diff --git a/2020-02-20_pubmlst_scheme_list.tsv b/scheme_list_snapshots/2020-02-20_pubmlst_scheme_list.tsv similarity index 100% rename from 2020-02-20_pubmlst_scheme_list.tsv rename to scheme_list_snapshots/2020-02-20_pubmlst_scheme_list.tsv diff --git a/scheme_list_snapshots/2020-05-25_pasteur_scheme_list.tsv b/scheme_list_snapshots/2020-05-25_pasteur_scheme_list.tsv new file mode 100644 index 0000000..ea6fec6 --- /dev/null +++ b/scheme_list_snapshots/2020-05-25_pasteur_scheme_list.tsv @@ -0,0 +1,35 @@ +name id description locus_count records last_added last_updated +klebsiella 20 AbST 5 63 2018-07-26 2018-07-26 +klebsiella 1 MLST 7 4992 2020-05-19 2020-05-19 +klebsiella 17 CbST 15 65 2016-12-19 2016-12-19 +klebsiella 11 Aminoglycoside resistance genes 74 None None None +klebsiella 5 Beta-lactamase genes 23 None None None +klebsiella 15 cgMLST_KpI 2537 None None None +klebsiella 10 cgMLST_ST258_ST512_ST1199 1371 None None None +klebsiella 13 cps cluster genes 2 None None None +klebsiella 6 Efflux systems and regulators 17 None None None +klebsiella 8 Heavy metal resistance genes 40 None None None +klebsiella 7 hvK2 multiplex PCR 5 None None None +klebsiella 22 otherResistanceGenes 2 None None None +klebsiella 12 Quinolone resistance genes 10 None None None +klebsiella 19 r_cg_MLST 0 None None None +klebsiella 18 scgMLST629_S 629 1729 2018-07-12 2018-07-12 +klebsiella 3 scgMLST634 632 None None None +klebsiella 21 SmST 4 35 2018-07-12 2018-07-12 +klebsiella 9 Species-specific markers 7 None None None +klebsiella 14 Urease-Nickel cluster 6 None None None +klebsiella 4 Virulence genes 80 None None None +klebsiella 2 wzi 1 589 2020-04-27 2020-04-27 +klebsiella 16 YbST 11 346 2018-07-26 2018-07-26 +listeria 2 MLST 7 2133 2020-05-20 2020-05-20 +listeria 3 cgMLST1748 1748 18534 2020-04-14 2020-04-14 +listeria 4 PCR-serogroup 5 149 2020-05-20 2020-05-20 +listeria 5 Virulence 92 None None None +listeria 6 Antibiotic Resistance 17 None None None +listeria 7 Metal & Detergent Resistance 8 None None None +listeria 8 Stress Islands 7 None None None +listeria 10 Listeria Stress Islands 88 None None None +listeria 11 sigB operon 8 None None None +listeria 12 Rhamnose operon 5 None None None +listeria 13 Clonogrouping 0 None None None +listeria 14 PBPs 0 None None None diff --git a/scheme_list_snapshots/2020-05-25_pubmlst_scheme_list.tsv b/scheme_list_snapshots/2020-05-25_pubmlst_scheme_list.tsv new file mode 100644 index 0000000..4816176 --- /dev/null +++ b/scheme_list_snapshots/2020-05-25_pubmlst_scheme_list.tsv @@ -0,0 +1,409 @@ +name id description locus_count records last_added last_updated +achromobacter 1 MLST 7 481 2020-05-21 2020-05-21 +abaumannii 1 MLST (Oxford) 7 2131 2020-04-06 2020-04-06 +abaumannii 2 MLST (Pasteur) 7 1476 2020-05-12 2020-05-12 +aeromonas 1 MLST 6 689 2020-04-13 2020-04-13 +aphagocytophilum 1 MLST 7 184 2019-11-14 2019-11-14 +arcobacter 1 MLST 7 831 2019-02-19 2019-02-19 +bcereus 1 MLST 7 2555 2020-05-18 2020-05-18 +blicheniformis 14 MLST 6 47 2018-05-04 2018-05-04 +bsubtilis 1 MLST 7 245 2020-05-12 