[med-svn] [sistr] 01/02: New upstream version 1.0.2
Andreas Tille
tille at debian.org
Wed Oct 11 12:28:15 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository sistr.
commit eb7ce6d99a7e43eaa00cc41c9fb6e45ab121bdce
Author: Andreas Tille <tille at debian.org>
Date: Wed Oct 11 14:24:25 2017 +0200
New upstream version 1.0.2
---
.gitignore | 16 +
LICENSE | 201 +
MANIFEST.in | 6 +
README.rst | 542 +
setup.py | 61 +
sistr/__init__.py | 0
...a-serotype_serogroup_antigen_table-WHO_2007.csv | 3 +
sistr/data/antigens/fliC.fasta | 3 +
sistr/data/antigens/fljB.fasta | 3 +
sistr/data/antigens/wzx.fasta | 3 +
sistr/data/antigens/wzy.fasta | 3 +
sistr/data/cgmlst/README.md | 22 +
sistr/data/cgmlst/cgmlst-centroid.fasta | 3 +
sistr/data/cgmlst/cgmlst-full.fasta | 3 +
sistr/data/cgmlst/cgmlst-profiles.csv | 3 +
sistr/data/cgmlst/cgmlst-profiles.hdf | 3 +
sistr/data/genomes-to-serovar.txt | 52790 +++++++++++++++++++
sistr/data/genomes-to-subspecies.txt | 52790 +++++++++++++++++++
sistr/data/sistr.msh | Bin 0 -> 96169728 bytes
sistr/misc/__init__.py | 0
sistr/misc/add_ref_genomes.py | 427 +
sistr/misc/hc_clusters_from_cgmlst_profiles.py | 97 +
sistr/misc/reduce_to_centroid_alleles.py | 161 +
sistr/sistr_cmd.py | 367 +
sistr/src/__init__.py | 0
sistr/src/blast_wrapper/__init__.py | 309 +
sistr/src/blast_wrapper/helpers.py | 51 +
sistr/src/cgmlst/__init__.py | 413 +
sistr/src/cgmlst/extras/__init__.py | 0
sistr/src/cgmlst/extras/centroid_cgmlst_alleles.py | 169 +
sistr/src/cgmlst/extras/hclust_cutree.py | 76 +
sistr/src/cgmlst/msa.py | 77 +
sistr/src/logger.py | 11 +
sistr/src/mash.py | 67 +
sistr/src/parsers.py | 110 +
sistr/src/qc/__init__.py | 55 +
sistr/src/qc/constants.py | 4 +
sistr/src/serovar_prediction/__init__.py | 540 +
sistr/src/serovar_prediction/constants.py | 153 +
sistr/src/writers.py | 188 +
sistr/version.py | 1 +
tests/00_0163.fasta | 3 +
tests/conftest.py | 26 +
tests/test_cgmlst.py | 39 +
tests/test_hclust_cutree.py | 32 +
tests/test_mash.py | 15 +
tests/test_msa.py | 51 +
tests/test_parse_blast.py | 89 +
tests/test_writer_util.py | 115 +
49 files changed, 110101 insertions(+)
diff --git a/.gitignore b/.gitignore
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+.idea/
+.venv/
+venv/
+.cache/
+.ipynb_checkpoints/
+dist/
+*.egg-info/
+__pycache__/
+tmp
+*.db
+*.pyc
+*.bak
+*.ipynb
+*.b6
+.RData
+.Rhistory
diff --git a/LICENSE b/LICENSE
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+++ b/LICENSE
@@ -0,0 +1,201 @@
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diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 0000000..a66c0ac
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1,6 @@
+include LICENSE
+include README.rst
+include MANIFEST.in
+include setup.py
+
+recursive-include sistr/data/ *.fasta *.txt *.csv *.msh
diff --git a/README.rst b/README.rst
new file mode 100644
index 0000000..2b3cc8e
--- /dev/null
+++ b/README.rst
@@ -0,0 +1,542 @@
+****************************************************************************
+``sistr_cmd``: Salmonella In Silico Typing Resource (SISTR) commandline tool
+****************************************************************************
+
+
+Serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST.
+`Mash MinHash <https://mash.readthedocs.io/en/latest/>`_ can also be used for serovar prediction.
+
+**Latest stable version: `v0.3.4 <https://github.com/peterk87/sistr_cmd/releases/tag/v0.3.4>`_ **
+
+
+*Don't want to use a command-line app?* Try the `SISTR web app <https://lfz.corefacility.ca/sistr-app/>`_
+
+
+Citation
+========
+
+If you find this tool useful, please cite as:
+
+.. epigraph::
+
+ The *Salmonella In Silico* Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft *Salmonella* genome assemblies. Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada. PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101
+
+ -- Paper Link: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147101
+
+BibTeX
+------
+
+.. code-block:: none
+
+ @article{Yoshida2016,
+ doi = {10.1371/journal.pone.0147101},
+ url = {http://dx.doi.org/10.1371/journal.pone.0147101},
+ year = {2016},
+ month = {jan},
+ publisher = {Public Library of Science ({PLoS})},
+ volume = {11},
+ number = {1},
+ pages = {e0147101},
+ author = {Catherine E. Yoshida and Peter Kruczkiewicz and Chad R. Laing and Erika J. Lingohr and Victor P. J. Gannon and John H. E. Nash and Eduardo N. Taboada},
+ editor = {Michael Hensel},
+ title = {The Salmonella In Silico Typing Resource ({SISTR}): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies},
+ journal = {{PLOS} {ONE}}
+ }
+
+
+Installation
+============
+
+Using Conda [Recommended]
+-----------
+
+You can install ``sistr_cmd`` using `Conda <https://conda.io/miniconda.html>`_ from the `BioConda channel <https://bioconda.github.io/>`_:
+
+.. code-block:: bash
+
+ # Install conda. Miniconda is recommended if you don't have Conda installed already
+ # see https://conda.io/miniconda.html
+ # Add Bioconda channel and other channels https://bioconda.github.io/#set-up-channels
+ conda config --add channels conda-forge
+ conda config --add channels defaults
+ conda config --add channels r
+ conda config --add channels bioconda
+ # Install sistr_cmd and its dependencies
+ conda install sistr_cmd
+ # sistr_cmd should be installed in your $PATH
+ sistr --help
+
+Installing ``sistr_cmd`` is recommended for the least amount of headache since Conda will ensure that all necessary external dependencies are installed along with ``sistr_cmd`` (i.e. ``blast+``, ``mafft``, ``mash``). This will also help you get ``sistr_cmd`` running on older systems (e.g. CentOS 5) or where you may not have many user privileges.
+
+
+Using ``pip``
+-------------
+
+You can install ``sistr_cmd`` using ``pip``:
+
+.. code-block:: bash
+
+ pip install sistr_cmd
+
+
+``sistr_cmd`` is available from PYPI at https://pypi.python.org/pypi/sistr-cmd
+
+**NOTE:** You will need to ensure that external dependencies are installed (i.e. ``blast+``, ``mafft``, ``mash`` [optionally])
+
+
+Dependencies
+============
+
+These are the external dependencies required for ``sistr_cmd``:
+
+- Python (>= v2.7 OR >= v3.4)
+- BLAST+ (>= v2.2.30)
+- MAFFT (>=v7.271 (2016/1/6))
+- `Mash v1.0+ <https://github.com/marbl/Mash/releases>`_ [optional]
+
+Python Dependencies
+-------------------
+
+``sistr_cmd`` requires the following Python libraries:
+
+- numpy (>=1.11.1)
+- pandas (>=0.18.1)
+
+
+You can run the following commands to get up-to-date versions of ``numpy`` and ``pandas``
+
+.. code-block:: bash
+
+ pip install --upgrade pip
+ pip install wheel
+ pip install numpy pandas
+
+Usage
+=====
+
+If you run ``sistr -h``, you should see the following usage info:
+
+.. code-block:: none
+
+ usage: sistr_cmd [-h] [-i fasta_path genome_name] [-f OUTPUT_FORMAT]
+ [-o OUTPUT_PREDICTION] [-p CGMLST_PROFILES]
+ [-n NOVEL_ALLELES] [-a ALLELES_OUTPUT] [-T TMP_DIR] [-K]
+ [--use-full-cgmlst-db] [--no-cgmlst] [-m] [--qc] [-t THREADS]
+ [-v] [-V]
+ [F [F ...]]
+
+ SISTR (Salmonella In Silico Typing Resource) Command-line Tool
+ ==============================================================
+ Serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST.
+
+ Note about using the "--use-full-cgmlst-db" flag:
+ The "centroid" allele database is ~10% the size of the full set so analysis is much quicker with the "centroid" vs "full" set of alleles. Results between 2 cgMLST allele sets should not differ.
+
+ If you find this program useful in your research, please cite as:
+
+ The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies.
+ Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada.
+ PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101
+
+ positional arguments:
+ F Input genome FASTA file
+
+ optional arguments:
+ -h, --help show this help message and exit
+ -i fasta_path genome_name, --input-fasta-genome-name fasta_path genome_name
+ fasta file path to genome name pair
+ -f OUTPUT_FORMAT, --output-format OUTPUT_FORMAT
+ Output format (json, csv, pickle)
+ -o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION
+ SISTR serovar prediction output path
+ -p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES
+ Output CSV file destination for cgMLST allelic
+ profiles
+ -n NOVEL_ALLELES, --novel-alleles NOVEL_ALLELES
+ Output FASTA file destination of novel cgMLST alleles
+ from input genomes
+ -a ALLELES_OUTPUT, --alleles-output ALLELES_OUTPUT
+ Output path of allele sequences and info to JSON
+ -T TMP_DIR, --tmp-dir TMP_DIR
+ Base temporary working directory for intermediate
+ analysis files.
+ -K, --keep-tmp Keep temporary analysis files.
+ --use-full-cgmlst-db Use the full set of cgMLST alleles which can include
+ highly similar alleles. By default the smaller
+ "centroid" alleles or representative alleles are used
+ for each marker.
+ --no-cgmlst Do not run cgMLST serovar prediction
+ -m, --run-mash Determine Mash MinHash genomic distances to Salmonella
+ genomes with trusted serovar designations. Mash binary
+ must be in accessible via $PATH (e.g. /usr/bin).
+ --qc Perform basic QC to provide level of confidence in
+ serovar prediction results.
+ -t THREADS, --threads THREADS
+ Number of parallel threads to run sistr_cmd analysis.
+ -v, --verbose Logging verbosity level (-v == show warnings; -vvv ==
+ show debug info)
+ -V, --version show program's version number and exit
+
+
+
+Example Usage
+-------------
+
+By running the following command on a FASTA file of *Salmonella enterica* strain LT2 (https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP014051.1):
+
+.. code-block:: bash
+
+ sistr --qc -vv --alleles-output allele-results.json --novel-alleles novel-alleles.fasta --cgmlst-profiles cgmlst-profiles.csv -f tab -o sistr-output.tab LT2.fasta
+
+
+You should see some log messages like so:
+
+.. code-block:: none
+
+ <time> INFO: Running sistr_cmd 0.3.4 [in /usr/lib/python2.7/site-packages/sistr/sistr_cmd.py:290]
+ <time> INFO: Serial single threaded run mode on 1 genomes [in /usr/lib/python2.7/site-packages/sistr/sistr_cmd.py:319]
+ <time> INFO: Initializing temporary analysis directory "/tmp/20170309104912-SISTR-LT2" and preparing for BLAST searching. [in /usr/lib/python2.7/site-packages/sistr/sistr_cmd.py:175]
+ <time> INFO: Temporary FASTA file copied to /tmp/20170309104912-SISTR-LT2/LT2_fasta [in /usr/lib/python2.7/site-packages/sistr/sistr_cmd.py:177]
+ <time> INFO: Running BLAST on serovar predictive cgMLST330 alleles [in /usr/lib/python2.7/site-packages/sistr/src/cgmlst/__init__.py:319]
+ <time> INFO: Reading BLAST output file "/tmp/20170309104912-SISTR-LT2/cgmlst-centroid.fasta-LT2_fasta-2017Mar09_10_49_13.blast" [in /usr/lib/python2.7/site-packages/sistr/src/cgmlst/__init__.py:322]
+ <time> INFO: Found 6525 cgMLST330 allele BLAST results [in /usr/lib/python2.7/site-packages/sistr/src/cgmlst/__init__.py:333]
+ <time> INFO: Marker NZ_AOXE01000081.1_201 | Recovered novel allele with gaps (n=0) of length 477 vs length 477 for ref allele NZ_AOXE01000081.1_201|2823059714. Novel allele name=3250876267 [in /usr/lib/python2.7/site-packages/sistr/src/cgmlst/__init__.py:181]
+ <time> INFO: Type retrieved_marker_alleles <type 'dict'> [in /usr/lib/python2.7/site-packages/sistr/src/cgmlst/__init__.py:343]
+ <time> INFO: Calculating number of matching alleles to serovar predictive cgMLST330 profiles [in /usr/lib/python2.7/site-packages/sistr/src/cgmlst/__init__.py:360]
+ <time> INFO: Top subspecies by cgMLST is "enterica" (min dist=0.00909090909091, Counter={'enterica': 11532}) [in /usr/lib/python2.7/site-packages/sistr/src/cgmlst/__init__.py:369]
+ <time> INFO: Top serovar by cgMLST profile matching: "Typhimurium" with 327 matching alleles, distance=0.9% [in /usr/lib/python2.7/site-packages/sistr/src/cgmlst/__init__.py:385]
+ <time> INFO: cgMLST330 Sequence Type=660408169 [in /usr/lib/python2.7/site-packages/sistr/src/cgmlst/__init__.py:404]
+ <time> INFO: LT2 | Antigen gene BLAST serovar prediction: "Typhimurium" serogroup=B 1,4,[5],12:i:1,2 [in /usr/lib/python2.7/site-packages/sistr/sistr_cmd.py:207]
+ <time> INFO: LT2 | Subspecies prediction: enterica [in /usr/lib/python2.7/site-packages/sistr/sistr_cmd.py:210]
+ <time> INFO: LT2 | Overall serovar prediction: Typhimurium [in /usr/lib/python2.7/site-packages/sistr/sistr_cmd.py:213]
+ <time> INFO: Genome size=4857473 (within gsize thresholds? True) [in /usr/lib/python2.7/site-packages/sistr/src/qc/__init__.py:13]
+ <time> INFO: Deleting temporary working directory at /tmp/20170309104912-SISTR-LT2 [in /usr/lib/python2.7/site-packages/sistr/sistr_cmd.py:220]
+ <time> INFO: Writing output "tab" file to "sistr-output.tab" [in /usr/lib/python2.7/site-packages/sistr/src/writers.py:38]
+ <time> INFO: cgMLST allelic profiles written to cgmlst-profiles.csv [in /usr/lib/python2.7/site-packages/sistr/sistr_cmd.py:340]
+ <time> INFO: JSON of allele data written to allele-results.json for 1 cgMLST allele results [in /usr/lib/python2.7/site-packages/sistr/sistr_cmd.py:343]
+ <time> INFO: Wrote 330 alleles to novel-alleles.fasta [in /usr/lib/python2.7/site-packages/sistr/sistr_cmd.py:346]
+
+
+``sistr_cmd`` Output
+====================
+
+``sistr_cmd`` has several output options. The primary output is the serovar prediction and in silico typing results output (e.g. ``-o sistr-results.tab``).
+
+Summary of output options:
+
+- primary results output
+ + serovar prediction, cgMLST results, Mash results
+ + format (``-f <format>``): ``tab``, ``csv``, ``json``, ``pickle``
+ + ``-o sistr-results``
+- cgMLST allele results
+ + in-depth allele search results for each input genome for each cgMLST locus (330 loci in total)
+ + includes extracted allele sequences, top ``blastn`` results and summarized ``mafft`` results
+ + format: JSON
+ + ``-a allele-results.json``
+- cgMLST allelic profiles
+ + table of allele designations for each genome for each cgMLST locus
+ + row names: genome names
+ + column names: cgMLST marker names
+ + format: CSV
+ + ``--cgmlst-profiles cgmlst-profiles.csv``
+
+
+Primary results output (``-o sistr-results``)
+------------------------------------------
+
+Tab-delimited results output (``-f tab``):
+
+.. code-block:: tab
+
+ cgmlst_ST cgmlst_distance cgmlst_genome_match cgmlst_matching_alleles cgmlst_subspecies fasta_filepath genome h1 h2 o_antigen qc_messages qc_status serogroup serovar serovar_antigen serovar_cgmlst
+ 660408169 0.00909090909091 LT2 327 enterica /home/peter/Downloads/sistr-LT2-example/LT2.fasta LT2 i 1,2 1,4,[5],12 PASS B Typhimurium Typhimurium Typhimurium
+
+CSV results output (``-f csv``):
+
+.. code-block:: csv
+
+ cgmlst_ST,cgmlst_distance,cgmlst_genome_match,cgmlst_matching_alleles,cgmlst_subspecies,fasta_filepath,genome,h1,h2,o_antigen,qc_messages,qc_status,serogroup,serovar,serovar_antigen,serovar_cgmlst
+ 660408169,0.00909090909091,LT2,327,enterica,/home/peter/Downloads/sistr-LT2-example/LT2.fasta,LT2,i,"1,2","1,4,[5],12",,PASS,B,Typhimurium,Typhimurium,Typhimurium
+
+How the results should look in a table:
+
+.. csv-table::
+
+ cgmlst_ST,cgmlst_distance,cgmlst_genome_match,cgmlst_matching_alleles,cgmlst_subspecies,fasta_filepath,genome,h1,h2,o_antigen,qc_messages,qc_status,serogroup,serovar,serovar_antigen,serovar_cgmlst
+ 660408169,0.00909090909091,LT2,327,enterica,/home/peter/Downloads/sistr-LT2-example/LT2.fasta,LT2,i,"1,2","1,4,[5],12",,PASS,B,Typhimurium,Typhimurium,Typhimurium
+
+
+JSON results output:
+
+.. code-block:: json
+
+ [
+ {
+ "serovar_cgmlst": "Typhimurium",
+ "cgmlst_matching_alleles": 327,
+ "h1": "i",
+ "serovar_antigen": "Typhimurium",
+ "cgmlst_distance": 0.009090909090909038,
+ "h2": "1,2",
+ "cgmlst_genome_match": "LT2",
+ "cgmlst_ST": 660408169,
+ "serovar": "Typhimurium",
+ "fasta_filepath": "/full/path/to/LT2.fasta",
+ "genome": "LT2",
+ "serogroup": "B",
+ "qc_messages": "",
+ "qc_status": "PASS",
+ "o_antigen": "1,4,[5],12",
+ "cgmlst_subspecies": "enterica"
+ }
+ ]
+
+cgMLST allele search results
+-------------------------------------
+
+You can produce in-depth allele search results with the ``-a``/``--alleles-output`` commandline argument.
+These results may be useful for understanding unexpected or low confidence serovar predictions.
+
+Schema:
+~~~~~~~
+
+.. code-block:: json
+
+ {
+ <genome name>: {
+ // for each
+ <cgMLST marker id>: {
+ // top blast result on largest contig
+ blast_result: {
+ // perfect match to a previously identified allele?
+ "is_perfect": boolean,
+ // blastn subject sequence length
+ "slen": integer,
+ // blastn percent identity
+ "pident": numeric,
+ // cgMLST marker name
+ "marker": string,
+ // blastn query sequence id
+ "qseqid": string,
+ // blastn query sequence start index
+ "qstart": integer,
+ // is match truncated by end of sequence?
+ "is_trunc": boolean,
+ // number of MSA gaps in subject sequence
+ "sseq_msa_gaps": integer,
+ // blastn subject sequence
+ "sseq": string,
+ // blastn bitscore
+ "bitscore": numeric,
+ // proportion of subject sequence MSA with gaps
+ "sseq_msa_p_gaps": numeric,
+ // blastn E-value
+ "evalue": numeric,
+ // blastn gap open
+ "gapopen": integer,
+ // blastn subject sequence end index
+ "send": integer,
+ // does this allele have a perfect match?
+ "has_perfect_match": boolean,
+ // matching allele name
+ "allele": integer,
+ // subject sequence start index
+ "sstart": integer,
+ // extracted allele name (CRC32 of subject nucleotide sequence)
+ "allele_name": integer,
+ // adjusted subject sequence start index
+ "start_idx": numeric,
+ // blastn query end index
+ "qend": integer,
+ // did the extracted allele sequence need to be reverse complemented?
+ "needs_revcomp": boolean,
+ // did the extracted allele sequence need to be extended to match the length of the query sequence?
+ "is_extended": boolean,
+ // blastn number of mismatches
+ "mismatch": integer,
+ // extracted allele coverage i.e. (length of extracted allele) / (length of closest matching allele)
+ "coverage": numeric,
+ // too many gaps within the MSA of extracted allele sequence and closest matching allele?
+ "too_many_gaps": boolean,
+ // adjusted subject end index
+ "end_idx": numeric,
+ // is extracted allele truncated by end of sequence?
+ "trunc": boolean,
+ // blastn subject sequence title
+ "stitle": string,
+ // blastn query sequence length
+ "qlen": integer,
+ // valid allele match found?
+ "is_match": true,
+ // blastn alignment length
+ "length": integer
+ },
+ // CRC32 unsigned 32-bit integer allele name from allele sequence
+ "name": integer,
+ // extracted allele sequence
+ "seq": string
+ }
+
+ }}
+
+Example:
+~~~~~~~~
+
+Here's some truncated example allele search results output:
+
+.. code-block:: json
+
+ {
+ "LT2": {
+ "NZ_AOXE01000034.1_82": {
+ "blast_result": {
+ "is_perfect": false,
+ "slen": 4857473,
+ "pident": 99.479,
+ "marker": "NZ_AOXE01000034.1_82",
+ "qseqid": "NZ_AOXE01000034.1_82|340989631",
+ "qstart": 1,
+ "is_trunc": false,
+ "sseq_msa_gaps": 0,
+ "sseq": "ATGCCAACCAGACCACCTTATCCGCGGGAAGCTTATATCGTCACCATTGAAAAAGGCACGCCGGGCCAGACGGTGACGTGGTATCAGCTACGGGCTGACCATCCGAAACCTGATTCGCTCATCAGCGAGCATCCGACCGCAGAAGAAGCGATGGATGCGAAAAATCGTTACGAAGATCCGGATAAATCATAG",
+ "bitscore": 350.0,
+ "sseq_msa_p_gaps": 0.0,
+ "evalue": 3.289999999999999E-97,
+ "gapopen": 0,
+ "send": 358277,
+ "has_perfect_match": false,
+ "allele": 340989631,
+ "sstart": 358468,
+ "allele_name": 1204520418,
+ "start_idx": 358276.0,
+ "qend": 192,
+ "needs_revcomp": true,
+ "is_extended": false,
+ "mismatch": 1,
+ "coverage": 1.0,
+ "too_many_gaps": false,
+ "end_idx": 358467.0,
+ "trunc": false,
+ "stitle": "NZ_CP014051.1 Salmonella enterica strain LT2, complete genome",
+ "qlen": 192,
+ "is_match": true,
+ "length": 192
+ },
+ "name": 1204520418,
+ "seq": "ATGCCAACCAGACCACCTTATCCGCGGGAAGCTTATATCGTCACCATTGAAAAAGGCACGCCGGGCCAGACGGTGACGTGGTATCAGCTACGGGCTGACCATCCGAAACCTGATTCGCTCATCAGCGAGCATCCGACCGCAGAAGAAGCGATGGATGCGAAAAATCGTTACGAAGATCCGGATAAATCATAG"
+ },
+ // 329 other cgMLST allele results
+ },
+ "another-genome": { /* allele results */}
+ }
+
+
+cgMLST allelic profiles output (``--cgmlst-profiles cgmlst-profiles.csv``)
+--------------------------------------------------------------------------
+
+With the ``-p``/``--cgmlst-profiles`` commandline argument, you can output the 330 loci cgMLST allelic profiles for your input genomes (i.e. the allele designation for each cgMLST locus for each input genome).
+You can use this information to construct phylogenetic trees from this data using a tool such as `Phyloviz Online <https://online.phyloviz.net/index>`_.
+This type of analysis may be useful to explore why unexpected serovar prediction results were generated (e.g. your genomes are genetically very different from each other).
+
+Example truncated cgMLST profiles output:
+
+.. csv-table::
+
+ ,NC_003198.1_3005,NC_006905.1_2841,NC_011149.1_467,...
+ LT2,419666160,2853045644,161888011,...
+
+
+
+QC by ``sistr_cmd`` (``--qc``)
+-------------------
+
+If you are running ``sistr_cmd`` with the ``--qc`` commandline argument, ``sistr_cmd`` will run some basic QC to determine the level of confidence in the serovar prediction.
+
+The ``qc_status`` field should contain a value of ``PASS`` if your genome passes all QC checks, otherwise, it will be ``WARNING`` or ``FAIL`` if there are issues with your results and/or input genome sequence.
+
+The ``qc_messages`` field will contain useful information about why you may have a low confidence serovar prediction result. The QC messages will be delimited by `` | ``.
+
+For example, here are the QC messages for an unusually small *Salmonella* assembly where the predicted serovar was "-:-:-":
+
+.. code-block:: none
+
+ FAIL: Large number of cgMLST330 loci missing (n=272 > 30)
+ FAIL: Wzx/Wzy genes missing. Cannot determine O-antigen group/serogroup. Cannot accurately predict serovar from antigen genes.
+ WARNING: H1 antigen gene (fliC) missing. Cannot determine H1 antigen. Cannot accurately predict serovar from antigen genes.
+ WARNING: Input genome size (699860 bp) not within expected range of 4000000-6000000 (bp) for Salmonella
+ WARNING: Only matched 57 cgMLST330 loci. Min threshold for confident serovar prediction from cgMLST is 297.0
+
+The QC messages produced by ``sistr_cmd`` should help you understand your serovar prediction results.
+
+
+Issues
+======
+
+If you encounter any problems or have any questions feel free to create an issue anonymously or not to let us know so we can address it!
+
+Feature requests and pull requests are welcome!
+
+
+Want to help improve this tool?
+===============================
+
+Do you have any *Salmonella* genomes with trustworthy serovar info? Would you like SISTR to provide better serovar predictions? You can help by contributing those genomes along with their serovar info!
+
+SISTR relies on a database of cgMLST allelic profiles from *Salmonella* genomes with validated serovar info to make accurate serovar predictions (since antigenic determinations from a handful of genes like wzx or fliC can only get you so far). So the more genomes there are in the SISTR database, the more accurate the serovar predictions, especially if those genomes belong to uncommon or rare serovars or lineages.
+
+Help us improve SISTR serovar predictions! Contribute *Salmonella* genomes to SISTR!
+
+
+You can contribute by:
+
+- let us know here: https://github.com/peterk87/sistr_cmd/issues/15
+- linking to your genome on NCBI SRA/BioSample/Assembly
+- sending us an email at sistr.salmonella at gmail.com
+- contacting the authors of SISTR
+
+
+Development
+===========
+
+Getting started
+
+.. code-block:: bash
+
+ git clone https://github.com/peterk87/sistr_cmd.git
+ cd sistr_cmd/
+ export PYTHONPATH=$(pwd)
+ # run tests
+ py.test tests/
+
+Pull requests for feature additions and bug fixes welcome!
+
+
+Using ``sistr_cmd`` in your Python application
+----------------------------------------------
+
+Want to use ``sistr_cmd`` directly in your Python application?
+
+Install ``sistr_cmd`` using pip or Conda.
+
+You can run SISTR serovar predictions like so:
+
+.. code-block:: python
+
+ from sistr.sistr_cmd import sistr_predict
+ # create mock commandline arguments class
+ class SistrCmdMockArgs:
+ run_mash = True
+ no_cgmlst = False
+ qc = True
+ use_full_cgmlst_db = False
+ # run SISTR serovar prediction
+ sistr_results, allele_results = sistr_predict(genome_fasta_path, genome_name, keep_tmp=False, tmp_dir='/tmp/sistr_cmd', args=SistrCmdMockArgs)
+ # use sistr_cmd results for something
+
+
+License
+=======
+
+Copyright 2016 Public Health Agency of Canada
+
+Distributed under the GNU Public License version 3.0
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..c0e6069
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,61 @@
+import os
+from distutils.core import setup
+from setuptools import find_packages
+
+classifiers = """
+Development Status :: 3 - Alpha
+Environment :: Console
+License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+Intended Audience :: Science/Research
+Topic :: Scientific/Engineering
+Topic :: Scientific/Engineering :: Bio-Informatics
+Programming Language :: Python
+Programming Language :: Python :: 2.7
+Programming Language :: Python :: 3.4
+Programming Language :: Python :: 3.5
+Programming Language :: Python :: 3.6
+Programming Language :: Python :: Implementation :: CPython
+Operating System :: POSIX :: Linux
+""".strip().split('\n')
+
+def read(fname):
+ return open(os.path.join(os.path.dirname(__file__), fname)).read()
+
+exec(open('sistr/version.py').read())
+
+setup(
+ name='sistr_cmd',
+ version=__version__,
+ packages=find_packages(exclude=['tests']),
+ url='https://github.com/peterk87/sistr_cmd',
+ license='GPLv3',
+ author='Peter Kruczkiewicz',
+ author_email='peter.kruczkiewicz at gmail.com',
+ description=('Serovar predictions from Salmonella whole-genome sequence assemblies by determination of antigen gene'
+ 'and cgMLST gene alleles using BLAST. Mash MinHash can also be used for serovar prediction.'),
+ keywords='Salmonella serotyping genotyping cgMLST BLAST Mash MinHash',
+ classifiers=classifiers,
+ package_dir={'sistr':'sistr'},
+ package_data={'sistr': ['data/*.msh',
+ 'data/*.csv',
+ 'data/*.txt',
+ 'data/antigens/*.fasta',
+ 'data/cgmlst/*.fasta',
+ 'data/cgmlst/*.txt',
+ 'data/cgmlst/*.csv',
+ 'data/cgmlst/*.hdf'
+ ]},
+ install_requires=[
+ 'numpy>=1.11.1',
+ 'pandas>=0.18.1',
+ 'tables>=3.3.0',
+ ],
+ extras_require={
+ 'test': ['pytest>=2.9.2',],
+ },
+ entry_points={
+ 'console_scripts': [
+ 'sistr=sistr.sistr_cmd:main',
+ ],
+ },
+)
diff --git a/sistr/__init__.py b/sistr/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/sistr/data/Salmonella-serotype_serogroup_antigen_table-WHO_2007.csv b/sistr/data/Salmonella-serotype_serogroup_antigen_table-WHO_2007.csv
new file mode 100755
index 0000000..09f8539
--- /dev/null
+++ b/sistr/data/Salmonella-serotype_serogroup_antigen_table-WHO_2007.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5a2ffa704a93582d7b3e2c5df8ca02dde1af769718a1cc289b80bf682e3f76cc
+size 120411
diff --git a/sistr/data/antigens/fliC.fasta b/sistr/data/antigens/fliC.fasta
new file mode 100755
index 0000000..6561765
--- /dev/null
+++ b/sistr/data/antigens/fliC.fasta
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9e9e11cde490dadd450231398df83a20add73431e24ae397732e32d0801d7be3
+size 1076904
diff --git a/sistr/data/antigens/fljB.fasta b/sistr/data/antigens/fljB.fasta
new file mode 100755
index 0000000..5704162
--- /dev/null
+++ b/sistr/data/antigens/fljB.fasta
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4f262ef9deb3ae152bef85e5471b66b4cef19166adbf99e28ab8417144a1f6f8
+size 214544
diff --git a/sistr/data/antigens/wzx.fasta b/sistr/data/antigens/wzx.fasta
new file mode 100644
index 0000000..0588843
--- /dev/null
+++ b/sistr/data/antigens/wzx.fasta
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1866bfb705d3dc4cece01835c87b25b27c8cde799bc8f540697c2d53c01e99f8
+size 129374
diff --git a/sistr/data/antigens/wzy.fasta b/sistr/data/antigens/wzy.fasta
new file mode 100755
index 0000000..129e381
--- /dev/null
+++ b/sistr/data/antigens/wzy.fasta
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:67c28ea7f8a65bf9554713a6f641e29e6ee66522feb0b224aa7f5f7574eeb8c3
+size 61004
diff --git a/sistr/data/cgmlst/README.md b/sistr/data/cgmlst/README.md
new file mode 100644
index 0000000..6d9b328
--- /dev/null
+++ b/sistr/data/cgmlst/README.md
@@ -0,0 +1,22 @@
+# 330 loci cgMLST scheme for *Salmonella*
+
+All alleles necessary for serovar prediction are included in `cgmlst.fasta`.
+
+## Header format
+
+Each fasta header contains the cgMLST330 marker name and allele number delimited by `|` (pipe):
+
+```
+>{cgMLST marker name}|{allele number}
+AGTC...
+```
+
+## Interpretation of results
+
+Only alleles that match with 100% identity and query coverage are considered for cgMLST profile matching.
+
+The closest matching cgMLST allele profile from the cgMLST allele database (`cgmlst-profiles.csv`) determines the cgMLST-derived serovar prediction.
+
+If the input genome's cgMLST profile matches at 90% or greater similarity, then the cgMLST-derived serovar prediction will be used to refine the antigen gene-derived serovar prediction and influence the overall prediction.
+
+
diff --git a/sistr/data/cgmlst/cgmlst-centroid.fasta b/sistr/data/cgmlst/cgmlst-centroid.fasta
new file mode 100644
index 0000000..a05d8d6
--- /dev/null
+++ b/sistr/data/cgmlst/cgmlst-centroid.fasta
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a467a14df0cd05e17f260e7dfe8f68c63da1e3a7c37adeed70bd59877fec4e59
+size 7712762
diff --git a/sistr/data/cgmlst/cgmlst-full.fasta b/sistr/data/cgmlst/cgmlst-full.fasta
new file mode 100644
index 0000000..e5dfef6
--- /dev/null
+++ b/sistr/data/cgmlst/cgmlst-full.fasta
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:534152518c1d29d2bba46d21a78612eedddae5f0de3564d4d9a64627ec583d20
+size 100743422
diff --git a/sistr/data/cgmlst/cgmlst-profiles.csv b/sistr/data/cgmlst/cgmlst-profiles.csv
new file mode 100644
index 0000000..a4e5d31
--- /dev/null
+++ b/sistr/data/cgmlst/cgmlst-profiles.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2b9085778a517bd9426e9080e0e7c921994e0b636480349f7994b57a58562335
+size 187489079
diff --git a/sistr/data/cgmlst/cgmlst-profiles.hdf b/sistr/data/cgmlst/cgmlst-profiles.hdf
new file mode 100644
index 0000000..b884ef4
--- /dev/null
+++ b/sistr/data/cgmlst/cgmlst-profiles.hdf
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:837322abe662fbecddcc041c04737abb46b267862da119d0676579292ed40f95
+size 140229904
diff --git a/sistr/data/genomes-to-serovar.txt b/sistr/data/genomes-to-serovar.txt
new file mode 100644
index 0000000..a7cf366
--- /dev/null
+++ b/sistr/data/genomes-to-serovar.txt
@@ -0,0 +1,52790 @@
+SRR1198880 Oranienburg
+SRR1198883 Typhimurium
+SRR1198885 Infantis
+SRR1198886 Enteritidis
+SRR1198887 Mbandaka
+SRR1198889 Typhimurium
+SRR1282366 Newport
+SRR1282365 I 4,[5],12:i:-
+SRR1030529 Kentucky
+SRR2002723 Oranienburg
+SRR1030526 Heidelberg
+SRR1030527 Typhimurium
+SRR1030525 Typhimurium
+51269 Saintpaul
+51268 Enteritidis
+51267 London
+51266 Oslo
+51265 Enteritidis
+51264 Typhimurium
+51263 Stanley
+51262 Enteritidis
+51261 Enteritidis
+SRR980354 Newport
+SRR980351 Muenchen
+SRR980350 Montevideo
+SRR980353 Ohio
+SRR980352 Muenchen
+SRR1122629 Ohio
+SRR1122628 Senftenberg
+46138 Agona
+00_0163 II 58:l,z13,z28:z6
+46136 Poona
+46135 Thompson
+46134 Bardo
+46133 Typhimurium
+46132 Enteritidis
+46131 Enteritidis
+46130 Enteritidis
+75948 Potsdam
+75949 Kentucky
+56123 Typhimurium
+56122 Braenderup
+56124 I 4,[5],12:i:-
+56127 I 4,[5],12:i:-
+56126 Typhi
+75940 Typhimurium
+75941 Kottbus
+75942 Typhimurium
+75943 I 4,[5],12:i:-
+75944 Montevideo
+75945 Thompson
+75946 Richmond
+75947 Typhimurium
+SRR1157968 Typhimurium
+SRR1157969 Poona
+SRR1157966 Kiambu
+SRR1157967 Enteritidis
+SRR1157965 Paratyphi B
+65396 Stourbridge
+A50 Choleraesuis
+80598 Derby
+73622 Enteritidis
+80594 Enteritidis
+80593 Enteritidis
+80591 Typhimurium
+54040 I 4,[5],12:i:-
+69726 Typhimurium
+60091 Virchow
+63027 I 4,[5],12:d:-
+63020 Stanley
+63021 Virchow
+9258 Typhimurium
+9259 I 4,[5],12:i:-
+9256 Infantis
+9257 Stanley
+SRR1257275 Oslo
+SRR1257274 Typhimurium
+63028 Infantis
+9253 Oranienburg
+9251 Ouakam
+69729 Stanley
+SRR1122701 Heidelberg
+69178 Kentucky
+37799 Enteritidis
+37798 Enteritidis
+37797 Coeln
+37794 I 4,[5],12:i:-
+37793 I 4,[5],12:i:-
+37792 I 4,[5],12:i:-
+37791 Typhimurium
+37790 Agama
+70662 Enteritidis
+70660 Typhimurium
+70661 Enteritidis
+70666 Enteritidis
+70667 Enteritidis
+70664 Enteritidis
+70665 Dublin
+70668 Enteritidis
+SRR1021942 Muenchen
+SRR1021940 Inverness
+SRR1021941 Rubislaw
+71539 Infantis
+71538 Enteritidis
+31947 Agona
+71535 I 4,[5],12:i:-
+71537 Kedougou
+71531 IIIb 48:z10:e,n,x,z15
+71530 Enteritidis
+71532 Newport
+12_3032 Kouka
+SRR1238795 Enteritidis
+78669 Chester
+ST4848 Typhimurium
+78668 Enteritidis
+48265 Enteritidis
+78662 Enteritidis
+78663 I 4,[5],12:i:-
+78660 Enteritidis
+78661 Infantis
+78666 Enteritidis
+78667 Potsdam
+78664 Enteritidis
+78665 Typhimurium
+41565 Heidelberg
+41566 Heidelberg
+515920_2 Montevideo
+41563 Heidelberg
+WA_14885 Newport
+WA_14881 Newport
+WA_14882 Newport
+99737 Stanley
+99736 I 4,[5],12:i:-
+29382 I 4,[5],12:i:-
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+SAL_AA9552AA Paratyphi B var. Java
+SAL_AA9553AA Paratyphi B
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+SAL_AA9556AA Paratyphi B
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+SAL_AA9589AA Paratyphi B
+SAL_AA9590AA Paratyphi B
+SAL_AA9591AA Paratyphi B
+SAL_AA9592AA Paratyphi B var. Java
+SAL_AA9594AA Typhi
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+SAL_AA9655AA Dublin
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+SAL_AA9657AA Dublin
+SAL_AA9658AA Gallinarum
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+SAL_AA9383AA Paratyphi B
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+SAL_BA1104AA Enteritidis
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+SAL_CA1511AA Montevideo
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+SAL_CA1513AA Montevideo
+SAL_CA1514AA Enteritidis
+SAL_CA1515AA Bareilly
+SAL_CA1516AA Typhi
+SAL_CA1519AA Enteritidis
+SAL_CA1521AA Enteritidis
+SAL_CA1524AA Kentucky
+SAL_CA1526AA Senftenberg
+SAL_CA1529AA Bareilly
+SAL_CA1532AA Oranienburg
+SAL_CA1533AA Typhimurium
+SAL_CA1534AA Bareilly
+SAL_CA1536AA Bareilly
+SAL_CA1538AA Bareilly
+SAL_CA1539AA Bareilly
+SAL_CA1540AA Enteritidis
+SAL_CA1542AA Stanley
+SAL_CA1543AA Enteritidis
+SAL_CA1545AA Typhi
+SAL_CA1551AA Bareilly
+SAL_CA1552AA Enteritidis
+SAL_CA1553AA Bareilly
+SAL_CA1554AA Tennessee
+SAL_CA1556AA Bareilly
+SAL_CA1558AA Enteritidis
+SAL_CA1560AA Enteritidis
+SAL_CA1562AA Enteritidis
+SAL_CA1564AA Oranienburg
+SAL_BA9798AA Typhi
+SAL_BA9822AA Enteritidis
+SAL_BA9852AA Typhimurium
+SAL_BA9890AA Cerro
+SAL_BA9919AA Nchanga
+SAL_BA9944AA Typhimurium
+SAL_BA9970AA Enteritidis
+SAL_CA0035AA Typhimurium
+SAL_CA0056AA Typhimurium
+SAL_CA0073AA Dublin
+SAL_CA0094AA Enteritidis
+SAL_CA0129AA Enteritidis
+SAL_CA0150AA Enteritidis
+SAL_CA0168AA Newport
+SAL_CA0188AA Enteritidis
+SAL_CA0206AA Weltevreden
+SAL_CA0224AA Typhimurium
+SAL_CA0244AA Enteritidis
+SAL_CA1568AA Enteritidis
+SAL_CA1569AA Bareilly
+SAL_CA1570AA Newport
+SAL_CA1575AA Enteritidis
+SAL_CA1577AA Mississippi
+SAL_CA1580AA Newport
+SAL_CA1583AA Typhimurium
+SAL_CA1586AA Havana
+SAL_CA1588AA Enteritidis
+SAL_CA1590AA Paratyphi A
+SAL_CA1591AA Oranienburg
+SAL_CA1593AA Newport
+SAL_CA1594AA Enteritidis
+SAL_CA1596AA Enteritidis
+SAL_CA1597AA Fanti
+SAL_CA1600AA Agama
+SAL_CA0131AA Typhimurium
+SAL_CA0132AA Agona
+SAL_CA0133AA Typhimurium
+SAL_CA0134AA Typhi
+SAL_CA0135AA Typhimurium
+SAL_CA0136AA Virchow
+SAL_CA0137AA Typhimurium
+SAL_CA0138AA Enteritidis
+SAL_CA0139AA Typhimurium
+SAL_CA0140AA Enteritidis
+SAL_CA0141AA Typhimurium
+SAL_CA0142AA Saintpaul
+SAL_CA0143AA Typhimurium
+SAL_CA0145AA Newport
+SAL_CA0146AA Stanley
+SAL_CA0149AA Newport
+SAL_CA1604AA Mikawasima
+SAL_CA1605AA Bareilly
+SAL_CA1607AA Jangwani
+SAL_CA1610AA Typhimurium
+SAL_CA1612AA Typhimurium
+SAL_CA1614AA Bareilly
+SAL_CA1615AA Takoradi
+SAL_CA1617AA Enteritidis
+SAL_CA1621AA Enteritidis
+SAL_CA1623AA Enteritidis
+SAL_CA1625AA Enteritidis
+SAL_CA1627AA Typhimurium
+SAL_CA1631AA Enteritidis
+SAL_CA1634AA Infantis
+SAL_CA1636AA Enteritidis
+SAL_CA1638AA Corvallis
+SAL_CA1644AA Enteritidis
+SAL_CA1648AA Enteritidis
+SAL_CA1649AA Bareilly
+SAL_CA1650AA Infantis
+SAL_CA1652AA Newport
+SAL_CA1654AA Enteritidis
+SAL_CA1656AA Typhimurium
+SAL_CA1658AA Hadar
+SAL_CA1660AA Infantis
+SAL_CA1664AA Colindale
+SAL_CA1670AA Infantis
+SAL_CA1672AA Saintpaul
+SAL_CA1676AA Typhimurium
+SAL_CA1678AA Enteritidis
+SAL_CA1680AA Enteritidis
+SAL_CA1682AA Enteritidis
+SAL_CA1687AA Paratyphi A
+SAL_CA1689AA Enteritidis
+SAL_CA1693AA Saintpaul
+SAL_CA1698AA Infantis
+SAL_CA1702AA Richmond
+SAL_CA1703AA Typhimurium
+SAL_CA1704AA Saintpaul
+SAL_CA1705AA Enteritidis
+SAL_CA1708AA Mbandaka
+SAL_CA1709AA Enteritidis
+SAL_CA1710AA Kentucky
+SAL_CA1712AA Kottbus
+SAL_CA1713AA Haifa
+SAL_CA1714AA Typhimurium
+SAL_CA1715AA Enteritidis
+SAL_CA1716AA Napoli
+SAL_CA1718AA Oranienburg
+SAL_CA1719AA Enteritidis
+SAL_CA1720AA Enteritidis
+SAL_CA1722AA Agona
+SAL_CA1723AA Enteritidis
+SAL_CA1725AA Infantis
+SAL_CA1727AA Enteritidis
+SAL_CA1729AA Typhimurium
+SAL_CA1733AA Enteritidis
+SAL_CA1735AA Enteritidis
+SAL_CA1737AA Enteritidis
+SAL_CA1739AA Infantis
+SAL_CA1741AA Enteritidis
+SAL_CA1743AA Enteritidis
+SAL_CA1745AA Typhi
+SAL_CA1747AA Enteritidis
+SAL_CA1751AA Typhimurium
+SAL_CA1753AA Enteritidis
+SAL_CA1755AA Enteritidis
+SAL_CA1761AA Oranienburg
+SAL_CA1763AA Enteritidis
+SAL_CA1765AA Enteritidis
+SAL_CA1769AA Typhimurium
+SAL_CA1771AA Enteritidis
+SAL_CA1775AA Newport
+SAL_CA1776AA Enteritidis
+SAL_CA1778AA Enteritidis
+SAL_CA1780AA Minnesota
+SAL_CA1781AA Enteritidis
+SAL_CA1784AA Enteritidis
+SAL_CA1786AA Senftenberg
+SAL_CA1788AA Rissen
+SAL_CA1794AA Enteritidis
+SAL_CA1797AA Enteritidis
+SAL_CA1799AA Montevideo
+SAL_CA1801AA Enteritidis
+SAL_CA1802AA Haifa
+SAL_CA1804AA Montevideo
+SAL_CA1806AA Enteritidis
+SAL_CA1809AA Tamberma
+SAL_CA1811AA Paratyphi A
+SAL_CA1813AA Braenderup
+SAL_CA1815AA Enteritidis
+SAL_CA1817AA Agbeni
+SAL_CA1818AA Paratyphi A
+SAL_CA1820AA Enteritidis
+SAL_CA1822AA Oranienburg
+SAL_CA1824AA Typhimurium
+SAL_CA0151AA Newport
+SAL_CA0152AA Curacao
+SAL_CA0153AA Newport
+SAL_CA0154AA Weltevreden
+SAL_CA0155AA Newport
+SAL_CA0157AA Paratyphi A
+SAL_CA0158AA Newport
+SAL_CA0159AA Colindale
+SAL_CA0160AA Newport
+SAL_CA0161AA Enteritidis
+SAL_CA0162AA Newport
+SAL_CA0163AA Enteritidis
+SAL_CA0164AA Newport
+SAL_CA0165AA Typhimurium
+SAL_CA0166AA Newport
+SAL_CA0167AA Kentucky
+SAL_CA1830AA Agama
+SAL_CA1832AA Poona
+SAL_CA1834AA Stanley
+SAL_CA1835AA Paratyphi A
+SAL_CA1838AA Enteritidis
+SAL_CA1840AA Thompson
+SAL_CA1841AA Corvallis
+SAL_CA1843AA Typhimurium
+SAL_CA1845AA Newport
+SAL_CA1856AA Infantis
+SAL_CA1860AA Poona
+SAL_CA1862AA Enteritidis
+SAL_CA1864AA Enteritidis
+SAL_CA1866AA Enteritidis
+SAL_CA1868AA Typhimurium
+SAL_CA1871AA Enteritidis
+SAL_CA1874AA Enteritidis
+SAL_CA1876AA Enteritidis
+SAL_CA1878AA Typhimurium
+SAL_CA1880AA Coeln
+SAL_CA1882AA Enteritidis
+SAL_CA1884AA Typhi
+SAL_CA1885AA Oranienburg
+SAL_CA1887AA Enteritidis
+SAL_CA1889AA Enteritidis
+SAL_CA1890AA Grumpensis
+SAL_CA1892AA Enteritidis
+SAL_CA1893AA Enteritidis
+SAL_CA1895AA Enteritidis
+SAL_CA1897AA Havana
+SAL_CA1899AA Kentucky
+SAL_CA1902AA Typhimurium
+SAL_CA1908AA Enteritidis
+SAL_CA1909AA Typhimurium
+SAL_CA1913AA Enteritidis
+SAL_CA1915AA Typhi
+SAL_CA1918AA Enteritidis
+SAL_CA1919AA Enteritidis
+SAL_CA1921AA Agona
+SAL_CA1923AA Heidelberg
+SAL_CA1925AA Enteritidis
+SAL_CA1927AA Infantis
+SAL_CA1930AA Hadar
+SAL_CA1932AA Infantis
+SAL_CA1934AA Hvittingfoss
+SAL_CA1938AA Paratyphi A
+SAL_CA1940AA Typhi
+SAL_CA1942AA Infantis
+SAL_CA1946AA Enteritidis
+SAL_CA1948AA Enteritidis
+SAL_CA1951AA Enteritidis
+SAL_CA1953AA Enteritidis
+SAL_CA1955AA Enteritidis
+SAL_CA1957AA Enteritidis
+SAL_CA1963AA Manchester
+SAL_CA1965AA Enteritidis
+SAL_CA1970AA Typhi
+SAL_CA1972AA Livingstone
+SAL_CA1974AA Bilthoven
+SAL_CA1976AA Enteritidis
+SAL_CA1977AA Paratyphi A
+SAL_CA1980AA Stanley
+SAL_CA1982AA Stanley
+SAL_CA1984AA Enteritidis
+SAL_CA1990AA Typhimurium
+SAL_CA1994AA Typhimurium
+SAL_CA1997AA Enteritidis
+SAL_CA1999AA Typhimurium
+SAL_CA2002AA Chandans
+SAL_CA2004AA Enteritidis
+SAL_CA2006AA Corvallis
+SAL_CA2008AA Stanley
+SAL_CA2010AA Enteritidis
+SAL_CA2012AA Poona
+SAL_CA2014AA Enteritidis
+SAL_CA2016AA Stanley
+SAL_CA2018AA Enteritidis
+SAL_CA2020AA Typhimurium
+SAL_CA2022AA Kentucky
+SAL_CA2024AA Enteritidis
+SAL_CA2030AA Typhimurium
+SAL_CA2034AA Agbeni
+SAL_CA2035AA Kottbus
+SAL_CA2037AA Enteritidis
+SAL_CA2039AA Enteritidis
+SAL_CA2043AA Infantis
+SAL_CA2045AA Enteritidis
+SAL_CA2047AA Monschaui
+SAL_CA2048AA Paratyphi A
+SAL_CA2050AA Enteritidis
+SAL_CA2052AA Enteritidis
+SAL_CA2055AA Enteritidis
+SAL_CA2059AA Enteritidis
+SAL_CA2060AA Enteritidis
+SAL_CA2062AA Hvittingfoss
+SAL_CA2064AA Virchow
+SAL_CA2068AA Newport
+SAL_CA2069AA Chester
+SAL_CA2072AA Enteritidis
+SAL_CA2075AA Typhimurium
+SAL_CA2077AA Enteritidis
+SAL_CA2079AA Corvallis
+SAL_CA2082AA Typhimurium
+SAL_CA2083AA Ouakam
+SAL_CA2084AA Enteritidis
+SAL_CA2085AA Newport
+SAL_CA2086AA Stanley
+SAL_CA2087AA Typhimurium
+SAL_CA2088AA Typhimurium
+SAL_CA2089AA Typhimurium
+SAL_CA2090AA Rissen
+SAL_CA2091AA Poona
+SAL_CA1508AA Montevideo
+SAL_CA1535AA Enteritidis
+SAL_CA1566AA Chandans
+SAL_CA1602AA Enteritidis
+SAL_CA1640AA Enteritidis
+SAL_CA1685AA Bareilly
+SAL_CA1717AA Enteritidis
+SAL_CA1749AA Typhimurium
+SAL_CA1792AA Typhimurium
+SAL_CA1826AA Typhi
+SAL_CA1873AA Enteritidis
+SAL_CA1904AA Potsdam
+SAL_CA1944AA Newport
+SAL_CA1988AA Typhimurium
+SAL_CA2028AA Muenchen
+SAL_CA2093AA Enteritidis
+SAL_CA2094AA Enteritidis
+SAL_CA2095AA Virchow
+SAL_CA2097AA Typhimurium
+SAL_CA2099AA Infantis
+SAL_CA2100AA Agona
+SAL_CA2101AA Poona
+SAL_CA2102AA Typhimurium
+SAL_CA2103AA Braenderup
+SAL_CA2105AA Senftenberg
+SAL_CA2106AA Newport
+SAL_CA2107AA Stanley
+SAL_CA2108AA Bareilly
+SAL_CA2109AA Enteritidis
+SAL_CA2110AA Blockley
+SAL_CA2111AA Give
+SAL_CA0169AA Haifa
+SAL_CA0170AA Newport
+SAL_CA0171AA Infantis
+SAL_CA0172AA Newport
+SAL_CA0175AA Typhi
+SAL_CA0176AA Newport
+SAL_CA0177AA Enteritidis
+SAL_CA0178AA Newport
+SAL_CA0180AA Newport
+SAL_CA0181AA Newport
+SAL_CA0182AA Amager
+SAL_CA0183AA Newport
+SAL_CA0184AA Enteritidis
+SAL_CA0185AA Newport
+SAL_CA0186AA Enteritidis
+SAL_CA0187AA Newport
+SAL_CA2113AA Enteritidis
+SAL_CA2114AA Paratyphi B
+SAL_CA2115AA Typhi
+SAL_CA2116AA Typhimurium
+SAL_CA2117AA Ago
+SAL_CA2120AA Corvallis
+SAL_CA2121AA Enteritidis
+SAL_CA2122AA Virchow
+SAL_CA2123AA Typhimurium
+SAL_CA2124AA Mississippi
+SAL_CA2126AA Coeln
+SAL_CA2127AA Typhi
+SAL_CA2128AA Typhimurium
+SAL_CA2132AA Enteritidis
+SAL_CA2133AA Enteritidis
+SAL_CA2134AA Enteritidis
+SAL_CA2137AA Typhimurium
+SAL_CA2138AA Enteritidis
+SAL_CA2139AA Orientalis
+SAL_CA2140AA Enteritidis
+SAL_CA2141AA Enteritidis
