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All species MLST databases and published schemes

MLST databases are hosted at the University of Oxford, UK; the University of Warwick, UK, and the Pasteur Institute, Paris, France.

Order by: Organism | Profiles | Isolates

Databases ordered by numbers of profiles

Chart shows databases with at least 1000 profiles or isolates.

* Data updated automatically: 2019-10-19.

Organism Website and link to database Sequence types Isolates Applications to date Selected references
Streptococcus pneumoniae https://pubmlst.org/spneumoniae/ 15059 * 39725 * Identification of antibiotic resistant clones, epidemiological surveillance, population analyses. Enright et al. (1998) Microbiology 144 ( Pt 11):3049-60.
Neisseria spp. https://pubmlst.org/neisseria/ 14809 * 49664 * Epidemiological surveillance, post-vaccine studies, population and evolutionary analyses. Maiden et al. (1998) Proc Natl Acad Sci U S A 95:3140-5.
Campylobacter jejuni https://pubmlst.org/campylobacter/ 10064 * 72343 * Epidemiological surveillance of food-borne infections, population structure analyses. Dingle et al. (2001) J Clin Microbiol 39:14-23.
Escherichia coli#1 http://mlst.warwick.ac.uk/mlst/dbs/Ecoli 9151 * 6492 * Examination of the evolution of virulence. Wirth et al. (2006) Mol Microbiol 60:1136-51.
Salmonella enterica http://mlst.warwick.ac.uk/mlst/dbs/Senterica 6317 * 6286 * -
Staphylococcus aureus https://pubmlst.org/saureus 5682 * 34571 * Identification of predominant epidemic MRSA isolates, species evolution, population analyses
Klebsiella pneumoniae http://bigsdb.web.pasteur.fr/klebsiella/ 4513 * 5772 * Isolate characterisation and epidemiological analyses
Candida albicans https://pubmlst.org/calbicans 3566 * 4392 * Isolate characterisation and identification of nosocomial outbreaks Bougnoux et al. (2003) J Clin Microbiol 41:5265-6.
Helicobacter pylori https://pubmlst.org/helicobacter/ 3495 * 2358 * Tracking the patterns of human migration. Wirth et al. (2004) Proc Natl Acad Sci U S A 101:4746-51.
Pseudomonas aeruginosa https://pubmlst.org/paeruginosa/ 3342 * 6880 * Population and evolutionary analyses. Curran et al. (2004) J Clin Microbiol 42:5644-9.
Bacillus cereus https://pubmlst.org/bcereus/ 2481 * 2649 * Population and evolutionary analyses. Priest et al. (2004) J Bacteriol 186:7959-70.
Vibrio parahaemolyticus https://pubmlst.org/vparahaemolyticus/ 2208 * 3184 * -
Haemophilus influenzae https://pubmlst.org/hinfluenzae/ 2197 * 4966 * Isolate characterisation and population structure analysis Meats et al. (2003) J Clin Microbiol 41:1623-36.
Acinetobacter baumannii#1 https://pubmlst.org/abaumannii/ 2013 * 4374 * Isolate characterisation and population structure analysis Bartual et al. (2005) J Clin Microbiol 43:4382-90.
Burkholderia pseudomallei https://pubmlst.org/bpseudomallei 1746 * 5906 * Isolate characterisation and species identification. Godoy et al. (2003) J Clin Microbiol 41:2068-79.
Burkholderia cepacia complex https://pubmlst.org/bcc/ 1691 * 3158 * Isolate characterisation and population structure analyses Baldwin et al. (2005) J Clin Microbiol 43:4665-73.
Enterococcus faecium https://pubmlst.org/efaecium/ 1639 * 3356 * Strain characterization and population structure analysis
Listeria monocytogenes http://bigsdb.web.pasteur.fr/listeria/ 1605 * 4060 * -
Staphylococcus pseudintermedius https://pubmlst.org/spseudintermedius/ 1567 * 1753 * Strain characterization and population structure analysis Solyman et al. (2013) J Clin Microbiol 51:306-10.