2020-05-12 +llactis_phage 1 MLST 5 221 2017-06-19 2017-06-19 +bbacilliformis 1 MLST 7 14 2017-06-17 2017-06-17 +bhenselae 1 MLST 8 36 2019-09-24 2019-09-24 +bwashoensis 1 MLST 6 21 2019-08-22 2019-08-22 +bordetella 3 MLST 7 96 2020-02-07 2020-02-07 +bordetella 1 Bordetella core genes 1415 None None None +bordetella 2 Bordetella virulence associated genes 20 None None None +borrelia 1 MLST 8 933 2020-03-19 2020-03-19 +brachyspira 5 B. hampsonii MLST 6 20 2015-02-18 2015-02-18 +brachyspira 2 B. hyodysenteriae MLST 7 263 2019-12-06 2019-12-06 +brachyspira 3 B. intermedia MLST 7 83 2015-07-20 2015-07-20 +brachyspira 4 B. pilosicoli MLST 7 94 2019-04-23 2019-04-23 +brachyspira 1 Brachyspira MLST 7 36 2012-01-18 2012-01-18 +brucella 1 MLST (9 locus) 9 98 2020-05-13 2020-05-13 +brucella 2 MLST (21 locus) 21 150 2019-09-11 2019-09-11 +bcc 1 MLST 7 1843 2020-05-06 2020-05-06 +bpseudomallei 1 MLST 7 1862 2020-04-29 2020-04-29 +campylobacter_nonjejuni 5 C. concisus/curvus MLST 7 130 2015-03-11 2015-03-11 +campylobacter_nonjejuni 9 C. fetus MLST 7 69 2017-02-24 2017-02-24 +campylobacter_nonjejuni 1 C. helveticus MLST 7 9 2015-01-12 2015-01-12 +campylobacter_nonjejuni 6 C. hyointestinalis MLST 7 134 2018-11-28 2018-11-28 +campylobacter_nonjejuni 2 C. insulaenigrae MLST 7 43 2011-11-10 2011-11-10 +campylobacter_nonjejuni 7 C. lanienae MLST 7 172 2018-11-27 2018-11-27 +campylobacter_nonjejuni 3 C. lari MLST 7 161 2018-11-28 2018-11-28 +campylobacter_nonjejuni 8 C. sputorum MLST 7 16 2011-11-18 2011-11-18 +campylobacter_nonjejuni 4 C. upsaliensis MLST 7 204 2017-08-28 2017-08-28 +campylobacter 1 MLST 7 10342 2020-05-20 2020-05-20 +campylobacter 3 1643 Gundogdu loci 1643 None None None +campylobacter 6 C. coli 15-537360 1588 None None None +campylobacter 4 C. jejuni / C. coli cgMLST v1.0 1343 34115 2020-04-30 2020-04-30 +campylobacter 7 ED pathway 7 None None None +campylobacter 2 eMLST (21 partial genes) 21 None None None +campylobacter 5 Ribosomal Protein Genes 52 None None None +calbicans 1 MLST 7 3569 2020-03-12 2020-03-12 +cglabrata 1 MLST 6 177 2020-01-28 2020-01-28 +ctropicalis 1 MLST 6 1046 2020-05-12 2020-05-12 +cmaltaromaticum 1 MLST 7 56 2018-04-11 2018-04-11 +chlamydiales 16 Aerobic and ATP Biogenesis 16 None None None +chlamydiales 7 Amino Acyl tRNA Synthesis 3 None None None +chlamydiales 17 Aromatic Amino Acids 10 None None None +chlamydiales 18 Aspartate Amino Acid 5 None None None +chlamydiales 20 Biotin, Lipoate and Ubiquinone 6 None None None +chlamydiales 26 Both Purine and Pyrimidine Metabolism 4 None None None +chlamydiales 44 C. abortus cgMLST v1.0 959 None None None +chlamydiales 30 Cell Division 9 None None None +chlamydiales 42 C. trachomatis cgMLST v1.0 817 369 2020-05-13 2020-05-13 +chlamydiales 3 DNA Replication 24 None None None +chlamydiales 14 Electron Transport Chain 4 None None None +chlamydiales 37 Eukaryotic Type Chromatin Factors 4 None None None +chlamydiales 29 Fatty Acid and Phospholipid Metabolism 27 None None None +chlamydiales 21 Folic Acid 5 None None None +chlamydiales 10 