+SAL_CA2142AA Kentucky
+SAL_CA2144AA Schwarzengrund
+SAL_CA2145AA Stanley
+SAL_CA2146AA Enteritidis
+SAL_CA2147AA Braenderup
+SAL_CA2148AA Muenchen
+SAL_CA2149AA Infantis
+SAL_CA2150AA Enteritidis
+SAL_CA2151AA Enteritidis
+SAL_CA2153AA Typhi
+SAL_CA2156AA Paratyphi A
+SAL_CA2159AA Oranienburg
+SAL_CA2160AA Enteritidis
+SAL_CA2162AA Enteritidis
+SAL_CA2163AA Glostrup
+SAL_CA2165AA Enteritidis
+SAL_CA2166AA Stanley
+SAL_CA2167AA Enteritidis
+SAL_CA2168AA Ohio
+SAL_CA2169AA Enteritidis
+SAL_CA2170AA Enteritidis
+SAL_CA2171AA Enteritidis
+SAL_CA2172AA Paratyphi A
+SAL_CA2174AA Agona
+SAL_CA2175AA Enteritidis
+SAL_CA2176AA Typhimurium
+SAL_CA2177AA Enteritidis
+SAL_CA2179AA Ago
+SAL_CA2180AA Newport
+SAL_CA2181AA Typhi
+SAL_CA2182AA Stanley
+SAL_CA2183AA Enteritidis
+SAL_CA2184AA Enteritidis
+SAL_CA2185AA Newport
+SAL_CA2190AA Enteritidis
+SAL_CA2191AA Enteritidis
+SAL_CA2192AA Virchow
+SAL_CA2197AA Virchow
+SAL_CA2198AA Eastbourne
+SAL_CA2199AA Enteritidis
+SAL_CA2200AA Enteritidis
+SAL_CA2201AA Paratyphi A
+SAL_CA2202AA Montevideo
+SAL_CA2204AA Stanleyville
+SAL_CA2205AA Enteritidis
+SAL_CA2206AA Kentucky
+SAL_CA2208AA Enteritidis
+SAL_CA2209AA Enteritidis
+SAL_CA2211AA Typhimurium
+SAL_CA2213AA Enteritidis
+SAL_CA2214AA Enteritidis
+SAL_CA2215AA Infantis
+SAL_CA2217AA Enteritidis
+SAL_CA2219AA Mbandaka
+SAL_CA2220AA Hadar
+SAL_CA2221AA Enteritidis
+SAL_CA2222AA Typhimurium
+SAL_CA2223AA Infantis
+SAL_CA2224AA Enteritidis
+SAL_CA2228AA Stanley
+SAL_CA2229AA Enteritidis
+SAL_CA2230AA Typhi
+SAL_CA2231AA Enteritidis
+SAL_CA2232AA Typhimurium
+SAL_CA2233AA Typhi
+SAL_CA2234AA Infantis
+SAL_CA2236AA Isangi
+SAL_CA2237AA Bredeney
+SAL_CA2238AA Kentucky
+SAL_CA2239AA Infantis
+SAL_CA2240AA Typhimurium
+SAL_CA2242AA Enteritidis
+SAL_CA2244AA Infantis
+SAL_CA2247AA Oranienburg
+SAL_CA2248AA Stanley
+SAL_CA2252AA Enteritidis
+SAL_CA2254AA Typhi
+SAL_CA2255AA Enteritidis
+SAL_CA2258AA Montevideo
+SAL_CA2259AA Enteritidis
+SAL_CA2260AA Hadar
+SAL_CA2261AA Typhimurium
+SAL_CA2262AA Mississippi
+SAL_CA2263AA Virchow
+SAL_CA2264AA Wangata
+SAL_CA2265AA Enteritidis
+SAL_CA2266AA Braenderup
+SAL_CA2267AA Typhimurium
+SAL_CA2268AA Typhimurium
+SAL_CA2269AA Virchow
+SAL_CA2270AA Typhimurium
+SAL_CA0189AA Newport
+SAL_CA0191AA Newport
+SAL_CA0192AA Newport
+SAL_CA0193AA Agbeni
+SAL_CA0194AA Newport
+SAL_CA0195AA Stanley
+SAL_CA0196AA Typhimurium
+SAL_CA0197AA Newport
+SAL_CA0198AA Newport
+SAL_CA0199AA Enteritidis
+SAL_CA0200AA Newport
+SAL_CA0201AA Stanley
+SAL_CA0202AA Newport
+SAL_CA0203AA Newport
+SAL_CA0204AA Enteritidis
+SAL_CA0205AA Newport
+SAL_CA2273AA Enteritidis
+SAL_CA2274AA Newport
+SAL_CA2275AA Virchow
+SAL_CA2276AA Kentucky
+SAL_CA2278AA Typhimurium
+SAL_CA2279AA Schwarzengrund
+SAL_CA2280AA Enteritidis
+SAL_CA2281AA Oslo
+SAL_CA2284AA Enteritidis
+SAL_CA2285AA Saintpaul
+SAL_CA2287AA Paratyphi A
+SAL_CA2289AA Enteritidis
+SAL_CA2290AA Enteritidis
+SAL_CA2291AA Agona
+SAL_CA2293AA Bareilly
+SAL_CA2296AA Typhi
+SAL_CA2298AA Enteritidis
+SAL_CA2299AA Typhimurium
+SAL_CA2301AA Enteritidis
+SAL_CA2302AA Braenderup
+SAL_CA2303AA Typhimurium
+SAL_CA2305AA Virchow
+SAL_CA2307AA Nima
+SAL_CA2308AA Poona
+SAL_CA2309AA Abony
+SAL_CA2310AA Stanley
+SAL_CA2312AA Saintpaul
+SAL_CA2313AA Enteritidis
+SAL_CA2314AA Virchow
+SAL_CA2315AA Enteritidis
+SAL_CA2316AA Bareilly
+SAL_CA2317AA Enteritidis
+SAL_CA2319AA Enteritidis
+SAL_CA2323AA Enteritidis
+SAL_CA2324AA Enteritidis
+SAL_CA2341AA Adelaide
+SAL_CA2342AA Enteritidis
+SAL_CA2345AA Bareilly
+SAL_CA2346AA Enteritidis
+SAL_CA2347AA Kentucky
+SAL_CA2348AA Paratyphi A
+SAL_CA2349AA Typhimurium
+SAL_CA2351AA Bareilly
+SAL_CA2353AA Newport
+SAL_CA2354AA Hadar
+SAL_CA2355AA Kirkee
+SAL_CA2356AA Typhi
+SAL_CA2357AA Bareilly
+SAL_CA2360AA Paratyphi B
+SAL_CA2361AA Newport
+SAL_CA2362AA Enteritidis
+SAL_CA2363AA Braenderup
+SAL_CA2364AA Enteritidis
+SAL_CA2365AA Typhimurium
+SAL_CA2367AA Tennessee
+SAL_CA2368AA Newport
+SAL_CA2369AA Agona
+SAL_CA2370AA Virchow
+SAL_CA2371AA Enteritidis
+SAL_CA2372AA Enteritidis
+SAL_CA2373AA Oranienburg
+SAL_CA2374AA Enteritidis
+SAL_CA2375AA Newport
+SAL_CA2376AA Apapa
+SAL_CA2379AA Enteritidis
+SAL_CA2380AA Newport
+SAL_CA2381AA Enteritidis
+SAL_CA2382AA Cotham
+SAL_CA2383AA Enteritidis
+SAL_CA2385AA Typhimurium
+SAL_CA2387AA Stanley
+SAL_CA2388AA Heidelberg
+SAL_CA2389AA Haifa
+SAL_CA2390AA Enteritidis
+SAL_CA2391AA Paratyphi B
+SAL_CA2392AA Enteritidis
+SAL_CA2395AA Enteritidis
+SAL_CA2396AA Typhi
+SAL_CA2397AA Enteritidis
+SAL_CA2398AA Agona
+SAL_CA2400AA Muenchen
+SAL_CA2402AA Typhimurium
+SAL_CA2403AA Enteritidis
+SAL_CA2404AA Paratyphi A
+SAL_CA2406AA Typhimurium
+SAL_CA2407AA Typhi
+SAL_CA2409AA Enteritidis
+SAL_CA2412AA Enteritidis
+SAL_CA2414AA Cotham
+SAL_CA2416AA Haifa
+SAL_CA2418AA Mbandaka
+SAL_CA2419AA Enteritidis
+SAL_CA2420AA Brancaster
+SAL_CA2421AA Enteritidis
+SAL_CA2422AA Enteritidis
+SAL_CA2423AA Enteritidis
+SAL_CA0207AA Newport
+SAL_CA0208AA Typhimurium
+SAL_CA0209AA Newport
+SAL_CA0210AA Newport
+SAL_CA0211AA Typhimurium
+SAL_CA0212AA Newport
+SAL_CA0213AA Typhimurium
+SAL_CA0214AA Newport
+SAL_CA0215AA Newport
+SAL_CA0216AA Poona
+SAL_CA0217AA Newport
+SAL_CA0219AA Newport
+SAL_CA0220AA Enteritidis
+SAL_CA0221AA Newport
+SAL_CA0222AA Typhimurium
+SAL_CA0223AA Newport
+SAL_CA2425AA Kentucky
+SAL_CA2426AA Nima
+SAL_CA2427AA Enteritidis
+SAL_CA2428AA Enteritidis
+SAL_CA2429AA Nima
+SAL_CA2430AA Enteritidis
+SAL_CA2431AA Enteritidis
+SAL_CA2432AA Enteritidis
+SAL_CA2433AA Typhi
+SAL_CA2435AA Typhimurium
+SAL_CA2437AA Braenderup
+SAL_CA2438AA Enteritidis
+SAL_CA2439AA Ealing
+SAL_CA2440AA Typhi
+SAL_CA2441AA Enteritidis
+SAL_CA2442AA Kentucky
+SAL_CA2445AA Enteritidis
+SAL_CA2446AA Typhimurium
+SAL_CA2449AA Enteritidis
+SAL_CA2450AA Chester
+SAL_CA2451AA Javiana
+SAL_CA2454AA Braenderup
+SAL_CA2455AA Enteritidis
+SAL_CA2456AA Typhi
+SAL_CA2457AA Typhimurium
+SAL_CA2458AA Enteritidis
+SAL_CA2459AA Typhi
+SAL_CA2460AA Oranienburg
+SAL_CA2461AA Enteritidis
+SAL_CA2462AA Paratyphi A
+SAL_CA2463AA Enteritidis
+SAL_CA2464AA Mbandaka
+SAL_CA2092AA Bareilly
+SAL_CA2112AA Stanley
+SAL_CA2136AA Javiana
+SAL_CA2157AA Enteritidis
+SAL_CA2178AA Enteritidis
+SAL_CA2203AA Enteritidis
+SAL_CA2225AA Kentucky
+SAL_CA2249AA Typhimurium
+SAL_CA2271AA Poona
+SAL_CA2297AA Typhimurium
+SAL_CA2318AA Paratyphi A
+SAL_CA2358AA Typhimurium
+SAL_CA2377AA Typhimurium
+SAL_CA2399AA Enteritidis
+SAL_CA2424AA Typhimurium
+SAL_CA2466AA Newport
+SAL_CA2468AA Typhi
+SAL_CA2469AA Bareilly
+SAL_CA2470AA Typhi
+SAL_CA2473AA Enteritidis
+SAL_CA2474AA Enteritidis
+SAL_CA2475AA Oranienburg
+SAL_CA2477AA Braenderup
+SAL_CA2478AA Typhimurium
+SAL_CA2480AA Typhi
+SAL_CA2482AA Ohio
+SAL_CA2484AA Poona
+SAL_CA2486AA Typhimurium
+SAL_CA2487AA Newport
+SAL_CA2488AA Montevideo
+SAL_CA2489AA Enteritidis
+SAL_CA2492AA Enteritidis
+SAL_CA2493AA Enteritidis
+SAL_CA2494AA Rissen
+SAL_CA2495AA Stanley
+SAL_CA2498AA Enteritidis
+SAL_CA2503AA Typhi
+SAL_CA2504AA Enteritidis
+SAL_CA2505AA Enteritidis
+SAL_CA2506AA Kottbus
+SAL_CA2507AA Enteritidis
+SAL_CA2508AA Kentucky
+SAL_CA2509AA Enteritidis
+SAL_CA2510AA Typhimurium
+SAL_CA2511AA Typhimurium
+SAL_CA2512AA Mikawasima
+SAL_CA2513AA Enteritidis
+SAL_CA2515AA Enteritidis
+SAL_CA2516AA Enteritidis
+SAL_CA2517AA Braenderup
+SAL_CA2518AA Livingstone
+SAL_CA2519AA Hadar
+SAL_CA2520AA Hadar
+SAL_CA2522AA Enteritidis
+SAL_CA2523AA Infantis
+SAL_CA2524AA Typhimurium
+SAL_CA2525AA Agona
+SAL_CA2528AA Mississippi
+SAL_CA2530AA Tees
+SAL_CA2532AA Typhimurium
+SAL_CA2533AA Typhimurium
+SAL_CA2534AA Kentucky
+SAL_CA2535AA Infantis
+SAL_CA2537AA Adelaide
+SAL_CA2538AA Enteritidis
+SAL_CA2539AA Enteritidis
+SAL_CA2543AA Typhi
+SAL_CA2544AA Paratyphi A
+SAL_CA2545AA Typhimurium
+SAL_CA2546AA Enteritidis
+SAL_CA2547AA Montevideo
+SAL_CA2549AA Enteritidis
+SAL_CA2551AA I 4,[5],12:i:-
+SAL_CA2552AA Typhimurium
+SAL_CA2553AA Richmond
+SAL_CA2554AA Typhimurium
+SAL_CA2555AA Enteritidis
+SAL_CA2557AA Enteritidis
+SAL_CA2558AA Typhimurium
+SAL_CA2560AA Newport
+SAL_CA2561AA Enteritidis
+SAL_CA2563AA London
+SAL_CA2564AA Enteritidis
+SAL_CA2565AA Typhimurium
+SAL_CA2566AA Cerro
+SAL_CA2567AA Enteritidis
+SAL_CA2568AA Enteritidis
+SAL_CA2569AA Curacao
+SAL_CA2570AA Enteritidis
+SAL_CA2571AA Worthington
+SAL_CA2572AA Enteritidis
+SAL_CA2573AA Bredeney
+SAL_CA2574AA Typhimurium
+SAL_CA2575AA Enteritidis
+SAL_CA2576AA Typhimurium
+SAL_CA2578AA Typhi
+SAL_CA2579AA Agona
+SAL_CA2580AA Enteritidis
+SAL_CA2581AA Kentucky
+SAL_CA2582AA Typhimurium
+SAL_CA2583AA Infantis
+SAL_CA2584AA Blockley
+SAL_CA2586AA Agona
+SAL_CA2587AA Saintpaul
+SAL_CA2588AA Enteritidis
+SAL_CA2590AA Corvallis
+SAL_CA2591AA Enteritidis
+SAL_CA2592AA Gaminara
+SAL_CA2593AA Enteritidis
+SAL_CA2594AA Stanley
+SAL_CA2595AA Corvallis
+SAL_CA2597AA Muenchen
+SAL_CA2598AA Typhimurium
+SAL_CA2600AA Abony
+SAL_CA2601AA Stanley
+SAL_CA2602AA Agona
+SAL_CA2604AA Enteritidis
+SAL_CA2605AA Enteritidis
+SAL_CA2607AA Typhi
+SAL_CA2608AA Kentucky
+SAL_CA2609AA Bareilly
+SAL_CA2610AA Infantis
+SAL_CA2611AA Enteritidis
+SAL_CA2612AA Paratyphi A
+SAL_CA2613AA Poona
+SAL_CA2615AA Enteritidis
+SAL_CA2617AA Enteritidis
+SAL_CA2619AA Enteritidis
+SAL_CA2620AA Brandenburg
+SAL_CA2621AA Paratyphi A
+SAL_CA2622AA Javiana
+SAL_CA2624AA Enteritidis
+SAL_CA2625AA Javiana
+SAL_CA2627AA Bareilly
+SAL_CA2628AA Saintpaul
+SAL_CA2629AA Mbandaka
+SAL_CA2630AA Stanley
+SAL_CA2631AA Enteritidis
+SAL_CA2633AA Virchow
+SAL_CA2634AA Montevideo
+SAL_CA2635AA Virchow
+SAL_CA2636AA Enteritidis
+SAL_CA2637AA Enteritidis
+SAL_CA2640AA Enteritidis
+SAL_CA2642AA Enteritidis
+SAL_CA2643AA Virchow
+SAL_CA2646AA Anatum
+SAL_CA2647AA Newport
+SAL_CA2649AA Poona
+SAL_CA2650AA Enteritidis
+SAL_CA2652AA Enteritidis
+SAL_CA2654AA Infantis
+SAL_CA2655AA Oranienburg
+SAL_CA2656AA Agona
+SAL_CA2657AA Agona
+SAL_CA2658AA Enteritidis
+SAL_CA2661AA Enteritidis
+SAL_CA2663AA Agona
+SAL_CA2664AA Enteritidis
+SAL_CA2666AA Agona
+SAL_CA2667AA Albany
+SAL_CA2668AA Enteritidis
+SAL_CA2669AA Livingstone
+SAL_CA2670AA Kentucky
+SAL_CA2671AA Enteritidis
+SAL_CA2673AA Enteritidis
+SAL_CA2674AA Enteritidis
+SAL_CA2676AA Typhimurium
+SAL_CA2677AA Braenderup
+SAL_CA2678AA Mbandaka
+SAL_CA2679AA Typhimurium
+SAL_CA2680AA Infantis
+SAL_CA2682AA Infantis
+SAL_CA2683AA Anatum
+SAL_CA2684AA Typhimurium
+SAL_CA2686AA Oranienburg
+SAL_CA2687AA Enteritidis
+SAL_CA2688AA Enteritidis
+SAL_CA2691AA Oranienburg
+SAL_CA2692AA I 4,[5],12:i:-
+SAL_CA2693AA Coeln
+SAL_CA2694AA Enteritidis
+SAL_CA2697AA Enteritidis
+SAL_CA2698AA Enteritidis
+SAL_CA2699AA Virchow
+SAL_CA2700AA Kentucky
+SAL_CA2701AA Enteritidis
+SAL_CA2702AA Montevideo
+SAL_CA2703AA Infantis
+SAL_CA2704AA Enteritidis
+SAL_CA2705AA Hadar
+SAL_CA2708AA Enteritidis
+SAL_CA2709AA Typhi
+SAL_CA2710AA Enteritidis
+SAL_CA2711AA Infantis
+SAL_CA2715AA Typhimurium
+SAL_CA2716AA Enteritidis
+SAL_CA2717AA Kentucky
+SAL_CA2718AA Typhimurium
+SAL_CA2719AA Infantis
+SAL_CA2721AA Agama
+SAL_CA2723AA Typhimurium
+SAL_CA2724AA Typhimurium
+SAL_CA2726AA Enteritidis
+SAL_CA2728AA Enteritidis
+SAL_CA2729AA Oranienburg
+SAL_CA2731AA Fluntern
+SAL_CA2733AA Derby
+SAL_CA2736AA Enteritidis
+SAL_CA2738AA Oranienburg
+SAL_CA2739AA Enteritidis
+SAL_CA2740AA Enteritidis
+SAL_CA2741AA Anatum
+SAL_CA2742AA Muenchen
+SAL_CA2743AA Enteritidis
+SAL_CA2744AA Stanley
+SAL_CA2745AA Infantis
+SAL_CA2748AA Infantis
+SAL_CA2749AA Enteritidis
+SAL_CA2750AA Typhimurium
+SAL_CA2751AA Agona
+SAL_CA2753AA Enteritidis
+SAL_CA2754AA Typhimurium
+SAL_CA0225AA Newport
+SAL_CA0226AA Newport
+SAL_CA0227AA Newport
+SAL_CA0228AA Newport
+SAL_CA0229AA Enteritidis
+SAL_CA0230AA Newport
+SAL_CA0231AA Oranienburg
+SAL_CA0232AA Newport
+SAL_CA0233AA Mgulani
+SAL_CA0235AA Newport
+SAL_CA0237AA Paratyphi A
+SAL_CA0239AA Paratyphi A
+SAL_CA0240AA Enteritidis
+SAL_CA0241AA Paratyphi A
+SAL_CA0242AA Paratyphi A
+SAL_CA0243AA Paratyphi A
+SAL_CA2756AA Enteritidis
+SAL_CA2758AA Hadar
+SAL_CA2760AA Newport
+SAL_CA2761AA Newport
+SAL_CA2765AA Derby
+SAL_CA2767AA Enteritidis
+SAL_CA2769AA Enteritidis
+SAL_CA2770AA Mikawasima
+SAL_CA2772AA Enteritidis
+SAL_CA2773AA Enteritidis
+SAL_CA2774AA Enteritidis
+SAL_CA2775AA Typhimurium
+SAL_CA2779AA Enteritidis
+SAL_CA2780AA Newport
+SAL_CA2781AA Newport
+SAL_CA2782AA Montevideo
+SAL_CA2786AA Enteritidis
+SAL_CA2787AA Kentucky
+SAL_CA2788AA Enteritidis
+SAL_CA2789AA Paratyphi A
+SAL_CA2790AA Typhi
+SAL_CA2791AA Alachua
+SAL_CA2792AA Enteritidis
+SAL_CA2793AA Enteritidis
+SAL_CA2794AA Enteritidis
+SAL_CA2795AA Durham
+SAL_CA2796AA Enteritidis
+SAL_CA2797AA Enteritidis
+SAL_CA2799AA Enteritidis
+SAL_CA2800AA Enteritidis
+SAL_CA2801AA Enteritidis
+SAL_CA2802AA Enteritidis
+SAL_CA2805AA Braenderup
+SAL_CA2806AA Oslo
+SAL_CA2807AA Enteritidis
+SAL_CA2808AA Oslo
+SAL_CA2809AA Enteritidis
+SAL_CA2811AA Enteritidis
+SAL_CA2812AA Coeln
+SAL_CA2813AA Enteritidis
+SAL_CA2814AA Senftenberg
+SAL_CA2815AA Kentucky
+SAL_CA2816AA Agama
+SAL_CA2818AA Kalina
+SAL_CA2820AA Chester
+SAL_CA2822AA Typhimurium
+SAL_CA2823AA Typhimurium
+SAL_CA2824AA Indiana
+SAL_CA2465AA Enteritidis
+SAL_CA2490AA Durham
+SAL_CA2514AA Brandenburg
+SAL_CA2536AA Newport
+SAL_CA2559AA Albany
+SAL_CA2577AA Enteritidis
+SAL_CA2596AA Enteritidis
+SAL_CA2618AA Napoli
+SAL_CA2639AA Typhimurium
+SAL_CA2665AA Anatum
+SAL_CA2685AA Enteritidis
+SAL_CA2707AA Wangata
+SAL_CA2732AA Oranienburg
+SAL_CA2755AA Enteritidis
+SAL_CA2784AA Enteritidis
+SAL_CA2826AA Fulica
+SAL_CA2827AA Infantis
+SAL_CA2828AA Jangwani
+SAL_CA2829AA Enteritidis
+SAL_CA2830AA Colindale
+SAL_CA2831AA Stanleyville
+SAL_CA2834AA Enteritidis
+SAL_CA2835AA Hadar
+SAL_CA2838AA Enteritidis
+SAL_CA2840AA Enteritidis
+SAL_CA2841AA Typhimurium
+SAL_CA2842AA Newport
+SAL_CA2844AA Bareilly
+SAL_CA2845AA Livingstone
+SAL_CA2847AA Typhimurium
+SAL_CA2848AA Enteritidis
+SAL_CA2851AA Tennessee
+SAL_CA2852AA Enteritidis
+SAL_CA2854AA Kentucky
+SAL_CA2855AA Paratyphi A
+SAL_CA2856AA Enteritidis
+SAL_CA2858AA Virchow
+SAL_CA2860AA Enteritidis
+SAL_CA2861AA Yarrabah
+SAL_CA2862AA Enteritidis
+SAL_CA2863AA Enteritidis
+SAL_CA2865AA Agama
+SAL_CA2866AA Infantis
+SAL_CA2867AA Typhimurium
+SAL_CA2868AA Typhimurium
+SAL_CA2870AA Kentucky
+SAL_CA2871AA Infantis
+SAL_CA2873AA Hadar
+SAL_CA2874AA Typhimurium
+SAL_CA2876AA Agona
+SAL_CA2877AA Enteritidis
+SAL_CA2878AA Typhimurium
+SAL_CA2879AA Enteritidis
+SAL_CA2880AA Enteritidis
+SAL_CA2881AA Newport
+SAL_CA2882AA Enteritidis
+SAL_CA2884AA Typhimurium
+SAL_CA2885AA Enteritidis
+SAL_CA2886AA Enteritidis
+SAL_CA2887AA Litchfield
+SAL_CA2889AA Livingstone
+SAL_CA2890AA Typhi
+SAL_CA2891AA Enteritidis
+SAL_CA2895AA Enteritidis
+SAL_CA2898AA Typhi
+SAL_CA2900AA Enteritidis
+SAL_CA2901AA Bareilly
+SAL_CA2902AA Typhimurium
+SAL_CA2903AA Bareilly
+SAL_CA2904AA Typhi
+SAL_CA2905AA Mississippi
+SAL_CA2906AA Virchow
+SAL_CA2907AA Overschie
+SAL_CA2908AA Enteritidis
+SAL_CA2909AA Typhimurium
+SAL_CA2910AA Enteritidis
+SAL_CA2911AA Newport
+SAL_CA2912AA Montevideo
+SAL_CA2914AA Enteritidis
+SAL_CA0245AA Paratyphi A
+SAL_CA0246AA Kenya
+SAL_CA0247AA Paratyphi A
+SAL_CA0248AA Paratyphi A
+SAL_CA0249AA Kentucky
+SAL_CA0250AA Paratyphi A
+SAL_CA0251AA Anatum
+SAL_CA0252AA Paratyphi A
+SAL_CA0253AA Enteritidis
+SAL_CA0254AA Paratyphi A
+SAL_CA0256AA Paratyphi A
+SAL_CA0257AA Enteritidis
+SAL_CA0258AA Paratyphi A
+SAL_CA0259AA Typhimurium
+SAL_CA0260AA Paratyphi A
+SAL_CA0261AA Enteritidis
+SAL_CA2916AA Weltevreden
+SAL_CA2917AA Virchow
+SAL_CA2918AA Enteritidis
+SAL_CA2919AA Enteritidis
+SAL_CA2920AA Typhimurium
+SAL_CA2921AA Enteritidis
+SAL_CA2922AA Typhi
+SAL_CA2923AA Typhimurium
+SAL_CA2924AA Brandenburg
+SAL_CA2925AA Enteritidis
+SAL_CA2926AA Typhimurium
+SAL_CA2927AA Derby
+SAL_CA2928AA Kentucky
+SAL_CA2929AA Infantis
+SAL_CA2930AA Enteritidis
+SAL_CA2931AA Braenderup
+SAL_CA2933AA Enteritidis
+SAL_CA2934AA Newport
+SAL_CA2936AA Typhi
+SAL_CA2937AA Enteritidis
+SAL_CA2938AA Enteritidis
+SAL_CA2939AA Brandenburg
+SAL_CA2940AA Typhimurium
+SAL_CA2941AA Infantis
+SAL_CA2942AA Enteritidis
+SAL_CA2943AA Enteritidis
+SAL_CA2944AA Typhimurium
+SAL_CA2946AA Typhi
+SAL_CA2947AA Kottbus
+SAL_CA2948AA Enteritidis
+SAL_CA2949AA Typhimurium
+SAL_CA2950AA Paratyphi A
+SAL_CA2952AA Enteritidis
+SAL_CA2953AA Enteritidis
+SAL_CA2954AA Mbandaka
+SAL_CA2955AA Jangwani
+SAL_CA2956AA Enteritidis
+SAL_CA2957AA Colindale
+SAL_CA2958AA Typhimurium
+SAL_CA2959AA Enteritidis
+SAL_CA2960AA Agbeni
+SAL_CA2961AA Monschaui
+SAL_CA2962AA Enteritidis
+SAL_CA2963AA Typhimurium
+SAL_CA2964AA Typhimurium
+SAL_CA2965AA Enteritidis
+SAL_CA2966AA Enteritidis
+SAL_CA2967AA Enteritidis
+SAL_CA2969AA Enteritidis
+SAL_CA2970AA Typhi
+SAL_CA2971AA Kentucky
+SAL_CA2972AA Paratyphi A
+SAL_CA2974AA Kottbus
+SAL_CA2976AA Enteritidis
+SAL_CA2980AA Typhi
+SAL_CA2981AA Braenderup
+SAL_CA2982AA Kentucky
+SAL_CA2985AA Typhimurium
+SAL_CA2986AA Enteritidis
+SAL_CA2987AA Enteritidis
+SAL_CA2989AA Typhimurium
+SAL_CA2990AA Enteritidis
+SAL_CA2991AA Typhimurium
+SAL_CA2993AA Enteritidis
+SAL_CA2996AA Newport
+SAL_CA2997AA Enteritidis
+SAL_CA2998AA Typhimurium
+SAL_CA2999AA Enteritidis
+SAL_CA3000AA Enteritidis
+SAL_CA3001AA Enteritidis
+SAL_CA3002AA Enteritidis
+SAL_CA3003AA Enteritidis
+SAL_CA3004AA Enteritidis
+SAL_CA3005AA Enteritidis
+SAL_CA3006AA Typhi
+SAL_CA3007AA Enteritidis
+SAL_CA3009AA Cubana
+SAL_CA3011AA Enteritidis
+SAL_CA3012AA Newport
+SAL_CA3013AA Agona
+SAL_CA3015AA Kentucky
+SAL_CA3016AA Virchow
+SAL_CA3017AA Mikawasima
+SAL_CA3018AA Jangwani
+SAL_CA3019AA Corvallis
+SAL_CA3020AA Enteritidis
+SAL_CA3021AA Oranienburg
+SAL_CA3022AA Javiana
+SAL_CA3025AA Enteritidis
+SAL_CA3026AA Mbandaka
+SAL_CA3027AA Vitkin
+SAL_CA3028AA Mikawasima
+SAL_CA3029AA Typhimurium
+SAL_CA3031AA Enteritidis
+SAL_CA3032AA Infantis
+SAL_CA3033AA Enteritidis
+SAL_CA3036AA Enteritidis
+SAL_CA3038AA Derby
+SAL_CA3039AA Typhimurium
+SAL_CA3040AA Enteritidis
+SAL_CA3041AA Infantis
+SAL_CA3042AA Typhimurium
+SAL_CA3043AA Enteritidis
+SAL_CA3045AA Enteritidis
+SAL_CA3046AA Enteritidis
+SAL_CA3047AA Enteritidis
+SAL_CA3048AA Enteritidis
+SAL_CA3049AA Enteritidis
+SAL_CA3050AA Enteritidis
+SAL_CA3052AA Enteritidis
+SAL_CA3053AA Jangwani
+SAL_CA3054AA Typhimurium
+SAL_CA3056AA Livingstone
+SAL_CA3057AA Braenderup
+SAL_CA3060AA Enteritidis
+SAL_CA3061AA Newport
+SAL_CA3062AA Enteritidis
+SAL_CA3063AA Muenchen
+SAL_CA3064AA Infantis
+SAL_CA3066AA Anatum
+SAL_CA3068AA Enteritidis
+SAL_CA3069AA Typhi
+SAL_CA3070AA Napoli
+SAL_CA3071AA Enteritidis
+SAL_CA3072AA Enteritidis
+SAL_CA3073AA Stanley
+SAL_CA3074AA Oranienburg
+SAL_CA3075AA Virchow
+SAL_CA0263AA Typhimurium
+SAL_CA0264AA Paratyphi A
+SAL_CA0265AA Paratyphi A
+SAL_CA0266AA Enteritidis
+SAL_CA0267AA Paratyphi A
+SAL_CA0269AA Paratyphi A
+SAL_CA0271AA Paratyphi A
+SAL_CA0273AA Paratyphi A
+SAL_CA0274AA I 4,[5],12:i:-
+SAL_CA0275AA Paratyphi A
+SAL_CA0276AA Typhimurium
+SAL_CA0277AA Paratyphi A
+SAL_CA0278AA Enteritidis
+SAL_CA0279AA Paratyphi A
+SAL_CA0280AA Paratyphi A
+SAL_CA0282AA Paratyphi A
+SAL_CA3077AA Enteritidis
+SAL_CA3078AA Enteritidis
+SAL_CA3079AA Enteritidis
+SAL_CA3080AA Isangi
+SAL_CA3082AA Herston
+SAL_CA3083AA Typhimurium
+SAL_CA3085AA Bareilly
+SAL_CA3086AA Richmond
+SAL_CA3087AA Enteritidis
+SAL_CA3090AA Kentucky
+SAL_CA3092AA Infantis
+SAL_CA3093AA Typhimurium
+SAL_CA3095AA Kentucky
+SAL_CA3097AA Enteritidis
+SAL_CA3098AA Newport
+SAL_CA3099AA Dublin
+SAL_CA3103AA Typhimurium
+SAL_CA3104AA Typhimurium
+SAL_CA3105AA Enteritidis
+SAL_CA3106AA Enteritidis
+SAL_CA3107AA Kentucky
+SAL_CA3108AA Enteritidis
+SAL_CA3110AA Enteritidis
+SAL_CA3111AA Enteritidis
+SAL_CA3113AA Enteritidis
+SAL_CA3114AA Enteritidis
+SAL_CA3116AA Enteritidis
+SAL_CA3118AA Enteritidis
+SAL_CA3120AA Enteritidis
+SAL_CA3121AA Infantis
+SAL_CA3125AA Enteritidis
+SAL_CA3126AA Typhi
+SAL_CA3129AA Paratyphi A
+SAL_CA3130AA Typhimurium
+SAL_CA3132AA Virchow
+SAL_CA3133AA Ealing
+SAL_CA3134AA Enteritidis
+SAL_CA3135AA Typhi
+SAL_CA3136AA Typhimurium
+SAL_CA3138AA Rissen
+SAL_CA3140AA Ohio
+SAL_CA3141AA Enteritidis
+SAL_CA3142AA Enteritidis
+SAL_CA3143AA Enteritidis
+SAL_CA3144AA Infantis
+SAL_CA3146AA Enteritidis
+SAL_CA3147AA Monschaui
+SAL_CA3148AA Bonn
+SAL_CA3152AA Livingstone
+SAL_CA3153AA Enteritidis
+SAL_CA3154AA Typhimurium
+SAL_CA3155AA Virchow
+SAL_CA3157AA Typhimurium
+SAL_CA3158AA Typhimurium
+SAL_CA3159AA Enteritidis
+SAL_CA3161AA Enteritidis
+SAL_CA3162AA Haifa
+SAL_CA3164AA Braenderup
+SAL_CA3165AA Enteritidis
+SAL_CA3166AA Enteritidis
+SAL_CA3167AA Enteritidis
+SAL_CA3168AA Enteritidis
+SAL_CA3169AA Stanley
+SAL_CA3170AA Newport
+SAL_CA2825AA Enteritidis
+SAL_CA2850AA Enteritidis
+SAL_CA2872AA Enteritidis
+SAL_CA2893AA Bredeney
+SAL_CA2915AA Enteritidis
+SAL_CA2932AA Enteritidis
+SAL_CA2951AA Enteritidis
+SAL_CA2968AA Typhimurium
+SAL_CA2995AA Enteritidis
+SAL_CA3014AA Haifa
+SAL_CA3034AA Enteritidis
+SAL_CA3055AA Enteritidis
+SAL_CA3076AA Manchester
+SAL_CA3101AA Newport
+SAL_CA3128AA Typhimurium
+SAL_CA3174AA Enteritidis
+SAL_CA3177AA Bareilly
+SAL_CA3178AA Oslo
+SAL_CA3179AA Paratyphi A
+SAL_CA3181AA Ohio
+SAL_CA3182AA Enteritidis
+SAL_CA3184AA Infantis
+SAL_CA3186AA Oranienburg
+SAL_CA3187AA Grancanaria
+SAL_CA3188AA Typhimurium
+SAL_CA3189AA Bareilly
+SAL_CA3190AA Enteritidis
+SAL_CA3191AA Typhimurium
+SAL_CA3192AA Kenya
+SAL_CA3193AA Enteritidis
+SAL_CA3195AA Saintpaul
+SAL_CA3197AA Derby
+SAL_CA3199AA Enteritidis
+SAL_CA3200AA Enteritidis
+SAL_CA3201AA Enteritidis
+SAL_CA3202AA Birkenhead
+SAL_CA3205AA Typhimurium
+SAL_CA3206AA Enteritidis
+SAL_CA3207AA Enteritidis
+SAL_CA3208AA Virchow
+SAL_CA3209AA Enteritidis
+SAL_CA3210AA Hadar
+SAL_CA3211AA Livingstone
+SAL_CA3212AA Enteritidis
+SAL_CA3213AA Tamale
+SAL_CA3216AA Enteritidis
+SAL_CA3217AA Enteritidis
+SAL_CA0284AA Paratyphi A
+SAL_CA0285AA Typhimurium
+SAL_CA0286AA Paratyphi A
+SAL_CA0288AA Paratyphi A
+SAL_CA0289AA Paratyphi A
+SAL_CA0291AA Paratyphi A
+SAL_CA0292AA Enteritidis
+SAL_CA0293AA Paratyphi A
+SAL_CA0294AA Dublin
+SAL_CA0296AA Paratyphi A
+SAL_CA0297AA Virchow
+SAL_CA0298AA Paratyphi A
+SAL_CA0299AA Paratyphi A
+SAL_CA0301AA Paratyphi A
+SAL_CA0302AA Enteritidis
+SAL_CA0303AA Paratyphi A
+SAL_CA3221AA Enteritidis
+SAL_CA3222AA Irumu
+SAL_CA3224AA Enteritidis
+SAL_CA3225AA Shubra
+SAL_CA3226AA Enteritidis
+SAL_CA3227AA Takoradi
+SAL_CA3228AA Stanley
+SAL_CA3229AA Albany
+SAL_CA3230AA Enteritidis
+SAL_CA3231AA Typhimurium
+SAL_CA3233AA Enteritidis
+SAL_CA3235AA Typhi
+SAL_CA3236AA Stanley
+SAL_CA3239AA Braenderup
+SAL_CA3241AA Enteritidis
+SAL_CA3242AA Mississippi
+SAL_CA3245AA Typhimurium
+SAL_CA3246AA Enteritidis
+SAL_CA3247AA Enteritidis
+SAL_CA3248AA Enteritidis
+SAL_CA3249AA Typhimurium
+SAL_CA3250AA Typhimurium
+SAL_CA3251AA Typhimurium
+SAL_CA3253AA Enteritidis
+SAL_CA3254AA Kentucky
+SAL_CA3255AA Enteritidis
+SAL_CA3256AA Enteritidis
+SAL_CA3257AA Paratyphi A
+SAL_CA3259AA Enteritidis
+SAL_CA3260AA Blockley
+SAL_CA3261AA Indiana
+SAL_CA3262AA Altona
+SAL_CA3264AA Braenderup
+SAL_CA3265AA Agona
+SAL_CA3268AA Corvallis
+SAL_CA3269AA Enteritidis
+SAL_CA3270AA Typhimurium
+SAL_CA3272AA Agama
+SAL_CA3273AA Paratyphi A
+SAL_CA3274AA Enteritidis
+SAL_CA3275AA Typhi
+SAL_CA3276AA Enteritidis
+SAL_CA3277AA Rissen
+SAL_CA3278AA Enteritidis
+SAL_CA3279AA Enteritidis
+SAL_CA3280AA Enteritidis
+SAL_CA3281AA Enteritidis
+SAL_CA3282AA Enteritidis
+SAL_CA3284AA Typhimurium
+SAL_CA3285AA Enteritidis
+SAL_CA3286AA Enteritidis
+SAL_CA3287AA Enteritidis
+SAL_CA3288AA Typhi
+SAL_CA3289AA Oslo
+SAL_CA3290AA Hartford
+SAL_CA3291AA Brandenburg
+SAL_CA3292AA Paratyphi A
+SAL_CA3294AA London
+SAL_CA3295AA Enteritidis
+SAL_CA3296AA Kentucky
+SAL_CA3297AA Newport
+SAL_CA3298AA Typhimurium
+SAL_CA3299AA Enteritidis
+SAL_CA3300AA Bredeney
+SAL_CA3303AA Stanley
+SAL_CA3306AA Stanley
+SAL_CA3307AA Stanley
+SAL_CA3308AA Enteritidis
+SAL_CA3310AA Newport
+SAL_CA3311AA Typhimurium
+SAL_CA3312AA Enteritidis
+SAL_CA3314AA Tees
+SAL_CA3316AA Hadar
+SAL_CA3317AA Typhimurium
+SAL_CA3320AA Panama
+SAL_CA3321AA Enteritidis
+SAL_CA3322AA Enteritidis
+SAL_CA3323AA Bareilly
+SAL_CA3324AA Enteritidis
+SAL_CA3325AA Enteritidis
+SAL_CA3327AA Enteritidis
+SAL_CA3328AA Enteritidis
+SAL_CA3330AA Poona
+SAL_CA3331AA Typhimurium
+SAL_CA3332AA Typhimurium
+SAL_CA3333AA Kentucky
+SAL_CA3335AA Typhimurium
+SAL_CA3336AA Haifa
+SAL_CA3337AA Enteritidis
+SAL_CA3338AA Bredeney
+SAL_CA3339AA Enteritidis
+SAL_CA3340AA Livingstone
+SAL_CA3342AA Enteritidis
+SAL_CA3343AA Enteritidis
+SAL_CA3344AA Hadar
+SAL_CA3345AA Enteritidis
+SAL_CA3347AA Enteritidis
+SAL_CA3348AA Typhimurium
+SAL_CA3350AA Typhimurium
+SAL_CA3351AA Enteritidis
+SAL_CA3357AA Newport
+SAL_CA3358AA Braenderup
+SAL_CA3359AA Enteritidis
+SAL_CA3360AA Newport
+SAL_CA3361AA Enteritidis
+SAL_CA3363AA Enteritidis
+SAL_CA3364AA Typhimurium
+SAL_CA3365AA Virchow
+SAL_CA3366AA Enteritidis
+SAL_CA3367AA Enteritidis
+SAL_CA3368AA Give
+SAL_CA3369AA Typhimurium
+SAL_CA3372AA Enteritidis
+SAL_CA3373AA Enteritidis
+SAL_CA3374AA Senftenberg
+SAL_CA3375AA Typhimurium
+SAL_CA3376AA Enteritidis
+SAL_CA3378AA Oranienburg
+SAL_CA3379AA Enteritidis
+SAL_CA3380AA Enteritidis
+SAL_CA3382AA Stanley
+SAL_CA3383AA Enteritidis
+SAL_CA3384AA Enteritidis
+SAL_CA3385AA Enteritidis
+SAL_CA3387AA Typhimurium
+SAL_CA3388AA Enteritidis
+SAL_CA3390AA Derby
+SAL_CA3392AA Monschaui
+SAL_CA3397AA Bareilly
+SAL_CA3398AA Ohio
+SAL_CA3399AA Enteritidis
+SAL_CA3401AA Infantis
+SAL_CA3402AA Kentucky
+SAL_CA3403AA Typhimurium
+SAL_CA3404AA Oranienburg
+SAL_CA3405AA Agona
+SAL_CA3407AA Give
+SAL_CA3408AA Enteritidis
+SAL_CA3409AA Napoli
+SAL_CA3411AA Infantis
+SAL_CA3412AA Typhi
+SAL_CA3413AA Enteritidis
+SAL_CA3414AA Enteritidis
+SAL_CA3415AA Enteritidis
+SAL_CA3418AA Typhimurium
+SAL_CA3419AA Amager
+SAL_CA3420AA Heidelberg
+SAL_CA3421AA Enteritidis
+SAL_CA3422AA Virchow
+SAL_CA3423AA Muenster
+SAL_CA3424AA Give
+SAL_CA3427AA Typhimurium
+SAL_CA3428AA Paratyphi A
+SAL_CA3430AA Bredeney
+SAL_CA3431AA Enteritidis
+SAL_CA3432AA Typhi
+SAL_CA3433AA Enteritidis
+SAL_CA3434AA Agama
+SAL_CA3435AA Enteritidis
+SAL_CA3437AA Typhimurium
+SAL_CA3439AA Corvallis
+SAL_CA3440AA Enteritidis
+SAL_CA3441AA Livingstone
+SAL_CA3442AA Enteritidis
+SAL_CA3444AA Newport
+SAL_CA3446AA Enteritidis
+SAL_CA3447AA Derby
+SAL_CA3454AA Enteritidis
+SAL_CA3455AA Enteritidis
+SAL_CA3456AA Enteritidis
+SAL_CA3457AA Typhimurium
+SAL_CA3458AA Enteritidis
+SAL_CA3459AA Enteritidis
+SAL_CA3460AA Typhimurium
+SAL_CA3461AA I 4,[5],12:i:-
+SAL_CA3462AA Enteritidis
+SAL_CA3467AA Typhimurium
+SAL_CA3468AA Enteritidis
+SAL_CA3469AA Enteritidis
+SAL_CA3470AA Durham
+SAL_CA3471AA Enteritidis
+SAL_CA3472AA Typhimurium
+SAL_CA3473AA Ituri
+SAL_CA3474AA Typhimurium
+SAL_CA3475AA Enteritidis
+SAL_CA3476AA Mbandaka
+SAL_CA3477AA Newport
+SAL_CA3478AA Enteritidis
+SAL_CA3479AA Enteritidis
+SAL_CA3480AA Enteritidis
+SAL_CA3482AA Paratyphi A
+SAL_CA3484AA Enteritidis
+SAL_CA3486AA Infantis
+SAL_CA3487AA Corvallis
+SAL_CA3488AA Enteritidis
+SAL_CA3489AA Enteritidis
+SAL_CA3490AA Montevideo
+SAL_CA3491AA Typhi
+SAL_CA3492AA Typhimurium
+SAL_CA3494AA Enteritidis
+SAL_CA3495AA Typhimurium
+SAL_CA3496AA Enteritidis
+SAL_CA3497AA Enteritidis
+SAL_CA3498AA Ibadan
+SAL_CA3502AA Stanley
+SAL_CA3503AA Hvittingfoss
+SAL_CA3504AA Enteritidis
+SAL_CA3505AA Enteritidis
+SAL_CA3507AA Typhimurium
+SAL_CA3508AA Kottbus
+SAL_CA3511AA Enteritidis
+SAL_CA3512AA Typhimurium
+SAL_CA3513AA Enteritidis
+SAL_CA3514AA Mikawasima
+SAL_CA3515AA Virchow
+SAL_CA3517AA London
+SAL_CA3518AA Enteritidis
+SAL_CA3519AA Enteritidis
+SAL_CA3520AA Saintpaul
+SAL_CA3521AA Agona
+SAL_CA3522AA Stanleyville
+SAL_CA3523AA Typhimurium
+SAL_CA3525AA Montevideo
+SAL_CA3526AA Typhimurium
+SAL_CA3171AA Infantis
+SAL_CA3196AA Enteritidis
+SAL_CA3220AA Paratyphi A
+SAL_CA3244AA Kentucky
+SAL_CA3263AA Typhimurium
+SAL_CA3283AA Bredeney
+SAL_CA3302AA Enteritidis
+SAL_CA3326AA Typhimurium
+SAL_CA3346AA Montevideo
+SAL_CA3370AA Bareilly
+SAL_CA3394AA Typhi
+SAL_CA3416AA Typhimurium
+SAL_CA3438AA Oranienburg
+SAL_CA3464AA Enteritidis
+SAL_CA3485AA Enteritidis
+SAL_CA3528AA Virchow
+SAL_CA3529AA Virchow
+SAL_CA3531AA Bonariensis
+SAL_CA3533AA Typhimurium
+SAL_CA3534AA Typhimurium
+SAL_CA3536AA Enteritidis
+SAL_CA3538AA Agona
+SAL_CA3539AA Braenderup
+SAL_CA3540AA Enteritidis
+SAL_CA3541AA Enteritidis
+SAL_CA3542AA Anecho
+SAL_CA3543AA Typhimurium
+SAL_CA3544AA Enteritidis
+SAL_CA3545AA Enteritidis
+SAL_CA3546AA Enteritidis
+SAL_CA3547AA Enteritidis
+SAL_CA0305AA Paratyphi A
+SAL_CA0306AA Enteritidis
+SAL_CA0307AA Paratyphi A
+SAL_CA0308AA Enteritidis
+SAL_CA0309AA Paratyphi A
+SAL_CA0311AA Enteritidis
+SAL_CA0312AA Paratyphi A
+SAL_CA0314AA Paratyphi A
+SAL_CA0315AA Enteritidis
+SAL_CA0316AA Paratyphi A
+SAL_CA0317AA Enteritidis
+SAL_CA0318AA Paratyphi A
+SAL_CA0320AA Paratyphi A
+SAL_CA0321AA Paratyphi A
+SAL_CA0322AA Rissen
+SAL_CA0323AA Paratyphi A
+SAL_CA3549AA Typhimurium
+SAL_CA3550AA Enteritidis
+SAL_CA3552AA Enteritidis
+SAL_CA3555AA Enteritidis
+SAL_CA3556AA Stanley
+SAL_CA3557AA Typhimurium
+SAL_CA3558AA Virchow
+SAL_CA3559AA Typhimurium
+SAL_CA3560AA Infantis
+SAL_CA3561AA Enteritidis
+SAL_CA3563AA Typhimurium
+SAL_CA3565AA Kentucky
+SAL_CA3566AA Typhimurium
+SAL_CA3568AA Typhimurium
+SAL_CA3569AA Fluntern
+SAL_CA3570AA Infantis
+SAL_CA3572AA Agona
+SAL_CA3573AA Mbandaka
+SAL_CA3574AA Enteritidis
+SAL_CA3576AA Enteritidis
+SAL_CA3577AA Paratyphi B
+SAL_CA3578AA Rissen
+SAL_CA3579AA Enteritidis
+SAL_CA3580AA Enteritidis
+SAL_CA3581AA Bareilly
+SAL_CA3583AA Agona
+SAL_CA3584AA Enteritidis
+SAL_CA3585AA Virchow
+SAL_CA3586AA Enteritidis
+SAL_CA3587AA Typhimurium
+SAL_CA3588AA Tees
+SAL_CA3589AA Newport
+SAL_CA3591AA Haifa
+SAL_CA3592AA Madras
+SAL_CA3593AA Virchow
+SAL_CA3594AA Typhimurium
+SAL_CA3598AA Kentucky
+SAL_CA3600AA Typhimurium
+SAL_CA3602AA Enteritidis
+SAL_CA3603AA Tennessee
+SAL_CA3604AA Enteritidis
+SAL_CA3605AA Enteritidis
+SAL_CA3606AA Enteritidis
+SAL_CA3607AA Enteritidis
+SAL_CA3608AA I 4,[5],12:i:-
+SAL_CA3609AA Chester
+SAL_CA3610AA Virchow
+SAL_CA3611AA Enteritidis
+SAL_CA3613AA Virchow
+SAL_CA3614AA Enteritidis
+SAL_CA3615AA Enteritidis
+SAL_CA3616AA Enteritidis
+SAL_CA3617AA Oranienburg
+SAL_CA3618AA Enteritidis
+SAL_CA3619AA Typhimurium
+SAL_CA3620AA Rubislaw
+SAL_CA3621AA Dublin
+SAL_CA3622AA Enteritidis
+SAL_CA3623AA Enteritidis
+SAL_CA3624AA Kentucky
+SAL_CA3626AA Newport
+SAL_CA3627AA Enteritidis
+SAL_CA3628AA Enteritidis
+SAL_CA3629AA Enteritidis
+SAL_CA3631AA Livingstone
+SAL_CA3632AA Newport
+SAL_CA3634AA Enteritidis
+SAL_CA3635AA Enteritidis
+SAL_CA3637AA Kentucky
+SAL_CA3638AA Kentucky
+SAL_CA3639AA Typhimurium
+SAL_CA3640AA Enteritidis
+SAL_CA3641AA Typhi
+SAL_CA3642AA Enteritidis
+SAL_CA3643AA Muenchen
+SAL_CA3644AA Agona
+SAL_CA3646AA Typhi
+SAL_CA3647AA Livingstone
+SAL_CA3648AA Enteritidis
+SAL_CA3649AA Enteritidis
+SAL_CA3651AA Typhi
+SAL_CA3652AA Typhimurium
+SAL_CA3653AA Richmond
+SAL_CA3654AA Ago
+SAL_CA3655AA Oslo
+SAL_CA3656AA Enteritidis
+SAL_CA3658AA Enteritidis
+SAL_CA3660AA Enteritidis
+SAL_CA3662AA Infantis
+SAL_CA3663AA I 4,[5],12:i:-
+SAL_CA3667AA Enteritidis
+SAL_CA3669AA Newport
+SAL_CA3670AA Chester
+SAL_CA3671AA Ibadan
+SAL_CA3672AA Infantis
+SAL_CA3673AA Enteritidis
+SAL_CA3678AA Enteritidis
+SAL_CA3679AA Enteritidis
+SAL_CA3681AA Paratyphi A
+SAL_CA3682AA Agona
+SAL_CA3683AA Montevideo
+SAL_CA3684AA Typhimurium
+SAL_CA3685AA Typhi
+SAL_CA3686AA Bareilly
+SAL_CA3688AA Enteritidis
+SAL_CA3689AA Richmond
+SAL_CA3690AA Enteritidis
+SAL_CA3691AA Typhimurium
+SAL_CA3692AA Typhimurium
+SAL_CA3693AA Aberdeen
+SAL_CA3694AA Infantis
+SAL_CA3695AA Newport
+SAL_CA0326AA Paratyphi A
+SAL_CA0327AA Uganda
+SAL_CA0328AA Paratyphi A
+SAL_CA0329AA Typhimurium
+SAL_CA0330AA Paratyphi A
+SAL_CA0331AA Infantis
+SAL_CA0332AA Typhimurium
+SAL_CA0333AA Typhimurium
+SAL_CA0334AA Typhimurium
+SAL_CA0335AA Typhimurium
+SAL_CA0336AA Infantis
+SAL_CA0337AA Typhimurium
+SAL_CA0338AA Typhimurium
+SAL_CA0339AA Typhimurium
+SAL_CA0340AA Indiana
+SAL_CA0341AA Typhimurium
+SAL_CA3697AA Typhimurium
+SAL_CA3700AA Typhi
+SAL_CA3701AA Virchow
+SAL_CA3702AA Typhimurium
+SAL_CA3704AA Kentucky
+SAL_CA3705AA Enteritidis
+SAL_CA3706AA Litchfield
+SAL_CA3707AA Enteritidis
+SAL_CA3708AA Enteritidis
+SAL_CA3709AA Enteritidis
+SAL_CA3710AA Typhimurium
+SAL_CA3711AA Montevideo
+SAL_CA3712AA Haifa
+SAL_CA3713AA Infantis
+SAL_CA3715AA Enteritidis
+SAL_CA3716AA Paratyphi A
+SAL_CA3718AA Agama
+SAL_CA3719AA Oranienburg
+SAL_CA3720AA Paratyphi A
+SAL_CA3721AA Agona
+SAL_CA3722AA Rissen
+SAL_CA3723AA Agona
+SAL_CA3724AA Typhimurium
+SAL_CA3726AA Enteritidis
+SAL_CA3727AA Enteritidis
+SAL_CA3729AA Newport
+SAL_CA3730AA Mbandaka
+SAL_CA3731AA Enteritidis
+SAL_CA3734AA Enteritidis
+SAL_CA3735AA Typhimurium
+SAL_CA3736AA Enteritidis
+SAL_CA3737AA Typhimurium
+SAL_CA3739AA Adelaide
+SAL_CA3740AA Panama
+SAL_CA3741AA Typhimurium
+SAL_CA3742AA Enteritidis
+SAL_CA3743AA Heidelberg
+SAL_CA3744AA Enteritidis
+SAL_CA3746AA Typhi
+SAL_CA3747AA Typhimurium
+SAL_CA3748AA Enteritidis
+SAL_CA3751AA Enteritidis
+SAL_CA3752AA Enteritidis
+SAL_CA3754AA Virchow
+SAL_CA3757AA Enteritidis
+SAL_CA3758AA Livingstone
+SAL_CA3759AA Enteritidis
+SAL_CA3761AA Enteritidis
+SAL_CA3763AA Typhimurium
+SAL_CA3766AA Enteritidis
+SAL_CA3767AA Enteritidis
+SAL_CA3770AA Typhimurium
+SAL_CA3771AA Enteritidis
+SAL_CA3772AA Enteritidis
+SAL_CA3773AA Enteritidis
+SAL_CA3774AA Typhi
+SAL_CA3775AA Infantis
+SAL_CA3776AA Bareilly
+SAL_CA3778AA Typhimurium
+SAL_CA3779AA Typhimurium
+SAL_CA3783AA Enteritidis
+SAL_CA3787AA Enteritidis
+SAL_CA3788AA Typhimurium
+SAL_CA3789AA Stanley
+SAL_CA0037AA Typhimurium
+SAL_CA0038AA Typhimurium
+SAL_CA0040AA Ajiobo
+SAL_CA0041AA Typhimurium
+SAL_CA0042AA Typhimurium
+SAL_CA0043AA Typhimurium
+SAL_CA0044AA Weltevreden
+SAL_CA0045AA Typhimurium
+SAL_CA0047AA Typhimurium
+SAL_CA0048AA Kentucky
+SAL_CA0049AA Typhimurium
+SAL_CA0050AA Muenchen
+SAL_CA0051AA Typhimurium
+SAL_CA0052AA Agona
+SAL_CA0054AA Typhimurium
+SAL_CA0055AA Agona
+SAL_CA3791AA Enteritidis
+SAL_CA3792AA Typhi
+SAL_CA3793AA Krefeld
+SAL_CA3794AA Enteritidis
+SAL_CA3796AA Senftenberg
+SAL_CA3813AA Typhimurium
+SAL_CA3814AA Enteritidis
+SAL_CA3815AA Typhimurium
+SAL_CA3817AA Enteritidis
+SAL_CA3818AA Typhimurium
+SAL_CA3821AA Stanleyville
+SAL_CA3822AA Typhimurium
+SAL_CA3823AA Abony
+SAL_CA3825AA Virchow
+SAL_CA3827AA Bareilly
+SAL_CA3845AA Enteritidis
+SAL_CA3851AA Enteritidis
+SAL_CA3852AA Muenchen
+SAL_CA3854AA Infantis
+SAL_CA3855AA Infantis
+SAL_CA3856AA Panama
+SAL_CA3857AA Typhimurium
+SAL_CA3859AA Infantis
+SAL_CA3860AA Enteritidis
+SAL_CA3861AA Coeln
+SAL_CA3862AA Enteritidis
+SAL_CA3863AA Hvittingfoss
+SAL_CA3864AA Poona
+SAL_CA3867AA Paratyphi B
+SAL_CA3868AA Chester
+SAL_CA3871AA Kentucky
+SAL_CA3873AA Montevideo
+SAL_CA0343AA Typhimurium
+SAL_CA0344AA Enteritidis
+SAL_CA0345AA Typhimurium
+SAL_CA0346AA Weltevreden
+SAL_CA0347AA Typhimurium
+SAL_CA0348AA Enteritidis
+SAL_CA0349AA Typhimurium
+SAL_CA0350AA Typhimurium
+SAL_CA0351AA Typhimurium
+SAL_CA0352AA Typhimurium
+SAL_CA0353AA Typhimurium
+SAL_CA0355AA Typhimurium
+SAL_CA0356AA Enteritidis
+SAL_CA0357AA Typhimurium
+SAL_CA0358AA Enteritidis
+SAL_CA0359AA Typhimurium
+SAL_CA3877AA Enteritidis
+SAL_CA3878AA Typhi
+SAL_CA3879AA Albany
+SAL_CA3880AA Enteritidis
+SAL_CA3881AA Enteritidis
+SAL_CA3882AA Paratyphi A
+SAL_CA3886AA Enteritidis
+SAL_CA3887AA Enteritidis
+SAL_CA3888AA Enteritidis
+SAL_CA3890AA Enteritidis
+SAL_CA3891AA Agona
+SAL_CA3892AA Virchow
+SAL_CA3893AA Enteritidis
+SAL_CA3894AA Braenderup
+SAL_CA3895AA Enteritidis
+SAL_CA3896AA Typhimurium
+SAL_CA3900AA Enteritidis
+SAL_CA3901AA Enteritidis
+SAL_CA3902AA Typhimurium
+SAL_CA3903AA Oranienburg
+SAL_CA3904AA Typhi
+SAL_CA3908AA Enteritidis
+SAL_CA3909AA Jangwani
+SAL_CA3910AA Enteritidis
+SAL_CA3911AA Haifa
+SAL_CA3912AA Enteritidis
+SAL_CA3913AA Typhi
+SAL_CA3916AA Typhimurium
+SAL_CA3917AA Chester
+SAL_CA3918AA Infantis
+SAL_CA3920AA Newport
+SAL_CA3921AA Poona
+SAL_CA3527AA Poona
+SAL_CA3548AA Infantis
+SAL_CA3571AA Oranienburg
+SAL_CA3590AA Albany
+SAL_CA3612AA Typhi
+SAL_CA3630AA Enteritidis
+SAL_CA3650AA Typhi
+SAL_CA3676AA Typhimurium
+SAL_CA3696AA Typhimurium
+SAL_CA3717AA Dublin
+SAL_CA3738AA Enteritidis
+SAL_CA3762AA Infantis
+SAL_CA3790AA Potsdam
+SAL_CA3849AA Weltevreden
+SAL_CA3876AA Enteritidis
+SAL_BA5415AA Newport
+SAL_BA5981AA Typhi
+SAL_BA6444AA Cotham
+SAL_BA7047AA Paratyphi A
+SAL_BA7646AA Typhimurium
+SAL_BA8241AA Enteritidis
+SAL_BA8623AA Enteritidis
+SAL_BA8989AA Typhi
+SAL_BA9388AA Enteritidis
+SAL_BA9775AA Enteritidis
+SAL_CA0262AA Paratyphi A
+SAL_CA0709AA Agona
+SAL_CA1486AA Enteritidis
+SAL_CA2066AA Enteritidis
+SAL_CA2444AA Typhimurium
+SAL_CA3923AA Saintpaul
+SAL_CA3925AA Typhimurium
+SAL_CA3926AA Typhi
+SAL_CA3928AA Enteritidis
+SAL_CA3930AA Enteritidis
+SAL_CA3931AA Typhi
+SAL_CA3932AA Enteritidis
+SAL_CA3933AA Thompson
+SAL_CA3934AA Enteritidis
+SAL_CA3935AA Weltevreden
+SAL_CA3936AA Typhi
+SAL_CA3937AA Typhimurium
+SAL_CA3939AA Virchow
+SAL_CA3940AA Typhimurium
+SAL_CA3941AA Enteritidis
+SAL_CA3942AA Enteritidis
+SAL_CA3944AA Typhimurium
+SAL_CA3946AA Braenderup
+SAL_CA3947AA Enteritidis
+SAL_CA3948AA Montevideo
+SAL_CA3949AA Enteritidis
+SAL_CA3950AA Abony
+SAL_CA3951AA Oranienburg
+SAL_CA3952AA Typhimurium
+SAL_CA3953AA Chester
+SAL_CA3954AA Typhi
+SAL_CA3955AA Enteritidis
+SAL_CA3956AA Enteritidis
+SAL_CA3957AA Reading
+SAL_CA3958AA Typhimurium
+SAL_CA3959AA Hvittingfoss
+SAL_CA3963AA Bareilly
+SAL_CA3966AA Braenderup
+SAL_CA3969AA Infantis
+SAL_CA3970AA Kentucky
+SAL_CA3971AA Enteritidis
+SAL_CA3973AA Enteritidis
+SAL_CA3974AA Enteritidis
+SAL_CA3975AA Infantis
+SAL_CA3976AA Enteritidis
+SAL_CA3977AA Typhimurium
+SAL_CA3978AA Enteritidis
+SAL_CA3979AA Typhi
+SAL_CA3982AA Newport
+SAL_CA3983AA Enteritidis
+SAL_CA3984AA Enteritidis
+SAL_CA3985AA Enteritidis
+SAL_CA3988AA Umbilo
+SAL_CA3990AA Kentucky
+SAL_CA3991AA Agama
+SAL_CA3992AA Enteritidis
+SAL_CA3994AA Typhimurium
+SAL_CA3995AA Enteritidis
+SAL_CA3996AA Monschaui
+SAL_CA3998AA Enteritidis
+SAL_CA4000AA Enteritidis
+SAL_CA4001AA Newport
+SAL_CA4003AA Stanley
+SAL_CA4004AA Oranienburg
+SAL_CA4008AA London
+SAL_CA4010AA Enteritidis
+SAL_CA4011AA Kentucky
+SAL_CA4013AA Give
+SAL_CA4015AA Newport
+SAL_CA0363AA Typhimurium
+SAL_CA0364AA Kingston
+SAL_CA0365AA Typhimurium
+SAL_CA0366AA Senftenberg
+SAL_CA0367AA Typhimurium
+SAL_CA0368AA Enteritidis
+SAL_CA0369AA Typhimurium
+SAL_CA0370AA Enteritidis
+SAL_CA0371AA Typhimurium
+SAL_CA0372AA Oranienburg
+SAL_CA0373AA Typhimurium
+SAL_CA0375AA Typhimurium
+SAL_CA0376AA Javiana
+SAL_CA0377AA Typhimurium
+SAL_CA0378AA Enteritidis
+SAL_CA0379AA Typhimurium
+SAL_CA4020AA Enteritidis
+SAL_CA4021AA Dublin
+SAL_CA4022AA Enteritidis
+SAL_CA4023AA Stanley
+SAL_CA4024AA Thompson
+SAL_CA4025AA Amsterdam
+SAL_CA4026AA Enteritidis
+SAL_CA4028AA Virchow
+SAL_CA4029AA Kentucky
+SAL_CA4031AA Braenderup
+SAL_CA4032AA Mbandaka
+SAL_CA4033AA Enteritidis
+SAL_CA4034AA Enteritidis
+SAL_CA4036AA Agona
+SAL_CA4038AA Mbandaka
+SAL_CA4039AA Enteritidis
+SAL_CA4043AA Enteritidis
+SAL_CA4045AA Enteritidis
+SAL_CA4046AA Enteritidis
+SAL_CA4048AA Agama
+SAL_CA4051AA Enteritidis
+SAL_CA4053AA Enteritidis
+SAL_CA4055AA Blockley
+SAL_CA4056AA Newport
+SAL_CA4057AA Enteritidis
+SAL_CA4060AA Typhimurium
+SAL_CA4061AA Enteritidis
+SAL_CA4064AA Newport
+SAL_CA4065AA Enteritidis
+SAL_CA4066AA Bareilly
+SAL_CA4067AA Oranienburg
+SAL_CA4068AA Typhimurium
+SAL_CA4071AA Monschaui
+SAL_CA4072AA Enteritidis
+SAL_CA4073AA Enteritidis
+SAL_CA4074AA Enteritidis
+SAL_CA4076AA Typhimurium
+SAL_CA4077AA Enteritidis
+SAL_CA4079AA Enteritidis
+SAL_CA4080AA Enteritidis
+SAL_CA4081AA Enteritidis
+SAL_CA4084AA Enteritidis
+SAL_CA4085AA Kisangani
+SAL_CA4086AA Litchfield
+SAL_CA4087AA Emek
+SAL_CA4088AA Enteritidis
+SAL_CA4089AA Enteritidis
+SAL_CA4090AA Typhi
+SAL_CA4092AA Huddinge
+SAL_CA4093AA Kentucky
+SAL_CA4095AA Enteritidis
+SAL_CA4096AA Typhimurium
+SAL_CA4098AA Richmond
+SAL_CA4102AA Virchow
+SAL_CA4103AA Stanley
+SAL_CA4106AA Enteritidis
+SAL_CA4107AA Enteritidis
+SAL_CA4108AA Saintpaul
+SAL_CA4109AA Kentucky
+SAL_CA4110AA Durham
+SAL_CA4113AA Enteritidis
+SAL_CA4115AA Give
+SAL_CA4116AA Coeln
+SAL_CA4150AA Saphra
+SAL_CA4152AA Enteritidis
+SAL_CA4154AA Richmond
+SAL_CA4155AA Enteritidis
+SAL_CA4156AA Saintpaul
+SAL_CA4157AA Enteritidis
+SAL_CA4158AA Enteritidis
+SAL_CA4160AA Enteritidis
+SAL_CA4162AA Enteritidis
+SAL_CA4163AA Infantis
+SAL_CA4164AA Enteritidis
+SAL_CA4165AA Enteritidis
+SAL_CA4166AA Stanley
+SAL_CA4167AA Livingstone
+SAL_CA4168AA Enteritidis
+SAL_CA4170AA Enteritidis
+SAL_CA4171AA Typhimurium
+SAL_CA4173AA Enteritidis
+SAL_CA4174AA Enteritidis
+SAL_CA4175AA Enteritidis
+SAL_CA4176AA Enteritidis
+SAL_CA4178AA Kentucky
+SAL_CA4179AA Anatum
+SAL_CA4181AA Enteritidis
+SAL_CA4182AA Paratyphi A
+SAL_CA4183AA Poona
+SAL_CA4185AA Emek
+SAL_CA4187AA Enteritidis
+SAL_CA4188AA Javiana
+SAL_CA4189AA Enteritidis
+SAL_CA4190AA Albany
+SAL_CA4191AA Anatum
+SAL_CA4192AA Enteritidis
+SAL_CA0381AA Typhimurium
+SAL_CA0383AA Typhimurium
+SAL_CA0384AA Typhimurium
+SAL_CA0386AA Typhimurium
+SAL_CA0387AA Coeln
+SAL_CA0388AA Typhimurium
+SAL_CA0389AA Enteritidis
+SAL_CA0390AA Typhimurium
+SAL_CA0391AA Haifa
+SAL_CA0392AA Typhimurium
+SAL_CA0394AA Typhimurium
+SAL_CA0395AA Fluntern
+SAL_CA0396AA Typhimurium
+SAL_CA0397AA Virchow
+SAL_CA0398AA Typhimurium
+SAL_CA0399AA Enteritidis
+SAL_CA4194AA Enteritidis
+SAL_CA4196AA Anatum
+SAL_CA4197AA Enteritidis
+SAL_CA4198AA Paratyphi A
+SAL_CA4200AA Enteritidis
+SAL_CA4201AA Typhimurium
+SAL_CA4202AA Lome
+SAL_CA4203AA Enteritidis
+SAL_CA4204AA Montevideo
+SAL_CA4205AA Typhimurium
+SAL_CA4206AA Enteritidis
+SAL_CA4207AA Enteritidis
+SAL_CA4209AA Enteritidis
+SAL_CA4210AA Mbandaka
+SAL_CA4211AA Braenderup
+SAL_CA4213AA Enteritidis
+SAL_CA4215AA Stanley
+SAL_CA4217AA Enteritidis
+SAL_CA4218AA Montevideo
+SAL_CA4220AA Javiana
+SAL_CA4222AA Montevideo
+SAL_CA4224AA Enteritidis
+SAL_CA4225AA Enteritidis
+SAL_CA4226AA Virchow
+SAL_CA4227AA Agona
+SAL_CA4228AA Enteritidis
+SAL_CA4261AA Corvallis
+SAL_CA4263AA Paratyphi A
+SAL_CA4264AA Virchow
+SAL_CA4266AA Enteritidis
+SAL_CA4267AA Kentucky
+SAL_CA4268AA Enteritidis
+SAL_CA4272AA Hadar
+SAL_CA4273AA Typhimurium
+SAL_CA4274AA Typhimurium
+SAL_CA4278AA Typhi
+SAL_CA4279AA Enteritidis
+SAL_CA4280AA Coeln
+SAL_CA4281AA Infantis
+SAL_CA4282AA Derby
+SAL_CA4283AA Concord
+SAL_CA4285AA Enteritidis
+SAL_CA4286AA Agona
+SAL_CA4287AA Derby
+SAL_CA4289AA Bareilly
+SAL_CA4290AA Poona
+SAL_CA4291AA Stanley
+SAL_CA4292AA Typhimurium
+SAL_CA4295AA Infantis
+SAL_CA4296AA Enteritidis
+SAL_CA4298AA Typhimurium
+SAL_CA4299AA Enteritidis
+SAL_CA4300AA Agbeni
+SAL_CA4302AA Paratyphi A
+SAL_CA4303AA Marseille
+SAL_CA4304AA Napoli
+SAL_CA4305AA Enteritidis
+SAL_CA4306AA Braenderup
+SAL_CA4307AA Newport
+SAL_CA4309AA Agama
+SAL_CA4310AA Infantis
+SAL_CA4311AA Oranienburg
+SAL_CA4312AA Enteritidis
+SAL_CA4314AA Oranienburg
+SAL_CA4316AA Enteritidis
+SAL_CA4317AA Enteritidis
+SAL_CA4318AA Javiana
+SAL_CA4319AA Enteritidis
+SAL_CA4320AA Enteritidis
+SAL_CA4322AA Enteritidis
+SAL_CA4324AA Virchow
+SAL_CA4325AA Enteritidis
+SAL_CA4326AA Enteritidis
+SAL_CA4327AA Agona
+SAL_CA4329AA Enteritidis
+SAL_CA4330AA Agona
+SAL_CA4331AA Newport
+SAL_CA4332AA Enteritidis
+SAL_CA4333AA Javiana
+SAL_CA4334AA Dublin
+SAL_CA4336AA Enteritidis
+SAL_CA4337AA Typhimurium
+SAL_CA4339AA Enteritidis
+SAL_CA4340AA Enteritidis