Streptococcus agalactiae https://pubmlst.org/sagalactiae/ 1400 * 12099 * Identification of clones associated with neonatal infections. Jones et al. (2003) J Clin Microbiol 41:2530-6.
Acinetobacter baumannii#2 https://pubmlst.org/abaumannii/ 1385 * 4374 * -
Enterobacter cloacae https://pubmlst.org/ecloacae/ 1320 * - Strain characterization and population structure analysis
Streptococcus suis https://pubmlst.org/ssuis 1244 * 2293 * Population characterisation and population structure analysis
Streptococcus pyogenes https://pubmlst.org/spyogenes 1165 * 4007 * Identification of relationships between emm-type and clonal complex Enright et al. (2001) Infect Immun 69:2416-27.
Streptococcus uberis https://pubmlst.org/suberis/ 1165 * 1179 * - Coffey et al. (2006) Appl Environ Microbiol 72:1420-8.
Vibrio cholerae https://pubmlst.org/vcholerae/ 984 * 2923 * Strain characterization and population structure analysis
Escherichia coli#2 http://bigsdb.web.pasteur.fr/ecoli/ 966 * 1122 * -
Enterococcus faecalis https://pubmlst.org/efaecalis/ 938 * 1858 * Isolate characterisation and population structure analysis
Borrelia spp. https://pubmlst.org/borrelia/ 929 * 2671 * Isolate characterisation and epidemiological analyses
Staphylococcus epidermidis https://pubmlst.org/sepidermidis/ 910 * 1500 * Isolate characterisation and population structure analysis Thomas et al. (2007) J Clin Microbiol 45:616-9.
Candida tropicalis https://pubmlst.org/ctropicalis/ 871 * 1019 * Isolate characterisation and epidemiological analyses Tavanti et al. (2005) J Clin Microbiol 43:5593-600.
Mycobacteria spp. http://pubmlst.org/mycobacteria 839 * 9425 * Strain characterisation
Arcobacter spp. https://pubmlst.org/arcobacter/ 831 * 893 * Isolate characterisation and population structure
Moraxella catarrhalis http://mlst.warwick.ac.uk/mlst/dbs/Mcatarrhalis 772 * 346 * -
Cronobacter spp. https://pubmlst.org/cronobacter/ 697 * 2847 * -
Aeromonas spp. https://pubmlst.org/aeromonas/ 648 * 747 * Strain characterization
Corynebacterium diphtheriae https://pubmlst.org/cdiphtheriae/ 636 * 767 * -
Clostridioides difficile https://pubmlst.org/cdifficile 631 * 1716 * Isolate characterisation and population structure analysis Griffiths et al. (2010) J Clin Microbiol 48:770-8.
Vibrio vulnificus https://pubmlst.org/vvulnificus/ 530 * 706 * Isolate characterisation and epidemiological analyses. Bisharat et al. (2005) Emerg Infect Dis 11:30-5.
Wolbachia https://pubmlst.org/wolbachia/ 524 * 1928 * Isolate characterisation and population structure analyses Baldo et al. (2006) Appl Environ Microbiol 72:7098-110.
Citrobacter freundii https://pubmlst.org/cfreundii 521 * 421 * Isolate characterisation and population structure analysis Bai et al. (2012) PLoS One 7:e33054.
Yersinia pseudotuberculosis http://mlst.warwick.ac.uk/mlst/dbs/Ypseudotuberculosis 515 * 748 * Population and evolutionary analyses.
Streptococcus dysgalactiae equisimilis https://pubmlst.org/sdysgalactiae/ 515 * 1501 * Isolate characterisation and population structure analysis McMillan et al. (2010) PLoS One 5:e11741.
Achromobacter spp. https://pubmlst.org/achromobacter 469 * 1080 * Isolate characterisation Spilker et al. (2012) J Clin Microbiol 50:3010-5.
Vibrio cholerae#2 http://pubmlst.org/vcholerae 422 * 2923 * Isolate characterisation
Haemophilus parasuis https://pubmlst.org/hparasuis/ 397 * 396 * Population and evolutionary analyses.
