├── pubmlst_client ├── __init__.py ├── util.py ├── download.py └── list.py ├── .gitignore ├── setup.py ├── LICENSE ├── scheme_list_snapshots ├── 2020-05-25_pasteur_scheme_list.tsv ├── 2020-02-20_pubmlst_scheme_list.tsv ├── 2020-05-25_pubmlst_scheme_list.tsv ├── 2021-10-25_pubmlst_scheme_list.tsv └── 2024-10-14_pubmlst_scheme_list.tsv └── README.md /pubmlst_client/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *.egg-info 2 | __pycache__ 3 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | import pathlib 2 | from setuptools import setup 3 | 4 | HERE = pathlib.Path(__file__).parent 5 | 6 | README = (HERE / "README.md").read_text() 7 | 8 | setup( 9 | name="pubmlst_client", 10 | version="0.1.0", 11 | description="Find and download schemes from pubmlst.org", 12 | long_description=README, 13 | long_description_content_type="text/markdown", 14 | url="https://github.com/Public-Health-Bioinformatics/pubmlst_client", 15 | author="Dan Fornika", 16 | author_email="dan.fornika@bccdc.ca", 17 | license="MIT", 18 | classifiers=[ 19 | "License :: OSI Approved :: MIT License", 20 | "Programming Language :: Python :: 3", 21 | "Programming Language :: Python :: 3.7", 22 | ], 23 | packages=["pubmlst_client"], 24 | include_package_data=True, 25 | install_requires=[], 26 | entry_points={ 27 | "console_scripts": [ 28 | "pubmlst_list=pubmlst_client.list:main", 29 | "pubmlst_download=pubmlst_client.download:main", 30 | ] 31 | }, 32 | ) 33 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2020 Dan Fornika 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /pubmlst_client/util.py: -------------------------------------------------------------------------------- 1 | import datetime 2 | import json 3 | import sys 4 | import time 5 | import urllib.request 6 | 7 | 8 | def get(api_url, headers={'Content-Type': 'application/json'}, max_retries=5): 9 | response = None 10 | retries = 0 11 | request = urllib.request.Request(api_url, headers=headers) 12 | while retries < max_retries: 13 | time.sleep(1) # give the api a rest 14 | try: 15 | with urllib.request.urlopen(request) as response: 16 | response_content = response.read() 17 | if response.status == 200: 18 | retries = 0 19 | break 20 | except: 21 | log_msg = { 22 | 'timestamp': str(datetime.datetime.now().isoformat()), 23 | 'event': 'connection_error', 24 | 'url': api_url, 25 | 'retries': retries, 26 | } 27 | print(json.dumps(log_msg), file=sys.stderr) 28 | retries += 1 29 | 30 | if response and response.status == 200: 31 | return response_content 32 | elif response and response.status == 401: 33 | log_msg = { 34 | 'timestamp': str(datetime.datetime.now().isoformat()), 35 | 'event': 'connection_error', 36 | 'url': api_url, 37 | 'message': 'Unauthorized', 38 | } 39 | print(json.dumps(log_msg), file=sys.stderr) 40 | return None 41 | else: 42 | if retries == max_retries: 43 | log_msg = { 44 | 'timestamp': str(datetime.datetime.now().isoformat()), 45 | 'event': 'max_retries', 46 | 'url': api_url, 47 | } 48 | print(json.dumps(log_msg), file=sys.stderr) 49 | return None 50 | -------------------------------------------------------------------------------- /scheme_list_snapshots/2020-05-25_pasteur_scheme_list.tsv: -------------------------------------------------------------------------------- 1 | name id description locus_count records last_added last_updated 2 | klebsiella 20 AbST 5 63 2018-07-26 2018-07-26 3 | klebsiella 1 MLST 7 4992 2020-05-19 2020-05-19 4 | klebsiella 17 CbST 15 65 2016-12-19 2016-12-19 5 | klebsiella 11 Aminoglycoside resistance genes 74 None None None 6 | klebsiella 5 Beta-lactamase genes 23 None None None 7 | klebsiella 15 cgMLST_KpI 2537 None None None 8 | klebsiella 10 cgMLST_ST258_ST512_ST1199 1371 None None None 9 | klebsiella 13 cps cluster genes 2 None None None 10 | klebsiella 6 Efflux systems and regulators 17 None None None 11 | klebsiella 8 Heavy metal resistance genes 40 None None None 12 | klebsiella 7 hvK2 multiplex PCR 5 None None None 13 | klebsiella 22 otherResistanceGenes 2 None None None 14 | klebsiella 12 Quinolone resistance genes 10 None None None 15 | klebsiella 19 r_cg_MLST 0 None None None 16 | klebsiella 18 scgMLST629_S 629 1729 2018-07-12 2018-07-12 17 | klebsiella 3 scgMLST634 632 None None None 18 | klebsiella 21 SmST 4 35 2018-07-12 2018-07-12 19 | klebsiella 9 Species-specific markers 7 None None None 20 | klebsiella 14 Urease-Nickel cluster 6 None None None 21 | klebsiella 4 Virulence genes 80 None None None 22 | klebsiella 2 wzi 1 589 2020-04-27 2020-04-27 23 | klebsiella 16 YbST 11 346 2018-07-26 2018-07-26 24 | listeria 2 MLST 7 2133 2020-05-20 2020-05-20 25 | listeria 3 cgMLST1748 1748 18534 2020-04-14 2020-04-14 26 | listeria 4 PCR-serogroup 5 149 2020-05-20 2020-05-20 27 | listeria 5 Virulence 92 None None None 28 | listeria 6 Antibiotic Resistance 17 None None None 29 | listeria 7 Metal & Detergent Resistance 8 None None None 30 | listeria 8 Stress Islands 7 None None None 31 | listeria 10 Listeria Stress Islands 88 None None None 32 | listeria 11 sigB operon 8 None None None 33 | listeria 12 Rhamnose operon 5 None None None 34 | listeria 13 Clonogrouping 0 None None None 35 | listeria 14 PBPs 0 None None None 36 | -------------------------------------------------------------------------------- /pubmlst_client/download.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import argparse 4 | import datetime 5 | import json 6 | import os 7 | import sys 8 | import time 9 | 10 | from pubmlst_client.util import get 11 | 12 | 13 | def main(): 14 | 15 | parser = argparse.ArgumentParser() 16 | parser.add_argument("--scheme_name", "-s", dest="scheme_name", help="scheme name", required=True) 17 | parser.add_argument("--scheme_id", "-i", dest="scheme_id", default="1", help="scheme id") 18 | parser.add_argument("--outdir", "-o", dest="outdir", default='.', help="output directory") 19 | parser.add_argument("--base-url", "-b", dest="base_url", default='http://rest.pubmlst.org/db', help="Base URL for the API. Suggested values are: http://rest.pubmlst.org/db (default), https://bigsdb.pasteur.fr/api/db") 20 | args = parser.parse_args() 21 | 22 | if not os.path.exists(args.outdir): 23 | os.mkdir(args.outdir) 24 | 25 | api_url_base = args.base_url 26 | 27 | scheme_url = '/'.join([ 28 | api_url_base, 29 | 'pubmlst_' + args.scheme_name + '_seqdef', 30 | 'schemes', 31 | args.scheme_id 32 | ]) 33 | 34 | scheme_response = json.loads(get(scheme_url)) 35 | 36 | for locus_url in scheme_response['loci']: 37 | locus = json.loads(get(locus_url)) 38 | plaintext_header = {'Content-Type': 'text/plain'} 39 | alleles_fasta = get(locus['alleles_fasta'], headers=plaintext_header).decode('utf-8') 40 | output_filename = os.path.join(args.outdir, locus['id'] + '.fasta') 41 | with open(output_filename, 'w') as f: 42 | f.write(alleles_fasta) 43 | log_msg = { 44 | 'timestamp': str(datetime.datetime.now().isoformat()), 45 | 'event': 'file_downloaded', 46 | 'filename': output_filename, 47 | } 48 | print(json.dumps(log_msg), file=sys.stderr) 49 | 50 | 51 | 52 | if __name__ == '__main__': 53 | main() 54 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # pubMLST Client 2 | 3 | ## Usage 4 | 5 | ### List available schemes 6 | 7 | ``` 8 | usage: pubmlst_list [-h] [--pattern PATTERN] [--exclude_pattern EXCLUDE_PATTERN] [--names_only] [--base-url BASE_URL] 9 | 10 | optional arguments: 11 | -h, --help show this help message and exit 12 | --pattern PATTERN, -p PATTERN 13 | regex pattern to filter scheme names 14 | --exclude_pattern EXCLUDE_PATTERN, -e EXCLUDE_PATTERN 15 | regex pattern to filter scheme names 16 | --names_only, -n Only show scheme names 17 | --base-url BASE_URL, -b BASE_URL 18 | Base URL for the API. Suggested values are: http://rest.pubmlst.org/db (default), https://bigsdb.pasteur.fr/api/db 19 | ``` 20 | 21 | #### Example Output 22 | 23 | | name | id | description | locus_count | records | last_added | last_updated | 24 | |:------------- | --:|:-------------- | -----------:| -------:| ----------:| ------------:| 25 | | achromobacter | 1 | MLST | 7 | 480 | 2020-02-20 | 2020-02-20 | 26 | | abaumannii | 1 | MLST (Oxford) | 7 | 2088 | 2020-02-07 | 2020-02-07 | 27 | | abaumannii | 2 | MLST (Pasteur) | 7 | 1438 | 2020-02-18 | 2020-02-18 | 28 | | aeromonas | 1 | MLST | 6 | 656 | 2020-01-07 | 2020-01-08 | 29 | 30 | 31 | ### Download schemes 32 | 33 | ``` 34 | usage: pubmlst_download [-h] --scheme_name SCHEME_NAME [--scheme_id SCHEME_ID] [--outdir OUTDIR] [--base-url BASE_URL] 35 | 36 | optional arguments: 37 | -h, --help show this help message and exit 38 | --scheme_name SCHEME_NAME, -s SCHEME_NAME 39 | scheme name 40 | --scheme_id SCHEME_ID, -i SCHEME_ID 41 | scheme id 42 | --outdir OUTDIR, -o OUTDIR 43 | output directory 44 | --base-url BASE_URL, -b BASE_URL 45 | Base URL for the API. Suggested values are: http://rest.pubmlst.org/db (default), https://bigsdb.pasteur.fr/api/db 46 | ``` 47 | -------------------------------------------------------------------------------- /pubmlst_client/list.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import argparse 4 | import json 5 | import os 6 | import re 7 | import urllib.request 8 | import sys 9 | import time 10 | 11 | from pubmlst_client.util import get 12 | 13 | 14 | def main(): 15 | parser = argparse.ArgumentParser() 16 | parser.add_argument('--pattern', '-p', default="", help="regex pattern to filter scheme names") 17 | parser.add_argument('--exclude_pattern', '-e', default="", help="regex pattern to filter scheme names") 18 | parser.add_argument('--names_only', '-n', default="", action='store_true', help="Only show scheme names") 19 | parser.add_argument("--base-url", "-b", dest="base_url", default='http://rest.pubmlst.org/db', help="Base URL for the API. Suggested values are: http://rest.pubmlst.org/db (default), https://bigsdb.pasteur.fr/api/db") 20 | 21 | args = parser.parse_args() 22 | 23 | details_fields = [ 24 | 'id', 25 | 'description', 26 | 'locus_count', 27 | 'records', 28 | 'last_added', 29 | 'last_updated', 30 | ] 31 | 32 | if args.names_only: 33 | print('name') 34 | else: 35 | print('\t'.join(['name'] + details_fields)) 36 | 37 | api_url_base = args.base_url 38 | 39 | url_base_response = json.loads(get(api_url_base)) 40 | 41 | 42 | for db in url_base_response: 43 | databases = db['databases'] 44 | for database in databases: 45 | if args.exclude_pattern != "": 46 | if re.search('pubmlst_(' + '.*' + args.exclude_pattern + '.*' + ')_seqdef$', database['name']): 47 | continue 48 | scheme_match = re.search('pubmlst_(' + '.*' + args.pattern + '.*' + ')_seqdef$', database['name']) 49 | if scheme_match: 50 | scheme_name = scheme_match.group(1) 51 | if args.names_only: 52 | print(scheme_name) 53 | break 54 | seqdef_response = get(database['href']) 55 | if seqdef_response: 56 | schemes_response = get(json.loads(seqdef_response)['schemes']) 57 | if schemes_response: 58 | for scheme in json.loads(schemes_response)['schemes']: 59 | scheme_details_response = get(scheme['scheme']) 60 | if scheme_details_response: 61 | details = {} 62 | for field in details_fields: 63 | try: 64 | details[field] = json.loads(scheme_details_response)[field] 65 | except KeyError: 66 | details[field] = None 67 | print('\t'.join(map(str, [scheme_name] + list(details.values()))), flush=True) 68 | 69 | 70 | if __name__ == '__main__': 71 | main() 72 | -------------------------------------------------------------------------------- /scheme_list_snapshots/2020-02-20_pubmlst_scheme_list.tsv: -------------------------------------------------------------------------------- 1 | name id description locus_count records last_added last_updated 2 | achromobacter 1 MLST 7 480 2020-02-20 2020-02-20 3 | abaumannii 1 MLST (Oxford) 7 2088 2020-02-07 2020-02-07 4 | abaumannii 2 MLST (Pasteur) 7 1438 2020-02-18 2020-02-18 5 | aeromonas 1 MLST 6 656 2020-01-07 2020-01-08 6 | aphagocytophilum 1 MLST 7 184 2019-11-14 2019-11-14 7 | arcobacter 1 MLST 7 831 2019-02-19 2019-02-19 8 | bcereus 1 MLST 7 2485 2020-01-28 2020-01-28 9 | blicheniformis 14 MLST 6 47 2018-05-04 2018-05-04 10 | bsubtilis 1 MLST 7 175 2019-12-04 2019-12-04 11 | llactis_phage 1 MLST 5 221 2017-06-19 2017-06-19 12 | bbacilliformis 1 MLST 7 14 2017-06-17 2017-06-17 13 | bhenselae 1 MLST 8 36 2019-09-24 2019-09-24 14 | bwashoensis 1 MLST 6 21 2019-08-22 2019-08-22 15 | bordetella 3 MLST 7 96 2020-02-07 2020-02-07 16 | bordetella 1 Bordetella core genes 1415 None None None 17 | bordetella 2 Bordetella virulence associated genes 20 None None None 18 | borrelia 1 MLST 8 932 2020-01-02 2020-01-02 19 | brachyspira 5 B. hampsonii MLST 6 20 2015-02-18 2015-02-18 20 | brachyspira 2 B. hyodysenteriae MLST 7 263 2019-12-06 2019-12-06 21 | brachyspira 3 B. intermedia MLST 7 83 2015-07-20 2015-07-20 22 | brachyspira 4 B. pilosicoli MLST 7 94 2019-04-23 2019-04-23 23 | brachyspira 1 Brachyspira MLST 7 36 2012-01-18 2012-01-18 24 | brucella 1 MLST (9 locus) 9 96 2019-09-11 2019-09-11 25 | brucella 2 MLST (21 locus) 21 150 2019-09-11 2019-09-11 26 | bcc 1 MLST 7 1728 2020-02-20 2020-02-20 27 | bpseudomallei 1 MLST 7 1773 2020-01-24 2020-01-24 28 | campylobacter_nonjejuni 5 C. concisus/curvus MLST 7 130 2015-03-11 2015-03-11 29 | campylobacter_nonjejuni 9 C. fetus MLST 7 69 2017-02-24 2017-02-24 30 | campylobacter_nonjejuni 1 C. helveticus MLST 7 9 2015-01-12 2015-01-12 31 | campylobacter_nonjejuni 6 C. hyointestinalis MLST 7 134 2018-11-28 2018-11-28 32 | campylobacter_nonjejuni 2 C. insulaenigrae MLST 7 43 2011-11-10 2011-11-10 33 | campylobacter_nonjejuni 7 C. lanienae MLST 7 172 2018-11-27 2018-11-27 34 | campylobacter_nonjejuni 3 C. lari MLST 7 161 2018-11-28 2018-11-28 35 | campylobacter_nonjejuni 8 C. sputorum MLST 7 16 2011-11-18 2011-11-18 36 | campylobacter_nonjejuni 4 C. upsaliensis MLST 7 204 2017-08-28 2017-08-28 37 | campylobacter 1 MLST 7 10207 2020-02-18 2020-02-18 38 | campylobacter 3 1643 Gundogdu loci 1643 None None None 39 | campylobacter 6 C. coli 15-537360 1588 None None None 40 | campylobacter 4 C. jejuni / C. coli cgMLST v1.0 1343 33469 2020-01-29 2020-01-29 41 | campylobacter 7 ED pathway 7 None None None 42 | campylobacter 2 eMLST (21 partial genes) 21 None None None 43 | campylobacter 5 Ribosomal Protein Genes 52 None None None 44 | calbicans 1 MLST 7 3566 2018-10-31 2018-10-31 45 | cglabrata 1 MLST 6 177 2020-01-28 2020-01-28 46 | ctropicalis 1 MLST 6 930 2020-01-24 2020-01-24 47 | cmaltaromaticum 1 MLST 7 56 2018-04-11 2018-04-11 48 | chlamydiales 16 Aerobic and ATP Biogenesis 16 None None None 49 | chlamydiales 7 Amino Acyl tRNA Synthesis 3 None None None 50 | chlamydiales 17 Aromatic Amino Acids 10 None None None 51 | chlamydiales 18 Aspartate Amino Acid 5 None None None 52 | chlamydiales 20 Biotin, Lipoate and Ubiquinone 6 None None None 53 | chlamydiales 26 Both Purine and Pyrimidine Metabolism 4 None None None 54 | chlamydiales 44 C. abortus cgMLST v1.0 959 None None None 55 | chlamydiales 30 Cell Division 9 None None None 56 | chlamydiales 42 C. trachomatis cgMLST v1.0 817 366 2019-12-02 2019-12-02 57 | chlamydiales 3 DNA Replication 24 None None None 58 | chlamydiales 14 Electron Transport Chain 4 None None None 59 | chlamydiales 37 Eukaryotic Type Chromatin Factors 4 None None None 60 | chlamydiales 29 Fatty Acid and Phospholipid Metabolism 27 None None None 61 | chlamydiales 21 Folic Acid 5 None None None 62 | chlamydiales 10 Glycolysis, Gluconeogensis, Glycogen 20 None None None 63 | chlamydiales 27 Membrane Proteins, Lipoproteins, Porins 9 None None None 64 | chlamydiales 36 Miscellaneous Enzymes/Conserved Proteins 44 None None None 65 | chlamydiales 1 MLST (Chlamydiales) 7 280 2020-02-17 2020-02-17 66 | chlamydiales 38 MLST (C. trachomatis) 7 88 2019-11-18 2019-11-18 67 | chlamydiales 41 MLST (C. trachomatis Uppsala) 5 520 2015-10-12 2016-02-22 