+SAL_CA4341AA Typhimurium
+SAL_CA4342AA Matopeni
+SAL_CA4343AA Enteritidis
+SAL_CA4345AA Hvittingfoss
+SAL_CA4346AA Colindale
+SAL_CA4347AA Montevideo
+SAL_CA4348AA Anatum
+SAL_CA4349AA Typhimurium
+SAL_CA4351AA Enteritidis
+SAL_CA4352AA Enteritidis
+SAL_CA4353AA Weltevreden
+SAL_CA4354AA Enteritidis
+SAL_CA3922AA Bonariensis
+SAL_CA3943AA Enteritidis
+SAL_CA3965AA Kentucky
+SAL_CA3989AA Enteritidis
+SAL_CA4019AA Paratyphi A
+SAL_CA4040AA Enteritidis
+SAL_CA4069AA Enteritidis
+SAL_CA4091AA Typhimurium
+SAL_CA4151AA Enteritidis
+SAL_CA4172AA Enteritidis
+SAL_CA4193AA Typhimurium
+SAL_CA4214AA Enteritidis
+SAL_CA4271AA Hadar
+SAL_CA4294AA Infantis
+SAL_CA4315AA Enteritidis
+SAL_CA4357AA Enteritidis
+SAL_CA4358AA Typhi
+SAL_CA4359AA Enteritidis
+SAL_CA4360AA Enteritidis
+SAL_CA4361AA Enteritidis
+SAL_CA4362AA Virchow
+SAL_CA4364AA Muenchen
+SAL_CA4366AA Braenderup
+SAL_CA4367AA Blockley
+SAL_CA4368AA Typhimurium
+SAL_CA4369AA Thompson
+SAL_CA4370AA Florida
+SAL_CA4371AA Braenderup
+SAL_CA4372AA Enteritidis
+SAL_CA4373AA Hull
+SAL_CA4374AA Virchow
+SAL_CA4376AA Typhimurium
+SAL_CA4377AA Enteritidis
+SAL_CA4378AA Typhimurium
+SAL_CA4379AA Braenderup
+SAL_CA4380AA Agona
+SAL_CA4381AA Enteritidis
+SAL_CA4383AA Enteritidis
+SAL_CA4384AA Typhi
+SAL_CA4385AA Paratyphi A
+SAL_CA4386AA Enteritidis
+SAL_CA4387AA Saintpaul
+SAL_CA4388AA Agona
+SAL_CA4389AA Braenderup
+SAL_CA4390AA Typhimurium
+SAL_CA4391AA Enteritidis
+SAL_CA4393AA Derby
+SAL_CA4395AA Enteritidis
+SAL_CA4396AA Bareilly
+SAL_CA4397AA Enteritidis
+SAL_CA4398AA Enteritidis
+SAL_CA4399AA Enteritidis
+SAL_CA4400AA Typhimurium
+SAL_CA4402AA Enteritidis
+SAL_CA4403AA Virchow
+SAL_CA4404AA Enteritidis
+SAL_CA4405AA Newport
+SAL_CA4408AA Enteritidis
+SAL_CA4409AA Enteritidis
+SAL_CA4410AA Typhimurium
+SAL_CA4411AA Saintpaul
+SAL_CA4412AA Agona
+SAL_CA4413AA Ohio
+SAL_CA4415AA Typhimurium
+SAL_CA4416AA Typhimurium
+SAL_CA4417AA Enteritidis
+SAL_CA4418AA Enteritidis
+SAL_CA4420AA Enteritidis
+SAL_CA4421AA Infantis
+SAL_CA4422AA Infantis
+SAL_CA4423AA Paratyphi B
+SAL_CA4427AA Enteritidis
+SAL_CA4428AA Coeln
+SAL_CA4430AA Carmel
+SAL_CA4431AA Enteritidis
+SAL_CA4432AA Typhi
+SAL_CA4433AA Enteritidis
+SAL_CA4434AA Bareilly
+SAL_CA4435AA Enteritidis
+SAL_CA4438AA Enteritidis
+SAL_CA4439AA Braenderup
+SAL_CA4440AA Enteritidis
+SAL_CA4443AA Dublin
+SAL_CA4444AA Enteritidis
+SAL_CA4447AA Typhi
+SAL_CA4450AA Enteritidis
+SAL_CA4451AA Vitkin
+SAL_CA4454AA Typhimurium
+SAL_CA4455AA Typhimurium
+SAL_CA4457AA Enteritidis
+SAL_CA4458AA Enteritidis
+SAL_CA4461AA Richmond
+SAL_CA4462AA Enteritidis
+SAL_CA4463AA Enteritidis
+SAL_CA4464AA Enteritidis
+SAL_CA4466AA Enteritidis
+SAL_CA4468AA Paratyphi A
+SAL_CA4469AA Typhimurium
+SAL_CA4471AA Agona
+SAL_CA4472AA Virchow
+SAL_CA4473AA Virchow
+SAL_CA4474AA Typhimurium
+SAL_CA4475AA Stanley
+SAL_CA4476AA Enteritidis
+SAL_CA4477AA Stanley
+SAL_CA4479AA Braenderup
+SAL_CA4480AA Agona
+SAL_CA4481AA Enteritidis
+SAL_CA4482AA Takoradi
+SAL_CA4483AA Enteritidis
+SAL_CA4487AA Kentucky
+SAL_CA4489AA Braenderup
+SAL_CA4491AA Saintpaul
+SAL_CA4493AA Poona
+SAL_CA4494AA Agona
+SAL_CA4495AA Newport
+SAL_CA4496AA Enteritidis
+SAL_CA4497AA Typhimurium
+SAL_CA4498AA Stanley
+SAL_CA4500AA Typhi
+SAL_CA4503AA Infantis
+SAL_CA4504AA Infantis
+SAL_CA4505AA Lattenkamp
+SAL_CA4507AA Kentucky
+SAL_CA4508AA Enteritidis
+SAL_CA4509AA Enteritidis
+SAL_CA4510AA Enteritidis
+SAL_CA0401AA Enteritidis
+SAL_CA0402AA Typhimurium
+SAL_CA0404AA Typhimurium
+SAL_CA0405AA Enteritidis
+SAL_CA0406AA Typhimurium
+SAL_CA0407AA Enteritidis
+SAL_CA0408AA Typhimurium
+SAL_CA0410AA Typhimurium
+SAL_CA0411AA Enteritidis
+SAL_CA0412AA Typhimurium
+SAL_CA0413AA Enteritidis
+SAL_CA0414AA Enteritidis
+SAL_CA0415AA Typhimurium
+SAL_CA0416AA Typhimurium
+SAL_CA0417AA Enteritidis
+SAL_CA0418AA Typhimurium
+SAL_CA4512AA Enteritidis
+SAL_CA4516AA Enteritidis
+SAL_CA4517AA Enteritidis
+SAL_CA4550AA Enteritidis
+SAL_CA4551AA Dublin
+SAL_CA4552AA Cerro
+SAL_CA4553AA Enteritidis
+SAL_CA4554AA Infantis
+SAL_CA4555AA Typhimurium
+SAL_CA4556AA Oranienburg
+SAL_CA4557AA Newport
+SAL_CA4558AA Apapa
+SAL_CA4559AA Enteritidis
+SAL_CA4560AA Enteritidis
+SAL_CA4562AA Derby
+SAL_CA4563AA Weltevreden
+SAL_CA4565AA Senftenberg
+SAL_CA4566AA Enteritidis
+SAL_CA4567AA Rubislaw
+SAL_CA4568AA Enteritidis
+SAL_CA4569AA Bareilly
+SAL_CA4570AA Enteritidis
+SAL_CA4571AA Enteritidis
+SAL_CA4572AA Claibornei
+SAL_CA4573AA Enteritidis
+SAL_CA4574AA Enteritidis
+SAL_CA4575AA Enteritidis
+SAL_CA4578AA Typhimurium
+SAL_CA4579AA Oranienburg
+SAL_CA4580AA Enteritidis
+SAL_CA4581AA Virchow
+SAL_CA4582AA Enteritidis
+SAL_CA4586AA Agona
+SAL_CA4587AA Typhimurium
+SAL_CA4588AA Enteritidis
+SAL_CA4591AA Enteritidis
+SAL_CA4592AA Senftenberg
+SAL_CA4593AA Enteritidis
+SAL_CA4594AA Typhimurium
+SAL_CA4595AA Blockley
+SAL_CA4596AA Stanley
+SAL_CA4597AA Typhimurium
+SAL_CA4598AA Enteritidis
+SAL_CA4599AA Enteritidis
+SAL_CA4600AA Typhimurium
+SAL_CA4601AA Enteritidis
+SAL_CA4602AA Montevideo
+SAL_CA4604AA Typhimurium
+SAL_CA4606AA Typhimurium
+SAL_CA4607AA Typhimurium
+SAL_CA4610AA Dublin
+SAL_CA4611AA Paratyphi B
+SAL_CA4612AA Cerro
+SAL_CA4614AA Give
+SAL_CA4615AA Enteritidis
+SAL_CA4616AA Enteritidis
+SAL_CA4617AA Enteritidis
+SAL_CA4618AA Livingstone
+SAL_CA4619AA Oranienburg
+SAL_CA4620AA Typhimurium
+SAL_CA4622AA Paratyphi A
+SAL_CA4623AA Paratyphi A
+SAL_CA4624AA Infantis
+SAL_CA4625AA Infantis
+SAL_CA0421AA Newport
+SAL_CA0422AA Typhimurium
+SAL_CA0423AA Typhimurium
+SAL_CA0427AA Hvittingfoss
+SAL_CA0429AA Infantis
+SAL_CA0431AA Infantis
+SAL_CA0433AA Paratyphi A
+SAL_CA0439AA Newport
+SAL_CA0441AA Nottingham
+SAL_CA0443AA Enteritidis
+SAL_CA0445AA Enteritidis
+SAL_CA0447AA Typhimurium
+SAL_CA0449AA Kentucky
+SAL_CA0451AA Enteritidis
+SAL_CA0453AA Braenderup
+SAL_CA0455AA Enteritidis
+SAL_CA4627AA Weltevreden
+SAL_CA4628AA Enteritidis
+SAL_CA4629AA Manchester
+SAL_CA4662AA Heidelberg
+SAL_CA4663AA Enteritidis
+SAL_CA4664AA Enteritidis
+SAL_CA4666AA Enteritidis
+SAL_CA4667AA Kentucky
+SAL_CA4668AA Kenya
+SAL_CA4669AA Enteritidis
+SAL_CA4671AA Duisburg
+SAL_CA4673AA Typhimurium
+SAL_CA4674AA Bournemouth
+SAL_CA4675AA Enteritidis
+SAL_CA4676AA Agama
+SAL_CA4678AA Bareilly
+SAL_CA4680AA Enteritidis
+SAL_CA4681AA Enteritidis
+SAL_CA4682AA Meleagridis
+SAL_CA4683AA Enteritidis
+SAL_CA4684AA Agona
+SAL_CA4685AA Enteritidis
+SAL_CA4688AA Enteritidis
+SAL_CA4689AA Typhimurium
+SAL_CA4690AA Enteritidis
+SAL_CA4691AA Enteritidis
+SAL_CA4692AA Infantis
+SAL_CA4694AA Enteritidis
+SAL_CA4695AA Typhimurium
+SAL_CA4696AA Braenderup
+SAL_CA4697AA Enteritidis
+SAL_CA4698AA Typhimurium
+SAL_CA4701AA Enteritidis
+SAL_CA4703AA Enteritidis
+SAL_CA4704AA London
+SAL_CA4705AA Enteritidis
+SAL_CA4707AA Enteritidis
+SAL_CA4708AA Typhimurium
+SAL_CA4711AA Corvallis
+SAL_CA4712AA Mbandaka
+SAL_CA4713AA Enteritidis
+SAL_CA4714AA Enteritidis
+SAL_CA4715AA Stanley
+SAL_CA4716AA Litchfield
+SAL_CA4719AA Enteritidis
+SAL_CA4723AA Agbeni
+SAL_CA4724AA Enteritidis
+SAL_CA4725AA Enteritidis
+SAL_CA4727AA Enteritidis
+SAL_CA4728AA Coeln
+SAL_CA4729AA Mikawasima
+SAL_CA4731AA Kentucky
+SAL_CA4732AA Kisarawe
+SAL_CA4733AA Enteritidis
+SAL_CA4734AA Typhimurium
+SAL_CA4736AA Typhi
+SAL_CA4737AA Infantis
+SAL_CA4738AA Haifa
+SAL_CA4739AA Paratyphi A
+SAL_CA4740AA Enteritidis
+SAL_CA4741AA Enteritidis
+SAL_CA4758AA Typhimurium
+SAL_CA4759AA Typhimurium
+SAL_CA4763AA Thompson
+SAL_CA4765AA Enteritidis
+SAL_CA4767AA Kentucky
+SAL_CA4768AA Enteritidis
+SAL_CA4769AA Braenderup
+SAL_CA4770AA Enteritidis
+SAL_CA4773AA Typhimurium
+SAL_CA4774AA Tennessee
+SAL_CA4775AA Heidelberg
+SAL_CA4777AA Muenchen
+SAL_CA4779AA Enteritidis
+SAL_CA4780AA Enteritidis
+SAL_CA4781AA Infantis
+SAL_CA4784AA Enteritidis
+SAL_CA4785AA Enteritidis
+SAL_CA4786AA Enteritidis
+SAL_CA4787AA Havana
+SAL_CA4355AA Enteritidis
+SAL_CA4375AA Enteritidis
+SAL_CA4394AA Enteritidis
+SAL_CA4414AA Agama
+SAL_CA4437AA Enteritidis
+SAL_CA4465AA Kottbus
+SAL_CA4488AA Enteritidis
+SAL_CA4511AA Newport
+SAL_CA4564AA Saintpaul
+SAL_CA4585AA Typhimurium
+SAL_CA4605AA Enteritidis
+SAL_CA4626AA Blockley
+SAL_CA4679AA Infantis
+SAL_CA4699AA Newport
+SAL_CA4726AA Derby
+SAL_CA4789AA Enteritidis
+SAL_CA4790AA Virchow
+SAL_CA4791AA Corvallis
+SAL_CA4792AA Enteritidis
+SAL_CA4794AA Paratyphi A
+SAL_CA4795AA Infantis
+SAL_CA4796AA Florida
+SAL_CA4797AA Enteritidis
+SAL_CA4798AA Typhimurium
+SAL_CA4799AA Enteritidis
+SAL_CA4800AA Enteritidis
+SAL_CA4801AA Typhimurium
+SAL_CA4802AA Enteritidis
+SAL_CA4803AA Orientalis
+SAL_CA4804AA Enteritidis
+SAL_CA4805AA Enteritidis
+SAL_CA4823AA Nima
+SAL_CA4824AA Typhi
+SAL_CA4825AA Typhimurium
+SAL_CA4826AA Limete
+SAL_CA4827AA Javiana
+SAL_CA4828AA Enteritidis
+SAL_CA4829AA Kentucky
+SAL_CA4830AA Stanley
+SAL_CA4831AA Saintpaul
+SAL_CA4832AA Typhimurium
+SAL_CA4833AA Enteritidis
+SAL_CA4834AA Stanley
+SAL_CA4835AA Typhimurium
+SAL_CA4836AA Agona
+SAL_CA4837AA Enteritidis
+SAL_CA4854AA Typhi
+SAL_CA4856AA Typhi
+SAL_CA4857AA Typhimurium
+SAL_CA4859AA Typhimurium
+SAL_CA4860AA Enteritidis
+SAL_CA4861AA Enteritidis
+SAL_CA4862AA Enteritidis
+SAL_CA4863AA Enteritidis
+SAL_CA4864AA Stanley
+SAL_CA4866AA Enteritidis
+SAL_CA4867AA Typhi
+SAL_CA4868AA Infantis
+SAL_CA4869AA Oslo
+SAL_CA4870AA Typhimurium
+SAL_CA4873AA Potsdam
+SAL_CA4874AA Oranienburg
+SAL_CA4882AA Stanley
+SAL_CA4886AA Kenya
+SAL_CA4887AA Enteritidis
+SAL_CA4888AA Enteritidis
+SAL_CA4889AA Enteritidis
+SAL_CA4890AA Typhimurium
+SAL_CA4891AA Orientalis
+SAL_CA4892AA Dublin
+SAL_CA4894AA Enteritidis
+SAL_CA4895AA Weltevreden
+SAL_CA4896AA Typhimurium
+SAL_CA4897AA Typhimurium
+SAL_CA4898AA Enteritidis
+SAL_CA4900AA Typhimurium
+SAL_CA4901AA Typhimurium
+SAL_CA4903AA Enteritidis
+SAL_CA4904AA Kentucky
+SAL_CA4906AA Weltevreden
+SAL_CA4909AA Typhimurium
+SAL_CA4910AA Enteritidis
+SAL_CA4911AA Enteritidis
+SAL_CA4912AA Enteritidis
+SAL_CA4913AA Stanley
+SAL_CA4914AA Krefeld
+SAL_CA4915AA Newport
+SAL_CA4916AA Weltevreden
+SAL_CA4917AA Typhimurium
+SAL_CA4918AA Typhi
+SAL_CA4919AA Havana
+SAL_CA4920AA Typhimurium
+SAL_CA4921AA I 4,[5],12:i:-
+SAL_CA4922AA Enteritidis
+SAL_CA4924AA Kentucky
+SAL_CA4927AA Enteritidis
+SAL_CA4928AA Give
+SAL_CA4929AA Haifa
+SAL_CA4932AA Anatum
+SAL_CA4933AA Paratyphi A
+SAL_CA4934AA Kenya
+SAL_CA4935AA Enteritidis
+SAL_CA4936AA Enteritidis
+SAL_CA4937AA Enteritidis
+SAL_CA4938AA Typhimurium
+SAL_CA4939AA Enteritidis
+SAL_CA4940AA Newport
+SAL_CA4941AA Derby
+SAL_CA4942AA Enteritidis
+SAL_CA4943AA Enteritidis
+SAL_CA4945AA Enteritidis
+SAL_CA4947AA Enteritidis
+SAL_CA4948AA Typhimurium
+SAL_CA4950AA Kentucky
+SAL_CA4951AA Typhimurium
+SAL_CA4952AA Enteritidis
+SAL_CA4953AA Enteritidis
+SAL_CA4954AA Enteritidis
+SAL_CA4955AA Heidelberg
+SAL_CA4956AA Krefeld
+SAL_CA4958AA Enteritidis
+SAL_CA4959AA Dublin
+SAL_CA4960AA Meleagridis
+SAL_CA4962AA Typhimurium
+SAL_CA4963AA Typhi
+SAL_CA4966AA Enteritidis
+SAL_CA4967AA Enteritidis
+SAL_CA0458AA Saintpaul
+SAL_CA0461AA Enteritidis
+SAL_CA0463AA Infantis
+SAL_CA0466AA Ajiobo
+SAL_CA0467AA Enteritidis
+SAL_CA0468AA Enteritidis
+SAL_CA0471AA Emek
+SAL_CA0472AA Enteritidis
+SAL_CA0473AA Enteritidis
+SAL_CA0474AA Abony
+SAL_CA0475AA Enteritidis
+SAL_CA0477AA Senftenberg
+SAL_CA0481AA Panama
+SAL_CA0483AA Shubra
+SAL_CA0485AA Kiambu
+SAL_CA0489AA Zanzibar
+SAL_CA4969AA Enteritidis
+SAL_CA4970AA Zaiman
+SAL_CA4972AA Derby
+SAL_CA4973AA Typhi
+SAL_CA4974AA Typhi
+SAL_CA4975AA Newport
+SAL_CA4976AA Typhimurium
+SAL_CA4977AA Galiema
+SAL_CA4979AA Enteritidis
+SAL_CA4980AA Enteritidis
+SAL_CA4981AA Enteritidis
+SAL_CA4998AA Enteritidis
+SAL_CA4999AA Enteritidis
+SAL_CA5002AA Mikawasima
+SAL_CA5004AA Enteritidis
+SAL_CA5006AA Oranienburg
+SAL_CA5008AA Agama
+SAL_CA5009AA Typhimurium
+SAL_CA5010AA Typhimurium
+SAL_CA5011AA Typhimurium
+SAL_CA5012AA Oranienburg
+SAL_CA5014AA Pomona
+SAL_CA5015AA Typhimurium
+SAL_CA5017AA Stanley
+SAL_CA5018AA Stanley
+SAL_CA5019AA Typhimurium
+SAL_CA5021AA Muenchen
+SAL_CA5023AA Enteritidis
+SAL_CA5024AA Muenchen
+SAL_CA5025AA Heidelberg
+SAL_CA5026AA Enteritidis
+SAL_CA5027AA Enteritidis
+SAL_CA5031AA Singapore
+SAL_CA5033AA Enteritidis
+SAL_CA5034AA Give
+SAL_CA5036AA Newport
+SAL_CA5037AA Montevideo
+SAL_CA5038AA Oranienburg
+SAL_CA5039AA Enteritidis
+SAL_CA5040AA Enteritidis
+SAL_CA5041AA Dublin
+SAL_CA5042AA Derby
+SAL_CA5043AA Typhimurium
+SAL_CA5045AA Typhimurium
+SAL_CA5046AA Kentucky
+SAL_CA5048AA Enteritidis
+SAL_CA5049AA Enteritidis
+SAL_CA5051AA Infantis
+SAL_CA5055AA Typhimurium
+SAL_CA5056AA Typhimurium
+SAL_CA5058AA Virchow
+SAL_CA5059AA Schwarzengrund
+SAL_CA5061AA Enteritidis
+SAL_CA5062AA Albany
+SAL_CA5063AA Enteritidis
+SAL_CA5064AA Typhi
+SAL_CA5065AA Enteritidis
+SAL_CA5066AA Enteritidis
+SAL_CA5067AA Enteritidis
+SAL_CA5068AA Enteritidis
+SAL_CA5069AA Typhimurium
+SAL_CA5070AA Enteritidis
+SAL_CA5071AA Paratyphi A
+SAL_CA5072AA Infantis
+SAL_CA5074AA Typhimurium
+SAL_CA5075AA Ohio
+SAL_CA5077AA Typhimurium
+SAL_CA5078AA Szentes
+SAL_CA5079AA Aberdeen
+SAL_CA5082AA Kentucky
+SAL_CA5083AA Enteritidis
+SAL_CA5084AA Enteritidis
+SAL_CA5085AA Braenderup
+SAL_CA5087AA Oranienburg
+SAL_CA5090AA Enteritidis
+SAL_CA5091AA Newport
+SAL_CA5093AA Typhi
+SAL_CA5094AA Enteritidis
+SAL_CA5095AA Dublin
+SAL_CA5101AA Enteritidis
+SAL_CA5105AA Mikawasima
+SAL_CA5106AA Ohio
+SAL_CA5107AA Enteritidis
+SAL_CA5108AA Enteritidis
+SAL_CA5109AA Corvallis
+SAL_CA5111AA Typhimurium
+SAL_CA5112AA Chester
+SAL_CA5113AA Corvallis
+SAL_CA5115AA Enteritidis
+SAL_CA5116AA Typhimurium
+SAL_CA5117AA Enteritidis
+SAL_CA5118AA Enteritidis
+SAL_CA5119AA Derby
+SAL_CA5120AA Corvallis
+SAL_CA5121AA Stanley
+SAL_CA5123AA Enteritidis
+SAL_CA5125AA Mississippi
+SAL_CA5126AA Enteritidis
+SAL_CA5128AA Kottbus
+SAL_CA5129AA Stanley
+SAL_CA5130AA Chester
+SAL_CA5131AA Haifa
+SAL_CA5132AA Enteritidis
+SAL_CA5133AA Typhimurium
+SAL_CA5134AA Typhimurium
+SAL_CA5135AA Virchow
+SAL_CA5138AA Enteritidis
+SAL_CA5139AA Enteritidis
+SAL_CA5140AA Virchow
+SAL_CA5141AA Typhimurium
+SAL_CA5142AA Newport
+SAL_CA5143AA Enteritidis
+SAL_CA0494AA Eastbourne
+SAL_CA0496AA Enteritidis
+SAL_CA0500AA Mbandaka
+SAL_CA0505AA Enteritidis
+SAL_CA0507AA Mbandaka
+SAL_CA0509AA Enteritidis
+SAL_CA0512AA Enteritidis
+SAL_CA0514AA Montevideo
+SAL_CA0516AA Enteritidis
+SAL_CA0518AA Braenderup
+SAL_CA0520AA Mbandaka
+SAL_CA0522AA Braenderup
+SAL_CA0524AA Senftenberg
+SAL_CA0526AA Mbandaka
+SAL_CA0528AA Typhimurium
+SAL_CA0534AA Typhi
+SAL_CA0283AA Infantis
+SAL_CA0304AA Infantis
+SAL_CA0325AA Poona
+SAL_CA0342AA Virchow
+SAL_CA0362AA Typhimurium
+SAL_CA0380AA Braenderup
+SAL_CA0400AA Typhimurium
+SAL_CA0420AA Typhimurium
+SAL_CA0457AA Livingstone
+SAL_CA0492AA Enteritidis
+SAL_CA0538AA Typhimurium
+SAL_CA0587AA Enteritidis
+SAL_CA0609AA Typhimurium
+SAL_CA0646AA Enteritidis
+SAL_CA0680AA Coeln
+SAL_CA5145AA Enteritidis
+SAL_CA5146AA Panama
+SAL_CA5147AA Tennessee
+SAL_CA5148AA Enteritidis
+SAL_CA5149AA Enteritidis
+SAL_CA5150AA Livingstone
+SAL_CA5151AA Enteritidis
+SAL_CA5152AA Enteritidis
+SAL_CA5153AA Livingstone
+SAL_CA5154AA Kentucky
+SAL_CA5155AA Newport
+SAL_CA5157AA Emek
+SAL_CA5159AA Typhimurium
+SAL_CA5160AA Typhimurium
+SAL_CA5161AA Enteritidis
+SAL_CA5163AA Typhimurium
+SAL_CA5166AA Enteritidis
+SAL_CA5168AA Typhimurium
+SAL_CA5169AA Enteritidis
+SAL_CA5170AA Bareilly
+SAL_CA5171AA Bareilly
+SAL_CA5172AA Emek
+SAL_CA5174AA Virchow
+SAL_CA5175AA Enteritidis
+SAL_CA5176AA Enteritidis
+SAL_CA5177AA Paratyphi A
+SAL_CA5178AA Typhimurium
+SAL_CA5179AA Typhi
+SAL_CA5180AA Oslo
+SAL_CA5181AA Thompson
+SAL_CA5182AA Typhimurium
+SAL_CA5183AA Infantis
+SAL_CA4788AA Saintpaul
+SAL_CA4822AA Enteritidis
+SAL_CA4855AA Dublin
+SAL_CA4883AA Kentucky
+SAL_CA4905AA Orion
+SAL_CA4925AA Mbandaka
+SAL_CA4946AA Oranienburg
+SAL_CA4968AA Enteritidis
+SAL_CA5007AA Enteritidis
+SAL_CA5029AA Infantis
+SAL_CA5052AA Enteritidis
+SAL_CA5073AA Enteritidis
+SAL_CA5104AA Enteritidis
+SAL_CA5124AA Newport
+SAL_CA5144AA Typhimurium
+SAL_CA5185AA Infantis
+SAL_CA5186AA Typhi
+SAL_CA5187AA Paratyphi A
+SAL_CA5189AA Havana
+SAL_CA5191AA Typhi
+SAL_CA5192AA Rissen
+SAL_CA5193AA Enteritidis
+SAL_CA5194AA Oranienburg
+SAL_CA5196AA Enteritidis
+SAL_CA5197AA Senftenberg
+SAL_CA5198AA Tennessee
+SAL_CA5199AA Enteritidis
+SAL_CA5200AA Typhimurium
+SAL_CA5201AA Newport
+SAL_CA5203AA Enteritidis
+SAL_CA5204AA Kedougou
+SAL_CA5206AA Enteritidis
+SAL_CA5207AA Enteritidis
+SAL_CA5209AA Enteritidis
+SAL_CA5210AA Typhimurium
+SAL_CA5212AA Enteritidis
+SAL_CA5213AA Dublin
+SAL_CA5215AA Enteritidis
+SAL_CA5216AA Derby
+SAL_CA5218AA Saintpaul
+SAL_CA5219AA Enteritidis
+SAL_CA5221AA Haifa
+SAL_CA5222AA Enteritidis
+SAL_CA5225AA Stanleyville
+SAL_CA5226AA Enteritidis
+SAL_CA5227AA Stanley
+SAL_CA5229AA Typhimurium
+SAL_CA5231AA Agona
+SAL_CA5232AA Braenderup
+SAL_CA5233AA Enteritidis
+SAL_CA5235AA Krefeld
+SAL_CA5237AA Typhimurium
+SAL_CA5238AA Enteritidis
+SAL_CA5239AA Virchow
+SAL_CA5240AA Thompson
+SAL_CA5241AA Newport
+SAL_CA5243AA Enteritidis
+SAL_CA5245AA Mbandaka
+SAL_CA5246AA Paratyphi A
+SAL_CA5248AA Virchow
+SAL_CA5249AA Enteritidis
+SAL_CA5250AA Enteritidis
+SAL_CA5251AA Enteritidis
+SAL_CA5253AA Javiana
+SAL_CA5254AA Panama
+SAL_CA5256AA Enteritidis
+SAL_CA5257AA Enteritidis
+SAL_CA5258AA Javiana
+SAL_CA5259AA Typhi
+SAL_CA5260AA Enteritidis
+SAL_CA5261AA Enteritidis
+SAL_CA5263AA Virchow
+SAL_CA5264AA Enteritidis
+SAL_CA5267AA Enteritidis
+SAL_CA5268AA Paratyphi A
+SAL_CA5269AA Infantis
+SAL_CA5270AA Chester
+SAL_CA5271AA Typhimurium
+SAL_CA5272AA Enteritidis
+SAL_CA5274AA Saintpaul
+SAL_CA5275AA Enteritidis
+SAL_CA5276AA Enteritidis
+SAL_CA5277AA Stanley
+SAL_CA5279AA Ohio
+SAL_CA5280AA Typhimurium
+SAL_CA5281AA Lattenkamp
+SAL_CA5283AA Enteritidis
+SAL_CA5284AA Enteritidis
+SAL_CA5285AA Enteritidis
+SAL_CA5286AA Agona
+SAL_CA5287AA Enteritidis
+SAL_CA5289AA Dublin
+SAL_CA5290AA Enteritidis
+SAL_CA5291AA Stanley
+SAL_CA5292AA Mbandaka
+SAL_CA5294AA Typhimurium
+SAL_CA5295AA Enteritidis
+SAL_CA5297AA Paratyphi A
+SAL_CA5298AA Enteritidis
+SAL_CA5299AA Typhimurium
+SAL_CA5300AA Virchow
+SAL_CA5301AA Enteritidis
+SAL_CA5302AA Enteritidis
+SAL_CA5304AA Kintambo
+SAL_CA5305AA Enteritidis
+SAL_CA5307AA Javiana
+SAL_CA5308AA Stanleyville
+SAL_CA5309AA Potsdam
+SAL_CA5310AA Lattenkamp
+SAL_CA5312AA Enteritidis
+SAL_CA5313AA Typhimurium
+SAL_CA5316AA Agona
+SAL_CA5317AA Enteritidis
+SAL_CA5318AA Mbandaka
+SAL_CA5319AA Adelaide
+SAL_CA5320AA Typhimurium
+SAL_CA5321AA Adelaide
+SAL_CA5322AA Poona
+SAL_CA5323AA Virchow
+SAL_CA5324AA Livingstone
+SAL_CA5325AA Enteritidis
+SAL_CA5328AA Enteritidis
+SAL_CA5329AA Enteritidis
+SAL_CA5330AA Typhimurium
+SAL_CA5331AA Typhimurium
+SAL_CA5333AA Kentucky
+SAL_CA5334AA Enteritidis
+SAL_CA5336AA Typhimurium
+SAL_CA5337AA Typhimurium
+SAL_CA5338AA Enteritidis
+SAL_CA5339AA Chester
+SAL_CA5341AA Enteritidis
+SAL_CA5342AA Saintpaul
+SAL_CA5345AA Typhimurium
+SAL_CA5348AA Typhimurium
+SAL_CA5350AA Hvittingfoss
+SAL_CA5351AA Neukoelln
+SAL_CA5352AA Typhimurium
+SAL_CA5354AA Poona
+SAL_CA5357AA Montevideo
+SAL_CA5358AA Enteritidis
+SAL_CA5359AA Typhimurium
+SAL_CA5360AA Idikan
+SAL_CA5363AA Enteritidis
+SAL_CA5364AA Braenderup
+SAL_CA5365AA Enteritidis
+SAL_CA5366AA Newport
+SAL_CA5367AA Typhimurium
+SAL_CA5369AA Typhimurium
+SAL_CA5370AA Enteritidis
+SAL_CA5374AA Typhimurium
+SAL_CA5376AA Mbandaka
+SAL_CA5377AA Enteritidis
+SAL_CA5383AA Paratyphi A
+SAL_CA5392AA Enteritidis
+SAL_CA5394AA Mbandaka
+SAL_CA5395AA Enteritidis
+SAL_CA5397AA Richmond
+SAL_CA5399AA Typhimurium
+SAL_CA0057AA Typhimurium
+SAL_CA0058AA Typhimurium
+SAL_CA0059AA Paratyphi A
+SAL_CA0060AA Typhimurium
+SAL_CA0061AA Newport
+SAL_CA0062AA Typhimurium
+SAL_CA0063AA Typhimurium
+SAL_CA0064AA Typhimurium
+SAL_CA0065AA Typhimurium
+SAL_CA0066AA Typhimurium
+SAL_CA0067AA Enteritidis
+SAL_CA0068AA Typhimurium
+SAL_CA0069AA Typhi
+SAL_CA0070AA Typhimurium
+SAL_CA0071AA Weltevreden
+SAL_CA0072AA Typhimurium
+SAL_CA5412AA Muenchen
+SAL_CA5413AA I 4,[5],12:i:-
+SAL_CA5414AA Enteritidis
+SAL_CA5415AA Enteritidis
+SAL_CA5416AA Enteritidis
+SAL_CA5419AA Virchow
+SAL_CA5421AA Enteritidis
+SAL_CA5425AA Typhimurium
+SAL_CA5431AA Agona
+SAL_CA5433AA Enteritidis
+SAL_CA5435AA Thompson
+SAL_CA5436AA Enteritidis
+SAL_CA5437AA Typhimurium
+SAL_CA5438AA Stanley
+SAL_CA5439AA Virchow
+SAL_CA5440AA Enteritidis
+SAL_CA5443AA Mikawasima
+SAL_CA5444AA Saintpaul
+SAL_CA5445AA Enteritidis
+SAL_CA5446AA Enteritidis
+SAL_CA5447AA Bredeney
+SAL_CA5448AA Enteritidis
+SAL_CA5449AA Enteritidis
+SAL_CA5450AA Enteritidis
+SAL_CA5451AA Derby
+SAL_CA5452AA Typhimurium
+SAL_CA5454AA Enteritidis
+SAL_CA5455AA Enteritidis
+SAL_CA5456AA Kentucky
+SAL_CA5457AA Litchfield
+SAL_CA5458AA Braenderup
+SAL_CA5459AA Enteritidis
+SAL_CA0540AA Rissen
+SAL_CA0544AA Enteritidis
+SAL_CA0546AA Agona
+SAL_CA0556AA Infantis
+SAL_CA0560AA Enteritidis
+SAL_CA0564AA Nima
+SAL_CA0566AA Agama
+SAL_CA0569AA Typhi
+SAL_CA0570AA Enteritidis
+SAL_CA0571AA Typhi
+SAL_CA0576AA Gatow
+SAL_CA0578AA Schwarzengrund
+SAL_CA0580AA Montevideo
+SAL_CA0582AA Typhimurium
+SAL_CA0585AA Enteritidis
+SAL_CA0586AA Newport
+SAL_CA5461AA Enteritidis
+SAL_CA5462AA Typhimurium
+SAL_CA5464AA Typhimurium
+SAL_CA5466AA Litchfield
+SAL_CA5467AA Litchfield
+SAL_CA5469AA Kentucky
+SAL_CA5471AA Enteritidis
+SAL_CA5472AA Enteritidis
+SAL_CA5474AA Typhi
+SAL_CA5475AA Enteritidis
+SAL_CA5476AA Infantis
+SAL_CA5477AA Enteritidis
+SAL_CA5478AA Typhimurium
+SAL_CA5479AA Agona
+SAL_CA5480AA Potsdam
+SAL_CA5482AA Kentucky
+SAL_CA5484AA Agona
+SAL_CA5486AA Braenderup
+SAL_CA5487AA Albany
+SAL_CA5489AA Mikawasima
+SAL_CA5490AA Enteritidis
+SAL_CA5491AA Enteritidis
+SAL_CA5492AA Livingstone
+SAL_CA5496AA Typhimurium
+SAL_CA5497AA Typhimurium
+SAL_CA5498AA Typhimurium
+SAL_CA5499AA Bredeney
+SAL_CA5500AA Typhimurium
+SAL_CA5501AA Enteritidis
+SAL_CA5503AA Typhimurium
+SAL_CA5505AA Kentucky
+SAL_CA5507AA Enteritidis
+SAL_CA5510AA Enteritidis
+SAL_CA5512AA Dublin
+SAL_CA5513AA Saintpaul
+SAL_CA5514AA Mikawasima
+SAL_CA5515AA Typhimurium
+SAL_CA5516AA Infantis
+SAL_CA5517AA Enteritidis
+SAL_CA5518AA Enteritidis
+SAL_CA5519AA Enteritidis
+SAL_CA5520AA Worb
+SAL_CA5521AA Albany
+SAL_CA5522AA Typhimurium
+SAL_CA5523AA Enteritidis
+SAL_CA5525AA Reading
+SAL_CA5526AA Enteritidis
+SAL_CA5527AA Typhimurium
+SAL_CA5529AA Livingstone
+SAL_CA5530AA Stanley
+SAL_CA5532AA Chester
+SAL_CA5533AA Stanley
+SAL_CA5535AA I 4,[5],12:i:-
+SAL_CA5536AA Braenderup
+SAL_CA5537AA Stanley
+SAL_CA5538AA Chester
+SAL_CA5539AA Typhi
+SAL_CA5541AA Plymouth
+SAL_CA5542AA Agona
+SAL_CA5544AA Enteritidis
+SAL_CA5545AA Typhi
+SAL_CA5546AA Livingstone
+SAL_CA5547AA Enteritidis
+SAL_CA5548AA Enteritidis
+SAL_CA5550AA Enteritidis
+SAL_CA5551AA Enteritidis
+SAL_CA5553AA Montevideo
+SAL_CA5554AA Newport
+SAL_CA5556AA Enteritidis
+SAL_CA5557AA Enteritidis
+SAL_CA5558AA Typhimurium
+SAL_CA5560AA Havana
+SAL_CA5561AA Enteritidis
+SAL_CA5562AA Virchow
+SAL_CA5579AA Saintpaul
+SAL_CA5580AA Enteritidis
+SAL_CA5581AA Enteritidis
+SAL_CA5583AA Agona
+SAL_CA5584AA Paratyphi A
+SAL_CA5585AA Typhimurium
+SAL_CA5184AA Braenderup
+SAL_CA5205AA Livingstone
+SAL_CA5230AA Enteritidis
+SAL_CA5252AA I 4,[5],12:i:-
+SAL_CA5273AA Enteritidis
+SAL_CA5293AA Enteritidis
+SAL_CA5315AA Enteritidis
+SAL_CA5335AA Heidelberg
+SAL_CA5361AA Enteritidis
+SAL_CA5410AA Newport
+SAL_CA5441AA Enteritidis
+SAL_CA5460AA Enteritidis
+SAL_CA5483AA Arechavaleta
+SAL_CA5508AA Typhimurium
+SAL_CA5528AA Enteritidis
+SAL_CA5587AA Virchow
+SAL_CA5588AA Mississippi
+SAL_CA5589AA Typhimurium
+SAL_CA5591AA Durban
+SAL_CA5592AA Kentucky
+SAL_CA5593AA Montevideo
+SAL_CA5594AA Typhimurium
+SAL_CA5611AA Enteritidis
+SAL_CA5612AA Newport
+SAL_CA5613AA Javiana
+SAL_CA5614AA Typhimurium
+SAL_CA5615AA Enteritidis
+SAL_CA5616AA Typhi
+SAL_CA5617AA Enteritidis
+SAL_CA5619AA Mbandaka
+SAL_CA5621AA Typhi
+SAL_CA5625AA Typhimurium
+SAL_CA5626AA Typhimurium
+SAL_CA5627AA Enteritidis
+SAL_CA5629AA Kentucky
+SAL_CA5630AA I 4,[5],12:i:-
+SAL_CA5631AA Virchow
+SAL_CA5632AA Typhimurium
+SAL_CA5634AA Butantan
+SAL_CA5636AA Enteritidis
+SAL_CA5637AA Typhimurium
+SAL_CA5638AA Enteritidis
+SAL_CA5639AA Enteritidis
+SAL_CA5640AA Infantis
+SAL_CA5641AA Montevideo
+SAL_CA5643AA Enteritidis
+SAL_CA5644AA Typhimurium
+SAL_CA5646AA Newport
+SAL_CA5647AA Infantis
+SAL_CA5648AA Virchow
+SAL_CA5650AA Typhimurium
+SAL_CA5652AA Virchow
+SAL_CA5653AA Typhimurium
+SAL_CA5654AA Enteritidis
+SAL_CA5656AA Virchow
+SAL_CA5658AA Agona
+SAL_CA5659AA Enteritidis
+SAL_CA5661AA Enteritidis
+SAL_CA5663AA Enteritidis
+SAL_CA5664AA Enteritidis
+SAL_CA5665AA Enteritidis
+SAL_CA5666AA Mikawasima
+SAL_CA5667AA Enteritidis
+SAL_CA5669AA Typhi
+SAL_CA5670AA Typhimurium
+SAL_CA5671AA Bareilly
+SAL_CA5672AA Agona
+SAL_CA5674AA Rubislaw
+SAL_CA5675AA Mbandaka
+SAL_CA5676AA Kentucky
+SAL_CA5677AA Chester
+SAL_CA5678AA Enteritidis
+SAL_CA5679AA Miami
+SAL_CA5680AA Kisangani
+SAL_CA5681AA Richmond
+SAL_CA5682AA Virchow
+SAL_CA5683AA Bareilly
+SAL_CA5684AA Derby
+SAL_CA5685AA Enteritidis
+SAL_CA5687AA Typhimurium
+SAL_CA5688AA Braenderup
+SAL_CA5689AA Enteritidis
+SAL_CA5690AA Wangata
+SAL_CA5691AA Typhimurium
+SAL_CA5692AA Enteritidis
+SAL_CA5693AA Kentucky
+SAL_CA5694AA Typhi
+SAL_CA5695AA Typhimurium
+SAL_CA5696AA Derby
+SAL_CA5697AA Kentucky
+SAL_CA5698AA Kentucky
+SAL_CA5699AA Enteritidis
+SAL_CA5701AA Livingstone
+SAL_CA5702AA London
+SAL_CA5703AA Newport
+SAL_CA5708AA Typhimurium
+SAL_CA5709AA Enteritidis
+SAL_CA5710AA Mikawasima
+SAL_CA5711AA Virchow
+SAL_CA5712AA Braenderup
+SAL_CA5713AA Paratyphi A
+SAL_CA5714AA Corvallis
+SAL_CA5716AA Enteritidis
+SAL_CA5718AA Potsdam
+SAL_CA5719AA Richmond
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+SAL_CA5721AA Enteritidis
+SAL_CA5722AA Enteritidis
+SAL_CA5723AA Javiana
+SAL_CA5724AA Enteritidis
+SAL_CA5725AA Mikawasima
+SAL_CA5727AA Derby
+SAL_CA5728AA Haifa
+SAL_CA5730AA Enteritidis
+SAL_CA5731AA Enteritidis
+SAL_CA5732AA Paratyphi A
+SAL_CA5733AA Blockley
+SAL_CA5734AA Enteritidis
+SAL_CA5737AA Stanley
+SAL_CA5738AA Kingston
+SAL_CA5740AA Paratyphi A
+SAL_CA5742AA Enteritidis
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+SAL_CA5745AA Typhimurium
+SAL_CA5747AA Enteritidis
+SAL_CA5748AA Albany
+SAL_CA5749AA Mbandaka
+SAL_CA5751AA Enteritidis
+SAL_CA5752AA Enteritidis
+SAL_CA5754AA Typhimurium
+SAL_CA5755AA Hadar
+SAL_CA5756AA Chester
+SAL_CA5757AA Enteritidis
+SAL_CA5758AA Typhimurium
+SAL_CA5759AA Muenster
+SAL_CA5760AA Enteritidis
+SAL_CA5761AA Typhimurium
+SAL_CA5762AA Infantis
+SAL_CA5763AA Schwarzengrund
+SAL_CA5764AA Mbandaka
+SAL_CA5765AA Enteritidis
+SAL_CA5766AA Eastbourne
+SAL_CA5767AA Heidelberg
+SAL_CA5770AA Braenderup
+SAL_CA5771AA Mbandaka
+SAL_CA5772AA Bareilly
+SAL_CA5773AA Infantis
+SAL_CA5774AA Enteritidis
+SAL_CA5775AA Mbandaka
+SAL_CA5777AA Stanley
+SAL_CA5778AA Enteritidis
+SAL_CA5779AA Adelaide
+SAL_CA5780AA Thompson
+SAL_CA5782AA Enteritidis
+SAL_CA5783AA Enteritidis
+SAL_CA5784AA Enteritidis
+SAL_CA5785AA Muenchen
+SAL_CA5787AA Enteritidis
+SAL_CA5788AA Typhimurium
+SAL_CA0588AA Typhimurium
+SAL_CA0590AA Typhimurium
+SAL_CA0591AA Oranienburg
+SAL_CA0593AA Enteritidis
+SAL_CA0594AA Typhimurium
+SAL_CA0595AA Hvittingfoss
+SAL_CA0596AA Typhimurium
+SAL_CA0597AA Enteritidis
+SAL_CA0598AA Bareilly
+SAL_CA0600AA Kentucky
+SAL_CA0602AA Infantis
+SAL_CA0603AA Typhimurium
+SAL_CA0604AA Kambole
+SAL_CA0606AA Typhimurium
+SAL_CA0607AA Enteritidis
+SAL_CA0608AA Newport
+SAL_CA5790AA Kentucky
+SAL_CA5791AA Enteritidis
+SAL_CA5792AA Braenderup
+SAL_CA5793AA Enteritidis
+SAL_CA5794AA Typhimurium
+SAL_CA5795AA Derby
+SAL_CA5797AA Enteritidis
+SAL_CA5798AA Typhimurium
+SAL_CA5799AA Enteritidis
+SAL_CA5800AA Enteritidis
+SAL_CA5801AA Mbandaka
+SAL_CA5802AA Enteritidis
+SAL_CA5803AA Enteritidis
+SAL_CA5804AA Takoradi
+SAL_CA5805AA Derby
+SAL_CA5806AA Oranienburg
+SAL_CA5809AA Bareilly
+SAL_CA5810AA Paratyphi A
+SAL_CA5811AA Virchow
+SAL_CA5814AA Enteritidis
+SAL_CA5815AA Shubra
+SAL_CA5816AA Infantis
+SAL_CA5818AA Enteritidis
+SAL_CA5819AA Livingstone
+SAL_CA5820AA Typhi
+SAL_CA5822AA Litchfield
+SAL_CA5823AA Saintpaul
+SAL_CA5825AA Agama
+SAL_CA5826AA Agona
+SAL_CA5829AA Enteritidis
+SAL_CA5832AA Abony
+SAL_CA5835AA Tennessee
+SAL_CA5837AA Poona
+SAL_CA5841AA Aberdeen
+SAL_CA5842AA Typhi
+SAL_CA5843AA Enteritidis
+SAL_CA5844AA Potsdam
+SAL_CA5845AA Enteritidis
+SAL_CA5846AA Enteritidis
+SAL_CA5850AA Enteritidis
+SAL_CA5852AA Lerum
+SAL_CA5853AA Typhimurium
+SAL_CA5854AA Enteritidis
+SAL_CA5862AA Heidelberg
+SAL_CA5863AA Anatum
+SAL_CA5864AA Anatum
+SAL_CA5865AA Javiana
+SAL_CA5866AA Anatum
+SAL_CA5868AA Newport
+SAL_CA5869AA Anatum
+SAL_CA5870AA Anatum
+SAL_CA5871AA Typhimurium
+SAL_CA5872AA Newport
+SAL_CA5873AA Newport
+SAL_CA5874AA Newport
+SAL_CA5875AA Anatum
+SAL_CA5877AA Typhimurium
+SAL_CA5878AA Anatum
+SAL_CA5879AA Anatum
+SAL_CA5880AA Newport
+SAL_CA5881AA Newport
+SAL_CA5882AA Newport
+SAL_CA5884AA Agona
+SAL_CA5885AA Typhimurium
+SAL_CA5887AA Montevideo
+SAL_CA5888AA Enteritidis
+SAL_CA5889AA Typhimurium
+SAL_CA5890AA Braenderup
+SAL_CA5891AA Typhimurium
+SAL_CA5892AA Augustenborg
+SAL_CA5893AA Enteritidis
+SAL_CA5894AA Kentucky
+SAL_CA5896AA Bispebjerg
+SAL_CA5897AA Hadar
+SAL_CA5898AA Enteritidis
+SAL_CA5899AA Enteritidis
+SAL_CA5900AA Paratyphi B
+SAL_CA5901AA Enteritidis
+SAL_CA5902AA Typhimurium
+SAL_CA5905AA Paratyphi A
+SAL_CA5907AA Typhimurium
+SAL_CA5908AA Mbandaka
+SAL_CA5909AA Enteritidis
+SAL_CA5910AA Schwarzengrund
+SAL_CA5912AA Agona
+SAL_CA5913AA Enteritidis
+SAL_CA5915AA Anatum
+SAL_CA5916AA Canastel
+SAL_CA5917AA Enteritidis
+SAL_CA5919AA Gaillac
+SAL_CA5920AA Typhi
+SAL_CA5921AA Kenya
+SAL_CA5923AA Kentucky
+SAL_CA5924AA Stanley
+SAL_CA5925AA Typhimurium
+SAL_CA5926AA Enteritidis
+SAL_CA5928AA Haifa
+SAL_CA5929AA Montevideo
+SAL_CA5930AA Enteritidis
+SAL_CA5931AA Enteritidis
+SAL_CA5933AA Haifa
+SAL_CA5935AA Kentucky
+SAL_CA5936AA Newport
+SAL_CA5939AA Dublin
+SAL_CA5940AA Stanleyville
+SAL_CA5941AA Kentucky
+SAL_CA5943AA Kentucky
+SAL_CA5944AA Enteritidis
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+SAL_CA5949AA Enteritidis
+SAL_CA5950AA Agbeni
+SAL_CA5951AA Kenya
+SAL_CA5586AA Newport
+SAL_CA5624AA Enteritidis
+SAL_CA5645AA Ibadan
+SAL_CA5668AA Typhimurium
+SAL_CA5686AA Enteritidis
+SAL_CA5705AA Enteritidis
+SAL_CA5726AA Glostrup
+SAL_CA5750AA Stanley
+SAL_CA5769AA Agona
+SAL_CA5789AA Umbilo
+SAL_CA5807AA Virchow
+SAL_CA5836AA Heidelberg
+SAL_CA5867AA Newport
+SAL_CA5886AA Enteritidis
+SAL_CA5906AA Enteritidis
+SAL_CA5954AA Infantis
+SAL_CA5955AA Montevideo
+SAL_CA5956AA Paratyphi A
+SAL_CA5957AA Typhimurium
+SAL_CA5958AA Oranienburg
+SAL_CA5959AA Typhi
+SAL_CA5960AA Enteritidis
+SAL_CA5961AA Kentucky
+SAL_CA5962AA Agama
+SAL_CA5963AA Enteritidis
+SAL_CA5964AA Oranienburg
+SAL_CA5965AA Durham
+SAL_CA5966AA Bonn
+SAL_CA5967AA Enteritidis
+SAL_CA5969AA Virchow
+SAL_CA5970AA Typhi
+SAL_CA5972AA Agona
+SAL_CA5973AA Litchfield
+SAL_CA5974AA Montevideo
+SAL_CA5975AA Montevideo
+SAL_CA5977AA Enteritidis
+SAL_CA5978AA Worthington
+SAL_CA5979AA Dublin
+SAL_CA5980AA Enteritidis
+SAL_CA5982AA Enteritidis
+SAL_CA5983AA Enteritidis
+SAL_CA5985AA Oranienburg
+SAL_CA5987AA Mbandaka
+SAL_CA5988AA Virchow
+SAL_CA5989AA Typhimurium
+SAL_CA5990AA Canastel
+SAL_CA5991AA Havana
+SAL_CA5994AA Enteritidis
+SAL_CA5995AA Agona
+SAL_CA5996AA Enteritidis
+SAL_CA5997AA Enteritidis
+SAL_CA5998AA Stanley
+SAL_CA5999AA Enteritidis
+SAL_CA6001AA Coeln
+SAL_CA6002AA Enteritidis
+SAL_CA6003AA Enteritidis
+SAL_CA6005AA Durham
+SAL_CA6006AA Enteritidis
+SAL_CA6008AA Chingola
+SAL_CA6009AA Oranienburg
+SAL_CA6010AA Kottbus
+SAL_CA6011AA Ajiobo
+SAL_CA6012AA Enteritidis
+SAL_CA6014AA Typhimurium
+SAL_CA6015AA Paratyphi A
+SAL_CA6016AA Typhi
+SAL_CA6017AA Enteritidis
+SAL_CA6018AA Enteritidis
+SAL_CA6019AA Enteritidis
+SAL_CA6022AA Enteritidis
+SAL_CA6023AA Kottbus
+SAL_CA6026AA Typhimurium
+SAL_CA6027AA Enteritidis
+SAL_CA6028AA Virchow
+SAL_CA6030AA Enteritidis
+SAL_CA6031AA Enteritidis
+SAL_CA6033AA Agama
+SAL_CA6036AA Virchow
+SAL_CA6037AA Kentucky
+SAL_CA6040AA Enteritidis
+SAL_CA6041AA Enteritidis
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+SAL_CA6043AA Bredeney
+SAL_CA6044AA Typhimurium
+SAL_CA6046AA Newport
+SAL_CA6047AA Enteritidis
+SAL_CA6048AA Mikawasima
+SAL_CA6049AA Enteritidis
+SAL_CA6050AA Oranienburg
+SAL_CA6051AA Enteritidis
+SAL_CA6053AA Newport
+SAL_CA6054AA Agona
+SAL_CA6056AA Montevideo
+SAL_CA6057AA Newport
+SAL_CA6058AA Enteritidis
+SAL_CA6060AA Enteritidis
+SAL_CA6062AA Braenderup
+SAL_CA6065AA Virchow
+SAL_CA6066AA Enteritidis
+SAL_CA6067AA Enteritidis
+SAL_CA6068AA Manhattan
+SAL_CA6069AA Infantis
+SAL_CA6071AA Newport
+SAL_CA6072AA Schwarzengrund
+SAL_CA6073AA Enteritidis
+SAL_CA6074AA Agama
+SAL_CA6076AA Hadar
+SAL_CA6079AA Montevideo
+SAL_CA6080AA Poona
+SAL_CA6081AA Mbandaka
+SAL_CA6082AA Infantis
+SAL_CA6084AA Enteritidis
+SAL_CA6085AA Typhimurium
+SAL_CA6086AA Infantis
+SAL_CA6087AA Enteritidis
+SAL_CA6088AA Enteritidis
+SAL_CA6089AA Heidelberg
+SAL_CA6091AA Enteritidis
+SAL_CA6092AA Colindale
+SAL_CA6093AA Enteritidis
+SAL_CA6094AA Typhimurium
+SAL_CA6095AA Agama
+SAL_CA6096AA Typhimurium
+SAL_CA6097AA Paratyphi A
+SAL_CA6098AA Enteritidis
+SAL_CA6099AA Weltevreden
+SAL_CA6100AA Typhimurium
+SAL_CA6102AA Durham
+SAL_CA6103AA Bareilly
+SAL_CA6106AA Give
+SAL_CA6107AA Typhimurium
+SAL_CA6108AA Montevideo
+SAL_CA6109AA Virchow
+SAL_CA6110AA Typhimurium
+SAL_CA6111AA Mbandaka
+SAL_CA6112AA Typhimurium
+SAL_CA6114AA Mbandaka
+SAL_CA6115AA Kottbus
+SAL_CA6116AA Abony
+SAL_CA6117AA Enteritidis
+SAL_CA6118AA Typhimurium
+SAL_CA6120AA Livingstone
+SAL_CA6121AA Gaminara
+SAL_CA0611AA Durham
+SAL_CA0612AA Typhi
+SAL_CA0613AA Typhimurium
+SAL_CA0616AA Typhimurium
+SAL_CA0618AA Enteritidis
+SAL_CA0622AA Bareilly
+SAL_CA0625AA Tudu
+SAL_CA0626AA Typhimurium
+SAL_CA0628AA Weltevreden
+SAL_CA0632AA Heidelberg
+SAL_CA0634AA Enteritidis
+SAL_CA0636AA Enteritidis
+SAL_CA0638AA Kentucky
+SAL_CA0640AA Typhi
+SAL_CA0642AA Typhi
+SAL_CA0644AA Enteritidis
+SAL_CA6123AA Enteritidis
+SAL_CA6124AA Liverpool
+SAL_CA6125AA Corvallis
+SAL_CA6127AA Oranienburg
+SAL_CA6129AA Enteritidis
+SAL_CA6130AA Bareilly
+SAL_CA6131AA Havana
+SAL_CA6133AA Typhimurium
+SAL_CA6136AA Chester
+SAL_CA6138AA Kentucky
+SAL_CA6140AA Typhimurium
+SAL_CA6141AA Enteritidis
+SAL_CA6142AA Enteritidis
+SAL_CA6143AA Typhimurium
+SAL_CA6145AA Enteritidis
+SAL_CA6146AA Enteritidis
+SAL_CA6148AA Enteritidis
+SAL_CA6149AA Enteritidis
+SAL_CA6150AA Enteritidis
+SAL_CA6151AA Enteritidis
+SAL_CA6152AA Newport
+SAL_CA6153AA Enteritidis
+SAL_CA6155AA Enteritidis
+SAL_CA6156AA Enteritidis
+SAL_CA6157AA Thompson
+SAL_CA6158AA Enteritidis
+SAL_CA6160AA Kentucky
+SAL_CA6161AA Kentucky
+SAL_CA6163AA Enteritidis
+SAL_CA6164AA Enteritidis
+SAL_CA6165AA Bardo
+SAL_CA6166AA Montevideo
+SAL_CA6168AA Enteritidis
+SAL_CA6169AA Potsdam
+SAL_CA6170AA Typhimurium
+SAL_CA6172AA Typhimurium
+SAL_CA6174AA Enteritidis
+SAL_CA6175AA Typhimurium
+SAL_CA6176AA Deversoir
+SAL_CA6177AA Paratyphi A
+SAL_CA6179AA Enteritidis
+SAL_CA6180AA Enteritidis
+SAL_CA6182AA Typhimurium
+SAL_CA6183AA Typhimurium
+SAL_CA6184AA Stanley
+SAL_CA6185AA Enteritidis
+SAL_CA6186AA Agona
+SAL_CA6187AA Enteritidis
+SAL_CA6190AA Kottbus
+SAL_CA6191AA Typhimurium
+SAL_CA6192AA Enteritidis
+SAL_CA6193AA Bareilly
+SAL_CA6194AA Enteritidis
+SAL_CA6195AA Enteritidis
+SAL_CA6196AA Enteritidis
+SAL_CA6197AA Rubislaw
+SAL_CA6198AA Enteritidis
+SAL_CA6199AA Virchow
+SAL_CA6200AA Weltevreden
+SAL_CA6201AA Typhimurium
+SAL_CA6202AA Liverpool
+SAL_CA6203AA Newport
+SAL_CA6204AA Enteritidis
+SAL_CA6205AA Infantis
+SAL_CA6207AA Enteritidis
+SAL_CA6208AA Enteritidis
+SAL_CA6209AA Enteritidis
+SAL_CA6210AA Enteritidis
+SAL_CA6211AA Paratyphi A
+SAL_CA6212AA Albany
+SAL_CA6213AA Enteritidis
+SAL_CA6214AA Virchow
+SAL_CA6215AA Thompson
+SAL_CA6216AA Enteritidis
+SAL_CA6218AA Enteritidis
+SAL_CA6219AA Indiana
+SAL_CA6220AA Oranienburg
+SAL_CA6224AA Typhimurium
+SAL_CA6225AA Stanley
+SAL_CA6227AA Braenderup
+SAL_CA6229AA Stanley
+SAL_CA6230AA Enteritidis
+SAL_CA6232AA Ajiobo
+SAL_CA6234AA Mikawasima
+SAL_CA6235AA Chester
+SAL_CA6237AA Kentucky
+SAL_CA6238AA Napoli
+SAL_CA6239AA Enteritidis
+SAL_CA6241AA Enteritidis
+SAL_CA6243AA Paratyphi A
+SAL_CA6245AA Enteritidis
+SAL_CA6246AA Typhimurium
+SAL_CA6247AA Oranienburg
+SAL_CA6248AA Enteritidis
+SAL_CA6249AA Infantis
+SAL_CA6250AA Thompson
+SAL_CA6252AA Enteritidis
+SAL_CA6253AA Enteritidis
+SAL_CA6255AA Typhimurium
+SAL_CA6256AA Enteritidis
+SAL_CA6257AA Typhimurium
+SAL_CA6258AA Tennessee
+SAL_CA6259AA Enteritidis
+SAL_CA6260AA Typhimurium
+SAL_CA6263AA Enteritidis
+SAL_CA6264AA Typhimurium
+SAL_CA6265AA Poona
+SAL_CA6267AA Enteritidis
+SAL_CA6268AA Enteritidis
+SAL_CA6269AA Stanley
+SAL_CA6270AA Enteritidis
+SAL_CA6271AA Typhimurium
+SAL_CA6274AA Typhimurium
+SAL_CA6275AA Bredeney
+SAL_CA6277AA Ealing
+SAL_CA6278AA Enteritidis
+SAL_CA6279AA Typhimurium
+SAL_CA6280AA Newport
+SAL_CA6281AA Paratyphi A
+SAL_CA6282AA Enteritidis
+SAL_CA6284AA Enteritidis
+SAL_CA6285AA Derby
+SAL_CA6286AA Virchow
+SAL_CA6287AA Enteritidis
+SAL_CA6288AA Virchow
+SAL_CA6289AA Typhimurium
+SAL_CA6290AA Virchow
+SAL_CA6291AA Agama
+SAL_CA5953AA Paratyphi A
+SAL_CA5971AA Enteritidis
+SAL_CA5992AA Enteritidis
+SAL_CA6013AA Virchow
+SAL_CA6038AA Enteritidis
+SAL_CA6059AA Typhimurium
+SAL_CA6083AA Enteritidis
+SAL_CA6101AA Typhimurium
+SAL_CA6122AA Oranienburg
+SAL_CA6147AA Enteritidis
+SAL_CA6167AA Enteritidis
+SAL_CA6188AA Virchow
+SAL_CA6206AA Typhimurium
+SAL_CA6228AA Braenderup
+SAL_CA6251AA Oranienburg
+SAL_CA6294AA Typhi
+SAL_CA6295AA Enteritidis
+SAL_CA6296AA Typhimurium
+SAL_CA6297AA Enteritidis
+SAL_CA6298AA Montevideo
+SAL_CA6299AA Haifa
+SAL_CA6301AA Liverpool
+SAL_CA6302AA Enteritidis
+SAL_CA6303AA Newport
+SAL_CA6304AA Hadar
+SAL_CA6305AA Enteritidis
+SAL_CA6306AA Weltevreden
+SAL_CA6307AA Enteritidis
+SAL_CA6308AA Enteritidis
+SAL_CA6309AA Enteritidis
+SAL_CA6310AA Typhimurium
+SAL_CA6312AA Braenderup
+SAL_CA6313AA Enteritidis
+SAL_CA6314AA Kimuenza
+SAL_CA6315AA Enteritidis
+SAL_CA6316AA Coeln
+SAL_CA6318AA Kingston
+SAL_CA6319AA Mikawasima
+SAL_CA6320AA Hadar
+SAL_CA6321AA Bareilly
+SAL_CA6323AA Enteritidis
+SAL_CA6324AA Enteritidis
+SAL_CA6325AA Enteritidis
+SAL_CA6326AA Enteritidis
+SAL_CA6327AA Virchow
+SAL_CA6328AA Kentucky
+SAL_CA6329AA Kottbus
+SAL_CA6332AA Coeln
+SAL_CA6333AA Panama
+SAL_CA6334AA Typhimurium
+SAL_CA6335AA Enteritidis
+SAL_CA6336AA Typhimurium
+SAL_CA6337AA Ibadan
+SAL_CA6338AA Hadar
+SAL_CA6339AA Stanley
+SAL_CA6341AA Enteritidis
+SAL_CA6342AA Enteritidis
+SAL_CA6343AA Hadar
+SAL_CA6345AA Virchow
+SAL_CA6346AA Braenderup
+SAL_CA6347AA Enteritidis
+SAL_CA6348AA Braenderup
+SAL_CA6349AA Haifa
+SAL_CA6351AA Enteritidis
+SAL_CA6352AA Hadar
+SAL_CA6353AA Muenchen
+SAL_CA6355AA Typhi
+SAL_CA6357AA Virchow
+SAL_CA6358AA Enteritidis
+SAL_CA6359AA Durham
+SAL_CA6360AA Kentucky
+SAL_CA6361AA Typhi
+SAL_CA6362AA Kentucky
+SAL_CA6363AA Typhimurium
+SAL_CA6364AA Senftenberg
+SAL_CA6365AA Ohio
+SAL_CA6366AA Elisabethville
+SAL_CA6367AA Enteritidis
+SAL_CA6368AA Typhimurium
+SAL_CA6371AA Typhimurium
+SAL_CA6372AA Typhimurium
+SAL_CA6373AA Enteritidis
+SAL_CA6376AA I 4,[5],12:i:-
+SAL_CA6377AA Dublin
+SAL_CA6378AA Newport
+SAL_CA6379AA Enteritidis
+SAL_CA6380AA Monschaui
+SAL_CA6381AA Enteritidis
+SAL_CA6382AA Oranienburg
+SAL_CA6384AA Typhimurium
+SAL_CA6385AA Give
+SAL_CA6386AA Virchow
+SAL_CA6387AA Enteritidis
+SAL_CA6388AA Typhimurium
+SAL_CA6390AA Enteritidis
+SAL_CA6393AA Gaminara
+SAL_CA6394AA Newport
+SAL_CA6396AA Enteritidis
+SAL_CA6397AA Braenderup
+SAL_CA6398AA Newport
+SAL_CA6399AA Typhimurium
+SAL_CA6400AA Bredeney
+SAL_CA6401AA Virchow
+SAL_CA6404AA Litchfield
+SAL_CA6405AA Agama
+SAL_CA6406AA Enteritidis
+SAL_CA6408AA Enteritidis
+SAL_CA6409AA Kenya
+SAL_CA6410AA Mbandaka
+SAL_CA6413AA Enteritidis
+SAL_CA6414AA Enteritidis
+SAL_CA6417AA Agama
+SAL_CA6418AA Enteritidis
+SAL_CA6419AA Infantis
+SAL_CA6420AA Enteritidis
+SAL_CA6421AA Gaminara
+SAL_CA6422AA Ohio
+SAL_CA6426AA Enteritidis
+SAL_CA6427AA Enteritidis
+SAL_CA6428AA Enteritidis
+SAL_CA6431AA Enteritidis
+SAL_CA6432AA Mikawasima
+SAL_CA6433AA Enteritidis
+SAL_CA6434AA Enteritidis
+SAL_CA6435AA Enteritidis
+SAL_CA6436AA Enteritidis
+SAL_CA6439AA Enteritidis
+SAL_CA0648AA Enteritidis
+SAL_CA0650AA Enteritidis
+SAL_CA0652AA Hadar
+SAL_CA0654AA Coeln
+SAL_CA0656AA Enteritidis
+SAL_CA0657AA Typhimurium
+SAL_CA0658AA Abony
+SAL_CA0662AA Bredeney
+SAL_CA0663AA Typhimurium
+SAL_CA0665AA Corvallis
+SAL_CA0666AA Enteritidis
+SAL_CA0668AA Enteritidis
+SAL_CA0670AA Typhimurium
+SAL_CA0672AA Typhimurium
+SAL_CA0674AA Stanley
+SAL_CA0676AA Infantis
+SAL_CA6441AA Enteritidis
+SAL_CA6442AA Typhimurium
+SAL_CA6443AA Obogu
+SAL_CA6444AA Braenderup
+SAL_CA6445AA Virchow
+SAL_CA6446AA Typhimurium
+SAL_CA6448AA Paratyphi A
+SAL_CA6449AA Enteritidis
+SAL_CA6450AA Typhimurium
+SAL_CA6451AA Enteritidis
+SAL_CA6452AA Enteritidis
+SAL_CA6453AA Enteritidis
+SAL_CA6455AA Enteritidis
+SAL_CA6456AA Infantis
+SAL_CA6457AA Enteritidis
+SAL_CA6458AA Dublin
+SAL_CA6462AA Enteritidis
+SAL_CA6464AA Enteritidis
+SAL_CA6465AA Bareilly
+SAL_CA6466AA Coeln
+SAL_CA6467AA Enteritidis
+SAL_CA6468AA Enteritidis
+SAL_CA6471AA Takoradi
+SAL_CA6473AA Enteritidis
+SAL_CA6474AA Amager
+SAL_CA6475AA Enteritidis
+SAL_CA6476AA Typhimurium
+SAL_CA6478AA Enteritidis
+SAL_CA6479AA Enteritidis
+SAL_CA6480AA Mikawasima
+SAL_CA6481AA Enteritidis
+SAL_CA6482AA Enteritidis
+SAL_CA6484AA Corvallis
+SAL_CA6485AA Eastbourne
+SAL_CA6487AA Bispebjerg
+SAL_CA6488AA Paratyphi A
+SAL_CA6489AA Kottbus
+SAL_CA6490AA Bredeney
+SAL_CA6491AA Coeln
+SAL_CA6492AA Montevideo
+SAL_CA6493AA Enteritidis
+SAL_CA6494AA Enteritidis
+SAL_CA6496AA Enteritidis
+SAL_CA6498AA Enteritidis
+SAL_CA6500AA Agama
+SAL_CA6501AA Virchow
+SAL_CA6502AA Enteritidis
+SAL_CA6503AA Enteritidis
+SAL_CA6505AA Enteritidis
+SAL_CA6506AA Enteritidis
+SAL_CA6508AA Bredeney
+SAL_CA6509AA Typhimurium
+SAL_CA6510AA Enteritidis
+SAL_CA6512AA Infantis
+SAL_CA6513AA Kenya
+SAL_CA6514AA Gaminara
+SAL_CA6517AA Enteritidis
+SAL_CA6518AA Enteritidis
+SAL_CA6519AA Oranienburg
+SAL_CA6520AA Infantis
+SAL_CA6522AA Bareilly
+SAL_CA6523AA Enteritidis
+SAL_CA6524AA Agama
+SAL_CA6525AA Oranienburg
+SAL_CA6527AA Typhimurium
+SAL_CA6528AA Newport
+SAL_CA6529AA Enteritidis
+SAL_CA6531AA Panama
+SAL_CA6534AA Enteritidis
+SAL_CA6536AA Enteritidis
+SAL_CA6537AA Agama
+SAL_CA6538AA Oranienburg
+SAL_CA6539AA Agona
+SAL_CA6540AA Virchow
+SAL_CA6541AA Enteritidis
+SAL_CA6542AA Enteritidis
+SAL_CA6543AA Typhimurium
+SAL_CA6546AA Enteritidis
+SAL_CA6547AA Enteritidis
+SAL_CA6548AA Kentucky
+SAL_CA6550AA Enteritidis
+SAL_CA6551AA Enteritidis
+SAL_CA6553AA Typhimurium
+SAL_CA6555AA Paratyphi A
+SAL_CA6556AA Typhimurium
+SAL_CA6557AA Enteritidis
+SAL_CA6558AA Heidelberg
+SAL_CA6560AA Indiana
+SAL_CA6562AA Typhimurium
+SAL_CA6563AA Enteritidis
+SAL_CA6565AA Mbandaka
+SAL_CA6566AA Newport
+SAL_CA6567AA Brandenburg
+SAL_CA6568AA Enteritidis
+SAL_CA6571AA Kentucky
+SAL_CA6572AA Stanley
+SAL_CA6575AA Enteritidis
+SAL_CA6576AA Infantis
+SAL_CA6580AA Enteritidis
+SAL_CA6581AA Infantis
+SAL_CA6582AA Enteritidis
+SAL_CA6583AA Duisburg
+SAL_CA6584AA Stanley
+SAL_CA6585AA Enteritidis
+SAL_CA6587AA Enteritidis
+SAL_CA6588AA Nima
+SAL_CA6589AA Enteritidis
+SAL_CA6590AA Enteritidis
+SAL_CA6591AA Kintambo
+SAL_CA6592AA Enteritidis
+SAL_CA6593AA Enteritidis
+SAL_CA6594AA Enteritidis