Streptococcus zooepidemicus https://pubmlst.org/szooepidemicus/ 396 * 1487 * Isolate characterisation and population structure analysis
Pasteurella multocida#1 https://pubmlst.org/pmultocida/ 372 * 562 * Isolate characterisation and population structure analysis
Stenotrophomonas maltophilia https://pubmlst.org/smaltophilia/ 366 * 520 * -
Leptospira spp. https://pubmlst.org/leptospira/ 297 * 1465 * Isolate characterisation and epidemiological analyses
Chlamydiales spp. https://pubmlst.org/chlamydiales/ 279 * 4516 * Isolate characterisation and population structure analysis Pannekoek et al. (2008) BMC Microbiol 8:42.
Leptospira spp.#2 https://pubmlst.org/leptospira/ 273 * 1465 * Strain characterization and population structure analysis Varni et al. (2014) Infect Genet Evol 22:216-22.
Klebsiella oxytoca https://pubmlst.org/koxytoca/ 259 * 190 * Isolate characterisation and population structure analysis
Brachyspira hyodysenteriae https://pubmlst.org/brachyspira/ 256 * 815 * Molecular epidemiology and population structure analyses.
Clonorchis sinensis https://pubmlst.org/csinensis/ 254 * 256 * Strain characterization and population structure analysis
Streptomyces spp https://pubmlst.org/streptomyces/ 234 * 270 * Species identification
Streptococcus bovis/equinus complex (SBSEC) https://pubmlst.org/sbsec/ 214 * 272 * Isolate characterisation and population structure analysis Jans et al. (2016) BMC Microbiol 16:117.
Campylobacter upsaliensis https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
204 * 582 * -
Klebsiella aerogenes http://pubmlst.org/kaerogenes/ 198 * 201 * Isolate characterisation and population structure analysis
Flavobacterium psychrophilum https://pubmlst.org/fpsychrophilum/ 194 * 1097 * Strain characterization and population structure analysis
Candida krusei https://pubmlst.org/ckrusei/ 188 * 245 * Isolate characterisation and population structure analyses Jacobsen et al. (2007) J Clin Microbiol 45:317-23.
Mycoplasma bovis https://pubmlst.org/mbovis 180 * 709 * Isolate characterisation and population structure analysis Register et al. (2015) Vet Microbiol 175:92-8.
Anaplasma phagocytophilum https://pubmlst.org/aphagocytophilum/ 179 * 515 * Strain characterization and population structure analysis
Bacillus subtilis https://pubmlst.org/bsubtilis/ 174 * 352 * Isolate characterisation and population structure analysis
Campylobacter lanienae https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
172 * 582 * Isolate characterisation and population structure analysis
Yersinia spp. https://pubmlst.org/yersinia/ 170 * 389 * Speciation and isolate characterisation
Candida glabrata https://pubmlst.org/cglabrata/ 168 * 1365 * Isolate characterisation and population structure analyses Dodgson et al. (2003) J Clin Microbiol 41:5709-17.
Ureaplasma spp. http://pubmlst.org/ureaplasma 164 * 583 * Isolate characterisation
Campylobacter lari https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
161 * 582 * -
Vibrio spp. https://pubmlst.org/vibrio 160 * 180 * Species identification
Leptospira spp.#3 https://pubmlst.org/leptospira 153 * 1465 * Strain characterization and population structure analysis Ahmed et al. (2006) Ann Clin Microbiol Antimicrob 5:28.
Propionibacterium acnes https://pubmlst.org/pacnes/ 152 * 215 * Isolate characterisation and population structure analyses
Porphyromonas gingivalis https://pubmlst.org/pgingivalis/ 138 * 144 * Isolate characterisation and population structure analyses Enersen et al. (2006) J Clin Microbiol 44:35-41.