Glycolysis, Gluconeogensis, Glycogen 20 None None None +chlamydiales 27 Membrane Proteins, Lipoproteins, Porins 9 None None None +chlamydiales 36 Miscellaneous Enzymes/Conserved Proteins 44 None None None +chlamydiales 1 MLST (Chlamydiales) 7 298 2020-05-04 2020-05-04 +chlamydiales 38 MLST (C. trachomatis) 7 88 2019-11-18 2019-11-18 +chlamydiales 41 MLST (C. trachomatis Uppsala) 5 520 2015-10-12 2016-02-22 +chlamydiales 4 Nucleotide Excision and Repair 18 None None None +chlamydiales 33 Pathogenesis Associated Proteins 25 None None None +chlamydiales 15 Pentose Phosphate Pathway 8 None None None +chlamydiales 8 Peptide Synthesis 14 None None None +chlamydiales 28 Peptidoglycan 16 None None None +chlamydiales 11 Phosphorous and Sulphur 4 None None None +chlamydiales 2 Plasmid loci 8 None None None +chlamydiales 40 Plasmid MLST 8 47 2015-10-06 2015-10-06 +chlamydiales 22 Porphyrin 9 None None None +chlamydiales 9 Protein Folding, Assembly, Modification 37 None None None +chlamydiales 24 Purine Metabolism 3 None None None +chlamydiales 25 Pyrimidine Metabolism 7 None None None +chlamydiales 12 Pyruvate Dehydrogenase 7 None None None +chlamydiales 5 Recombination 8 None None None +chlamydiales 23 Riboflavin 5 None None None +chlamydiales 43 Ribosomal Protein genes 52 None None None +chlamydiales 6 RNA Associated 44 None None None +chlamydiales 19 Serine Amino Acid 2 None None None +chlamydiales 31 Signal Transduction 18 None None None +chlamydiales 35 Specific Proteins 11 None None None +chlamydiales 13 TCA Cycle 11 None None None +chlamydiales 34 Transport Related Proteins 54 None None None +chlamydiales 39 Type III Effector Proteins 0 None None None +chlamydiales 32 Type III Secretion Systems 58 None None None +cfreundii 1 MLST 7 526 2020-03-09 2020-03-09 +csinensis 1 MLST 8 254 2012-01-07 2012-01-07 +cdifficile 2 cwp cluster genes 6 None None None +cdifficile 1 MLST 7 689 2020-05-20 2020-05-20 +cbotulinum 1 MLST 7 120 2019-12-16 2019-12-16 +cbotulinum 2 Extended MLST 14 0 None None +csepticum 1 MLST 7 8 2008-07-29 2008-07-29 +cdiphtheriae 1 MLST 7 696 2020-04-20 2020-04-20 +cronobacter 4 cogMLST 1865 None None None +cronobacter 3 Ext-MLST 3 0 None None +cronobacter 5 Gcog 222 None None None +cronobacter 1 MLST 7 738 2020-05-11 2020-05-11 +cronobacter 6 O-serotype 2 0 None None +cronobacter 2 Tax-MLST 2 None None None +pacnes 3 MLST 8 153 2020-03-01 2020-03-01 +dnodosus 3 cgMLST 714 None None None +dnodosus 1 MLST 7 115 2017-09-13 2017-09-13 +edwardsiella 1 MLST 10 22 2020-04-23 2020-04-23 +ecloacae 1 MLST 7 1395 2020-05-17 2020-05-17 +efaecalis 1 MLST 7 1000 2020-05-15 2020-05-15 +efaecium 1 MLST 7 1709 2020-04-03 2020-04-03 +escherichia 1 MLST (Achtman) 7 9860 2020-05-25 2020-05-25 +escherichia 2 MLST (Pasteur) 8 997 2020-04-22 2020-04-22 +escherichia 10 accessory genome 22489 None None None +escherichia 3 beta-lactamase resistance 9 None None None +escherichia 6 cgMLST 2513 None None None +escherichia 12 IncL/M 3 None None None +escherichia 4 locus of enterocyte effacement (LEE) island 40 None None None +escherichia 14 oxa-48 