+SAL_CA6597AA Typhimurium
+SAL_CA6599AA Enteritidis
+SAL_CA6600AA Agona
+SAL_CA6601AA Enteritidis
+SAL_CA6603AA Typhimurium
+SAL_CA6604AA Mississippi
+SAL_CA6605AA Montevideo
+SAL_CA6606AA Minnesota
+SAL_CA6607AA Muenchen
+SAL_CA6608AA Montevideo
+SAL_CA6609AA Typhi
+SAL_CA6610AA Enteritidis
+SAL_CA6611AA Hadar
+SAL_CA6612AA Stanley
+SAL_CA6613AA Potsdam
+SAL_CA6614AA Enteritidis
+SAL_CA6618AA Enteritidis
+SAL_CA6619AA Enteritidis
+SAL_CA6620AA Haifa
+SAL_CA6623AA Weltevreden
+SAL_CA6624AA Kingston
+SAL_CA6625AA Kottbus
+SAL_CA6626AA Enteritidis
+SAL_CA6629AA Enteritidis
+SAL_CA6630AA Typhi
+SAL_CA6631AA Bredeney
+SAL_CA6632AA Concord
+SAL_CA6633AA Alachua
+SAL_CA6634AA Senftenberg
+SAL_CA6635AA Enteritidis
+SAL_CA6636AA Mikawasima
+SAL_CA6637AA Derby
+SAL_CA6293AA Enteritidis
+SAL_CA6311AA Saintpaul
+SAL_CA6331AA Virchow
+SAL_CA6350AA Senftenberg
+SAL_CA6369AA Enteritidis
+SAL_CA6391AA Mississippi
+SAL_CA6415AA Abony
+SAL_CA6440AA Enteritidis
+SAL_CA6459AA Montevideo
+SAL_CA6483AA Muenchen
+SAL_CA6504AA Paratyphi A
+SAL_CA6526AA Enteritidis
+SAL_CA6549AA Corvallis
+SAL_CA6574AA Typhimurium
+SAL_CA6596AA Derby
+SAL_CA6640AA Typhi
+SAL_CA6641AA Virchow
+SAL_CA6642AA Montevideo
+SAL_CA6643AA Paratyphi A
+SAL_CA6644AA Stanley
+SAL_CA6646AA Newport
+SAL_CA6647AA Enteritidis
+SAL_CA6649AA Enteritidis
+SAL_CA6650AA Enteritidis
+SAL_CA6651AA Weltevreden
+SAL_CA6652AA Typhi
+SAL_CA6654AA Enteritidis
+SAL_CA6655AA Newport
+SAL_CA6657AA Enteritidis
+SAL_CA6659AA Typhimurium
+SAL_CA6660AA Typhimurium
+SAL_CA6662AA Typhimurium
+SAL_CA6663AA Oranienburg
+SAL_CA6664AA Enteritidis
+SAL_CA6665AA Derby
+SAL_CA6666AA Typhimurium
+SAL_CA6668AA Typhimurium
+SAL_CA6669AA Typhimurium
+SAL_CA6670AA Enteritidis
+SAL_CA6673AA Typhimurium
+SAL_CA6674AA Bredeney
+SAL_CA6675AA Enteritidis
+SAL_CA6677AA Paratyphi A
+SAL_CA6678AA Saintpaul
+SAL_CA6680AA Enteritidis
+SAL_CA6682AA Enteritidis
+SAL_CA6683AA Typhimurium
+SAL_CA6686AA Typhimurium
+SAL_CA6688AA Enteritidis
+SAL_CA6689AA Enteritidis
+SAL_CA6690AA Enteritidis
+SAL_CA6691AA Enteritidis
+SAL_CA6693AA Enteritidis
+SAL_CA6694AA Typhimurium
+SAL_CA6695AA Enteritidis
+SAL_CA6696AA Enteritidis
+SAL_CA6698AA Typhimurium
+SAL_CA6699AA Montevideo
+SAL_CA6700AA Bredeney
+SAL_CA6701AA Thompson
+SAL_CA6702AA Gaminara
+SAL_CA6703AA Enteritidis
+SAL_CA6704AA Enteritidis
+SAL_CA6706AA Bredeney
+SAL_CA6707AA Typhimurium
+SAL_CA6708AA Typhimurium
+SAL_CA6709AA Kentucky
+SAL_CA6711AA Stanley
+SAL_CA6712AA Poona
+SAL_CA6715AA Enteritidis
+SAL_CA6716AA Enteritidis
+SAL_CA6717AA Mikawasima
+SAL_CA6718AA Panama
+SAL_CA6720AA Anatum
+SAL_CA6721AA Enteritidis
+SAL_CA6723AA Typhimurium
+SAL_CA6724AA Kentucky
+SAL_CA6725AA Newport
+SAL_CA6726AA Enteritidis
+SAL_CA6731AA Aberdeen
+SAL_CA6732AA Kedougou
+SAL_CA6733AA Stanley
+SAL_CA6734AA Montevideo
+SAL_CA6735AA Kenya
+SAL_CA6736AA Typhimurium
+SAL_CA6738AA Enteritidis
+SAL_CA6739AA Typhimurium
+SAL_CA6740AA Kingston
+SAL_CA6741AA Montevideo
+SAL_CA6742AA Enteritidis
+SAL_CA6743AA Typhimurium
+SAL_CA6745AA Stanley
+SAL_CA6746AA Enteritidis
+SAL_CA6748AA Enteritidis
+SAL_CA6749AA Hadar
+SAL_CA0682AA Enteritidis
+SAL_CA0684AA Napoli
+SAL_CA0686AA Enteritidis
+SAL_CA0694AA Enteritidis
+SAL_CA0696AA Agona
+SAL_CA0697AA Enteritidis
+SAL_CA0698AA Agona
+SAL_CA0699AA Enteritidis
+SAL_CA0700AA Agona
+SAL_CA0701AA Glostrup
+SAL_CA0702AA Agona
+SAL_CA0704AA Enteritidis
+SAL_CA0705AA Agona
+SAL_CA0706AA Virchow
+SAL_CA0707AA Agona
+SAL_CA0708AA Enteritidis
+SAL_CA6752AA Gaminara
+SAL_CA6753AA Adelaide
+SAL_CA6754AA Enteritidis
+SAL_CA6755AA Typhi
+SAL_CA6756AA Enteritidis
+SAL_CA6757AA Enteritidis
+SAL_CA6758AA Oslo
+SAL_CA6759AA Enteritidis
+SAL_CA6760AA Enteritidis
+SAL_CA6761AA Typhi
+SAL_CA6762AA Virchow
+SAL_CA6764AA Enteritidis
+SAL_CA6766AA Enteritidis
+SAL_CA6767AA Typhimurium
+SAL_CA6769AA Saintpaul
+SAL_CA6770AA Abony
+SAL_CA6772AA Duisburg
+SAL_CA6773AA Enteritidis
+SAL_CA6774AA Enteritidis
+SAL_CA6775AA Typhi
+SAL_CA6776AA Enteritidis
+SAL_CA6777AA Montevideo
+SAL_CA6778AA Enteritidis
+SAL_CA6779AA Virchow
+SAL_CA6780AA Enteritidis
+SAL_CA6781AA Stanley
+SAL_CA6782AA Enteritidis
+SAL_CA6784AA Braenderup
+SAL_CA6785AA Chester
+SAL_CA6786AA Enteritidis
+SAL_CA6787AA Enteritidis
+SAL_CA6788AA Enteritidis
+SAL_CA6792AA Infantis
+SAL_CA6793AA Agbeni
+SAL_CA6794AA Enteritidis
+SAL_CA6795AA Enteritidis
+SAL_CA6796AA Newport
+SAL_CA6797AA Enteritidis
+SAL_CA6798AA Enteritidis
+SAL_CA6801AA Enteritidis
+SAL_CA6802AA Enteritidis
+SAL_CA6803AA Typhi
+SAL_CA6805AA Enteritidis
+SAL_CA6806AA Enteritidis
+SAL_CA6807AA Enteritidis
+SAL_CA6808AA Senftenberg
+SAL_CA6809AA Mbandaka
+SAL_CA6810AA Enteritidis
+SAL_CA6812AA London
+SAL_CA6813AA Enteritidis
+SAL_CA6814AA Enteritidis
+SAL_CA6816AA Oslo
+SAL_CA6817AA Minnesota
+SAL_CA6818AA Enteritidis
+SAL_CA6819AA Enteritidis
+SAL_CA6820AA Enteritidis
+SAL_CA6821AA Enteritidis
+SAL_CA6822AA Enteritidis
+SAL_CA6823AA Bareilly
+SAL_CA6824AA Enteritidis
+SAL_CA6825AA Javiana
+SAL_CA6826AA Enteritidis
+SAL_CA6827AA Enteritidis
+SAL_CA6828AA London
+SAL_CA6830AA Kedougou
+SAL_CA6831AA Enteritidis
+SAL_CA6832AA Newport
+SAL_CA6833AA Paratyphi B
+SAL_CA6836AA Enteritidis
+SAL_CA6837AA Enteritidis
+SAL_CA6838AA Enteritidis
+SAL_CA6840AA Virchow
+SAL_CA6841AA Enteritidis
+SAL_CA6842AA Typhi
+SAL_CA6843AA Indiana
+SAL_CA6845AA Bareilly
+SAL_CA6846AA Hadar
+SAL_CA6847AA Newport
+SAL_CA6848AA Hadar
+SAL_CA6849AA Enteritidis
+SAL_CA6859AA Enteritidis
+SAL_CA6860AA Enteritidis
+SAL_CA6879AA Enteritidis
+SAL_CA6880AA Enteritidis
+SAL_CA6881AA Enteritidis
+SAL_CA6882AA Enteritidis
+SAL_CA6883AA Enteritidis
+SAL_CA6884AA Enteritidis
+SAL_CA6886AA Enteritidis
+SAL_CA6887AA Enteritidis
+SAL_CA6888AA Enteritidis
+SAL_CA6889AA Enteritidis
+SAL_CA6890AA Enteritidis
+SAL_CA6891AA Enteritidis
+SAL_CA6892AA Enteritidis
+SAL_CA6893AA Enteritidis
+SAL_CA6895AA Enteritidis
+SAL_CA6896AA Enteritidis
+SAL_CA6897AA Enteritidis
+SAL_CA6898AA Enteritidis
+SAL_CA6899AA Enteritidis
+SAL_CA6900AA Enteritidis
+SAL_CA6901AA Enteritidis
+SAL_CA6902AA Enteritidis
+SAL_CA6903AA Enteritidis
+SAL_CA6904AA Enteritidis
+SAL_CA6905AA Enteritidis
+SAL_CA6906AA Enteritidis
+SAL_CA6907AA Enteritidis
+SAL_CA6909AA Enteritidis
+SAL_CA6910AA Enteritidis
+SAL_CA6911AA Enteritidis
+SAL_CA6913AA Enteritidis
+SAL_CA6914AA Enteritidis
+SAL_CA6915AA Enteritidis
+SAL_CA6916AA Enteritidis
+SAL_CA6917AA Enteritidis
+SAL_CA6918AA Enteritidis
+SAL_CA6919AA Enteritidis
+SAL_CA6920AA Enteritidis
+SAL_CA6921AA Enteritidis
+SAL_CA6922AA Enteritidis
+SAL_CA6923AA Enteritidis
+SAL_CA6924AA Enteritidis
+SAL_CA6925AA Enteritidis
+SAL_CA6926AA Enteritidis
+SAL_CA6927AA Enteritidis
+SAL_CA6928AA Enteritidis
+SAL_CA6930AA Enteritidis
+SAL_CA6931AA Enteritidis
+SAL_CA6932AA Enteritidis
+SAL_CA6933AA Enteritidis
+SAL_CA6934AA Enteritidis
+SAL_CA6935AA Enteritidis
+SAL_CA6937AA Newport
+SAL_CA6938AA Tucson
+SAL_CA6939AA Mbandaka
+SAL_CA6947AA Typhimurium
+SAL_CA6949AA Saintpaul
+SAL_CA6951AA Muenchen
+SAL_CA6952AA Heidelberg
+SAL_CA6953AA Heidelberg
+SAL_CA6954AA Hadar
+SAL_CA6955AA Senftenberg
+SAL_CA6958AA Kentucky
+SAL_CA6959AA Hadar
+SAL_CA6960AA Hadar
+SAL_CA6961AA Montevideo
+SAL_CA6962AA Kentucky
+SAL_CA6963AA Agona
+SAL_CA6964AA Johannesburg
+SAL_CA6965AA Kentucky
+SAL_CA6966AA Senftenberg
+SAL_CA6967AA Hadar
+SAL_CA6968AA Kentucky
+SAL_CA6969AA Saintpaul
+SAL_CA6970AA Thompson
+SAL_CA6971AA Hadar
+SAL_CA6972AA Agona
+SAL_CA6973AA Kentucky
+SAL_CA0074AA Typhimurium
+SAL_CA0075AA Weltevreden
+SAL_CA0076AA Typhimurium
+SAL_CA0078AA Typhimurium
+SAL_CA0079AA Enteritidis
+SAL_CA0080AA Typhimurium
+SAL_CA0081AA Oranienburg
+SAL_CA0082AA Typhimurium
+SAL_CA0084AA Typhimurium
+SAL_CA0086AA Typhimurium
+SAL_CA0087AA Senftenberg
+SAL_CA0088AA Typhimurium
+SAL_CA0089AA Enteritidis
+SAL_CA0090AA Javiana
+SAL_CA0091AA Typhimurium
+SAL_CA0093AA Typhimurium
+SAL_CA6975AA Saintpaul
+SAL_CA6976AA Kentucky
+SAL_CA6977AA Heidelberg
+SAL_CA6978AA Kentucky
+SAL_CA6980AA Hadar
+SAL_CA7024AA Heidelberg
+SAL_CA7025AA Kentucky
+SAL_CA7027AA Bere
+SAL_CA7028AA Derby
+SAL_CA7031AA Bredeney
+SAL_CA7033AA London
+SAL_CA7034AA Montevideo
+SAL_CA7035AA Brunei
+SAL_CA7036AA Senftenberg
+SAL_CA7037AA Weltevreden
+SAL_CA7038AA Enteritidis
+SAL_CA6638AA Oslo
+SAL_CA6661AA Enteritidis
+SAL_CA6684AA Typhimurium
+SAL_CA6705AA Enteritidis
+SAL_CA6727AA Newport
+SAL_CA6751AA Agona
+SAL_CA6771AA Mbandaka
+SAL_CA6791AA Enteritidis
+SAL_CA6811AA Enteritidis
+SAL_CA6829AA Enteritidis
+SAL_CA6850AA Derby
+SAL_CA6894AA Enteritidis
+SAL_CA6912AA Enteritidis
+SAL_CA6929AA Enteritidis
+SAL_CA6956AA Saintpaul
+SAL_CA7047AA Heidelberg
+SAL_CA7049AA Cerro
+SAL_CA7051AA Derby
+SAL_CA7052AA Cerro
+SAL_CA7053AA Javiana
+SAL_CA7055AA Enteritidis
+SAL_CA7056AA Cerro
+SAL_CA7059AA Weltevreden
+SAL_CA7060AA Montevideo
+SAL_CA7062AA Sandiego
+SAL_CA7064AA Typhimurium
+SAL_CA7065AA Agona
+SAL_CA7066AA Derby
+SAL_CA7068AA Newport
+SAL_CA7069AA Typhimurium
+SAL_CA7071AA Kentucky
+SAL_CA0710AA Typhimurium
+SAL_CA0711AA Agona
+SAL_CA0712AA Tennessee
+SAL_CA0713AA Agona
+SAL_CA0714AA Newport
+SAL_CA0715AA Agona
+SAL_CA0716AA Enteritidis
+SAL_CA0717AA Agona
+SAL_CA0719AA Agona
+SAL_CA0720AA Enteritidis
+SAL_CA0721AA Agona
+SAL_CA0722AA Typhimurium
+SAL_CA0723AA Agona
+SAL_CA0725AA Agona
+SAL_CA0726AA Livingstone
+SAL_CA0727AA Agona
+SAL_CA7074AA Potsdam
+SAL_CA7075AA Montevideo
+SAL_CA7078AA Kentucky
+SAL_CA7079AA Aberdeen
+SAL_CA7080AA Weltevreden
+SAL_CA7083AA Give
+SAL_CA7086AA Senftenberg
+SAL_CA7087AA Montevideo
+SAL_CA7088AA Typhimurium
+SAL_CA7090AA Saintpaul
+SAL_CA7091AA Agona
+SAL_CA7094AA Kentucky
+SAL_CA7096AA Brunei
+SAL_CA7097AA Weltevreden
+SAL_CA7098AA Heidelberg
+SAL_CA7100AA Schwarzengrund
+SAL_CA7105AA Weltevreden
+SAL_CA7109AA Senftenberg
+SAL_CA7110AA Newport
+SAL_CA7113AA Oranienburg
+SAL_CA7115AA Senftenberg
+SAL_CA7116AA Hadar
+SAL_CA7117AA Yoruba
+SAL_CA7118AA Weltevreden
+SAL_CA7120AA Hadar
+SAL_CA7121AA Weltevreden
+SAL_CA7124AA Lille
+SAL_CA7126AA Kentucky
+SAL_CA7128AA Anatum
+SAL_CA7130AA Cerro
+SAL_CA7132AA Agona
+SAL_CA7134AA Heidelberg
+SAL_CA7141AA Anatum
+SAL_CA7144AA Heidelberg
+SAL_CA7147AA Mbandaka
+SAL_CA7148AA Johannesburg
+SAL_CA7150AA Agona
+SAL_CA7151AA Schwarzengrund
+SAL_CA7154AA Agona
+SAL_CA7156AA Enteritidis
+SAL_CA7157AA Weltevreden
+SAL_CA7158AA Montevideo
+SAL_CA7161AA Tennessee
+SAL_CA7163AA Typhimurium
+SAL_CA7170AA Anatum
+SAL_CA7173AA Virchow
+SAL_CA7190AA Typhimurium
+SAL_CA7191AA Montevideo
+SAL_CA7193AA Heidelberg
+SAL_CA7194AA Typhimurium
+SAL_CA7195AA Enteritidis
+SAL_CA7196AA Typhimurium
+SAL_CA7197AA Derby
+SAL_CA7198AA Anatum
+SAL_CA7199AA Derby
+SAL_CA7200AA Derby
+SAL_CA7201AA Derby
+SAL_CA7202AA Derby
+SAL_CA7203AA Derby
+SAL_CA7204AA Derby
+SAL_CA7205AA Molade
+SAL_CA7206AA Enteritidis
+SAL_CA7209AA Derby
+SAL_CA7210AA Derby
+SAL_CA7212AA Derby
+SAL_CA7213AA Derby
+SAL_CA7214AA Derby
+SAL_CA7215AA Derby
+SAL_CA7216AA Derby
+SAL_CA7217AA Sandiego
+SAL_CA7218AA Potsdam
+SAL_CA7219AA Enteritidis
+SAL_CA7220AA Augustenborg
+SAL_CA7221AA Derby
+SAL_CA7222AA Derby
+SAL_CA7223AA Derby
+SAL_CA7224AA Derby
+SAL_CA7225AA Derby
+SAL_CA7226AA Derby
+SAL_CA7227AA Derby
+SAL_CA0729AA Agona
+SAL_CA0730AA Kentucky
+SAL_CA0731AA Agona
+SAL_CA0732AA Virchow
+SAL_CA0733AA Haifa
+SAL_CA0734AA Agona
+SAL_CA0735AA Enteritidis
+SAL_CA0736AA Agona
+SAL_CA0737AA Typhimurium
+SAL_CA0738AA Agona
+SAL_CA0740AA Agona
+SAL_CA0741AA Enteritidis
+SAL_CA0742AA Agona
+SAL_CA0743AA Enteritidis
+SAL_CA0745AA Paratyphi A
+SAL_CA0746AA Agona
+SAL_CA7229AA Idikan
+SAL_CA7231AA Corvallis
+SAL_CA7233AA Abaetetuba
+SAL_CA7235AA Stanley
+SAL_CA7236AA Caracas
+SAL_CA7240AA Weltevreden
+SAL_CA7249AA Javiana
+SAL_CA7262AA Anatum
+SAL_CA7263AA Senftenberg
+SAL_CA7264AA Muenchen
+SAL_CA7265AA Nottingham
+SAL_CA7266AA Poona
+SAL_CA7273AA Senftenberg
+SAL_CA7274AA Muenchen
+SAL_CA7275AA Weltevreden
+SAL_CA7276AA Senftenberg
+SAL_CA7279AA Wandsworth
+SAL_CA7282AA Enteritidis
+SAL_CA7283AA Sandiego
+SAL_CA7285AA Weltevreden
+SAL_CA7286AA Kumasi
+SAL_CA7287AA Wandsworth
+SAL_CA7289AA Eastbourne
+SAL_CA7290AA Brunei
+SAL_CA7293AA Weltevreden
+SAL_CA7294AA Agona
+SAL_CA7296AA Derby
+SAL_CA7297AA Virchow
+SAL_CA7298AA Weltevreden
+SAL_CA7300AA Weltevreden
+SAL_CA7302AA Typhimurium
+SAL_CA7303AA Weltevreden
+SAL_CA7305AA Weltevreden
+SAL_CA7306AA Enteritidis
+SAL_CA7308AA Rissen
+SAL_CA7309AA Give
+SAL_CA7311AA Tennessee
+SAL_CA7312AA Oranienburg
+SAL_CA7313AA Tennessee
+SAL_CA7315AA Potsdam
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+SAL_DA1147AA Enteritidis
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+SAL_DA1192AA Enteritidis
+SAL_DA1193AA Enteritidis
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+SAL_DA1200AA Enteritidis
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+SAL_DA1244AA Enteritidis
+SAL_DA1245AA Enteritidis
+SAL_DA1247AA Agona
+SAL_DA1248AA Give
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+SAL_CA9768AA Give
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+SAL_CA9978AA Weltevreden
+SAL_DA0016AA Oranienburg
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+SAL_DA0380AA Enteritidis
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+SAL_CA3899AA Enteritidis
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+SAL_CA6974AA Heidelberg
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+SAL_DA7743AA Paratyphi A
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+SAL_GA4668AA Muenchen
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+SAL_DA1266AA Paratyphi A
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+SAL_DA1295AA Enteritidis
+SAL_DA1297AA Infantis
+SAL_DA1300AA Enteritidis
+SAL_DA1303AA Kibusi
+SAL_DA1305AA Irumu
+SAL_DA1306AA Enteritidis
+SAL_DA1309AA Enteritidis
+SAL_DA1310AA Enteritidis
+SAL_DA1312AA Enteritidis
+SAL_DA1315AA Enteritidis
+SAL_DA1318AA Enteritidis
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+SAL_DA1346AA Thompson
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+SAL_DA1349AA Alachua
+SAL_DA1350AA Mikawasima
+SAL_DA1351AA Ago
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+SAL_DA1358AA Ealing
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+SAL_DA1364AA Gafsa
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+SAL_DA1367AA Galiema
+SAL_DA1368AA Vejle
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+SAL_DA1370AA Anecho
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+SAL_DA1377AA Ajiobo
+SAL_DA1378AA Agbeni
+SAL_DA1381AA Coeln
+SAL_DA1382AA Anecho
+SAL_DA1385AA Gafsa
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+SAL_DA1388AA Abony
+SAL_DA1393AA Nima
+SAL_DA1394AA Mikawasima
+SAL_DA1395AA Coeln
+SAL_DA1397AA Mikawasima
+SAL_DA1399AA Altona
+SAL_DA1401AA Agama
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+SAL_DA1419AA Ajiobo
+SAL_DA1423AA Coeln
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+SAL_DA1427AA Ago
+SAL_DA1432AA Ealing
+SAL_DA1433AA Coeln
+SAL_DA1434AA Agama
+SAL_DA1436AA Vitkin
+SAL_DA1438AA Alachua
+SAL_DA1442AA Enteritidis
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+SAL_DA1475AA Tennessee
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+SAL_DA1480AA Derby
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+SAL_DA1487AA Javiana
+SAL_DA1488AA Enteritidis
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+SAL_DA1493AA Enteritidis
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+SAL_DA1496AA Mgulani
+SAL_DA1497AA Wangata
+SAL_DA1498AA Eastbourne
+SAL_DA1499AA Mgulani
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+SAL_DA1504AA Enteritidis
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+SAL_DA1506AA Stanleyville
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+SAL_DA1523AA Hull
+SAL_DA1524AA Enteritidis
+SAL_DA1525AA Hull
+SAL_DA1526AA Richmond
+SAL_DA1527AA Napoli
+SAL_DA1529AA Enteritidis
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+SAL_DA1889AA Enteritidis
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+SAL_DA1909AA Enteritidis
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+SAL_DA2224AA Enteritidis
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+SAL_DA2320AA Enteritidis
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+SAL_DA2341AA Thompson
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+SAL_DA2946AA Uganda
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+SAL_DA2986AA Enteritidis
+SAL_DA2988AA Enteritidis
+SAL_DA3000AA Typhimurium
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+SAL_DA3121AA Enteritidis
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+SAL_DA3135AA Enteritidis
+SAL_DA3141AA Enteritidis
+SAL_DA3144AA Enteritidis
+SAL_DA3145AA Enteritidis
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+SAL_DA0408AA Enteritidis
+SAL_DA0410AA Wangata
+SAL_DA0411AA Paratyphi A
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+SAL_DA0414AA Typhi
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+SAL_DA4335AA Heidelberg
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+SAL_DA4363AA Montevideo
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+SAL_DA4399AA Enteritidis
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+SAL_DA7739AA Paratyphi A
+SAL_DA7740AA Paratyphi A
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+SAL_DA7744AA Paratyphi A
+SAL_DA7745AA Paratyphi A
+SAL_DA7746AA Paratyphi A
+SAL_DA7747AA Paratyphi A
+SAL_DA7748AA Paratyphi A
+SAL_DA7749AA Paratyphi A
+SAL_DA7750AA Paratyphi A
+SAL_DA7751AA Paratyphi A
+SAL_DA7752AA Paratyphi A
+SAL_DA7753AA Paratyphi A
+SAL_DA7754AA Paratyphi A
+SAL_DA7755AA Paratyphi A
+SAL_DA7756AA Paratyphi A
+SAL_DA7757AA Paratyphi A
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+SAL_DA7618AA Paratyphi A
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+SAL_DA8132AA Enteritidis
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+SAL_DA8175AA Sandiego
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+SAL_DA0055AA Enteritidis
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+SAL_DA0080AA Weltevreden
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+SAL_DA0097AA Newport
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+SAL_DA0099AA Gaminara
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+SAL_DA0104AA Senftenberg
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+SAL_DA0110AA Senftenberg
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+SAL_DA8485AA Enteritidis
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+SAL_DA8529AA Nchanga
+SAL_DA8531AA Teko
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+SAL_DA0872AA Enteritidis
+SAL_DA0875AA Montevideo
+SAL_DA0876AA Enteritidis
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+SAL_EA7693AA Enteritidis
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+SAL_HA1498AA Enteritidis
+SAL_HA1499AA Enteritidis
+SAL_HA1500AA Enteritidis
+SAL_HA1501AA Enteritidis
+SAL_HA1502AA Enteritidis
+SAL_HA1503AA Enteritidis
+SAL_HA1504AA Enteritidis
+SAL_HA1505AA Enteritidis
+SAL_HA1506AA Enteritidis
+SAL_HA0182AA Enteritidis
+SAL_HA0183AA Enteritidis
+SAL_HA0184AA Enteritidis
+SAL_HA0185AA Enteritidis
+SAL_HA0186AA Enteritidis
+SAL_HA0187AA Enteritidis
+SAL_HA0188AA Enteritidis
+SAL_HA0189AA Enteritidis
+SAL_HA0190AA Enteritidis
+SAL_HA0191AA Enteritidis
+SAL_HA0192AA Enteritidis
+SAL_HA0193AA Enteritidis
+SAL_HA0194AA Enteritidis
+SAL_HA0195AA Enteritidis
+SAL_HA0196AA Enteritidis
+SAL_HA0197AA Enteritidis
+SAL_HA1508AA Enteritidis
+SAL_HA1509AA Enteritidis
+SAL_HA1510AA Enteritidis
+SAL_HA1511AA Enteritidis
+SAL_HA1512AA Enteritidis
+SAL_HA1513AA Enteritidis
+SAL_HA1514AA Enteritidis
+SAL_HA1515AA Enteritidis
+SAL_HA1516AA Enteritidis
+SAL_HA1517AA Enteritidis
+SAL_HA1518AA Enteritidis
+SAL_HA1519AA Enteritidis
+SAL_HA1520AA Enteritidis
+SAL_HA1652AA Enteritidis
+SAL_HA1653AA Enteritidis
+SAL_HA1654AA Enteritidis
+SAL_HA1656AA Enteritidis
+SAL_HA1657AA Enteritidis
+SAL_HA1658AA Enteritidis
+SAL_HA1659AA Enteritidis
+SAL_HA1660AA Enteritidis
+SAL_HA1661AA Enteritidis
+SAL_HA1662AA Enteritidis
+SAL_HA1663AA Enteritidis
+SAL_HA1664AA Enteritidis
+SAL_HA1665AA Enteritidis
+SAL_HA1666AA Enteritidis
+SAL_HA1667AA Enteritidis
+SAL_HA1668AA Enteritidis
+SAL_HA1669AA Enteritidis
+SAL_HA1670AA Enteritidis
+SAL_HA1671AA Enteritidis
+SAL_HA1673AA Enteritidis
+SAL_HA1674AA Enteritidis
+SAL_HA1675AA Enteritidis
+SAL_HA1676AA Enteritidis
+SAL_HA1677AA Enteritidis
+SAL_HA1678AA Enteritidis
+SAL_HA1679AA Enteritidis
+SAL_HA1680AA Enteritidis
+SAL_HA1681AA Enteritidis
+SAL_HA1701AA Paratyphi C
+SAL_HA1702AA Johannesburg
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+SAL_HA0199AA Enteritidis
+SAL_HA0200AA Enteritidis
+SAL_HA0201AA Enteritidis
+SAL_HA0202AA Enteritidis
+SAL_HA0203AA Enteritidis
+SAL_HA0204AA Enteritidis
+SAL_HA0205AA Enteritidis
+SAL_HA0206AA Enteritidis
+SAL_HA0207AA Enteritidis
+SAL_HA0208AA Enteritidis
+SAL_HA0209AA Enteritidis
+SAL_HA0210AA Enteritidis
+SAL_HA0211AA Enteritidis
+SAL_HA0212AA Enteritidis
+SAL_HA0213AA Enteritidis
+SAL_HA0214AA Enteritidis
+SAL_HA1709AA Johannesburg
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+SAL_HA1756AA Infantis
+SAL_HA1757AA Kentucky
+SAL_HA1772AA Enteritidis
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+SAL_HA1775AA Enteritidis
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+SAL_HA1777AA Enteritidis
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+SAL_HA1779AA Enteritidis
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+SAL_HA1781AA Enteritidis
+SAL_HA1782AA Enteritidis
+SAL_HA1783AA Enteritidis
+SAL_HA1784AA Enteritidis
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+SAL_HA1786AA Enteritidis
+SAL_HA1787AA Enteritidis
+SAL_HA1788AA Enteritidis
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+SAL_HA1790AA Enteritidis
+SAL_HA1792AA Enteritidis
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+SAL_HA1797AA Enteritidis
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+SAL_HA1800AA Enteritidis
+SAL_HA1801AA Enteritidis
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+SAL_HA1804AA Enteritidis
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+SAL_HA1806AA Enteritidis
+SAL_HA1807AA Enteritidis
+SAL_HA0216AA Enteritidis
+SAL_HA0217AA Enteritidis
+SAL_HA0218AA Enteritidis
+SAL_HA0219AA Enteritidis
+SAL_HA0220AA Enteritidis
+SAL_HA0221AA Enteritidis
+SAL_HA0222AA Enteritidis
+SAL_HA0223AA Enteritidis
+SAL_HA0224AA Enteritidis
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+SAL_HA1809AA Enteritidis
+SAL_HA1810AA Enteritidis
+SAL_HA1811AA Enteritidis
+SAL_HA1812AA Enteritidis
+SAL_HA1813AA Enteritidis
+SAL_HA1814AA Enteritidis
+SAL_HA1815AA Enteritidis
+SAL_HA1816AA Enteritidis
+SAL_HA1817AA Enteritidis
+SAL_HA1818AA Enteritidis
+SAL_HA1819AA Enteritidis
+SAL_HA1820AA Enteritidis
+SAL_HA1821AA Enteritidis
+SAL_HA2391AA Enteritidis
+SAL_HA2392AA Enteritidis
+SAL_HA2393AA Enteritidis
+SAL_HA2395AA Enteritidis
+SAL_HA2396AA Enteritidis
+SAL_HA2397AA Enteritidis
+SAL_HA2398AA Enteritidis
+SAL_HA2399AA Enteritidis
+SAL_HA2400AA Enteritidis
+SAL_HA2401AA Enteritidis
+SAL_HA2402AA Enteritidis
+SAL_HA2403AA Enteritidis
+SAL_HA2404AA Enteritidis
+SAL_HA2405AA Enteritidis
+SAL_HA2406AA Enteritidis
+SAL_HA2407AA Enteritidis
+SAL_HA2408AA Enteritidis
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+SAL_HA2410AA Enteritidis
+SAL_HA2412AA Enteritidis
+SAL_HA2413AA Enteritidis
+SAL_HA2414AA Enteritidis
+SAL_HA2415AA Enteritidis
+SAL_HA2416AA Enteritidis
+SAL_HA2417AA Enteritidis
+SAL_HA2418AA Enteritidis
+SAL_HA2419AA Enteritidis
+SAL_HA2420AA Enteritidis
+SAL_HA2421AA Enteritidis
+SAL_HA2422AA Enteritidis
+SAL_HA2423AA Enteritidis
+SAL_HA2424AA Enteritidis
+SAL_HA2425AA Enteritidis
+SAL_HA2426AA Enteritidis
+SAL_HA2427AA Enteritidis
+SAL_HA1269AA Aberdeen
+SAL_HA1290AA Hadar
+SAL_HA1310AA Give
+SAL_HA1340AA Enteritidis
+SAL_HA1424AA Enteritidis
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+SAL_HA1507AA Enteritidis
+SAL_HA1655AA Enteritidis
+SAL_HA1672AA Enteritidis
+SAL_HA1708AA London
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+SAL_HA2394AA Enteritidis
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+SAL_HA2430AA Enteritidis
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+SAL_HA2694AA Enteritidis
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+SAL_HA2697AA Enteritidis
+SAL_HA2698AA Enteritidis
+SAL_HA2699AA Enteritidis
+SAL_HA2700AA Enteritidis
+SAL_HA2701AA Enteritidis
+SAL_HA2702AA Enteritidis
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+SAL_HA2791AA Bovismorbificans
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+SAL_HA2836AA Enteritidis
+SAL_HA2837AA Enteritidis
+SAL_HA2838AA Enteritidis
+SAL_HA2839AA Enteritidis
+SAL_HA2841AA Enteritidis
+SAL_HA2842AA Enteritidis
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+SAL_HA2847AA Enteritidis
+SAL_HA2848AA Enteritidis
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+SAL_HA3125AA Dublin
+SAL_HA3126AA Kentucky
+SAL_HA3140AA Enteritidis
+SAL_HA3141AA Enteritidis
+SAL_HA3142AA Enteritidis
+SAL_HA3144AA Enteritidis
+SAL_HA3145AA Enteritidis
+SAL_HA3146AA Enteritidis
+SAL_HA3147AA Enteritidis
+SAL_HA3148AA Enteritidis
+SAL_HA3149AA Enteritidis
+SAL_HA3223AA Enteritidis
+SAL_HA3224AA Enteritidis
+SAL_HA3225AA Enteritidis
+SAL_HA3226AA Enteritidis
+SAL_HA3227AA Enteritidis
+SAL_HA3228AA Enteritidis
+SAL_HA3229AA Enteritidis
+SAL_HA3230AA Enteritidis
+SAL_HA3231AA Enteritidis
+SAL_HA3232AA Enteritidis
+SAL_HA3234AA Enteritidis
+SAL_HA3235AA Enteritidis
+SAL_HA3236AA Enteritidis
+SAL_HA3237AA Enteritidis
+SAL_HA3238AA Enteritidis
+SAL_HA3239AA Enteritidis
+SAL_HA3240AA Enteritidis
+SAL_HA3241AA Enteritidis
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+SAL_HA3244AA Heidelberg
+SAL_HA3245AA Infantis
+SAL_HA3246AA Infantis
+SAL_HA3247AA Typhimurium
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+SAL_HA3446AA Enteritidis
+SAL_HA3447AA Enteritidis
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+SAL_HA3450AA Enteritidis
+SAL_HA3451AA Enteritidis
+SAL_HA3452AA Enteritidis
+SAL_HA3453AA Enteritidis
+SAL_HA3454AA Enteritidis
+SAL_HA3455AA Enteritidis
+SAL_HA3456AA Enteritidis
+SAL_HA3457AA Enteritidis
+SAL_HA3458AA Enteritidis
+SAL_HA3459AA Enteritidis
+SAL_HA3460AA Enteritidis
+SAL_HA3461AA Enteritidis
+SAL_HA3463AA Enteritidis
+SAL_HA3464AA Enteritidis
+SAL_HA3465AA Enteritidis
+SAL_HA3466AA Enteritidis
+SAL_HA3467AA Enteritidis
+SAL_HA3468AA Enteritidis
+SAL_HA3469AA Enteritidis
+SAL_HA3470AA Enteritidis
+SAL_HA3471AA Enteritidis
+SAL_HA3472AA Enteritidis
+SAL_HA3473AA Enteritidis
+SAL_HA3474AA Enteritidis
+SAL_HA3475AA Enteritidis
+SAL_HA3476AA Enteritidis
+SAL_HA3477AA Enteritidis
+SAL_HA3478AA Enteritidis
+SAL_HA3480AA Enteritidis
+SAL_HA3481AA Enteritidis
+SAL_HA3482AA Enteritidis
+SAL_HA3483AA Enteritidis
+SAL_HA3484AA Enteritidis
+SAL_HA3485AA Enteritidis
+SAL_HA3486AA Enteritidis
+SAL_HA3487AA Enteritidis
+SAL_HA3488AA Enteritidis
+SAL_HA3489AA Enteritidis
+SAL_HA3490AA Enteritidis
+SAL_HA3491AA Enteritidis
+SAL_HA3492AA Enteritidis
+SAL_HA3493AA Enteritidis
+SAL_HA3494AA Enteritidis
+SAL_HA3495AA Enteritidis
+SAL_HA2428AA Enteritidis
+SAL_HA2693AA Enteritidis
+SAL_HA2711AA Montevideo
+SAL_HA2775AA Rissen
+SAL_HA2800AA Senftenberg
+SAL_HA2840AA Enteritidis
+SAL_HA2899AA Berta
+SAL_HA2926AA Ouakam
+SAL_HA2947AA Montevideo
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+SAL_HA3113AA Typhimurium
+SAL_HA3143AA Enteritidis
+SAL_HA3233AA Enteritidis
+SAL_HA3251AA Infantis
+SAL_HA3462AA Enteritidis
+SAL_HA3497AA Enteritidis
+SAL_HA3498AA Enteritidis
+SAL_HA3499AA Enteritidis
+SAL_HA3500AA Enteritidis
+SAL_HA3501AA Enteritidis
+SAL_HA3502AA Enteritidis
+SAL_HA3503AA Enteritidis
+SAL_HA3504AA Enteritidis
+SAL_HA3505AA Enteritidis
+SAL_HA3507AA Enteritidis
+SAL_HA3508AA Enteritidis
+SAL_HA3509AA Enteritidis
+SAL_HA3510AA Enteritidis
+SAL_HA3511AA Enteritidis
+SAL_HA3512AA Enteritidis
+SAL_HA3513AA Enteritidis
+SAL_HA3515AA Enteritidis
+SAL_HA3516AA Enteritidis
+SAL_HA3517AA Enteritidis
+SAL_HA3518AA Enteritidis
+SAL_HA3519AA Enteritidis
+SAL_HA3520AA Enteritidis
+SAL_HA3521AA Hartford
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+SAL_HA3524AA Oranienburg
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+SAL_HA3527AA Anatum
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+SAL_HA3531AA Agona
+SAL_HA3535AA Enteritidis
+SAL_HA3544AA Enteritidis
+SAL_HA3545AA Enteritidis
+SAL_HA3546AA Enteritidis
+SAL_HA3547AA Enteritidis
+SAL_HA3548AA Enteritidis
+SAL_HA3549AA Enteritidis
+SAL_HA3550AA Enteritidis
+SAL_HA3551AA Enteritidis
+SAL_HA3552AA Enteritidis
+SAL_HA3553AA Enteritidis
+SAL_HA3554AA Enteritidis
+SAL_HA3555AA Enteritidis
+SAL_HA3556AA Enteritidis
+SAL_HA3557AA Enteritidis
+SAL_HA3558AA Enteritidis
+SAL_HA3559AA Enteritidis
+SAL_HA3561AA Enteritidis
+SAL_HA3562AA Enteritidis
+SAL_HA3563AA Enteritidis
+SAL_HA3564AA Enteritidis
+SAL_HA3565AA Enteritidis
+SAL_HA3566AA Enteritidis
+SAL_HA3567AA Enteritidis
+SAL_HA3568AA Enteritidis
+SAL_HA3569AA Enteritidis
+SAL_HA3570AA Enteritidis
+SAL_HA3571AA Enteritidis
+SAL_HA3572AA Enteritidis
+SAL_HA3573AA Enteritidis
+SAL_HA3574AA Enteritidis
+SAL_HA3575AA Enteritidis
+SAL_HA3576AA Enteritidis
+SAL_HA3578AA Enteritidis
+SAL_HA3579AA Enteritidis
+SAL_HA3580AA Enteritidis
+SAL_HA3581AA Enteritidis
+SAL_HA3582AA Enteritidis
+SAL_HA3583AA Enteritidis
+SAL_HA3584AA Enteritidis
+SAL_HA3585AA Enteritidis
+SAL_HA3586AA Enteritidis
+SAL_HA3587AA Enteritidis
+SAL_HA3588AA Enteritidis
+SAL_HA3589AA Enteritidis
+SAL_HA3590AA Enteritidis
+SAL_HA3591AA Enteritidis
+SAL_HA3592AA Enteritidis
+SAL_HA3593AA Enteritidis
+SAL_HA3595AA Enteritidis
+SAL_HA3596AA Enteritidis
+SAL_HA3597AA Enteritidis
+SAL_HA3598AA Enteritidis
+SAL_HA3599AA Enteritidis
+SAL_HA3600AA Enteritidis
+SAL_HA3601AA Enteritidis
+SAL_HA3602AA Enteritidis
+SAL_HA3603AA Enteritidis
+SAL_HA3604AA Enteritidis
+SAL_HA3605AA Enteritidis
+SAL_HA3606AA Enteritidis
+SAL_HA3607AA Enteritidis
+SAL_HA3608AA Enteritidis
+SAL_HA3609AA Enteritidis
+SAL_HA3610AA Enteritidis
+SAL_HA3612AA Enteritidis
+SAL_HA3613AA Enteritidis
+SAL_HA3663AA Kentucky
+SAL_HA3664AA Kentucky
+SAL_HA3920AA Heidelberg
+SAL_HA3921AA Kentucky
+SAL_HA3922AA Kentucky
+SAL_HA3923AA Kentucky
+SAL_HA3925AA Infantis
+SAL_HA3926AA Kentucky
+SAL_HA3927AA Enteritidis
+SAL_HA3935AA Hadar
+SAL_HA3936AA Gaminara
+SAL_HA3937AA Mgulani
+SAL_HA3941AA Hadar
+SAL_HA3942AA Typhimurium
+SAL_HA3944AA Anatum
+SAL_HA3945AA Anatum
+SAL_HA3946AA Infantis
+SAL_HA3947AA Enteritidis
+SAL_HA3948AA Kentucky
+SAL_HA3949AA Kentucky
+SAL_HA3950AA Infantis
+SAL_HA3951AA Anatum
+SAL_HA3952AA Infantis
+SAL_HA3953AA Newport
+SAL_HA3955AA Montevideo
+SAL_HA3956AA Montevideo
+SAL_HA3958AA Enteritidis
+SAL_HA3959AA Mbandaka
+SAL_HA3960AA Infantis
+SAL_HA3961AA Muenchen
+SAL_HA3964AA Kentucky
+SAL_HA3966AA Typhimurium
+SAL_HA3967AA Kentucky
+SAL_HA3968AA Kentucky
+SAL_HA3969AA Uganda
+SAL_HA3970AA Altona
+SAL_HA3971AA London
+SAL_HA3972AA Agona
+SAL_HA3973AA Anatum
+SAL_HA3974AA Uganda
+SAL_HA3975AA Tennessee
+SAL_HA3976AA Typhimurium
+SAL_HA3977AA Infantis
+SAL_HA3978AA Johannesburg
+SAL_HA3979AA Infantis
+SAL_HA3980AA Montevideo
+SAL_HA3982AA Saintpaul
+SAL_HA3983AA Anatum
+SAL_HA3984AA Enteritidis
+SAL_HA3985AA Mbandaka
+SAL_HA3986AA Reading
+SAL_HA3988AA Anatum
+SAL_HA3989AA Johannesburg
+SAL_HA3990AA Newport
+SAL_HA3991AA Anatum
+SAL_HA3992AA Bredeney
+SAL_HA3993AA Anatum
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+SAL_JA0467AA Hadar
+SAL_JA0468AA Kentucky
+SAL_JA0469AA Typhimurium
+SAL_JA0472AA Typhimurium
+SAL_JA0475AA Typhimurium
+SAL_JA0476AA Anatum
+SAL_JA0477AA Agona
+SAL_JA0483AA Anatum
+SAL_JA0485AA Thompson
+SAL_JA0487AA Thompson
+SAL_JA0490AA Typhimurium
+SAL_JA0491AA Bredeney
+SAL_JA0493AA Montevideo
+SAL_JA0494AA Enteritidis
+SAL_JA0586AA Rissen
+SAL_JA0587AA Rissen
+SAL_JA0594AA Mbandaka
+SAL_JA0596AA Derby
+SAL_JA0598AA Cerro
+SAL_JA0600AA Cerro
+SAL_JA0602AA Cerro
+SAL_JA0603AA Rissen
+SAL_JA0606AA Dublin
+SAL_JA0608AA Johannesburg
+SAL_JA0610AA Johannesburg
+SAL_JA0612AA Derby
+SAL_JA0614AA Rissen
+SAL_JA0842AA Anatum
+SAL_JA0845AA Bredeney
+SAL_JA0846AA Uganda
+SAL_JA0849AA Bredeney
+SAL_JA0851AA Sandiego
+SAL_JA0854AA Oranienburg
+SAL_JA0868AA Senftenberg
+SAL_JA0872AA Heidelberg
+SAL_JA0873AA Typhimurium
+SAL_JA1130AA Heidelberg
+SAL_JA1131AA Schwarzengrund
+SAL_JA1132AA Heidelberg
+SAL_JA1134AA Agona
+SAL_JA1135AA Newport
+SAL_JA1136AA Heidelberg
+SAL_JA1144AA Mbandaka
+SAL_JA1146AA Mbandaka
+SAL_JA1147AA Mbandaka
+SAL_JA1148AA Mbandaka
+SAL_JA1149AA Mbandaka
+SAL_JA1150AA Mbandaka
+SAL_JA0081AA Weltevreden
+SAL_JA0099AA Weltevreden
+SAL_JA0111AA Muenchen
+SAL_JA0115AA Muenchen
+SAL_JA0119AA Enteritidis
+SAL_JA0134AA Rissen
+SAL_JA0208AA Litchfield
+SAL_JA0209AA Kirkee
+SAL_JA0210AA Mbandaka
+SAL_JA0235AA Enteritidis
+SAL_JA0265AA Enteritidis
+SAL_JA0269AA Mbandaka
+SAL_JA0270AA Worthington
+SAL_JA0296AA Kentucky
+SAL_JA0299AA Stanley
+SAL_JA0300AA Weltevreden
+SAL_JA0301AA Braenderup
+SAL_JA0327AA Mbandaka
+SAL_JA0330AA Mbandaka
+SAL_AA9333AA Gallinarum
+SAL_AA9670AA Paratyphi B var. Java
+SAL_AA9671AA Gallinarum
+SAL_AA9677AA Dublin
+SAL_BA0698AA I 4,[5],12:i:-
+SAL_BA0711AA I 4,[5],12:i:-
+SAL_BA0712AA I 4,[5],12:i:-
+SAL_BA0713AA I 4,[5],12:i:-
+SAL_BA0739AA I 4,[5],12:i:-
+SAL_BA0745AA I 4,[5],12:i:-
+SAL_BA0784AA Paratyphi B var. Java
+SAL_BA0812AA Newport
+SAL_BA0816AA Paratyphi B var. Java
+SAL_BA0817AA Paratyphi B var. Java
+SAL_BA0827AA Paratyphi B var. Java
+SAL_BA0830AA I 4,[5],12:b:-
+SAL_BA1500AA Orion
+SAL_BA1504AA IV 43:z4,z23:-
+SAL_BA1507AA IV 43:z4,z23:-
+SAL_BA1529AA Anatum
+SAL_BA1531AA I 4,[5],12:b:-
+SAL_BA1537AA I 4,[5],12:b:-
+SAL_BA1598AA Typhimurium
+SAL_BA1603AA Typhimurium
+SAL_BA1626AA Typhimurium
+SAL_BA1630AA IV 48:z4,z32:-
+SAL_BA1660AA I 4,[5],12:i:-
+SAL_BA1671AA IIIb 61:l,v:z35
+SAL_BA1686AA Typhimurium
+SAL_BA1690AA I 47:z4,z23:-
+SAL_BA1698AA I 4,[5],12:i:-
+SAL_BA1846AA Paratyphi B
+SAL_BA1877AA IV 43:z4,z23:-
+SAL_BA1903AA Paratyphi B
+SAL_BA1912AA Oranienburg
+SAL_BA1940AA Oranienburg
+SAL_BA1980AA Oranienburg
+SAL_BA1988AA Oranienburg
+SAL_BA1991AA II 48:d:z6
+SAL_BA1995AA II 48:d:z6
+SAL_BA2007AA I 4,[5],12:b:-
+SAL_BA2039AA Typhimurium
+SAL_BA2046AA Senftenberg
+SAL_BA2051AA II 48:d:z6
+SAL_BA2147AA II 40:z4,z24:z39
+SAL_BA2153AA Orion
+SAL_BA2550AA Weltevreden
+SAL_BA2566AA Itami
+SAL_BA2624AA I 4,[5],12:b:-
+SAL_BA2638AA IV 43:z4,z23:-
+SAL_BA2659AA Paratyphi B var. Java
+SAL_BA2758AA Heidelberg
+SAL_BA2894AA Orion
+SAL_BA3007AA Heidelberg
+SAL_BA3015AA IIIb 50:r:z:[z67]
+SAL_BA3018AA Heidelberg
+SAL_BA3020AA Heidelberg
+SAL_BA3161AA I 4,[5],12:i:-
+SAL_BA3404AA Brazzaville
+SAL_BA3482AA Javiana
+SAL_BA3523AA Oranienburg
+SAL_BA3532AA IIIb 38:(k):z35
+SAL_BA3533AA Newport
+SAL_BA3537AA Javiana
+SAL_BA0836AA Paratyphi B var. Java
+SAL_BA0980AA Bovismorbificans
+SAL_BA1448AA IV 43:z4,z23:-
+SAL_BA1849AA Paratyphi B
+SAL_BA2589AA I 4,[5],12:i:-
+SAL_BA3554AA IV 45:g,z51:-
+SAL_BA4478AA IIIb 61:l,v:z35
+SAL_BA5469AA Colobane
+SAL_BA6536AA Typhimurium
+SAL_BA7568AA Paratyphi B var. Java
+SAL_BA8554AA Paratyphi B var. Java
+SAL_BA9121AA Paratyphi B var. Java
+SAL_CA0435AA Goldcoast
+SAL_CA1313AA Paratyphi B var. Java
+SAL_CA2081AA Hvittingfoss
+SAL_BA3567AA Newport
+SAL_BA3569AA Newport
+SAL_BA3581AA Oranienburg
+SAL_BA3600AA Oranienburg
+SAL_BA3663AA IV 11:g,z51:-
+SAL_BA3870AA Paratyphi B var. Java
+SAL_BA3872AA Paratyphi B var. Java
+SAL_BA3874AA Paratyphi B var. Java
+SAL_BA3875AA Paratyphi B var. Java
+SAL_BA3877AA Paratyphi B var. Java
+SAL_BA3880AA Paratyphi B var. Java
+SAL_BA3882AA Paratyphi B var. Java
+SAL_BA3884AA Paratyphi B var. Java
+SAL_BA3886AA Paratyphi B var. Java
+SAL_BA4264AA Mbandaka
+SAL_BA4472AA I 4,[5],12:i:-
+SAL_BA4513AA Rissen
+SAL_BA4746AA Typhimurium
+SAL_BA4789AA Typhimurium
+SAL_BA4830AA Choleraesuis
+SAL_BA4832AA Gallinarum
+SAL_BA4834AA Gallinarum
+SAL_BA4836AA Bispebjerg
+SAL_BA4840AA Bispebjerg
+SAL_BA4843AA Choleraesuis
+SAL_BA4853AA Wentworth
+SAL_BA4903AA Orion
+SAL_BA5003AA Denver
+SAL_BA5034AA Soahanina
+SAL_BA5427AA IV 11:g,z51:-
+SAL_BA5434AA Itami
+SAL_BA5443AA Oranienburg
+SAL_BA5473AA Colobane
+SAL_BA5478AA Colobane
+SAL_BA5536AA Typhimurium
+SAL_BA5634AA Gallinarum
+SAL_BA5643AA Typhimurium
+SAL_BA5777AA Gallinarum
+SAL_BA5794AA Choleraesuis
+SAL_BA5795AA Paratyphi B var. Java monophasic
+SAL_BA5832AA Bispebjerg
+SAL_BA5877AA Gallinarum
+SAL_BA6141AA Stormont
+SAL_BA6358AA Paratyphi B var. Java
+SAL_BA6380AA I 4,[5],12:d:-
+SAL_BA6381AA Paratyphi B var. Java
+SAL_BA6409AA Nessziona
+SAL_BA6430AA Ebrie
+SAL_BA6541AA Benue
+SAL_BA6551AA Benue
+SAL_BA6563AA Lexington
+SAL_BA6641AA Rostock
+SAL_BA6667AA Oranienburg
+SAL_BA6678AA Paratyphi B var. Java
+SAL_BA6957AA Typhimurium
+SAL_BA7023AA I 4,[5],12:d:-
+SAL_BA7283AA Uganda
+SAL_BA7307AA I 4,[5],12:d:-
+SAL_BA7333AA II 1,4,[5],12,[27]:b:[e,n,x]
+SAL_BA7337AA I 4,[5],12:d:-
+SAL_BA7448AA Paratyphi B var. Java
+SAL_BA7468AA Goldcoast
+SAL_BA7524AA Paratyphi B var. Java
+SAL_BA7545AA Bovismorbificans
+SAL_BA7616AA Goldcoast
+SAL_BA7869AA Goldcoast
+SAL_BA7909AA Paratyphi B var. Java
+SAL_BA7935AA Goldcoast
+SAL_BA7940AA I 4,[5],12:i:-
+SAL_BA8033AA Paratyphi B var. Java
+SAL_BA8035AA Paratyphi B var. Java
+SAL_BA8135AA Bovismorbificans
+SAL_BA8179AA Paratyphi B var. Java
+SAL_BA8327AA Goldcoast
+SAL_BA8400AA Paratyphi B var. Java
+SAL_BA8407AA Duesseldorf
+SAL_BA8413AA Onireke
+SAL_BA8453AA Telelkebir
+SAL_BA8460AA IV 50:g,z51:-
+SAL_BA8524AA Carno
+SAL_BA8619AA Paratyphi B var. Java
+SAL_BA8663AA IV 50:g,z51:-
+SAL_BA8667AA Sandiego
+SAL_BA8673AA Paratyphi B var. Java
+SAL_BA8701AA Typhimurium
+SAL_BA8708AA Bovismorbificans
+SAL_BA8712AA IV 1,40:z4,z32:-
+SAL_BA8719AA Florida
+SAL_BA8747AA Typhimurium
+SAL_BA8755AA Typhimurium
+SAL_BA8803AA I 4,[5],12:i:-
+SAL_BA8883AA IV 1,40:z4,z32:-
+SAL_BA8890AA IV 1,40:z4,z32:-
+SAL_BA8917AA IIIb 50:r:z:[z67]
+SAL_BA8919AA IIIa 41:z4,z23:-
+SAL_BA8926AA Bovismorbificans
+SAL_BA0844AA Paratyphi B var. Java
+SAL_BA0845AA Paratyphi B var. Java
+SAL_BA0852AA Paratyphi B var. Java
+SAL_BA0854AA Paratyphi B var. Java
+SAL_BA0873AA Paratyphi B var. Java
+SAL_BA0917AA Paratyphi B var. Java
+SAL_BA0921AA Typhimurium
+SAL_BA0927AA Paratyphi B var. Java
+SAL_BA0928AA Paratyphi B var. Java
+SAL_BA0946AA Cannstatt
+SAL_BA0952AA Paratyphi B var. Java
+SAL_BA0974AA Bovismorbificans
+SAL_BA0975AA Bovismorbificans
+SAL_BA0976AA Bovismorbificans
+SAL_BA0977AA Bovismorbificans
+SAL_BA0978AA Bovismorbificans
+SAL_BA0979AA Bovismorbificans
+SAL_BA0981AA Bovismorbificans
+SAL_BA0982AA Bovismorbificans
+SAL_BA0983AA Bovismorbificans
+SAL_BA0984AA Bovismorbificans
+SAL_BA0985AA Bovismorbificans
+SAL_BA0986AA Bovismorbificans
+SAL_BA0987AA Bovismorbificans
+SAL_BA0988AA Bovismorbificans
+SAL_BA0989AA Bovismorbificans
+SAL_BA0991AA Bovismorbificans
+SAL_BA0992AA Bovismorbificans
+SAL_BA0993AA I 4,[5],12:i:-
+SAL_BA1227AA I 4,[5],12:i:-
+SAL_BA1234AA I 4,[5],12:i:-
+SAL_BA1278AA I 4,[5],12:i:-
+SAL_BA1283AA IIIa 18:z4,z23:-
+SAL_BA1303AA Typhimurium
+SAL_BA1306AA Typhimurium
+SAL_BA1325AA I 4,[5],12:b:-
+SAL_BA1328AA Paratyphi B var. Java monophasic
+SAL_BA1331AA I 4,[5],12:i:-
+SAL_BA1357AA Paratyphi B var. Java monophasic
+SAL_BA1366AA I 4,[5],12:b:-
+SAL_BA1369AA Telhashomer
+SAL_BA9129AA Paratyphi B var. Java
+SAL_BA9147AA Choleraesuis
+SAL_BA9244AA Goldcoast
+SAL_BA9250AA Goldcoast
+SAL_BA9315AA Goldcoast
+SAL_BA9392AA Goldcoast
+SAL_BA9433AA Paratyphi B var. Java
+SAL_BA9471AA Telelkebir
+SAL_BA9486AA Weltevreden
+SAL_BA9511AA Choleraesuis
+SAL_BA9642AA Goldcoast
+SAL_BA9714AA Paratyphi B var. Java
+SAL_BA9789AA Goldcoast
+SAL_BA9826AA Orion
+SAL_CA0354AA Paratyphi B var. Java monophasic
+SAL_CA0393AA Goldcoast
+SAL_CA1400AA Paratyphi B var. Java
+SAL_CA1432AA Goldcoast
+SAL_CA1433AA Goldcoast
+SAL_CA1517AA Paratyphi B var. Java
+SAL_CA1578AA Paratyphi B var. Java
+SAL_CA1691AA Paratyphi B var. Java
+SAL_CA1695AA Bovismorbificans
+SAL_CA1773AA Goldcoast
+SAL_CA1808AA Goldcoast
+SAL_CA1850AA Bovismorbificans
+SAL_CA1911AA Paratyphi B var. Java
+SAL_CA1936AA Bovismorbificans
+SAL_CA1959AA Anatum
+SAL_CA1969AA Sandiego
+SAL_CA1992AA Sandiego
+SAL_CA2080AA Goldcoast
+SAL_CA2104AA Paratyphi B var. Java
+SAL_CA2125AA Goldcoast
+SAL_CA2129AA Paratyphi B var. Java
+SAL_CA2155AA Paratyphi B var. Java
+SAL_CA2243AA Paratyphi B var. Java
+SAL_CA2257AA Telelkebir
+SAL_CA2288AA Paratyphi B var. Java
+SAL_CA2304AA Paratyphi B var. Java
+SAL_CA2467AA Paratyphi B var. Java
+SAL_CA2485AA Paratyphi B var. Java
+SAL_CA2529AA Bovismorbificans
+SAL_CA2531AA Paratyphi B var. Java
+SAL_CA2541AA Bovismorbificans
+SAL_CA2644AA Fluntern
+SAL_CA2648AA Paratyphi B var. Java
+SAL_CA2720AA Amherstiana
+SAL_CA2883AA Bovismorbificans
+SAL_CA2888AA IV 50:g,z51:-
+SAL_CA2892AA Paratyphi B var. Java
+SAL_CA2896AA Kottbus
+SAL_CA2994AA Sandiego
+SAL_CA3044AA IV 50:g,z51:-
+SAL_CA3058AA Paratyphi B var. Java
+SAL_CA3096AA Bovismorbificans
+SAL_CA3122AA Bovismorbificans
+SAL_CA3139AA Bovismorbificans
+SAL_CA3173AA Goldcoast
+SAL_CA3180AA Paratyphi B var. Java
+SAL_CA3194AA Paratyphi B var. Java
+SAL_CA3214AA Paratyphi B var. Java
+SAL_CA3234AA Goldcoast
+SAL_CA3238AA Paratyphi B var. Java
+SAL_CA3258AA Paratyphi B var. Java
+SAL_CA3267AA Paratyphi B var. Java
+SAL_CA3319AA Paratyphi B var. Java monophasic
+SAL_CA3334AA Paratyphi B var. Java
+SAL_CA3393AA Goldcoast
+SAL_CA3400AA Goldcoast
+SAL_CA3406AA Bovismorbificans
+SAL_CA3417AA Goldcoast
+SAL_CA3425AA Paratyphi B var. Java
+SAL_CA3445AA Mkamba
+SAL_CA3595AA Sandiego
+SAL_CA3680AA Paratyphi B var. Java
+SAL_CA3698AA Bovismorbificans
+SAL_CA3699AA Goldcoast
+SAL_CA3760AA Goldcoast
+SAL_CA3769AA Duesseldorf
+SAL_CA3858AA Sandiego
+SAL_CA3874AA Paratyphi B var. Java
+SAL_CA3960AA Goldcoast
+SAL_CA3967AA Goldcoast
+SAL_CA3980AA Bovismorbificans
+SAL_CA3997AA Goldcoast
+SAL_CA4027AA Paratyphi B var. Java
+SAL_CA4037AA Goldcoast
+SAL_CA4082AA Goldcoast
+SAL_CA4094AA Paratyphi B var. Java
+SAL_CA4114AA Sandiego
+SAL_CA4186AA Telelkebir
+SAL_CA4212AA Teko
+SAL_CA4216AA Uganda
+SAL_CA4219AA Bovismorbificans
+SAL_CA4276AA IV 50:g,z51:-
+SAL_CA4313AA Goldcoast
+SAL_CA4365AA Goldcoast
+SAL_CA4407AA Uganda
+SAL_CA4484AA Paratyphi B var. Java
+SAL_CA4486AA Paratyphi B var. Java
+SAL_CA4584AA Bovismorbificans
+SAL_CA4609AA Goldcoast
+SAL_CA4670AA Paratyphi B var. Java
+SAL_CA4677AA Paratyphi B var. Java
+SAL_CA4693AA Paratyphi B var. Java monophasic
+SAL_CA4717AA Paratyphi B var. Java
+SAL_CA4718AA Goldcoast
+SAL_CA4722AA Goldcoast
+SAL_CA4762AA IV 11:z4,z23:-
+SAL_CA4793AA Sandiego
+SAL_CA4858AA Paratyphi B var. Java
+SAL_CA4878AA II 1,4,[5],12,[27]:b:[e,n,x]
+SAL_CA4893AA IV 50:g,z51:-
+SAL_CA4902AA Paratyphi B var. Java
+SAL_CA4930AA Paratyphi B var. Java
+SAL_CA5013AA Paratyphi B var. Java
+SAL_CA5016AA Uganda
+SAL_CA5076AA Simi
+SAL_CA5122AA Paratyphi B var. Java
+SAL_CA5127AA Bovismorbificans
+SAL_CA5136AA Paratyphi B var. Java monophasic
+SAL_CA5165AA Paratyphi B var. Java
+SAL_CA5173AA Paratyphi B var. Java
+SAL_CA5217AA Lomita
+SAL_CA5247AA Paratyphi B var. Java
+SAL_CA5262AA Sandiego
+SAL_CA5265AA Uganda
+SAL_CA5332AA Paratyphi B var. Java
+SAL_CA5343AA Hadar
+SAL_CA5396AA Paratyphi B var. Java
+SAL_CA5463AA Paratyphi B var. Java
+SAL_CA5494AA Sandiego