68 | chlamydiales 4 Nucleotide Excision and Repair 18 None None None 69 | chlamydiales 33 Pathogenesis Associated Proteins 25 None None None 70 | chlamydiales 15 Pentose Phosphate Pathway 8 None None None 71 | chlamydiales 8 Peptide Synthesis 14 None None None 72 | chlamydiales 28 Peptidoglycan 16 None None None 73 | chlamydiales 11 Phosphorous and Sulphur 4 None None None 74 | chlamydiales 2 Plasmid loci 8 None None None 75 | chlamydiales 40 Plasmid MLST 8 47 2015-10-06 2015-10-06 76 | chlamydiales 22 Porphyrin 9 None None None 77 | chlamydiales 9 Protein Folding, Assembly, Modification 37 None None None 78 | chlamydiales 24 Purine Metabolism 3 None None None 79 | chlamydiales 25 Pyrimidine Metabolism 7 None None None 80 | chlamydiales 12 Pyruvate Dehydrogenase 7 None None None 81 | chlamydiales 5 Recombination 8 None None None 82 | chlamydiales 23 Riboflavin 5 None None None 83 | chlamydiales 43 Ribosomal Protein genes 52 None None None 84 | chlamydiales 6 RNA Associated 44 None None None 85 | chlamydiales 19 Serine Amino Acid 2 None None None 86 | chlamydiales 31 Signal Transduction 18 None None None 87 | chlamydiales 35 Specific Proteins 11 None None None 88 | chlamydiales 13 TCA Cycle 11 None None None 89 | chlamydiales 34 Transport Related Proteins 54 None None None 90 | chlamydiales 39 Type III Effector Proteins 0 None None None 91 | chlamydiales 32 Type III Secretion Systems 58 None None None 92 | cfreundii 1 MLST 7 525 2020-01-24 2020-01-24 93 | csinensis 1 MLST 8 254 2012-01-07 2012-01-07 94 | cdifficile 2 cwp cluster genes 6 None None None 95 | cdifficile 1 MLST 7 669 2020-02-13 2020-02-13 96 | cbotulinum 1 MLST 7 120 2019-12-16 2019-12-16 97 | cbotulinum 2 Extended MLST 14 0 None None 98 | csepticum 1 MLST 7 8 2008-07-29 2008-07-29 99 | cdiphtheriae 1 MLST 7 664 2020-02-11 2020-02-11 100 | cronobacter 4 cogMLST 1865 None None None 101 | cronobacter 3 Ext-MLST 3 0 None None 102 | cronobacter 5 Gcog 222 None None None 103 | cronobacter 1 MLST 7 729 2020-02-20 2020-02-20 104 | cronobacter 6 O-serotype 2 0 None None 105 | cronobacter 2 Tax-MLST 2 None None None 106 | pacnes 3 MLST 8 152 2019-08-19 2019-08-19 107 | dnodosus 3 cgMLST 714 None None None 108 | dnodosus 1 MLST 7 115 2017-09-13 2017-09-13 109 | edwardsiella 1 MLST 10 18 2015-12-03 2015-12-03 110 | ecloacae 1 MLST 7 1337 2020-02-13 2020-02-13 111 | efaecalis 1 MLST 7 979 2020-02-10 2020-02-10 112 | efaecium 1 MLST 7 1697 2020-02-17 2020-02-17 113 | escherichia 1 MLST (Achtman) 7 9506 2020-02-20 2020-02-20 114 | escherichia 2 MLST (Pasteur) 8 986 2020-01-30 2020-01-30 115 | escherichia 10 accessory genome 22489 None None None 116 | escherichia 3 beta-lactamase resistance 9 None None None 117 | escherichia 6 cgMLST 2513 None None None 118 | escherichia 12 IncL/M 3 None None None 119 | escherichia 4 locus of enterocyte effacement (LEE) island 40 None None None 120 | escherichia 14 oxa-48 chromosome loci 29 None None None 121 | escherichia 8 pO157 plasmid 49 None None None 122 | escherichia 13 pOXA-48 plasmid 71 None None None 123 | escherichia 11 quinolone resistance 4 None None None 124 | escherichia 5 shiga toxins 4 None None None 125 | escherichia 9 virulence genes 16 None None None 126 | escherichia 7 wgMLST 25002 None None None 127 | fpsychrophilum 1 MLST 7 194 2018-02-09 2018-02-09 128 | gallibacterium 1 MLST 8 81 2012-06-12 2012-06-12 129 | hinfluenzae 42 Alanine, aspartate and glutamate metabolism 13 None None None 130 | hinfluenzae 14 Aminoacyl-tRNA biosynthesis 24 None None None 131 | hinfluenzae 19 Amino sugar and nucleotide sugar metabolism 21 None None None 132 | hinfluenzae 52 Antimicrobial Resistance 6 None None None 133 | hinfluenzae 43 Arginine and proline metabolism 20 None None None 134 | hinfluenzae 21 Butanoate metabolism 8 None None None 135 | hinfluenzae 2 Capsule - Region I 7 None None None 136 | hinfluenzae 4 Capsule - Region III 4 None None None 137 | hinfluenzae 7 Capsule - serotype A 2 None None None 138 | hinfluenzae 3 Capsule - serotype B 8 None None None 139 | hinfluenzae 8 Capsule - serotype C 4 None None None 140 | hinfluenzae 9 Capsule - serotype D 5 None None None 141 | hinfluenzae 6 Capsule - Serotype E 8 None None None 142 | hinfluenzae 5 Capsule - serotype F 3 None None None 143 | hinfluenzae 38 Cysteine and methionine metabolism 17 None None None 144 | hinfluenzae 10 DNA Replication 13 None None None 145 | hinfluenzae 32 Fatty acid biosynthesis 11 None None None 146 | hinfluenzae 31 Fatty acid metabolism 3 None None None 147 | hinfluenzae 23 Fructose and mannose metabolism 13 None None None 148 | hinfluenzae 20 Galactose Metabolism 6 None None None 149 | hinfluenzae 33 Glycerolipid metabolism 6 None None None 150 | hinfluenzae 34 Glycerophospholipid metabolism 19 None None None 151 | hinfluenzae 39 Glycine, serine and threonine metabolism 19 None None None 152 | hinfluenzae 15 Glycolysis 15 None None None 153 | hinfluenzae 16 Glyoxylate and dicarboxylate metabolism 11 None None None 154 | hinfluenzae 45 Histidine metabolism 8 None None None 155 | hinfluenzae 50 LOS Biosynthesis 23 None None None 156 | hinfluenzae 40 Lysine biosynthesis 14 None None None 157 | hinfluenzae 47 Lysine degradation 4 None None None 158 | hinfluenzae 26 Methane metabolism 26 None None None 159 | hinfluenzae 1 MLST 7 2280 2020-01-21 2020-01-21 160 | hinfluenzae 27 Nitrogen Metabolism 10 None None None 161 | hinfluenzae 11 Nucleotide Excision Repair 12 None None None 162 | hinfluenzae 29 Oxidative phosphorylation 10 None None None 163 | hinfluenzae 25 Pentose and glucuronate interconversions 4 None None None 164 | hinfluenzae 24 Pentose Phosphate Pathway 15 None None None 165 | hinfluenzae 37 Phenylalanine metabolism 4 None None None 166 | hinfluenzae 44 Phenylalanine, tyrosine, tryptophan biosynthesis 19 None None None 167 | hinfluenzae 51 Pilus Biosynthesis 6 None None None 168 | hinfluenzae 22 Propanoate metabolism 10 None None None 169 | hinfluenzae 35 Purine Metabolism 58 None None None 170 | hinfluenzae 36 Pyrimidine Metabolism 43 None None None 171 | hinfluenzae 18 Pyruvate Metabolism 20 None None None 172 | hinfluenzae 30 Reductive carboxylate cycle (CO2 fixation) 13 None None None 173 | hinfluenzae 13 Ribosomal Protein Genes 56 None None None 174 | hinfluenzae 12 RNA Polymerase 11 None None None 175 | hinfluenzae 28 Sulphur Metabolism 8 None None None 176 | hinfluenzae 17 TCA Cycle 12 None None None 177 | hinfluenzae 41 Tryptophan metabolism 6 None None None 178 | hinfluenzae 46 Tyrosine metabolism 4 None None None 179 | hinfluenzae 48 Valine, leucine and isoleucine biosynthesis 11 None None None 180 | hinfluenzae 49 Valine, leucine and isoleucine degradation 3 None None None 181 | hparasuis 1 MLST 7 397 2019-08-05 2019-08-05 182 | hcinaedi 1 MLST 7 20 2019-12-06 2019-12-06 183 | helicobacter 1 MLST 7 3687 2020-01-10 2020-01-10 184 | hsuis 1 MLST 7 138 2017-05-17 2017-05-17 185 | kaerogenes 1 MLST 7 203 2020-01-15 2020-01-15 186 | koxytoca 1 MLST 7 271 2020-01-25 2020-01-25 187 | kseptempunctata 1 MLST 2 3 2014-12-22 2014-12-22 188 | lsalivarius 1 MLST 5 25 2010-12-07 2010-12-07 189 | leptospira 1 MLST (scheme 1) 7 322 2019-12-17 2019-12-17 190 | leptospira 2 MLST (scheme 2) 7 273 2019-04-24 2019-04-24 191 | leptospira 3 MLST (scheme 3) 6 194 2020-02-10 2020-02-10 192 | leptospira 5 LPS 21 None None None 193 | leptospira 4 Pathogenic cgMLST 1565 None None None 194 | liberibacter 1 MLST 7 10 2019-01-15 2019-01-15 195 | mcanis 1 MLST 7 83 2019-10-21 2019-10-21 196 | mcaseolyticus 1 MLST 7 67 2019-10-21 2019-10-21 197 | mplutonius 1 MLST 4 36 2020-01-29 2020-01-29 198 | mabscessus 1 M. abscessus MLST 7 26 2012-04-25 2012-04-25 199 | mabscessus 2 M. massiliense MLST 7 12 2012-03-27 2012-04-25 200 | mycobacteria 1 Core genome (H37Rv ref vs 19 finished species) 744 5626 2017-08-25 2017-08-25 201 | mycobacteria 2 MLST 8 873 2019-11-15 2019-11-15 202 | magalactiae 1 MLST 5 35 2019-04-24 2019-04-24 203 | mbovis 1 MLST 7 185 2020-01-10 2020-01-10 204 | mbovis 2 MLST (revised) 7 88 2020-01-09 2020-01-09 205 | mflocculare 1 MLST 3 8 2018-07-03 2018-07-03 206 | mgallisepticum 1 MLST#1 (Ghanem) 7 55 2019-03-09 2019-03-09 207 | mgallisepticum 2 MLST#2 (Bekő) 6 57 2019-03-24 2019-03-24 208 | mhominis 1 MLST 5 23 2019-10-16 2019-10-16 209 | mhominis 2 MVLST 5 31 2019-10-16 2019-10-16 210 | mhominis 3 eMLST 10 32 2019-10-16 2019-10-16 211 | mhyopneumoniae 1 MLST 3 143 2020-01-15 2020-01-15 212 | mhyorhinis 1 MLST 6 104 2019-04-26 2019-04-26 213 | miowae 1 MLST 6 35 2019-05-05 2019-05-05 214 | mpneumoniae 1 MLST 8 37 2019-12-18 2019-12-18 215 | msynoviae 1 MLST 7 139 2020-01-27 2020-01-27 216 | neisseria 1 MLST 7 15322 2020-02-19 2020-02-19 217 | neisseria 2 Finetyping antigens 3 None None None 218 | neisseria 42 rplF species 1 211 2019-02-06 2019-02-06 219 | neisseria 7 ADP-heptose biosynthesis 5 None None None 220 | neisseria 5 Antibiotic resistance 11 None None None 221 | neisseria 3 Antigen genes 7 None None None 222 | neisseria 52 beta lactamase plasmid 8 18 2018-04-17 2018-04-17 223 | neisseria 53 Bexsero Antigen Sequence Typing (BAST) 5 3478 2020-02-16 2020-02-16 224 | neisseria 63 Capsule Null (cnl) 1 None None None 225 | neisseria 29 Capsule Region A - Serogroup A 4 None None None 226 | neisseria 36 Capsule Region A - Serogroup B 5 None None None 227 | neisseria 37 Capsule Region A - Serogroup C 6 None None None 228 | neisseria 35 Capsule Region A - Serogroup E 7 None None None 229 | neisseria 32 Capsule Region A - Serogroup H 4 None None None 230 | neisseria 33 Capsule Region A - Serogroup L 3 None None None 231 | neisseria 38 Capsule Region A - Serogroup W 6 None None None 232 | neisseria 30 Capsule Region A - Serogroup X 3 None None None 233 | neisseria 39 Capsule Region A - Serogroup Y 6 None None None 234 | neisseria 31 Capsule Region A - Serogroup Z 4 None None None 235 | neisseria 41 Capsule Region B 2 None None None 236 | neisseria 40 Capsule Region C 4 None None None 237 | neisseria 48 Capsule Region D and D' 6 None None None 238 | neisseria 49 Conjugative Plasmid 50 242 2018-04-25 2018-04-25 239 | neisseria 66 Cryptic Plasmid 9 96 2018-05-15 2018-05-15 240 | neisseria 25 DNA replication 16 None None None 241 | neisseria 4 eMLST (20 locus partial genes) 20 None None None 242 | neisseria 12 eMLST (20 locus whole genes) 20 None None None 243 | neisseria 6 Factor H binding protein 10 None None None 244 | neisseria 15 Glycolysis 11 None None None 245 | neisseria 50 Gonococcal Genetic Island 73 None None None 246 | neisseria 72 Human-restricted Neisseria cgMLST v1.0 1441 None None None 247 | neisseria 21 Iron acquisition 7 None None None 248 | neisseria 19 Kdo addition 5 None None None 249 | neisseria 45 L3_cgMLST 1742 None None None 250 | neisseria 68 L44_cgMLST 1699 None None None 251 | neisseria 69 L44_pgMLST 1786 None None None 252 | neisseria 17 Lipid A biosynthesis: acyltransferases 4 None None None 253 | neisseria 18 Lipid A biosynthesis: other 5 None None None 254 | neisseria 9 LOS alpha chain transferases 7 None None None 255 | neisseria 8 LOS inner core transferases 7 None None None 256 | neisseria 20 LOS transport/export 5 None None None 257 | neisseria 43 Methyltransferases 0 None None None 258 | neisseria 54 MGI-1 7 None None None 259 | neisseria 55 MGI-2 21 None None None 260 | neisseria 56 MGI-3 18 None None None 261 | neisseria 46 NadA 2 None None None 262 | neisseria 44 Neisseria Heparin Binding Antigen (NHBA) 2 None None None 263 | neisseria 71 NG MAST 2 19070 2020-02-18 2020-02-18 264 | neisseria 57 N. gonorrhoeae Beta-lactam AMR 5 None None None 265 | neisseria 62 N. gonorrhoeae cgMLST v1.0 1649 6744 2020-02-05 2020-02-05 266 | neisseria 61 N. gonorrhoeae Efflux Pumps AMR 10 None None None 267 | neisseria 58 N. gonorrhoeae Fluoroquinolone AMR 4 None None None 268 | neisseria 59 N. gonorrhoeae Macrolides AMR 2 None None None 269 | neisseria 60 N. gonorrhoeae plasmid mediated AMR 2 None None None 270 | neisseria 67 NG STAR 7 1450 2019-12-18 2019-12-18 271 | neisseria 47 N. meningitidis cgMLST v1.0 1605 18083 2020-02-20 2020-02-20 272 | neisseria 27 Nucleotide excision repair 8 None None None 273 | neisseria 64 OMV peptide 50 None None None 274 | neisseria 65 OMV peptide typing 24 4248 2019-05-15 2019-05-15 275 | neisseria 13 Pilus genes 27 None None None 276 | neisseria 28 Protein glycosylation 14 None None None 277 | neisseria 22 Purine metabolism 39 None None None 278 | neisseria 23 Pyrimidine metabolism 32 None None None 279 | neisseria 14 Pyruvate dehydrogenase complex 3 None None None 280 | neisseria 24 Ribosomal protein genes 55 None None None 281 | neisseria 26 RNA polymerase 4 None None None 282 | neisseria 34 Small regulatory RNAs 3 None None None 283 | neisseria 16 TCA cycle 16 None None None 284 | neisseria 70 tRNA molecules 21 None None None 285 | neisseria 11 UDP-GlcNAc synthesis 1 None None None 286 | neisseria 10 UDP-glucose and UDP-galactose biosynthesis 2 None None None 287 | neisseria 51 VirB T4SS 31 None None None 288 | otsutsugamushi 1 MLST 7 98 2019-05-10 2019-05-10 289 | orhinotracheale 1 MLST 7 35 2018-01-03 2018-01-03 290 | plarvae 1 MLST 7 25 2020-01-30 2020-01-30 291 | pmultocida 1 Multiple host MLST 7 122 2020-02-06 2020-02-06 292 | pmultocida 2 RIRDC MLST 7 373 2019-11-28 2019-11-28 293 | ppentosaceus 1 MLST 7 17 2013-02-19 2013-02-19 294 | pdamselae 1 MLST 6 56 2018-08-09 2018-08-09 295 | psalmonis 1 MLST 7 24 2017-04-07 2017-04-07 296 | plasmid 7 IncA/C cgPMLST 28 41 2018-01-05 2018-01-05 297 | plasmid 6 IncA/C PMLST 4 13 2018-01-05 2018-01-05 298 | plasmid 3 IncF RST 7 None None None 299 | plasmid 5 IncHI1 MLST 6 15 2018-05-30 2018-05-30 300 | plasmid 2 IncHI2 DLST 2 15 2018-09-05 2018-09-05 301 | plasmid 1 IncI1 MLST 5 313 2019-07-25 2019-07-25 302 | plasmid 4 IncN MLST 3 22 2019-03-12 2019-03-12 303 | plasmid 8 pBSSB1-family 3 35 2019-04-09 2019-04-09 304 | pgingivalis 1 MLST 7 138 2007-08-12 2007-08-12 305 | paeruginosa 1 MLST 7 3375 2020-01-29 2020-01-29 306 | paeruginosa 5 pAMBL1 30 None None None 307 | paeruginosa 4 pCOL-1 29 None None None 308 | paeruginosa 6 pCOOP-101 32 None None None 309 | paeruginosa 2 pMATVIM-7 29 None None None 310 | paeruginosa 3 pNOR-2000 24 None None None 311 | pfluorescens 1 MLST 7 110 2019-06-28 2019-06-28 312 | pputida 1 MLST 8 93 2019-08-22 2019-08-22 313 | ranatipestifer 1 MLST 7 44 2017-09-12 2017-09-12 314 | rhodococcus 1 MLST 7 39 2016-02-22 2016-02-22 315 | salmonella 4 cgMLST v2 (Enterobase) 3002 None None None 316 | salmonella 2 MLST 7 6624 2020-02-20 2020-02-20 317 | salmonella 1 Oxford loci 3633 None None None 318 | salmonella 3 SalmcgMLST v1.0 2750 13722 2020-02-06 2020-02-06 319 | sparasitica 1 MLST 7 15 2018-03-26 2018-03-26 320 | sinorhizobium 1 MLST 10 136 2010-05-07 2010-05-07 321 | smaltophilia 1 MLST 7 473 2020-02-13 2020-02-13 322 | saureus 1 MLST 7 5859 2020-02-14 2020-02-14 323 | saureus 2 Core 2208 2208 None None None 324 | sepidermidis 1 MLST 7 967 2019-11-11 2019-11-11 325 | shaemolyticus 1 MLST 7 69 2019-10-22 2019-10-22 326 | shominis 1 MLST 6 57 2017-10-19 2017-10-19 327 | spseudintermedius 1 MLST 7 1601 2020-01-31 2020-01-31 328 | oralstrep 2 S. mutans MLST (Do) 8 179 2019-10-08 2019-10-08 329 | oralstrep 3 S. mutans MLST (Nakano) 8 269 2020-01-22 2020-01-22 330 | oralstrep 1 S. oralis MLST 7 78 2015-10-23 2015-10-23 331 | sagalactiae 1 MLST 7 1442 2020-01-30 2020-01-30 332 | sagalactiae 37 Adherence Regulation 2 None None None 333 | sagalactiae 29 Alp Family Proteins 5 None None None 334 | sagalactiae 23 Amino Acid Metabolism 85 None None None 335 | sagalactiae 17 Ascorbate and Aldarate Metabolism 28 None None None 336 | sagalactiae 3 Biosynthesis and activation of sialic acid 5 None None None 337 | sagalactiae 30 C5a Peptidase 2 None None None 338 | sagalactiae 4 Capsular polysaccharide Biosynthesis 