chromosome loci 29 None None None +escherichia 8 pO157 plasmid 49 None None None +escherichia 13 pOXA-48 plasmid 71 None None None +escherichia 11 quinolone resistance 4 None None None +escherichia 5 shiga toxins 4 None None None +escherichia 9 virulence genes 16 None None None +escherichia 7 wgMLST 25002 None None None +fpsychrophilum 1 MLST 7 194 2018-02-09 2018-02-09 +gallibacterium 1 MLST 8 81 2012-06-12 2012-06-12 +hinfluenzae 42 Alanine, aspartate and glutamate metabolism 13 None None None +hinfluenzae 14 Aminoacyl-tRNA biosynthesis 24 None None None +hinfluenzae 19 Amino sugar and nucleotide sugar metabolism 21 None None None +hinfluenzae 52 Antimicrobial Resistance 6 None None None +hinfluenzae 43 Arginine and proline metabolism 20 None None None +hinfluenzae 21 Butanoate metabolism 8 None None None +hinfluenzae 2 Capsule - Region I 7 None None None +hinfluenzae 4 Capsule - Region III 4 None None None +hinfluenzae 7 Capsule - serotype A 2 None None None +hinfluenzae 3 Capsule - serotype B 8 None None None +hinfluenzae 8 Capsule - serotype C 4 None None None +hinfluenzae 9 Capsule - serotype D 5 None None None +hinfluenzae 6 Capsule - Serotype E 8 None None None +hinfluenzae 5 Capsule - serotype F 3 None None None +hinfluenzae 38 Cysteine and methionine metabolism 17 None None None +hinfluenzae 10 DNA Replication 13 None None None +hinfluenzae 32 Fatty acid biosynthesis 11 None None None +hinfluenzae 31 Fatty acid metabolism 3 None None None +hinfluenzae 23 Fructose and mannose metabolism 13 None None None +hinfluenzae 20 Galactose Metabolism 6 None None None +hinfluenzae 33 Glycerolipid metabolism 6 None None None +hinfluenzae 34 Glycerophospholipid metabolism 19 None None None +hinfluenzae 39 Glycine, serine and threonine metabolism 19 None None None +hinfluenzae 15 Glycolysis 15 None None None +hinfluenzae 16 Glyoxylate and dicarboxylate metabolism 11 None None None +hinfluenzae 45 Histidine metabolism 8 None None None +hinfluenzae 53 Iron Acquisition 13 None None None +hinfluenzae 50 LOS Biosynthesis 23 None None None +hinfluenzae 40 Lysine biosynthesis 14 None None None +hinfluenzae 47 Lysine degradation 4 None None None +hinfluenzae 26 Methane metabolism 26 None None None +hinfluenzae 1 MLST 7 2311 2020-05-18 2020-05-18 +hinfluenzae 27 Nitrogen Metabolism 10 None None None +hinfluenzae 11 Nucleotide Excision Repair 12 None None None +hinfluenzae 29 Oxidative phosphorylation 10 None None None +hinfluenzae 25 Pentose and glucuronate interconversions 4 None None None +hinfluenzae 24 Pentose Phosphate Pathway 15 None None None +hinfluenzae 37 Phenylalanine metabolism 4 None None None +hinfluenzae 44 Phenylalanine, tyrosine, tryptophan biosynthesis 19 None None None +hinfluenzae 51 Pilus Biosynthesis 6 None None None +hinfluenzae 22 Propanoate metabolism 10 None None None +hinfluenzae 35 Purine Metabolism 58 None None None +hinfluenzae 36 Pyrimidine Metabolism 43 None None None +hinfluenzae 18 Pyruvate Metabolism 20 None None None +hinfluenzae 30 Reductive carboxylate cycle (CO2 fixation) 13 None None None +hinfluenzae 