+SAL_CA5618AA Paratyphi B var. Java
+SAL_CA5633AA Paratyphi B var. Java
+SAL_CA5635AA IV 43:z4,z23:-
+SAL_CA5642AA Paratyphi B var. Java
+SAL_CA5707AA Sangalkam
+SAL_CA5715AA IV 50:g,z51:-
+SAL_CA5717AA Paratyphi B var. Java
+SAL_CA5729AA Bovismorbificans
+SAL_CA5768AA Sandiego
+SAL_CA5796AA IV 50:g,z51:-
+SAL_CA5876AA I 4,[5],12:i:-
+SAL_CA5947AA Paratyphi B var. Java
+SAL_CA6024AA Paratyphi B var. Java
+SAL_CA6055AA Sandiego
+SAL_CA6144AA IV 50:g,z51:-
+SAL_CA6171AA Orion
+SAL_CA6181AA Paratyphi B var. Java
+SAL_CA6226AA Bovismorbificans
+SAL_CA6412AA Paratyphi B var. Java
+SAL_CA6595AA Paratyphi B var. Java
+SAL_CA6645AA Orion
+SAL_CA6648AA Paratyphi B var. Java
+SAL_CA6679AA Telelkebir
+SAL_CA6730AA Paratyphi B var. Java
+SAL_CA7023AA IV 50:g,z51:-
+SAL_CA7032AA I 4,[5],12:i:-
+SAL_CA7054AA Paratyphi B var. Java
+SAL_CA7089AA I 4,[5],12:i:-
+SAL_CA7103AA I 4,[5],12:i:-
+SAL_CA7108AA I 4,[5],12:i:-
+SAL_CA7129AA Bangkok
+SAL_CA7242AA Paratyphi B var. Java monophasic
+SAL_CA7280AA Paratyphi B var. Java monophasic
+SAL_CA7281AA IV 43:z4,z23:-
+SAL_CA7284AA II 40:z4,z24:z39
+SAL_CA7292AA IV 51:z4,z23:-
+SAL_CA7295AA Typhimurium
+SAL_CA7301AA II 48:d:z6
+SAL_CA7307AA Paratyphi B var. Java
+SAL_CA7397AA Typhimurium
+SAL_CA7398AA Typhimurium
+SAL_CA7399AA Typhimurium
+SAL_CA7403AA Typhimurium
+SAL_CA7456AA I 4,[5],12:i:-
+SAL_CA7612AA Typhimurium
+SAL_CA7621AA Typhimurium
+SAL_CA7715AA Paratyphi B var. Java monophasic
+SAL_CA7723AA I 4,[5],12:b:-
+SAL_CA7919AA Paratyphi B var. Java
+SAL_CA7995AA Muenster
+SAL_CA8011AA Weltevreden
+SAL_CA8022AA IV 43:z4,z23:-
+SAL_CA8041AA Muenster
+SAL_CA8062AA Denver
+SAL_CA8092AA Mbandaka
+SAL_CA8135AA I 4,[5],12:i:-
+SAL_CA8180AA Typhimurium
+SAL_CA8182AA I 4,[5],12:i:-
+SAL_CA8183AA I 4,[5],12:i:-
+SAL_CA8185AA I 4,[5],12:i:-
+SAL_CA8186AA I 4,[5],12:i:-
+SAL_CA8188AA I 4,[5],12:i:-
+SAL_CA8189AA I 4,[5],12:i:-
+SAL_CA8190AA I 4,[5],12:i:-
+SAL_CA8191AA I 4,[5],12:i:-
+SAL_CA8237AA Nessziona
+SAL_CA8254AA IIIa 48:z4,z23,z32:-
+SAL_CA8270AA I 4,[5],12:i:-
+SAL_CA8276AA I 4,[5],12:d:-
+SAL_CA8331AA Typhimurium
+SAL_CA8383AA O61:k:1,5,7
+SAL_CA8415AA I 4,[5],12:b:-
+SAL_CA8515AA Oranienburg
+SAL_CA8531AA I 4,[5],12:i:-
+SAL_CA8541AA I 4,[5],12:i:-
+SAL_CA0487AA Goldcoast
+SAL_CA0542AA Paratyphi B var. Java
+SAL_CA0633AA V 48:z35:-
+SAL_CA0639AA V 66:z65:-
+SAL_CA0641AA V 48:z35:-
+SAL_CA0643AA V 48:z41:-
+SAL_CA0655AA V 48:z35:-
+SAL_CA0659AA V 66:z35:-
+SAL_CA0661AA V 48:z35:-
+SAL_CA0692AA Sandiego
+SAL_CA0774AA Goldcoast
+SAL_CA0803AA Goldcoast
+SAL_CA0807AA Goldcoast
+SAL_CA0883AA Paratyphi B var. Java
+SAL_CA0909AA Paratyphi B var. Java
+SAL_CA1074AA Gallinarum
+SAL_CA1083AA Goldcoast
+SAL_CA1091AA Paratyphi B var. Java
+SAL_CA1260AA Paratyphi B var. Java
+SAL_CA1274AA Sandiego
+SAL_CA8561AA I 4,[5],12:d:-
+SAL_CA8573AA IV 43:z4,z23:-
+SAL_CA8586AA IV 48:z4,z32:-
+SAL_CA8608AA Poona
+SAL_CA8614AA I 4,[5],12:i:-
+SAL_CA8621AA Heidelberg
+SAL_CA8623AA Oranienburg
+SAL_CA8628AA Poona
+SAL_CA8695AA I 4,[5],12:i:-
+SAL_CA8715AA Oranienburg
+SAL_CA8721AA Denver
+SAL_CA8722AA Oranienburg
+SAL_CA8758AA Typhimurium
+SAL_CA8763AA I 4,[5],12:i:-
+SAL_CA8847AA Paratyphi B var. Java
+SAL_CA8969AA Virchow
+SAL_CA9018AA Typhimurium
+SAL_CA9030AA Typhimurium
+SAL_CA9040AA Typhimurium
+SAL_CA9250AA Caracas
+SAL_CA9259AA Paratyphi B var. Java monophasic
+SAL_CA9272AA Virchow
+SAL_CA9281AA Caracas
+SAL_CA9287AA Virchow
+SAL_CA9302AA Typhimurium
+SAL_CA9306AA Typhimurium
+SAL_CA9320AA Typhimurium
+SAL_CA9679AA Javiana
+SAL_CA9705AA Typhimurium
+SAL_CA9713AA Lomita
+SAL_CA9771AA Bere
+SAL_CA9841AA Heidelberg
+SAL_CA9868AA Typhimurium
+SAL_CA9875AA Typhimurium
+SAL_CA9924AA I 4,[5],12:i:-
+SAL_CA9935AA I 4,[5],12:i:-
+SAL_CA9961AA Weltevreden
+SAL_CA9969AA IV 50:g,z51:-
+SAL_CA9974AA IV 50:g,z51:-
+SAL_DA0077AA Uganda
+SAL_DA0078AA Altona
+SAL_DA0083AA Altona
+SAL_DA0092AA Paratyphi B var. Java monophasic
+SAL_DA0143AA Altona
+SAL_DA0148AA Uganda
+SAL_DA0238AA Typhimurium
+SAL_DA0249AA I 42:z4,z23:-
+SAL_DA0252AA I 4,[5],12:i:-
+SAL_DA0255AA Banana
+SAL_DA0263AA Typhimurium
+SAL_DA0271AA I 4,[5],12:d:-
+SAL_DA0272AA I 4,[5],12:d:-
+SAL_DA1275AA Paratyphi B var. Java monophasic
+SAL_DA1277AA IV 48:g,z51:-
+SAL_DA1285AA Paratyphi B var. Java
+SAL_DA1301AA I 4,[5],12:b:-
+SAL_DA1327AA Orion
+SAL_DA1340AA Orion
+SAL_DA1375AA Edinburg
+SAL_DA1407AA Ramatgan
+SAL_DA1410AA Ramatgan
+SAL_DA1429AA I Rough:z38:-
+SAL_DA1439AA Edinburg
+SAL_DA1482AA Warragul
+SAL_DA1489AA Paratyphi B var. Java
+SAL_DA1491AA IV 50:g,z51:-
+SAL_DA1571AA I 4,[5],12:i:-
+SAL_DA1578AA I 4,[5],12:i:-
+SAL_DA1642AA Newport
+SAL_DA1643AA Newport
+SAL_DA1666AA IV 43:z4,z23:-
+SAL_DA1707AA I 4,[5],12:i:-
+SAL_DA1752AA I 4,[5],12:b:-
+SAL_DA1753AA I 4,[5],12:b:-
+SAL_DA1754AA I 4,[5],12:b:-
+SAL_DA1805AA I 4,[5],12:b:-
+SAL_DA1810AA Paratyphi B var. Java
+SAL_DA1814AA Paratyphi B var. Java
+SAL_DA1876AA I 4,[5],12:b:-
+SAL_DA1890AA VI [1],6,14,[25]:a:e,n,x
+SAL_DA1901AA I 4,[5],12:b:-
+SAL_DA1925AA I 4,[5],12:b:-
+SAL_DA1927AA Typhimurium
+SAL_DA1928AA Typhimurium
+SAL_DA1959AA Ouakam
+SAL_DA2004AA IIIb 42:z10:e,n,x,z15:[z60]
+SAL_DA2011AA I 4,[5],12:i:-
+SAL_DA2022AA Weltevreden
+SAL_DA2024AA Typhimurium
+SAL_DA2030AA II 42:z:1,5
+SAL_DA2033AA Amsterdam
+SAL_DA2163AA Newport
+SAL_DA2164AA Orion
+SAL_DA2431AA Newport
+SAL_DA2433AA Nchanga
+SAL_DA2438AA Paratyphi B var. Java
+SAL_DA2439AA Paratyphi B var. Java
+SAL_DA2440AA Paratyphi B var. Java
+SAL_DA2445AA Choleraesuis
+SAL_DA2459AA I 4,[5],12:i:-
+SAL_DA2999AA Edinburg
+SAL_DA3019AA Choleraesuis
+SAL_DA3137AA Paratyphi B
+SAL_DA3138AA Typhimurium
+SAL_DA3253AA Typhimurium
+SAL_DA3275AA Typhimurium
+SAL_DA3277AA Typhimurium
+SAL_DA3278AA Typhimurium
+SAL_DA3279AA Typhimurium
+SAL_DA3283AA Typhimurium
+SAL_DA3285AA Typhimurium
+SAL_DA3286AA Typhimurium
+SAL_DA3287AA Typhimurium
+SAL_DA3288AA Typhimurium
+SAL_DA3290AA Typhimurium
+SAL_DA3590AA Paratyphi B var. Java monophasic
+SAL_CA3243AA Goldcoast
+SAL_CA3826AA Goldcoast
+SAL_CA4297AA Bovismorbificans
+SAL_CA4877AA Paratyphi B var. Java monophasic
+SAL_CA5306AA Sandiego
+SAL_CA5895AA Sandiego
+SAL_CA7058AA Paratyphi B var. Java
+SAL_CA7404AA Uganda
+SAL_CA8184AA I 4,[5],12:i:-
+SAL_CA8548AA I 4,[5],12:i:-
+SAL_CA9005AA IV 43:z4,z23:-
+SAL_CA9860AA Typhimurium
+SAL_DA0313AA Bere
+SAL_DA0645AA IV 50:g,z51:-
+SAL_DA1255AA Paratyphi B var. Java
+SAL_DA3645AA Paratyphi B var. Java monophasic
+SAL_DA3686AA Paratyphi B var. Java monophasic
+SAL_DA3704AA Paratyphi B var. Java monophasic
+SAL_DA3706AA Paratyphi B var. Java monophasic
+SAL_DA3751AA Paratyphi B var. Java monophasic
+SAL_DA3760AA Paratyphi B var. Java monophasic
+SAL_DA3854AA I 1,6,14,25:b:e,n,x
+SAL_DA3890AA Typhimurium
+SAL_DA3896AA Typhimurium
+SAL_DA3925AA Hato
+SAL_DA3954AA Brunei
+SAL_DA3960AA I 50:y:-
+SAL_DA3965AA I 4,[5],12:b:-
+SAL_DA3967AA VI [1],6,14,[25]:a:e,n,x
+SAL_DA3996AA Bispebjerg
+SAL_DA4050AA I 4,[5],12:i:-
+SAL_DA4087AA I 4,[5],12:d:-
+SAL_DA4094AA Choleraesuis
+SAL_DA4139AA Give
+SAL_DA4274AA Woodinville
+SAL_DA4276AA Typhimurium
+SAL_DA4287AA II 1,9,12,46,27:l,w:e,n,x
+SAL_DA4305AA Typhimurium
+SAL_DA4371AA IV 43:z4,z23:-
+SAL_DA4372AA II 48:d:z6
+SAL_DA4430AA Choleraesuis
+SAL_DA4449AA Choleraesuis
+SAL_DA4451AA Choleraesuis
+SAL_DA4453AA Choleraesuis
+SAL_DA4457AA Choleraesuis
+SAL_DA4459AA Choleraesuis
+SAL_DA4460AA Choleraesuis
+SAL_DA4463AA V 44:r:-
+SAL_DA4464AA V 44:z39:-
+SAL_DA4465AA V 1,40:z35:-
+SAL_DA4467AA V 1,13,22:i:-
+SAL_DA4468AA V 48:z39:-
+SAL_DA4469AA V 61:z35:-
+SAL_DA4471AA V 66:z39:-
+SAL_DA4473AA V 13,22:r:-
+SAL_DA4474AA V 48:i:-
+SAL_DA4518AA Choleraesuis
+SAL_DA4519AA Choleraesuis
+SAL_DA4520AA Choleraesuis
+SAL_DA4522AA Choleraesuis
+SAL_DA4525AA Choleraesuis
+SAL_DA4526AA Choleraesuis
+SAL_DA4531AA Choleraesuis
+SAL_DA4545AA Choleraesuis
+SAL_DA4547AA Choleraesuis
+SAL_DA4548AA Choleraesuis
+SAL_DA4549AA Choleraesuis
+SAL_DA4550AA Choleraesuis
+SAL_DA4552AA Choleraesuis
+SAL_DA4553AA Choleraesuis
+SAL_DA4554AA Choleraesuis
+SAL_DA4555AA Choleraesuis
+SAL_DA5037AA IV 16:z4,z32:-
+SAL_DA5099AA Typhimurium
+SAL_DA5103AA Waycross
+SAL_DA5119AA Choleraesuis
+SAL_DA5161AA Choleraesuis
+SAL_DA5253AA II 42:r:-
+SAL_DA5275AA Telhashomer
+SAL_DA0330AA Bere
+SAL_DA0347AA I 4,[5],12:i:-
+SAL_DA0354AA Bere
+SAL_DA0371AA Bovismorbificans
+SAL_DA0383AA Bovismorbificans
+SAL_DA0398AA Carno
+SAL_DA0441AA Goelzau
+SAL_DA0524AA II 1,4,[5],12,[27]:b:[e,n,x]
+SAL_DA0533AA Paratyphi B var. Java
+SAL_DA0537AA Paratyphi B var. Java
+SAL_DA0551AA Paratyphi B var. Java
+SAL_DA0574AA Paratyphi B var. Java
+SAL_DA0605AA Sandiego
+SAL_DA0617AA Paratyphi B var. Java
+SAL_DA0619AA Paratyphi B var. Java
+SAL_DA0639AA Goelzau
+SAL_DA5426AA I 4,[5],12:d:-
+SAL_DA5467AA IV 43:z4,z23:-
+SAL_DA5599AA Farmsen
+SAL_DA5600AA I 4,[5],12:b:-
+SAL_DA5610AA I 4,[5],12:b:-
+SAL_DA5611AA I 4,[5],12:b:-
+SAL_DA5648AA Typhimurium
+SAL_DA5650AA Anatum
+SAL_DA5739AA Benin
+SAL_DA5743AA Meleagridis
+SAL_DA5762AA Meleagridis
+SAL_DA5902AA I 1,6,14,25:b:1,6
+SAL_DA6034AA Choleraesuis
+SAL_DA6078AA Coromandel
+SAL_DA6086AA Weltevreden
+SAL_DA6090AA Cerro
+SAL_DA6121AA Edinburg
+SAL_DA6182AA Meleagridis
+SAL_DA6186AA Typhimurium
+SAL_DA6207AA Choleraesuis
+SAL_DA6223AA Paratyphi B var. Java
+SAL_DA6229AA Paratyphi B var. Java
+SAL_DA6270AA Virchow
+SAL_DA6271AA I 4,[5],12:i:-
+SAL_DA6299AA Farmsen
+SAL_DA6366AA Poona
+SAL_DA6383AA I 4,[5],12:b:-
+SAL_DA6412AA Anatum
+SAL_DA6413AA Newport
+SAL_DA6416AA Kentucky
+SAL_DA6436AA Anatum
+SAL_DA6515AA Kentucky
+SAL_DA6520AA Meleagridis
+SAL_DA6558AA Typhimurium
+SAL_DA6572AA Typhimurium
+SAL_DA6609AA Typhimurium
+SAL_DA6664AA II 9,12:z29:1,5
+SAL_DA6678AA Paratyphi B
+SAL_DA6797AA Paratyphi B var. Java
+SAL_DA6798AA Paratyphi B var. Java
+SAL_DA6802AA Paratyphi B var. Java
+SAL_DA6807AA Paratyphi B var. Java
+SAL_DA6812AA Paratyphi B var. Java
+SAL_DA6893AA Weltevreden
+SAL_DA6904AA Newport
+SAL_DA6912AA Give
+SAL_DA6913AA Senftenberg
+SAL_DA6956AA IIIb 58:r:z53:[z47],[z57],[z70],[z73]
+SAL_DA7006AA Newport
+SAL_DA7034AA I 4,[5],12:i:-
+SAL_DA7036AA Typhimurium
+SAL_DA7037AA Typhimurium
+SAL_DA7038AA Choleraesuis
+SAL_DA7049AA Typhimurium
+SAL_DA7053AA Heidelberg
+SAL_DA7059AA Heidelberg
+SAL_DA7061AA Typhimurium
+SAL_DA7062AA Typhimurium
+SAL_DA7067AA Typhimurium
+SAL_DA7076AA Typhimurium
+SAL_DA7077AA Typhimurium
+SAL_DA7116AA Choleraesuis
+SAL_DA7120AA Typhimurium
+SAL_DA7139AA Typhimurium
+SAL_DA7177AA Typhimurium
+SAL_DA7224AA Mbandaka
+SAL_DA7226AA I 4,[5],12:i:-
+SAL_DA7233AA IIIb 61:l,v:1,5,7:[z57]
+SAL_DA7237AA Ouakam
+SAL_DA7348AA IV 43:z4,z23:-
+SAL_DA7359AA Choleraesuis
+SAL_DA7371AA IV 44:z4,z32:-
+SAL_DA7377AA Typhimurium
+SAL_DA7392AA Typhimurium
+SAL_DA7393AA Newport
+SAL_DA7397AA Enteritidis
+SAL_DA7402AA Meleagridis
+SAL_DA7404AA Anatum
+SAL_DA7498AA IIIb 11:k:z53
+SAL_DA7814AA Choleraesuis
+SAL_DA8046AA Typhimurium
+SAL_DA8052AA I 4,[5],12:b:-
+SAL_DA8054AA Kentucky
+SAL_DA8057AA Typhimurium
+SAL_DA8066AA Anatum
+SAL_DA8075AA Kentucky
+SAL_DA8099AA Paratyphi B var. Java monophasic
+SAL_DA8101AA Newport
+SAL_DA8110AA II 40:z4,z24:z39
+SAL_DA8117AA II 42:b:e,n,x,z15
+SAL_DA8127AA Senftenberg
+SAL_DA8134AA Orion
+SAL_DA8154AA Kentucky
+SAL_DA8182AA Typhimurium
+SAL_DA8192AA Typhimurium
+SAL_DA8405AA Braenderup
+SAL_DA8447AA IV 1,40:z4,z24:-
+SAL_DA8458AA IV 1,40:z4,z24:-
+SAL_DA8471AA Schwarzengrund
+SAL_DA8486AA Typhimurium
+SAL_DA8494AA Anatum
+SAL_DA8524AA Thompson
+SAL_DA8592AA Albany
+SAL_DA8621AA Typhimurium
+SAL_DA8636AA I 4,[5],12:d:-
+SAL_DA8668AA Typhimurium
+SAL_DA8673AA Typhimurium
+SAL_DA8683AA I 4,[5],12:i:-
+SAL_DA8686AA Typhimurium
+SAL_DA8703AA IV 50:z4,z23:-
+SAL_DA8710AA IV 1,40:z4,z24:-
+SAL_DA8712AA IIIa 44:z4,z32:-
+SAL_DA0715AA Sandiego
+SAL_DA0772AA II 42:r:-
+SAL_DA0783AA Paratyphi B var. Java
+SAL_DA0790AA Paratyphi B var. Java
+SAL_DA0791AA Bovismorbificans
+SAL_DA0794AA Bovismorbificans
+SAL_DA0802AA Paratyphi B var. Java
+SAL_DA0853AA Paratyphi B var. Java
+SAL_DA0869AA IV 48:g,z51:-
+SAL_DA0879AA Goldcoast
+SAL_DA0936AA Paratyphi B var. Java
+SAL_DA1008AA Bovismorbificans
+SAL_DA1039AA II 1,4,[5],12,[27]:b:[e,n,x]
+SAL_DA1115AA IV 50:g,z51:-
+SAL_DA1135AA Paratyphi B var. Java
+SAL_DA1166AA Paratyphi B var. Java
+SAL_DA1207AA IV 50:g,z51:-
+SAL_DA1250AA Bovismorbificans
+SAL_DA1252AA Paratyphi B var. Java
+SAL_DA8720AA Heidelberg
+SAL_DA8763AA Anatum
+SAL_DA8772AA Typhimurium
+SAL_DA8786AA Typhimurium
+SAL_DA8787AA Typhimurium
+SAL_DA8812AA IIIa 53:z4,z23:-
+SAL_DA8817AA Typhimurium
+SAL_DA8822AA Typhimurium
+SAL_DA8855AA Heidelberg
+SAL_DA8861AA I 4,[5],12:i:-
+SAL_DA8870AA I 4,[5],12:i:-
+SAL_DA8883AA I 4,[5],12:i:-
+SAL_DA8896AA I 4,[5],12:i:-
+SAL_DA9114AA Weltevreden
+SAL_DA9349AA Amsterdam
+SAL_DA9412AA Anatum
+SAL_DA9435AA Typhimurium
+SAL_DA9453AA Typhimurium
+SAL_DA9458AA Thompson
+SAL_DA9471AA Typhimurium
+SAL_DA9482AA I 4,[5],12:i:-
+SAL_DA9495AA Meleagridis
+SAL_DA9497AA I 4,[5],12:i:-
+SAL_DA9517AA Anatum
+SAL_DA9559AA Typhimurium
+SAL_DA9595AA Virchow
+SAL_DA9638AA Lomalinda
+SAL_DA9655AA IIIb 60:r:e,n,x,z15
+SAL_DA9658AA Corvallis
+SAL_DA9667AA IIIb 60:r:e,n,x,z15
+SAL_DA9670AA Lexington
+SAL_DA9674AA I 9,12:d:1,2
+SAL_DA9741AA Paratyphi B var. Java monophasic
+SAL_DA9763AA Enteritidis
+SAL_DA9765AA Paratyphi B var. Java monophasic
+SAL_DA9782AA Brunei
+SAL_DA9801AA IV 43:z4,z23:-
+SAL_DA9815AA Typhimurium
+SAL_DA9850AA I 45:d:-
+SAL_DA9852AA Typhimurium
+SAL_DA9860AA Enteritidis
+SAL_DA9938AA Wandsworth
+SAL_DA9943AA Typhimurium
+SAL_DA9948AA Schleissheim
+SAL_DA9950AA Typhimurium
+SAL_DA9990AA IIIa Rough:z36:-
+SAL_DA9997AA IIIb 60:r:e,n,x,z15
+SAL_EA0032AA Drac
+SAL_DA1929AA Typhimurium
+SAL_DA2493AA Anatum
+SAL_DA3644AA Paratyphi B var. Java monophasic
+SAL_DA4081AA Typhimurium
+SAL_DA4461AA V 48:z39:-
+SAL_DA4544AA Choleraesuis
+SAL_DA5288AA Typhimurium
+SAL_DA6118AA Paratyphi B var. Java
+SAL_DA6519AA Typhimurium
+SAL_DA6978AA Paratyphi B var. Java monophasic
+SAL_DA7158AA Paratyphi B var. Java
+SAL_DA7863AA Typhimurium
+SAL_DA8439AA IIIb 50:k:z35
+SAL_DA8719AA I 4,[5],12:i:-
+SAL_DA9424AA Typhimurium
+SAL_EA1240AA Paratyphi B var. Java
+SAL_EA1241AA Paratyphi B var. Java
+SAL_EA1242AA Paratyphi B var. Java
+SAL_EA1245AA Paratyphi B var. Java
+SAL_EA1246AA Paratyphi B var. Java monophasic
+SAL_EA1247AA Paratyphi B var. Java
+SAL_EA1248AA I 4,[5],12:b:-
+SAL_EA1249AA Paratyphi B var. Java
+SAL_EA1250AA Paratyphi B var. Java
+SAL_EA1251AA Paratyphi B var. Java
+SAL_EA1255AA Paratyphi B var. Java monophasic
+SAL_EA1256AA Paratyphi B var. Java
+SAL_EA1257AA Paratyphi B var. Java
+SAL_EA1258AA Paratyphi B var. Java
+SAL_EA1261AA Paratyphi B var. Java
+SAL_EA1262AA Paratyphi B var. Java
+SAL_EA1265AA Paratyphi B var. Java
+SAL_EA1266AA Paratyphi B var. Java
+SAL_EA1269AA Paratyphi B var. Java
+SAL_EA1270AA Paratyphi B var. Java
+SAL_EA1271AA Paratyphi B var. Java
+SAL_EA1272AA Paratyphi B var. Java
+SAL_EA1275AA Paratyphi B var. Java
+SAL_EA1276AA Paratyphi B var. Java
+SAL_EA1277AA Paratyphi B var. Java
+SAL_EA1278AA Paratyphi B var. Java monophasic
+SAL_EA1280AA Paratyphi B var. Java
+SAL_EA1282AA Paratyphi B var. Java
+SAL_EA1358AA Typhimurium
+SAL_EA1361AA IV 1,40:z4,z32:-
+SAL_EA1476AA Alachua
+SAL_EA1655AA Muenster
+SAL_EA1902AA Typhimurium
+SAL_EA1904AA Typhimurium
+SAL_EA1908AA Typhimurium
+SAL_EA1911AA Typhimurium
+SAL_EA1918AA Typhimurium
+SAL_EA1936AA Typhimurium
+SAL_EA1952AA I 4,[5],12:i:-
+SAL_EA1956AA Typhimurium
+SAL_EA1964AA Typhimurium
+SAL_EA1971AA Typhimurium
+SAL_EA1983AA Typhimurium
+SAL_EA1985AA I 4,[5],12:i:-
+SAL_EA1989AA Typhimurium
+SAL_EA1990AA Typhimurium
+SAL_EA2007AA Typhimurium
+SAL_EA2011AA I 4,[5],12:d:-
+SAL_EA2016AA Typhimurium
+SAL_EA2030AA Typhimurium
+SAL_EA2033AA Typhimurium
+SAL_EA2034AA Typhimurium
+SAL_EA2035AA Typhimurium
+SAL_EA2038AA I 4,[5],12:d:-
+SAL_EA2040AA Typhimurium
+SAL_EA2043AA Typhimurium
+SAL_EA2048AA Typhimurium
+SAL_EA2049AA I 4,[5],12:i:-
+SAL_EA2053AA I 4,[5],12:i:-
+SAL_EA2067AA Typhimurium
+SAL_EA2070AA Typhimurium
+SAL_EA2074AA Typhimurium
+SAL_EA2075AA Typhimurium
+SAL_EA2076AA Typhimurium
+SAL_EA2093AA Typhimurium
+SAL_EA2103AA Typhimurium
+SAL_EA2110AA Typhimurium
+SAL_EA2111AA Typhimurium
+SAL_EA2117AA Typhimurium
+SAL_EA2119AA Typhimurium
+SAL_EA2120AA Typhimurium
+SAL_EA2121AA Typhimurium
+SAL_EA2123AA Typhimurium
+SAL_EA2132AA Typhimurium
+SAL_EA2147AA I 4,[5],12:i:-
+SAL_EA2345AA Typhimurium
+SAL_EA2357AA I 4,[5],12:d:-
+SAL_EA2358AA Typhimurium
+SAL_EA2359AA Typhimurium
+SAL_EA2360AA Typhimurium
+SAL_EA2362AA Typhimurium
+SAL_EA2364AA Typhimurium
+SAL_EA2366AA Typhimurium
+SAL_EA2367AA Typhimurium
+SAL_EA2429AA Typhimurium
+SAL_EA2461AA Typhimurium
+SAL_EA2463AA IV 43:z4,z23:-
+SAL_EA2465AA IV 43:z4,z23:-
+SAL_EA2525AA Typhimurium
+SAL_EA2526AA Typhimurium
+SAL_EA2528AA Typhimurium
+SAL_EA2529AA Typhimurium
+SAL_EA2530AA Typhimurium
+SAL_EA2537AA I 4,[5],12:i:-
+SAL_EA2560AA Typhimurium
+SAL_EA2561AA Typhimurium
+SAL_EA2569AA Typhimurium
+SAL_EA2570AA Typhimurium
+SAL_EA2577AA I 4,[5],12:i:-
+SAL_EA2611AA Typhimurium
+SAL_EA2631AA I 4,[5],12:i:-
+SAL_EA2633AA Typhimurium
+SAL_EA2638AA Typhimurium
+SAL_EA2649AA I 4,[5],12:i:-
+SAL_EA2696AA Typhimurium
+SAL_EA2702AA Weltevreden
+SAL_EA2715AA Onderstepoort
+SAL_EA2725AA Cerro
+SAL_EA2726AA Cerro
+SAL_EA2731AA Newport
+SAL_EA2734AA Typhimurium
+SAL_EA2830AA Amsterdam
+SAL_EA2874AA Bahrenfeld
+SAL_EA2899AA VI [1],6,14,[25]:a:e,n,x
+SAL_EA2932AA I 50:y:-
+SAL_EA2966AA Choleraesuis
+SAL_EA2972AA I 4,[5],12:i:-
+SAL_EA2977AA I 4,[5],12:d:-
+SAL_EA3000AA Typhimurium
+SAL_EA3025AA Infantis
+SAL_EA3111AA Typhimurium
+SAL_EA3112AA Typhimurium
+SAL_EA3152AA Typhimurium
+SAL_EA3192AA Typhimurium
+SAL_EA3198AA I 4,[5],12:i:-
+SAL_EA3199AA Typhimurium
+SAL_EA3200AA I 4,[5],12:i:-
+SAL_EA3227AA Weltevreden
+SAL_EA3262AA IV 50:z4,z23:-
+SAL_EA3554AA I 4,[5],12:i:-
+SAL_EA3557AA Typhimurium
+SAL_EA3559AA Typhimurium
+SAL_EA3560AA Typhimurium
+SAL_EA3564AA Typhimurium
+SAL_EA3573AA I 4,[5],12:i:-
+SAL_EA3585AA Typhimurium
+SAL_EA3588AA Typhimurium
+SAL_EA3590AA I 4,[5],12:i:-
+SAL_EA3591AA Typhimurium
+SAL_EA3592AA Typhimurium
+SAL_EA3605AA Typhimurium
+SAL_EA3620AA I 4,[5],12:i:-
+SAL_EA3626AA I 4,[5],12:i:-
+SAL_EA3629AA I 4,[5],12:i:-
+SAL_EA3641AA Typhimurium
+SAL_EA3646AA Typhimurium
+SAL_EA3651AA I 4,[5],12:i:-
+SAL_EA3656AA Typhimurium
+SAL_EA3673AA I 4,[5],12:i:-
+SAL_EA3674AA Typhimurium
+SAL_EA3675AA Typhimurium
+SAL_EA3684AA Typhimurium
+SAL_EA3685AA Typhimurium
+SAL_EA3687AA Typhimurium
+SAL_EA3688AA Typhimurium
+SAL_EA3693AA Typhimurium
+SAL_EA3706AA Typhimurium
+SAL_EA3711AA Typhimurium
+SAL_EA3712AA Typhimurium
+SAL_EA3720AA Typhimurium
+SAL_EA3724AA Typhimurium
+SAL_EA3727AA Typhimurium
+SAL_EA3728AA Typhimurium
+SAL_EA3729AA Typhimurium
+SAL_EA3731AA Typhimurium
+SAL_EA3732AA Typhimurium
+SAL_EA3738AA Typhimurium
+SAL_EA3744AA Typhimurium
+SAL_EA3746AA Typhimurium
+SAL_EA3747AA Typhimurium
+SAL_EA3748AA Typhimurium
+SAL_EA3770AA Typhimurium
+SAL_EA3779AA Typhimurium
+SAL_EA3781AA Typhimurium
+SAL_EA3782AA Typhimurium
+SAL_EA3796AA Typhimurium
+SAL_EA3801AA Typhimurium
+SAL_EA3802AA Typhimurium
+SAL_EA3803AA Typhimurium
+SAL_EA3815AA Typhimurium
+SAL_EA3816AA Typhimurium
+SAL_EA3817AA Typhimurium
+SAL_EA3818AA Typhimurium
+SAL_EA3819AA Typhimurium
+SAL_EA3820AA Typhimurium
+SAL_EA3821AA Typhimurium
+SAL_EA3822AA Typhimurium
+SAL_EA3825AA Typhimurium
+SAL_EA3841AA Typhimurium
+SAL_EA3846AA Typhimurium
+SAL_EA3851AA Typhimurium
+SAL_EA3852AA Typhimurium
+SAL_EA3859AA Typhimurium
+SAL_EA3860AA Typhimurium
+SAL_EA3861AA Typhimurium
+SAL_EA3869AA I 4,[5],12:i:-
+SAL_EA3877AA Typhimurium
+SAL_EA3879AA I 4,[5],12:i:-
+SAL_EA3883AA I 4,[5],12:i:-
+SAL_EA4224AA Typhimurium
+SAL_EA4229AA Paratyphi B var. Java
+SAL_EA4238AA I 4,[5],12:i:-
+SAL_EA4280AA Onderstepoort
+SAL_EA4282AA Typhimurium
+SAL_EA4354AA I 4,[5],12:i:-
+SAL_EA4359AA I 4,[5],12:i:-
+SAL_EA4365AA I 4,[5],12:i:-
+SAL_EA4410AA I 4,[5],12:i:-
+SAL_EA0068AA IV 43:z4,z23:-
+SAL_EA0078AA Typhimurium
+SAL_EA0108AA Typhimurium
+SAL_EA0204AA Paratyphi B var. Java
+SAL_EA0235AA Duesseldorf
+SAL_EA0285AA Bere
+SAL_EA0303AA Oslo
+SAL_EA0311AA Meleagridis
+SAL_EA0318AA Schleissheim
+SAL_EA0393AA IV 43:z4,z23:-
+SAL_EA0394AA Javiana
+SAL_EA0413AA Anatum
+SAL_EA0421AA Anatum
+SAL_EA0440AA Newport
+SAL_EA0485AA Anatum
+SAL_EA0493AA IIIb 60:r:e,n,x,z15
+SAL_EA0497AA Muenchen
+SAL_EA4445AA I 4,[5],12:i:-
+SAL_EA4573AA I 4,[5],12:i:-
+SAL_EA4576AA I 4,[5],12:i:-
+SAL_EA4923AA Typhimurium
+SAL_EA4924AA Typhimurium
+SAL_EA5201AA Typhimurium
+SAL_EA5267AA I 4,[5],12:b:-
+SAL_EA5268AA Typhimurium
+SAL_EA5313AA Typhimurium
+SAL_EA5316AA Typhimurium
+SAL_EA5320AA Typhimurium
+SAL_EA5345AA Meleagridis
+SAL_EA5488AA I 4,[5],12:i:-
+SAL_EA5490AA Typhimurium
+SAL_EA5491AA I 4,[5],12:i:-
+SAL_EA5497AA I 4,[5],12:i:-
+SAL_EA5564AA Typhimurium
+SAL_EA5566AA Typhimurium
+SAL_EA5567AA Typhimurium
+SAL_EA5569AA Typhimurium
+SAL_EA5570AA Typhimurium
+SAL_EA5573AA I 4,[5],12:i:-
+SAL_EA5584AA I 4,[5],12:r:-
+SAL_EA5727AA Infantis
+SAL_EA5804AA Typhimurium
+SAL_EA5805AA Typhimurium
+SAL_EA5806AA Typhimurium
+SAL_EA5812AA Typhimurium
+SAL_EA5813AA Typhimurium
+SAL_EA5814AA Typhimurium
+SAL_EA5815AA Typhimurium
+SAL_EA5816AA Typhimurium
+SAL_EA0066AA IV 43:z4,z23:-
+SAL_EA0499AA Chiredzi
+SAL_EA1239AA Paratyphi B var. Java
+SAL_EA1263AA Paratyphi B var. Java
+SAL_EA1893AA Typhimurium
+SAL_EA2013AA Typhimurium
+SAL_EA2077AA Typhimurium
+SAL_EA2361AA Typhimurium
+SAL_EA2567AA Typhimurium
+SAL_EA2841AA Orion
+SAL_EA3228AA Orion
+SAL_EA3638AA Typhimurium
+SAL_EA3721AA Typhimurium
+SAL_EA3798AA Typhimurium
+SAL_EA3853AA Typhimurium
+SAL_CA2725AA Paratyphi B var. Java
+SAL_DA1610AA Heidelberg
+SAL_DA9680AA II 48:d:z6
+SAL_EA4444AA I 4,[5],12:i:-
+SAL_FA0710AA Typhimurium
+SAL_FA7733AA Oranienburg
+SAL_GA3188AA I 4,[5],12:d:-
+SAL_GA9555AA I 4,[5],12:i:-
+SAL_EA5934AA Saintpaul
+SAL_EA5941AA Typhimurium
+SAL_EA5943AA Typhimurium
+SAL_EA5944AA Typhimurium
+SAL_EA5957AA Typhimurium
+SAL_EA6167AA Typhimurium
+SAL_EA6168AA I 4,[5],12:i:-
+SAL_EA6170AA Typhimurium
+SAL_EA6180AA I 4,[5],12:i:-
+SAL_EA6219AA Paratyphi B var. Java monophasic
+SAL_EA6386AA Typhimurium
+SAL_EA6387AA Typhimurium
+SAL_EA6389AA Typhimurium
+SAL_EA6390AA Typhimurium
+SAL_EA6391AA Typhimurium
+SAL_EA6392AA Typhimurium
+SAL_EA6543AA I 4,[5],12:i:-
+SAL_EA6544AA I 4,[5],12:i:-
+SAL_EA6545AA I 4,[5],12:i:-
+SAL_EA6546AA I 4,[5],12:i:-
+SAL_EA6547AA I 4,[5],12:i:-
+SAL_EA6548AA I 4,[5],12:i:-
+SAL_EA6549AA I 4,[5],12:i:-
+SAL_EA6724AA Typhimurium
+SAL_EA6727AA Typhimurium
+SAL_EA6728AA Typhimurium
+SAL_EA6732AA Typhimurium
+SAL_EA6772AA Butantan
+SAL_EA6867AA Typhimurium
+SAL_EA6869AA Typhimurium
+SAL_EA6870AA Typhimurium
+SAL_EA6871AA Typhimurium
+SAL_EA6924AA Paratyphi B var. Java
+SAL_EA6926AA Telelkebir
+SAL_EA7014AA Bovismorbificans
+SAL_EA7025AA Paratyphi B var. Java
+SAL_EA7064AA Telelkebir
+SAL_EA7065AA Paratyphi B var. Java
+SAL_EA7264AA Paratyphi B var. Java monophasic
+SAL_EA7287AA IV 50:g,z51:-
+SAL_EA7317AA Paratyphi B var. Java
+SAL_EA7339AA Paratyphi B var. Java
+SAL_EA7375AA Itami
+SAL_EA7480AA Bovismorbificans
+SAL_EA7526AA Bovismorbificans
+SAL_EA7539AA Bovismorbificans
+SAL_EA7547AA Paratyphi B var. Java
+SAL_EA7562AA Paratyphi B var. Java
+SAL_EA7676AA Bovismorbificans
+SAL_EA7680AA Paratyphi B var. Java
+SAL_EA7712AA Telelkebir
+SAL_EA7755AA Telelkebir
+SAL_EA7793AA Paratyphi B var. Java
+SAL_EA7796AA Paratyphi B var. Java
+SAL_EA7834AA Goldcoast
+SAL_EA7837AA Bovismorbificans
+SAL_EA7855AA Paratyphi B var. Java
+SAL_EA8009AA Weltevreden
+SAL_EA8125AA Typhimurium
+SAL_EA8130AA Typhimurium
+SAL_EA8131AA Typhimurium
+SAL_EA8166AA Typhimurium
+SAL_EA8167AA Typhimurium
+SAL_EA8168AA I 4,[5],12:r:-
+SAL_EA8175AA Typhimurium
+SAL_EA8177AA Typhimurium
+SAL_EA8182AA I 4,[5],12:i:-
+SAL_EA8197AA Typhimurium
+SAL_EA8198AA Typhimurium
+SAL_EA8204AA Typhimurium
+SAL_EA8401AA I 4,[5],12:i:-
+SAL_EA8404AA I 4,[5],12:i:-
+SAL_EA8423AA I 4,[5],12:i:-
+SAL_EA8512AA I 4,[5],12:i:-
+SAL_EA8513AA Typhimurium
+SAL_EA8514AA Typhimurium
+SAL_EA8518AA Typhimurium
+SAL_EA8541AA Virchow
+SAL_EA8546AA Typhimurium
+SAL_EA8550AA Typhimurium
+SAL_EA0504AA I 4,[5],12:i:-
+SAL_EA0513AA Typhimurium
+SAL_EA0574AA Newport
+SAL_EA0598AA Thompson
+SAL_EA0632AA IV 43:z4,z23:-
+SAL_EA0639AA Brunei
+SAL_EA0640AA Anatum
+SAL_EA0641AA I 28:e,h:-
+SAL_EA0644AA Newport
+SAL_EA0655AA Saintpaul
+SAL_EA0716AA I 18:z44:1,5
+SAL_EA0728AA IIIa 35:z36:-
+SAL_EA0763AA Aberdeen
+SAL_EA0826AA Gallinarum
+SAL_EA0850AA Rostock
+SAL_EA0870AA Enteritidis
+SAL_EA1108AA Enteritidis
+SAL_EA1238AA Paratyphi B var. Java
+SAL_EA8556AA Typhimurium
+SAL_EA8557AA Typhimurium
+SAL_EA8564AA Typhimurium
+SAL_EA8566AA Typhimurium
+SAL_EA8572AA I 4,[5],12:i:-
+SAL_EA8722AA I 4,[5],12:i:-
+SAL_EA8737AA Typhimurium
+SAL_EA8757AA Typhimurium
+SAL_EA8758AA Typhimurium
+SAL_EA8760AA Typhimurium
+SAL_EA8761AA Typhimurium
+SAL_EA8807AA Typhimurium
+SAL_EA8809AA Typhimurium
+SAL_EA8812AA Typhimurium
+SAL_EA8835AA Typhimurium
+SAL_EA8837AA I 4,[5],12:r:-
+SAL_EA8841AA Typhimurium
+SAL_EA8844AA Typhimurium
+SAL_EA8851AA Typhimurium
+SAL_EA8907AA I 4,[5],12:i:-
+SAL_EA8950AA I 4,[5],12:i:-
+SAL_EA8951AA I 4,[5],12:i:-
+SAL_EA8957AA I 4,[5],12:i:-
+SAL_EA8961AA I 4,[5],12:i:-
+SAL_EA8963AA Enteritidis
+SAL_EA8967AA I 4,[5],12:i:-
+SAL_EA8969AA Typhimurium
+SAL_EA8970AA I 4,[5],12:i:-
+SAL_EA8971AA I 4,[5],12:i:-
+SAL_EA8972AA I 4,[5],12:i:-
+SAL_EA8973AA I 4,[5],12:i:-
+SAL_EA8974AA I 4,[5],12:i:-
+SAL_EA8977AA I 4,[5],12:i:-
+SAL_EA8978AA I 4,[5],12:i:-
+SAL_EA8979AA I 4,[5],12:i:-
+SAL_EA8980AA I 4,[5],12:i:-
+SAL_EA8981AA I 4,[5],12:i:-
+SAL_EA8982AA I 4,[5],12:i:-
+SAL_EA9009AA I 4,[5],12:i:-
+SAL_EA9017AA I 4,[5],12:i:-
+SAL_EA9037AA Typhimurium
+SAL_EA9041AA Typhimurium
+SAL_EA9042AA I 4,[5],12:i:-
+SAL_EA9049AA Typhimurium
+SAL_EA9052AA Typhimurium
+SAL_EA9053AA I 4,[5],12:i:-
+SAL_EA9054AA I 4,[5],12:i:-
+SAL_EA9055AA I 4,[5],12:i:-
+SAL_EA9057AA I 4,[5],12:i:-
+SAL_EA9058AA I 4,[5],12:i:-
+SAL_EA9059AA I 4,[5],12:i:-
+SAL_EA9060AA I 4,[5],12:i:-
+SAL_EA9061AA I 4,[5],12:i:-
+SAL_EA9062AA I 4,[5],12:i:-
+SAL_EA9063AA I 4,[5],12:i:-
+SAL_EA9064AA I 4,[5],12:i:-
+SAL_EA9065AA I 4,[5],12:i:-
+SAL_EA9066AA I 4,[5],12:i:-
+SAL_EA9067AA I 4,[5],12:i:-
+SAL_EA9068AA Typhimurium
+SAL_EA9069AA Typhimurium
+SAL_EA9070AA Typhimurium
+SAL_EA9071AA Heidelberg
+SAL_EA9077AA Typhimurium
+SAL_EA9081AA Typhimurium
+SAL_EA9098AA I 4,[5],12:d:-
+SAL_EA9099AA Typhimurium
+SAL_EA9133AA Livingstone
+SAL_EA9144AA I 4,[5],12:i:-
+SAL_EA9146AA I 4,[5],12:d:-
+SAL_EA9148AA Typhimurium
+SAL_EA9149AA I 4,[5],12:d:-
+SAL_EA9152AA I 4,[5],12:d:-
+SAL_EA9154AA Typhimurium
+SAL_EA9157AA Typhimurium
+SAL_EA9158AA Typhimurium
+SAL_EA9167AA Choleraesuis
+SAL_EA9169AA Choleraesuis
+SAL_EA9170AA Choleraesuis
+SAL_EA9173AA Choleraesuis
+SAL_EA9194AA Choleraesuis
+SAL_EA9203AA Choleraesuis
+SAL_EA9206AA Choleraesuis
+SAL_EA9208AA Paratyphi C
+SAL_EA9245AA Typhimurium
+SAL_EA9253AA I 4,[5],12:i:-
+SAL_EA9254AA I 4,[5],12:i:-
+SAL_EA9255AA I 4,[5],12:i:-
+SAL_EA9256AA I 4,[5],12:i:-
+SAL_EA9257AA I 4,[5],12:i:-
+SAL_EA9287AA Paratyphi B var. Java
+SAL_EA9299AA Paratyphi B var. Java
+SAL_EA9311AA Paratyphi B var. Java
+SAL_EA9312AA Sandiego
+SAL_EA9465AA I 4,[5],12:i:-
+SAL_EA9467AA I 4,[5],12:i:-
+SAL_EA9469AA I 4,[5],12:i:-
+SAL_EA9470AA I 4,[5],12:i:-
+SAL_EA9516AA Typhimurium
+SAL_EA9517AA Typhimurium
+SAL_EA9518AA Typhimurium
+SAL_EA9522AA Typhimurium
+SAL_EA9523AA Typhimurium
+SAL_EA9525AA Typhimurium
+SAL_EA9530AA Thompson
+SAL_EA9573AA I 4,[5],12:i:-
+SAL_EA9574AA Typhimurium
+SAL_EA9575AA Typhimurium
+SAL_EA9582AA Typhimurium
+SAL_EA9584AA Typhimurium
+SAL_EA9585AA Typhimurium
+SAL_EA9727AA Gallinarum
+SAL_EA9763AA V 48:z41:-
+SAL_EA9769AA Gallinarum
+SAL_EA9778AA IIIa 41:z4,z23:-
+SAL_EA9784AA Choleraesuis
+SAL_EA9793AA Typhimurium
+SAL_EA9799AA Typhimurium
+SAL_EA9800AA Typhimurium
+SAL_EA9804AA Typhimurium
+SAL_EA9863AA II 42:r:-
+SAL_EA9865AA Uzaramo
+SAL_EA9866AA Telhashomer
+SAL_FA0404AA Braenderup
+SAL_FA0515AA Typhimurium
+SAL_FA0525AA Bahrenfeld
+SAL_FA0546AA Typhimurium
+SAL_FA0547AA Typhimurium
+SAL_FA1153AA I 4,[5],12:d:-
+SAL_FA1271AA Typhimurium
+SAL_FA1273AA Typhimurium
+SAL_FA1274AA Typhimurium
+SAL_FA1315AA Typhimurium
+SAL_FA1318AA Typhimurium
+SAL_FA1507AA I 4,[5],12:r:-
+SAL_FA1508AA I 4,[5],12:r:-
+SAL_FA1511AA I 4,[5],12:r:-
+SAL_FA1541AA Typhimurium
+SAL_FA1542AA Typhimurium
+SAL_FA1543AA Typhimurium
+SAL_FA1544AA Typhimurium
+SAL_FA1546AA Typhimurium
+SAL_FA1547AA Typhimurium
+SAL_FA1548AA Typhimurium
+SAL_FA1608AA Typhimurium
+SAL_FA1874AA Typhimurium
+SAL_FA2211AA Typhimurium
+SAL_FA2215AA Typhimurium
+SAL_FA2223AA Typhimurium
+SAL_FA2281AA Hidalgo
+SAL_FA2315AA Enteritidis
+SAL_FA2320AA I 4,[5],12:d:-
+SAL_FA2321AA Typhimurium
+SAL_FA2325AA Typhimurium
+SAL_FA2327AA Typhimurium
+SAL_FA2330AA Typhimurium
+SAL_FA2331AA Typhimurium
+SAL_FA2332AA Enteritidis
+SAL_FA2563AA Typhimurium
+SAL_FA2564AA Typhimurium
+SAL_EA5563AA Typhimurium
+SAL_EA5822AA IV 50:z4,z23:-
+SAL_EA6458AA IV 43:z4,z23:-
+SAL_EA6885AA Mountpleasant
+SAL_EA7625AA Goldcoast
+SAL_EA8170AA Typhimurium
+SAL_EA8555AA Typhimurium
+SAL_EA8840AA Typhimurium
+SAL_EA8975AA I 4,[5],12:i:-
+SAL_EA9056AA I 4,[5],12:i:-
+SAL_EA9080AA Typhimurium
+SAL_EA9178AA Choleraesuis
+SAL_EA9468AA I 4,[5],12:i:-
+SAL_EA9749AA IIIa 62:z36:-
+SAL_FA0548AA I 4,[5],12:d:-
+SAL_FA2568AA Typhimurium
+SAL_FA2569AA Typhimurium
+SAL_FA2572AA Typhimurium
+SAL_FA2573AA Typhimurium
+SAL_FA2642AA Typhimurium
+SAL_FA2645AA Typhimurium
+SAL_FA2646AA Typhimurium
+SAL_FA2652AA Typhimurium
+SAL_FA2657AA Paratyphi B var. Java
+SAL_FA2661AA I 4,[5],12:i:-
+SAL_FA2687AA I 4,[5],12:i:-
+SAL_FA2715AA I 4,[5],12:i:-
+SAL_FA2741AA I 4,[5],12:i:-
+SAL_FA2770AA I 4,[5],12:i:-
+SAL_FA2783AA I 4,[5],12:i:-
+SAL_FA2793AA I 4,[5],12:i:-
+SAL_FA2912AA I 4,[5],12:i:-
+SAL_FA2920AA I 4,[5],12:i:-
+SAL_FA2922AA I 4,[5],12:i:-
+SAL_FA2940AA I 4,[5],12:i:-
+SAL_FA2941AA I 4,[5],12:i:-
+SAL_FA2959AA I 4,[5],12:i:-
+SAL_FA2992AA I 4,[5],12:i:-
+SAL_FA2993AA I 4,[5],12:i:-
+SAL_FA2994AA I 4,[5],12:i:-
+SAL_FA2997AA Typhimurium
+SAL_FA3001AA I 4,[5],12:i:-
+SAL_FA3044AA I 4,[5],12:i:-
+SAL_FA3045AA I 4,[5],12:i:-
+SAL_FA3075AA Typhimurium
+SAL_FA3097AA I 4,[5],12:i:-
+SAL_FA3279AA Typhimurium
+SAL_FA3303AA Enteritidis
+SAL_FA3306AA Typhimurium
+SAL_FA3307AA Typhimurium
+SAL_FA3309AA Typhimurium
+SAL_FA3310AA Typhimurium
+SAL_FA3512AA Paratyphi B var. Java
+SAL_FA3525AA Paratyphi B var. Java
+SAL_FA3563AA Louisiana
+SAL_FA3642AA Sandiego
+SAL_FA3706AA I 4,[5],12:i:-
+SAL_FA3712AA I 4,[5],12:i:-
+SAL_FA3714AA I 4,[5],12:i:-
+SAL_FA3718AA I 4,[5],12:i:-
+SAL_FA3740AA I 4,[5],12:i:-
+SAL_FA3744AA I 4,[5],12:i:-
+SAL_FA3749AA I 4,[5],12:i:-
+SAL_FA3765AA I 4,[5],12:i:-
+SAL_FA3766AA I 4,[5],12:i:-
+SAL_FA3771AA I 4,[5],12:i:-
+SAL_FA3773AA I 4,[5],12:i:-
+SAL_FA3775AA I 4,[5],12:i:-
+SAL_FA3805AA I 4,[5],12:i:-
+SAL_FA3809AA I 4,[5],12:i:-
+SAL_FA3820AA I 4,[5],12:i:-
+SAL_FA3832AA I 4,[5],12:i:-
+SAL_FA3833AA I 4,[5],12:i:-
+SAL_FA3835AA I 4,[5],12:i:-
+SAL_FA3838AA I 4,[5],12:i:-
+SAL_FA3842AA I 4,[5],12:i:-
+SAL_FA3848AA I 4,[5],12:i:-
+SAL_FA3878AA I 4,[5],12:i:-
+SAL_FA3879AA I 4,[5],12:i:-
+SAL_FA3894AA I 4,[5],12:i:-
+SAL_FA3898AA I 4,[5],12:i:-
+SAL_FA3900AA I 4,[5],12:i:-
+SAL_FA3908AA I 4,[5],12:i:-
+SAL_FA3910AA I 4,[5],12:i:-
+SAL_FA3926AA I 4,[5],12:i:-
+SAL_FA3936AA I 4,[5],12:i:-
+SAL_FA3940AA I 4,[5],12:i:-
+SAL_FA3943AA I 4,[5],12:i:-
+SAL_FA3950AA I 4,[5],12:i:-
+SAL_FA3954AA I 4,[5],12:i:-
+SAL_FA3959AA I 4,[5],12:i:-
+SAL_FA3962AA I 4,[5],12:i:-
+SAL_FA3965AA I 4,[5],12:i:-
+SAL_FA3973AA I 4,[5],12:i:-
+SAL_FA3981AA I 4,[5],12:i:-
+SAL_FA4072AA Bovismorbificans
+SAL_FA4075AA I 4,[5],12:i:-
+SAL_FA4077AA I 4,[5],12:i:-
+SAL_FA4082AA I 4,[5],12:i:-
+SAL_FA4088AA I 4,[5],12:i:-
+SAL_FA4095AA Bovismorbificans
+SAL_FA4102AA I 4,[5],12:i:-
+SAL_FA4112AA I 4,[5],12:i:-
+SAL_FA4113AA I 4,[5],12:i:-
+SAL_FA4114AA I 4,[5],12:i:-
+SAL_FA4115AA I 4,[5],12:i:-
+SAL_FA4125AA I 4,[5],12:i:-
+SAL_FA4126AA I 4,[5],12:i:-
+SAL_FA4128AA Kottbus
+SAL_FA4146AA I 4,[5],12:i:-
+SAL_FA4153AA Hadar
+SAL_FA4168AA I 4,[5],12:i:-
+SAL_FA4181AA I 4,[5],12:i:-
+SAL_FA4183AA Bovismorbificans
+SAL_FA4202AA I 4,[5],12:i:-
+SAL_FA4212AA I 4,[5],12:i:-
+SAL_FA4223AA I 4,[5],12:i:-
+SAL_FA4245AA I 4,[5],12:i:-
+SAL_FA4247AA I 4,[5],12:i:-
+SAL_FA4248AA I 4,[5],12:i:-
+SAL_FA4253AA Sandiego
+SAL_FA4257AA I 4,[5],12:i:-
+SAL_FA4258AA I 4,[5],12:i:-
+SAL_FA4267AA Paratyphi B var. Java monophasic
+SAL_FA4277AA I 4,[5],12:i:-
+SAL_FA4279AA I 4,[5],12:i:-
+SAL_FA4286AA Sandiego
+SAL_FA4305AA I 4,[5],12:i:-
+SAL_FA4312AA I 4,[5],12:i:-
+SAL_FA4316AA Paratyphi B var. Java
+SAL_FA4324AA I 4,[5],12:i:-
+SAL_FA4326AA I 4,[5],12:i:-
+SAL_FA4328AA I 4,[5],12:i:-
+SAL_FA4337AA I 4,[5],12:i:-
+SAL_FA4352AA I 4,[5],12:i:-
+SAL_FA4360AA I 4,[5],12:i:-
+SAL_FA4361AA I 4,[5],12:i:-
+SAL_FA4363AA I 4,[5],12:i:-
+SAL_FA4373AA I 4,[5],12:i:-
+SAL_FA4394AA I 4,[5],12:i:-
+SAL_FA4395AA I 4,[5],12:i:-
+SAL_FA4403AA I 4,[5],12:i:-
+SAL_FA4439AA I 4,[5],12:i:-
+SAL_FA4461AA I 4,[5],12:i:-
+SAL_FA4465AA Telelkebir
+SAL_FA4475AA I 4,[5],12:i:-
+SAL_FA4483AA I 4,[5],12:i:-
+SAL_FA4485AA I 4,[5],12:i:-
+SAL_FA4486AA I 4,[5],12:i:-
+SAL_FA4487AA I 4,[5],12:i:-
+SAL_FA4493AA I 4,[5],12:i:-
+SAL_FA4551AA I 4,[5],12:i:-
+SAL_FA4583AA I 4,[5],12:i:-
+SAL_FA4604AA I 4,[5],12:i:-
+SAL_FA4612AA Bovismorbificans
+SAL_FA4621AA Losangeles
+SAL_FA4624AA Joal
+SAL_FA4632AA Sandiego
+SAL_FA4640AA Bovismorbificans
+SAL_FA4655AA I 4,[5],12:i:-
+SAL_FA4662AA Bovismorbificans
+SAL_FA4669AA I 4,[5],12:i:-
+SAL_FA4736AA Choleraesuis
+SAL_FA4799AA Typhimurium
+SAL_FA4801AA Typhimurium
+SAL_FA4807AA Typhimurium
+SAL_FA4809AA Typhimurium
+SAL_FA4818AA Typhimurium
+SAL_FA4832AA Typhimurium
+SAL_FA4833AA Typhimurium
+SAL_FA4839AA Typhimurium
+SAL_FA4851AA Typhimurium
+SAL_FA4867AA Javiana
+SAL_FA4958AA Typhimurium
+SAL_FA4959AA Typhimurium
+SAL_FA5168AA I 4,[5],12:i:-
+SAL_FA5169AA I 4,[5],12:i:-
+SAL_FA5427AA Meleagridis
+SAL_FA5740AA I 4,[5],12:i:-
+SAL_FA5741AA I 4,[5],12:i:-
+SAL_FA5743AA I 4,[5],12:i:-
+SAL_FA5744AA I 4,[5],12:i:-
+SAL_FA5757AA I 4,[5],12:i:-
+SAL_FA5764AA I 4,[5],12:i:-
+SAL_FA5769AA Paratyphi B var. Java
+SAL_FA5788AA Paratyphi B var. Java
+SAL_FA5789AA I 4,[5],12:i:-
+SAL_FA5793AA Paratyphi B var. Java
+SAL_FA5794AA Typhimurium
+SAL_FA5795AA Typhimurium
+SAL_FA5812AA I 4,[5],12:i:-
+SAL_FA5831AA Paratyphi B var. Java
+SAL_FA5832AA Paratyphi B var. Java
+SAL_FA5833AA Paratyphi B var. Java
+SAL_FA5834AA Paratyphi B var. Java
+SAL_FA5835AA Paratyphi B var. Java
+SAL_FA5837AA Paratyphi B var. Java
+SAL_FA5849AA Oranienburg
+SAL_FA5862AA Amsterdam
+SAL_FA5863AA Amsterdam
+SAL_FA5869AA Amsterdam
+SAL_FA5880AA I 4,[5],12:i:-
+SAL_FA5885AA I 4,[5],12:i:-
+SAL_FA6006AA Typhimurium
+SAL_FA6021AA Meleagridis
+SAL_FA6078AA I 4,[5],12:i:-
+SAL_FA6079AA I 4,[5],12:i:-
+SAL_FA0552AA Typhimurium
+SAL_FA0607AA Typhimurium
+SAL_FA0610AA Typhimurium
+SAL_FA0612AA Typhimurium
+SAL_FA0619AA Typhimurium
+SAL_FA0620AA Typhimurium
+SAL_FA0621AA Typhimurium
+SAL_FA0644AA Typhimurium
+SAL_FA0656AA Muenster
+SAL_FA0690AA Paratyphi B var. Java
+SAL_FA0693AA Paratyphi B var. Java
+SAL_FA0694AA Paratyphi B var. Java
+SAL_FA0703AA I 4,[5],12:r:-
+SAL_FA0705AA Typhimurium
+SAL_FA0706AA Typhimurium
+SAL_FA0709AA Typhimurium
+SAL_FA6081AA I 4,[5],12:i:-
+SAL_FA6082AA I 4,[5],12:i:-
+SAL_FA6083AA I 4,[5],12:i:-
+SAL_FA6394AA Heidelberg
+SAL_FA6395AA Heidelberg
+SAL_FA6396AA Typhimurium
+SAL_FA6411AA II 9,12:z29:1,5
+SAL_FA6561AA Enteritidis
+SAL_FA6670AA Typhimurium
+SAL_FA6832AA Typhimurium
+SAL_FA6836AA Typhimurium
+SAL_FA6838AA Typhimurium
+SAL_FA6842AA Typhimurium
+SAL_FA7304AA I 4,[5],12:i:-
+SAL_FA7307AA I 4,[5],12:i:-
+SAL_FA7516AA Paratyphi B var. Java
+SAL_FA0712AA Typhimurium
+SAL_FA0713AA Typhimurium
+SAL_FA0714AA Typhimurium
+SAL_FA0716AA Typhimurium
+SAL_FA0717AA Typhimurium
+SAL_FA0722AA Paratyphi B var. Java
+SAL_FA0724AA Paratyphi B var. Java
+SAL_FA0854AA Typhimurium
+SAL_FA0855AA Typhimurium
+SAL_FA0856AA Typhimurium
+SAL_FA0858AA Typhimurium
+SAL_FA0859AA Typhimurium
+SAL_FA0866AA Typhimurium
+SAL_FA0868AA Typhimurium
+SAL_FA0869AA Typhimurium
+SAL_FA0878AA Typhimurium
+SAL_FA0879AA Typhimurium
+SAL_FA0882AA Typhimurium
+SAL_FA0883AA I 4,[5],12:i:-
+SAL_FA0892AA I 4,[5],12:i:-
+SAL_FA1016AA Choleraesuis
+SAL_FA1017AA Choleraesuis
+SAL_FA1025AA Choleraesuis
+SAL_FA1026AA Choleraesuis
+SAL_FA1028AA Choleraesuis
+SAL_FA1045AA Choleraesuis
+SAL_FA1056AA Choleraesuis
+SAL_FA1115AA Typhimurium
+SAL_FA1120AA Typhimurium
+SAL_FA1122AA Typhimurium
+SAL_FA1134AA I 4,[5],12:d:-
+SAL_FA7838AA Paratyphi B var. Java
+SAL_FA8141AA Bovismorbificans
+SAL_FA8219AA Choleraesuis
+SAL_FA8260AA I 28:e,h:-
+SAL_FA8439AA IV 43:z4,z23:-
+SAL_FA8440AA IV 43:z4,z23:-
+SAL_FA8466AA Adelaide
+SAL_FA8496AA Typhimurium
+SAL_FA8502AA Typhimurium
+SAL_FA8507AA Typhimurium
+SAL_FA8510AA Typhimurium
+SAL_FA8511AA Typhimurium
+SAL_FA8515AA Typhimurium
+SAL_FA8516AA Typhimurium
+SAL_FA8517AA Typhimurium
+SAL_FA8519AA Typhimurium
+SAL_FA1152AA I 4,[5],12:d:-
+SAL_FA1550AA Typhimurium
+SAL_FA2567AA Typhimurium
+SAL_FA2858AA I 4,[5],12:i:-
+SAL_FA3301AA Typhimurium
+SAL_FA3757AA I 4,[5],12:i:-
+SAL_FA3891AA I 4,[5],12:i:-
+SAL_FA3997AA I 4,[5],12:i:-
+SAL_FA4156AA I 4,[5],12:i:-
+SAL_FA4292AA I 4,[5],12:i:-
+SAL_FA4455AA Bovismorbificans
+SAL_FA4647AA I 4,[5],12:i:-
+SAL_FA4960AA Typhimurium
+SAL_FA5816AA Paratyphi B var. Java
+SAL_FA6080AA I 4,[5],12:i:-
+SAL_FA8521AA Typhimurium
+SAL_FA8528AA Typhimurium
+SAL_FA8534AA I 4,[5],12:d:-
+SAL_FA8548AA Typhimurium
+SAL_FA8549AA Typhimurium
+SAL_FA8563AA Typhimurium
+SAL_FA8617AA Typhimurium
+SAL_FA8621AA Typhimurium
+SAL_FA8622AA Typhimurium
+SAL_FA8627AA Typhimurium
+SAL_FA8628AA Typhimurium
+SAL_FA8629AA Typhimurium
+SAL_FA8667AA Typhimurium
+SAL_FA8677AA Typhimurium
+SAL_FA8686AA Typhimurium
+SAL_FA8687AA Typhimurium
+SAL_FA8710AA Typhimurium
+SAL_FA8711AA Typhimurium
+SAL_FA8712AA Typhimurium
+SAL_FA8715AA Typhimurium
+SAL_FA8716AA Typhimurium
+SAL_FA8717AA Typhimurium
+SAL_FA8732AA Typhimurium
+SAL_FA8740AA Typhimurium
+SAL_FA8749AA Typhimurium
+SAL_FA8754AA I 4,[5],12:d:-
+SAL_FA8767AA Typhimurium
+SAL_FA8802AA Typhimurium
+SAL_FA8806AA Typhimurium
+SAL_FA8809AA Typhimurium
+SAL_FA8810AA Typhimurium
+SAL_FA8819AA Typhimurium
+SAL_FA8821AA Typhimurium
+SAL_FA8822AA Typhimurium
+SAL_FA8828AA Typhimurium
+SAL_FA8832AA Typhimurium
+SAL_FA8833AA Typhimurium
+SAL_FA8836AA Typhimurium
+SAL_FA8837AA Typhimurium
+SAL_FA8838AA Typhimurium
+SAL_FA8853AA Typhimurium
+SAL_FA8855AA Typhimurium
+SAL_FA8857AA Typhimurium
+SAL_FA8859AA Typhimurium
+SAL_FA8864AA Typhimurium
+SAL_FA8871AA Typhimurium
+SAL_FA8876AA I 4,[5],12:d:-
+SAL_FA8878AA Typhimurium
+SAL_FA8890AA Typhimurium
+SAL_FA8905AA Typhimurium
+SAL_FA8916AA Typhimurium
+SAL_FA8917AA Typhimurium
+SAL_FA8918AA Typhimurium
+SAL_FA8921AA Typhimurium
+SAL_FA8938AA Typhimurium
+SAL_FA8958AA Typhimurium
+SAL_FA8961AA Typhimurium
+SAL_FA8962AA Typhimurium
+SAL_FA8965AA Typhimurium
+SAL_FA8976AA Typhimurium
+SAL_FA8977AA Typhimurium
+SAL_FA8978AA Typhimurium
+SAL_FA8979AA Typhimurium
+SAL_FA8984AA Typhimurium
+SAL_FA8987AA Typhimurium
+SAL_FA8988AA I 4,[5],12:i:-
+SAL_FA8992AA Typhimurium
+SAL_FA8995AA Typhimurium
+SAL_FA8996AA Typhimurium
+SAL_FA9003AA Typhimurium
+SAL_FA9004AA Typhimurium
+SAL_FA9005AA Typhimurium
+SAL_FA9006AA Typhimurium
+SAL_FA9007AA Typhimurium
+SAL_FA9016AA I 4,[5],12:i:-
+SAL_FA9018AA I 4,[5],12:i:-
+SAL_FA9021AA Typhimurium
+SAL_FA9023AA Typhimurium
+SAL_FA9025AA Typhimurium
+SAL_FA9031AA Typhimurium
+SAL_FA9035AA Typhimurium
+SAL_FA9037AA Typhimurium
+SAL_FA9038AA Typhimurium
+SAL_FA9039AA Typhimurium
+SAL_FA9040AA Typhimurium
+SAL_FA9041AA Typhimurium
+SAL_FA9042AA Typhimurium
+SAL_FA9043AA Typhimurium
+SAL_FA9044AA Typhimurium
+SAL_FA9045AA Typhimurium
+SAL_FA9047AA Typhimurium
+SAL_FA9051AA Typhimurium
+SAL_FA9053AA Typhimurium
+SAL_FA9055AA Typhimurium
+SAL_FA9072AA Typhimurium
+SAL_FA9073AA Typhimurium
+SAL_FA9082AA Enteritidis
+SAL_FA9083AA Typhimurium
+SAL_FA9084AA Typhimurium
+SAL_FA9085AA Typhimurium
+SAL_FA9086AA Typhimurium
+SAL_FA9091AA I 4,[5],12:i:-
+SAL_FA9093AA Typhimurium
+SAL_FA9094AA Typhimurium
+SAL_FA9096AA Typhimurium
+SAL_FA9112AA Typhimurium
+SAL_FA9113AA Typhimurium
+SAL_FA9114AA Typhimurium
+SAL_FA9115AA Typhimurium
+SAL_FA9118AA Typhimurium
+SAL_FA9121AA Typhimurium
+SAL_FA9122AA Typhimurium
+SAL_FA9124AA Typhimurium
+SAL_FA9125AA Typhimurium
+SAL_FA9136AA Typhimurium
+SAL_FA9153AA Typhimurium
+SAL_FA9178AA Typhimurium
+SAL_FA9183AA Typhimurium
+SAL_FA9188AA Typhimurium
+SAL_FA9192AA Typhimurium
+SAL_FA9197AA IIIa 18:z4,z23:-
+SAL_FA9204AA Typhimurium
+SAL_FA9307AA Typhimurium
+SAL_FA9368AA Typhimurium
+SAL_FA9370AA I 4,[5],12:d:-
+SAL_FA9415AA Typhimurium
+SAL_FA9438AA Typhimurium
+SAL_FA9440AA Typhimurium
+SAL_FA9460AA Orion
+SAL_FA9474AA Typhimurium
+SAL_FA9475AA Typhimurium
+SAL_FA9476AA Typhimurium
+SAL_FA9477AA Typhimurium
+SAL_FA9481AA Enteritidis
+SAL_FA9530AA I 4,[5],12:i:-
+SAL_FA9531AA I 4,[5],12:i:-
+SAL_FA9532AA I 4,[5],12:i:-
+SAL_FA9533AA I 4,[5],12:i:-
+SAL_FA9551AA Typhimurium
+SAL_FA9552AA Typhimurium
+SAL_FA9555AA Typhimurium
+SAL_FA9558AA Typhimurium
+SAL_FA9560AA Typhimurium
+SAL_FA9604AA I 4,[5],12:r:-
+SAL_FA9607AA Typhimurium
+SAL_FA9612AA Typhimurium
+SAL_FA9640AA I 4,[5],12:d:-
+SAL_FA9643AA I 4,[5],12:d:-
+SAL_FA9645AA Typhimurium
+SAL_FA9646AA Typhimurium
+SAL_FA9647AA Typhimurium
+SAL_FA9651AA Typhimurium
+SAL_FA9652AA Typhimurium
+SAL_FA9653AA Typhimurium
+SAL_FA9654AA Typhimurium
+SAL_FA9655AA Typhimurium
+SAL_FA9713AA Orion
+SAL_FA9725AA Orion
+SAL_FA9729AA II 47:b:1,5
+SAL_GA1618AA IIIb 60:r:z
+SAL_GA1620AA IIIb 60:r:z
+SAL_GA1622AA Enteritidis
+SAL_GA1629AA Typhimurium
+SAL_GA1643AA Typhimurium
+SAL_GA1673AA Onireke
+SAL_GA1683AA Braenderup
+SAL_GA1685AA Vinohrady
+SAL_GA1687AA Weltevreden
+SAL_GA1695AA Vinohrady
+SAL_GA1699AA IIIa 56:z4,z23,z32:-
+SAL_GA1703AA Newport
+SAL_GA1705AA Paratyphi B var. Java
+SAL_GA1717AA Abaetetuba
+SAL_GA1719AA VI [1],6,14,[25]:a:e,n,x
+SAL_GA1720AA Typhimurium
+SAL_GA1721AA VI [1],6,14:a:1,5
+SAL_GA1728AA Typhimurium
+SAL_GA1731AA Heidelberg
+SAL_GA1733AA Heidelberg
+SAL_GA1735AA Heidelberg
+SAL_GA1736AA Heidelberg
+SAL_GA1738AA Heidelberg
+SAL_GA1740AA Heidelberg
+SAL_GA1753AA Typhimurium
+SAL_GA1756AA IIIa 18:z4,z23:-
+SAL_GA1758AA Typhimurium
+SAL_GA1765AA Typhimurium
+SAL_GA1768AA Typhimurium
+SAL_GA1771AA IIIa 18:z4,z23:-
+SAL_GA1772AA Typhimurium
+SAL_GA1776AA Thompson
+SAL_GA1777AA IIIa 18:z4,z23:-
+SAL_GA1780AA I 4,[5],12:i:-
+SAL_GA1783AA IV 48:g,z51:-
+SAL_GA1785AA IV 48:g,z51:-
+SAL_GA1787AA IV 1,40:g,z51:-
+SAL_GA1788AA II 30:l,z28:z6
+SAL_GA1789AA II 58:d:z6
+SAL_GA1790AA II 30:l,z28:z6
+SAL_GA1810AA VI 11:b:1,7
+SAL_GA1811AA V 48:z35:-
+SAL_GA1813AA IIIb 61:l,v:1,5,7:[z57]
+SAL_GA1814AA IIIa 48:g,z51:-
+SAL_GA1815AA II 50:b:z6
+SAL_GA2492AA Choleraesuis
+SAL_GA2499AA Javiana
+SAL_GA2511AA Choleraesuis
+SAL_GA2520AA Choleraesuis
+SAL_GA2535AA Lomalinda
+SAL_GA2538AA Lomalinda
+SAL_GA2541AA Edinburg
+SAL_GA2546AA Lomalinda
+SAL_GA2548AA Lomalinda
+SAL_GA2552AA Edinburg
+SAL_GA2555AA Edinburg
+SAL_GA2559AA Lomalinda
+SAL_GA2565AA Edinburg
+SAL_GA2569AA Lomalinda
+SAL_GA2645AA II 1,4,[5],12,[27]:b:[e,n,x]