7 None None None 339 | sagalactiae 22 Fatty Acid Biosynthesis 18 None None None 340 | sagalactiae 31 Fibrinogen Binding Proteins 2 None None None 341 | sagalactiae 14 Fructose and Mannose Metabolism 36 None None None 342 | sagalactiae 15 Galactose Metabolism 34 None None None 343 | sagalactiae 12 Glycolysis 44 None None None 344 | sagalactiae 32 Haemolysin Operon 9 None None None 345 | sagalactiae 38 h_S.agalactiae cgMLST v1.0 1405 None None None 346 | sagalactiae 33 Hyaluronidase Activity 1 None None None 347 | sagalactiae 40 ICESag1962 51 None None None 348 | sagalactiae 39 IMESp2907 16 None None None 349 | sagalactiae 35 LysR family 1 None None None 350 | sagalactiae 18 Oxidative phosphorylation 13 None None None 351 | sagalactiae 13 Pentose Phosphate Pathway 23 None None None 352 | sagalactiae 19 Photosynthesis 8 None None None 353 | sagalactiae 27 PI-1 6 None None None 354 | sagalactiae 28 PI-2a 5 None None None 355 | sagalactiae 26 PI-2b 5 None None None 356 | sagalactiae 34 Pilus Regulator 1 None None None 357 | sagalactiae 21 Purine Metabolism 63 None None None 358 | sagalactiae 20 Pyrimidine Metabolism 51 None None None 359 | sagalactiae 6 Serotype Ia 4 None None None 360 | sagalactiae 7 Serotype Ib 4 None None None 361 | sagalactiae 8 Serotype II 6 None None None 362 | sagalactiae 9 Serotype III 4 None None None 363 | sagalactiae 10 Serotype IV 5 None None None 364 | sagalactiae 5 Serotype V 6 None None None 365 | sagalactiae 41 Serotype VI 4 None None None 366 | sagalactiae 42 Serotype VII 2 None None None 367 | sagalactiae 16 Starch and Sucrose Metabolism 36 None None None 368 | sagalactiae 2 Synthesis of the group B carbohydrate 15 None None None 369 | sagalactiae 11 TCA Cycle 5 None None None 370 | sagalactiae 25 Transcription 4 None None None 371 | sagalactiae 36 Transcriptional Regulator 1 None None None 372 | sagalactiae 24 Translation 25 None None None 373 | sbsec 1 MLST 10 214 2017-09-25 2017-09-25 374 | scanis 1 MLST 7 54 2019-12-09 2019-12-09 375 | sdysgalactiae 1 MLST 7 522 2020-02-17 2020-02-17 376 | sgallolyticus 1 MLST 7 109 2017-02-22 2017-02-22 377 | spneumoniae 1 MLST 7 15251 2020-02-19 2020-02-19 378 | spneumoniae 2 cgMLST 1360 7149 2020-02-14 2020-02-14 379 | spyogenes 1 MLST 7 1192 2020-02-20 2020-02-20 380 | ssuis 1 MLST 7 1289 2020-02-12 2020-02-12 381 | sthermophilus 1 MLST 10 119 2015-06-18 2015-06-18 382 | suberis 1 MLST 7 1212 2020-02-20 2020-02-20 383 | suberis 2 vMLST 10 0 None None 384 | szooepidemicus 1 MLST 7 400 2020-02-17 2020-02-17 385 | streptomyces 1 MLST 6 234 2016-01-22 2016-01-22 386 | taylorella 1 MLST 7 71 2020-01-23 2020-01-23 387 | tenacibaculum 1 MLST 7 130 2020-01-15 2020-01-15 388 | tpallidum 1 MLST 3 72 2019-11-28 2019-11-28 389 | tvaginalis 1 MLST 7 60 2016-02-08 2016-02-08 390 | ureaplasma 1 MLST 4 164 2018-09-14 2018-09-14 391 | ureaplasma 2 eMLST 6 229 2018-09-14 2018-09-14 392 | vcholerae 1 MLST 7 985 2020-01-02 2020-01-02 393 | vcholerae 2 MLST (O1 and O139) 5 422 2019-09-13 2019-09-13 394 | vcholerae 3 cgMLST 2443 1035 2020-02-08 2020-02-08 395 | vibrio 1 MLST 4 178 2019-11-19 2019-11-19 396 | vparahaemolyticus 1 MLST 7 2243 2020-02-20 2020-02-20 397 | vparahaemolyticus 2 AA-MLST 7 244 2018-04-20 2018-04-20 398 | vparahaemolyticus 3 cgMLST 2254 None None None 399 | vparahaemolyticus 4 Virulence markers 3 None None None 400 | vtapetis 1 MLST 10 10 2011-09-22 2011-09-22 401 | vvulnificus 1 MLST 10 530 2019-09-19 2019-09-19 402 | wolbachia 1 MLST 5 574 2020-02-05 2020-02-05 403 | wolbachia 2 WSP 5 None None None 404 | xcitri 1 cgMLST 1618 228 2020-02-09 2020-02-09 405 | xfastidiosa 1 MLST 7 87 2019-03-06 2019-03-06 406 | yersinia 1 MLST 7 170 2015-06-16 2015-06-16 407 | yruckeri 1 MLST 6 30 2011-07-27 2011-07-27 408 | -------------------------------------------------------------------------------- /scheme_list_snapshots/2020-05-25_pubmlst_scheme_list.tsv: -------------------------------------------------------------------------------- 1 | name id description locus_count records last_added last_updated 2 | achromobacter 1 MLST 7 481 2020-05-21 2020-05-21 3 | abaumannii 1 MLST (Oxford) 7 2131 2020-04-06 2020-04-06 4 | abaumannii 2 MLST (Pasteur) 7 1476 2020-05-12 2020-05-12 5 | aeromonas 1 MLST 6 689 2020-04-13 2020-04-13 6 | aphagocytophilum 1 MLST 7 184 2019-11-14 2019-11-14 7 | arcobacter 1 MLST 7 831 2019-02-19 2019-02-19 8 | bcereus 1 MLST 7 2555 2020-05-18 2020-05-18 9 | blicheniformis 14 MLST 6 47 2018-05-04 2018-05-04 10 | bsubtilis 1 MLST 7 245 2020-05-12 2020-05-12 11 | llactis_phage 1 MLST 5 221 2017-06-19 2017-06-19 12 | bbacilliformis 1 MLST 7 14 2017-06-17 2017-06-17 13 | bhenselae 1 MLST 8 36 2019-09-24 2019-09-24 14 | bwashoensis 1 MLST 6 21 2019-08-22 2019-08-22 15 | bordetella 3 MLST 7 96 2020-02-07 2020-02-07 16 | bordetella 1 Bordetella core genes 1415 None None None 17 | bordetella 2 Bordetella virulence associated genes 20 None None None 18 | borrelia 1 MLST 8 933 2020-03-19 2020-03-19 19 | brachyspira 5 B. hampsonii MLST 6 20 2015-02-18 2015-02-18 20 | brachyspira 2 B. hyodysenteriae MLST 7 263 2019-12-06 2019-12-06 21 | brachyspira 3 B. intermedia MLST 7 83 2015-07-20 2015-07-20 22 | brachyspira 4 B. pilosicoli MLST 7 94 2019-04-23 2019-04-23 23 | brachyspira 1 Brachyspira MLST 7 36 2012-01-18 2012-01-18 24 | brucella 1 MLST (9 locus) 9 98 2020-05-13 2020-05-13 25 | brucella 2 MLST (21 locus) 21 150 2019-09-11 2019-09-11 26 | bcc 1 MLST 7 1843 2020-05-06 2020-05-06 27 | bpseudomallei 1 MLST 7 1862 2020-04-29 2020-04-29 28 | campylobacter_nonjejuni 5 C. concisus/curvus MLST 7 130 2015-03-11 2015-03-11 29 | campylobacter_nonjejuni 9 C. fetus MLST 7 69 2017-02-24 2017-02-24 30 | campylobacter_nonjejuni 1 C. helveticus MLST 7 9 2015-01-12 2015-01-12 31 | campylobacter_nonjejuni 6 C. hyointestinalis MLST 7 134 2018-11-28 2018-11-28 32 | campylobacter_nonjejuni 2 C. insulaenigrae MLST 7 43 2011-11-10 2011-11-10 33 | campylobacter_nonjejuni 7 C. lanienae MLST 7 172 2018-11-27 2018-11-27 34 | campylobacter_nonjejuni 3 C. lari MLST 7 161 2018-11-28 2018-11-28 35 | campylobacter_nonjejuni 8 C. sputorum MLST 7 16 2011-11-18 2011-11-18 36 | campylobacter_nonjejuni 4 C. upsaliensis MLST 7 204 2017-08-28 2017-08-28 37 | campylobacter 1 MLST 7 10342 2020-05-20 2020-05-20 38 | campylobacter 3 1643 Gundogdu loci 1643 None None None 39 | campylobacter 6 C. coli 15-537360 1588 None None None 40 | campylobacter 4 C. jejuni / C. coli cgMLST v1.0 1343 34115 2020-04-30 2020-04-30 41 | campylobacter 7 ED pathway 7 None None None 42 | campylobacter 2 eMLST (21 partial genes) 21 None None None 43 | campylobacter 5 Ribosomal Protein Genes 52 None None None 44 | calbicans 1 MLST 7 3569 2020-03-12 2020-03-12 45 | cglabrata 1 MLST 6 177 2020-01-28 2020-01-28 46 | ctropicalis 1 MLST 6 1046 2020-05-12 2020-05-12 47 | cmaltaromaticum 1 MLST 7 56 2018-04-11 2018-04-11 48 | chlamydiales 16 Aerobic and ATP Biogenesis 16 None None None 49 | chlamydiales 7 Amino Acyl tRNA Synthesis 3 None None None 50 | chlamydiales 17 Aromatic Amino Acids 10 None None None 51 | chlamydiales 18 Aspartate Amino Acid 5 None None None 52 | chlamydiales 20 Biotin, Lipoate and Ubiquinone 6 None None None 53 | chlamydiales 26 Both Purine and Pyrimidine Metabolism 4 None None None 54 | chlamydiales 44 C. abortus cgMLST v1.0 959 None None None 55 | chlamydiales 30 Cell Division 9 None None None 56 | chlamydiales 42 C. trachomatis cgMLST v1.0 817 369 2020-05-13 2020-05-13 57 | chlamydiales 3 DNA Replication 24 None None None 58 | chlamydiales 14 Electron Transport Chain 4 None None None 59 | chlamydiales 37 Eukaryotic Type Chromatin Factors 4 None None None 60 | chlamydiales 29 Fatty Acid and Phospholipid Metabolism 27 None None None 61 | chlamydiales 21 Folic Acid 5 None None None 62 | chlamydiales 10 Glycolysis, Gluconeogensis, Glycogen 20 None None None 63 | chlamydiales 27 Membrane Proteins, Lipoproteins, Porins 9 None None None 64 | chlamydiales 36 Miscellaneous Enzymes/Conserved Proteins 44 None None None 65 | chlamydiales 1 MLST (Chlamydiales) 7 298 2020-05-04 2020-05-04 66 | chlamydiales 38 MLST (C. trachomatis) 7 88 2019-11-18 2019-11-18 67 | chlamydiales 41 MLST (C. trachomatis Uppsala) 5 520 2015-10-12 2016-02-22 68 | chlamydiales 4 Nucleotide Excision and Repair 18 None None None 69 | chlamydiales 33 Pathogenesis Associated Proteins 25 None None None 70 | chlamydiales 15 Pentose Phosphate Pathway 8 None None None 71 | chlamydiales 8 Peptide Synthesis 14 None None None 72 | chlamydiales 28 Peptidoglycan 16 None None None 73 | chlamydiales 11 Phosphorous and Sulphur 4 None None None 74 | chlamydiales 2 Plasmid loci 8 None None None 75 | chlamydiales 40 Plasmid MLST 8 47 2015-10-06 2015-10-06 76 | chlamydiales 22 Porphyrin 9 None None None 77 | chlamydiales 9 Protein Folding, Assembly, Modification 37 None None None 78 | chlamydiales 24 Purine Metabolism 3 None None None 79 | chlamydiales 25 Pyrimidine Metabolism 7 None None None 80 | chlamydiales 12 Pyruvate Dehydrogenase 7 None None None 81 | chlamydiales 5 Recombination 8 None None None 82 | chlamydiales 23 Riboflavin 5 None None None 83 | chlamydiales 43 Ribosomal Protein genes 52 None None None 84 | chlamydiales 6 RNA Associated 44 None None None 85 | chlamydiales 19 Serine Amino Acid 2 None None None 86 | chlamydiales 31 Signal Transduction 18 None None None 87 | chlamydiales 35 Specific Proteins 11 None None None 88 | chlamydiales 13 TCA Cycle 11 None None None 89 | chlamydiales 34 Transport Related Proteins 54 None None None 90 | chlamydiales 39 Type III Effector Proteins 0 None None None 91 | chlamydiales 32 Type III Secretion Systems 58 None None None 92 | cfreundii 1 MLST 7 526 2020-03-09 2020-03-09 93 | csinensis 1 MLST 8 254 2012-01-07 2012-01-07 94 | cdifficile 2 cwp cluster genes 6 None None None 95 | cdifficile 1 MLST 7 689 2020-05-20 2020-05-20 96 | cbotulinum 1 MLST 7 120 2019-12-16 2019-12-16 97 | cbotulinum 2 Extended MLST 14 0 None None 98 | csepticum 1 MLST 7 8 2008-07-29 2008-07-29 99 | cdiphtheriae 1 MLST 7 696 2020-04-20 2020-04-20 100 | cronobacter 4 cogMLST 1865 None None None 101 | cronobacter 3 Ext-MLST 3 0 None None 102 | cronobacter 5 Gcog 222 None None None 103 | cronobacter 1 MLST 7 738 2020-05-11 2020-05-11 104 | cronobacter 6 O-serotype 2 0 None None 105 | cronobacter 2 Tax-MLST 2 None None None 106 | pacnes 3 MLST 8 153 2020-03-01 2020-03-01 107 | dnodosus 3 cgMLST 714 None None None 108 | dnodosus 1 MLST 7 115 2017-09-13 2017-09-13 109 | edwardsiella 1 MLST 10 22 2020-04-23 2020-04-23 110 | ecloacae 1 MLST 7 1395 2020-05-17 2020-05-17 111 | efaecalis 1 MLST 7 1000 2020-05-15 2020-05-15 112 | efaecium 1 MLST 7 1709 2020-04-03 2020-04-03 113 | escherichia 1 MLST (Achtman) 7 9860 2020-05-25 2020-05-25 114 | escherichia 2 MLST (Pasteur) 8 997 2020-04-22 2020-04-22 115 | escherichia 10 accessory genome 22489 None None None 116 | escherichia 3 beta-lactamase resistance 9 None None None 117 | escherichia 6 cgMLST 2513 None None None 118 | escherichia 12 IncL/M 3 None None None 119 | escherichia 4 locus of enterocyte effacement (LEE) island 40 None None None 120 | escherichia 14 oxa-48 chromosome loci 29 None None None 121 | escherichia 8 pO157 plasmid 49 None None None 122 | escherichia 13 pOXA-48 plasmid 71 None None None 123 | escherichia 11 quinolone resistance 4 None None None 124 | escherichia 5 shiga toxins 4 None None None 125 | escherichia 9 virulence genes 16 None None None 126 | escherichia 7 wgMLST 25002 None None None 127 | fpsychrophilum 1 MLST 7 194 2018-02-09 2018-02-09 128 | gallibacterium 1 MLST 8 81 2012-06-12 2012-06-12 129 | hinfluenzae 42 Alanine, aspartate and glutamate metabolism 13 None None None 130 | hinfluenzae 14 Aminoacyl-tRNA biosynthesis 24 None None None 131 | hinfluenzae 19 Amino sugar and nucleotide sugar metabolism 21 None None None 132 | hinfluenzae 52 Antimicrobial Resistance 6 None None None 133 | hinfluenzae 43 Arginine and proline metabolism 20 None None None 134 | hinfluenzae 21 Butanoate metabolism 8 None None None 135 | hinfluenzae 2 Capsule - Region I 7 None None None 136 | hinfluenzae 4 Capsule - Region III 4 None None None 137 | hinfluenzae 7 Capsule - serotype A 2 None None None 138 | hinfluenzae 3 Capsule - serotype B 8 None None None 139 | hinfluenzae 8 Capsule - serotype C 4 None None None 140 | hinfluenzae 9 Capsule - serotype D 5 None None None 141 | hinfluenzae 6 Capsule - Serotype E 8 None None None 142 | hinfluenzae 5 Capsule - serotype F 3 None None None 143 | hinfluenzae 38 Cysteine and methionine metabolism 17 None None None 144 | hinfluenzae 10 DNA Replication 13 None None None 145 | hinfluenzae 32 Fatty acid biosynthesis 11 None None None 146 | hinfluenzae 31 Fatty acid metabolism 3 None None None 147 | hinfluenzae 23 Fructose and mannose metabolism 13 None None None 148 | hinfluenzae 20 Galactose Metabolism 6 None None None 149 | hinfluenzae 33 Glycerolipid metabolism 6 None None None 150 | hinfluenzae 34 Glycerophospholipid metabolism 19 None None None 151 | hinfluenzae 39 Glycine, serine and threonine metabolism 19 None None None 152 | hinfluenzae 15 Glycolysis 15 None None None 153 | hinfluenzae 16 Glyoxylate and dicarboxylate metabolism 11 None None None 154 | hinfluenzae 45 Histidine metabolism 8 None None None 155 | hinfluenzae 53 Iron Acquisition 13 None None None 156 | hinfluenzae 50 LOS Biosynthesis 23 None None None 157 | hinfluenzae 40 Lysine biosynthesis 14 None None None 158 | hinfluenzae 47 Lysine degradation 4 None None None 159 | hinfluenzae 26 Methane metabolism 26 None None None 160 | hinfluenzae 1 MLST 7 2311 2020-05-18 2020-05-18 161 | hinfluenzae 27 Nitrogen Metabolism 10 None None None 162 | hinfluenzae 11 Nucleotide Excision Repair 12 None None None 163 | hinfluenzae 29 Oxidative phosphorylation 10 None None None 164 | hinfluenzae 25 Pentose and glucuronate interconversions 4 None None None 165 | hinfluenzae 24 Pentose Phosphate Pathway 15 None None None 166 | hinfluenzae 37 Phenylalanine metabolism 4 None None None 167 | hinfluenzae 44 Phenylalanine, tyrosine, tryptophan biosynthesis 19 None None None 168 | hinfluenzae 51 Pilus Biosynthesis 6 None None None 169 | hinfluenzae 22 Propanoate metabolism 10 None None None 170 | hinfluenzae 35 Purine Metabolism 58 None None None 171 | hinfluenzae 36 Pyrimidine Metabolism 43 None None None 172 | hinfluenzae 18 Pyruvate Metabolism 20 None None None 173 | hinfluenzae 30 Reductive carboxylate cycle (CO2 fixation) 13 None None None 174 | hinfluenzae 13 Ribosomal Protein Genes 56 None None None 175 | hinfluenzae 12 RNA Polymerase 11 None None None 176 | hinfluenzae 28 Sulphur Metabolism 8 None None None 177 | hinfluenzae 17 TCA Cycle 12 None None None 178 | hinfluenzae 41 Tryptophan metabolism 6 None None None 179 | hinfluenzae 46 Tyrosine metabolism 4 None None None 180 | hinfluenzae 48 Valine, leucine and isoleucine biosynthesis 11 None None None 181 | hinfluenzae 49 Valine, leucine and isoleucine degradation 3 None None None 182 | hparasuis 1 MLST 7 397 2019-08-05 2019-08-05 183 | hcinaedi 1 MLST 7 20 2019-12-06 2019-12-06 184 | helicobacter 1 MLST 7 3729 2020-04-06 2020-04-06 185 | hsuis 1 MLST 7 141 2020-03-06 2020-03-06 186 | kaerogenes 1 MLST 7 204 2020-05-21 2020-05-21 187 | koxytoca 1 MLST 7 323 2020-05-18 2020-05-18 188 | kseptempunctata 1 MLST 2 3 2014-12-22 2014-12-22 189 | lsalivarius 1 MLST 5 25 2010-12-07 2010-12-07 190 | leptospira 1 MLST (scheme 1) 7 326 2020-04-23 2020-04-23 191 | leptospira 2 MLST (scheme 2) 7 273 2019-04-24 2019-04-24 192 | leptospira 3 MLST (scheme 3) 6 194 2020-02-10 2020-02-10 193 | leptospira 4 cgMLST 1565 None None None 194 | leptospira 5 LPS 21 None None None 195 | liberibacter 1 MLST 7 14 2020-05-07 2020-05-07 196 | mcanis 1 MLST 7 83 2019-10-21 2019-10-21 197 | mcaseolyticus 1 MLST 7 67 2019-10-21 2019-10-21 