13 Ribosomal Protein Genes 56 None None None +hinfluenzae 12 RNA Polymerase 11 None None None +hinfluenzae 28 Sulphur Metabolism 8 None None None +hinfluenzae 17 TCA Cycle 12 None None None +hinfluenzae 41 Tryptophan metabolism 6 None None None +hinfluenzae 46 Tyrosine metabolism 4 None None None +hinfluenzae 48 Valine, leucine and isoleucine biosynthesis 11 None None None +hinfluenzae 49 Valine, leucine and isoleucine degradation 3 None None None +hparasuis 1 MLST 7 397 2019-08-05 2019-08-05 +hcinaedi 1 MLST 7 20 2019-12-06 2019-12-06 +helicobacter 1 MLST 7 3729 2020-04-06 2020-04-06 +hsuis 1 MLST 7 141 2020-03-06 2020-03-06 +kaerogenes 1 MLST 7 204 2020-05-21 2020-05-21 +koxytoca 1 MLST 7 323 2020-05-18 2020-05-18 +kseptempunctata 1 MLST 2 3 2014-12-22 2014-12-22 +lsalivarius 1 MLST 5 25 2010-12-07 2010-12-07 +leptospira 1 MLST (scheme 1) 7 326 2020-04-23 2020-04-23 +leptospira 2 MLST (scheme 2) 7 273 2019-04-24 2019-04-24 +leptospira 3 MLST (scheme 3) 6 194 2020-02-10 2020-02-10 +leptospira 4 cgMLST 1565 None None None +leptospira 5 LPS 21 None None None +liberibacter 1 MLST 7 14 2020-05-07 2020-05-07 +mcanis 1 MLST 7 83 2019-10-21 2019-10-21 +mcaseolyticus 1 MLST 7 67 2019-10-21 2019-10-21 +mplutonius 1 MLST 4 37 2020-03-11 2020-03-11 +mabscessus 1 M. abscessus MLST 7 26 2012-04-25 2012-04-25 +mabscessus 2 M. massiliense MLST 7 12 2012-03-27 2012-04-25 +mycobacteria 1 Core genome (H37Rv ref vs 19 finished species) 744 5626 2017-08-25 2017-08-25 +mycobacteria 2 MLST 8 873 2019-11-15 2019-11-15 +magalactiae 1 MLST 5 35 2019-04-24 2019-04-24 +mbovis 2 MLST 7 90 2020-05-14 2020-05-14 +mbovis 1 MLST (legacy) 7 185 2020-01-10 2020-01-10 +mflocculare 1 MLST 3 8 2018-07-03 2018-07-03 +mgallisepticum 1 MLST#1 (Ghanem) 7 60 2020-04-06 2020-04-06 +mgallisepticum 2 MLST#2 (Bekő) 6 79 2020-05-18 2020-05-18 +mhominis 1 MLST 5 23 2019-10-16 2019-10-16 +mhominis 2 MVLST 5 31 2019-10-16 2019-10-16 +mhominis 3 eMLST 10 32 2019-10-16 2019-10-16 +mhyopneumoniae 1 MLST 3 151 2020-03-20 2020-03-20 +mhyorhinis 1 MLST 6 128 2020-03-27 2020-03-27 +miowae 1 MLST 6 35 2019-05-05 2019-05-05 +mpneumoniae 1 MLST 8 37 2019-12-18 2019-12-18 +msynoviae 1 MLST 7 141 2020-04-17 2020-04-17 +neisseria 1 MLST 7 15480 2020-05-22 2020-05-22 +neisseria 2 Finetyping antigens 3 None None None +neisseria 42 rplF species 1 211 2019-02-06 2019-02-06 +neisseria 7 ADP-heptose biosynthesis 5 None None None +neisseria 5 Antibiotic resistance 11 None None None +neisseria 3 Antigen genes 7 None None None +neisseria 52 beta lactamase plasmid 8 18 2018-04-17 2018-04-17 +neisseria 53 Bexsero Antigen Sequence Typing (BAST) 5 3661 2020-05-22 2020-05-22 +neisseria 63 Capsule Null (cnl) 1 None None None +neisseria 29 Capsule Region A - Serogroup A 4 None None None +neisseria 36 Capsule Region A - Serogroup B 5 None None None +neisseria 37 Capsule Region A - Serogroup C 6 None None None +neisseria 35 Capsule Region A - Serogroup E 7 None None None +neisseria 32 Capsule Region A - Serogroup H 4 None None None +neisseria 33 Capsule Region A - Serogroup L 3 None None