+SAL_GA2651AA I 4,[5],12:b:-
+SAL_GA2658AA Paratyphi B var. Java monophasic
+SAL_GA2747AA O61:k:1,5,7
+SAL_GA2748AA O61:k:1,5,7
+SAL_GA2797AA II 48:d:z6
+SAL_GA2869AA Muenchen
+SAL_GA2913AA Paratyphi B var. Java monophasic
+SAL_GA2976AA Paratyphi B var. Java
+SAL_GA3084AA Typhimurium
+SAL_GA3089AA Rubislaw
+SAL_GA3102AA Typhimurium
+SAL_GA3103AA Typhimurium
+SAL_GA3128AA Typhimurium
+SAL_GA3129AA Typhimurium
+SAL_GA3147AA V 61:z35:-
+SAL_GA3148AA V 1,13,22:i:-
+SAL_GA3149AA V 1,40:z35:-
+SAL_GA3169AA I 4,[5],12:i:-
+SAL_GA3170AA Typhimurium
+SAL_GA3172AA Typhimurium
+SAL_GA3185AA Typhimurium
+SAL_GA3192AA IIIa 18:z4,z23:-
+SAL_GA3201AA Typhimurium
+SAL_GA3216AA Typhimurium
+SAL_GA3230AA Typhimurium
+SAL_GA3231AA Typhimurium
+SAL_GA3236AA Kentucky
+SAL_GA3239AA Typhimurium
+SAL_GA3241AA IIIa 18:z4,z23:-
+SAL_GA3242AA Typhimurium
+SAL_GA3250AA Typhimurium
+SAL_GA3251AA Typhimurium
+SAL_GA3252AA Typhimurium
+SAL_GA3256AA IIIa 18:z4,z23:-
+SAL_GA3260AA I 4,[5],12:r:-
+SAL_GA3261AA Typhimurium
+SAL_GA3265AA I 4,[5],12:d:-
+SAL_FA8520AA Typhimurium
+SAL_FA8701AA Typhimurium
+SAL_FA8820AA Typhimurium
+SAL_FA8889AA Typhimurium
+SAL_FA8985AA Typhimurium
+SAL_FA9032AA Typhimurium
+SAL_FA9077AA Typhimurium
+SAL_FA9123AA Typhimurium
+SAL_FA9459AA IV 50:z4,z23:-
+SAL_FA9606AA Typhimurium
+SAL_GA1619AA IIIb 60:r:z
+SAL_GA1722AA VI 11:b:e,n,x
+SAL_GA1778AA IIIa 18:z4,z23:-
+SAL_GA2522AA Javiana
+SAL_GA2799AA Anatum
+SAL_GA3270AA Typhimurium
+SAL_GA3271AA I 4,[5],12:r:-
+SAL_GA3272AA I 4,[5],12:d:-
+SAL_GA3273AA I 4,[5],12:r:-
+SAL_GA3278AA V 48:z35:-
+SAL_GA3279AA IV 50:z4,z23:-
+SAL_GA3280AA IV 44:z4,z24:-
+SAL_GA3281AA IV 45:g,z51:-
+SAL_GA3282AA II 58:d:z6
+SAL_GA3283AA II 18:z10:z6
+SAL_GA3284AA II 48:d:z6
+SAL_GA3285AA VI 45:a:e,n,x
+SAL_GA3287AA II 58:a:z6
+SAL_GA3289AA II 42:z:1,5
+SAL_GA3290AA Montevideo
+SAL_GA3292AA Typhimurium
+SAL_GA3308AA Duisburg
+SAL_GA3313AA Choleraesuis
+SAL_GA3341AA I 4,[5],12:i:-
+SAL_GA3368AA I 4,[5],12:i:-
+SAL_GA3377AA Heidelberg
+SAL_GA3381AA Enteritidis
+SAL_GA3403AA Typhimurium
+SAL_GA3407AA Typhimurium
+SAL_GA3411AA Typhimurium
+SAL_GA3412AA Typhimurium
+SAL_GA3416AA Typhimurium
+SAL_GA3418AA Typhimurium
+SAL_GA3423AA Typhimurium
+SAL_GA3427AA I 4,[5],12:b:-
+SAL_GA3477AA Oranienburg
+SAL_GA3488AA Bredeney
+SAL_GA3494AA Oranienburg
+SAL_GA3498AA Mbandaka
+SAL_GA3504AA I 4,[5],12:i:-
+SAL_GA3512AA Paratyphi B var. Java
+SAL_GA3516AA Manhattan
+SAL_GA3519AA Weltevreden
+SAL_GA3529AA Schwarzengrund
+SAL_GA3531AA Bredeney
+SAL_GA3535AA Wilhelmsburg
+SAL_GA3548AA II 55:z39:-
+SAL_GA3555AA O61:k:1,5,7
+SAL_GA3566AA Paratyphi B var. Java
+SAL_GA3571AA Oritamerin
+SAL_GA3609AA Itami
+SAL_GA3653AA VI 41:b:1,7
+SAL_GA3654AA VI 45:a:e,n,x
+SAL_GA3656AA V 60:z41:-
+SAL_GA3658AA Typhi
+SAL_GA3659AA Choleraesuis
+SAL_GA3660AA VI 11:a:1,5
+SAL_GA3661AA VI 6,7:z41:1,7
+SAL_GA3672AA Heidelberg
+SAL_GA3675AA Typhimurium
+SAL_GA3676AA Typhimurium
+SAL_GA3690AA Typhimurium
+SAL_GA3694AA Typhimurium
+SAL_GA3702AA Typhimurium
+SAL_GA3707AA Typhimurium
+SAL_GA3710AA IIIa 18:z4,z23:-
+SAL_GA3713AA Typhimurium
+SAL_GA3717AA Typhimurium
+SAL_GA3721AA Typhimurium
+SAL_GA3729AA V 66:z41:-
+SAL_GA3731AA IV 44:z36,[z38]:-
+SAL_GA3733AA IV 21:z4,z23:-
+SAL_GA3734AA IV 50:g,z51:-
+SAL_GA3735AA IV 45:g,z51:-
+SAL_GA3736AA IV 44:z36,[z38]:-
+SAL_GA3737AA IV 43:z4,z23:-
+SAL_GA3738AA IV 16:z4,z32:-
+SAL_GA3739AA IV 16:z4,z32:-
+SAL_GA3740AA IV 50:g,z51:-
+SAL_GA3742AA IV 44:z4,z24:-
+SAL_GA3744AA IV 1,40:z4,z24:-
+SAL_GA3745AA IV 44:z36,[z38]:-
+SAL_GA3746AA IV 50:g,z51:-
+SAL_GA3747AA IV 50:z4,z23:-
+SAL_GA3748AA II 58:d:z6
+SAL_GA3750AA II 48:d:z8
+SAL_GA3751AA II 47:a:1,5
+SAL_GA3752AA II 48:d:z6
+SAL_GA3754AA II 30:l,z28:z6
+SAL_GA3755AA II 60:g,m,t:z6
+SAL_GA3756AA II 58:d:z8
+SAL_GA3757AA IIIa 18:z4,z32:-
+SAL_GA3758AA IIIa 62:z36:-
+SAL_GA3759AA IIIa 41:z4,z23:-
+SAL_GA3760AA IIIb 38:(k):z35
+SAL_GA3761AA IIIb 50:k:z
+SAL_GA3762AA IIIb 65:(k):z
+SAL_GA3766AA Montevideo
+SAL_GA3842AA I 42:z4,z23:-
+SAL_GA3848AA I 4,[5],12:i:-
+SAL_GA3849AA I 4,[5],12:i:-
+SAL_GA3860AA VI 6,14,25:z10:1,(2),7
+SAL_GA3861AA V 44:z39:-
+SAL_GA3862AA V 48:i:-
+SAL_GA3864AA IV 16:z4,z32:-
+SAL_GA3865AA IV 45:g,z51:-
+SAL_GA3866AA IV 48:g,z51:-
+SAL_GA3868AA IIIb 38:z10:z53
+SAL_GA3869AA IIIb 48:z10:e,n,x,z15
+SAL_GA3871AA IIIb 60:r:e,n,x,z15
+SAL_GA3872AA IIIa 48:z4,z23,z32:-
+SAL_GA3874AA II 1,13,23:z29:1,7
+SAL_GA3875AA II 53:l,z28:z39
+SAL_GA3876AA II 48:d:z6
+SAL_GA3877AA II 47:d:z39
+SAL_GA3878AA II 58:l,z13,z28:z6
+SAL_GA4192AA Montevideo
+SAL_GA4379AA Typhimurium
+SAL_GA4380AA Typhimurium
+SAL_GA4384AA Enteritidis
+SAL_GA4385AA Typhimurium
+SAL_GA4388AA Typhimurium
+SAL_GA4389AA Typhimurium
+SAL_GA4503AA Pharr
+SAL_GA4505AA II 42:b:e,n,x,z15
+SAL_GA4532AA Warragul
+SAL_GA4533AA Warragul
+SAL_GA4546AA Typhimurium
+SAL_GA4548AA Typhimurium
+SAL_GA4549AA Typhimurium
+SAL_GA4550AA Typhimurium
+SAL_GA4552AA Typhimurium
+SAL_GA4633AA Braenderup
+SAL_GA4640AA Thompson
+SAL_GA4716AA Infantis
+SAL_GA5103AA I 4,[5],12:i:-
+SAL_GA5157AA I 4,[5],12:i:-
+SAL_GA5178AA I 4,[5],12:i:-
+SAL_GA5179AA Typhimurium
+SAL_GA5188AA I 4,[5],12:b:-
+SAL_GA5190AA I 4,[5],12:b:-
+SAL_GA5201AA I 4,[5],12:i:-
+SAL_GA5567AA Typhimurium
+SAL_GA5586AA I 4,[5],12:i:-
+SAL_GA5602AA I 4,[5],12:i:-
+SAL_GA5644AA Heidelberg
+SAL_GA5648AA I 4,[5],12:i:-
+SAL_GA5649AA Typhimurium
+SAL_GA5654AA Typhimurium
+SAL_GA5666AA Typhimurium
+SAL_GA5668AA Typhimurium
+SAL_GA5669AA Typhimurium
+SAL_GA5671AA Typhimurium
+SAL_GA5683AA I 4,[5],12:i:-
+SAL_GA5699AA Typhimurium
+SAL_GA5709AA Typhimurium
+SAL_GA5710AA Typhimurium
+SAL_GA5712AA Typhimurium
+SAL_GA5713AA Typhimurium
+SAL_GA5714AA Typhimurium
+SAL_GA5721AA Typhimurium
+SAL_GA5722AA Typhimurium
+SAL_GA5723AA Typhimurium
+SAL_GA5724AA Typhimurium
+SAL_GA5725AA Typhimurium
+SAL_GA5741AA Typhimurium
+SAL_GA5747AA Typhimurium
+SAL_GA5748AA Typhimurium
+SAL_GA5749AA Typhimurium
+SAL_GA5750AA Typhimurium
+SAL_GA5751AA Typhimurium
+SAL_GA5752AA Typhimurium
+SAL_GA5753AA Typhimurium
+SAL_GA5755AA Typhimurium
+SAL_GA5756AA Typhimurium
+SAL_GA5757AA Typhimurium
+SAL_GA5762AA Typhimurium
+SAL_GA5764AA Typhimurium
+SAL_GA5766AA Typhimurium
+SAL_GA5825AA Weltevreden
+SAL_GA5828AA Denver
+SAL_GA6037AA I 4,[5],12:i:-
+SAL_GA6038AA Typhimurium
+SAL_GA6315AA I 4,[5],12:i:-
+SAL_GA6961AA Westminster
+SAL_GA6967AA Anatum
+SAL_GA7185AA I 4,[5],12:d:-
+SAL_GA7186AA Bovismorbificans
+SAL_GA7376AA IIIa 42:g,z51:-
+SAL_GA7387AA Telhashomer
+SAL_GA7414AA Typhimurium
+SAL_GA7415AA Typhimurium
+SAL_GA7416AA Typhimurium
+SAL_GA7424AA Typhimurium
+SAL_GA7425AA Typhimurium
+SAL_GA7426AA Typhimurium
+SAL_GA7427AA Typhimurium
+SAL_GA8457AA Muenchen
+SAL_GA8458AA Muenchen
+SAL_GA8500AA II 1,4,[5],12,[27]:b:[e,n,x]
+SAL_GA8502AA Warragul
+SAL_GA8592AA I 4,[5],12:i:-
+SAL_GA8593AA Amsterdam
+SAL_GA8594AA I 4,[5],12:b:-
+SAL_GA8729AA I 4,[5],12:i:-
+SAL_GA8745AA I 4,[5],12:d:-
+SAL_GA8754AA IV 11:z4,z23:-
+SAL_GA8853AA Ouakam
+SAL_GA9079AA Muenchen
+SAL_GA9126AA Florian
+SAL_GA9132AA I 4,[5],12:i:-
+SAL_GA9136AA I 4,[5],12:i:-
+SAL_GA9146AA I 4,[5],12:i:-
+SAL_GA9180AA Eastbourne
+SAL_GA9200AA Enteritidis
+SAL_GA9201AA Enteritidis
+SAL_GA9203AA Hadar
+SAL_GA9204AA Hadar
+SAL_GA9233AA IIIa 42:z4,z23:-
+SAL_GA9320AA Cannstatt
+SAL_GA9368AA Typhimurium
+SAL_GA9370AA I 4,[5],12:i:-
+SAL_GA9371AA I 4,[5],12:i:-
+SAL_GA9470AA Typhimurium
+SAL_GA9471AA Typhimurium
+SAL_GA9472AA Typhimurium
+SAL_GA9473AA Typhimurium
+SAL_GA9475AA Typhimurium
+SAL_GA9476AA Typhimurium
+SAL_GA9496AA Typhimurium
+SAL_GA9500AA Typhimurium
+SAL_GA9501AA Typhimurium
+SAL_GA9502AA Typhimurium
+SAL_GA9505AA Typhimurium
+SAL_GA9506AA Typhimurium
+SAL_GA9507AA Typhimurium
+SAL_GA9508AA Typhimurium
+SAL_GA9510AA Typhimurium
+SAL_GA9511AA Typhimurium
+SAL_GA9526AA Typhimurium
+SAL_GA9531AA Typhimurium
+SAL_GA9532AA Typhimurium
+SAL_GA9534AA Typhimurium
+SAL_GA9543AA Typhimurium
+SAL_GA9554AA Typhimurium
+SAL_GA9562AA Thompson
+SAL_GA9629AA IIIa 41:z4,z23:-
+SAL_GA9641AA Paratyphi B var. Java monophasic
+SAL_GA9650AA I 4,[5],12:i:-
+SAL_GA9651AA I 4,[5],12:i:-
+SAL_GA9652AA I 4,[5],12:i:-
+SAL_GA9653AA I 4,[5],12:i:-
+SAL_GA9654AA I 4,[5],12:i:-
+SAL_GA9655AA I 4,[5],12:i:-
+SAL_GA9742AA Amsterdam
+SAL_GA9765AA I 4,[5],12:i:-
+SAL_GA9769AA IIIb 38:(k):z35
+SAL_HA0111AA Waycross
+SAL_HA0228AA I 4,[5],12:i:-
+SAL_HA0229AA I 4,[5],12:i:-
+SAL_HA0233AA I 4,[5],12:i:-
+SAL_HA0418AA I 4,[5],12:d:-
+SAL_HA0803AA Cerro
+SAL_HA0824AA Uganda
+SAL_GA3266AA I 4,[5],12:i:-
+SAL_GA3293AA Typhimurium
+SAL_GA3489AA Brandenburg
+SAL_GA3655AA V 48:z39:-
+SAL_GA3725AA Typhimurium
+SAL_GA3749AA II 58:d:z8
+SAL_GA3850AA I 4,[5],12:i:-
+SAL_GA4375AA Typhimurium
+SAL_GA4639AA Braenderup
+SAL_GA5659AA Typhimurium
+SAL_GA5731AA Typhimurium
+SAL_GA6036AA Typhimurium
+SAL_GA8456AA Muenchen
+SAL_GA9179AA Eastbourne
+SAL_GA9494AA I 4,[5],12:i:-
+SAL_HA2635AA Cannstatt
+SAL_HA2772AA I 4,[5],12:i:-
+SAL_HA2794AA I 4,[5],12:i:-
+SAL_HA2801AA I 4,[5],12:i:-
+SAL_HA2802AA I 4,[5],12:i:-
+SAL_HA2852AA Chester
+SAL_HA2857AA Chester
+SAL_HA4265AA I 18:z44:1,5
+SAL_HA4266AA I 18:z44:1,5
+SAL_HA4586AA Paratyphi B var. Java
+SAL_HA4588AA I 4,[5],12:i:-
+SAL_HA4601AA I 4,[5],12:i:-
+SAL_HA4603AA Paratyphi B var. Java monophasic
+SAL_HA4608AA I 4,[5],12:i:-
+SAL_HA4610AA IIIb 65:z10:e,n,x,z15
+SAL_HA4614AA I 4,[5],12:b:-
+SAL_HA4619AA Paratyphi B var. Java
+SAL_HA4620AA Paratyphi B var. Java
+SAL_HA4625AA I 4,[5],12:i:-
+SAL_HA4663AA IIIa 44:z4,z23,z32:-
+SAL_HA4664AA IIIb 11:k:z53
+SAL_HA4665AA IIIa 1,13,23:g,z51:-
+SAL_HA4666AA IIIa 48:g,z51:-
+SAL_HA4667AA IIIa 41:z4,z23:-
+SAL_HA4668AA IIIa 48:z4,z24:-
+SAL_HA4669AA IIIb 50:l,v:z35
+SAL_HA4670AA IIIa 41:z4,z23:-
+SAL_HA4671AA IIIb 50:z52:z
+SAL_HA4672AA IIIb 61:k:1,5,7
+SAL_HA4765AA I 4,[5],12:i:-
+SAL_HA4769AA I 4,[5],12:i:-
+SAL_HA4772AA Paratyphi B var. Java
+SAL_HA4779AA I 4,[5],12:i:-
+SAL_HA4789AA Paratyphi B var. Java
+SAL_HA4798AA Paratyphi B var. Java
+SAL_HA4800AA I 4,[5],12:i:-
+SAL_HA4809AA Paratyphi B var. Java monophasic
+SAL_HA4883AA Paratyphi B var. Java
+SAL_HA4888AA Paratyphi B var. Java monophasic
+SAL_HA4895AA I 4,[5],12:i:-
+SAL_HA4898AA Enteritidis
+SAL_HA4904AA Enteritidis
+SAL_HA4905AA Paratyphi B var. Java
+SAL_HA4910AA Paratyphi B var. Java monophasic
+SAL_HA4912AA Paratyphi B var. Java
+SAL_HA4914AA I 4,[5],12:i:-
+SAL_HA4915AA I 4,[5],12:i:-
+SAL_HA4916AA I 4,[5],12:b:-
+SAL_HA4936AA Paratyphi B var. Java
+SAL_HA4938AA Paratyphi B var. Java
+SAL_HA4941AA Paratyphi B var. Java
+SAL_HA4954AA I 4,[5],12:i:-
+SAL_HA4962AA Paratyphi B var. Java
+SAL_HA4969AA Paratyphi B var. Java
+SAL_HA4982AA Paratyphi B var. Java
+SAL_HA4986AA I 4,[5],12:i:-
+SAL_HA4993AA I 4,[5],12:i:-
+SAL_HA4999AA Paratyphi B var. Java
+SAL_HA5002AA I 4,[5],12:i:-
+SAL_HA5013AA Paratyphi B var. Java
+SAL_HA5018AA I 4,[5],12:i:-
+SAL_HA5020AA Paratyphi B var. Java
+SAL_HA5024AA Paratyphi B var. Java
+SAL_HA5026AA I 4,[5],12:b:-
+SAL_HA5043AA Paratyphi B var. Java
+SAL_HA5051AA Paratyphi B var. Java
+SAL_HA5066AA I 4,[5],12:b:-
+SAL_HA5148AA Enteritidis
+SAL_HA5151AA Paratyphi B var. Java
+SAL_HA5157AA Paratyphi B var. Java
+SAL_HA5172AA I 4,[5],12:i:-
+SAL_HA5180AA I 4,[5],12:b:-
+SAL_HA5182AA Paratyphi B var. Java
+SAL_HA5400AA Paratyphi B var. Java monophasic
+SAL_HA5414AA I 4,[5],12:b:-
+SAL_HA5420AA Paratyphi B var. Java monophasic
+SAL_HA5448AA I 4,[5],12:i:-
+SAL_HA5455AA I 4,[5],12:i:-
+SAL_HA5458AA I 4,[5],12:b:-
+SAL_HA5522AA IV 18:z36,z38:-
+SAL_HA5524AA IV 48:z4,z32:-
+SAL_HA5525AA IV 48:g,z51:-
+SAL_HA5526AA IV 50:g,z51:-
+SAL_HA5527AA II 58:l,z13,z28:z6
+SAL_HA5529AA II 47:b:1,5
+SAL_HA5531AA IV 44:z4,z23:-
+SAL_HA5532AA II 58:l,z13,z28:z6
+SAL_HA5533AA II 9,46:l,w:e,n,x
+SAL_HA6082AA Cannstatt
+SAL_HA6085AA Cannstatt
+SAL_HA6309AA Chester
+SAL_HA6379AA I 4,[5],12:i:-
+SAL_HA7656AA California
+SAL_HA7657AA California
+SAL_IA0679AA Paratyphi B var. Java
+SAL_IA0768AA Saintpaul
+SAL_IA0769AA I 4,[5],12:i:-
+SAL_IA0775AA I 4,[5],12:i:-
+SAL_IA0783AA Paratyphi B var. Java
+SAL_IA0816AA I 4,[5],12:i:-
+SAL_IA0902AA Saintpaul
+SAL_IA0945AA I 4,[5],12:i:-
+SAL_IA0990AA I 4,[5],12:i:-
+SAL_IA1024AA I 4,[5],12:i:-
+SAL_IA1061AA I 4,[5],12:i:-
+SAL_IA1118AA Bovismorbificans
+SAL_IA1283AA I 4,[5],12:i:-
+SAL_IA1292AA I 4,[5],12:i:-
+SAL_IA1321AA I 4,[5],12:i:-
+SAL_IA1336AA I 4,[5],12:i:-
+SAL_IA1433AA I 4,[5],12:i:-
+SAL_IA1528AA I 4,[5],12:i:-
+SAL_IA1561AA Saintpaul
+SAL_IA1621AA I 4,[5],12:i:-
+SAL_IA1679AA Goldcoast
+SAL_IA1704AA I 4,[5],12:i:-
+SAL_IA1736AA I 4,[5],12:i:-
+SAL_IA1760AA Saintpaul
+SAL_IA1769AA I 4,[5],12:i:-
+SAL_IA1792AA I 4,[5],12:i:-
+SAL_IA1828AA I 4,[5],12:i:-
+SAL_IA1859AA I 4,[5],12:i:-
+SAL_IA2096AA I 4,[5],12:i:-
+SAL_IA2224AA I 4,[5],12:i:-
+SAL_IA2225AA Paratyphi B var. Java
+SAL_IA2227AA I 4,[5],12:i:-
+SAL_IA2230AA I 4,[5],12:i:-
+SAL_IA2233AA I 4,[5],12:i:-
+SAL_IA2241AA I 4,[5],12:i:-
+SAL_IA2243AA I 4,[5],12:i:-
+SAL_IA2247AA Paratyphi B var. Java
+SAL_IA2248AA I 4,[5],12:i:-
+SAL_IA2249AA I 4,[5],12:i:-
+SAL_IA2256AA Paratyphi B var. Java
+SAL_IA2258AA I 4,[5],12:i:-
+SAL_IA2268AA I 4,[5],12:i:-
+SAL_IA2281AA IIIa 1,13,23:g,z51:-
+SAL_IA2381AA Cannstatt
+SAL_IA2615AA IV 43:z4,z23:-
+SAL_IA2684AA Typhimurium
+SAL_IA2736AA I 4,[5],12:i:-
+SAL_IA2739AA I 4,[5],12:i:-
+SAL_IA2742AA I 4,[5],12:i:-
+SAL_IA2744AA I 4,[5],12:i:-
+SAL_IA2745AA I 4,[5],12:i:-
+SAL_IA2762AA I 4,[5],12:i:-
+SAL_IA2768AA I 4,[5],12:i:-
+SAL_IA2792AA I 4,[5],12:i:-
+SAL_IA2904AA Telelkebir
+SAL_IA3097AA Saintpaul
+SAL_IA3146AA I 4,[5],12:i:-
+SAL_IA3203AA I 4,[5],12:i:-
+SAL_IA3215AA I 4,[5],12:i:-
+SAL_IA3392AA I 4,[5],12:i:-
+SAL_IA3473AA I 4,[5],12:i:-
+SAL_IA3534AA Saintpaul
+SAL_IA3592AA Bovismorbificans
+SAL_IA3688AA I 4,[5],12:i:-
+SAL_IA4703AA Orion
+SAL_IA4732AA I 4,[5],12:i:-
+SAL_IA4735AA I 4,[5],12:i:-
+SAL_IA4742AA I 4,[5],12:i:-
+SAL_IA4743AA I 4,[5],12:i:-
+SAL_IA4749AA I 4,[5],12:i:-
+SAL_IA4752AA I 4,[5],12:i:-
+SAL_IA4754AA I 4,[5],12:i:-
+SAL_IA4760AA IV 44:z4,z23:-
+SAL_IA4764AA I 4,[5],12:i:-
+SAL_IA4769AA I 4,[5],12:i:-
+SAL_IA4770AA I 4,[5],12:i:-
+SAL_IA4813AA I 4,[5],12:i:-
+SAL_IA4819AA Paratyphi B var. Java
+SAL_IA4825AA I 4,[5],12:i:-
+SAL_IA4878AA I 4,[5],12:i:-
+SAL_IA5058AA I 4,[5],12:i:-
+SAL_IA5070AA I 4,[5],12:i:-
+SAL_IA5101AA Typhimurium
+SAL_IA5106AA Typhimurium
+SAL_IA5107AA Paratyphi B var. Java
+SAL_IA5333AA Cerro
+SAL_IA5372AA I 4,[5],12:i:-
+SAL_IA5708AA I 4,[5],12:i:-
+SAL_IA5716AA I 4,[5],12:i:-
+SAL_IA5763AA I 4,[5],12:i:-
+SAL_IA5766AA I 4,[5],12:i:-
+SAL_IA5767AA I 4,[5],12:i:-
+SAL_IA5890AA I 4,[5],12:i:-
+SAL_IA5903AA I 4,[5],12:i:-
+SAL_IA5905AA Paratyphi B var. Java
+SAL_IA5907AA I 4,[5],12:i:-
+SAL_IA5912AA I 4,[5],12:i:-
+SAL_IA5931AA I 4,[5],12:i:-
+SAL_IA5935AA I 4,[5],12:i:-
+SAL_IA5938AA I 4,[5],12:i:-
+SAL_IA5952AA I 4,[5],12:i:-
+SAL_IA5956AA I 4,[5],12:i:-
+SAL_IA6112AA Paratyphi B var. Java
+SAL_IA6126AA Paratyphi B var. Java
+SAL_IA6139AA Paratyphi B var. Java
+SAL_IA6205AA Paratyphi B var. Java
+SAL_IA6223AA Paratyphi B var. Java
+SAL_IA6684AA I 4,[5],12:d:-
+SAL_IA6705AA I 4,[5],12:i:-
+SAL_IA6926AA Paratyphi B var. Java
+SAL_IA6928AA I 4,[5],12:i:-
+SAL_IA6942AA I 4,[5],12:i:-
+SAL_IA6944AA Paratyphi B var. Java
+SAL_IA6947AA Paratyphi B var. Java
+SAL_IA6950AA I 4,[5],12:i:-
+SAL_IA6969AA Paratyphi B var. Java
+SAL_IA6976AA IIIb 61:k:1,5,7
+SAL_IA6978AA IIIb 35:i:z35
+SAL_IA6983AA Denver
+SAL_IA7055AA I 4,[5],12:i:-
+SAL_IA7057AA I 4,[5],12:i:-
+SAL_IA7061AA Typhimurium
+SAL_IA7062AA Typhimurium
+SAL_IA7065AA Typhimurium
+SAL_IA7171AA I 4,[5],12:i:-
+SAL_IA7175AA I 4,[5],12:i:-
+SAL_IA7367AA Senftenberg
+SAL_IA7368AA IV 48:z4,z32:-
+SAL_IA7370AA IV 48:z4,z32:-
+SAL_IA7530AA IIIa 48:g,z51:-
+SAL_IA7646AA I 4,[5],12:i:-
+SAL_IA7647AA Paratyphi B var. Java
+SAL_IA7648AA I 4,[5],12:i:-
+SAL_IA7658AA I 4,[5],12:i:-
+SAL_IA7661AA I 4,[5],12:i:-
+SAL_IA7662AA I 4,[5],12:i:-
+SAL_IA7663AA Paratyphi B var. Java
+SAL_IA7677AA Cannstatt
+SAL_IA7684AA Amsterdam
+SAL_IA7697AA Paratyphi B var. Java
+SAL_IA7793AA Paratyphi B var. Java
+SAL_IA8326AA IIIb 53:k:e,n,x,z15
+SAL_IA8335AA IIIb 60:b:z
+SAL_IA8797AA Ruiru
+SAL_IA8884AA IV 43:z4,z23:-
+SAL_IA8901AA II 53:z4,z24:-
+SAL_IA9043AA Saintpaul
+SAL_IA9644AA I 4,[5],12:i:-
+SAL_IA9716AA IIIa 1,13,23:g,z51:-
+SAL_IA9782AA I 4,[5],12:i:-
+SAL_IA9995AA Paratyphi B var. Java monophasic
+SAL_IA9996AA Paratyphi B var. Java monophasic
+SAL_IA9998AA Paratyphi B var. Java monophasic
+SAL_JA0001AA Paratyphi B var. Java monophasic
+SAL_JA0003AA Paratyphi B var. Java
+SAL_JA0004AA Paratyphi B var. Java monophasic
+SAL_JA1160AA I 4,[5],12:i:-
+SAL_JA1179AA Typhimurium
+SAL_JA1278AA Bovismorbificans
+SAL_JA1280AA Bovismorbificans
+SAL_JA1281AA Bovismorbificans
+SAL_JA1282AA Bovismorbificans
+SAL_JA1283AA Bovismorbificans
+SAL_JA1284AA Bovismorbificans
+SAL_JA1285AA Bovismorbificans
+SAL_JA1286AA Bovismorbificans
+SAL_JA1287AA Bovismorbificans
+SAL_JA1288AA Bovismorbificans
+SAL_JA1289AA Bovismorbificans
+SAL_JA1290AA Bovismorbificans
+SAL_JA1291AA Bovismorbificans
+SAL_JA1292AA Bovismorbificans
+SAL_HA1256AA I 4,[5],12:i:-
+SAL_HA4616AA IIIb 50:k:z
+SAL_HA4773AA I 4,[5],12:b:-
+SAL_HA4927AA I 4,[5],12:i:-
+SAL_HA5032AA Paratyphi B var. Java
+SAL_HA5523AA II 42:r:-
+SAL_IA1271AA I 4,[5],12:i:-
+SAL_IA2082AA Choleraesuis
+SAL_IA2451AA II 1,4,[5],12,[27]:b:[e,n,x]
+SAL_IA3443AA I 4,[5],12:i:-
+SAL_IA4771AA I 4,[5],12:i:-
+SAL_IA5769AA I 4,[5],12:i:-
+SAL_IA6703AA I 4,[5],12:i:-
+SAL_IA7168AA Godesberg
+SAL_IA7789AA Paratyphi B var. Java
+SAL_JA0020AA IIIa 1,13,23:g,z51:-
+SAL_JA1155AA I 4,[5],12:i:-
+SAL_JA1293AA Bovismorbificans
+SAL_JA1313AA Bovismorbificans
+SAL_JA1348AA Bovismorbificans
+SAL_JA1379AA Bovismorbificans
+SAL_JA1294AA Bovismorbificans
+SAL_JA1295AA Bovismorbificans
+SAL_JA1296AA Bovismorbificans
+SAL_JA1297AA Bovismorbificans
+SAL_JA1298AA Bovismorbificans
+SAL_JA1299AA Bovismorbificans
+SAL_JA1300AA Bovismorbificans
+SAL_JA1301AA Bovismorbificans
+SAL_JA1302AA Bovismorbificans
+SAL_JA1303AA Bovismorbificans
+SAL_JA1304AA Bovismorbificans
+SAL_JA1305AA Bovismorbificans
+SAL_JA1306AA Bovismorbificans
+SAL_JA1307AA Bovismorbificans
+SAL_JA1309AA Bovismorbificans
+SAL_JA1310AA Bovismorbificans
+SAL_JA1314AA Bovismorbificans
+SAL_JA1315AA Bovismorbificans
+SAL_JA1316AA Bovismorbificans
+SAL_JA1317AA Bovismorbificans
+SAL_JA1318AA Bovismorbificans
+SAL_JA1320AA Bovismorbificans
+SAL_JA1321AA Bovismorbificans
+SAL_JA1338AA Bovismorbificans
+SAL_JA1339AA Bovismorbificans
+SAL_JA1340AA Bovismorbificans
+SAL_JA1341AA Bovismorbificans
+SAL_JA1342AA Bovismorbificans
+SAL_JA1343AA Bovismorbificans
+SAL_JA1344AA Bovismorbificans
+SAL_JA1345AA Bovismorbificans
+SAL_JA1346AA Bovismorbificans
+SAL_JA1349AA Bovismorbificans
+SAL_JA1352AA Bovismorbificans
+SAL_JA1353AA Bovismorbificans
+SAL_JA1354AA Bovismorbificans
+SAL_JA1355AA Bovismorbificans
+SAL_JA1356AA Bovismorbificans
+SAL_JA1357AA Bovismorbificans
+SAL_JA1359AA Bovismorbificans
+SAL_JA1361AA Bovismorbificans
+SAL_JA1371AA Bovismorbificans
+SAL_JA1372AA Bovismorbificans
+SAL_JA1373AA Bovismorbificans
+SAL_JA1375AA Bovismorbificans
+SAL_JA1376AA Bovismorbificans
+SAL_JA1377AA Bovismorbificans
+SAL_JA1378AA Bovismorbificans
+SAL_JA1380AA Bovismorbificans
+SAL_JA1381AA Bovismorbificans
+SAL_JA1382AA Bovismorbificans
+SAL_JA1384AA Bovismorbificans
+SAL_JA1387AA Bovismorbificans
+SAL_JA1392AA Bovismorbificans
+SAL_JA1394AA Bovismorbificans
+SAL_JA1396AA Bovismorbificans
+SAL_JA1397AA Bovismorbificans
+SAL_JA1398AA Bovismorbificans
+SAL_JA1400AA Bovismorbificans
+SAL_JA1406AA Bovismorbificans
+SAL_JA1410AA Bovismorbificans
+SAL_JA1445AA IV 38:z4,z23:-
+SAL_JA1446AA IV 48:g,z51:-
+SAL_JA1460AA IV 16:z4,z32:-
+SAL_JA1462AA IV 48:g,z51:-
+SAL_JA1463AA IV 48:g,z51:-
+SAL_JA0138AA Paratyphi B
+SAL_JA0333AA I 4,[5],12:i:-
+SAL_JA0334AA I 4,[5],12:i:-
+SAL_JA0335AA I 4,[5],12:i:-
+SAL_JA0470AA I 4,[5],12:i:-
+SAL_JA0471AA IV 16:z4,z32:-
+SAL_JA0473AA I 4,[5],12:i:-
+SAL_JA0474AA I 4,[5],12:i:-
+SAL_JA0486AA I 4,[5],12:i:-
+SAL_JA0592AA I 4,[5],12:i:-
+SAL_JA0593AA I 4,[5],12:i:-
+SAL_JA0595AA I 4,[5],12:i:-
+SAL_JA0599AA I 4,[5],12:i:-
+SAL_JA0601AA I 4,[5],12:i:-
+SAL_JA0605AA I 4,[5],12:i:-
+SAL_JA0867AA IV 16:z4,z32:-
+SAL_JA0874AA Typhimurium
diff --git a/sistr/data/genomes-to-subspecies.txt b/sistr/data/genomes-to-subspecies.txt
new file mode 100644
index 0000000..9187a96
--- /dev/null
+++ b/sistr/data/genomes-to-subspecies.txt
@@ -0,0 +1,52790 @@
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+SAL_BA1307AA enterica
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+SAL_BA0123AA enterica
+SAL_BA0124AA enterica
+SAL_BA0125AA enterica
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+SAL_HA6596AA enterica
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+SAL_HA8451AA enterica
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+SAL_HA8454AA enterica
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+SAL_HA8471AA enterica
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+SAL_HA7329AA enterica
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+SAL_HA8476AA enterica
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+SAL_HA8478AA enterica
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+SAL_HA8481AA enterica
+SAL_HA8482AA enterica
+SAL_HA8483AA enterica
+SAL_HA8484AA enterica
+SAL_HA8485AA enterica
+SAL_HA8486AA enterica
+SAL_HA8487AA enterica
+SAL_HA8488AA enterica
+SAL_HA8489AA enterica
+SAL_HA8490AA enterica
+SAL_HA8492AA enterica
+SAL_HA8493AA enterica
+SAL_HA8494AA enterica
+SAL_HA8495AA enterica
+SAL_HA8496AA enterica
+SAL_HA8497AA enterica
+SAL_HA8498AA enterica
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+SAL_HA8502AA enterica
+SAL_HA8503AA enterica
+SAL_HA8504AA enterica
+SAL_HA8505AA enterica
+SAL_HA8506AA enterica
+SAL_HA8507AA enterica
+SAL_HA8509AA enterica
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+SAL_HA8551AA enterica
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+SAL_HA8554AA enterica
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+SAL_HA8652AA enterica
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+SAL_HA8655AA enterica
+SAL_HA8656AA enterica
+SAL_HA8657AA enterica
+SAL_HA8658AA enterica
+SAL_HA8659AA enterica
+SAL_HA8660AA enterica
+SAL_HA8661AA enterica
+SAL_HA8663AA enterica
+SAL_HA8664AA enterica
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+SAL_HA8666AA enterica
+SAL_HA8667AA enterica
+SAL_HA8668AA enterica
+SAL_HA8669AA enterica
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+SAL_HA8684AA enterica
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+SAL_HA8687AA enterica
+SAL_HA8689AA enterica
+SAL_HA8690AA enterica
+SAL_HA8692AA enterica
+SAL_HA8693AA enterica
+SAL_HA8694AA enterica
+SAL_HA8695AA enterica
+SAL_HA8696AA enterica
+SAL_HA8697AA enterica
+SAL_HA8698AA enterica
+SAL_HA8699AA enterica
+SAL_HA8700AA enterica
+SAL_HA8701AA enterica
+SAL_HA8702AA enterica
+SAL_HA8716AA enterica
+SAL_HA8717AA enterica
+SAL_HA8718AA enterica
+SAL_HA8719AA enterica
+SAL_HA8734AA enterica
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+SAL_HA8738AA enterica
+SAL_HA8739AA enterica
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+SAL_HA8744AA enterica
+SAL_HA8745AA enterica
+SAL_HA8747AA enterica
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+SAL_HA8749AA enterica
+SAL_HA8750AA enterica
+SAL_HA8751AA enterica
+SAL_HA8752AA enterica
+SAL_HA8753AA enterica
+SAL_HA8757AA enterica
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+SAL_HA8804AA enterica
+SAL_HA8807AA enterica
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+SAL_HA8812AA enterica
+SAL_HA8813AA enterica
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+SAL_HA8817AA enterica
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+SAL_HA8821AA enterica
+SAL_HA8822AA enterica
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+SAL_HA8938AA enterica
+SAL_HA8939AA enterica
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+SAL_HA8944AA enterica
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+SAL_HA8946AA enterica
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+SAL_HA8952AA enterica
+SAL_HA8953AA enterica
+SAL_HA8954AA enterica
+SAL_HA8955AA enterica
+SAL_HA9091AA enterica
+SAL_HA9092AA enterica
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+SAL_HA9120AA enterica
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+SAL_HA9151AA enterica
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+SAL_HA9351AA enterica
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+SAL_HA9387AA enterica
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+SAL_HA9390AA enterica
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+SAL_HA8474AA enterica
+SAL_HA8491AA enterica
+SAL_HA8508AA enterica
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+SAL_HA8653AA enterica
+SAL_HA8671AA enterica
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+SAL_HA8814AA enterica
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+SAL_HA8951AA enterica
+SAL_HA9150AA enterica
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+SAL_HA9397AA enterica
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+SAL_HA9402AA enterica
+SAL_HA9403AA enterica
+SAL_HA9404AA enterica
+SAL_HA9405AA enterica
+SAL_HA9406AA enterica
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+SAL_HA9409AA enterica
+SAL_HA9410AA enterica
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+SAL_HA9426AA enterica
+SAL_HA9427AA enterica
+SAL_HA9428AA enterica
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+SAL_IA3534AA enterica
+SAL_IA3592AA enterica
+SAL_IA3688AA enterica
+SAL_IA4703AA enterica
+SAL_IA4732AA enterica
+SAL_IA4735AA enterica
+SAL_IA4742AA enterica
+SAL_IA4743AA enterica
+SAL_IA4749AA enterica
+SAL_IA4752AA enterica
+SAL_IA4754AA enterica
+SAL_IA4760AA houtenae
+SAL_IA4764AA enterica
+SAL_IA4769AA enterica
+SAL_IA4770AA enterica
+SAL_IA4813AA enterica
+SAL_IA4819AA enterica
+SAL_IA4825AA enterica
+SAL_IA4878AA enterica
+SAL_IA5058AA enterica
+SAL_IA5070AA enterica
+SAL_IA5101AA enterica
+SAL_IA5106AA enterica
+SAL_IA5107AA enterica
+SAL_IA5333AA enterica
+SAL_IA5372AA enterica
+SAL_IA5708AA enterica
+SAL_IA5716AA enterica
+SAL_IA5763AA enterica
+SAL_IA5766AA enterica
+SAL_IA5767AA enterica
+SAL_IA5890AA enterica
+SAL_IA5903AA enterica
+SAL_IA5905AA enterica
+SAL_IA5907AA enterica
+SAL_IA5912AA enterica
+SAL_IA5931AA enterica
+SAL_IA5935AA enterica
+SAL_IA5938AA enterica
+SAL_IA5952AA enterica
+SAL_IA5956AA enterica
+SAL_IA6112AA enterica
+SAL_IA6126AA enterica
+SAL_IA6139AA enterica
+SAL_IA6205AA enterica
+SAL_IA6223AA enterica
+SAL_IA6684AA enterica
+SAL_IA6705AA enterica
+SAL_IA6926AA enterica
+SAL_IA6928AA enterica
+SAL_IA6942AA enterica
+SAL_IA6944AA enterica
+SAL_IA6947AA enterica
+SAL_IA6950AA enterica
+SAL_IA6969AA enterica
+SAL_IA6976AA diarizonae
+SAL_IA6978AA diarizonae
+SAL_IA6983AA enterica
+SAL_IA7055AA enterica
+SAL_IA7057AA enterica
+SAL_IA7061AA enterica
+SAL_IA7062AA enterica
+SAL_IA7065AA enterica
+SAL_IA7171AA enterica
+SAL_IA7175AA enterica
+SAL_IA7367AA enterica
+SAL_IA7368AA houtenae
+SAL_IA7370AA houtenae
+SAL_IA7530AA arizonae
+SAL_IA7646AA enterica
+SAL_IA7647AA enterica
+SAL_IA7648AA enterica
+SAL_IA7658AA enterica
+SAL_IA7661AA enterica
+SAL_IA7662AA enterica
+SAL_IA7663AA enterica
+SAL_IA7677AA enterica
+SAL_IA7684AA enterica
+SAL_IA7697AA enterica
+SAL_IA7793AA enterica
+SAL_IA8326AA diarizonae
+SAL_IA8335AA diarizonae
+SAL_IA8797AA enterica
+SAL_IA8884AA houtenae
+SAL_IA8901AA salamae
+SAL_IA9043AA enterica
+SAL_IA9644AA enterica
+SAL_IA9716AA arizonae
+SAL_IA9782AA enterica
+SAL_IA9995AA enterica
+SAL_IA9996AA enterica
+SAL_IA9998AA enterica
+SAL_JA0001AA enterica
+SAL_JA0003AA enterica
+SAL_JA0004AA enterica
+SAL_JA1160AA enterica
+SAL_JA1179AA enterica
+SAL_JA1278AA enterica
+SAL_JA1280AA enterica
+SAL_JA1281AA enterica
+SAL_JA1282AA enterica
+SAL_JA1283AA enterica
+SAL_JA1284AA enterica
+SAL_JA1285AA enterica
+SAL_JA1286AA enterica
+SAL_JA1287AA enterica
+SAL_JA1288AA enterica
+SAL_JA1289AA enterica
+SAL_JA1290AA enterica
+SAL_JA1291AA enterica
+SAL_JA1292AA enterica
+SAL_HA1256AA enterica
+SAL_HA4616AA diarizonae
+SAL_HA4773AA enterica
+SAL_HA4927AA enterica
+SAL_HA5032AA enterica
+SAL_HA5523AA salamae
+SAL_IA1271AA enterica
+SAL_IA2082AA enterica
+SAL_IA2451AA salamae
+SAL_IA3443AA enterica
+SAL_IA4771AA enterica
+SAL_IA5769AA enterica
+SAL_IA6703AA enterica
+SAL_IA7168AA enterica
+SAL_IA7789AA enterica
+SAL_JA0020AA arizonae
+SAL_JA1155AA enterica
+SAL_JA1293AA enterica
+SAL_JA1313AA enterica
+SAL_JA1348AA enterica
+SAL_JA1379AA enterica
+SAL_JA1294AA enterica
+SAL_JA1295AA enterica
+SAL_JA1296AA enterica
+SAL_JA1297AA enterica
+SAL_JA1298AA enterica
+SAL_JA1299AA enterica
+SAL_JA1300AA enterica
+SAL_JA1301AA enterica
+SAL_JA1302AA enterica
+SAL_JA1303AA enterica
+SAL_JA1304AA enterica
+SAL_JA1305AA enterica
+SAL_JA1306AA enterica
+SAL_JA1307AA enterica
+SAL_JA1309AA enterica
+SAL_JA1310AA enterica
+SAL_JA1314AA enterica
+SAL_JA1315AA enterica
+SAL_JA1316AA enterica
+SAL_JA1317AA enterica
+SAL_JA1318AA enterica
+SAL_JA1320AA enterica
+SAL_JA1321AA enterica
+SAL_JA1338AA enterica
+SAL_JA1339AA enterica
+SAL_JA1340AA enterica
+SAL_JA1341AA enterica
+SAL_JA1342AA enterica
+SAL_JA1343AA enterica
+SAL_JA1344AA enterica
+SAL_JA1345AA enterica
+SAL_JA1346AA enterica
+SAL_JA1349AA enterica
+SAL_JA1352AA enterica
+SAL_JA1353AA enterica
+SAL_JA1354AA enterica
+SAL_JA1355AA enterica
+SAL_JA1356AA enterica
+SAL_JA1357AA enterica
+SAL_JA1359AA enterica
+SAL_JA1361AA enterica
+SAL_JA1371AA enterica
+SAL_JA1372AA enterica
+SAL_JA1373AA enterica
+SAL_JA1375AA enterica
+SAL_JA1376AA enterica
+SAL_JA1377AA enterica
+SAL_JA1378AA enterica
+SAL_JA1380AA enterica
+SAL_JA1381AA enterica
+SAL_JA1382AA enterica
+SAL_JA1384AA enterica
+SAL_JA1387AA enterica
+SAL_JA1392AA enterica
+SAL_JA1394AA enterica
+SAL_JA1396AA enterica
+SAL_JA1397AA enterica
+SAL_JA1398AA enterica
+SAL_JA1400AA enterica
+SAL_JA1406AA enterica
+SAL_JA1410AA enterica
+SAL_JA1445AA houtenae
+SAL_JA1446AA houtenae
+SAL_JA1460AA houtenae
+SAL_JA1462AA houtenae
+SAL_JA1463AA houtenae
+SAL_JA0138AA enterica
+SAL_JA0333AA enterica
+SAL_JA0334AA enterica
+SAL_JA0335AA enterica
+SAL_JA0470AA enterica
+SAL_JA0471AA houtenae
+SAL_JA0473AA enterica
+SAL_JA0474AA enterica
+SAL_JA0486AA enterica
+SAL_JA0592AA enterica
+SAL_JA0593AA enterica
+SAL_JA0595AA enterica
+SAL_JA0599AA enterica
+SAL_JA0601AA enterica
+SAL_JA0605AA enterica
+SAL_JA0867AA houtenae
+SAL_JA0874AA enterica
diff --git a/sistr/data/sistr.msh b/sistr/data/sistr.msh
new file mode 100644
index 0000000..e44e881
Binary files /dev/null and b/sistr/data/sistr.msh differ
diff --git a/sistr/misc/__init__.py b/sistr/misc/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/sistr/misc/add_ref_genomes.py b/sistr/misc/add_ref_genomes.py
new file mode 100644
index 0000000..58a689a
--- /dev/null
+++ b/sistr/misc/add_ref_genomes.py
@@ -0,0 +1,427 @@
+#!/usr/bin/env python
+import argparse
+from collections import defaultdict
+import logging
+import os
+from subprocess import Popen
+import re
+from datetime import datetime
+
+import pandas as pd
+import numpy as np
+
+from sistr.misc.reduce_to_centroid_alleles import run_allele_reduction
+from sistr.sistr_cmd import genome_name_from_fasta_path
+from sistr.src.blast_wrapper import BlastRunner
+from sistr.src.logger import init_console_logger
+from sistr.src.parsers import parse_fasta
+from sistr.src.serovar_prediction import SerovarPredictor, overall_serovar_call
+from sistr.src.cgmlst import CGMLST_PROFILES_PATH, run_cgmlst, allele_name, CGMLST_FULL_FASTA_PATH
+from sistr.src.serovar_prediction.constants import GENOMES_TO_SEROVAR_PATH, GENOMES_TO_SPP_PATH, SEROVAR_TABLE_PATH
+from sistr.src.mash import MASH_SKETCH_FILE
+
+
+def init_parser():
+ prog_desc = '''Add reference genomes to sistr_cmd
+Supply genome FASTA files and a table with genome name to serovar (and subspecies). If genome not present in table or table not supplied then the serovar and subspecies predictions will be used instead.
+
+sistr_cmd ref genome info files will be written to an output directory
+'''
+
+ parser = argparse.ArgumentParser(prog='predict_serovar',
+ formatter_class=argparse.RawDescriptionHelpFormatter,
+ description=prog_desc)
+
+ parser.add_argument('fastas',
+ metavar='F',
+ nargs='+',
+ help='Input genome FASTA file(s). Genome names in filenames before file extension (e.g. for "g1.fasta" genome name is "g1")')
+ parser.add_argument('-o',
+ '--outdir',
+ required=True,
+ help='Output destination')
+ parser.add_argument('-s',
+ '--serovar-table',
+ help='Table with serovar (and subspecies). CSV expected if extension is .csv; otherwise tab delimited expected. Columns=[genome,serovar, subspecies(optional)]')
+ parser.add_argument('--force',
+ action='store_true',
+ help='Force overwrite of output directory if it exists!')
+ parser.add_argument('-T',
+ '--tmp-dir',
+ default='/tmp',
+ help='Base temporary working directory for intermediate analysis files.')
+ parser.add_argument('-t', '--threads',
+ type=int,
+ default=1,
+ help='Number of parallel threads to run sistr_cmd analysis.')
+ parser.add_argument('-v',
+ '--verbose',
+ action='count',
+ default=2,
+ help='Logging verbosity level (-v to show warnings; -vvv to show debug info)')
+ return parser
+
+
+def sketch_fasta(fasta_path, outdir):
+ """Create a Mash sketch from an input fasta file
+
+ Args:
+ fasta_path (str): input fasta file path. Genome name in fasta filename
+ outdir (str): output directory path to write Mash sketch file to
+
+ Returns:
+ str: output Mash sketch file path
+ """
+ genome_name = genome_name_from_fasta_path(fasta_path)
+ outpath = os.path.join(outdir, genome_name)
+ args = ['mash', 'sketch', '-o', outpath, fasta_path]
+ logging.info('Running Mash sketch with command: %s', ' '.join(args))
+ p = Popen(args)
+ p.wait()
+ sketch_path = outpath + '.msh'
+ assert os.path.exists(sketch_path), 'Mash sketch for genome {} was not created at {}'.format(
+ genome_name,
+ sketch_path)
+ return sketch_path
+
+
+def merge_sketches(outdir, sketch_paths):
+ """Merge new Mash sketches with current Mash sketches
+
+ Args:
+ outdir (str): output directory to write merged Mash sketch file
+ sketch_paths (list of str): Mash sketch file paths for input fasta files
+
+ Returns:
+ str: output path for Mash sketch file with new and old sketches
+ """
+ merge_sketch_path = os.path.join(outdir, 'sistr.msh')
+ args = ['mash', 'paste', merge_sketch_path]
+ for x in sketch_paths:
+ args.append(x)
+ args.append(MASH_SKETCH_FILE)
+ logging.info('Running Mash paste with command: %s', ' '.join(args))
+ p = Popen(args)
+ p.wait()
+ assert os.path.exists(merge_sketch_path), 'Merged sketch was not created at {}'.format(merge_sketch_path)
+ return merge_sketch_path
+
+
+def create_subdirs(outdir, *args):
+ subdir = os.path.join(outdir, *args)
+ try:
+ os.makedirs(subdir)
+ return subdir
+ except Exception as ex:
+ if os.path.exists(subdir):
+ return subdir
+ logging.error(ex)
+
+
+def merge_cgmlst_prediction(serovar_prediction, cgmlst_prediction):
+ serovar_prediction.cgmlst_distance = cgmlst_prediction['distance']
+ serovar_prediction.cgmlst_genome_match = cgmlst_prediction['genome_match']
+ serovar_prediction.serovar_cgmlst = cgmlst_prediction['serovar']
+ serovar_prediction.cgmlst_matching_alleles = cgmlst_prediction['matching_alleles']
+ serovar_prediction.cgmlst_subspecies = cgmlst_prediction['subspecies']
+ return serovar_prediction
+
+
+def run_sistr(input_fasta, tmp_dir):
+ blast_runner = None
+ try:
+ assert os.path.exists(input_fasta), "Input fasta file '%s' must exist!" % input_fasta
+ fasta_filename = os.path.basename(input_fasta)
+ genome_name = genome_name_from_fasta_path(input_fasta)
+ dtnow = datetime.now()
+ genome_tmp_dir = os.path.join(tmp_dir, dtnow.strftime("%Y%m%d%H%M%S") + '-' + 'SISTR' + '-' + genome_name)
+ blast_runner = BlastRunner(input_fasta, genome_tmp_dir)
+ logging.info('Initializing temporary analysis directory "%s" and preparing for BLAST searching.',
+ genome_tmp_dir)
+ blast_runner.prep_blast()
+ logging.info('Temporary FASTA file copied to %s', blast_runner.tmp_fasta_path)
+
+ cgmlst_prediction, cgmlst_results = run_cgmlst(blast_runner)
+
+ spp = cgmlst_prediction['subspecies']
+
+ serovar_predictor = SerovarPredictor(blast_runner, spp)
+ serovar_predictor.predict_serovar_from_antigen_blast()
+ prediction = serovar_predictor.get_serovar_prediction()
+ merge_cgmlst_prediction(prediction, cgmlst_prediction)
+ overall_serovar_call(prediction, serovar_predictor)
+ logging.info('%s | Antigen gene BLAST serovar prediction: "%s" serogroup=%s:H1=%s:H2=%s',
+ fasta_filename,
+ prediction.serovar_antigen,
+ prediction.serogroup,
+ prediction.h1,
+ prediction.h2)
+ logging.info('%s | Subspecies prediction: %s',
+ fasta_filename,
+ spp)
+ logging.info('%s | Overall serovar prediction: %s',
+ fasta_filename,
+ prediction.serovar)
+ finally:
+ logging.info('Deleting temporary working directory at %s', blast_runner.tmp_work_dir)
+ blast_runner.cleanup()
+ return prediction, cgmlst_results
+
+
+def cgmlst_profiles_df(fastas, cgmlst_results):
+ genome_marker_cgmlst_result = {}
+ for fasta, res in zip(fastas, cgmlst_results):
+ genome = genome_name_from_fasta_path(fasta)
+ tmp = {}
+ for marker, res_dict in res.items():
+ aname = res_dict['name']
+ tmp[marker] = int(aname) if aname is not None else None
+ genome_marker_cgmlst_result[genome] = tmp
+ return pd.DataFrame(genome_marker_cgmlst_result).transpose()
+
+
+def write_cgmlst_fasta(outdir, cgmlst_results):
+ marker_allele_seqs = defaultdict(set)
+
+ allowed_nts = set('ATGCatgc')
+ for h, s in parse_fasta(CGMLST_FULL_FASTA_PATH):
+ marker, allele = h.split('|')
+ s = s.replace('-', '')
+ forbidden_char = set(s) - allowed_nts
+ if len(forbidden_char) > 0:
+ logging.warning('Forbidden nucleotide characters %s in allele "%s". Skipping this allele!',
+ forbidden_char,
+ h)
+ continue
+ marker_allele_seqs[marker].add(s)
+
+ # init default dict with int where values start as int 0
+ new_allele_count = defaultdict(int)
+
+ for x in cgmlst_results:
+ for marker, res in x.items():
+ seq = res['seq']
+ if seq is not None:
+ if seq not in marker_allele_seqs[marker]:
+ new_allele_count[marker] += 1
+ if '-' in seq:
+ logging.error('marker %s | result %s', marker, res)
+ marker_allele_seqs[marker].add(seq)
+
+ for marker in sorted(new_allele_count.keys()):
+ logging.info('Added %s new alleles for marker %s', new_allele_count[marker], marker)
+
+ new_cgmlst_fasta_path = os.path.join(outdir, 'cgmlst-full.fasta')
+ with open(new_cgmlst_fasta_path, 'w') as fout:
+ for marker in sorted(marker_allele_seqs.keys()):
+ seqs = marker_allele_seqs[marker]
+ for seq in seqs:
+ fout.write('>{}|{}\n{}\n'.format(marker, allele_name(seq), seq))
+ logging.info('cgMLST FASTA written to "%s" with %s novel alleles',
+ new_cgmlst_fasta_path,
+ sum([v for k, v in new_allele_count.items()]))
+ return new_cgmlst_fasta_path
+
+
+def write_cgmlst_profiles_csv(outdir, cgmlst_results, genome_names):
+ df_profiles_old = pd.read_csv(CGMLST_PROFILES_PATH, index_col=0)
+ markers = df_profiles_old.columns
+
+ genome_marker_allele_results = defaultdict(dict)
+ for genome, cgmlst_result in zip(genome_names, cgmlst_results):
+ for marker in markers:
+ allele = None
+ if marker in cgmlst_result:
+ r = cgmlst_result[marker]
+ if 'name' in r:
+ allele = int(r['name']) if r['name'] is not None else None
+ else:
+ allele = None
+ genome_marker_allele_results[genome][marker] = allele
+ df_profiles_new = pd.DataFrame(genome_marker_allele_results).transpose()
+ df_all_profiles = pd.concat([df_profiles_new, df_profiles_old])
+ profiles_output_path = os.path.join(outdir, 'cgmlst-profiles.csv')
+ df_all_profiles.to_csv(profiles_output_path, float_format='%.0f')
+ assert os.path.exists(profiles_output_path), 'cgMLST profiles CSV file was not written to "{}"'.format(
+ profiles_output_path)
+ logging.info('cgMLST profiles (dim=%s) CSV written to "%s"',
+ df_all_profiles.shape,
+ profiles_output_path)
+
+
+def read_genomes_to_x(path):
+ out = {}
+ with open(path) as f:
+ for l in f:
+ l = l.strip()
+ g, s = l.split('\t')
+ out[g] = s
+ return out
+
+
+def write_genomes_to_x_table(path, genome_to_x):
+ with open(path, 'w') as fout:
+ for k, v in genome_to_x.items():
+ fout.write('{}\t{}\n'.format(k, v))
+
+
+def write_serovar_and_spp_tables(outdir, df_serovar, predictions, genome_names):
+ genome_serovar = read_genomes_to_x(GENOMES_TO_SEROVAR_PATH)
+ genome_spp = read_genomes_to_x(GENOMES_TO_SPP_PATH)
+
+ # prediction serovars and subspecies
+ pred_genome_serovar = {}
+ pred_genome_spp = {}
+ for genome, prediction in zip(genome_names, predictions):
+ pred_dict = prediction.__dict__
+ pred_genome_serovar[genome] = pred_dict['serovar']
+ if 'cgmlst_subspecies' in pred_dict:
+ pred_genome_spp[genome] = pred_dict['cgmlst_subspecies']
+ else:
+ pred_genome_spp[genome] = None
+
+ if df_serovar is not None:
+ for i, row in df_serovar.iterrows():
+ genome = row['genome']
+ serovar = row['serovar']
+ if not serovar in pred_genome_serovar[genome]:
+ logging.warning('Genome "%s" user specified serovar "%s" not in serovar prediction "%s"',
+ genome,
+ serovar,
+ pred_genome_serovar[genome])
+ if 'subspecies' in df_serovar:
+ spp = row['subspecies']
+ if spp != pred_genome_spp[genome]:
+ logging.warning('Genome "%s" provided subspecies of "%s" does not match prediction of "%s"',
+ genome,
+ spp,
+ pred_genome_spp[genome])
+ else:
+ spp = pred_genome_spp[genome]
+ logging.warning('Genome "%s" subspecies info not provided. Using subspecies prediction of "%s"',
+ genome,
+ spp)
+ genome_serovar[genome] = serovar
+ genome_spp[genome] = spp
+ else:
+ logging.warning(
+ 'User did not specify serovar/subspecies table! Using SISTR serovar and subspecies predictions for all genomes.')
+ for genome in genome_names:
+ genome_serovar[genome] = pred_genome_serovar[genome]
+ genome_spp[genome] = pred_genome_spp[genome]
+ genomes_to_serovar_path = os.path.join(outdir, 'genomes-to-serovar.txt')
+ genomes_to_spp_path = os.path.join(outdir, 'genomes-to-subspecies.txt')
+ write_genomes_to_x_table(genomes_to_serovar_path, genome_serovar)
+ assert os.path.exists(genomes_to_serovar_path), '{} file could not be written!'.format(
+ genomes_to_serovar_path)
+ logging.info('Wrote genomes to serovars table at %s', genomes_to_serovar_path)
+ write_genomes_to_x_table(genomes_to_spp_path, genome_spp)
+ assert os.path.exists(genomes_to_spp_path), '{} file could not be written!'.format(
+ genomes_to_spp_path)
+ logging.info('Wrote genomes to subspecies table at %s', genomes_to_spp_path)
+
+
+def create_merge_mash_sketches(input_fastas, data_outdir, sketch_outdir):
+ sketch_paths = [sketch_fasta(fasta, sketch_outdir) for fasta in input_fastas]
+ merge_sketches(data_outdir, sketch_paths)
+
+
+def main():
+ parser = init_parser()
+ args = parser.parse_args()
+ init_console_logger(args.verbose)
+ logging.debug(args)
+ input_fastas = args.fastas
+ outdir = args.outdir
+ tmp_dir = args.tmp_dir
+ serovar_table_path = args.serovar_table
+ threads = args.threads
+ force = args.force
+
+ assert len(input_fastas) > 0, 'No FASTA files specified!'