198 | mplutonius 1 MLST 4 37 2020-03-11 2020-03-11 199 | mabscessus 1 M. abscessus MLST 7 26 2012-04-25 2012-04-25 200 | mabscessus 2 M. massiliense MLST 7 12 2012-03-27 2012-04-25 201 | mycobacteria 1 Core genome (H37Rv ref vs 19 finished species) 744 5626 2017-08-25 2017-08-25 202 | mycobacteria 2 MLST 8 873 2019-11-15 2019-11-15 203 | magalactiae 1 MLST 5 35 2019-04-24 2019-04-24 204 | mbovis 2 MLST 7 90 2020-05-14 2020-05-14 205 | mbovis 1 MLST (legacy) 7 185 2020-01-10 2020-01-10 206 | mflocculare 1 MLST 3 8 2018-07-03 2018-07-03 207 | mgallisepticum 1 MLST#1 (Ghanem) 7 60 2020-04-06 2020-04-06 208 | mgallisepticum 2 MLST#2 (Bekő) 6 79 2020-05-18 2020-05-18 209 | mhominis 1 MLST 5 23 2019-10-16 2019-10-16 210 | mhominis 2 MVLST 5 31 2019-10-16 2019-10-16 211 | mhominis 3 eMLST 10 32 2019-10-16 2019-10-16 212 | mhyopneumoniae 1 MLST 3 151 2020-03-20 2020-03-20 213 | mhyorhinis 1 MLST 6 128 2020-03-27 2020-03-27 214 | miowae 1 MLST 6 35 2019-05-05 2019-05-05 215 | mpneumoniae 1 MLST 8 37 2019-12-18 2019-12-18 216 | msynoviae 1 MLST 7 141 2020-04-17 2020-04-17 217 | neisseria 1 MLST 7 15480 2020-05-22 2020-05-22 218 | neisseria 2 Finetyping antigens 3 None None None 219 | neisseria 42 rplF species 1 211 2019-02-06 2019-02-06 220 | neisseria 7 ADP-heptose biosynthesis 5 None None None 221 | neisseria 5 Antibiotic resistance 11 None None None 222 | neisseria 3 Antigen genes 7 None None None 223 | neisseria 52 beta lactamase plasmid 8 18 2018-04-17 2018-04-17 224 | neisseria 53 Bexsero Antigen Sequence Typing (BAST) 5 3661 2020-05-22 2020-05-22 225 | neisseria 63 Capsule Null (cnl) 1 None None None 226 | neisseria 29 Capsule Region A - Serogroup A 4 None None None 227 | neisseria 36 Capsule Region A - Serogroup B 5 None None None 228 | neisseria 37 Capsule Region A - Serogroup C 6 None None None 229 | neisseria 35 Capsule Region A - Serogroup E 7 None None None 230 | neisseria 32 Capsule Region A - Serogroup H 4 None None None 231 | neisseria 33 Capsule Region A - Serogroup L 3 None None None 232 | neisseria 38 Capsule Region A - Serogroup W 6 None None None 233 | neisseria 30 Capsule Region A - Serogroup X 3 None None None 234 | neisseria 39 Capsule Region A - Serogroup Y 6 None None None 235 | neisseria 31 Capsule Region A - Serogroup Z 4 None None None 236 | neisseria 41 Capsule Region B 2 None None None 237 | neisseria 40 Capsule Region C 4 None None None 238 | neisseria 48 Capsule Region D and D' 6 None None None 239 | neisseria 49 Conjugative Plasmid 50 242 2018-04-25 2018-04-25 240 | neisseria 66 Cryptic Plasmid 9 96 2018-05-15 2018-05-15 241 | neisseria 25 DNA replication 16 None None None 242 | neisseria 4 eMLST (20 locus partial genes) 20 None None None 243 | neisseria 12 eMLST (20 locus whole genes) 20 None None None 244 | neisseria 6 Factor H binding protein 10 None None None 245 | neisseria 73 GC OMV peptide typing 26 2283 2020-03-31 2020-03-31 246 | neisseria 15 Glycolysis 11 None None None 247 | neisseria 50 Gonococcal Genetic Island 73 None None None 248 | neisseria 72 Human-restricted Neisseria cgMLST v1.0 1441 None None None 249 | neisseria 21 Iron acquisition 7 None None None 250 | neisseria 19 Kdo addition 5 None None None 251 | neisseria 45 L3_cgMLST 1742 None None None 252 | neisseria 68 L44_cgMLST 1699 None None None 253 | neisseria 69 L44_pgMLST 1786 None None None 254 | neisseria 17 Lipid A biosynthesis: acyltransferases 4 None None None 255 | neisseria 18 Lipid A biosynthesis: other 5 None None None 256 | neisseria 9 LOS alpha chain transferases 7 None None None 257 | neisseria 8 LOS inner core transferases 7 None None None 258 | neisseria 20 LOS transport/export 5 None None None 259 | neisseria 43 Methyltransferases 0 None None None 260 | neisseria 54 MGI-1 7 None None None 261 | neisseria 55 MGI-2 21 None None None 262 | neisseria 56 MGI-3 18 None None None 263 | neisseria 46 NadA 2 None None None 264 | neisseria 44 Neisseria Heparin Binding Antigen (NHBA) 2 None None None 265 | neisseria 71 NG MAST 2 19107 2020-03-26 2020-03-26 266 | neisseria 57 N. gonorrhoeae Beta-lactam AMR 5 None None None 267 | neisseria 62 N. gonorrhoeae cgMLST v1.0 1649 6950 2020-05-18 2020-05-18 268 | neisseria 61 N. gonorrhoeae Efflux Pumps AMR 10 None None None 269 | neisseria 58 N. gonorrhoeae Fluoroquinolone AMR 4 None None None 270 | neisseria 59 N. gonorrhoeae Macrolides AMR 2 None None None 271 | neisseria 60 N. gonorrhoeae plasmid mediated AMR 2 None None None 272 | neisseria 67 NG STAR 7 1891 2020-03-30 2020-03-30 273 | neisseria 47 N. meningitidis cgMLST v1.0 1605 18503 2020-05-22 2020-05-22 274 | neisseria 27 Nucleotide excision repair 8 None None None 275 | neisseria 64 OMV peptide 50 None None None 276 | neisseria 65 OMV peptide typing 24 4046 2019-05-15 2019-05-15 277 | neisseria 13 Pilus genes 27 None None None 278 | neisseria 28 Protein glycosylation 14 None None None 279 | neisseria 22 Purine metabolism 39 None None None 280 | neisseria 23 Pyrimidine metabolism 32 None None None 281 | neisseria 14 Pyruvate dehydrogenase complex 3 None None None 282 | neisseria 24 Ribosomal protein genes 55 None None None 283 | neisseria 26 RNA polymerase 4 None None None 284 | neisseria 34 Small regulatory RNAs 3 None None None 285 | neisseria 16 TCA cycle 16 None None None 286 | neisseria 70 tRNA molecules 21 None None None 287 | neisseria 11 UDP-GlcNAc synthesis 1 None None None 288 | neisseria 10 UDP-glucose and UDP-galactose biosynthesis 2 None None None 289 | neisseria 51 VirB T4SS 31 None None None 290 | otsutsugamushi 1 MLST 7 98 2019-05-10 2019-05-10 291 | orhinotracheale 1 MLST 7 35 2018-01-03 2018-01-03 292 | plarvae 1 MLST 7 29 2020-03-11 2020-03-11 293 | pmultocida 1 Multiple host MLST 7 124 2020-03-10 2020-03-10 294 | pmultocida 2 RIRDC MLST 7 373 2019-11-28 2019-11-28 295 | ppentosaceus 1 MLST 7 17 2013-02-19 2013-02-19 296 | pdamselae 1 MLST 6 56 2018-08-09 2018-08-09 297 | psalmonis 1 MLST 7 24 2017-04-07 2017-04-07 298 | plasmid 7 IncA/C cgPMLST 28 41 2018-01-05 2018-01-05 299 | plasmid 6 IncA/C PMLST 4 13 2018-01-05 2018-01-05 300 | plasmid 3 IncF RST 7 None None None 301 | plasmid 5 IncHI1 MLST 6 15 2018-05-30 2018-05-30 302 | plasmid 2 IncHI2 DLST 2 15 2018-09-05 2018-09-05 303 | plasmid 1 IncI1 MLST 5 316 2020-05-06 2020-05-06 304 | plasmid 4 IncN MLST 3 22 2019-03-12 2019-03-12 305 | plasmid 8 pBSSB1-family 3 35 2019-04-09 2019-04-09 306 | pgingivalis 1 MLST 7 138 2007-08-12 2007-08-12 307 | paeruginosa 1 MLST 7 3400 2020-05-11 2020-05-11 308 | paeruginosa 2 Plasmid loci 199 None None None 309 | pfluorescens 1 MLST 7 110 2019-06-28 2019-06-28 310 | pputida 1 MLST 8 115 2020-05-21 2020-05-21 311 | ranatipestifer 1 MLST 7 77 2020-05-08 2020-05-08 312 | rhodococcus 1 MLST 7 46 2020-04-15 2020-04-20 313 | salmonella 4 cgMLST v2 (Enterobase) 3002 None None None 314 | salmonella 2 MLST 7 6782 2020-05-25 2020-05-25 315 | salmonella 1 Oxford loci 3633 None None None 316 | salmonella 3 SalmcgMLST v1.0 2750 13722 2020-02-06 2020-02-06 317 | sparasitica 1 MLST 7 15 2018-03-26 2018-03-26 318 | sinorhizobium 1 MLST 10 136 2010-05-07 2010-05-07 319 | smaltophilia 1 MLST 7 490 2020-05-20 2020-05-20 320 | saureus 1 MLST 7 6071 2020-05-22 2020-05-22 321 | saureus 2 Core 2208 2208 None None None 322 | sepidermidis 1 MLST 7 972 2020-05-22 2020-05-22 323 | shaemolyticus 1 MLST 7 79 2020-05-20 2020-05-20 324 | shominis 1 MLST 6 57 2017-10-19 2017-10-19 325 | spseudintermedius 1 MLST 7 1685 2020-05-25 2020-05-25 326 | oralstrep 2 S. mutans MLST (Do) 8 179 2019-10-08 2019-10-08 327 | oralstrep 3 S. mutans MLST (Nakano) 8 269 2020-01-22 2020-01-22 328 | oralstrep 1 S. oralis MLST 7 78 2015-10-23 2015-10-23 329 | sagalactiae 1 MLST 7 1605 2020-04-17 2020-04-17 330 | sagalactiae 37 Adherence Regulation 2 None None None 331 | sagalactiae 29 Alp Family Proteins 5 None None None 332 | sagalactiae 23 Amino Acid Metabolism 85 None None None 333 | sagalactiae 44 Aminoglycosides 2 None None None 334 | sagalactiae 17 Ascorbate and Aldarate Metabolism 28 None None None 335 | sagalactiae 3 Biosynthesis and activation of sialic acid 5 None None None 336 | sagalactiae 30 C5a Peptidase 2 None None None 337 | sagalactiae 4 Capsular polysaccharide Biosynthesis 7 None None None 338 | sagalactiae 46 Chloramphenicol 1 None None None 339 | sagalactiae 22 Fatty Acid Biosynthesis 18 None None None 340 | sagalactiae 31 Fibrinogen Binding Proteins 2 None None None 341 | sagalactiae 14 Fructose and Mannose Metabolism 36 None None None 342 | sagalactiae 15 Galactose Metabolism 34 None None None 343 | sagalactiae 12 Glycolysis 44 None None None 344 | sagalactiae 32 Haemolysin Operon 9 None None None 345 | sagalactiae 38 h_S.agalactiae cgMLST v1.0 1405 None None None 346 | sagalactiae 33 Hyaluronidase Activity 1 None None None 347 | sagalactiae 40 ICESag1962 51 None None None 348 | sagalactiae 39 IMESp2907 16 None None None 349 | sagalactiae 35 LysR family 1 None None None 350 | sagalactiae 45 Macrolides, lincosamides, Streptogramins 5 None None None 351 | sagalactiae 18 Oxidative phosphorylation 13 None None None 352 | sagalactiae 13 Pentose Phosphate Pathway 23 None None None 353 | sagalactiae 19 Photosynthesis 8 None None None 354 | sagalactiae 27 PI-1 6 None None None 355 | sagalactiae 28 PI-2a 5 None None None 356 | sagalactiae 26 PI-2b 5 None None None 357 | sagalactiae 34 Pilus Regulator 1 None None None 358 | sagalactiae 21 Purine Metabolism 63 None None None 359 | sagalactiae 20 Pyrimidine Metabolism 51 None None None 360 | sagalactiae 6 Serotype Ia 4 None None None 361 | sagalactiae 7 Serotype Ib 4 None None None 362 | sagalactiae 8 Serotype II 6 None None None 363 | sagalactiae 9 Serotype III 4 None None None 364 | sagalactiae 10 Serotype IV 5 None None None 365 | sagalactiae 5 Serotype V 6 None None None 366 | sagalactiae 41 Serotype VI 4 None None None 367 | sagalactiae 42 Serotype VII 2 None None None 368 | sagalactiae 16 Starch and Sucrose Metabolism 36 None None None 369 | sagalactiae 2 Synthesis of the group B carbohydrate 15 None None None 370 | sagalactiae 11 TCA Cycle 5 None None None 371 | sagalactiae 43 Tetracyclines 2 None None None 372 | sagalactiae 25 Transcription 4 None None None 373 | sagalactiae 36 Transcriptional Regulator 1 None None None 374 | sagalactiae 24 Translation 25 None None None 375 | sbsec 1 MLST 10 214 2017-09-25 2017-09-25 376 | scanis 1 MLST 7 54 2019-12-09 2019-12-09 377 | sdysgalactiae 1 MLST 7 522 2020-02-17 2020-02-17 378 | sgallolyticus 1 MLST 7 109 2017-02-22 2017-02-22 379 | spneumoniae 1 MLST 7 15508 2020-05-21 2020-05-21 380 | spneumoniae 2 cgMLST 1360 6992 2020-02-14 2020-02-14 381 | spyogenes 1 MLST 7 1233 2020-05-12 2020-05-12 382 | ssuis 1 MLST 7 1299 2020-05-15 2020-05-15 383 | sthermophilus 1 MLST 10 119 2015-06-18 2015-06-18 384 | suberis 1 MLST 7 1230 2020-02-25 2020-02-25 385 | suberis 2 vMLST 10 0 None None 386 | szooepidemicus 1 MLST 7 402 2020-03-13 2020-03-13 387 | streptomyces 1 MLST 6 234 2016-01-22 2016-01-22 388 | taylorella 1 MLST 7 71 2020-01-23 2020-01-23 389 | tenacibaculum 1 MLST 7 168 2020-04-22 2020-04-22 390 | tpallidum 1 MLST 3 72 2019-11-28 2019-11-28 391 | tvaginalis 1 MLST 7 60 2016-02-08 2016-02-08 392 | ureaplasma 1 MLST 4 164 2018-09-14 2018-09-14 393 | ureaplasma 2 eMLST 6 229 2018-09-14 2018-09-14 394 | vcholerae 1 MLST 7 1403 2020-04-28 2020-04-28 395 | vcholerae 2 MLST (O1 and O139) 5 422 2019-09-13 2019-09-13 396 | vcholerae 3 cgMLST 2443 1048 2020-05-01 2020-05-01 397 | vibrio 1 MLST 4 179 2020-05-07 2020-05-07 398 | vparahaemolyticus 1 MLST 7 2347 2020-05-02 2020-05-02 399 | vparahaemolyticus 2 AA-MLST 7 244 2018-04-20 2018-04-20 400 | vparahaemolyticus 3 cgMLST 2254 None None None 401 | vparahaemolyticus 4 Virulence markers 3 None None None 402 | vtapetis 1 MLST 10 10 2011-09-22 2011-09-22 403 | vvulnificus 1 MLST 10 530 2019-09-19 2019-09-19 404 | wolbachia 1 MLST 5 576 2020-02-24 2020-02-24 405 | wolbachia 2 WSP 5 None None None 406 | xcitri 1 cgMLST 1618 228 2020-02-09 2020-02-09 407 | xfastidiosa 1 MLST 7 87 2019-03-06 2019-03-06 408 | yersinia 1 MLST 7 170 2015-06-16 2015-06-16 409 | yruckeri 1 MLST 6 30 2011-07-27 2011-07-27 410 | -------------------------------------------------------------------------------- /scheme_list_snapshots/2021-10-25_pubmlst_scheme_list.tsv: -------------------------------------------------------------------------------- 1 | name id description locus_count records last_added last_updated 2 | abaumannii 1 MLST (Oxford) 7 2461 2021-10-05 2021-10-05 3 | abaumannii 2 MLST (Pasteur) 7 1889 2021-09-30 2021-09-30 4 | aeromonas 1 MLST 6 1055 2021-10-20 2021-10-20 5 | aactinomycetemcomitans 1 MLST 7 57 2020-05-24 2020-05-24 6 | aphagocytophilum 1 MLST 7 184 2019-11-14 2019-11-14 7 | arcobacter 1 MLST 7 833 2021-02-25 2021-02-25 8 | afumigatus 1 MLST 7 48 2014-09-16 2014-09-16 9 | bcereus 1 MLST 7 2792 2021-10-20 2021-10-20 10 | bcereus 2 B. anthracis cgMLST 3803 648 2020-11-10 2020-11-10 11 | bcereus 3 B. anthracis accessory genes 1263 None None None 12 | bcereus 4 B. anthracis plasmids 10 40 2021-02-15 2021-02-15 13 | blicheniformis 14 MLST 6 50 2020-12-14 2020-12-14 14 | bsubtilis 1 MLST 7 251 2021-10-07 2021-10-07 15 | llactis_phage 1 MLST 5 221 2017-06-19 2017-06-19 16 | bbacilliformis 1 MLST 7 14 2017-06-17 2017-06-17 17 | bhenselae 1 MLST 8 37 2021-04-23 2021-04-23 18 | bwashoensis 1 MLST 6 21 2019-08-22 2019-08-22 19 | blastocystis 1 ST3 MLST 5 81 2019-05-20 2019-05-20 20 | blastocystis 2 ST4 MLST 6 6 2011-09-16 2011-09-16 21 | borrelia 1 MLST 8 974 2021-09-02 2021-09-02 22 | borrelia 2 MLSA (legacy) 7 None None None 23 | brucella 1 MLST (9 locus) 9 104 2021-10-11 2021-10-11 24 | brucella 2 MLST (21 locus) 21 153 2021-10-11 2021-10-11 25 | brucella 3 cgMLST 1665 0 None None 26 | bcc 1 MLST 7 2049 2021-10-19 2021-10-19 27 | bpseudomallei 1 MLST 7 1940 2021-10-14 2021-10-14 28 | campylobacter_nonjejuni 9 C. fetus MLST 7 73 2020-11-02 2020-11-02 29 | campylobacter_nonjejuni 1 C. helveticus MLST 7 9 2015-01-12 2015-01-12 30 | campylobacter_nonjejuni 6 C. hyointestinalis MLST 7 135 2021-02-16 2021-02-16 31 | campylobacter_nonjejuni 2 C. insulaenigrae MLST 7 43 2011-11-10 2011-11-10 32 | campylobacter_nonjejuni 7 C. lanienae MLST 7 172 2018-11-27 2018-11-27 33 | campylobacter_nonjejuni 3 C. lari MLST 7 299 2021-09-08 2021-09-08 34 | campylobacter_nonjejuni 8 C. sputorum MLST 7 16 2011-11-18 2011-11-18 35 | campylobacter_nonjejuni 4 C. upsaliensis MLST 7 211 2020-10-23 2020-10-23 36 | campylobacter 1 MLST 7 11537 2021-10-19 2021-10-19 37 | campylobacter 3 1643 Gundogdu loci 1643 None None None 38 | campylobacter 6 C. coli 15-537360 1588 None None None 39 | campylobacter 4 C. jejuni / C. coli cgMLST v1.0 1343 35308 2021-10-15 2021-10-15 40 | campylobacter 7 ED pathway 7 None None None 41 | campylobacter 2 eMLST (21 partial genes) 21 None None None 42 | campylobacter 5 Ribosomal Protein Genes 52 None None None 43 | calbicans 1 MLST 7 3668 2021-09-27 2021-09-27 44 | cglabrata 1 MLST 6 193 2021-07-22 2021-07-22 45 | ckrusei 1 MLST 6 239 2021-09-20 2021-09-20 46 | ctropicalis 1 MLST 6 1200 2021-10-14 2021-10-14 47 | cmaltaromaticum 1 MLST 7 56 2018-04-11 2018-04-11 48 | chlamydiales 16 Aerobic and ATP Biogenesis 16 None None None 49 | chlamydiales 7 Amino Acyl tRNA Synthesis 3 None None None 50 | chlamydiales 17 Aromatic Amino Acids 10 None None None 51 | chlamydiales 18 Aspartate Amino Acid 5 None None None 52 | chlamydiales 20 Biotin, Lipoate and Ubiquinone 6 None None None 53 | chlamydiales 26 Both Purine and Pyrimidine Metabolism 4 None None None 54 | chlamydiales 44 C. abortus cgMLST v1.0 959 None None None 55 | chlamydiales 30 Cell Division 9 None None None 56 | chlamydiales 42 C. trachomatis cgMLST v1.0 817 373 2020-09-30 2020-09-30 57 | chlamydiales 3 DNA Replication 24 None None None 58 | chlamydiales 14 Electron Transport Chain 4 None None None 59 | chlamydiales 37 Eukaryotic Type Chromatin Factors 4 None None None 60 | chlamydiales 29 Fatty Acid and Phospholipid Metabolism 27 None None None 61 | chlamydiales 21 Folic Acid 5 None None None 62 | chlamydiales 10 Glycolysis, Gluconeogensis, Glycogen 20 None None None 63 | chlamydiales 27 Membrane Proteins, Lipoproteins, Porins 9 None None None 64 | chlamydiales 36 Miscellaneous Enzymes/Conserved Proteins 44 None None None 65 | chlamydiales 1 MLST (Chlamydiales) 7 317 2021-10-14 2021-10-14 66 | chlamydiales 38 MLST (C. trachomatis) 7 88 2019-11-18 2019-11-18 67 | chlamydiales 41 MLST (C. trachomatis Uppsala) 5 527 2020-08-13 2020-08-13 68 | chlamydiales 4 Nucleotide Excision and Repair 18 None None None 69 | chlamydiales 33 Pathogenesis Associated Proteins 25 None None None 70 | chlamydiales 15 Pentose Phosphate Pathway 8 None None None 71 | chlamydiales 8 Peptide Synthesis 14 None None None 72 | chlamydiales 28 Peptidoglycan 16 None None None 73 | chlamydiales 11 Phosphorous and Sulphur 4 None None None 74 | chlamydiales 2 Plasmid loci 8 None None None 75 | chlamydiales 40 Plasmid MLST 8 47 2015-10-06 2015-10-06 76 | chlamydiales 22 Porphyrin 9 None None None 77 | chlamydiales 9 Protein Folding, Assembly, Modification 37 None None None 78 | chlamydiales 24 Purine Metabolism 3 None None None 79 | chlamydiales 25 Pyrimidine Metabolism 7 None None None 80 | chlamydiales 12 Pyruvate Dehydrogenase 7 None None None 81 | chlamydiales 5 Recombination 8 None None None 82 | chlamydiales 23 Riboflavin 5 None None None 83 | chlamydiales 43 Ribosomal Protein genes 52 None None None 84 | chlamydiales 6 RNA Associated 44 None None None 85 | chlamydiales 19 Serine Amino Acid 2 None None None 86 | chlamydiales 31 Signal Transduction 18 None None None 87 | chlamydiales 35 Specific Proteins 11 None None None 88 | chlamydiales 13 TCA Cycle 11 None None None 89 | chlamydiales 34 Transport Related Proteins 54 None None None 90 | chlamydiales 39 Type III Effector Proteins 0 None None None 91 | chlamydiales 32 Type III Secretion Systems 58 None None None 92 | cfreundii 1 MLST 7 601 2021-10-19 2021-10-19 93 | csinensis 1 MLST 8 254 2012-01-07 2012-01-07 94 | cdifficile 2 cwp cluster genes 6 None None None 95 | cdifficile 1 MLST 7 908 2021-10-19 2021-10-19 96 | cdifficile 3 Pathogenicity loci 5 None None None 97 | cbotulinum 1 MLST 7 154 2021-10-05 2021-10-05 98 | cbotulinum 2 Extended MLST 14 0 None None 99 | cchauvoei 2 agMLST 234 None None None 100 | cchauvoei 1 cgMLST 2223 60 2021-08-18 2021-08-18 101 | cperfringens 1 MLST 8 415 2021-10-19 2021-10-19 102 | cperfringens 2 cgMLST 1431 169 2021-08-04 2021-08-04 103 | csepticum 1 MLST 7 8 2008-07-29 2008-07-29 104 | cdiphtheriae 1 MLST 7 799 2021-09-23 2021-09-23 105 | cronobacter 4 cogMLST 1865 None None None 106 | cronobacter 3 Ext-MLST 3 0 None None 107 | cronobacter 5 Gcog 222 None None None 108 | cronobacter 1 MLST 7 768 2021-10-23 2021-10-23 109 | cronobacter 6 O-serotype 2 0 None None 110 | cronobacter 2 Tax-MLST 2 None None None 111 | pacnes 3 MLST 8 158 2021-02-20 2021-02-20 112 | dnodosus 3 cgMLST 714 None None None 113 | dnodosus 1 MLST 7 115 2017-09-13 2017-09-13 114 | edwardsiella 1 MLST 10 22 2020-04-23 2020-04-23 115 | ecloacae 1 MLST 7 1725 2021-10-21 2021-10-21 116 | efaecalis 1 MLST 7 1164 2021-10-05 2021-10-05 117 | efaecium 1 MLST 7 2082 2021-10-11 2021-10-11 118 | escherichia 1 MLST (Achtman) 7 11248 2021-10-22 2021-10-22 119 | escherichia 2 MLST (Pasteur) 8 1077 2021-07-19 2021-07-19 120 | escherichia 10 accessory genome 22489 None None None 121 | escherichia 3 beta-lactamase resistance 9 None None None 122 | escherichia 6 cgMLST 2513 None None None 123 | escherichia 12 IncL/M 3 None None None 124 | escherichia 4 locus of enterocyte effacement (LEE) island 40 None None None 125 | escherichia 14 oxa-48 chromosome loci 29 None None None 126 | escherichia 8 pO157 plasmid 49 None None None 127 | escherichia 13 pOXA-48 plasmid 71 None None None 128 | escherichia 11 quinolone resistance 4 None None None 129 | escherichia 5 shiga toxins 4 None None None 130 | escherichia 9 virulence genes 16 None None None 131 | escherichia 7 wgMLST 25002 None None None 132 | fpsychrophilum 1 MLST 7 264 2021-10-15 2021-10-15 133 | gallibacterium 1 MLST 8 81 2012-06-12 2012-06-12 134 | geotrichum 1 MLST 5 40 2015-07-29 2015-07-29 135 | hparasuis 1 MLST 7 461 2021-10-18 2021-10-18 136 | hinfluenzae 1 MLST 7 2500 2021-10-12 2021-10-12 137 | hinfluenzae 42 Alanine, aspartate and glutamate metabolism 13 None None None 138 | hinfluenzae 14 Aminoacyl-tRNA biosynthesis 24 None None None 139 | hinfluenzae 19 Amino sugar and nucleotide sugar metabolism 21 None None None 140 | hinfluenzae 52 Antimicrobial Resistance 6 None None None 141 | hinfluenzae 43 Arginine and proline metabolism 20 None None None 142 | hinfluenzae 21 Butanoate metabolism 8 None None None 143 | hinfluenzae 2 Capsule - Region I 4 None None None 144 | hinfluenzae 4 Capsule - Region III 2 None None None 145 | hinfluenzae 7 Capsule - serotype A 2 None None None 146 | hinfluenzae 3 Capsule - serotype B 8 None None None 147 | hinfluenzae 8 Capsule - serotype C 4 None None None 148 | hinfluenzae 9 Capsule - serotype D 5 None None None 149 | hinfluenzae 6 Capsule - Serotype E 8 None None None 150 | hinfluenzae 5 Capsule - serotype F 3 None None None 151 | hinfluenzae 38 Cysteine and methionine metabolism 17 None None None 152 | hinfluenzae 10 DNA Replication 13 None None None 153 | hinfluenzae 32 Fatty acid biosynthesis 11 None None None 154 | hinfluenzae 31 Fatty acid metabolism 3 None None None 155 | hinfluenzae 23 Fructose and mannose metabolism 13 None None None 156 | hinfluenzae 20 Galactose Metabolism 6 None None None 157 | hinfluenzae 33 Glycerolipid metabolism 6 None None None 158 | hinfluenzae 34 Glycerophospholipid metabolism 19 None None None 159 | hinfluenzae 39 Glycine, serine and threonine metabolism 19 None None None 160 | hinfluenzae 15 Glycolysis 15 None None None 161 | hinfluenzae 16 Glyoxylate and dicarboxylate metabolism 11 None None None 162 | hinfluenzae 45 Histidine metabolism 8 None None None 163 | hinfluenzae 53 Iron Acquisition 13 None None None 164 | hinfluenzae 50 LOS Biosynthesis 23 None None None 165 | hinfluenzae 40 Lysine biosynthesis 14 None None None 166 | hinfluenzae 47 Lysine degradation 4 None None None 167 | hinfluenzae 26 Methane metabolism 26 None None None 168 | hinfluenzae 27 Nitrogen Metabolism 10 None None None 169 | hinfluenzae 11 Nucleotide Excision Repair 12 None None None 170 | hinfluenzae 29 Oxidative phosphorylation 10 None None None 171 | hinfluenzae 25 Pentose and glucuronate interconversions 4 None None None 172 | hinfluenzae 24 Pentose Phosphate Pathway 15 None None None 173 | hinfluenzae 37 Phenylalanine metabolism 4 None None None 174 | hinfluenzae 44 Phenylalanine, tyrosine, tryptophan biosynthesis 19 None None None 175 | hinfluenzae 51 Pilus Biosynthesis 6 None None None 176 | hinfluenzae 22 Propanoate metabolism 10 None None None 177 | hinfluenzae 35 Purine Metabolism 58 None None None 178 | hinfluenzae 36 Pyrimidine Metabolism 43 None None None 179 | hinfluenzae 18 Pyruvate Metabolism 20 None None None 180 | hinfluenzae 30 Reductive carboxylate cycle (CO2 fixation) 13 None None None 181 | hinfluenzae 13 Ribosomal Protein Genes 56 None None None 182 | hinfluenzae 12 RNA Polymerase 11 None None None 183 | hinfluenzae 28 Sulphur Metabolism 8 None None None 184 | hinfluenzae 17 TCA Cycle 12 None None None 185 | hinfluenzae 41 Tryptophan metabolism 6 None None None 186 | hinfluenzae 46 Tyrosine metabolism 4 None None None 187 | hinfluenzae 48 Valine, leucine and isoleucine biosynthesis 11 None None None 188 | hinfluenzae 49 Valine, leucine and isoleucine degradation 3 None None None 189 | hcinaedi 1 MLST 7 21 2020-10-12 2020-10-12 190 | helicobacter 1 MLST 7 3941 2021-07-14 2021-07-14 191 | hsuis 1 MLST 7 141 2020-03-06 2020-03-06 192 | kaerogenes 1 MLST 7 241 2021-10-21 2021-10-21 193 | koxytoca 1 MLST 7 371 2021-10-12 2021-10-12 194 | kseptempunctata 1 MLST 2 3 2014-12-22 2014-12-22 195 | lsalivarius 1 MLST 5 25 2010-12-07 2010-12-07 196 | leptospira 1 MLST (scheme 1) 7 331 2021-03-29 2021-03-29 197 | leptospira 2 MLST (scheme 2) 7 273 2019-04-24 2019-04-24 198 | leptospira 3 MLST (scheme 3) 6 194 2020-02-10 2020-02-10 199 | leptospira 4 cgMLST 1565 None None None 200 | leptospira 5 LPS 21 None None None 201 | liberibacter 1 MLST 7 14 2020-05-07 2020-05-07 202 | mcanis 1 MLST 7 83 2019-10-21 2019-10-21 203 | mcaseolyticus 1 MLST 7 67 2019-10-21 2019-10-21 204 | msciuri 1 MLST 7 122 2021-09-28 2021-09-28 205 | mhaemolytica 1 MLST 7 53 2021-09-15 2021-09-15 206 | mplutonius 1 MLST 4 38 2021-10-12 2021-10-12 207 | mycobacteria 1 Core genome (H37Rv ref vs 19 finished species) 744 5626 2017-08-25 2017-08-25 208 | mycobacteria 2 MLST 8 873 2019-11-15 2019-11-15 209 | mabscessus 1 MLST 7 258 2021-10-17 2021-10-17 210 | magalactiae 1 MLST 5 35 2019-04-24 2019-04-24 211 | manserisalpingitidis 1 MLST 5 76 2020-11-10 2020-11-10 212 | mbovis 2 MLST 7 168 2021-10-18 2021-10-18 213 | mbovis 1 MLST (legacy) 7 185 2020-01-10 2020-01-10 214 | mflocculare 1 MLST 3 8 2018-07-03 2018-07-03 215 | mgallisepticum 1 MLST#1 (Ghanem) 7 78 2021-07-21 2021-07-21 216 | mgallisepticum 2 MLST#2 (Bekő) 6 118 2021-10-10 2021-10-10 217 | mhominis 1 MLST 5 28 2021-09-28 2021-09-28 218 | mhominis 2 MVLST 5 31 2019-10-16 2019-10-16 219 | mhominis 3 eMLST 10 32 2019-10-16 2019-10-16 220 | mhyopneumoniae 1 MLST 3 181 2021-02-24 2021-02-24 221 | mhyorhinis 1 MLST 6 143 2020-11-26 2020-11-26 222 | miowae 1 MLST 6 35 2019-05-05 2019-05-05 223 | mpneumoniae 1 MLST 8 46 2021-07-30 2021-07-30 224 | msynoviae 1 MLST 7 169 2021-10-21 2021-10-21 225 | neisseria 1 MLST 7 16527 2021-10-21 2021-10-21 226 | neisseria 2 Finetyping antigens 3 None None None 227 | neisseria 42 rplF species 1 211 2019-02-06 2019-02-06 228 | neisseria 7 ADP-heptose biosynthesis 5 None None None 229 | neisseria 5 Antibiotic resistance 11 None None None 230 | neisseria 3 Antigen genes 7 None None None 231 | neisseria 52 beta lactamase plasmid 8 18 2018-04-17 2018-04-17 232 | neisseria 53 Bexsero Antigen Sequence Typing (BAST) 5 4394 2021-10-19 2021-10-19 233 | neisseria 63 Capsule Null (cnl) 1 None None None 234 | neisseria 29 Capsule Region A - Serogroup A 4 None None None 235 | neisseria 36 Capsule Region A - Serogroup B 5 None None None 236 | neisseria 37 Capsule Region A - Serogroup C 6 None None None 237 | neisseria 35 Capsule Region A - Serogroup E 7 None None None 238 | neisseria 32 Capsule Region A - Serogroup H 4 None None None 239 | neisseria 33 Capsule Region A - Serogroup L 3 None None None 240 | neisseria 38 Capsule Region A - Serogroup W 6 None None None 241 | neisseria 30 Capsule Region A - Serogroup X 3 None None None 242 | neisseria 39 Capsule Region A - Serogroup Y 6 None None None 243 | neisseria 31 Capsule Region A - Serogroup Z 4 None None None 244 | neisseria 41 Capsule Region B 2 None None None 245 | neisseria 40 Capsule Region C 4 None None None 246 | neisseria 48 Capsule Region D and D' 6 None None None 247 | neisseria 74 Commensal cps: Group 1 6 None None None 248 | neisseria 75 Commensal cps: Group 2 8 None None None 249 | neisseria 76 Commensal cps: Group 3 12 None None None 250 | neisseria 49 Conjugative Plasmid 50 242 2018-04-25 2018-04-25 251 | neisseria 66 Cryptic Plasmid 9 96 2018-05-15 2018-05-15 252 | neisseria 25 DNA replication 16 None None None 253 | neisseria 4 eMLST (20 locus partial genes) 20 None None None 254 | neisseria 12 eMLST (20 locus whole genes) 20 None None None 255 | neisseria 6 Factor H binding protein 10 None None None 256 | neisseria 73 GC OMV peptide typing 26 2371 2021-07-26 2021-07-26 257 | neisseria 15 Glycolysis 11 None None None 258 | neisseria 50 Gonococcal Genetic Island 73 None None None 259 | neisseria 72 Human-restricted Neisseria cgMLST v1.0 1441 None None None 260 | neisseria 21 Iron acquisition 7 None None None 261 | neisseria 19 Kdo addition 5 None None None 262 | neisseria 45 L3 cgMLST 1742 None None None 263 | neisseria 68 L44 cgMLST 1699 None None None 264 | neisseria 69 L44 pgMLST 1786 None None None 265 | neisseria 17 Lipid A biosynthesis: acyltransferases 4 None None None 266 | neisseria 18 Lipid A biosynthesis: other 5 None None None 267 | neisseria 9 LOS alpha chain transferases 7 None None None 268 | neisseria 8 LOS inner core transferases 7 None None None 269 | neisseria 20 LOS transport/export 5 None None None 270 | neisseria 77 Mendevar 7 None None None 271 | neisseria 43 Methyltransferases 54 None None None 272 | neisseria 54 MGI-1 7 None None None 273 | neisseria 55 MGI-2 21 None None None 274 | neisseria 56 MGI-3 18 None None None 275 | neisseria 46 NadA 2 None None None 276 | neisseria 44 Neisseria Heparin Binding Antigen (NHBA) 2 None None None 277 | neisseria 71 NG MAST v2.0 2 19349 2021-10-19 2021-10-19 278 | neisseria 80 N. gonorrhoeae agMLST v1.0 251 None None None 279 | neisseria 57 N. gonorrhoeae Beta-lactam AMR 5 None None None 280 | neisseria 62 N. gonorrhoeae cgMLST v1.0 1649 12443 2021-10-25 2021-10-25 281 | neisseria 61 N. gonorrhoeae Efflux Pumps AMR 10 None None None 282 | neisseria 58 N. gonorrhoeae Fluoroquinolone AMR 4 None None None 283 | neisseria 59 N. gonorrhoeae Macrolides AMR 2 None None None 284 | neisseria 81 N. gonorrhoeae pgMLST v1.0 1907 None None None 285 | neisseria 60 N. gonorrhoeae plasmid mediated AMR 2 None None None 286 | neisseria 67 NG STAR 7 1947 2020-11-28 2020-11-28 287 | neisseria 47 N. meningitidis cgMLST v1.0 1605 23059 2021-10-25 2021-10-25 288 | neisseria 27 Nucleotide excision repair 8 None None None 289 | neisseria 64 OMV peptide 50 None None None 290 | neisseria 65 OMV peptide typing 24 4046 2019-05-15 2019-05-15 291 | neisseria 13 Pilus genes 27 None None None 292 | neisseria 78 PorB_loop_peptides 8 None None None 293 | neisseria 28 Protein glycosylation 14 None None None 294 | neisseria 22 Purine metabolism 39 None None None 295 | neisseria 23 Pyrimidine metabolism 32 None None None 296 | neisseria 14 Pyruvate dehydrogenase complex 3 None None None 297 | neisseria 24 Ribosomal protein genes 55 None None None 298 | neisseria 79 RMS in Neisseria gonorrhoeae 36 None None None 299 | neisseria 26 RNA polymerase 4 None None None 300 | neisseria 34 Small regulatory RNAs 3 None None None 301 | neisseria 16 TCA cycle 16 None None None 302 | neisseria 70 tRNA molecules 21 None None None 303 | neisseria 11 UDP-GlcNAc synthesis 1 None None None 304 | neisseria 10 UDP-glucose and UDP-galactose biosynthesis 2 None None None 305 | neisseria 51 VirB T4SS 31 None None None 306 | otsutsugamushi 1 MLST 7 98 2019-05-10 2019-05-10 307 | orhinotracheale 1 MLST 7 35 2018-01-03 2018-01-03 308 | plarvae 1 MLST 7 30 2020-12-10 2020-12-10 309 | pmultocida 1 Multiple host MLST 7 177 2021-06-18 2021-06-18 310 | pmultocida 2 RIRDC MLST 7 389 2021-06-01 2021-06-01 311 | ppentosaceus 1 MLST 7 17 2013-02-19 2013-02-19 312 | pdamselae 1 MLST 6 63 2021-05-06 2021-05-06 313 | psalmonis 1 MLST 7 28 2020-09-28 2020-09-28 314 | plasmid 7 IncA/C cgPMLST 28 41 2018-01-05 2018-01-05 315 | plasmid 6 IncA/C PMLST 4 13 2018-01-05 2018-01-05 316 | plasmid 3 IncF RST 7 None None None 317 | plasmid 5 IncHI1 MLST 6 16 2020-12-08 2020-12-08 318 | plasmid 2 IncHI2 DLST 2 16 2021-05-26 2021-05-26 319 | plasmid 1 IncI1 MLST 5 329 2021-03-05 2021-03-05 320 | plasmid 4 IncN MLST 3 23 2020-11-25 2020-11-25 321 | plasmid 8 pBSSB1-family 3 35 2019-04-09 2019-04-09 322 | pgingivalis 1 MLST 7 138 2007-08-12 2007-08-12 323 | paeruginosa 1 MLST 7 3833 2021-10-18 2021-10-18 324 | paeruginosa 2 Plasmid loci 199 None None None 325 | pfluorescens 1 MLST 7 121 2021-10-15 2021-10-15 326 | pputida 1 MLST 