None +neisseria 38 Capsule Region A - Serogroup W 6 None None None +neisseria 30 Capsule Region A - Serogroup X 3 None None None +neisseria 39 Capsule Region A - Serogroup Y 6 None None None +neisseria 31 Capsule Region A - Serogroup Z 4 None None None +neisseria 41 Capsule Region B 2 None None None +neisseria 40 Capsule Region C 4 None None None +neisseria 48 Capsule Region D and D' 6 None None None +neisseria 49 Conjugative Plasmid 50 242 2018-04-25 2018-04-25 +neisseria 66 Cryptic Plasmid 9 96 2018-05-15 2018-05-15 +neisseria 25 DNA replication 16 None None None +neisseria 4 eMLST (20 locus partial genes) 20 None None None +neisseria 12 eMLST (20 locus whole genes) 20 None None None +neisseria 6 Factor H binding protein 10 None None None +neisseria 73 GC OMV peptide typing 26 2283 2020-03-31 2020-03-31 +neisseria 15 Glycolysis 11 None None None +neisseria 50 Gonococcal Genetic Island 73 None None None +neisseria 72 Human-restricted Neisseria cgMLST v1.0 1441 None None None +neisseria 21 Iron acquisition 7 None None None +neisseria 19 Kdo addition 5 None None None +neisseria 45 L3_cgMLST 1742 None None None +neisseria 68 L44_cgMLST 1699 None None None +neisseria 69 L44_pgMLST 1786 None None None +neisseria 17 Lipid A biosynthesis: acyltransferases 4 None None None +neisseria 18 Lipid A biosynthesis: other 5 None None None +neisseria 9 LOS alpha chain transferases 7 None None None +neisseria 8 LOS inner core transferases 7 None None None +neisseria 20 LOS transport/export 5 None None None +neisseria 43 Methyltransferases 0 None None None +neisseria 54 MGI-1 7 None None None +neisseria 55 MGI-2 21 None None None +neisseria 56 MGI-3 18 None None None +neisseria 46 NadA 2 None None None +neisseria 44 Neisseria Heparin Binding Antigen (NHBA) 2 None None None +neisseria 71 NG MAST 2 19107 2020-03-26 2020-03-26 +neisseria 57 N. gonorrhoeae Beta-lactam AMR 5 None None None +neisseria 62 N. gonorrhoeae cgMLST v1.0 1649 6950 2020-05-18 2020-05-18 +neisseria 61 N. gonorrhoeae Efflux Pumps AMR 10 None None None +neisseria 58 N. gonorrhoeae Fluoroquinolone AMR 4 None None None +neisseria 59 N. gonorrhoeae Macrolides AMR 2 None None None +neisseria 60 N. gonorrhoeae plasmid mediated AMR 2 None None None +neisseria 67 NG STAR 7 1891 2020-03-30 2020-03-30 +neisseria 47 N. meningitidis cgMLST v1.0 1605 18503 2020-05-22 2020-05-22 +neisseria 27 Nucleotide excision repair 8 None None None +neisseria 64 OMV peptide 50 None None None +neisseria 65 OMV peptide typing 24 4046 2019-05-15 2019-05-15 +neisseria 13 Pilus genes 27 None None None +neisseria 28 Protein glycosylation 14 None None None +neisseria 22 Purine metabolism 39 None None None +neisseria 23 Pyrimidine metabolism 32 None None None +neisseria 14 Pyruvate dehydrogenase complex 3 None None None +neisseria 24 Ribosomal protein genes 55 None None None +neisseria 26 RNA polymerase 4 None None None +neisseria 34 Small regulatory RNAs 3 None None None +neisseria 16 TCA cycle 16 None None None +neisseria 70 tRNA molecules 21 None None None +neisseria 11 UDP-GlcNAc synthesis 1 None