+ for input_fasta in input_fastas:
+ assert os.path.exists(input_fasta), 'Genome FASTA file does not exist at "{}"'.format(input_fasta)
+ genome_names = [genome_name_from_fasta_path(x) for x in input_fastas]
+ logging.info('You have specified %s genomes to add to current sistr_cmd data files! %s',
+ len(genome_names),
+ genome_names)
+
+ if os.path.exists(outdir):
+ if not force:
+ raise Exception('Output directory already exists at {}!'.format(outdir))
+ else:
+ logging.warning('Using existing output directory at %s', outdir)
+ try:
+ os.makedirs(outdir)
+ except:
+ pass
+ assert os.path.exists(outdir), 'Output directory could not be created!'
+
+ if serovar_table_path:
+ assert os.path.exists(serovar_table_path), 'Provided serovar table path does not exist! {}'.format(
+ serovar_table_path)
+ logging.info('Parsing serovar table from "%s"', serovar_table_path)
+ if re.match(r'.*.csv$', serovar_table_path):
+ logging.info('Trying to read serovar table "%s" as CSV', serovar_table_path)
+ df_serovar = pd.read_csv(serovar_table_path)
+ else:
+ logging.info('Trying to read serovar table "%s" as tab-delimited', serovar_table_path)
+ df_serovar = pd.read_table(serovar_table_path)
+ expected_columns = ['genome', 'serovar']
+ assert np.all(
+ df_serovar.columns.isin(expected_columns)), 'User serovar table did not contain expected columns {}'.format(
+ expected_columns)
+ if 'subspecies' not in df_serovar.columns:
+ logging.warning(
+ 'User serovar table did not contain "subspecies" column so the sistr_cmd subspecies prediction will be used!')
+ genome_names_series = pd.Series(genome_names)
+ genomes_in_serovar_table = genome_names_series.isin(df_serovar.genome)
+ if not np.all(genomes_in_serovar_table):
+ missing_genomes = ', '.join([x for x in genome_names_series[~genomes_in_serovar_table]])
+ logging.error('The following genomes were not found in the serovar table: %s', missing_genomes)
+ raise Exception('Not all user provided genome FASTA files in the provided serovar table!')
+
+ df_wklm = pd.read_csv(SEROVAR_TABLE_PATH)
+ logging.info('Checking for non-standard serovar designations')
+ serovars_not_in_wklm = df_serovar.serovar[~df_serovar.serovar.isin(df_wklm.Serovar)]
+ for row_idx, serovar in serovars_not_in_wklm.iteritems():
+ logging.warning('Non-standard serovar %s at row %s for genome %s!', serovar, row_idx,
+ df_serovar.ix[row_idx]['genome'])
+ else:
+ logging.warning('No genome to serovar table specified! Using SISTR serovar predictions')
+ df_serovar = None
+
+ if threads == 1:
+ logging.info('Serial single threaded run mode on %s genomes', len(input_fastas))
+ outputs = [run_sistr(input_fasta, tmp_dir) for input_fasta in input_fastas]
+ else:
+ from multiprocessing import Pool
+
+ logging.info('Initializing thread pool with %s threads', threads)
+ pool = Pool(processes=threads)
+ logging.info('Running SISTR analysis asynchronously on %s genomes', len(input_fastas))
+ res = [pool.apply_async(run_sistr, (input_fasta, tmp_dir)) for input_fasta in input_fastas]
+
+ logging.info('Getting SISTR analysis results')
+ outputs = [x.get() for x in res]
+ # collect results from sistr analysis
+ prediction_outputs = [x for x, y in outputs]
+ cgmlst_results = [y for x, y in outputs]
+ # create some output dirs
+ data_outdir = create_subdirs(outdir, 'data')
+ cgmlst_outdir = create_subdirs(outdir, 'data', 'cgmlst')
+ sketch_outdir = create_subdirs(outdir, 'mash-sketches')
+ # write files with new and old data
+ cgmlst_fasta = write_cgmlst_fasta(cgmlst_outdir, cgmlst_results)
+ write_cgmlst_profiles_csv(cgmlst_outdir, cgmlst_results, genome_names)
+ write_serovar_and_spp_tables(data_outdir, df_serovar, prediction_outputs, genome_names)
+ create_merge_mash_sketches(input_fastas, data_outdir, sketch_outdir)
+
+ centroid_alleles_path = os.path.join(cgmlst_outdir, 'cgmlst-centroid.fasta')
+ run_allele_reduction(cgmlst_fasta, centroid_alleles_path, threads=threads)
+
+ logging.info('Done!')
+
+
+if __name__ == '__main__':
+ main()
diff --git a/sistr/misc/hc_clusters_from_cgmlst_profiles.py b/sistr/misc/hc_clusters_from_cgmlst_profiles.py
new file mode 100644
index 0000000..3162da3
--- /dev/null
+++ b/sistr/misc/hc_clusters_from_cgmlst_profiles.py
@@ -0,0 +1,97 @@
+#!/usr/bin/env python
+import logging
+import os
+import argparse
+import numpy as np
+
+from sistr.src.logger import init_console_logger
+from sistr.src.cgmlst.extras.hclust_cutree import profiles_to_np_array, nr_profiles, dist_matrix_hamming, complete_linkage, cutree, expand_clusters_dataframe
+
+
+def init_arg_parser():
+ prog_desc = 'Hierarchical clustering flat clusters from cgMLST profiles'
+ parser = argparse.ArgumentParser(prog='hc_clusters_from_cgmlst_profiles',
+ formatter_class=argparse.RawDescriptionHelpFormatter,
+ description=prog_desc)
+
+ parser.add_argument('-i', '--input',
+ required=True,
+ help='cgMLST allelic profiles. Column names == marker names; row names == genome names. First row is column header. First column is genome names.')
+ parser.add_argument('-o', '--output',
+ required=True,
+ help='Output path for CSV of hierarchical clustering flat clusters table.')
+ parser.add_argument('-b', '--begin-threshold',
+ type=float,
+ default=0.0,
+ help='Flat cluster distance threshold range start (default: 0.0)')
+ parser.add_argument('-e', '--end-threshold',
+ type=float,
+ default=1.0,
+ help='Flat cluster distance threshold range end inclusive (default: 1.0)')
+ parser.add_argument('-s', '--step-threshold',
+ type=float,
+ default=0.01,
+ help='Flat cluster distance threshold range step value (default: 0.01).')
+ parser.add_argument('-v', '--verbose',
+ action='count',
+ default=0,
+ help='Logging verbosity (-v to log warnings; -vvv to log debug info)')
+ return parser
+
+
+def main():
+ parser = init_arg_parser()
+ args = parser.parse_args()
+ init_console_logger(args.verbose)
+ input_profiles = args.input
+ if not os.path.exists(input_profiles):
+ err_msg = 'Input cgMLST profiles file does not exist at {}. cgMLST profiles file required!'.format(input_profiles)
+ logging.error(err_msg)
+ raise Exception(err_msg)
+ output_path = args.output
+ if os.path.exists(output_path):
+ err_msg = 'File already exists at the output path "{}"! Specify a different output path.'.format(output_path)
+ logging.error(err_msg)
+ raise Exception(err_msg)
+
+ begin_threshold = args.begin_threshold
+ end_threshold = args.end_threshold
+ step_threshold = args.step_threshold
+ assert begin_threshold >= 0.0, "-b/--begin-threshold must be positive number!"
+ assert begin_threshold <= 1.0, "-b/--begin-threshold must be less than or equal to 1.0"
+ assert begin_threshold < end_threshold, "-b/--begin-threshold must be less than -e/--end-threshold"
+ assert end_threshold >= 0.0, "-e/--end-threshold must be positive number!"
+ assert end_threshold <= 1.0, "-e/--end-threshold must be less than or equal to 1.0"
+ assert step_threshold <= 1.0, "-s/--step-threshold must be less than or equal to 1.0"
+ assert step_threshold >= 0.0, "-s/--step-threshold must be positive number!"
+
+ logging.info('Reading profiles from %s', input_profiles)
+ profiles_matrix, genomes, markers = profiles_to_np_array(input_profiles)
+ logging.info('Profiles matrix shape: %s', profiles_matrix.shape)
+ logging.debug('Genomes: %s', genomes)
+ logging.debug('Markers: %s', markers)
+ logging.info('Finding non-redundant profiles. Grouping genomes by distinct profiles.')
+ nr_profiles_matrix, genome_groups = nr_profiles(profiles_matrix, genomes)
+ logging.info('Non-redundant profiles matrix shape: %s', nr_profiles_matrix.shape)
+ logging.debug('Genome groups: %s', genome_groups)
+ logging.info('Computing Hamming distance matrix from profiles')
+ dm = dist_matrix_hamming(nr_profiles_matrix)
+ logging.info('Complete linkage of Hamming distance matrix')
+ hc = complete_linkage(dm)
+ thresholds = np.arange(begin_threshold, end_threshold + step_threshold, step_threshold)
+ logging.info('Generating flat clusters from %s to %s with step %s',
+ begin_threshold,
+ end_threshold,
+ step_threshold)
+ logging.debug('Thresholds: %s', thresholds)
+ df_clusters = cutree(hc, thresholds)
+ logging.info('Flat clusters generated for non-redundant profiles. Expanding to all profiles.')
+ logging.debug('df_clusters: %s', df_clusters)
+ df_clusters = expand_clusters_dataframe(df_clusters, genome_groups)
+ df_clusters.to_csv(output_path)
+ logging.info('HC flat clusters written to "%s"', output_path)
+ logging.info('Done!')
+
+
+if __name__ == '__main__':
+ main()
diff --git a/sistr/misc/reduce_to_centroid_alleles.py b/sistr/misc/reduce_to_centroid_alleles.py
new file mode 100644
index 0000000..e71186c
--- /dev/null
+++ b/sistr/misc/reduce_to_centroid_alleles.py
@@ -0,0 +1,161 @@
+#!/usr/bin/env python
+from collections import defaultdict
+
+import logging
+import os
+import argparse
+import re
+from sistr.src.cgmlst import allele_name
+
+from sistr.src.logger import init_console_logger
+from sistr.src.parsers import parse_fasta
+from sistr.src.cgmlst.extras.centroid_cgmlst_alleles import find_centroid_alleles
+
+
+def init_arg_parser():
+ prog_desc = 'Output centroid alleles for cgMLST markers'
+ parser = argparse.ArgumentParser(prog='reduce_to_centroid_alleles',
+ formatter_class=argparse.RawDescriptionHelpFormatter,
+ description=prog_desc)
+
+ parser.add_argument('-i', '--input',
+ required=True,
+ help='cgMLST FASTA file with header format ">{marker name}|{allele name}"')
+ parser.add_argument('-o', '--output',
+ help='Reduced centroid cgMLST alleles FASTA output path (default: "<input_filename>.centroid.fasta"')
+ parser.add_argument('-w', '--word_size',
+ type=int,
+ default=28,
+ help='Number of bp at ends of each allele to group by. Related to blastn word size.')
+ parser.add_argument('-t', '--cluster-threshold',
+ type=float,
+ default=0.025,
+ help='Flat cluster generation threshold from hierarchically clustered alleles.')
+ parser.add_argument('--threads',
+ type=int,
+ default=1)
+ parser.add_argument('-v', '--verbose',
+ action='count',
+ default=0,
+ help='Logging verbosity (-v to log warnings; -vvv to log debug info)')
+ return parser
+
+
+def parse_cgmlst_alleles(cgmlst_fasta):
+ """Parse cgMLST alleles from fasta file
+ cgMLST FASTA file must have a header format of ">{marker name}|{allele name}"
+
+ Args:
+ cgmlst_fasta (str): cgMLST fasta file path
+
+ Returns:
+ dict of list: Marker name to list of allele sequences
+ """
+ out = defaultdict(list)
+ for header, seq in parse_fasta(cgmlst_fasta):
+ if not '|' in header:
+ raise Exception('Unexpected format for cgMLST fasta file header. No "|" (pipe) delimiter present! Header="{}"'.format(header))
+ marker_name, allele_name = header.split('|')
+ out[marker_name].append(seq)
+ return out
+
+
+def find_all_centroid_alleles(marker_alleles, threads=1, word_size=28, cluster_threshold=0.025):
+ out = {}
+ if threads == 1:
+ logging.info('Running centroid allele finding in serial single-threaded mode')
+ for marker_name, alleles in marker_alleles.items():
+ centroids = find_centroid_alleles(alleles, bp=word_size, t=cluster_threshold)
+ logging.info('Found {} centroid alleles for marker {} ({}% reduction from {})'.format(
+ len(centroids),
+ marker_name,
+ (1.0 - len(centroids) / float(len(alleles))) * 100),
+ len(alleles))
+ out[marker_name] = centroids
+ else:
+ logging.info('Running centroid allele finding in parallel mode with %s threads', threads)
+ from multiprocessing import Pool
+ pool = Pool(processes=threads)
+ jobs = []
+ markers = sorted(marker_alleles.keys())
+ for marker_name in markers:
+ alleles = marker_alleles[marker_name]
+ job = pool.apply_async(find_centroid_alleles,
+ (alleles,),
+ {'bp': word_size, 't': cluster_threshold})
+ jobs.append(job)
+ logging.info('Queued all markers for centroid allele finding; awaiting results')
+ for marker_name, job in zip(markers, jobs):
+ out[marker_name] = job.get()
+ for marker_name, centroids in out.items():
+ alleles = marker_alleles[marker_name]
+ logging.info('Found {} centroid alleles for marker {} ({}% reduction from {})'.format(
+ len(centroids),
+ marker_name,
+ (1.0 - len(centroids) / float(len(alleles))) * 100,
+ len(alleles)))
+ return out
+
+
+def write_alleles(marker_alleles, output_path):
+ with open(output_path, 'w') as fout:
+ for marker_name, seqs in marker_alleles.items():
+ for seq in seqs:
+ aname = allele_name(seq)
+ fout.write('>{}|{}\n{}\n'.format(marker_name, aname, seq))
+
+
+def run_allele_reduction(input_fasta, output_path, threads=1, word_size=28, cluster_threshold=0.025):
+ logging.info('Parsing alleles from input fasta %s', input_fasta)
+ marker_alleles = parse_cgmlst_alleles(input_fasta)
+ n_total_alleles = sum([len(v) for k,v in marker_alleles.items()])
+ logging.info('Parsed %s alleles for %s markers from %s',
+ n_total_alleles,
+ len(marker_alleles),
+ input_fasta)
+
+ logging.info('Finding centroid alleles for each marker')
+ marker_centroids = find_all_centroid_alleles(marker_alleles,
+ threads=threads,
+ word_size=word_size,
+ cluster_threshold=cluster_threshold)
+ n_centroids = sum([len(v) for k,v in marker_centroids.items()])
+ logging.info('Found {} centroid alleles ({}% of input)'.format(
+ n_centroids,
+ (n_centroids / float(n_total_alleles)) * 100))
+
+ logging.info('Outputting centroid alleles to output path "%s"', output_path)
+ write_alleles(marker_centroids, output_path)
+ logging.info('Centroid alleles written to "%s"', output_path)
+ logging.info('Done!')
+
+
+def main():
+ parser = init_arg_parser()
+ args = parser.parse_args()
+ init_console_logger(args.verbose)
+ input_fasta = args.input
+ if not os.path.exists(input_fasta):
+ err_msg = 'Input fasta file does not exist at {}. cgMLST fasta file required!'.format(input_fasta)
+ logging.error(err_msg)
+ raise Exception(err_msg)
+ output_path = args.output
+ if output_path is None:
+ input_fasta_dir = os.path.dirname(input_fasta)
+ input_filename = os.path.basename(input_fasta)
+ output_filename = re.sub(r'(\.fasta$)|(\.\w{1,}$)', '', input_filename) + '-centroid.fasta'
+ output_path = os.path.join(input_fasta_dir, output_filename)
+ logging.info('No output path specified. Using "%s"', output_path)
+ if os.path.exists(output_path):
+ err_msg = 'File already exists at the output path "{}"! Specify a different output path.'.format(output_path)
+ logging.error(err_msg)
+ raise Exception(err_msg)
+
+ run_allele_reduction(input_fasta, output_path,
+ threads=args.threads,
+ word_size=args.word_size,
+ cluster_threshold=args.cluster_threshold)
+
+
+if __name__ == '__main__':
+ main()
\ No newline at end of file
diff --git a/sistr/sistr_cmd.py b/sistr/sistr_cmd.py
new file mode 100755
index 0000000..a41c00a
--- /dev/null
+++ b/sistr/sistr_cmd.py
@@ -0,0 +1,367 @@
+#!/usr/bin/env python
+from __future__ import print_function
+
+import argparse
+from collections import Counter
+from datetime import datetime
+import logging
+import os
+import re
+
+from sistr.version import __version__
+from sistr.src.blast_wrapper import BlastRunner
+from sistr.src.cgmlst import run_cgmlst
+from sistr.src.logger import init_console_logger
+from sistr.src.qc import qc
+from sistr.src.serovar_prediction import SerovarPredictor, overall_serovar_call, serovar_table
+
+
+def init_parser():
+ prog_desc = '''
+SISTR (Salmonella In Silico Typing Resource) Command-line Tool
+==============================================================
+Serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST.
+
+Note about using the "--use-full-cgmlst-db" flag:
+ The "centroid" allele database is ~10% the size of the full set so analysis is much quicker with the "centroid" vs "full" set of alleles. Results between 2 cgMLST allele sets should not differ.
+
+If you find this program useful in your research, please cite as:
+
+The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies.
+Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada.
+PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101
+'''
+
+ parser = argparse.ArgumentParser(prog='sistr_cmd',
+ formatter_class=argparse.RawDescriptionHelpFormatter,
+ description=prog_desc)
+
+ parser.add_argument('fastas',
+ metavar='F',
+ nargs='*',
+ help='Input genome FASTA file')
+ parser.add_argument('-i',
+ '--input-fasta-genome-name',
+ nargs=2,
+ metavar=('fasta_path', 'genome_name'),
+ action='append',
+ help='fasta file path to genome name pair')
+ parser.add_argument('-f',
+ '--output-format',
+ default='json',
+ help='Output format (json, csv, pickle)')
+ parser.add_argument('-o',
+ '--output-prediction',
+ help='SISTR serovar prediction output path')
+ parser.add_argument('-M',
+ '--more-results',
+ action='count',
+ default=0,
+ help='Output more detailed results (-M) and all antigen search blastn results (-MM)')
+ parser.add_argument('-p',
+ '--cgmlst-profiles',
+ help='Output CSV file destination for cgMLST allelic profiles')
+ parser.add_argument('-n',
+ '--novel-alleles',
+ help='Output FASTA file destination of novel cgMLST alleles from input genomes')
+ parser.add_argument('-a',
+ '--alleles-output',
+ help='Output path of allele sequences and info to JSON')
+ parser.add_argument('-T',
+ '--tmp-dir',
+ default='/tmp',
+ help='Base temporary working directory for intermediate analysis files.')
+ parser.add_argument('-K',
+ '--keep-tmp',
+ action='store_true',
+ help='Keep temporary analysis files.')
+ parser.add_argument('--use-full-cgmlst-db',
+ action='store_true',
+ help='Use the full set of cgMLST alleles which can include highly similar alleles. By default the smaller "centroid" alleles or representative alleles are used for each marker. ')
+ parser.add_argument('--no-cgmlst',
+ action='store_true',
+ help='Do not run cgMLST serovar prediction')
+ parser.add_argument('-m', '--run-mash',
+ action='store_true',
+ help='Determine Mash MinHash genomic distances to Salmonella genomes with trusted serovar designations. Mash binary must be in accessible via $PATH (e.g. /usr/bin).')
+ parser.add_argument('--qc',
+ action='store_true',
+ help='Perform basic QC to provide level of confidence in serovar prediction results.')
+ parser.add_argument('-t', '--threads',
+ type=int,
+ default=1,
+ help='Number of parallel threads to run sistr_cmd analysis.')
+ parser.add_argument('-v',
+ '--verbose',
+ action='count',
+ default=0,
+ help='Logging verbosity level (-v == show warnings; -vvv == show debug info)')
+ parser.add_argument('-V', '--version', action='version', version='%(prog)s {}'.format(__version__))
+ return parser
+
+
+def run_mash(input_fasta):
+ from sistr.src.mash import mash_dist_trusted, mash_output_to_pandas_df, mash_subspeciation
+
+ mash_out = mash_dist_trusted(input_fasta)
+ df_mash = mash_output_to_pandas_df(mash_out)
+ df_mash_top_5 = df_mash[['ref', 'dist', 'n_match', 'serovar']].head(n=5)
+ logging.debug('Mash top 5 results:\n{}\n'.format(df_mash_top_5))
+ mash_spp_tuple = mash_subspeciation(df_mash)
+ spp = None
+ if mash_spp_tuple is not None:
+ spp, spp_dict, spp_counter = mash_spp_tuple
+ logging.info('Mash spp %s (dist=%s; counter=%s)', spp, spp_dict, spp_counter)
+
+ else:
+ logging.error('Could not perform Mash subspeciation!')
+
+ for idx, row in df_mash_top_5.iterrows():
+ mash_genome = row['ref']
+ mash_serovar = row['serovar']
+ mash_distance = row['dist']
+ mash_match = row['n_match']
+
+ log_msg = 'Top serovar by Mash: "{}" with dist={}, # matching sketches={}, matching genome={}'
+ logging.info(log_msg.format(mash_serovar, mash_distance, mash_match, mash_genome))
+
+ mash_result_dict = {
+ 'mash_genome': mash_genome,
+ 'mash_serovar': mash_serovar,
+ 'mash_distance': mash_distance,
+ 'mash_match': mash_match,
+ 'mash_subspecies': spp,
+ 'mash_top_5': df_mash_top_5.to_dict(),
+ }
+ return mash_result_dict
+
+
+def merge_mash_prediction(prediction, mash_prediction):
+ for k in mash_prediction:
+ prediction.__dict__[k] = mash_prediction[k]
+ return prediction
+
+
+def merge_cgmlst_prediction(serovar_prediction, cgmlst_prediction):
+ serovar_prediction.cgmlst_distance = cgmlst_prediction['distance']
+ serovar_prediction.cgmlst_genome_match = cgmlst_prediction['genome_match']
+ serovar_prediction.serovar_cgmlst = cgmlst_prediction['serovar']
+ serovar_prediction.cgmlst_matching_alleles = cgmlst_prediction['matching_alleles']
+ serovar_prediction.cgmlst_subspecies = cgmlst_prediction['subspecies']
+ serovar_prediction.cgmlst_ST = cgmlst_prediction['cgmlst330_ST']
+ return serovar_prediction
+
+
+def infer_o_antigen(prediction):
+ df_serovar = serovar_table()
+ predicted_serovars = prediction.serovar.split('|') if '|' in prediction.serovar else [prediction.serovar]
+ series_o_antigens = df_serovar.O_antigen[df_serovar.Serovar.isin(predicted_serovars)]
+ if series_o_antigens.size == 0:
+ sg = prediction.serogroup
+ if sg is None or sg == '' or sg == '-':
+ prediction.o_antigen = '-'
+ else:
+ series_o_antigens = df_serovar.O_antigen[df_serovar.Serogroup == sg]
+ counter_o_antigens = Counter(series_o_antigens)
+ prediction.o_antigen = counter_o_antigens.most_common(1)[0][0]
+ else:
+ counter_o_antigens = Counter(series_o_antigens)
+ prediction.o_antigen = counter_o_antigens.most_common(1)[0][0]
+
+
+def sistr_predict(input_fasta, genome_name, tmp_dir, keep_tmp, args):
+ blast_runner = None
+ try:
+ assert os.path.exists(input_fasta), "Input fasta file '%s' must exist!" % input_fasta
+ if genome_name is None or genome_name == '':
+ genome_name = genome_name_from_fasta_path(input_fasta)
+ dtnow = datetime.now()
+ genome_name_no_spaces = re.sub(r'\W', '_', genome_name)
+ genome_tmp_dir = os.path.join(tmp_dir, dtnow.strftime("%Y%m%d%H%M%S") + '-' + 'SISTR' + '-' + genome_name_no_spaces)
+ blast_runner = BlastRunner(input_fasta, genome_tmp_dir)
+ logging.info('Initializing temporary analysis directory "%s" and preparing for BLAST searching.', genome_tmp_dir)
+ blast_runner.prep_blast()
+ logging.info('Temporary FASTA file copied to %s', blast_runner.tmp_fasta_path)
+ spp = None
+ mash_prediction = None
+ if args.run_mash:
+ mash_prediction = run_mash(input_fasta)
+ spp = mash_prediction['mash_subspecies']
+
+ cgmlst_prediction = None
+ cgmlst_results = None
+ if not args.no_cgmlst:
+ cgmlst_prediction, cgmlst_results = run_cgmlst(blast_runner, full=args.use_full_cgmlst_db)
+ spp = cgmlst_prediction['subspecies']
+
+ serovar_predictor = SerovarPredictor(blast_runner, spp)
+ serovar_predictor.predict_serovar_from_antigen_blast()
+ prediction = serovar_predictor.get_serovar_prediction()
+ prediction.genome = genome_name
+ prediction.fasta_filepath = os.path.abspath(input_fasta)
+ if cgmlst_prediction:
+ merge_cgmlst_prediction(prediction, cgmlst_prediction)
+ if mash_prediction:
+ merge_mash_prediction(prediction, mash_prediction)
+ overall_serovar_call(prediction, serovar_predictor)
+ infer_o_antigen(prediction)
+ logging.info('%s | Antigen gene BLAST serovar prediction: "%s" serogroup=%s %s:%s:%s',
+ genome_name,
+ prediction.serovar_antigen,
+ prediction.serogroup,
+ prediction.o_antigen,
+ prediction.h1,
+ prediction.h2)
+ logging.info('%s | Subspecies prediction: %s',
+ genome_name,
+ spp)
+ logging.info('%s | Overall serovar prediction: %s',
+ genome_name,
+ prediction.serovar)
+ if args.qc:
+ qc_status, qc_msgs = qc(blast_runner.tmp_fasta_path, cgmlst_results, prediction)
+ prediction.qc_status = qc_status
+ prediction.qc_messages = ' | '.join(qc_msgs)
+ finally:
+ if not keep_tmp:
+ logging.info('Deleting temporary working directory at %s', blast_runner.tmp_work_dir)
+ blast_runner.cleanup()
+ else:
+ logging.info('Keeping temp dir at %s', blast_runner.tmp_work_dir)
+ return prediction, cgmlst_results
+
+
+def genome_name_from_fasta_path(fasta_path):
+ """Extract genome name from fasta filename
+
+ Get the filename without directory and remove the file extension.
+
+ Example:
+ With fasta file path ``/path/to/genome_1.fasta``::
+
+ fasta_path = '/path/to/genome_1.fasta'
+ genome_name = genome_name_from_fasta_path(fasta_path)
+ print(genome_name)
+ # => "genome_1"
+
+ Args:
+ fasta_path (str): fasta file path
+
+ Returns:
+ str: genome name
+ """
+ filename = os.path.basename(fasta_path)
+ return re.sub(r'(\.fa$)|(\.fas$)|(\.fasta$)|(\.fna$)|(\.\w{1,}$)', '', filename)
+
+
+def write_cgmlst_profiles(fastas, cgmlst_results, output_path):
+ genome_marker_cgmlst_result = {}
+ for genome, res in zip(fastas, cgmlst_results):
+ tmp = {}
+ for marker, res_dict in res.items():
+ aname = res_dict['name']
+ tmp[marker] = int(aname) if aname is not None else None
+ genome_marker_cgmlst_result[genome] = tmp
+ import pandas as pd
+ df = pd.DataFrame(genome_marker_cgmlst_result).transpose()
+ df.to_csv(output_path, float_format='%.0f')
+
+
+def write_cgmlst_results_json(input_fastas, cgmlst_results, output_path):
+ import json
+ with open(output_path, 'w') as fout:
+ json.dump({x:y for x,y in zip(input_fastas, cgmlst_results)}, fout)
+
+
+def write_novel_alleles(cgmlst_results, output_path):
+ count = 0
+ with open(output_path, 'w') as fout:
+ for x in cgmlst_results:
+ for marker, res in x.items():
+ name = res['name']
+ seq = res['seq']
+ br = res['blast_result']
+ if br is not None and isinstance(br, dict):
+ trunc = br['trunc']
+ if not trunc:
+ fout.write('>{}|{}\n{}\n'.format(marker, name, seq))
+ count += 1
+ return count
+
+
+def main():
+ parser = init_parser()
+ args = parser.parse_args()
+ init_console_logger(args.verbose)
+ logging.info('Running sistr_cmd {}'.format(__version__))
+ input_fastas = args.fastas
+ paths_names = args.input_fasta_genome_name
+ if len(input_fastas) == 0 and (paths_names is None or len(paths_names) == 0):
+ raise Exception('No FASTA files specified!')
+ if paths_names is None:
+ genome_names = [genome_name_from_fasta_path(x) for x in input_fastas]
+ else:
+ if len(input_fastas) == 0 and len(paths_names) > 0:
+ input_fastas = [x for x,y in paths_names]
+ genome_names = [y for x,y in paths_names]
+ elif len(input_fastas) > 0 and len(paths_names) > 0:
+ tmp = input_fastas
+ input_fastas = [x for x,y in paths_names] + tmp
+ genome_names = [y for x,y in paths_names] + [genome_name_from_fasta_path(x) for x in tmp]
+ else:
+ raise Exception('Unhandled fasta input args: input_fastas="{}" | input_fasta_genome_name="{}"'.format(
+ input_fastas,
+ paths_names))
+
+ tmp_dir = args.tmp_dir
+ keep_tmp = args.keep_tmp
+ output_format = args.output_format
+ output_path = args.output_prediction
+
+ n_threads = args.threads
+ if n_threads == 1:
+ logging.info('Serial single threaded run mode on %s genomes', len(input_fastas))
+ outputs = [sistr_predict(input_fasta, genome_name, tmp_dir, keep_tmp, args) for input_fasta, genome_name in zip(input_fastas, genome_names)]
+ else:
+ from multiprocessing import Pool
+ logging.info('Initializing thread pool with %s threads', n_threads)
+ pool = Pool(processes=n_threads)
+ logging.info('Running SISTR analysis asynchronously on %s genomes', len(input_fastas))
+ res = [pool.apply_async(sistr_predict, (input_fasta, genome_name, tmp_dir, keep_tmp, args)) for input_fasta, genome_name in zip(input_fastas, genome_names)]
+
+ logging.info('Getting SISTR analysis results')
+ outputs = [x.get() for x in res]
+
+ prediction_outputs = [x for x,y in outputs]
+ cgmlst_results = [y for x,y in outputs]
+
+ if output_path:
+ from sistr.src.writers import write
+ logging.info('Writing results with %s verbosity',
+ args.more_results)
+ write(output_path, output_format, prediction_outputs, more_results=args.more_results)
+ else:
+ import json
+ from sistr.src.writers import to_dict
+ logging.warning('No prediction results output file written! Writing results summary to stdout as JSON')
+ exclude_keys_in_output = {'blast_results', 'sseq'}
+ if args.more_results >= 2:
+ exclude_keys_in_output.remove('blast_results')
+ exclude_keys_in_output.remove('sseq')
+ elif args.more_results == 1:
+ exclude_keys_in_output.remove('sseq')
+ outs = [to_dict(x, 0, exclude_keys=exclude_keys_in_output) for x in prediction_outputs]
+ print(json.dumps(outs))
+ if args.cgmlst_profiles:
+ write_cgmlst_profiles(genome_names, cgmlst_results, args.cgmlst_profiles)
+ logging.info('cgMLST allelic profiles written to %s', args.cgmlst_profiles)
+ if args.alleles_output:
+ write_cgmlst_results_json(genome_names, cgmlst_results, args.alleles_output)
+ logging.info('JSON of allele data written to %s for %s cgMLST allele results', args.alleles_output, len(cgmlst_results))
+ if args.novel_alleles:
+ count = write_novel_alleles(cgmlst_results, args.novel_alleles)
+ logging.info('Wrote %s alleles to %s', count, args.novel_alleles)
+
+
+if __name__ == '__main__':
+ main()
diff --git a/sistr/src/__init__.py b/sistr/src/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/sistr/src/blast_wrapper/__init__.py b/sistr/src/blast_wrapper/__init__.py
new file mode 100644
index 0000000..871dcc3
--- /dev/null
+++ b/sistr/src/blast_wrapper/__init__.py
@@ -0,0 +1,309 @@
+from datetime import datetime
+import logging
+import shutil
+
+from subprocess import Popen, PIPE
+import os
+import pandas as pd
+import numpy as np
+from pandas.io.common import EmptyDataError
+import re
+
+
+BLAST_TABLE_COLS = '''
+qseqid
+stitle
+pident
+length
+mismatch
+gapopen
+qstart
+qend
+sstart
+send
+evalue
+bitscore
+qlen
+slen
+sseq
+'''.strip().split('\n')
+
+
+class BlastRunner:
+ blast_db_created = False
+
+ def __init__(self, fasta_path, tmp_work_dir):
+ self.tmp_work_dir = tmp_work_dir
+ self.fasta_path = fasta_path
+
+
+ def _create_tmp_folder(self):
+ count = 1
+ tmp_dir = self.tmp_work_dir
+ while True:
+ try:
+ logging.info('Trying to create analysis directory at: %s', tmp_dir)
+ os.makedirs(tmp_dir)
+ break
+ except OSError as e:
+ logging.warning('Error on creation of tmp analysis directory "{}"! {}'.format(
+ tmp_dir,
+ e
+ ))
+
+ tmp_dir = '{}_{}'.format(self.tmp_work_dir, count)
+ count += 1
+
+ self.tmp_work_dir = tmp_dir
+ return self.tmp_work_dir
+
+ def _copy_fasta_to_work_dir(self):
+ filename = os.path.basename(self.fasta_path)
+ filename_no_spaces = re.sub(r'\W', '_', filename)
+ dest_path = os.path.join(self.tmp_work_dir, filename_no_spaces)
+ if self.fasta_path == dest_path:
+ self.tmp_fasta_path = dest_path
+ return dest_path
+ shutil.copyfile(self.fasta_path, dest_path)
+ self.tmp_fasta_path = dest_path
+ return dest_path
+
+ def _run_makeblastdb(self):
+ work_dir = os.path.dirname(self.tmp_fasta_path)
+ filename = os.path.basename(self.tmp_fasta_path)
+ nin_filepath = os.path.join(work_dir, filename + '.nin')
+ if os.path.exists(nin_filepath):
+ self.blast_db_created = True
+ return self.tmp_fasta_path
+
+ p = Popen(['makeblastdb',
+ '-in', '{}'.format(self.tmp_fasta_path),
+ '-dbtype', 'nucl'],
+ stdout=PIPE,
+ stderr=PIPE)
+ p.wait()
+ stdout = p.stdout.read()
+ stderr = p.stderr.read()
+ if stdout is not None and stdout != '':
+ logging.debug('makeblastdb on {0} STDOUT: {1}'.format(self.tmp_fasta_path, stdout))
+ if stderr is not None and stderr != '':
+ logging.debug('makeblastdb on {0} STDERR: {1}'.format(self.tmp_fasta_path, stderr))
+
+ if os.path.exists(nin_filepath):
+ self.blast_db_created = True
+ return self.tmp_fasta_path
+ else:
+ ex_msg = 'makeblastdb was not able to create a BLAST DB for {0}. STDERR: {1}'.format(filename, stderr)
+ logging.error(ex_msg)
+ raise Exception(ex_msg)
+
+ def blast_against_query(self, query_fasta_path, blast_task='megablast', evalue=1e-20, min_pid=85):
+
+ if not self.blast_db_created:
+ self.prep_blast()
+
+ gene_filename = os.path.basename(query_fasta_path)
+ genome_filename = os.path.basename(self.tmp_fasta_path)
+ timestamp = '{:%Y%b%d_%H_%M_%S}'.format(datetime.now())
+ outfile = os.path.join(self.tmp_work_dir, '{}-{}-{}.blast'.format(gene_filename,
+ genome_filename,
+ timestamp))
+ p = Popen(['blastn',
+ '-task', blast_task,
+ '-query', query_fasta_path,
+ '-db', '{}'.format(self.tmp_fasta_path),
+ '-evalue', '{}'.format(evalue),
+ '-dust', 'no',
+ '-perc_identity', '{}'.format(min_pid),
+ '-out', outfile,
+ '-outfmt', '6 {}'.format(' '.join(BLAST_TABLE_COLS))],
+ stdout=PIPE,
+ stderr=PIPE)
+
+ p.wait()
+
+ stdout = p.stdout.read()
+ stderr = p.stderr.read()
+ if stdout is not None and stdout != '':
+ logging.debug('blastn on db {} and query {} STDOUT: {}'.format(genome_filename, gene_filename, stdout))
+ if stderr is not None and stderr != '':
+ logging.debug('blastn on db {} and query {} STDERR: {}'.format(genome_filename, gene_filename, stderr))
+
+ if os.path.exists(outfile):
+ return outfile
+ else:
+ ex_msg = 'blastn on db {} and query {} did not produce expected output file at {}'.format(genome_filename,
+ gene_filename,
+ outfile)
+ logging.error(ex_msg)
+ raise Exception(ex_msg)
+
+ def cleanup(self):
+ self.blast_db_created = False
+ shutil.rmtree(self.tmp_work_dir)
+
+ def prep_blast(self):
+ self._create_tmp_folder()
+ self._copy_fasta_to_work_dir()
+ self._run_makeblastdb()
+
+ def run_blast(self, query_fasta_path):
+ self.prep_blast()
+ blast_outfile = self.blast_against_query(query_fasta_path)
+ return blast_outfile
+
+
+class BlastReader:
+ is_missing = True
+ is_perfect_match = False
+ is_trunc = False
+ df = None
+
+
+ def __init__(self, blast_outfile):
+ """Read BLASTN output file into a pandas DataFrame
+ Sort the DataFrame by BLAST bitscore.
+ If there are no BLASTN results, then no results can be returned.
+
+ Args:
+ blast_outfile (str): `blastn` output file path
+
+ Raises:
+ EmptyDataError: No data could be parsed from the `blastn` output file
+ """
+ self.blast_outfile = blast_outfile
+ try:
+ self.df = pd.read_table(self.blast_outfile, header=None)
+ self.df.columns = BLAST_TABLE_COLS
+ # calculate the coverage for when results need to be validated
+ self.df.loc[:, 'coverage'] = self.df.length / self.df.qlen
+ self.df.sort_values(by='bitscore', ascending=False, inplace=True)
+ self.df.loc[:, 'is_trunc'] = BlastReader.trunc(qstart=self.df.qstart,
+ qend=self.df.qend,
+ qlen=self.df.qlen,
+ sstart=self.df.sstart,
+ send=self.df.send,
+ slen=self.df.slen)
+
+ logging.debug(self.df.head())
+ self.is_missing = False
+ except EmptyDataError as exc:
+ logging.warning('No BLASTN results to parse from file %s', blast_outfile)
+ self.is_missing = True
+
+
+ def df_dict(self):
+ if not self.is_missing:
+ return self.df.to_dict()
+
+ @staticmethod
+ def df_first_row_to_dict(df):
+ """First DataFrame row to list of dict
+
+ Args:
+ df (pandas.DataFrame): A DataFrame with at least one row
+
+ Returns:
+ A list of dict that looks like:
+
+ [{'C1': 'x'}, {'C2': 'y'}, {'C3': 'z'}]
+
+ from a DataFrame that looks like:
+
+ C1 C2 C3
+ 1 x y z
+
+ Else if `df` is `None`, returns `None`
+ """
+ if df is not None:
+ return [dict(r) for i, r in df.head(1).iterrows()][0]
+
+ @staticmethod
+ def is_blast_result_trunc(qstart, qend, sstart, send, qlen, slen):
+ """Check if a query sequence is truncated by the end of a subject sequence
+
+ Args:
+ qstart (int): Query sequence start index
+ qend (int): Query sequence end index
+ sstart (int): Subject sequence start index
+ send (int): Subject sequence end index
+ qlen (int): Query sequence length
+ slen (int): Subject sequence length
+
+ Returns:
+ bool: Result truncated by subject sequence end?
+ """
+ q_match_len = abs(qstart - qend) + 1
+ s_max = max(sstart, send)
+ s_min = min(sstart, send)
+ return (q_match_len < qlen) and (s_max >= slen or s_min <= 1)
+
+ @staticmethod
+ def trunc(qstart, qend, sstart, send, qlen, slen):
+ """Check if a query sequence is truncated by the end of a subject sequence
+
+ Args:
+ qstart (int pandas.Series): Query sequence start index
+ qend (int pandas.Series): Query sequence end index
+ sstart (int pandas.Series): Subject sequence start index
+ send (int pandas.Series): Subject sequence end index
+ qlen (int pandas.Series): Query sequence length
+ slen (int pandas.Series): Subject sequence length
+
+ Returns:
+ Boolean pandas.Series: Result truncated by subject sequence end?
+ """
+ ssum2 = (send + sstart) / 2.0
+ sabs2 = np.abs(send - sstart) / 2.0
+ smax = ssum2 + sabs2
+ smin = ssum2 - sabs2
+ q_match_len = np.abs(qstart - qend) + 1
+ return (q_match_len < qlen) & ((smax >= slen) | (smin <= 1))
+
+
+ def perfect_matches(self):
+ """
+ Return pandas DataFrame with perfect BLAST matches (100% identity and coverage)
+
+ Returns:
+ pandas.DataFrame or None: DataFrame of perfect BLAST matches or None if no perfect matches exist
+ """
+ if self.is_missing:
+ return None
+
+ df_perfect_matches = self.df[(self.df['coverage'] == 1.0) & (self.df['pident'] == 100.0)]
+ if df_perfect_matches.shape[0] == 0:
+ return None
+ return df_perfect_matches
+
+
+
+ def top_result(self):
+ """Return top `blastn` result
+ Try to find a 100% identity and coverage result (perfect match).
+ If one does not exist, then retrieve the result with the highest bitscore.
+
+ Returns:
+ Ordered dict of BLASTN results or None if no BLASTN results generated
+ """
+
+ if self.is_missing:
+ return None
+
+ df_perfect_matches = self.df[(self.df['coverage'] == 1.0) & (self.df['pident'] == 100.0)]
+ if df_perfect_matches.shape[0]:
+ self.is_perfect_match = True
+ return BlastReader.df_first_row_to_dict(df_perfect_matches)
+
+ # Return the result with the highest bitscore.
+ # This is the first result in dataframe since the df is ordered by
+ # bitscore in descending order.
+ result_dict = BlastReader.df_first_row_to_dict(self.df)
+ result_trunc = BlastReader.is_blast_result_trunc(qstart=result_dict['qstart'],
+ qend=result_dict['qend'],
+ sstart=result_dict['sstart'],
+ send=result_dict['send'],
+ qlen=result_dict['qlen'],
+ slen=result_dict['slen'])
+ self.is_trunc = result_trunc
+ return result_dict
\ No newline at end of file
diff --git a/sistr/src/blast_wrapper/helpers.py b/sistr/src/blast_wrapper/helpers.py
new file mode 100644
index 0000000..ac5d258
--- /dev/null
+++ b/sistr/src/blast_wrapper/helpers.py
@@ -0,0 +1,51 @@
+import numpy as np
+
+
+NT_SUB = {x:y for x,y in zip('acgtrymkswhbvdnxACGTRYMKSWHBVDNX', 'tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX')}
+
+
+revcomp = lambda s: ''.join([NT_SUB[c] for c in s[::-1]])
+
+
+def extend_subj_match_vec(df):
+ """
+ Get the extended clipped (clamped) start and end subject sequence indices
+
+ Also get whether each match needs to be reverse complemented and whether each extended match would be truncated by
+ the end of the subject sequence.
+
+ Args:
+ df (pandas.DataFrame): blastn results dataframe
+
+ Returns:
+ int pandas.Series: extended and clipped start indices
+ int pandas.Series: extended and clipped end indices
+ bool pandas.Series: does extracted seq need to be reverse complemented?
+ bool pandas.Series: would the extended seq be truncated by the ends of the subject sequence?
+ bool pandas.Series: was the subject seq extended?
+ """
+ needs_revcomp = df.sstart > df.send
+ add_to_end = df.qlen - df.qend
+ add_to_start = df.qstart - 1
+ ssum2 = (df.send + df.sstart) / 2.0
+ sabs2 = np.abs(df.send - df.sstart) / 2.0
+ end_idx = ssum2 + sabs2 - 1
+ start_idx = ssum2 - sabs2 - 1
+ start_idx[needs_revcomp] -= add_to_end
+ start_idx[~needs_revcomp] -= add_to_start
+ end_idx[needs_revcomp] += add_to_start
+ end_idx[~needs_revcomp] += add_to_end
+ clipped_start_idx = np.clip(start_idx, 0, (df.slen - 1))
+ clipped_end_idx = np.clip(end_idx, 0, (df.slen - 1))
+ trunc = (clipped_start_idx != start_idx) | (clipped_end_idx != end_idx)
+ is_extended = (add_to_start > 0) | (add_to_end > 0)
+ return clipped_start_idx, clipped_end_idx, needs_revcomp, trunc, is_extended
+
+
+def retrieve_seq(seq, start, end, needs_revcomp):
+ start = int(start)
+ end = int(end)
+ out_seq = seq[start:(end + 1)]
+ if needs_revcomp:
+ out_seq = revcomp(out_seq)
+ return out_seq
diff --git a/sistr/src/cgmlst/__init__.py b/sistr/src/cgmlst/__init__.py
new file mode 100644
index 0000000..2ec4dfc
--- /dev/null
+++ b/sistr/src/cgmlst/__init__.py
@@ -0,0 +1,413 @@
+from pkg_resources import resource_filename
+import logging
+import zlib
+from collections import Counter, defaultdict
+import numpy as np
+import pandas as pd
+from sistr.src.blast_wrapper import BlastReader
+from sistr.src.blast_wrapper.helpers import extend_subj_match_vec, retrieve_seq
+from sistr.src.cgmlst.msa import msa_ref_vs_novel, number_gapped_ungapped, MSA_GAP_PROP_THRESHOLD
+from sistr.src.parsers import parse_fasta
+from sistr.src.serovar_prediction.constants import CGMLST_SUBSPECIATION_DISTANCE_THRESHOLD, genomes_to_subspecies
+
+
+CGMLST_CENTROID_FASTA_PATH = resource_filename('sistr', 'data/cgmlst/cgmlst-centroid.fasta')
+CGMLST_FULL_FASTA_PATH = resource_filename('sistr', 'data/cgmlst/cgmlst-full.fasta')
+CGMLST_PROFILES_PATH = resource_filename('sistr', 'data/cgmlst/cgmlst-profiles.hdf')
+BLASTN_PIDENT_THRESHOLD = 90.0
+
+
+def allele_name(seq):
+ """CRC32 unsigned integer from allele nucleotide sequence.
+ The "& 0xffffffff" is used to generate an unsigned integer and
+ will generate the same number for both Python 2 and 3
+ (https://docs.python.org/2/library/zlib.html#zlib.crc32).
+
+ Args:
+ seq (str): nucleotide string
+
+ Returns:
+ int: CRC32 checksum as unsigned 32bit integer
+ """
+ seq = str(seq).encode()
+ return zlib.crc32(seq) & 0xffffffff
+
+
+def ref_cgmlst_profiles():
+ return pd.read_hdf(CGMLST_PROFILES_PATH, key='cgmlst')
+
+
+def process_cgmlst_results(df):
+ """Append informative fields to cgMLST330 BLAST results DataFrame
+
+ The `qseqid` column must contain cgMLST330 query IDs with `{marker name}|{allele number}` format.
+ The `qseqid` parsed allele numbers and marker names are appended as new fields.
+
+ `is_perfect` column contains boolean values for whether an allele result is 100% identity and coverage.
+ `has_perfect_match` denotes if a cgMLST330 marker has a perfect allele match.
+ The top result with the largest bitscore for a marker with no perfect match is used to retrieve the allele present
+ at that marker locus.
+
+ Args:
+ df (pandas.DataFrame): DataFrame of cgMLST330 BLAST results
+
+ Returns:
+ pandas.DataFrame: cgMLST330 BLAST results DataFrame with extra fields (`marker`, `allele`, `is_perfect`, `has_perfect_match`)
+ """
+ assert isinstance(df, pd.DataFrame)
+ markers = []
+ alleles = []
+ for x in df['qseqid']:
+ marker, allele = x.split('|')
+ markers.append(marker)
+ alleles.append(int(allele))
+ df.loc[:, 'marker'] = markers
+ df.loc[:, 'allele'] = alleles
+ df.loc[:, 'is_match'] = (df['coverage'] >= 1.0) & (df['pident'] >= 90.0) & ~(df['is_trunc'])
+ df.loc[:, 'allele_name'] = df.apply(lambda x: allele_name(x.sseq.replace('-', '')), axis=1)
+ df.loc[:, 'is_perfect'] = (df['coverage'] == 1.0) & (df['pident'] == 100.0)
+ df_perf = df[df['is_perfect']]
+ perf_markers = df_perf['marker'].unique()
+ df.loc[:, 'has_perfect_match'] = df['marker'].isin(perf_markers)
+ start_idxs, end_idxs, needs_revcomps, trunc, is_extended = extend_subj_match_vec(df)
+ df.loc[:, 'start_idx'] = start_idxs
+ df.loc[:, 'end_idx'] = end_idxs
+ df.loc[:, 'needs_revcomp'] = needs_revcomps
+ df.loc[:, 'trunc'] = trunc
+ df.loc[:, 'is_extended'] = is_extended
+ df.loc[:, 'sseq_msa_gaps'] = np.zeros(df.shape[0], dtype=np.int64)
+ df.loc[:, 'sseq_msa_p_gaps'] = np.zeros(df.shape[0], dtype=np.float64)
+ df.loc[:, 'too_many_gaps'] = trunc
+
+ return df
+
+
+def alleles_to_retrieve(df):
+ """Alleles to retrieve from genome fasta
+
+ Get a dict of the genome fasta contig title to a list of blastn results of the allele sequences that must be
+ retrieved from the genome contig.
+
+ Args:
+ df (pandas.DataFrame): blastn results dataframe
+
+ Returns:
+ {str:[pandas.Series]}: dict of contig title (header name) to list of top blastn result records for each marker
+ for which the allele sequence must be retrieved from the original sequence.
+ """
+ contig_blastn_records = defaultdict(list)
+ markers = df.marker.unique()
+ for m in markers:
+ dfsub = df[df.marker == m]
+ for i, r in dfsub.iterrows():
+ if r.coverage < 1.0:
+ contig_blastn_records[r.stitle].append(r)
+ break
+ return contig_blastn_records
+
+
+def allele_result_dict(name, seq, blast_result):
+ return {'name': name,
+ 'seq': seq,
+ 'blast_result': blast_result, }
+
+
+def get_allele_sequences(genome_fasta_path, contig_blastn_records, full=False):
+ cgmlst_fasta_path = CGMLST_CENTROID_FASTA_PATH if not full else CGMLST_FULL_FASTA_PATH
+ out = {}
+ for header, seq in parse_fasta(genome_fasta_path):
+ if header in contig_blastn_records:
+ for r in contig_blastn_records[header]:
+ start_idx = r['start_idx']
+ end_idx = r['end_idx']
+ needs_revcomp = r['needs_revcomp']
+ logging.debug('seq len {}| start {}| end {}| revcomp? {}'.format(len(seq), start_idx, end_idx, needs_revcomp))
+ allele_seq = retrieve_seq(seq, start_idx, end_idx, needs_revcomp)
+ ref_seqid = r['qseqid']
+ ref_seq = None
+ for h, s in parse_fasta(cgmlst_fasta_path):
+ if h == ref_seqid:
+ ref_seq = s
+ break
+ if ref_seq is None:
+ raise Exception('Could not retrieve allele %s from %s', ref_seqid, cgmlst_fasta_path)
+ msa_ref, msa_novel = msa_ref_vs_novel(ref_seq, allele_seq)
+ # if there are gaps at the start or end of the ref allele MSA then trim those from both MSAs
+ trim_left = 0
+ while (msa_ref[trim_left] == '-'):
+ trim_left += 1
+ trim_right = len(msa_ref)
+ while (msa_ref[trim_right - 1] == '-'):
+ trim_right -= 1
+
+ trimmed_msa_ref = msa_ref[trim_left:trim_right]
+ trimmed_msa_novel = msa_novel[trim_left:trim_right]
+ logging.debug(msa_ref)
+ logging.debug(msa_novel)
+ logging.debug('%s:%s', trim_left, trim_right)
+ logging.debug(trimmed_msa_ref)
+ logging.debug(trimmed_msa_novel)
+ gapped, ungapped = number_gapped_ungapped(trimmed_msa_ref, trimmed_msa_novel)
+ p_gapped = gapped / float((gapped + ungapped))
+ r['qseq_msa'] = msa_ref
+ r['qseq_msa_trimmed'] = trimmed_msa_ref
+ r['sseq_msa'] = msa_novel
+ r['sseq_msa_trimmed'] = trimmed_msa_novel
+ r['sseq_msa_gaps'] = gapped
+ r['sseq_msa_p_gaps'] = p_gapped
+ # if there are too many gaps within the trimmed extracted allele seq then result is equivalent
+ # to missing or contig trunc
+ if p_gapped > MSA_GAP_PROP_THRESHOLD:
+ logging.error('Too many gapped sites in extracted allele seq for marker %s contained %s gaps out of %s bp (%s > %s); stitle: %s',
+ r['marker'],
+ gapped,
+ (gapped + ungapped),
+ p_gapped,
+ MSA_GAP_PROP_THRESHOLD,
+ r['stitle'])
+ r['too_many_gaps'] = True
+ out[r.marker] = allele_result_dict(None, None, r.to_dict())
+ continue
+ # otherwise if there are an acceptable number of gaps then remove gap characters and uppercase
+ # Mafft MSA extracted and trimmed seq
+ allele_seq = trimmed_msa_novel.replace('-', '').upper()
+ new_allele_name = allele_name(allele_seq)
+ logging.info('Marker %s | Recovered novel allele with gaps (n=%s) of length %s vs length %s for ref allele %s. Novel allele name=%s',
+ r['marker'],
+ gapped,
+ len(allele_seq),
+ r['qlen'],
+ r['qseqid'],
+ new_allele_name)
+ out[r.marker] = allele_result_dict(new_allele_name, allele_seq, r.to_dict())
+ return out
+
+
+def matches_to_marker_results(df):
+ """Perfect BLAST matches to marker results dict
+
+ Parse perfect BLAST matches to marker results dict.
+
+
+ Args:
+ df (pandas.DataFrame): DataFrame of perfect BLAST matches
+
+ Returns:
+ dict: cgMLST330 marker names to matching allele numbers
+ """
+ assert isinstance(df, pd.DataFrame)
+ from collections import defaultdict
+ d = defaultdict(list)
+ for idx, row in df.iterrows():
+ marker = row['marker']
+ d[marker].append(row)
+
+ marker_results = {}
+ for k,v in d.items():
+ if len(v) > 1:
+ logging.debug('Multiple potential cgMLST allele matches (n=%s) found for marker %s. Selecting match on longest contig.', len(v), k)
+ df_marker = pd.DataFrame(v)
+ df_marker.sort_values('slen', ascending=False, inplace=True)
+ for i,r in df_marker.iterrows():
+ allele = r['allele_name']
+ slen = r['slen']
+ logging.debug('Selecting allele %s from contig with length %s', allele, slen)
+ seq = r['sseq']
+ if '-' in seq:
+ logging.warning('Gaps found in allele. Removing gaps. %s', r)
+ seq = seq.replace('-', '').upper()
+ allele = allele_name(seq)
+ marker_results[k] = allele_result_dict(allele, seq, r.to_dict())
+ break
+ elif len(v) == 1:
+ row = v[0]
+ seq = row['sseq']
+ if '-' in seq:
+ logging.warning('Gaps found in allele. Removing gaps. %s', row)
+ seq = seq.replace('-', '').upper()
+ allele = allele_name(seq)
+ marker_results[k] = allele_result_dict(allele, seq, row.to_dict())
+ else:
+ err_msg = 'Empty list of matches for marker {}'.format(k)
+ logging.error(err_msg)
+ raise Exception(err_msg)
+ return marker_results
+
+
+def find_closest_related_genome(marker_results, df_genome_profiles):
+ """
+
+ Args:
+ df_genome_profiles (pandas.DataFrame):
+
+ Returns:
+ (dict, list): Most closely related Genome and list of other related Genomes_ in order of relatedness
+ """
+ marker_names = df_genome_profiles.columns
+ n_markers = len(marker_names)
+
+ profile = [marker_results[marker_name] if marker_name in marker_results else None for marker_name in marker_names]
+ genome_profile = np.array(profile, dtype=np.float64)
+ profiles_matrix = np.array(df_genome_profiles, dtype=np.float64)
+ genome_profile_similarity_counts = np.apply_along_axis(lambda x: (x == genome_profile).sum(), 1, profiles_matrix)
+
+ df_relatives = pd.DataFrame()
+ df_relatives['matching'] = genome_profile_similarity_counts
+ df_relatives['distance'] = 1.0 - (df_relatives['matching'] / float(n_markers))
+ df_relatives.index = df_genome_profiles.index
+ df_relatives.sort_values(by='distance', inplace=True)
+ return df_relatives
+
+
+def cgmlst_subspecies_call(df_relatives):
+ """Call Salmonella subspecies based on cgMLST results
+
+ This method attempts to find the majority subspecies type within curated
+ public genomes above a cgMLST allelic profile distance threshold.
+
+ Note:
+ ``CGMLST_SUBSPECIATION_DISTANCE_THRESHOLD`` is the cgMLST distance
+ threshold used to determine the subspecies by cgMLST. It is set at a
+ distance of 0.9 which translates to a cgMLST allelic similarity of 10%.
+ A threshold of 0.9 is generous and reasonable given the congruence
+ between subspecies designations and 10% cgMLST clusters by Adjusted
+ Rand (~0.850) and Adjusted Wallace metrics (~0.850 both ways).
+
+ Args:
+ df_relatives (pandas.DataFrame): Table of genomes related by cgMLST to input genome
+
+ Returns:
+ None: if no curated public genomes found to have a cgMLST profile similarity of 10% or greater
+ (string, float, dict): most common subspecies, closest related public genome distance, subspecies frequencies
+ """
+
+ closest_distance = df_relatives['distance'].min()
+
+ if closest_distance > CGMLST_SUBSPECIATION_DISTANCE_THRESHOLD:
+ logging.warning('Min cgMLST distance (%s) above subspeciation distance threshold (%s)',
+ closest_distance,
+ CGMLST_SUBSPECIATION_DISTANCE_THRESHOLD)
+ return None
+ else:
+ df_relatives = df_relatives.loc[df_relatives.distance <= CGMLST_SUBSPECIATION_DISTANCE_THRESHOLD, :]
+ df_relatives = df_relatives.sort_values('distance', ascending=True)
+ logging.debug('df_relatives by cgmlst %s', df_relatives.head())
+ genome_spp = genomes_to_subspecies()
+ subspecies_below_threshold = [genome_spp[member_genome] if member_genome in genome_spp else None for member_genome in df_relatives.index]
+ subspecies_below_threshold = filter(None, subspecies_below_threshold)
+ subspecies_counter = Counter(subspecies_below_threshold)
+ logging.debug('Subspecies counter: %s', subspecies_counter)
+ return (subspecies_counter.most_common(1)[0][0], closest_distance, dict(subspecies_counter))
+
+
+def run_cgmlst(blast_runner, full=False):
+ """Perform in silico cgMLST on an input genome
+
+ Args:
+ blast_runner (sistr.src.blast_wrapper.BlastRunner): blastn runner object with genome fasta initialized
+
+ Returns:
+ dict: cgMLST ref genome match, distance to closest ref genome, subspecies and serovar predictions
+ dict: marker allele match results (seq, allele name, blastn results)
+ """
+ from sistr.src.serovar_prediction.constants import genomes_to_serovar
+
+ df_cgmlst_profiles = ref_cgmlst_profiles()
+
+ logging.debug('{} distinct cgMLST330 profiles'.format(df_cgmlst_profiles.shape[0]))
+
+ logging.info('Running BLAST on serovar predictive cgMLST330 alleles')
+ cgmlst_fasta_path = CGMLST_CENTROID_FASTA_PATH if not full else CGMLST_FULL_FASTA_PATH
+ blast_outfile = blast_runner.blast_against_query(cgmlst_fasta_path)
+ logging.info('Reading BLAST output file "{}"'.format(blast_outfile))
+ blast_reader = BlastReader(blast_outfile)
+ if blast_reader.df is None:
+ logging.error('No cgMLST330 alleles found!')
+ return ({'distance': 1.0,
+ 'genome_match': None,
+ 'serovar': None,
+ 'matching_alleles': 0,
+ 'subspecies': None,
+ 'cgmlst330_ST': None,},
+ {}, )
+ logging.info('Found {} cgMLST330 allele BLAST results'.format(blast_reader.df.shape[0]))
+
+
+ df_cgmlst_blastn = process_cgmlst_results(blast_reader.df)
+
+ marker_match_results = matches_to_marker_results(df_cgmlst_blastn[df_cgmlst_blastn.is_match])
+ contig_blastn_records = alleles_to_retrieve(df_cgmlst_blastn)
+ retrieved_marker_alleles = get_allele_sequences(blast_runner.fasta_path,
+ contig_blastn_records,
+ full=full)
+ logging.info('Type retrieved_marker_alleles %s', type(retrieved_marker_alleles))
+ all_marker_results = marker_match_results.copy()
+ for marker, res in retrieved_marker_alleles.items():
+ all_marker_results[marker] = res
+ for marker in df_cgmlst_profiles.columns:
+ if marker not in all_marker_results:
+ all_marker_results[marker] = {'blast_result': None,
+ 'name': None,
+ 'seq': None,}
+ cgmlst_results = {}
+ for marker, res in all_marker_results.items():
+ try:
+ cgmlst_results[marker] = int(res['name'])
+ except:
+ logging.error('Missing cgmlst_results for %s', marker)
+ logging.debug(res)
+
+ logging.info('Calculating number of matching alleles to serovar predictive cgMLST330 profiles')
+ df_relatives = find_closest_related_genome(cgmlst_results, df_cgmlst_profiles)
+ genome_serovar_dict = genomes_to_serovar()
+ df_relatives['serovar'] = [genome_serovar_dict[genome] for genome in df_relatives.index]
+ logging.debug('Top 5 serovar predictive cgMLST profiles:\n{}'.format(df_relatives.head()))
+ spp = None
+ subspeciation_tuple = cgmlst_subspecies_call(df_relatives)
+ if subspeciation_tuple is not None:
+ spp, distance, spp_counter = subspeciation_tuple
+ logging.info('Top subspecies by cgMLST is "{}" (min dist={}, Counter={})'.format(spp, distance, spp_counter))
+ else:
+ logging.warning('Subspeciation by cgMLST was not possible!')
+
+ cgmlst_serovar = None
+ cgmlst_matching_genome = None
+ cgmlst_matching_alleles = 0
+ cgmlst_distance = 1.0
+ for idx, row in df_relatives.iterrows():
+ cgmlst_distance = row['distance']
+ cgmlst_matching_alleles = row['matching']
+ cgmlst_serovar = row['serovar'] if cgmlst_distance <= 1.0 else None
+ cgmlst_matching_genome = idx if cgmlst_distance <= 1.0 else None
+ logging.info('Top serovar by cgMLST profile matching: "{}" with {} matching alleles, distance={:.1%}'.format(
+ cgmlst_serovar,
+ cgmlst_matching_alleles,
+ cgmlst_distance
+ ))
+ break
+
+ cgmlst_st = None
+ cgmlst_markers_sorted = sorted(all_marker_results.keys())
+ cgmlst_allele_names = []
+ marker = None
+ for marker in cgmlst_markers_sorted:
+ try:
+ aname = all_marker_results[marker]['name']
+ if aname:
+ cgmlst_allele_names.append(str(aname))
+ else:
+ break
+ except:
+ break
+ if len(cgmlst_allele_names) == len(cgmlst_markers_sorted):
+ cgmlst_st = allele_name('-'.join(cgmlst_allele_names))
+ logging.info('cgMLST330 Sequence Type=%s', cgmlst_st)
+ else:
+ logging.warning('Could not compute cgMLST330 Sequence Type due to missing data (marker %s)', marker)
+ return ({'distance': cgmlst_distance,
+ 'genome_match': cgmlst_matching_genome,
+ 'serovar': cgmlst_serovar,
+ 'matching_alleles': cgmlst_matching_alleles,
+ 'subspecies': spp,
+ 'cgmlst330_ST': cgmlst_st,},
+ all_marker_results, )
diff --git a/sistr/src/cgmlst/extras/__init__.py b/sistr/src/cgmlst/extras/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/sistr/src/cgmlst/extras/centroid_cgmlst_alleles.py b/sistr/src/cgmlst/extras/centroid_cgmlst_alleles.py
new file mode 100644
index 0000000..98e298b
--- /dev/null
+++ b/sistr/src/cgmlst/extras/centroid_cgmlst_alleles.py
@@ -0,0 +1,169 @@
+import zlib
+from collections import defaultdict
+import numpy as np
+from scipy.spatial.distance import pdist, squareform
+from scipy.cluster.hierarchy import fcluster, linkage
+
+
+NT_TO_INT = {'A':1,'C':2,'G':3,'T':4}
+INT_TO_NT = {1:'A',2:'C',3:'G',4:'T'}
+
+
+def group_alleles_by_size(alleles):
+ allele_size_seqs = defaultdict(list)
+ for allele in alleles:
+ allele_size_seqs[len(allele)].append(allele)
+ return allele_size_seqs
+
+
+def seq_int_arr(seqs):
+ """Convert list of ACGT strings to matix of 1-4 ints
+
+ Args:
+ seqs (list of str): nucleotide sequences with only 'ACGT' characters
+
+ Returns:
+ numpy.array of int: matrix of integers from 1 to 4 inclusive representing A, C, G, and T
+ str: nucleotide sequence string
+ """
+ return np.array([[NT_TO_INT[c] for c in x.upper()] for x in seqs])
+
+
+def group_alleles_by_start_end_Xbp(arr, bp=28):
+ """Group alleles by matching ends
+
+ Args:
+ arr (numpy.array): 2D int matrix of alleles
+ bp (int): length of ends to group by
+
+ Returns:
+ dict of lists: key of start + end strings to list of indices of alleles with matching ends
+ """
+ starts = arr[:,0:bp]
+ ends = arr[:,-bp:]
+ starts_ends_idxs = defaultdict(list)
+ l, seq_len = arr.shape
+ for i in range(l):
+ start_i = starts[i]
+ end_i = ends[i]
+ start_i_str = ''.join([str(x) for x in start_i])
+ end_i_str = ''.join([str(x) for x in end_i])
+ starts_ends_idxs[start_i_str + end_i_str].append(i)
+ return starts_ends_idxs
+
+
+def allele_clusters(dists, t=0.025):
+ """Flat clusters from distance matrix
+
+ Args:
+ dists (numpy.array): pdist distance matrix
+ t (float): fcluster (tree cutting) distance threshold
+
+ Returns:
+ dict of lists: cluster number to list of indices of distances in cluster
+ """
+ clusters = fcluster(linkage(dists), 0.025, criterion='distance')
+ cluster_idx = defaultdict(list)
+ for idx, cl in enumerate(clusters):
+ cluster_idx[cl].append(idx)
+ return cluster_idx
+
+
+def dm_subset(dm_sq, idxs):
+ """Get subset of distance matrix given list of indices
+
+ Args:
+ dm_sq (numpy.array): squareform distance matrix from pdist
+ idxs (list of int): list of indices
+ Returns:
+ numpy.array: subset of `dm_sq` with `shape == (len(idxs), len(idxs))`
+ """
+ return dm_sq[idxs][:,idxs]
+
+
+def min_row_dist_sum_idx(dists):
+ """Find the index of the row with the minimum row distance sum
+
+ This should return the index of the row index with the least distance overall
+ to all other rows.