8 146 2021-10-21 2021-10-21 327 | ranatipestifer 1 MLST 7 82 2020-10-15 2020-10-15 328 | rhodococcus 1 MLST 7 46 2020-04-15 2020-04-20 329 | salmonella 4 cgMLST v2 (Enterobase) 3002 None None None 330 | salmonella 2 MLST 7 7680 2021-10-25 2021-10-25 331 | salmonella 1 Oxford loci 3633 None None None 332 | salmonella 3 SalmcgMLST v1.0 2750 13727 2021-02-08 2021-02-08 333 | sparasitica 1 MLST 7 15 2018-03-26 2018-03-26 334 | shewanella 1 MLST 8 74 2021-08-15 2021-08-15 335 | sinorhizobium 1 MLST 10 136 2010-05-07 2010-05-07 336 | smaltophilia 1 MLST 7 751 2021-10-19 2021-10-19 337 | saureus 1 MLST 7 7169 2021-10-23 2021-10-23 338 | saureus 2 Core 2208 2208 None None None 339 | schromogenes 1 MLST 7 127 2021-01-26 2021-01-26 340 | sepidermidis 1 MLST 7 1133 2021-10-13 2021-10-13 341 | shaemolyticus 1 MLST 7 92 2021-02-04 2021-02-04 342 | shominis 1 MLST 6 74 2020-09-04 2020-09-04 343 | spseudintermedius 1 MLST 7 2192 2021-08-20 2021-08-20 344 | oralstrep 2 S. mutans MLST (Do) 8 179 2019-10-08 2019-10-08 345 | oralstrep 3 S. mutans MLST (Nakano) 8 273 2020-12-30 2020-12-30 346 | oralstrep 1 S. oralis MLST 7 78 2015-10-23 2015-10-23 347 | sagalactiae 1 MLST 7 1861 2021-10-12 2021-10-12 348 | sagalactiae 37 Adherence Regulation 2 None None None 349 | sagalactiae 29 Alp Family Proteins 5 None None None 350 | sagalactiae 23 Amino Acid Metabolism 85 None None None 351 | sagalactiae 44 Aminoglycosides 2 None None None 352 | sagalactiae 17 Ascorbate and Aldarate Metabolism 28 None None None 353 | sagalactiae 3 Biosynthesis and activation of sialic acid 5 None None None 354 | sagalactiae 30 C5a Peptidase 2 None None None 355 | sagalactiae 4 Capsular polysaccharide Biosynthesis 7 None None None 356 | sagalactiae 46 Chloramphenicol 1 None None None 357 | sagalactiae 22 Fatty Acid Biosynthesis 18 None None None 358 | sagalactiae 31 Fibrinogen Binding Proteins 2 None None None 359 | sagalactiae 14 Fructose and Mannose Metabolism 36 None None None 360 | sagalactiae 15 Galactose Metabolism 34 None None None 361 | sagalactiae 12 Glycolysis 44 None None None 362 | sagalactiae 32 Haemolysin Operon 9 None None None 363 | sagalactiae 38 h_S.agalactiae cgMLST v1.0 1405 None None None 364 | sagalactiae 33 Hyaluronidase Activity 1 None None None 365 | sagalactiae 40 ICESag1962 51 None None None 366 | sagalactiae 39 IMESp2907 16 None None None 367 | sagalactiae 35 LysR family 1 None None None 368 | sagalactiae 45 Macrolides, lincosamides, Streptogramins 5 None None None 369 | sagalactiae 18 Oxidative phosphorylation 13 None None None 370 | sagalactiae 13 Pentose Phosphate Pathway 23 None None None 371 | sagalactiae 19 Photosynthesis 8 None None None 372 | sagalactiae 27 PI-1 6 None None None 373 | sagalactiae 28 PI-2a 5 None None None 374 | sagalactiae 26 PI-2b 5 None None None 375 | sagalactiae 34 Pilus Regulator 1 None None None 376 | sagalactiae 21 Purine Metabolism 63 None None None 377 | sagalactiae 20 Pyrimidine Metabolism 51 None None None 378 | sagalactiae 6 Serotype Ia 4 None None None 379 | sagalactiae 7 Serotype Ib 4 None None None 380 | sagalactiae 8 Serotype II 5 None None None 381 | sagalactiae 9 Serotype III 5 None None None 382 | sagalactiae 10 Serotype IV 6 None None None 383 | sagalactiae 5 Serotype V 6 None None None 384 | sagalactiae 41 Serotype VI 5 None None None 385 | sagalactiae 42 Serotype VII 4 None None None 386 | sagalactiae 16 Starch and Sucrose Metabolism 36 None None None 387 | sagalactiae 2 Synthesis of the group B carbohydrate 15 None None None 388 | sagalactiae 11 TCA Cycle 5 None None None 389 | sagalactiae 43 Tetracyclines 2 None None None 390 | sagalactiae 25 Transcription 4 None None None 391 | sagalactiae 36 Transcriptional Regulator 1 None None None 392 | sagalactiae 24 Translation 25 None None None 393 | sbsec 1 MLST 10 228 2020-12-15 2020-12-15 394 | scanis 1 MLST 7 62 2021-10-18 2021-10-18 395 | sdysgalactiae 1 MLST 7 557 2021-08-03 2021-08-03 396 | sgallolyticus 1 MLST 7 115 2021-07-27 2021-07-27 397 | siniae 1 MLST 8 13 2021-09-23 2021-09-23 398 | spneumoniae 1 MLST 7 17165 2021-10-07 2021-10-07 399 | spneumoniae 2 cgMLST 1360 6992 2020-02-14 2020-02-14 400 | spyogenes 2 FCT-AP1 4 None None None 401 | spyogenes 3 FCT-BP 4 None None None 402 | spyogenes 1 MLST 7 1280 2021-09-07 2021-09-07 403 | ssuis 1 MLST 7 1670 2021-10-15 2021-10-15 404 | sthermophilus 1 MLST 10 119 2015-06-18 2015-06-18 405 | suberis 1 MLST 7 1367 2021-06-04 2021-06-04 406 | suberis 2 vMLST 10 0 None None 407 | szooepidemicus 1 MLST 7 516 2021-05-20 2021-05-20 408 | streptomyces 1 MLST 6 236 2021-03-17 2021-03-17 409 | taylorella 1 MLST 7 77 2021-09-30 2021-09-30 410 | tenacibaculum 1 MLST 7 174 2020-12-04 2020-12-04 411 | tpallidum 1 MLST 3 90 2021-08-31 2021-08-31 412 | tvaginalis 1 MLST 7 60 2016-02-08 2016-02-08 413 | ureaplasma 1 MLST 4 170 2021-01-01 2021-01-01 414 | ureaplasma 2 eMLST 6 229 2018-09-14 2018-09-14 415 | vcholerae 1 MLST 7 1505 2021-10-01 2021-10-01 416 | vcholerae 2 MLST (O1 and O139) 5 422 2019-09-13 2019-09-13 417 | vcholerae 3 cgMLST 2443 1074 2021-04-02 2021-04-02 418 | vibrio 1 MLST 4 212 2021-10-15 2021-10-15 419 | vparahaemolyticus 1 MLST 7 2561 2021-10-22 2021-10-22 420 | vparahaemolyticus 2 AA-MLST 7 244 2018-04-20 2018-04-20 421 | vparahaemolyticus 3 cgMLST 2254 None None None 422 | vparahaemolyticus 4 Virulence markers 3 None None None 423 | vtapetis 1 MLST 10 10 2011-09-22 2011-09-22 424 | vvulnificus 1 MLST 10 601 2021-07-15 2021-07-15 425 | wolbachia 1 MLST 5 579 2020-09-01 2020-09-01 426 | wolbachia 2 WSP 5 None None None 427 | xcitri 1 cgMLST 1618 228 2020-02-09 2020-02-09 428 | xfastidiosa 1 MLST 7 89 2021-10-22 2021-10-22 429 | yruckeri 1 MLST 6 30 2011-07-27 2011-07-27 430 | -------------------------------------------------------------------------------- /scheme_list_snapshots/2024-10-14_pubmlst_scheme_list.tsv: -------------------------------------------------------------------------------- 1 | name id description locus_count records last_added last_updated 2 | achromobacter 1 MLST 7 583 2024-02-07 2024-02-07 3 | abaumannii 1 MLST (Oxford) 7 3377 2024-10-14 2024-10-14 4 | abaumannii 2 MLST (Pasteur) 7 2722 2024-10-14 2024-10-14 5 | abaumannii 3 cgMLST v1 2133 14813 2024-10-09 2024-10-09 6 | abaumannii 13 Adherence 28 None None None 7 | abaumannii 4 Biofilm 14 None None None 8 | abaumannii 9 Class A beta-lactamases 5 None None None 9 | abaumannii 10 Class B beta-lactamases (MBLs) 7 None None None 10 | abaumannii 11 Class C beta-lactamases 1 None None None 11 | abaumannii 12 Class D beta-lactamases (OXAs) 7 None None None 12 | abaumannii 15 Effector delivery system 30 None None None 13 | abaumannii 5 Efflux pumps 14 None None None 14 | abaumannii 8 Enzymes 4 None None None 15 | abaumannii 14 Immune modulation 9 None None None 16 | abaumannii 6 Iron uptake 19 None None None 17 | abaumannii 7 Quorum sensing 2 None None None 18 | aeromonas 1 MLST 6 2747 2024-09-24 2024-09-24 19 | aactinomycetemcomitans 1 MLST 7 57 2020-05-24 2020-05-24 20 | aphagocytophilum 2 ankA 1 154 2023-11-28 2023-11-28 21 | aphagocytophilum 3 groEL 1 199 2023-05-14 2023-05-14 22 | aphagocytophilum 1 MLST 7 197 2023-11-28 2023-11-28 23 | arcobacter 1 MLST 7 833 2021-02-25 2021-02-25 24 | afumigatus 1 MLST 7 48 2014-09-16 2014-09-16 25 | aparagallinarum 1 MLST 7 11 2023-11-01 2023-11-01 26 | bcereus 1 MLST 7 3314 2024-09-23 2024-09-23 27 | bcereus 2 B. anthracis cgMLST 3803 1958 2023-11-28 2023-11-28 28 | bcereus 3 B. anthracis accessory genes 1263 None None None 29 | bcereus 4 B. anthracis plasmids 10 40 2021-02-15 2021-02-15 30 | bcereus 5 B. cereus cgMLST 1568 3963 2024-10-07 2024-10-07 31 | blicheniformis 14 MLST 6 59 2023-12-13 2023-12-13 32 | bsubtilis 1 MLST 7 268 2023-11-14 2023-11-14 33 | llactis_phage 1 MLST 5 371 2023-02-20 2023-02-20 34 | bfragilis 1 MLST 7 231 2024-09-27 2024-09-27 35 | bbacilliformis 1 MLST 7 14 2017-06-17 2017-06-17 36 | bhenselae 1 MLST 8 38 2024-04-11 2024-04-11 37 | bwashoensis 1 MLST 6 22 2023-04-04 2023-04-04 38 | blastocystis 1 ST3 MLST 5 81 2019-05-20 2019-05-20 39 | blastocystis 2 ST4 MLST 6 6 2011-09-16 2011-09-16 40 | borrelia 1 MLST 8 1159 2024-09-11 2024-09-11 41 | borrelia 2 MLSA (legacy) 7 None None None 42 | borrelia 3 cgMLST 639 435 2024-06-03 2024-06-03 43 | borrelia 4 OspA IST typing 1 86 2024-02-15 2024-02-15 44 | brachyspira 5 B. hampsonii MLST 6 23 2022-03-28 2022-03-28 45 | brachyspira 2 B. hyodysenteriae MLST 7 342 2024-08-01 2024-08-01 46 | brachyspira 3 B. intermedia MLST 7 83 2015-07-20 2015-07-20 47 | brachyspira 4 B. pilosicoli MLST 7 140 2021-06-01 2021-06-01 48 | brachyspira 1 Brachyspira MLST 7 36 2012-01-18 2012-01-18 49 | brucella 1 MLST (9 locus) 9 122 2024-08-30 2024-08-30 50 | brucella 2 MLST (21 locus) 21 177 2023-02-07 2023-02-07 51 | brucella 3 cgMLST 1764 1133 2024-08-14 2024-08-14 52 | bcc 1 MLST 7 2413 2024-09-26 2024-09-26 53 | bmallei 1 cgMLST 3311 197 2024-08-12 2024-08-12 54 | bpseudomallei 1 MLST 7 2205 2024-10-14 2024-10-14 55 | bpseudomallei 2 cgMLST 4090 986 2024-09-10 2024-09-10 56 | campylobacter_nonjejuni 5 C. concisus/curvus MLST 7 177 2024-07-16 2024-07-16 57 | campylobacter_nonjejuni 9 C. fetus MLST 7 81 2024-06-03 2024-06-03 58 | campylobacter_nonjejuni 1 C. helveticus MLST 7 9 2015-01-12 2015-01-12 59 | campylobacter_nonjejuni 6 C. hyointestinalis MLST 7 136 2024-07-24 2024-07-24 60 | campylobacter_nonjejuni 2 C. insulaenigrae MLST 7 43 2011-11-10 2011-11-10 61 | campylobacter_nonjejuni 7 C. lanienae MLST 7 178 2023-12-01 2023-12-01 62 | campylobacter_nonjejuni 3 C. lari MLST 7 339 2024-07-24 2024-07-24 63 | campylobacter_nonjejuni 8 C. sputorum MLST 7 16 2011-11-18 2011-11-18 64 | campylobacter_nonjejuni 4 C. upsaliensis MLST 7 283 2024-04-09 2024-04-09 65 | campylobacter 1 MLST 7 14407 2024-10-11 2024-10-11 66 | campylobacter 3 1643 Gundogdu loci 1643 None None None 67 | campylobacter 10 Aerotolerance 8 None None None 68 | campylobacter 16 Aminoglycoside AMR 12 None None None 69 | campylobacter 12 Antimicrobial resistance 1 None None None 70 | campylobacter 11 Biofilm formation 12 None None None 71 | campylobacter 6 C. coli 15-537360 1588 None None None 72 | campylobacter 4 C. jejuni / C. coli cgMLST v1 1343 162905 2024-10-11 2024-10-11 73 | campylobacter 8 C. jejuni / C. coli cgMLST v2 1142 83281 2024-10-11 2024-10-11 74 | campylobacter 7 ED pathway 7 None None None 75 | campylobacter 2 eMLST (21 partial genes) 21 None None None 76 | campylobacter 13 Fluoroquinolone AMR 7 None None None 77 | campylobacter 18 Lincosomide AMR 1 None None None 78 | campylobacter 15 Macrolide AMR 2 None None None 79 | campylobacter 17 Phenicol AMR 2 None None None 80 | campylobacter 5 Ribosomal Protein Genes 52 None None None 81 | campylobacter 14 Tetracycline AMR 4 None None None 82 | campylobacter 9 Virulence 8 None None None 83 | calbicans 1 MLST 7 4277 2024-09-23 2024-09-23 84 | cglabrata 1 MLST 6 291 2024-07-14 2024-07-14 85 | ckrusei 1 MLST 6 239 2021-09-20 2021-09-20 86 | ctropicalis 1 MLST 6 1544 2024-07-18 2024-07-18 87 | cmaltaromaticum 1 MLST 7 56 2018-04-11 2018-04-11 88 | chlamydiales 16 Aerobic and ATP Biogenesis 16 None None None 89 | chlamydiales 7 Amino Acyl tRNA Synthesis 3 None None None 90 | chlamydiales 17 Aromatic Amino Acids 10 None None None 91 | chlamydiales 18 Aspartate Amino Acid 5 None None None 92 | chlamydiales 20 Biotin, Lipoate and Ubiquinone 6 None None None 93 | chlamydiales 26 Both Purine and Pyrimidine Metabolism 4 None None None 94 | chlamydiales 44 C. abortus cgMLST v1.0 959 None None None 95 | chlamydiales 30 Cell Division 9 None None None 96 | chlamydiales 42 C. trachomatis cgMLST v1.0 817 953 2023-10-09 2023-10-09 97 | chlamydiales 3 DNA Replication 24 None None None 98 | chlamydiales 14 Electron Transport Chain 4 None None None 99 | chlamydiales 37 Eukaryotic Type Chromatin Factors 4 None None None 100 | chlamydiales 29 Fatty Acid and Phospholipid Metabolism 27 None None None 101 | chlamydiales 21 Folic Acid 5 None None None 102 | chlamydiales 10 Glycolysis, Gluconeogensis, Glycogen 20 None None None 103 | chlamydiales 27 Membrane Proteins, Lipoproteins, Porins 9 None None None 104 | chlamydiales 36 Miscellaneous Enzymes/Conserved Proteins 44 None None None 105 | chlamydiales 1 MLST (Chlamydiales) 7 358 2024-09-19 2024-09-19 106 | chlamydiales 38 MLST (C. trachomatis) 7 89 2023-10-23 2023-10-23 107 | chlamydiales 41 MLST (C. trachomatis Uppsala) 5 629 2024-06-20 2024-06-20 108 | chlamydiales 4 Nucleotide Excision and Repair 18 None None None 109 | chlamydiales 33 Pathogenesis Associated Proteins 25 None None None 110 | chlamydiales 15 Pentose Phosphate Pathway 8 None None None 111 | chlamydiales 8 Peptide Synthesis 14 None None None 112 | chlamydiales 28 Peptidoglycan 16 None None None 113 | chlamydiales 11 Phosphorous and Sulphur 4 None None None 114 | chlamydiales 2 Plasmid loci 8 None None None 115 | chlamydiales 40 Plasmid MLST 8 47 2015-10-06 2015-10-06 116 | chlamydiales 22 Porphyrin 9 None None None 117 | chlamydiales 9 Protein Folding, Assembly, Modification 37 None None None 118 | chlamydiales 24 Purine Metabolism 3 None None None 119 | chlamydiales 25 Pyrimidine Metabolism 7 None None None 120 | chlamydiales 12 Pyruvate Dehydrogenase 7 None None None 121 | chlamydiales 5 Recombination 8 None None None 122 | chlamydiales 23 Riboflavin 5 None None None 123 | chlamydiales 43 Ribosomal Protein genes 52 None None None 124 | chlamydiales 6 RNA Associated 44 None None None 125 | chlamydiales 19 Serine Amino Acid 2 None None None 126 | chlamydiales 31 Signal Transduction 18 None None None 127 | chlamydiales 35 Specific Proteins 11 None None None 128 | chlamydiales 13 TCA Cycle 11 None None None 129 | chlamydiales 34 Transport Related Proteins 54 None None None 130 | chlamydiales 39 Type III Effector Proteins 0 None None None 131 | chlamydiales 32 Type III Secretion Systems 58 None None None 132 | cfreundii 1 MLST 7 1244 2024-10-01 2024-10-01 133 | csinensis 1 MLST 8 254 2012-01-07 2012-01-07 134 | cdifficile 2 cwp cluster genes 6 None None None 135 | cdifficile 1 MLST 7 1201 2024-10-07 2024-10-07 136 | cdifficile 3 Pathogenicity loci 5 None None None 137 | cbotulinum 1 MLST 7 192 2024-10-03 2024-10-03 138 | cbotulinum 2 Extended MLST 14 0 None None 139 | cchauvoei 2 agMLST 234 None None None 140 | cchauvoei 1 cgMLST 2223 60 2021-08-18 2021-08-18 141 | cperfringens 1 MLST 8 866 2024-08-30 2024-08-30 142 | cperfringens 2 cgMLST 1431 808 2024-02-05 2024-02-05 143 | csepticum 1 MLST 7 8 2008-07-29 2008-07-29 144 | cronobacter 1 MLST 7 1033 2024-09-08 2024-09-08 145 | cronobacter 4 cogMLST 1865 None None None 146 | cronobacter 3 Ext-MLST 3 0 None None 147 | cronobacter 5 Gcog 222 None None None 148 | cronobacter 6 O-serotype 2 0 None None 149 | cronobacter 2 Tax-MLST 2 None None None 150 | pacnes 3 MLST 8 264 2024-07-04 2024-10-06 151 | dnodosus 3 cgMLST 714 None None None 152 | dnodosus 1 MLST 7 120 2022-04-11 2022-04-11 153 | edwardsiella 1 MLST 10 24 2024-09-12 2024-09-12 154 | ecloacae 1 MLST 7 3230 2024-10-10 2024-10-10 155 | efaecalis 1 MLST 7 1952 2024-10-10 2024-10-10 156 | efaecium 1 MLST 7 2724 2024-10-10 2024-10-10 157 | efaecium 2 MLST (Bezdíček et al.) 8 1191 2024-09-30 2024-09-30 158 | escherichia 1 MLST (Achtman) 7 15616 2024-10-11 2024-10-11 159 | escherichia 2 MLST (Pasteur) 8 1793 2024-09-13 2024-09-13 160 | escherichia 3 beta-lactamase resistance 9 None None None 161 | escherichia 6 cgMLST 2513 None None None 162 | escherichia 12 IncL/M 3 None None None 163 | escherichia 4 locus of enterocyte effacement (LEE) island 40 None None None 164 | escherichia 14 oxa-48 chromosome loci 29 None None None 165 | escherichia 8 pO157 plasmid 49 None None None 166 | escherichia 13 pOXA-48 plasmid 71 None None None 167 | escherichia 11 quinolone resistance 4 None None None 168 | escherichia 5 shiga toxins 4 None None None 169 | escherichia 9 virulence genes 16 None None None 170 | fpsychrophilum 1 MLST 7 267 2024-06-13 2024-06-13 171 | gallibacterium 1 MLST 8 91 2023-08-04 2023-08-04 172 | geotrichum 1 MLST 5 40 2015-07-29 2015-07-29 173 | hparasuis 1 MLST 7 795 2024-08-22 2024-08-22 174 | hinfluenzae 1 MLST 7 2891 2024-10-04 2024-10-04 175 | hinfluenzae 42 Alanine, aspartate and glutamate metabolism 13 None None None 176 | hinfluenzae 14 Aminoacyl-tRNA biosynthesis 24 None None None 177 | hinfluenzae 19 Amino sugar and nucleotide sugar metabolism 21 None None None 178 | hinfluenzae 52 Antimicrobial Resistance 7 None None None 179 | hinfluenzae 43 Arginine and proline metabolism 20 None None None 180 | hinfluenzae 21 Butanoate metabolism 8 None None None 181 | hinfluenzae 2 Capsule - Region I 4 None None None 182 | hinfluenzae 4 Capsule - Region III 2 None None None 183 | hinfluenzae 7 Capsule - serotype A 2 None None None 184 | hinfluenzae 3 Capsule - serotype B 4 None None None 185 | hinfluenzae 8 Capsule - serotype C 4 None None None 186 | hinfluenzae 9 Capsule - serotype D 5 None None None 187 | hinfluenzae 6 Capsule - Serotype E 8 None None None 188 | hinfluenzae 5 Capsule - serotype F 3 None None None 189 | hinfluenzae 56 cgMLST v1 1037 13679 2024-10-10 2024-10-10 190 | hinfluenzae 38 Cysteine and methionine metabolism 17 None None None 191 | hinfluenzae 10 DNA Replication 13 None None None 192 | hinfluenzae 32 Fatty acid biosynthesis 11 None None None 193 | hinfluenzae 31 Fatty acid metabolism 3 None None None 194 | hinfluenzae 23 Fructose and mannose metabolism 13 None None None 195 | hinfluenzae 20 Galactose Metabolism 6 None None None 196 | hinfluenzae 33 Glycerolipid metabolism 6 None None None 197 | hinfluenzae 34 Glycerophospholipid metabolism 19 None None None 198 | hinfluenzae 39 Glycine, serine and threonine metabolism 19 None None None 199 | hinfluenzae 15 Glycolysis 15 None None None 200 | hinfluenzae 16 Glyoxylate and dicarboxylate metabolism 11 None None None 201 | hinfluenzae 45 Histidine metabolism 8 None None None 202 | hinfluenzae 53 Iron Acquisition 13 None None None 203 | hinfluenzae 50 LOS Biosynthesis 23 None None None 204 | hinfluenzae 40 Lysine biosynthesis 14 None None None 205 | hinfluenzae 47 Lysine degradation 4 None None None 206 | hinfluenzae 26 Methane metabolism 26 None None None 207 | hinfluenzae 27 Nitrogen Metabolism 10 None None None 208 | hinfluenzae 55 NTHi_clade_system 17 None None None 209 | hinfluenzae 11 Nucleotide Excision Repair 12 None None None 210 | hinfluenzae 29 Oxidative phosphorylation 10 None None None 211 | hinfluenzae 25 Pentose and glucuronate interconversions 4 None None None 212 | hinfluenzae 24 Pentose Phosphate Pathway 15 None None None 213 | hinfluenzae 37 Phenylalanine metabolism 4 None None None 214 | hinfluenzae 44 Phenylalanine, tyrosine, tryptophan biosynthesis 19 None None None 215 | hinfluenzae 51 Pilus Biosynthesis 6 None None None 216 | hinfluenzae 22 Propanoate metabolism 10 None None None 217 | hinfluenzae 35 Purine Metabolism 58 None None None 218 | hinfluenzae 36 Pyrimidine Metabolism 43 None None None 219 | hinfluenzae 18 Pyruvate Metabolism 20 None None None 220 | hinfluenzae 30 Reductive carboxylate cycle (CO2 fixation) 13 None None None 221 | hinfluenzae 13 Ribosomal Protein Genes 56 None None None 222 | hinfluenzae 12 RNA Polymerase 11 None None None 223 | hinfluenzae 28 Sulphur Metabolism 8 None None None 224 | hinfluenzae 17 TCA Cycle 12 None None None 225 | hinfluenzae 54 Translation regulator 1 None None None 226 | hinfluenzae 41 Tryptophan metabolism 6 None None None 227 | hinfluenzae 46 Tyrosine metabolism 4 None None None 228 | hinfluenzae 48 Valine, leucine and isoleucine biosynthesis 11 None None None 229 | hinfluenzae 49 Valine, leucine and isoleucine degradation 3 None None None 230 | hcinaedi 1 MLST 7 21 2020-10-12 2020-10-12 231 | helicobacter 1 MLST 7 4509 2024-09-09 2024-09-09 232 | hsuis 1 MLST 7 172 2024-06-18 2024-06-18 233 | kaerogenes 1 MLST 7 770 2024-09-14 2024-09-14 234 | koxytoca 1 MLST 7 643 2024-10-11 2024-10-11 235 | kseptempunctata 1 MLST 2 3 2014-12-22 2014-12-22 236 | lsalivarius 1 MLST 5 25 2010-12-07 2010-12-07 237 | lgarvieae 1 MLST 7 156 2024-09-30 2024-09-30 238 | leptospira 1 MLST (scheme 1) 7 383 2024-05-24 2024-05-24 239 | leptospira 2 MLST (scheme 2) 7 296 2024-09-25 2024-09-25 240 | leptospira 3 MLST (scheme 3) 6 198 2024-06-11 2024-06-11 241 | leptospira 4 cgMLST 1565 None None None 242 | leptospira 5 LPS 21 None None None 243 | liberibacter 1 MLST 7 14 2020-05-07 2020-05-07 244 | mcanis 1 MLST 7 83 2019-10-21 2019-10-21 245 | mcaseolyticus 1 MLST 7 68 2023-12-13 2023-12-13 246 | msciuri 1 MLST 7 360 2024-09-27 2024-09-27 247 | mhaemolytica 1 MLST 7 61 2024-03-13 2024-03-13 248 | mplutonius 1 MLST 4 47 2023-07-06 2024-10-04 249 | mycobacteria 1 Core genome (H37Rv ref vs 19 finished species) 744 6437 2023-08-10 2023-08-10 250 | mycobacteria 2 MLST 8 1042 2024-10-09 2024-10-09 251 | mabscessus 1 MLST 7 344 2024-08-22 2024-08-22 252 | mabscessus 2 cgMLST 2904 2803 2024-07-01 2024-07-01 253 | magalactiae 1 MLST 5 35 2019-04-24 2019-04-24 254 | manserisalpingitidis 1 MLST 5 76 2020-11-10 2020-11-10 255 | mbovis 2 MLST 7 286 2024-10-10 2024-10-10 256 | mbovis 1 MLST (legacy) 7 187 2024-10-10 2024-10-10 257 | mflocculare 1 MLST 3 8 2018-07-03 2018-07-03 258 | mgallisepticum 1 MLST#1 (Ghanem) 7 109 2024-09-16 2024-09-16 259 | mgallisepticum 2 MLST#2 (Bekő) 6 148 2024-08-30 2024-08-30 260 | mgenitalium 1 MG191-MG309 typing 2 468 2024-10-09 2024-10-09 261 | mgenitalium 2 MLST 6 0 None None 262 | mhominis 1 MLST 5 65 2023-11-05 2023-11-05 263 | mhominis 2 MVLST 5 41 2023-11-05 2023-11-05 264 | mhominis 3 eMLST 10 42 2023-11-05 2023-11-05 265 | mhyopneumoniae 1 MLST 3 239 2024-01-11 2024-01-11 266 | mhyorhinis 1 MLST 6 224 2024-10-11 2024-10-11 267 | mhyosynoviae 1 MLST 7 73 2024-09-15 2024-09-15 268 | miowae 1 MLST 6 48 2023-07-17 2023-07-17 269 | mpneumoniae 1 MLST 8 47 2024-06-21 2024-06-21 270 | msynoviae 1 MLST 7 224 2024-10-08 2024-10-08 271 | neisseria 1 MLST 7 18414 2024-10-10 2024-10-10 272 | neisseria 2 Finetyping antigens 3 None None None 273 | neisseria 42 rplF species 1 226 2024-09-01 2024-09-01 274 | neisseria 7 ADP-heptose biosynthesis 5 None None None 275 | neisseria 5 Antibiotic resistance 12 None None None 276 | neisseria 3 Antigen genes 7 None None None 277 | neisseria 52 beta lactamase plasmid 8 18 2018-04-17 2018-04-17 278 | neisseria 53 Bexsero Antigen Sequence Typing (BAST) 5 4904 2024-09-09 2024-09-09 279 | neisseria 63 Capsule Null (cnl) 1 None None None 280 | neisseria 29 Capsule Region A - Serogroup A 4 None None None 281 | neisseria 36 Capsule Region A - Serogroup B 5 None None None 282 | neisseria 37 Capsule Region A - Serogroup C 6 None None None 283 | neisseria 35 Capsule Region A - Serogroup E 7 None None None 284 | neisseria 32 Capsule Region A - Serogroup H 4 None None None 285 | neisseria 33 Capsule Region A - Serogroup L 3 None None None 286 | neisseria 38 Capsule Region A - Serogroup W 6 None None None 287 | neisseria 30 Capsule Region A - Serogroup X 3 None None None 288 | neisseria 39 Capsule Region A - Serogroup Y 6 None None None 289 | neisseria 31 Capsule Region A - Serogroup Z 4 None None None 290 | neisseria 41 Capsule Region B 2 None None None 291 | neisseria 40 Capsule Region C 4 None None None 292 | neisseria 48 Capsule Region D and D' 6 None None None 293 | neisseria 74 Commensal cps: Group 1 6 None None None 294 | neisseria 75 Commensal cps: Group 2 8 None None None 295 | neisseria 76 Commensal cps: Group 3 12 None None None 296 | neisseria 49 Conjugative Plasmid 50 796 2022-10-20 2022-10-20 297 | neisseria 66 Cryptic Plasmid 9 96 2018-05-15 2018-05-15 298 | neisseria 25 DNA replication 16 None None None 299 | neisseria 4 eMLST (20 locus partial genes) 20 None None None 300 | neisseria 12 eMLST (20 locus whole genes) 20 None None None 301 | neisseria 6 Factor H binding protein 10 None None None 302 | neisseria 73 GC OMV peptide typing 26 2371 2021-07-26 2021-07-26 303 | neisseria 15 Glycolysis 11 None None None 304 | neisseria 50 Gonococcal Genetic Island 73 None None None 305 | neisseria 72 Human-restricted Neisseria cgMLST v1.0 1441 None None None 306 | neisseria 21 Iron acquisition 7 None None None 307 | neisseria 19 Kdo addition 5 None None None 308 | neisseria 45 L3 cgMLST 1742 None None None 309 | neisseria 68 L44 cgMLST 1699 None None None 310 | neisseria 69 L44 pgMLST 1786 None None None 311 | neisseria 17 Lipid A biosynthesis: acyltransferases 4 None None None 312 | neisseria 18 Lipid A biosynthesis: other 5 None None None 313 | neisseria 9 LOS alpha chain transferases 7 None None None 314 | neisseria 8 LOS inner core transferases 7 None None None 315 | neisseria 20 LOS transport/export 5 None None None 316 | neisseria 77 Mendevar 7 None None None 317 | neisseria 43 Methylases 53 None None None 318 | neisseria 54 MGI-1 7 None None None 319 | neisseria 55 MGI-2 21 None None None 320 | neisseria 56 MGI-3 18 None None None 321 | neisseria 46 NadA 2 None None None 322 | neisseria 44 Neisseria Heparin Binding Antigen (NHBA) 2 None None None 323 | neisseria 71 NG MAST v2.0 2 22603 2024-10-09 2024-10-09 324 | neisseria 80 N. gonorrhoeae agMLST v1.0 251 None None None 325 | neisseria 57 N. gonorrhoeae Beta-lactam AMR 5 None None None 326 | neisseria 62 N. gonorrhoeae cgMLST v1.0 1649 71463 2024-10-14 2024-10-14 327 | neisseria 89 N. gonorrhoeae cgMLST v2 1430 36276 2024-10-14 2024-10-14 328 | neisseria 61 N. gonorrhoeae Efflux Pumps AMR 10 None None None 329 | neisseria 58 N. gonorrhoeae Fluoroquinolone AMR 4 None None None 330 | neisseria 59 N. gonorrhoeae Macrolides AMR 2 None None None 331 | neisseria 81 N. gonorrhoeae pgMLST v1.0 1907 None None None 332 | neisseria 60 N. gonorrhoeae plasmid mediated AMR 2 None None None 333 | neisseria 87 Ng_pblaST 8 5 2023-03-17 2023-03-17 334 | neisseria 67 NG STAR 7 6213 2024-07-23 2024-07-23 335 | neisseria 47 N. meningitidis cgMLST v1 1605 None None None 336 | neisseria 85 N. meningitidis cgMLST v2 1422 None None None 337 | neisseria 88 N. meningitidis cgMLST v3 1329 62606 2024-10-14 2024-10-14 338 | neisseria 27 Nucleotide excision repair 8 None None None 339 | neisseria 64 OMV peptide 50 None None None 340 | neisseria 65 OMV peptide typing 24 4046 2019-05-15 2019-05-15 341 | neisseria 86 Other RMS 1 None None None 342 | neisseria 82 PenA locus 15 None None None 343 | neisseria 83 Peptidoglycan pathway 23 None None None 344 | neisseria 13 Pilus genes 29 None None None 345 | neisseria 78 PorB_loop_peptides 8 None None None 346 | neisseria 28 Protein glycosylation 14 None None None 347 | neisseria 22 Purine metabolism 39 None None None 348 | neisseria 23 Pyrimidine metabolism 32 None None None 349 | neisseria 14 Pyruvate dehydrogenase complex 3 None None None 350 | neisseria 24 Ribosomal protein genes 55 None None None 351 | neisseria 79 RMS in Neisseria gonorrhoeae 36 None None None 352 | neisseria 26 RNA polymerase 4 None None None 353 | neisseria 84 Secreted peptides 9 None None None 354 | neisseria 34 Small regulatory RNAs 3 None None None 355 | neisseria 16 TCA cycle 16 None None None 356 | neisseria 70 tRNA molecules 21 None None None 357 | neisseria 11 UDP-GlcNAc synthesis 1 None None None 358 | neisseria 10 UDP-glucose and UDP-galactose biosynthesis 2 None None None 359 | neisseria 51 VirB T4SS 31 None None None 360 | otsutsugamushi 1 MLST 7 161 2024-09-19 2024-09-19 361 | orhinotracheale 1 MLST 7 43 2023-11-28 2023-11-28 362 | plarvae 1 MLST 7 45 2023-06-09 2023-06-09 363 | pmultocida 3 cgMLST (draft) 1238 985 2024-10-02 2024-10-02 364 | pmultocida 1 Multiple host MLST 7 360 2024-10-14 2024-10-14 365 | pmultocida 2 RIRDC MLST 7 562 2024-10-04 2024-10-04 366 | ppentosaceus 1 MLST 7 17 2013-02-19 2013-02-19 367 | pdamselae 1 MLST 6 67 2023-08-11 2023-08-11 368 | psalmonis 1 MLST 7 33 2023-04-28 2023-05-17 369 | plasmid 7 IncA/C cgPMLST 28 41 2018-01-05 2018-01-05 370 | plasmid 6 IncA/C PMLST 4 13 2018-01-05 2018-01-05 371 | plasmid 3 IncF RST 7 None None None 372 | plasmid 5 IncHI1 MLST 6 17 2022-07-21 2022-07-21 373 | plasmid 2 IncHI2 DLST 2 17 2023-04-17 2023-04-17 374 | plasmid 1 IncI1 MLST 5 333 2024-07-16 2024-07-16 375 | plasmid 4 IncN MLST 3 24 2023-02-08 2023-02-08 376 | plasmid 8 pBSSB1-family 3 35 2019-04-09 2019-04-09 377 | plasmid 9 Shigella flexneri 3 13 2022-04-28 2022-04-28 378 | pgingivalis 1 MLST 7 172 2023-05-11 2023-05-11 379 | proteus 1 MLST 6 636 2024-08-26 2024-08-26 380 | proteus 3 Antibiotic resistance 1 None None None 381 | proteus 2 Virulence 12 575 2024-07-30 2024-07-30 382 | paeruginosa 1 MLST 7 5090 2024-10-07 2024-10-07 383 | paeruginosa 2 Plasmid loci 199 None None None 384 | pfluorescens 1 MLST 7 129 2022-01-12 2022-01-12 385 | pputida 1 MLST 8 302 2024-08-21 2024-08-21 386 | ranatipestifer 1 MLST 7 229 2024-06-26 2024-06-26 387 | rhodococcus 1 MLST 7 82 2024-06-11 2024-06-11 388 | salmonella 4 cgMLST v2 (Enterobase) 3002 None None None 389 | salmonella 2 MLST 7 10956 2024-10-11 2024-10-11 390 | salmonella 1 Oxford loci 3633 None None None 391 | salmonella 3 SalmcgMLST v1.0 2750 19528 2024-10-07 2024-10-07 392 | sparasitica 1 MLST 7 15 2018-03-26 2018-03-26 393 | serratia 1 MLST 6 639 2024-09-12 2024-09-12 394 | serratia 2 cgMLST 2692 None None None 395 | shewanella 1 MLST 8 80 2024-10-08 2024-10-08 396 | sinorhizobium 1 MLST 10 136 2010-05-07 2010-05-07 397 | smaltophilia 1 MLST 7 1166 2024-10-01 2024-10-01 398 | saureus 1 MLST 7 9340 2024-10-11 2024-10-11 399 | saureus 20 cgMLST 1716 23136 2024-04-24 2024-04-24 400 | saureus 2 Core 2208 2208 None None None 401 | saureus 12 TCS-10: phoPR 2 None None None 402 | saureus 13 TCS-11: airSR 2 None None None 403 | saureus 14 TCS-12: vraSR 4 None None None 404 | saureus 15 TCS-13: agrCA 7 None None None 405 | saureus 16 TCS-14: kdpDE 2 None None None 406 | saureus 17 TCS-15: hssRS 2 None None None 407 | saureus 18 TCS-16: nreBC 7 None None None 408 | saureus 19 TCS-17: braRS 3 None None None 409 | saureus 3 TCS-1: walRK 4 None None None 410 | saureus 4 TCS-2: kdpED (SCCmec) 2 None None None 411 | saureus 5 TCS-3: hptSR 3 None None None 412 | saureus 6 TCS-4: lytSR 2 None None None 413 | saureus 7 TCS-5: graRS 3 None None None 414 | saureus 8 TCS-6: saeRS 4 None None None 415 | saureus 9 TCS-7 4 None None None 416 | saureus 10 TCS-8: arlRS 2 None None None 417 | saureus 11 TCS-9: srrAB 2 None None None 418 | schromogenes 1 MLST 7 193 2024-10-02 2024-10-02 419 | sepidermidis 1 MLST 7 1252 2024-10-08 2024-10-08 420 | shaemolyticus 1 MLST 7 179 2024-10-01 2024-10-01 421 | shominis 1 MLST 6 215 2024-08-22 2024-08-22 422 | spseudintermedius 1 MLST 7 2790 2024-09-30 2024-09-30 423 | oralstrep 2 S. mutans MLST (Do) 8 179 2019-10-08 2019-10-08 424 | oralstrep 3 S. mutans MLST (Nakano) 8 352 2022-09-18 2022-09-18 425 | oralstrep 1 S. oralis MLST 7 79 2024-07-23 2024-07-23 426 | sagalactiae 1 MLST 7 2288 2024-10-07 2024-10-07 427 | sagalactiae 37 Adherence Regulation 2 None None None 428 | sagalactiae 29 Alp Family Proteins 5 None None None 429 | sagalactiae 23 Amino Acid Metabolism 85 None None None 430 | sagalactiae 44 Aminoglycosides 2 None None None 431 | sagalactiae 17 Ascorbate and Aldarate Metabolism 28 None None None 432 | sagalactiae 3 Biosynthesis and activation of sialic acid 5 None None None 433 | sagalactiae 30 C5a Peptidase 2 None None None 434 | sagalactiae 4 Capsular polysaccharide Biosynthesis 7 None None None 435 | sagalactiae 46 Chloramphenicol 1 None None None 436 | sagalactiae 22 Fatty Acid Biosynthesis 18 None None None 437 | sagalactiae 31 Fibrinogen Binding Proteins 2 None None None 438 | sagalactiae 14 Fructose and Mannose Metabolism 36 None None None 439 | sagalactiae 