None None +neisseria 10 UDP-glucose and UDP-galactose biosynthesis 2 None None None +neisseria 51 VirB T4SS 31 None None None +otsutsugamushi 1 MLST 7 98 2019-05-10 2019-05-10 +orhinotracheale 1 MLST 7 35 2018-01-03 2018-01-03 +plarvae 1 MLST 7 29 2020-03-11 2020-03-11 +pmultocida 1 Multiple host MLST 7 124 2020-03-10 2020-03-10 +pmultocida 2 RIRDC MLST 7 373 2019-11-28 2019-11-28 +ppentosaceus 1 MLST 7 17 2013-02-19 2013-02-19 +pdamselae 1 MLST 6 56 2018-08-09 2018-08-09 +psalmonis 1 MLST 7 24 2017-04-07 2017-04-07 +plasmid 7 IncA/C cgPMLST 28 41 2018-01-05 2018-01-05 +plasmid 6 IncA/C PMLST 4 13 2018-01-05 2018-01-05 +plasmid 3 IncF RST 7 None None None +plasmid 5 IncHI1 MLST 6 15 2018-05-30 2018-05-30 +plasmid 2 IncHI2 DLST 2 15 2018-09-05 2018-09-05 +plasmid 1 IncI1 MLST 5 316 2020-05-06 2020-05-06 +plasmid 4 IncN MLST 3 22 2019-03-12 2019-03-12 +plasmid 8 pBSSB1-family 3 35 2019-04-09 2019-04-09 +pgingivalis 1 MLST 7 138 2007-08-12 2007-08-12 +paeruginosa 1 MLST 7 3400 2020-05-11 2020-05-11 +paeruginosa 2 Plasmid loci 199 None None None +pfluorescens 1 MLST 7 110 2019-06-28 2019-06-28 +pputida 1 MLST 8 115 2020-05-21 2020-05-21 +ranatipestifer 1 MLST 7 77 2020-05-08 2020-05-08 +rhodococcus 1 MLST 7 46 2020-04-15 2020-04-20 +salmonella 4 cgMLST v2 (Enterobase) 3002 None None None +salmonella 2 MLST 7 6782 2020-05-25 2020-05-25 +salmonella 1 Oxford loci 3633 None None None +salmonella 3 SalmcgMLST v1.0 2750 13722 2020-02-06 2020-02-06 +sparasitica 1 MLST 7 15 2018-03-26 2018-03-26 +sinorhizobium 1 MLST 10 136 2010-05-07 2010-05-07 +smaltophilia 1 MLST 7 490 2020-05-20 2020-05-20 +saureus 1 MLST 7 6071 2020-05-22 2020-05-22 +saureus 2 Core 2208 2208 None None None +sepidermidis 1 MLST 7 972 2020-05-22 2020-05-22 +shaemolyticus 1 MLST 7 79 2020-05-20 2020-05-20 +shominis 1 MLST 6 57 2017-10-19 2017-10-19 +spseudintermedius 1 MLST 7 1685 2020-05-25 2020-05-25 +oralstrep 2 S. mutans MLST (Do) 8 179 2019-10-08 2019-10-08 +oralstrep 3 S. mutans MLST (Nakano) 8 269 2020-01-22 2020-01-22 +oralstrep 1 S. oralis MLST 7 78 2015-10-23 2015-10-23 +sagalactiae 1 MLST 7 1605 2020-04-17 2020-04-17 +sagalactiae 37 Adherence Regulation 2 None None None +sagalactiae 29 Alp Family Proteins 5 None None None +sagalactiae 23 Amino Acid Metabolism 85 None None None +sagalactiae 44 Aminoglycosides 2 None None None +sagalactiae 17 Ascorbate and Aldarate Metabolism 28 None None None +sagalactiae 3 Biosynthesis and activation of sialic acid 5 None None None +sagalactiae 30 C5a Peptidase 2 None None None +sagalactiae 4 Capsular polysaccharide Biosynthesis 7 None None None +sagalactiae 46 Chloramphenicol 1 None None None +sagalactiae 22 Fatty Acid Biosynthesis 18 None None None +sagalactiae 31 Fibrinogen Binding Proteins 2 None None None +sagalactiae 14 Fructose and Mannose Metabolism 36 None None None +sagalactiae 15 Galactose Metabolism 34 None None None +sagalactiae 12 Glycolysis 44 None None None +sagalactiae 32 Haemolysin Operon 9 None None None +sagalactiae 38 h_S.agalactiae cgMLST v1.0 1405 None None None +sagalactiae 33 Hyaluronidase