+
+ Args:
+ dists (np.array): must be square distance matrix
+
+ Returns:
+ int: index of row with min dist row sum
+ """
+ row_sums = np.apply_along_axis(arr=dists, axis=0, func1d=np.sum)
+ return row_sums.argmin()
+
+
+def seq_int_arr_to_nt(arr):
+ """Convert 1-4 int array to ACGT string
+
+ Args:
+ arr (numpy.array of int): array of integers from 1 to 4 inclusive representing A, C, G, and T
+
+ Returns:
+ str: nucleotide sequence string
+ """
+ return ''.join([INT_TO_NT[x] for x in arr])
+
+
+def find_centroid_alleles(alleles, bp=28, t=0.025):
+ """Reduce list of alleles to set of centroid alleles based on size grouping, ends matching and hierarchical clustering
+
+ Workflow for finding centroid alleles:
+
+ - grouping by size (e.g. 100bp, 101bp, 103bp, etc)
+ - then grouped by `bp` nucleotides at ends matching
+ - size and ends grouped alleles hierarchically clustered (Hamming distance, complete linkage)
+ - tree cutting at threshold `t`
+ - select allele with minimum distance to other alleles in cluster as centroid
+
+ Args:
+ alleles (iterable): collection of allele nucleotide sequences
+ bp (int): number of bp matching at allele ends for size grouping (default=28 due to default blastn megablast word size)
+ t (float): cluster generation (tree cutting) distance threshold for size grouped alleles
+
+ Returns:
+ set of str: centroid alleles
+ """
+ centroid_alleles = set()
+ len_allele = group_alleles_by_size(alleles)
+ for length, seqs in len_allele.items():
+ # if only one alelle of a particular size, add as centroid, move onto next size group
+ if len(seqs) == 1:
+ centroid_alleles.add(seqs[0])
+ continue
+ # convert allele nucleotide sequences to integer matrix
+ seq_arr = seq_int_arr(seqs)
+ # group alleles by matching ends
+ starts_ends_idxs = group_alleles_by_start_end_Xbp(seq_arr, bp=bp)
+ for k, idxs in starts_ends_idxs.items():
+ # if only one allele for a particular matching ends group, then add as centroid and move onto next ends group
+ if len(idxs) == 1:
+ centroid_alleles.add(seqs[idxs[0]])
+ continue
+ # fetch subset of int allele sequences for a matching ends group
+ seq_arr_subset = seq_arr[idxs]
+ # Hamming distances between alleles
+ dists = pdist(seq_arr_subset, 'hamming')
+ # create flat clusters (tree cut) at t threshold
+ cl = allele_clusters(dists, t=t)
+ # for each allele cluster
+ dm_sq = squareform(dists)
+ for cl_key, cl_idxs in cl.items():
+ # if only 1 or 2 alleles in cluster then return first
+ if len(cl_idxs) == 1 or len(cl_idxs) == 2:
+ # get first cluster index and get nt seq for that index
+ centroid_alleles.add(seq_int_arr_to_nt(seq_arr_subset[cl_idxs[0]]))
+ continue
+ # else find allele with min distances to all other alleles in cluster
+ dm_sub = dm_subset(dm_sq, cl_idxs)
+ min_idx = min_row_dist_sum_idx(dm_sub)
+ # add nucleotide seq for cluster centroid allele to centroids set
+ centroid_alleles.add(seq_int_arr_to_nt(seq_arr_subset[min_idx]))
+ #end for cl_key, cl_idxs in cl.iteritems():
+ #end for k, idxs in starts_ends_idxs.iteritems():
+ #end for length, seqs in alleles.iteritems():
+ return centroid_alleles
diff --git a/sistr/src/cgmlst/extras/hclust_cutree.py b/sistr/src/cgmlst/extras/hclust_cutree.py
new file mode 100644
index 0000000..ef5cb6b
--- /dev/null
+++ b/sistr/src/cgmlst/extras/hclust_cutree.py
@@ -0,0 +1,76 @@
+from fastcluster import linkage
+from scipy.spatial.distance import pdist
+from scipy.cluster.hierarchy import fcluster
+import pandas as pd
+import numpy as np
+
+
+def profiles_to_np_array(profiles_csv_path):
+ """
+
+ """
+ df = pd.read_csv(profiles_csv_path, index_col=0)
+ arr = np.array(df, dtype=np.float64)
+ genomes = df.index
+ markers = df.columns
+ return arr, genomes, markers
+
+
+def nr_profiles(arr, genomes):
+ """
+ Get a condensed cgMLST pairwise distance matrix for specified Genomes_
+ where condensed means redundant cgMLST profiles are only represented once in the distance matrix.
+
+ Args:
+ user_name (list): List of Genome_ names to retrieve condensed distance matrix for
+
+ Returns:
+ (numpy.array, list): tuple of condensed cgMLST distance matrix and list of grouped Genomes_
+ """
+ gs_collapse = []
+ genome_idx_dict = {}
+ indices = []
+ patt_dict = {}
+ for i, g in enumerate(genomes):
+ p = arr[i, :].tostring()
+ if p in patt_dict:
+ parent = patt_dict[p]
+ idx = genome_idx_dict[parent]
+ gs_collapse[idx].append(g)
+ else:
+ indices.append(i)
+ patt_dict[p] = g
+ genome_idx_dict[g] = len(gs_collapse)
+ gs_collapse.append([g])
+ return arr[indices, :], gs_collapse
+
+
+def dist_matrix_hamming(arr):
+ return pdist(arr, metric='hamming')
+
+
+def complete_linkage(dm):
+ """
+ Perform complete linkage hierarchical clustering on a distance matrix.
+
+ Args:
+ dm (numpy.array): Distance matrix
+
+ Returns:
+ (object): fastcluster complete linkage hierarchical clustering object
+ """
+ return linkage(dm, 'complete')
+
+
+def cutree(Z, thresholds):
+ out = {}
+ for t in thresholds:
+ out[t] = fcluster(Z, t, criterion='distance')
+ return pd.DataFrame(out)
+
+def expand_clusters_dataframe(df_clusters, genome_groups):
+ lens_genome_groups = [len(xs) for xs in genome_groups]
+ idxs = np.repeat(df_clusters.index.values, lens_genome_groups)
+ df_cl_exp = df_clusters.reindex(idxs, method='ffill')
+ df_cl_exp.index = [g for gs in genome_groups for g in gs]
+ return df_cl_exp
\ No newline at end of file
diff --git a/sistr/src/cgmlst/msa.py b/sistr/src/cgmlst/msa.py
new file mode 100644
index 0000000..0b9a3be
--- /dev/null
+++ b/sistr/src/cgmlst/msa.py
@@ -0,0 +1,77 @@
+from subprocess import PIPE, Popen
+
+
+MSA_GAP_PROP_THRESHOLD = 0.05
+
+
+def parse_aln_out(out):
+ lines = out.split('\n')
+ seqs = []
+ header = ''
+ for line in lines:
+ line = line.strip()
+ if line == '': continue
+ if line[0] == '>':
+ if header == '':
+ header = line.replace('>','')
+ else:
+ yield header, ''.join(seqs)
+ seqs = []
+ header = line.replace('>','')
+ else:
+ seqs.append(line)
+ yield header, ''.join(seqs)
+
+
+def msa_mafft(seqs):
+
+ if isinstance(seqs, list):
+ mafft_stdin = '\n'.join(['>{}\n{}'.format(i, x.lower()) for i, x in enumerate(seqs)])
+ elif isinstance(seqs, dict):
+ mafft_stdin = '\n'.join(['>{}\n{}'.format(k, v.lower()) for k, v in seqs.items()])
+ elif isinstance(seqs, (str,)):
+ mafft_stdin = seqs
+ else:
+ raise Exception('Unexpected type for param seqs of "{}"'.format(type(seqs)))
+
+ p = Popen(['mafft', '-'], stdin=PIPE, stdout=PIPE, stderr=PIPE)
+ stdout, stderr = p.communicate(input=mafft_stdin.encode())
+ if isinstance(stdout, bytes):
+ stdout = stdout.decode()
+ if stdout[0] == '>':
+ if isinstance(seqs, list):
+ return [s for h,s in parse_aln_out(stdout)]
+ elif isinstance(seqs, (dict, str)):
+ return {h:s for h,s in parse_aln_out(stdout)}
+ else:
+ raise Exception('MSA not generated by MAFFT stdout=\n{}\n\nstderr=\n{}\n'.format(stdout, stderr))
+
+
+
+def msa_ref_vs_novel(ref_seq, novel_seq):
+ str_format_input_fasta = """>ref
+{}
+>novel
+{}
+"""
+ input_fasta = str_format_input_fasta.format(ref_seq.lower(), novel_seq.lower())
+ msa_out_dict = msa_mafft(input_fasta)
+ assert 'ref' in msa_out_dict
+ assert 'novel' in msa_out_dict
+ return msa_out_dict['ref'], msa_out_dict['novel']
+
+
+def number_gapped_ungapped(aln1, aln2):
+ ungapped = 0
+ total_gapped = 0
+ for c1, c2 in zip(aln1, aln2):
+ if c1 == '-' and c2 == '-':
+ continue
+ if c1 == '-':
+ total_gapped += 1
+ elif c2 == '-':
+ total_gapped += 1
+ else:
+ ungapped += 1
+
+ return total_gapped, ungapped
\ No newline at end of file
diff --git a/sistr/src/logger.py b/sistr/src/logger.py
new file mode 100644
index 0000000..07cdc3a
--- /dev/null
+++ b/sistr/src/logger.py
@@ -0,0 +1,11 @@
+import logging
+
+LOG_FORMAT = '%(asctime)s %(levelname)s: %(message)s [in %(pathname)s:%(lineno)d]'
+
+def init_console_logger(logging_verbosity=3):
+ logging_levels = [logging.ERROR, logging.WARN, logging.INFO, logging.DEBUG]
+ if logging_verbosity > (len(logging_levels) - 1):
+ logging_verbosity = 3
+ lvl = logging_levels[logging_verbosity]
+
+ logging.basicConfig(format=LOG_FORMAT, level=lvl)
diff --git a/sistr/src/mash.py b/sistr/src/mash.py
new file mode 100644
index 0000000..8ba5495
--- /dev/null
+++ b/sistr/src/mash.py
@@ -0,0 +1,67 @@
+import logging
+import re, os
+from pkg_resources import resource_filename
+from subprocess import Popen, PIPE
+import pandas as pd
+from sistr.src.serovar_prediction.constants import genomes_to_serovar, genomes_to_subspecies
+from sistr.src.serovar_prediction.constants import MASH_SUBSPECIATION_DISTANCE_THRESHOLD
+
+
+MASH_BIN = 'mash'
+MASH_SKETCH_FILE = resource_filename('sistr', 'data/sistr.msh')
+
+
+def mash_dist_trusted(fasta_path):
+ """
+ Compute Mash distances of sketch file of genome fasta to RefSeq sketch DB.
+
+ Args:
+ mash_bin (str): Mash binary path
+
+ Returns:
+ (str): Mash STDOUT string
+ """
+ args = [MASH_BIN,
+ 'dist',
+ MASH_SKETCH_FILE,
+ fasta_path]
+ p = Popen(args, stderr=PIPE, stdout=PIPE)
+ (stdout, stderr) = p.communicate()
+ retcode = p.returncode
+ if retcode != 0:
+ raise Exception('Could not run Mash dist {}'.format(stderr))
+
+ return stdout
+
+
+def mash_output_to_pandas_df(mash_out):
+ from io import BytesIO
+ df = pd.read_table(BytesIO(mash_out), header=None)
+ df.columns = ['ref', 'query', 'dist', 'pval', 'matching']
+ refs = [re.sub(r'(\.fa$)|(\.fas$)|(\.fasta$)|(\.fna$)', '', os.path.basename(r)) for r in df['ref']]
+ df['ref'] = refs
+ genome_serovar_dict = genomes_to_serovar()
+ df['serovar'] = [genome_serovar_dict[genome] for genome in refs]
+ df['n_match'] = [int(x.split('/')[0]) for x in df['matching']]
+ df.sort_values(by='dist', inplace=True)
+ df = df[df['dist'] < 1.0]
+ return df
+
+
+def mash_subspeciation(df_mash):
+ closest_distance = df_mash['dist'].min()
+ if closest_distance > MASH_SUBSPECIATION_DISTANCE_THRESHOLD:
+ logging.warning('Min Mash distance (%s) above subspeciation distance threshold (%s)',
+ closest_distance,
+ MASH_SUBSPECIATION_DISTANCE_THRESHOLD)
+ return None
+ else:
+ df_mash_spp = df_mash[df_mash['dist'] <= MASH_SUBSPECIATION_DISTANCE_THRESHOLD]
+ genomes = df_mash_spp['ref']
+ from collections import Counter
+ genome_spp = genomes_to_subspecies()
+ subspecies_below_threshold = [genome_spp[g] if g in genome_spp else None for g in genomes]
+ subspecies_below_threshold = filter(None, subspecies_below_threshold)
+ subspecies_counter = Counter(subspecies_below_threshold)
+ logging.info('Mash subspecies counter: %s', subspecies_counter)
+ return (subspecies_counter.most_common(1)[0][0], closest_distance, dict(subspecies_counter))
diff --git a/sistr/src/parsers.py b/sistr/src/parsers.py
new file mode 100644
index 0000000..46479dd
--- /dev/null
+++ b/sistr/src/parsers.py
@@ -0,0 +1,110 @@
+# TODO: check format of file? guess format maybe; use BioPython to parse variety of formats?
+
+#: set: valid IUPAC nucleotide characters for checking FASTA format
+VALID_NUCLEOTIDES = {'A', 'a',
+ 'C', 'c',
+ 'G', 'g',
+ 'T', 't',
+ 'R', 'r',
+ 'Y', 'y',
+ 'S', 's',
+ 'W', 'w',
+ 'K', 'k',
+ 'M', 'm',
+ 'B', 'b',
+ 'D', 'd',
+ 'H', 'h',
+ 'V', 'v',
+ 'N', 'n',
+ 'X', 'x', } # X for masked nucleotides
+
+
+def parse_fasta(filepath):
+ '''
+ Parse a fasta file returning a generator yielding tuples of fasta headers to sequences.
+
+ Note:
+ This function should give equivalent results to SeqIO from BioPython
+
+ .. code-block:: python
+
+ from Bio import SeqIO
+ # biopython to dict of header-seq
+ hseqs_bio = {r.description:str(r.seq) for r in SeqIO.parse(fasta_path, 'fasta')}
+ # this func to dict of header-seq
+ hseqs = {header:seq for header, seq in parse_fasta(fasta_path)}
+ # both methods should return the same dict
+ assert hseqs == hseqs_bio
+
+ Args:
+ filepath (str): Fasta file path
+
+ Returns:
+ generator: yields tuples of (<fasta header>, <fasta sequence>)
+ '''
+ with open(filepath, 'r') as f:
+ seqs = []
+ header = ''
+ for line in f:
+ line = line.strip()
+ if line == '':
+ continue
+ if line[0] == '>':
+ if header == '':
+ header = line.replace('>','')
+ else:
+ yield header, ''.join(seqs)
+ seqs = []
+ header = line.replace('>','')
+ else:
+ seqs.append(line)
+ yield header, ''.join(seqs)
+
+
+def fasta_format_check(fasta_path, logger):
+ """
+ Check that a file is valid FASTA format.
+
+ - First non-blank line needs to begin with a '>' header character.
+ - Sequence can only contain valid IUPAC nucleotide characters
+
+ Args:
+ fasta_str (str): FASTA file contents string
+
+ Raises:
+ Exception: If invalid FASTA format
+ """
+
+ header_count = 0
+ line_count = 1
+ nt_count = 0
+ with open(fasta_path) as f:
+ for l in f:
+ l = l.strip()
+ if l == '':
+ continue
+ if l[0] == '>':
+ header_count += 1
+ continue
+ if header_count == 0 and l[0] != '>':
+ error_msg = 'First non-blank line (L:{line_count}) does not contain FASTA header. Line beginning with ">" expected.' \
+ .format(line_count=line_count)
+ logger.error(error_msg)
+ raise Exception(error_msg)
+ non_nucleotide_chars_in_line = set(l) - VALID_NUCLEOTIDES
+
+ if len(non_nucleotide_chars_in_line) > 0:
+ error_msg = 'Line {line} contains the following non-nucleotide characters: {non_nt_chars}' \
+ .format(line=line_count,
+ non_nt_chars=', '.join([x for x in non_nucleotide_chars_in_line]))
+ logger.error(error_msg)
+ raise Exception(error_msg)
+ nt_count += len(l)
+ line_count += 1
+
+ if nt_count == 0:
+ error_msg = 'File "{}" does not contain any nucleotide sequence.'.format(fasta_path)
+ logger.error(error_msg)
+ raise Exception(error_msg)
+
+ logger.info('Valid FASTA format "{}" ({} bp)'.format(fasta_path, nt_count))
diff --git a/sistr/src/qc/__init__.py b/sistr/src/qc/__init__.py
new file mode 100644
index 0000000..650fc5c
--- /dev/null
+++ b/sistr/src/qc/__init__.py
@@ -0,0 +1,55 @@
+import logging
+from sistr.src.parsers import parse_fasta
+from sistr.src.qc.constants import ERR_MISSING_CGMLST_MARKERS, WARN_MISSING_CGMLST_MARKERS, SALMONELLA_GENOME_SIZE_MBP
+from sistr.src.serovar_prediction import CGMLST_DISTANCE_THRESHOLD
+
+
+def qc(fasta_path, cgmlst_results, prediction):
+ qc_status = 'PASS'
+ qc_msgs = []
+ genome_size = sum([len(s) for h, s in parse_fasta(fasta_path)])
+ lb_salm_gsize, ub_salm_gsize = SALMONELLA_GENOME_SIZE_MBP
+ is_gsize_acceptable = (genome_size >= lb_salm_gsize and genome_size <= ub_salm_gsize)
+ logging.info('Genome size=%s (within gsize thresholds? %s)', genome_size, is_gsize_acceptable)
+ if not is_gsize_acceptable:
+ qc_status = 'WARNING'
+ qc_msgs.append('WARNING: Input genome size ({} bp) not within expected range of {}-{} (bp) for Salmonella'.format(genome_size, lb_salm_gsize, ub_salm_gsize))
+ if cgmlst_results is not None:
+ if len(cgmlst_results) == 0:
+ missing_cgmlst_count = 330
+ else:
+ missing_cgmlst_count = 0
+ for marker, results in cgmlst_results.items():
+ if results['name'] is None:
+ missing_cgmlst_count += 1
+
+ if missing_cgmlst_count >= ERR_MISSING_CGMLST_MARKERS:
+ qc_status = 'FAIL'
+ qc_msgs.append('FAIL: Large number of cgMLST330 loci missing (n={} > {})'.format(
+ missing_cgmlst_count,
+ ERR_MISSING_CGMLST_MARKERS))
+ elif missing_cgmlst_count >= WARN_MISSING_CGMLST_MARKERS:
+ qc_status = 'WARNING'
+ qc_msgs.append('FAIL: Moderate number of cgMLST330 loci missing (n={} > {})'.format(
+ missing_cgmlst_count,
+ WARN_MISSING_CGMLST_MARKERS))
+
+ matching_cgmlst_alleles_threshold = (1.0 - CGMLST_DISTANCE_THRESHOLD) * 330
+ if prediction.cgmlst_matching_alleles < matching_cgmlst_alleles_threshold:
+ if qc_status != 'FAIL':
+ qc_status = 'WARNING'
+ qc_msgs.append('WARNING: Only matched {} cgMLST330 loci. Min threshold for confident serovar prediction from cgMLST is {}'.format(prediction.cgmlst_matching_alleles, matching_cgmlst_alleles_threshold))
+
+ if prediction.h1 is None or prediction.h1 == '-':
+ if qc_status != 'FAIL':
+ qc_status = 'WARNING'
+ qc_msgs.append('WARNING: H1 antigen gene (fliC) missing. Cannot determine H1 antigen. Cannot accurately predict serovar from antigen genes.')
+
+ if prediction.serogroup is None \
+ or prediction.serogroup == '-' \
+ or prediction.serogroup == '':
+ qc_status = 'FAIL'
+ qc_msgs.append('FAIL: Wzx/Wzy genes missing. Cannot determine O-antigen group/serogroup. Cannot accurately predict serovar from antigen genes.')
+
+ qc_msgs.sort()
+ return qc_status, qc_msgs
diff --git a/sistr/src/qc/constants.py b/sistr/src/qc/constants.py
new file mode 100644
index 0000000..7a56ea0
--- /dev/null
+++ b/sistr/src/qc/constants.py
@@ -0,0 +1,4 @@
+
+SALMONELLA_GENOME_SIZE_MBP = (4000000, 6000000)
+WARN_MISSING_CGMLST_MARKERS = 10
+ERR_MISSING_CGMLST_MARKERS = 30
diff --git a/sistr/src/serovar_prediction/__init__.py b/sistr/src/serovar_prediction/__init__.py
new file mode 100644
index 0000000..d0dde80
--- /dev/null
+++ b/sistr/src/serovar_prediction/__init__.py
@@ -0,0 +1,540 @@
+import logging
+import pandas as pd
+
+from sistr.src.blast_wrapper import BlastReader
+from sistr.src.serovar_prediction.constants import \
+ FLJB_FASTA_PATH, \
+ FLIC_FASTA_PATH, \
+ H2_FLJB_SIMILARITY_GROUPS, \
+ H1_FLIC_SIMILARITY_GROUPS, \
+ WZY_FASTA_PATH, \
+ WZX_FASTA_PATH, \
+ SEROGROUP_SIMILARITY_GROUPS, \
+ SEROVAR_TABLE_PATH, \
+ CGMLST_DISTANCE_THRESHOLD, MASH_DISTANCE_THRESHOLD
+
+spp_name_to_roman = {'enterica': 'I',
+ 'salamae': 'II',
+ 'arizonae': 'IIIa',
+ 'diarizonae': 'IIIb',
+ 'houtenae': 'IV',
+ 'bongori': 'V',
+ 'indica': 'VI'}
+
+
+class BlastResultMixin(object):
+ blast_results = None
+ top_result = None
+ is_trunc = False
+ is_missing = False
+ is_perfect_match = False
+
+
+class WzxPrediction(BlastResultMixin):
+ serogroup = None
+
+
+class WzyPrediction(BlastResultMixin):
+ serogroup = None
+
+
+class SerogroupPrediction():
+ serogroup = None
+
+ wzx_prediction = None
+ wzy_prediction = None
+
+
+class H1FliCPrediction(BlastResultMixin):
+ h1 = None
+
+
+class H2FljBPrediction(BlastResultMixin):
+ h2 = None
+
+
+class SerovarPrediction():
+ genome = None
+ serovar = None
+ serovar_cgmlst = None
+ cgmlst_distance = 1.0
+ cgmlst_matching_alleles = 0
+ cgmlst_genome_match = None
+ cgmlst_subspecies = None
+
+ serovar_antigen = None
+ serogroup = None
+ serogroup_prediction = None
+ h1 = None
+ h1_flic_prediction = None
+ h2 = None
+ h2_fljb_prediction = None
+
+
+def get_antigen_name(qseqid):
+ """
+ Get the antigen name from the BLASTN result query ID.
+ The last item delimited by | characters is the antigen name for all
+ antigens (H1, H2, serogroup)
+
+ @type qseqid: str
+ @param qseqid: BLASTN result query ID
+ @return: antigen name
+ """
+ if qseqid:
+ return qseqid.split('|')[-1]
+
+
+def serovar_table():
+ """
+ Get the WHO 2007 Salmonella enterica serovar table with serogroup, H1 and
+ H2 antigen info as a Pandas DataFrame.
+ @return: Pandas DataFrame of serovar table
+ """
+ return pd.read_csv(SEROVAR_TABLE_PATH)
+
+
+class BlastAntigenGeneMixin:
+ def get_antigen_gene_blast_results(self, model_obj, antigen_gene_fasta):
+ blast_outfile = self.blast_runner.blast_against_query(antigen_gene_fasta)
+ blast_reader = BlastReader(blast_outfile)
+ is_missing = blast_reader.is_missing
+ model_obj.is_missing = is_missing
+ if not is_missing:
+ model_obj.blast_results = blast_reader.df_dict()
+
+ model_obj.top_result = blast_reader.top_result()
+ model_obj.is_perfect_match = blast_reader.is_perfect_match
+ model_obj.is_trunc = blast_reader.is_trunc
+
+ return model_obj
+
+
+class SerogroupPredictor(BlastAntigenGeneMixin):
+ def __init__(self, blast_runner):
+ """
+ SerogroupPredictor takes a initialized BlastRunner object where the
+ temp work folder has been created and the genome fasta has been copied
+ over and a BLASTN DB has been made for it.
+ This class then queries wzx and wzy against the genome using the
+ BlastRunner to get the wzx and wzy serogroup predictions.
+
+ @type blast_runner: app.blast_wrapper.BlastRunner
+ @param blast_runner: Initialized BlastRunner object
+ """
+ self.blast_runner = blast_runner
+
+ self.wzx_prediction = WzxPrediction()
+ self.wzy_prediction = WzyPrediction()
+ self.serogroup_prediction = SerogroupPrediction()
+
+
+ def search_for_wzx(self):
+ self.wzx_prediction = self.get_antigen_gene_blast_results(self.wzx_prediction, WZX_FASTA_PATH)
+ if not self.wzx_prediction.is_missing:
+ top_result = self.wzx_prediction.top_result
+ top_result_pident = top_result['pident']
+ top_result_length = top_result['length']
+
+ if top_result_pident < 88.0:
+ self.wzx_prediction.is_missing = True
+ self.wzx_prediction.serogroup = None
+ return
+
+ if top_result_length < 400:
+ self.wzx_prediction.is_missing = True
+ self.wzx_prediction.serogroup = None
+ return
+
+ self.wzx_prediction.serogroup = get_antigen_name(top_result['qseqid'])
+
+
+ def search_for_wzy(self):
+ self.wzy_prediction = self.get_antigen_gene_blast_results(self.wzy_prediction, WZY_FASTA_PATH)
+ if not self.wzy_prediction.is_missing:
+ top_result = self.wzy_prediction.top_result
+ top_result_pident = top_result['pident']
+ top_result_length = top_result['length']
+
+ if top_result_pident < 88.0:
+ self.wzy_prediction.is_missing = True
+ self.wzy_prediction.serogroup = None
+ return
+
+ if top_result_length < 600:
+ self.wzy_prediction.is_missing = True
+ self.wzy_prediction.serogroup = None
+ return
+
+ self.wzy_prediction.serogroup = get_antigen_name(top_result['qseqid'])
+
+
+ def predict(self):
+ self.search_for_wzx()
+ self.search_for_wzy()
+ self.serogroup_prediction.wzx_prediction = self.wzx_prediction
+ self.serogroup_prediction.wzy_prediction = self.wzy_prediction
+ if self.wzx_prediction.is_perfect_match:
+ self.serogroup_prediction.serogroup = self.wzx_prediction.serogroup
+ if self.wzy_prediction.is_perfect_match:
+ self.serogroup_prediction.serogroup = self.wzy_prediction.serogroup
+ if self.wzy_prediction.is_perfect_match or self.wzx_prediction.is_perfect_match:
+ return
+
+ if self.wzx_prediction.is_missing and self.wzy_prediction.is_missing:
+ return
+ if self.wzx_prediction.is_missing:
+ self.serogroup_prediction.serogroup = self.wzy_prediction.serogroup
+ return
+ if self.wzy_prediction.is_missing:
+ self.serogroup_prediction.serogroup = self.wzx_prediction.serogroup
+ return
+
+ if self.wzy_prediction.serogroup == self.wzx_prediction.serogroup:
+ self.serogroup_prediction.serogroup = self.wzx_prediction.serogroup
+ return
+
+ top_wzy_result = self.wzy_prediction.top_result
+ top_wzx_result = self.wzx_prediction.top_result
+
+ wzx_cov = top_wzx_result['coverage']
+ wzx_pident = top_wzx_result['pident']
+
+ wzy_cov = top_wzy_result['coverage']
+ wzy_pident = top_wzy_result['pident']
+
+ if wzx_cov >= wzy_cov and wzx_pident >= wzy_pident:
+ self.serogroup_prediction.serogroup = self.wzx_prediction.serogroup
+ elif wzx_cov < wzy_cov and wzx_pident < wzy_pident:
+ self.serogroup_prediction.serogroup = self.wzy_prediction.serogroup
+ else:
+ self.serogroup_prediction.serogroup = self.wzx_prediction.serogroup
+
+
+class H1Predictor(BlastAntigenGeneMixin):
+ def __init__(self, blast_runner):
+ self.blast_runner = blast_runner
+ self.h1_prediction = H1FliCPrediction()
+
+ def predict(self):
+ self.h1_prediction = self.get_antigen_gene_blast_results(self.h1_prediction, FLIC_FASTA_PATH)
+ if not self.h1_prediction.is_missing:
+ if not self.h1_prediction.is_perfect_match:
+ df_blast_results = pd.DataFrame(self.h1_prediction.blast_results)
+ df_blast_results = df_blast_results[
+ (df_blast_results['mismatch'] <= 25) & (df_blast_results['length'] >= 700)]
+
+ if df_blast_results.shape[0] == 0:
+ self.h1_prediction.is_missing = True
+ self.h1_prediction.top_result = None
+ self.h1_prediction.h1 = None
+ return
+
+ df_blast_results_over1000 = df_blast_results[
+ (df_blast_results['mismatch'] <= 5) & (df_blast_results['length'] >= 1000)]
+
+ if df_blast_results_over1000.shape[0] > 0:
+ df_blast_results = df_blast_results_over1000.sort_values(by='mismatch')
+ else:
+ df_blast_results = df_blast_results.sort_values(by='bitscore', ascending=False)
+
+ result_dict = BlastReader.df_first_row_to_dict(df_blast_results)
+ result_trunc = BlastReader.is_blast_result_trunc(qstart=result_dict['qstart'],
+ qend=result_dict['qend'],
+ sstart=result_dict['sstart'],
+ send=result_dict['send'],
+ qlen=result_dict['qlen'],
+ slen=result_dict['slen'])
+ self.h1_prediction.top_result = result_dict
+ self.h1_prediction.is_trunc = result_trunc
+ self.h1_prediction.h1 = get_antigen_name(self.h1_prediction.top_result['qseqid'])
+
+
+class H2Predictor(BlastAntigenGeneMixin):
+ def __init__(self, blast_runner):
+ self.blast_runner = blast_runner
+ self.h2_prediction = H2FljBPrediction()
+
+ def predict(self):
+ self.h2_prediction = self.get_antigen_gene_blast_results(self.h2_prediction, FLJB_FASTA_PATH)
+ if not self.h2_prediction.is_missing:
+ if not self.h2_prediction.is_perfect_match:
+ top_result = self.h2_prediction.top_result
+ match_len = top_result['length']
+ pident = top_result['pident']
+
+ # short lower %ID matches are treated as missing or '-' for H2
+ if match_len <= 600 and pident < 88.0:
+ self.h2_prediction.h2 = '-'
+ self.h2_prediction.is_missing = True
+ return
+
+ if match_len <= 600 and not self.h2_prediction.is_trunc:
+ self.h2_prediction.h2 = '-'
+ self.h2_prediction.is_missing = True
+ return
+
+ df_blast_results = pd.DataFrame(self.h2_prediction.blast_results)
+ df_blast_results = df_blast_results[
+ (df_blast_results['mismatch'] <= 50) & (df_blast_results['length'] >= 700)]
+
+ if df_blast_results.shape[0] == 0:
+ self.h2_prediction.is_missing = True
+ self.h2_prediction.top_result = None
+ self.h2_prediction.h2 = '-'
+ return
+
+ df_blast_results_over1000 = df_blast_results[
+ (df_blast_results['mismatch'] <= 5) & (df_blast_results['length'] >= 1000)]
+
+ if df_blast_results_over1000.shape[0] > 0:
+ df_blast_results = df_blast_results_over1000.sort_values(by='mismatch')
+ else:
+ df_blast_results = df_blast_results.sort_values(by='bitscore', ascending=False)
+
+ result_dict = BlastReader.df_first_row_to_dict(df_blast_results)
+ result_trunc = BlastReader.is_blast_result_trunc(qstart=result_dict['qstart'],
+ qend=result_dict['qend'],
+ sstart=result_dict['sstart'],
+ send=result_dict['send'],
+ qlen=result_dict['qlen'],
+ slen=result_dict['slen'])
+ self.h2_prediction.top_result = result_dict
+ self.h2_prediction.is_trunc = result_trunc
+ self.h2_prediction.h2 = get_antigen_name(self.h2_prediction.top_result['qseqid'])
+
+ if self.h2_prediction.is_missing:
+ self.h2_prediction.h2 = '-'
+
+
+class SerovarPredictor:
+ serogroup = None
+ h1 = None
+ h2 = None
+ serovar = None
+ subspecies = None
+
+ def __init__(self, blast_runner, subspecies):
+ """
+
+ """
+ self.blast_runner = blast_runner
+ self.subspecies = subspecies
+ self.serogroup_predictor = SerogroupPredictor(self.blast_runner)
+ self.h1_predictor = H1Predictor(self.blast_runner)
+ self.h2_predictor = H2Predictor(self.blast_runner)
+
+ def predict_antigens(self):
+ self.h1_predictor.predict()
+ self.h2_predictor.predict()
+ self.serogroup_predictor.predict()
+ self.h1 = self.h1_predictor.h1_prediction.h1
+ self.h2 = self.h2_predictor.h2_prediction.h2
+ self.serogroup = self.serogroup_predictor.serogroup_prediction.serogroup
+ return self.serogroup, self.h1, self.h2
+
+ @staticmethod
+ def get_serovar(df, sg, h1, h2, spp):
+ h2_is_missing = '-' in h2
+ b_sg = df['Serogroup'].isin(sg)
+ b_h1 = df['H1'].isin(h1)
+ if h2_is_missing:
+ b_h2 = df['can_h2_be_missing']
+ else:
+ b_h2 = df['H2'].isin(h2)
+
+ if spp is not None:
+ b_spp = df['subspecies'] == spp
+ else:
+ b_spp = b_sg
+ df_prediction = df[(b_spp & b_sg & b_h1 & b_h2)]
+ logging.debug('Serovar prediction for %s %s:%s:%s is %s', spp, sg, h1, h2, list(df_prediction['Serovar']))
+ if df_prediction.shape[0] > 0:
+ return '|'.join(list(df_prediction['Serovar']))
+
+
+ def predict_serovar_from_antigen_blast(self):
+ if not self.serogroup or not self.h2 or not self.h1:
+ self.predict_antigens()
+
+ df = serovar_table()
+ sg = self.serogroup
+ h1 = self.h1
+ h2 = self.h2
+
+ # no antigen results then serovar == '-:-:-'
+ if sg is None \
+ and h1 is None \
+ and h2 == '-':
+ self.serovar = '-:-:-'
+ return self.serovar
+
+ for sg_groups in SEROGROUP_SIMILARITY_GROUPS:
+ if sg in sg_groups:
+ sg = sg_groups
+ break
+ if sg is None:
+ sg = list(df['Serogroup'].unique())
+ if not isinstance(sg, list):
+ sg = [sg]
+
+ for h1_groups in H1_FLIC_SIMILARITY_GROUPS:
+ if h1 in h1_groups:
+ h1 = h1_groups
+ break
+ if h1 is None:
+ h1 = list(df['H1'].unique())
+ if not isinstance(h1, list):
+ h1 = [h1]
+
+ for h2_groups in H2_FLJB_SIMILARITY_GROUPS:
+ if h2 in h2_groups:
+ h2 = h2_groups
+ break
+
+ if not isinstance(h2, list):
+ h2 = [h2]
+
+ self.serovar = SerovarPredictor.get_serovar(df, sg, h1, h2, self.subspecies)
+ if self.serovar is None:
+ try:
+ spp_roman = spp_name_to_roman[self.subspecies]
+ except:
+ spp_roman = None
+ from collections import Counter
+ c = Counter(df.O_antigen[df.Serogroup.isin(sg)])
+ o_antigen = c.most_common()[0][0]
+ h1_first = h1[0]
+ h2_first = h2[0]
+ if spp_roman:
+ self.serovar = '{} {}:{}:{}'.format(spp_roman, o_antigen, h1_first, h2_first)
+ else:
+ self.serovar = '{}:{}:{}'.format(o_antigen, h1_first, h2_first)
+ return self.serovar
+
+ def get_serovar_prediction(self):
+ serovar_pred = SerovarPrediction()
+ sg_pred = self.serogroup_predictor.serogroup_prediction
+
+ h1_pred = self.h1_predictor.h1_prediction
+ h2_pred = self.h2_predictor.h2_prediction
+
+ serovar_pred.serogroup_prediction = sg_pred
+ serovar_pred.serogroup = self.serogroup
+
+ serovar_pred.h1_flic_prediction = h1_pred
+ serovar_pred.h1 = self.h1
+
+ serovar_pred.h2_fljb_prediction = h2_pred
+ serovar_pred.h2 = self.h2
+
+ return serovar_pred
+
+
+def overall_serovar_call(serovar_prediction, antigen_predictor):
+ """
+ Predict serovar from cgMLST cluster membership analysis and antigen BLAST results.
+ SerovarPrediction object is assigned H1, H2 and Serogroup from the antigen BLAST results.
+ Antigen BLAST results will predict a particular serovar or list of serovars, however,
+ the cgMLST membership may be able to help narrow down the list of potential serovars.
+
+ Notes:
+ If the cgMLST predicted serovar is within the list of antigen BLAST predicted serovars,
+ then the serovar is assigned the cgMLST predicted serovar.
+
+
+ If all antigens are found, but an antigen serovar is not found then the serovar is assigned
+ a pseudo-antigenic formula (Serogroup:H1:H2), otherwise the serovar is assigned the cgMLST prediction.
+
+
+ If the antigen predicted serovar does not match the cgMLST predicted serovar,
+
+ - the serovar is the cgMLST serovar if the cgMLST cluster level is <= 0.1 (10% or less)
+ - otherwise, the serovar is antigen predicted serovar(s)
+
+ Args:
+ serovar_prediction (src.serovar_prediction.SerovarPrediction): Serovar prediction results (antigen+cgMLST[+Mash])
+ antigen_predictor (src.serovar_prediction.SerovarPredictor): Antigen search results
+
+ Returns:
+ src.serovar_prediction.SerovarPrediction: Serovar prediction results with overall prediction from antigen + cgMLST
+ """
+ assert isinstance(serovar_prediction, SerovarPrediction)
+ assert isinstance(antigen_predictor, SerovarPredictor)
+
+ h1 = antigen_predictor.h1
+ h2 = antigen_predictor.h2
+ sg = antigen_predictor.serogroup
+ spp = serovar_prediction.cgmlst_subspecies
+ if spp is None:
+ if 'mash_match' in serovar_prediction.__dict__:
+ spp = serovar_prediction.__dict__['mash_subspecies']
+
+ serovar_prediction.serovar_antigen = antigen_predictor.serovar
+
+ cgmlst_serovar = serovar_prediction.serovar_cgmlst
+ cgmlst_distance = float(serovar_prediction.cgmlst_distance)
+
+ null_result = '-:-:-'
+
+
+ try:
+ spp_roman = spp_name_to_roman[spp]
+ except:
+ spp_roman = None
+
+ is_antigen_null = lambda x: (x is None or x == '' or x == '-')
+
+
+ if antigen_predictor.serovar is None:
+ if is_antigen_null(sg) and is_antigen_null(h1) and is_antigen_null(h2):
+ if spp_roman is not None:
+ serovar_prediction.serovar = '{} {}:{}:{}'.format(spp_roman, sg, h1, h2)
+ else:
+ serovar_prediction.serovar = '{}:{}:{}'.format(spp_roman, sg, h1, h2)
+ elif cgmlst_serovar is not None and cgmlst_distance <= CGMLST_DISTANCE_THRESHOLD:
+ serovar_prediction.serovar = cgmlst_serovar
+ else:
+ serovar_prediction.serovar = null_result
+ if 'mash_match' in serovar_prediction.__dict__:
+ spd = serovar_prediction.__dict__
+ mash_dist = float(spd['mash_distance'])
+ if mash_dist <= MASH_DISTANCE_THRESHOLD:
+ serovar_prediction.serovar = spd['mash_serovar']
+ else:
+ serovars_from_antigen = antigen_predictor.serovar.split('|')
+ if not isinstance(serovars_from_antigen, list):
+ serovars_from_antigen = [serovars_from_antigen]
+ if cgmlst_serovar is not None:
+ if cgmlst_serovar in serovars_from_antigen:
+ serovar_prediction.serovar = cgmlst_serovar
+ else:
+ if float(cgmlst_distance) <= CGMLST_DISTANCE_THRESHOLD:
+ serovar_prediction.serovar = cgmlst_serovar
+ elif 'mash_match' in serovar_prediction.__dict__:
+ spd = serovar_prediction.__dict__
+ mash_serovar = spd['mash_serovar']
+ mash_dist = float(spd['mash_distance'])
+ if mash_serovar in serovars_from_antigen:
+ serovar_prediction.serovar = mash_serovar
+ else:
+ if mash_dist <= MASH_DISTANCE_THRESHOLD:
+ serovar_prediction.serovar = mash_serovar
+
+ if serovar_prediction.serovar is None:
+ serovar_prediction.serovar = serovar_prediction.serovar_antigen
+
+ if serovar_prediction.h1 is None:
+ serovar_prediction.h1 = '-'
+ if serovar_prediction.h2 is None:
+ serovar_prediction.h2 = '-'
+ if serovar_prediction.serogroup is None:
+ serovar_prediction.serogroup = '-'
+ if serovar_prediction.serovar_antigen is None:
+ if spp_roman is not None:
+ serovar_prediction.serovar_antigen = '{} -:-:-'.format(spp_roman)
+ else:
+ serovar_prediction.serovar_antigen = '-:-:-'
+ if serovar_prediction.serovar is None:
+ serovar_prediction.serovar = serovar_prediction.serovar_antigen
+ return serovar_prediction
\ No newline at end of file
diff --git a/sistr/src/serovar_prediction/constants.py b/sistr/src/serovar_prediction/constants.py
new file mode 100644
index 0000000..4260a63
--- /dev/null
+++ b/sistr/src/serovar_prediction/constants.py
@@ -0,0 +1,153 @@
+from __future__ import print_function
+
+from pkg_resources import resource_filename
+
+# cgMLST330 distance threshold for refining overall serovar prediction
+CGMLST_DISTANCE_THRESHOLD = 0.1
+MASH_DISTANCE_THRESHOLD = 0.005
+CGMLST_SUBSPECIATION_DISTANCE_THRESHOLD = 0.9
+MASH_SUBSPECIATION_DISTANCE_THRESHOLD = 0.01
+
+SEROVAR_TABLE_PATH = resource_filename('sistr', 'data/Salmonella-serotype_serogroup_antigen_table-WHO_2007.csv')
+WZX_FASTA_PATH = resource_filename('sistr', 'data/antigens/wzx.fasta')
+WZY_FASTA_PATH = resource_filename('sistr', 'data/antigens/wzy.fasta')
+FLIC_FASTA_PATH = resource_filename('sistr', 'data/antigens/fliC.fasta')
+FLJB_FASTA_PATH = resource_filename('sistr', 'data/antigens/fljB.fasta')
+
+
+GENOMES_TO_SEROVAR_PATH = resource_filename('sistr', 'data/genomes-to-serovar.txt')
+GENOMES_TO_SPP_PATH = resource_filename('sistr', 'data/genomes-to-subspecies.txt')
+
+
+def genomes_to_serovar():
+ rtn = {}
+ with open(GENOMES_TO_SEROVAR_PATH) as f:
+ for l in f:
+ l = l.strip()
+ genome, serovar = l.split('\t')
+ rtn[genome] = serovar
+ return rtn
+
+def genomes_to_subspecies():
+ rtn = {}
+ with open(GENOMES_TO_SPP_PATH) as f:
+ for l in f:
+ l = l.strip()
+ genome, spp = l.split('\t')
+ rtn[genome] = spp
+ return rtn
+
+
+SEROGROUP_SIMILARITY_GROUPS = [
+ ['E1', 'E4'],
+ ['A', 'D1', 'D2'],
+ ['C1', 'F'],
+ ['S', 'O62']
+]
+
+# Determined the following H1 antigen similarity groups based on a
+# phylogenetic tree of fliC allele sequences.
+# The cluster of g antigen sequences was very convoluted hence the complex
+# groupings in the list of lists below.
+H1_FLIC_SIMILARITY_GROUPS = [
+ ['r',
+ 'r,[i]',
+ 'r,i', ],
+ ['l,[z13],[z28]',
+ 'l,[z13],z28',
+ 'l,z13',
+ 'l,z13,[z28]',
+ 'l,z13,z28',
+ 'l,z28', ],
+ ['(g),m,[s],t',
+ 'g,(m),[s],t',
+ 'm,t',
+ 'm,p,t,[u]',
+ '[g],m,t',
+ 'g,m,t',
+ 'g,m,[t]',
+ 'g,m,[s],t',
+ 'g,m,[s],[t]',
+ 'g,[m],[s],[t]',
+ 'g,[m],s,t',
+ 'g,[m],t',
+ 'g,m,[s],[t]', ],
+ ['f,g,m,t',
+ 'm,t',
+ 'g,m,t',
+ 'g,m,[t]',
+ 'g,m,[s],t',
+ '[g],m,t',
+ 'g,[m],t',
+ 'g,m,[s],t',
+ 'g,m,[s],[t]',
+ 'g,[m],[s],[t]', ],
+ ['g,m,s,t',
+ 'g,[m],[s],[t]',
+ 'g,[m],[s],t',
+ 'g,[m],s,t',
+ 'g,m,[s],[t]', ],
+ ['g,(t)',
+ 'g,[m],[s],[t]',
+ 'g,[m],[s],t',
+ 'g,[m],s,t',
+ 'g,m,[s],[t]',
+ 'g,[m],t', ],
+ ['g,m',
+ 'g,m,[p],s',
+ 'g,m,[s]',
+ 'g,m,[t]',
+ 'g,[m],[s],[t]',
+ 'g,[m],[s],t',
+ 'g,m,[s],[t]',
+ 'g,m,q',
+ 'g,m,s',
+ 'g,p',
+ 'g,p,s',
+ 'g,p,u',
+ 'g,q',
+ 'g,s,q', ],
+ ['[f],g,[t]',
+ 'f,g',
+ 'f,g,[s]',
+ 'f,g,s',
+ 'f,g,[t]',
+ '[f],g,[t]',
+ 'f,g,t',
+ 'g,t',
+ '[f],g,[t]',
+ 'f,g,[s]',
+ 'f,g,[t]',
+ 'f,g,s', ],
+ ['[g,t]',
+ 'g,[s],t',
+ 'g,s,[t]',
+ 'g,s,t'
+ 'g,t', ],
+ ['z36,[z38]',
+ 'z36,z38', ],
+ ['z36,[z38]',
+ 'z36', ]
+]
+
+H2_FLJB_SIMILARITY_GROUPS = [
+ ['1,2,7',
+ '1,[2],7', ],
+ ['1,5',
+ '1,[2],5',
+ '1,5,[7]',
+ '[1,5]', ],
+ ['1,6',
+ '1,6,[7]', ],
+ ['1,7',
+ '1,[2],7',
+ '1,[5],7', ],
+ ['e,n,[x],z15',
+ 'e,n,z15',
+ '[e,n,z15]',
+ '[e,n,x,z15]', ],
+ ['e,n,x',
+ '[e,n,x]',
+ 'e,n,x,[z15]',
+ '[e,n,x,z15]', ]
+]
diff --git a/sistr/src/writers.py b/sistr/src/writers.py
new file mode 100644
index 0000000..2772de9
--- /dev/null
+++ b/sistr/src/writers.py
@@ -0,0 +1,188 @@
+import logging
+import numpy as np
+
+
+def listattrs(x):
+ """Get all instance and class attributes for an object
+
+ Get all instance and class attributes for an object except those that start
+ with "__" (double underscore).
+
+ __dict__ of an object only reports the instance attributes while dir()
+ reports all of the attributes of an object including private ones.
+
+ Callable attrs are filtered out.
+
+ Args:
+ x (object): Some object
+
+ Returns:
+ list str: List of non-callable non-private attributes of object x
+ """
+ return [attr for attr in dir(x) if not attr.startswith("__") and not callable(getattr(x, attr))]
+
+
+def to_dict(x, depth, exclude_keys=set(), depth_threshold=8):
+ """Transform a nested object/dict/list into a regular dict
+
+ json.dump(s) and pickle don't like to un/serialize regular Python objects so
+ this function should handle arbitrarily nested objects to be serialized to
+ regular string, float, int, bool, None values.
+
+ This is a recursive function so by default it will exit at a certain depth (depth_threshold=8).
+
+ Args:
+ x (object): Some object to dict-ify unless x is a scalar/literal then return x as is
+ depth (int): Starting depth must be 0 (cannot supply default value due to weird Pythonisms)
+ exclude_keys (set): Keys to avoid adding to the output dict
+ depth_threshold (int): object/dict nesting depth to stop at
+
+ Returns:
+ dict: dict with only scalar/literal leaf values
+ """
+ if x is None or isinstance(x, (str, int, float, bool)):
+ return x
+ if isinstance(x, np.int_):
+ return int(x)
+ if isinstance(x, np.int64):
+ return int(x)
+ if isinstance(x, np.float_):
+ return float(x)
+ if isinstance(x, np.float64):
+ return float(x)
+ if isinstance(x, np.bool_):
+ return bool(x)
+ if depth + 1 > depth_threshold: return {}
+ if isinstance(x, list):
+ out = []
+ for v in x:
+ tmp = to_dict(v, depth + 1, exclude_keys, depth_threshold)
+ if tmp == {}: continue
+ out.append(tmp)
+ return out
+ out = {}
+ if isinstance(x, dict):
+ for k, v in x.items():
+ if k in exclude_keys: continue
+ if not isinstance(k, (str,)):
+ k = str(k)
+ tmp = to_dict(v, depth + 1, exclude_keys, depth_threshold)
+ if tmp == {}: continue
+ out[k] = tmp
+ return out
+ for attr in listattrs(x):
+ if attr in exclude_keys: continue
+ v = getattr(x, attr)
+ tmp = to_dict(v, depth + 1, exclude_keys, depth_threshold)
+ if tmp == {}: continue
+ out[attr] = tmp
+ return out
+
+
+def _recur_flatten(key, x, out, sep='.'):
+ """Helper function to flatten_dict
+
+ Recursively flatten all nested values within a dict
+
+ Args:
+ key (str): parent key
+ x (object): object to flatten or add to out dict
+ out (dict): 1D output dict
+ sep (str): flattened key separator string
+
+ Returns:
+ dict: flattened 1D dict
+ """
+ if x is None or isinstance(x, (str, int, float, bool)):
+ out[key] = x
+ return out
+ if isinstance(x, list):
+ for i, v in enumerate(x):
+ new_key = '{}{}{}'.format(key, sep, i)
+ out = _recur_flatten(new_key, v, out, sep)
+ if isinstance(x, dict):
+ for k, v in x.items():
+ new_key = '{}{}{}'.format(key, sep, k)
+ out = _recur_flatten(new_key, v, out, sep)
+ return out
+
+
+def flatten_dict(x):
+ """Flatten a dict
+
+ Flatten an arbitrarily nested dict as output by to_dict
+
+ .. note::
+
+ Keys in the flattened dict may get very long.
+
+ Args:
+ x (dict): Arbitrarily nested dict (maybe resembling a tree) with literal/scalar leaf values
+
+ Returns:
+ dict: flattened 1D dict
+ """
+ out = {}
+ for k, v in x.items():
+ out = _recur_flatten(k, v, out)
+ return out
+
+
+def write_json(fh, output):
+ import json
+ json.dump(output, fh)
+
+
+def write_pickle(fh, output):
+ import cPickle
+ cPickle.dump(output, fh)
+
+
+def write_csv(fh, output):
+ import pandas as pd
+ df = pd.DataFrame(output)
+ df.to_csv(fh, index=False)
+
+
+def write_tab(fh, output):
+ import pandas as pd
+ df = pd.DataFrame(output)
+ df.to_csv(fh, index=False, sep='\t')
+
+
+fmt_to_write_func = {'json': write_json,
+ 'pickle': write_pickle,
+ 'csv': write_csv,
+ 'tab': write_tab, }
+
+
+def write(dest, fmt, serovar_predictions, more_results=0):
+ assert isinstance(serovar_predictions, list)
+ if not fmt in fmt_to_write_func:
+ logging.warn('Invalid output format "%s". Defaulting to "json"', fmt)
+ fmt = 'json'
+ if '.' + fmt not in dest:
+ dest += '.' + fmt
+ logging.info('Writing output "%s" file to "%s"', fmt, dest)
+ fh = open(dest, 'w')
+ try:
+ # write in whatever format necessary
+ write_func = fmt_to_write_func[fmt]
+ exclude_keys_in_output = {'blast_results', 'sseq'}
+ if more_results >= 2:
+ exclude_keys_in_output.remove('blast_results')
+ exclude_keys_in_output.remove('sseq')
+ elif more_results == 1:
+ exclude_keys_in_output.remove('sseq')
+ if fmt in {'pickle', 'json'}:
+ output_dict = [to_dict(v, 0, exclude_keys=exclude_keys_in_output) for v in serovar_predictions]
+ else:
+ if more_results > 0:
+ output_dict = [flatten_dict(to_dict(v, 0, exclude_keys=exclude_keys_in_output)) for v in
+ serovar_predictions]
+ else:
+ output_dict = [to_dict(v, 0, exclude_keys=exclude_keys_in_output, depth_threshold=1) for v in
+ serovar_predictions]
+ write_func(fh, output_dict)
+ finally:
+ fh.close()
diff --git a/sistr/version.py b/sistr/version.py
new file mode 100644
index 0000000..a6221b3
--- /dev/null
+++ b/sistr/version.py
@@ -0,0 +1 @@
+__version__ = '1.0.2'
diff --git a/tests/00_0163.fasta b/tests/00_0163.fasta
new file mode 100644
index 0000000..d268f8d
--- /dev/null
+++ b/tests/00_0163.fasta
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ce8eecbde216ed2b5864427ff46fb8a783994d590a8a227a6e92d0225773774c
+size 5184980
diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 0000000..be4978b
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,26 @@
+import os
+
+import pytest
+import shutil
+
+from sistr.src.blast_wrapper import BlastRunner
+
+ at pytest.fixture(scope='module')
+def fasta_path():
+ return 'tests/00_0163.fasta'
+
+ at pytest.yield_fixture(scope='module')
+def tmp_dir():
+ tmp = '/tmp/test-blast-runner/'
+ yield tmp
+ if os.path.exists(tmp):
+ shutil.rmtree(tmp)
+
+ at pytest.yield_fixture(scope='module')
+def blast_runner(fasta_path, tmp_dir):
+ _blast_runner = BlastRunner(fasta_path, tmp_dir)
+ _blast_runner.prep_blast()
+
+ yield _blast_runner
+
+ _blast_runner.cleanup()
diff --git a/tests/test_cgmlst.py b/tests/test_cgmlst.py
new file mode 100644
index 0000000..a723b93
--- /dev/null
+++ b/tests/test_cgmlst.py
@@ -0,0 +1,39 @@
+'''
+Test running cgMLST
+
+This is a longer test (>20 sec) due to running blastn of all alleles of all 330 cgMLST loci against a subject genome.
+'''
+from __future__ import print_function
+
+from sistr.sistr_cmd import run_cgmlst
+from sistr.src.cgmlst import allele_name
+
+
+def test_hash_allele():
+ seq = 'ATGC'
+ chksum = allele_name(seq)
+ assert chksum == 968142784
+
+ seq_unicode = u'ATGC'
+ chksum = allele_name(seq_unicode)
+ assert chksum == 968142784
+
+
+def test_run_cgmlst(blast_runner):
+ """
+ Expected perfect match against test genome 00_0163 since it is one of the ref genomes.
+ """
+ cgmlst_serovar_pred, marker_res = run_cgmlst(blast_runner)
+ assert isinstance(cgmlst_serovar_pred, dict)
+ spp = cgmlst_serovar_pred['subspecies']
+ serovar = cgmlst_serovar_pred['serovar']
+ genome_match = cgmlst_serovar_pred['genome_match']
+ matching_alleles = cgmlst_serovar_pred['matching_alleles']
+ distance = cgmlst_serovar_pred['distance']
+ assert matching_alleles == 326
+ assert distance >= 0.0
+ assert spp == 'salamae'
+ assert serovar == 'II 58:l,z13,z28:z6'
+ assert isinstance(marker_res, dict)
+ # 330 marker results for 330 cgMLST loci
+ assert len(marker_res) == 330
diff --git a/tests/test_hclust_cutree.py b/tests/test_hclust_cutree.py
new file mode 100644
index 0000000..9605266
--- /dev/null
+++ b/tests/test_hclust_cutree.py
@@ -0,0 +1,32 @@
+from sistr.src.cgmlst.extras.hclust_cutree import profiles_to_np_array, dist_matrix_hamming, complete_linkage, cutree, nr_profiles, expand_clusters_dataframe
+
+from sistr.src.cgmlst import CGMLST_PROFILES_PATH
+
+
+def test_read_profiles():
+ M, genomes, markers = profiles_to_np_array(CGMLST_PROFILES_PATH)
+ print(M.shape)
+ print(genomes)
+ print(markers)
+ assert M.shape == (len(genomes), len(markers))
+
+
+def test_cutree():
+ M, genomes, markers = profiles_to_np_array(CGMLST_PROFILES_PATH)
+ print(M.shape)
+ M_nr, genome_groups = nr_profiles(M, genomes)
+ print(M_nr.shape)
+ dm = dist_matrix_hamming(M_nr)
+ print(dm.shape)
+ Z = complete_linkage(dm)
+ print(Z.shape)
+ df_clusters = cutree(Z, [0, 0.1, 0.2, 0.3, 0.4])
+ print(df_clusters)
+ df_clusters = expand_clusters_dataframe(df_clusters, genome_groups)
+ print(df_clusters)
+ # check that each genome group of size >= 2 is part of the same 0.0 dist cluster
+ for gs in genome_groups:
+ if len(gs) == 1:
+ continue
+ df = df_clusters.ix[gs]
+ assert df[0.0].unique().size == 1
diff --git a/tests/test_mash.py b/tests/test_mash.py
new file mode 100644
index 0000000..e2a50de
--- /dev/null
+++ b/tests/test_mash.py
@@ -0,0 +1,15 @@
+from sistr.sistr_cmd import run_mash
+
+
+def test_run_mash(fasta_path):
+ out = run_mash(fasta_path)
+ assert 'mash_match' in out
+ assert 'mash_genome' in out
+ assert 'mash_distance' in out
+ assert 'mash_subspecies' in out
+ spp = out['mash_subspecies']
+ serovar = out['mash_serovar']
+ genome = out['mash_genome']
+ assert spp == 'salamae'
+ assert serovar == 'II 58:l,z13,z28:z6'
+ assert genome == '00_0163'
diff --git a/tests/test_msa.py b/tests/test_msa.py
new file mode 100644
index 0000000..0e4cc64
--- /dev/null
+++ b/tests/test_msa.py
@@ -0,0 +1,51 @@
+from __future__ import print_function
+from sistr.src.cgmlst.msa import msa_mafft, msa_ref_vs_novel, parse_aln_out
+
+
+def test_parse_aln_out_string():
+ test_aln_str = """
+>1
+atgc-
+>2
+-tgca
+>3
+atgca
+"""
+ aln_dict = {h:s for h,s in parse_aln_out(test_aln_str)}
+ assert "1" in aln_dict
+ assert "2" in aln_dict
+ assert "3" in aln_dict
+ assert aln_dict['1'] == 'atgc-'
+ assert aln_dict['2'] == '-tgca'
+ assert aln_dict['3'] == 'atgca'
+ print(aln_dict)
+
+
+def test_msa_mafft_str():
+ test_input_str = """
+>1
+atgc
+>2
+tgca
+>3
+atgca
+"""
+ aln_dict = msa_mafft(test_input_str)
+ assert isinstance(aln_dict, dict)
+ assert "1" in aln_dict
+ assert "2" in aln_dict
+ assert "3" in aln_dict
+ assert aln_dict['1'] == 'atgc-'
+ assert aln_dict['2'] == '-tgca'
+ assert aln_dict['3'] == 'atgca'
+ print(aln_dict)
+
+
+def test_msa_ref_vs_novel():
+ ref_nt = 'atgtgc'
+ novel_nt = 'atgcatgc'
+ ref_msa, novel_msa = msa_ref_vs_novel(ref_nt, novel_nt)
+ assert novel_msa == novel_nt
+ assert ref_msa == '--atgtgc'
+ print(ref_nt, novel_nt)
+ print(ref_msa, novel_msa)
diff --git a/tests/test_parse_blast.py b/tests/test_parse_blast.py
new file mode 100644
index 0000000..d01155f
--- /dev/null
+++ b/tests/test_parse_blast.py
@@ -0,0 +1,89 @@
+import os
+import pandas as pd
+import shutil
+
+from sistr.src.blast_wrapper import BlastRunner, BLAST_TABLE_COLS, BlastReader
+from sistr.src.serovar_prediction import WZX_FASTA_PATH, get_antigen_name, SerovarPredictor
+
+
+def test_BlastRunner(fasta_path):
+ tmp_dir = '/tmp/test_BlastRunner'
+ try:
+ br = BlastRunner(fasta_path, tmp_dir)
+ blast_outfile = br.run_blast(WZX_FASTA_PATH)
+ assert os.path.exists(tmp_dir)
+ assert os.path.exists(br.tmp_fasta_path)
+ nin_path = br.tmp_fasta_path + '.nin'
+ assert os.path.exists(nin_path)
+ assert os.path.exists(blast_outfile)
+ # Pandas should be able to parse in the table
+ df = pd.read_table(blast_outfile)
+ # the number of columns needs to be the expected number based on blastn outfmt specs
+ assert len(df.columns) == len(BLAST_TABLE_COLS)
+ br.cleanup()
+ assert not os.path.exists(br.tmp_work_dir)
+ finally:
+ if os.path.exists(tmp_dir):
+ shutil.rmtree(tmp_dir)
+
+
+def test_BlastReader(blast_runner):
+ blast_outfile = blast_runner.run_blast(WZX_FASTA_PATH)
+ blast_reader = BlastReader(blast_outfile)
+ top_result = blast_reader.top_result()
+ assert get_antigen_name(top_result['qseqid']) == 'O58'
+
+
+def test_BlastReader_is_blast_result_trunc():
+
+ # not truncated; match found in the middle of the subject sequence
+ assert not BlastReader.is_blast_result_trunc(qstart=1,
+ qend=100,
+ sstart=101,
+ send=200,
+ qlen=100,
+ slen=1000)
+
+ # not truncated; shorter match (-10bp) found in the middle of the subject
+ # sequence
+ assert not BlastReader.is_blast_result_trunc(qstart=1,
+ qend=90,
+ sstart=101,
+ send=190,
+ qlen=100,
+ slen=1000)
+
+ # not truncated; shorter match (-20bp) found in the middle of the subject
+ # sequence
+ assert not BlastReader.is_blast_result_trunc(qstart=1,
+ qend=80,
+ sstart=101,
+ send=180,
+ qlen=100,
+ slen=1000)
+
+
+ # truncated at the start of the subject
+ assert BlastReader.is_blast_result_trunc(qstart=51,
+ qend=100,
+ sstart=1,
+ send=50,
+ qlen=100,
+ slen=1000)
+
+ # truncated at the end of the subject
+ assert BlastReader.is_blast_result_trunc(qstart=51,
+ qend=100,
+ sstart=951,
+ send=1000,
+ qlen=100,
+ slen=1000)
+
+
+def test_SerovarPredictor(blast_runner):
+ sp = SerovarPredictor(blast_runner, "salamae")
+ sp.predict_serovar_from_antigen_blast()
+ assert sp.serogroup == 'O58'
+ assert sp.h1 == 'l,z13,z28'
+ assert sp.h2 == 'z6'
+ assert sp.serovar == 'II 58:l,z13,z28:z6'
diff --git a/tests/test_writer_util.py b/tests/test_writer_util.py
new file mode 100644
index 0000000..f438c87
--- /dev/null
+++ b/tests/test_writer_util.py
@@ -0,0 +1,115 @@
+from sistr.src.writers import to_dict, flatten_dict
+import numpy as np
+import pandas as pd
+
+class Test1:
+ a = 1
+ b = 3.2
+ c = 'abc'
+ z = False
+
+ def __init__(self):
+ self.i = 9
+ self.j = 0.56
+ self.k = 'test'
+ self.l = [1, 2, 3]
+ self.d = {'a':1, 'b':2}
+
+class Test2:
+ q = 6
+ w = True
+ e = 5.678
+ r = [8.9, 10.1, 2.3, 4.5]
+
+ def __init__(self, test1):
+ self.test1 = test1
+ a = 6
+ b = 7.8
+ c = 'string'
+ d = {'key1': 'val1', 'key2': 'val2'}
+ l = ['a', 'b', 'c']
+
+
+def test_complex_obj_to_dict():
+ t1 = Test1()
+ t2 = Test2(t1)
+ t2_dict = to_dict(t2, 0)
+ assert isinstance(t2_dict, dict)
+ exp_t2_dict = {'q': 6,
+ 'test1': {'a': 1,
+ 'c': 'abc',
+ 'b': 3.2,
+ 'd': {'a': 1,
+ 'b': 2},
+ 'i': 9,
+ 'k': 'test',
+ 'j': 0.56,
+ 'l': [1, 2, 3],
+ 'z': False},
+ 'r': [8.9, 10.1, 2.3, 4.5],
+ 'e': 5.678,
+ 'w': True}
+ assert t2_dict == exp_t2_dict
+
+ exp_t2_dict_depth2 = {'q': 6,
+ 'test1': {'a': 1,
+ 'c': 'abc',
+ 'b': 3.2,
+ 'i': 9,
+ 'k': 'test',
+ 'j': 0.56,
+ 'z': False},
+ 'r': [8.9, 10.1, 2.3, 4.5],
+ 'e': 5.678,
+ 'w': True}
+ t2_dict_depth2 = to_dict(t2, 0, depth_threshold=2)
+ assert t2_dict_depth2 == exp_t2_dict_depth2
+
+ exp_t2_dict = {
+ 'r': [8.9, 10.1, 2.3, 4.5],
+ 'e': 5.678,
+ 'w': True}
+ t2_dict = to_dict(t2, 0, exclude_keys={'test1', 'q'})
+ assert t2_dict == exp_t2_dict
+
+ exp_t2_dict = {'q': 6,
+ 'test1': {
+ 'c': 'abc',
+ 'b': 3.2,
+ 'd': {
+ 'b': 2},
+ 'i': 9,
+ 'k': 'test',
+ 'j': 0.56,
+ 'l': [1, 2, 3],
+ 'z': False},
+ 'r': [8.9, 10.1, 2.3, 4.5],
+ 'e': 5.678,
+ 'w': True}
+ t2_dict = to_dict(t2, 0, exclude_keys={'a'})
+ assert t2_dict == exp_t2_dict
+
+
+def test_numpy_numbers_to_dict():
+ import json
+ class ABC:
+ def __init__(self, a, b, c):
+ self.a = a
+ self.b = b
+ self.c = c
+
+ t = [{'a': 1.90,
+ 'b': 7.8,
+ 'c': 99},
+ {'a': 1.90,
+ 'b': 80.6,
+ 'c': 9999},
+ {'a': 13.90,
+ 'b': 78.5,
+ 'c': 999},]
+ df = pd.DataFrame(t)
+ for i, r in df.iterrows():
+ c = r.c
+ c = c.astype(np.int64)
+ abc = ABC(r.a, r.b, c)
+ assert json.dumps(to_dict(abc, 0), sort_keys=True) == json.dumps(t[i], sort_keys=True)
--
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