15 Galactose Metabolism 34 None None None 440 | sagalactiae 12 Glycolysis 44 None None None 441 | sagalactiae 32 Haemolysin Operon 9 None None None 442 | sagalactiae 38 h_S.agalactiae cgMLST v1.0 1405 None None None 443 | sagalactiae 33 Hyaluronidase Activity 1 None None None 444 | sagalactiae 40 ICESag1962 51 None None None 445 | sagalactiae 39 IMESp2907 16 None None None 446 | sagalactiae 35 LysR family 1 None None None 447 | sagalactiae 45 Macrolides, lincosamides, Streptogramins 5 None None None 448 | sagalactiae 18 Oxidative phosphorylation 13 None None None 449 | sagalactiae 13 Pentose Phosphate Pathway 23 None None None 450 | sagalactiae 19 Photosynthesis 8 None None None 451 | sagalactiae 27 PI-1 6 None None None 452 | sagalactiae 28 PI-2a 5 None None None 453 | sagalactiae 26 PI-2b 5 None None None 454 | sagalactiae 34 Pilus Regulator 1 None None None 455 | sagalactiae 21 Purine Metabolism 63 None None None 456 | sagalactiae 20 Pyrimidine Metabolism 51 None None None 457 | sagalactiae 6 Serotype Ia 5 None None None 458 | sagalactiae 7 Serotype Ib 5 None None None 459 | sagalactiae 8 Serotype II 7 None None None 460 | sagalactiae 9 Serotype III 5 None None None 461 | sagalactiae 10 Serotype IV 6 None None None 462 | sagalactiae 48 Serotype IX 6 None None None 463 | sagalactiae 5 Serotype V 7 None None None 464 | sagalactiae 41 Serotype VI 5 None None None 465 | sagalactiae 42 Serotype VII 5 None None None 466 | sagalactiae 47 Serotype VIII 5 None None None 467 | sagalactiae 16 Starch and Sucrose Metabolism 36 None None None 468 | sagalactiae 2 Synthesis of the group B carbohydrate 15 None None None 469 | sagalactiae 11 TCA Cycle 5 None None None 470 | sagalactiae 43 Tetracyclines 2 None None None 471 | sagalactiae 25 Transcription 4 None None None 472 | sagalactiae 36 Transcriptional Regulator 1 None None None 473 | sagalactiae 24 Translation 25 None None None 474 | sbsec 1 MLST 10 239 2023-10-30 2023-10-30 475 | scanis 1 MLST 7 101 2024-03-04 2024-03-04 476 | sdysgalactiae 1 MLST 7 788 2024-09-13 2024-09-13 477 | sgallolyticus 1 MLST 7 121 2023-09-25 2023-09-25 478 | siniae 1 MLST 8 13 2021-09-23 2021-09-23 479 | smitis 1 MLST 7 260 2024-06-20 2024-06-20 480 | spneumoniae 1 MLST 7 19306 2024-10-07 2024-10-07 481 | spneumoniae 2 cgMLST 1222 80400 2024-10-11 2024-10-11 482 | spyogenes 4 Emm typing 10 None None None 483 | spyogenes 6 FCT-other 7 None None None 484 | spyogenes 2 FCT-pilA 5 None None None 485 | spyogenes 3 FCT-pilB 7 None None None 486 | spyogenes 7 FCT-pilL 7 None None None 487 | spyogenes 10 FnBP domains 8 None None None 488 | spyogenes 9 GAC biosynthesis 12 None None None 489 | spyogenes 1 MLST 7 1492 2024-09-20 2024-09-20 490 | spyogenes 8 M protein domains 5 None None None 491 | spyogenes 5 Resistance 15 None None None 492 | ssuis 1 MLST 7 2909 2024-10-09 2024-10-09 493 | sthermophilus 1 MLST 10 140 2023-06-15 2023-06-15 494 | suberis 1 MLST 7 2137 2024-09-30 2024-09-30 495 | suberis 8 cgMLST 1447 1247 2024-06-10 2024-06-10 496 | suberis 19 diag_GWAS_1gen+milk&serum_PIMMS 693 None None None 497 | suberis 3 Growth in milk 415 None None None 498 | suberis 4 Growth in milk and adult bovine serum 555 None None None 499 | suberis 5 Growth in Todd Hewitt broth 265 None None None 500 | suberis 6 GWAS growth in milk 572 None None None 501 | suberis 7 GWAS growth in milk and adult bovine serum 506 None None None 502 | suberis 17 milk_GWAS_1_gen+PIMMS_milk 516 None None None 503 | suberis 15 new_GWAS_diagonal_+-1_gen 140 None None None 504 | suberis 16 new_GWAS_diagonal_+-2_gen 61 None None None 505 | suberis 11 new_milk_GWAS_+-1_gen 118 None None None 506 | suberis 12 new_milk_GWAS_+-2_gen 134 None None None 507 | suberis 13 new_serum_GWAS_+-1_gen 152 None None None 508 | suberis 14 new_serum_GWAS_+-2_gen 162 None None None 509 | suberis 18 serum_GWAS_1_gen+PIMMS_serum 685 None None None 510 | suberis 2 vMLST 10 0 None None 511 | szooepidemicus 1 MLST 7 553 2024-09-24 2024-09-24 512 | streptomyces 1 MLST 6 806 2024-07-11 2024-07-11 513 | taylorella 1 MLST 7 92 2024-02-01 2024-02-01 514 | tenacibaculum 1 MLST 7 193 2024-01-24 2024-01-24 515 | tpallidum 1 MLST (Grillová) 3 130 2024-07-01 2024-07-01 516 | tpallidum 181 MLST (Pla-Díaz) 7 0 None None 517 | tpallidum 90 1,4-dichlorobenzene Metabolism 1 None None None 518 | tpallidum 12 ABC Transporters 55 None None None 519 | tpallidum 66 Alanine Metabolism 5 None None None 520 | tpallidum 19 Alanine Transport 2 None None None 521 | tpallidum 94 Aldarate Metabolism 1 None None None 522 | tpallidum 170 All Membrane-Associated 71 None None None 523 | tpallidum 147 Amino Sugar Biosynthesis 1 None None None 524 | tpallidum 50 Amino Sugar Metabolism 9 None None None 525 | tpallidum 167 Ansamycin Biosynthesis 2 None None None 526 | tpallidum 38 Antimicrobial Peptide Transport 3 None None None 527 | tpallidum 56 Arginine Metabolism 9 None None None 528 | tpallidum 93 Ascorbate Metabolism 1 None None None 529 | tpallidum 67 Aspartic Acid Metabolism 4 None None None 530 | tpallidum 179 Bactofilins 3 None None None 531 | tpallidum 91 Benzoate Metabolism 1 None None None 532 | tpallidum 24 Betaine Transport 1 None None None 533 | tpallidum 158 Biotin Biosynthesis 3 None None None 534 | tpallidum 98 Biotin Metabolism 2 None None None 535 | tpallidum 28 Biotin Transport 3 None None None 536 | tpallidum 71 Butanoate Metabolism 3 None None None 537 | tpallidum 11 Calcium Transport 1 None None None 538 | tpallidum 73 Carbon Metabolism 21 None None None 539 | tpallidum 162 Cardiolipin Biosynthesis 1 None None None 540 | tpallidum 25 Carnitine Transport 1 None None None 541 | tpallidum 2 Cell Cycle 27 None None None 542 | tpallidum 3 Cell Division 29 None None None 543 | tpallidum 26 Choline Transport 1 None None None 544 | tpallidum 5 Cobalt Transport 3 None None None 545 | tpallidum 145 Cofactor Biosynthesis 24 None None None 546 | tpallidum 139 C-type Cytochrome Biogenesis 6 None None None 547 | tpallidum 81 Cyanoamino Acid Metabolism 2 None None None 548 | tpallidum 64 Cysteine Metabolism 3 None None None 549 | tpallidum 83 D-glutamic Acid Metabolism 2 None None None 550 | tpallidum 36 Dicarboxylate Transport 2 None None None 551 | tpallidum 108 DNA Recombination 24 None None None 552 | tpallidum 107 DNA Repair 41 None None None 553 | tpallidum 106 DNA Replication 23 None None None 554 | tpallidum 109 DNA Uptake and Competence 6 None None None 555 | tpallidum 101 Drug Metabolism 3 None None None 556 | tpallidum 41 Drug Transport 4 None None None 557 | tpallidum 55 Entner Doudoroff Pathway 5 None None None 558 | tpallidum 86 Ether Lipid Metabolism 1 None None None 559 | tpallidum 89 Ethylbenzene Metabolism 1 None None None 560 | tpallidum 143 Export System 20 None None None 561 | tpallidum 169 Fatty Acid Biosynthesis 2 None None None 562 | tpallidum 103 Fermentation 2 None None None 563 | tpallidum 180 FeS Cluster Assembly 3 None None None 564 | tpallidum 175 Flagellar 41 None None None 565 | tpallidum 149 Folate Biosynthesis 10 None None None 566 | tpallidum 45 Fructose Metabolism 7 None None None 567 | tpallidum 14 Fructose Transport 1 None None None 568 | tpallidum 47 Galactose Metabolism 4 None None None 569 | tpallidum 15 Galactose Transport 4 None None None 570 | tpallidum 68 Glutamic Acid Metabolism 4 None None None 571 | tpallidum 23 Glutamine Transport 1 None None None 572 | tpallidum 72 Glutathione Metabolism 6 None None None 573 | tpallidum 35 Glycerol Transport 1 None None None 574 | tpallidum 79 Glycerophospholipid/Glycerolipid Metabolism 6 None None None 575 | tpallidum 60 Glycine Metabolism 2 None None None 576 | tpallidum 20 Glycine Transport 2 None None None 577 | tpallidum 53 Glycolysis and Gluconeogenesis 15 None None None 578 | tpallidum 95 Glycosaminoglycan Metabolism 1 None None None 579 | tpallidum 82 Glyoxylate/Dicarboxylate Metabolism 3 None None None 580 | tpallidum 69 Histidine Metabolism 1 None None None 581 | tpallidum 85 Inositol Phosphate Metabolism 1 None None None 582 | tpallidum 8 Iron Transport 6 None None None 583 | tpallidum 165 Isoquinoline Alkoloid Biosynthesis 3 None None None 584 | tpallidum 87 Linolene Metabolism 2 None None None 585 | tpallidum 40 Lipopolysaccharide Transport 6 None None None 586 | tpallidum 30 Lipoprotein Transport 3 None None None 587 | tpallidum 156 Lysine Biosynthesis 2 None None None 588 | tpallidum 58 Lysine Metabolism 2 None None None 589 | tpallidum 4 Magnesium Transport 6 None None None 590 | tpallidum 13 Maltose Transport 3 None None None 591 | tpallidum 7 Manganese Transport 4 None None None 592 | tpallidum 46 Mannose Metabolism 7 None None None 593 | tpallidum 102 Metabolic Interconversions 5 None None None 594 | tpallidum 74 Methane Metabolism 23 None None None 595 | tpallidum 65 Methionine Metabolism 3 None None None 596 | tpallidum 18 Methionine Transport 3 None None None 597 | tpallidum 77 Nicotinate/Nicotinamide Metabolism 8 None None None 598 | tpallidum 99 Nitrogen Metabolism 2 None None None 599 | tpallidum 159 Novobiocin Biosynthesis 1 None None None 600 | tpallidum 146 Nucleotide Sugar Biosynthesis 6 None None None 601 | tpallidum 49 Nucleotide Sugar Metabolism 8 None None None 602 | tpallidum 157 Other Amino Acid Biosynthesis 16 None None None 603 | tpallidum 151 Other Lipopolysaccharide Biosynthesis 3 None None None 604 | tpallidum 178 Other Metabolism 2 None None None 605 | tpallidum 176 Other Motility and/or Chemotaxis 23 None None None 606 | tpallidum 138 Other Protein Processing 16 None None None 607 | tpallidum 39 Other Protein Transport 12 None None None 608 | tpallidum 141 Other Respiration 5 None None None 609 | tpallidum 174 Other Signalling 11 None None None 610 | tpallidum 113 Other Transcription 3 None None None 611 | tpallidum 121 Other tRNA Biosynthesis 4 None None None 612 | tpallidum 171 Outer Membrane-Associated 10 None None None 613 | tpallidum 140 Oxidative Phosphorylation 15 None None None 614 | tpallidum 163 Pantothenate Biosynthesis 4 None None None 615 | tpallidum 105 Pentose Phosphate Pathway 15 None None None 616 | tpallidum 150 Peptidoglycan Biosynthesis 19 None None None 617 | tpallidum 152 Phenylalanine Biosynthesis 1 None None None 618 | tpallidum 63 Phenylalanine Metabolism 2 None None None 619 | tpallidum 33 Phosphate Transport 1 None None None 620 | tpallidum 78 Phosphonate/Phosphinate Metabolism 1 None None None 621 | tpallidum 142 Phosphotransferase System 4 None None None 622 | tpallidum 88 Pinene Metabolism 2 None None None 623 | tpallidum 161 Piperidine Biosynthesis 2 None None None 624 | tpallidum 96 Polyamine Metabolism 3 None None None 625 | tpallidum 168 Polyketide Biosynthesis 2 None None None 626 | tpallidum 97 Porphyrin Metabolism 2 None None None 627 | tpallidum 10 Potassium Transport 4 None None None 628 | tpallidum 155 Proline Biosynthesis 3 None None None 629 | tpallidum 57 Proline Metabolism 8 None None None 630 | tpallidum 75 Propionate Metabolism 2 None None None 631 | tpallidum 137 Protein Folding 20 None None None 632 | tpallidum 43 Purine Metabolism 26 None None None 633 | tpallidum 42 Purine Transport 3 None None None 634 | tpallidum 32 Putrescine Transport 4 None None None 635 | tpallidum 44 Pyrimidine Metabolism 29 None None None 636 | tpallidum 52 Pyruvate Metabolism 10 None None None 637 | tpallidum 173 Quorum Sensing 10 None None None 638 | tpallidum 104 Reductive Carboxylate Cycle 2 None None None 639 | tpallidum 100 Riboflavin Metabolism 2 None None None 640 | tpallidum 29 Riboflavin Transport 5 None None None 641 | tpallidum 115 Ribosome 61 None None None 642 | tpallidum 112 RNA Degredation 11 None None None 643 | tpallidum 110 RNA Polymerase 7 None None None 644 | tpallidum 114 RNA Processing 24 None None None 645 | tpallidum 116 rRNA Processing 10 None None None 646 | tpallidum 148 Secondary Metabolite Biosynthesis 49 None None None 647 | tpallidum 92 Selenocompound Metabolism 2 None None None 648 | tpallidum 61 Serine Metabolism 2 None None None 649 | tpallidum 21 Serine Transport 1 None None None 650 | tpallidum 9 Sodium Transport 2 None None None 651 | tpallidum 31 Spermidine Transport 4 None None None 652 | tpallidum 51 Starch Metabolism 6 None None None 653 | tpallidum 166 Streptomycin Biosynthesis 2 None None None 654 | tpallidum 48 Sucrose Metabolism 5 None None None 655 | tpallidum 76 Taurine/Hypotaurine Metabolism 2 None None None 656 | tpallidum 54 TCA Cycle 2 None None None 657 | tpallidum 164 Terpenoid Backbone Biosynthesis 9 None None None 658 | tpallidum 84 Thiamine Metabolism 7 None None None 659 | tpallidum 27 Thiamine Transport 3 None None None 660 | tpallidum 59 Threonine Metabolism 2 None None None 661 | tpallidum 22 Threonine Transport 1 None None None 662 | tpallidum 144 TPR Genes 10 None None None 663 | tpallidum 111 Transcriptional Regulation 26 None None None 664 | tpallidum 117 Translational Regulation 20 None None None 665 | tpallidum 135 tRNA-Ala Biosynthesis 1 None None None 666 | tpallidum 133 tRNA-Arg Biosynthesis 1 None None None 667 | tpallidum 124 tRNA-Asp Biosynthesis 5 None None None 668 | tpallidum 120 tRNA-Cys Biosynthesis 1 None None None 669 | tpallidum 131 tRNA-Glut Biosynthesis 4 None None None 670 | tpallidum 130 tRNA-Gly Biosynthesis 1 None None None 671 | tpallidum 126 tRNA-His Biosynthesis 1 None None None 672 | tpallidum 122 tRNA-Iso Biosynthesis 1 None None None 673 | tpallidum 123 tRNA-Leu Biosynthesis 1 None None None 674 | tpallidum 127 tRNA-Lys Biosynthesis 1 None None None 675 | tpallidum 132 tRNA-Meth Biosynthesis 2 None None None 676 | tpallidum 119 tRNA-Phe Biosynthesis 2 None None None 677 | tpallidum 128 tRNA-Ser Biosynthesis 1 None None None 678 | tpallidum 129 tRNA-Thre Biosynthesis 3 None None None 679 | tpallidum 125 tRNA-Trypt Biosynthesis 1 None None None 680 | tpallidum 134 tRNA-Tyr Biosynthesis 1 None None None 681 | tpallidum 136 tRNA-Val Biosynthesis 1 None None None 682 | tpallidum 160 Tropane Biosynthesis 2 None None None 683 | tpallidum 154 Tryptophan Biosynthesis 1 None None None 684 | tpallidum 172 Two Component System 23 None None None 685 | tpallidum 153 Tyrosine Biosynthesis 1 None None None 686 | tpallidum 62 Tyrosine Metabolism 2 None None None 687 | tpallidum 118 Universal GTPases 11 None None None 688 | tpallidum 70 Unknown Amino Acid Metabolism 1 None None None 689 | tpallidum 17 Unknown Amino Acid Transport 3 None None None 690 | tpallidum 34 Unknown Metal Transport 3 None None None 691 | tpallidum 37 Unknown Substrate Transport 20 None None None 692 | tpallidum 16 Unknown Sugar Transport 1 None None None 693 | tpallidum 177 Virulence-Associated 48 None None None 694 | tpallidum 80 Vitamin B6 Metabolism 1 None None None 695 | tpallidum 6 Zinc Transport 7 None None None 696 | tvaginalis 1 MLST 7 72 2024-02-09 2024-02-09 697 | ureaplasma 1 MLST 4 192 2024-01-16 2024-01-16 698 | ureaplasma 2 eMLST 6 277 2024-01-26 2024-01-26 699 | vcholerae 1 MLST 7 1853 2024-10-11 2024-10-11 700 | vcholerae 2 MLST (O1 and O139) 5 422 2019-09-13 2019-09-13 701 | vcholerae 3 cgMLST 2443 1897 2024-10-11 2024-10-11 702 | vibrio 1 MLST 4 702 2024-07-22 2024-07-22 703 | vparahaemolyticus 1 MLST 7 3661 2024-10-11 2024-10-11 704 | vparahaemolyticus 2 AA-MLST 7 244 2018-04-20 2018-04-20 705 | vparahaemolyticus 3 cgMLST 2254 5994 2024-10-11 2024-10-11 706 | vparahaemolyticus 4 Virulence markers 3 None None None 707 | vtapetis 1 MLST 10 10 2011-09-22 2011-09-22 708 | vvulnificus 1 MLST 10 717 2024-08-14 2024-08-14 709 | wolbachia 1 MLST 5 579 2020-09-01 2020-09-01 710 | wolbachia 2 WSP 5 None None None 711 | xcitri 1 cgMLST 1618 889 2024-06-17 2024-06-17 712 | xfastidiosa 1 MLST 7 90 2022-06-29 2022-06-29 713 | yruckeri 1 MLST 6 54 2023-10-17 2023-10-17 714 | --------------------------------------------------------------------------------