Activity 1 None None None +sagalactiae 40 ICESag1962 51 None None None +sagalactiae 39 IMESp2907 16 None None None +sagalactiae 35 LysR family 1 None None None +sagalactiae 45 Macrolides, lincosamides, Streptogramins 5 None None None +sagalactiae 18 Oxidative phosphorylation 13 None None None +sagalactiae 13 Pentose Phosphate Pathway 23 None None None +sagalactiae 19 Photosynthesis 8 None None None +sagalactiae 27 PI-1 6 None None None +sagalactiae 28 PI-2a 5 None None None +sagalactiae 26 PI-2b 5 None None None +sagalactiae 34 Pilus Regulator 1 None None None +sagalactiae 21 Purine Metabolism 63 None None None +sagalactiae 20 Pyrimidine Metabolism 51 None None None +sagalactiae 6 Serotype Ia 4 None None None +sagalactiae 7 Serotype Ib 4 None None None +sagalactiae 8 Serotype II 6 None None None +sagalactiae 9 Serotype III 4 None None None +sagalactiae 10 Serotype IV 5 None None None +sagalactiae 5 Serotype V 6 None None None +sagalactiae 41 Serotype VI 4 None None None +sagalactiae 42 Serotype VII 2 None None None +sagalactiae 16 Starch and Sucrose Metabolism 36 None None None +sagalactiae 2 Synthesis of the group B carbohydrate 15 None None None +sagalactiae 11 TCA Cycle 5 None None None +sagalactiae 43 Tetracyclines 2 None None None +sagalactiae 25 Transcription 4 None None None +sagalactiae 36 Transcriptional Regulator 1 None None None +sagalactiae 24 Translation 25 None None None +sbsec 1 MLST 10 214 2017-09-25 2017-09-25 +scanis 1 MLST 7 54 2019-12-09 2019-12-09 +sdysgalactiae 1 MLST 7 522 2020-02-17 2020-02-17 +sgallolyticus 1 MLST 7 109 2017-02-22 2017-02-22 +spneumoniae 1 MLST 7 15508 2020-05-21 2020-05-21 +spneumoniae 2 cgMLST 1360 6992 2020-02-14 2020-02-14 +spyogenes 1 MLST 7 1233 2020-05-12 2020-05-12 +ssuis 1 MLST 7 1299 2020-05-15 2020-05-15 +sthermophilus 1 MLST 10 119 2015-06-18 2015-06-18 +suberis 1 MLST 7 1230 2020-02-25 2020-02-25 +suberis 2 vMLST 10 0 None None +szooepidemicus 1 MLST 7 402 2020-03-13 2020-03-13 +streptomyces 1 MLST 6 234 2016-01-22 2016-01-22 +taylorella 1 MLST 7 71 2020-01-23 2020-01-23 +tenacibaculum 1 MLST 7 168 2020-04-22 2020-04-22 +tpallidum 1 MLST 3 72 2019-11-28 2019-11-28 +tvaginalis 1 MLST 7 60 2016-02-08 2016-02-08 +ureaplasma 1 MLST 4 164 2018-09-14 2018-09-14 +ureaplasma 2 eMLST 6 229 2018-09-14 2018-09-14 +vcholerae 1 MLST 7 1403 2020-04-28 2020-04-28 +vcholerae 2 MLST (O1 and O139) 5 422 2019-09-13 2019-09-13 +vcholerae 3 cgMLST 2443 1048 2020-05-01 2020-05-01 +vibrio 1 MLST 4 179 2020-05-07 2020-05-07 +vparahaemolyticus 1 MLST 7 2347 2020-05-02 2020-05-02 +vparahaemolyticus 2 AA-MLST 7 244 2018-04-20 2018-04-20 +vparahaemolyticus 3 cgMLST 2254 None None None +vparahaemolyticus 4 Virulence markers 3 None None None +vtapetis 1 MLST 10 10 2011-09-22 2011-09-22 +vvulnificus 1 MLST 10 530 2019-09-19 2019-09-19 +wolbachia 1 MLST 5 576 2020-02-24 2020-02-24 +wolbachia 2 WSP 5 None None None +xcitri 1 cgMLST 1618 228 2020-02-09 2020-02-09 +xfastidiosa 1 MLST 7 87 2019-03-06 2019-03-06 +yersinia 1 MLST 7 170 2015-06-16 2015-06-16 +yruckeri 1 MLST 6 30 2011-07-27 2011-07-27