Helicobacter suis https://pubmlst.org/hsuis/ 138 * 181 * Strain characterization and population structure analysis
Sinorhizobium spp. https://pubmlst.org/sinorhizobium/ 136 * 550 * -
Campylobacter hyointestinalis https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
134 * 582 * Isolate characterisation and population structure analysis
Campylobacter concisus/curvus https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
130 * 582 * Isolate characterisation and population structure analysis
Mycoplasma hyopneumoniae https://pubmlst.org/mhyopneumoniae/ 130 * 265 * Strain characterization and population structure analysis Mayor et al. (2008) Vet Microbiol 127:63-72.
Tenacibaculum spp. https://pubmlst.org/tenacibaculum/ 125 * 114 * Isolate characterisation and populations structure analysis
Streptococcus thermophilus http://bigsdb.web.pasteur.fr/streptococcus/ 125 * 174 * -
Pasteurella multocida#2 https://pubmlst.org/pmultocida/ 124 * 125 * Evolutionary analyses between isolates from different host species
Streptococcus thermophilus#2 https://pubmlst.org/sthermophilus 119 * 257 * Isolate characterisation and population structure analysis
Dichelobacter nodosus http://pubmlst.org/dnodosus 115 * 173 * Isolate characterisation and population structure analysis
Clostridium botulinum https://pubmlst.org/cbotulinum/ 114 * 276 * Isolate characterisation and evolutionary analyses
Pseudomonas fluorescens https://pubmlst.org/pfluorescens/ 110 * 118 * Strain characterization and population structure analysis
Streptococcus gallolyticus https://pubmlst.org/sgallolyticus/ 109 * 364 * Strain characterization and population structure analysis Dumke et al. (2014) J Clin Microbiol 52:2472-8.
Mycoplasma hyorhinis https://pubmlst.org/mhyorhinis/ 104 * 133 * Isolate characterisation and population structure analysis
Mycoplasma synoviae https://pubmlst.org/msynoviae/ 104 * 157 * Isolate characterisation and population structure analysis
Orientia tsutsugamushi https://pubmlst.org/otsutsugamushi/ 98 * 169 * Population and evolutionary analyses
Brucella spp. https://pubmlst.org/brucella 96 * 868 * Isolate characterisation and population structure analysis
Brachyspira pilosicoli https://pubmlst.org/brachyspira/ 94 * 815 * Strain characterization and population structure analysis
Pseudomonas putida http://pubmlst.org/pputida 93 * 161 * Isolate characterisation and population structure analysis
Xylella fastidiosa https://pubmlst.org/xfastidiosa/ 87 * 293 * Isolate characterisation and population structure.
Bordetella spp. https://pubmlst.org/bordetella/ 87 * 1734 * -
Brachyspira intermedia https://pubmlst.org/brachyspira/ 83 * 815 * Molecular epidemiology and population structure analyses.
Macrococcus canis https://pubmlst.org/mcanis/ 82 * 26 * Isolate characterisation and population structure
Gallibacterium anatis http://pubmlst.org/gallibacterium 81 * 89 * Isolate characterisation and population structure analysis Johnson et al. (2013) PLoS One 8:e54844.
Streptococcus oralis https://pubmlst.org/soralis/ 78 * 784 * Isolate characterisation and population structure analyses Do et al. (2009) Microbiology 155:2593-602.
Kingella kingae http://bigsdb.web.pasteur.fr/kingella/ 70 * 137 * -
Campylobacter fetus https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
69 * 582 * Isolate characterisation and population structure analyses van Bergen et al. (2005) J Clin Microbiol 43:5888-98.
Staphylococcus haemolyticus https://pubmlst.org/shaemolyticus/ 68 * 107 * Strain characterisation and population structure analysis
Macrococcus caseolyticus https://pubmlst.org/mcaseolyticus/ 66 * 68 * Isolate characterisation and population structure
Treponema pallidum http://pubmlst.org/tpallidum 66 * 796 * Isolate characterisation and population structure analysis Grillová et al. (2018) PLoS One 13:e0200773.
Taylorella spp. https://pubmlst.org/taylorella/ 60 * 286 * Strain characterization and population structure analysis Duquesne et al. (2013) Vet Microbiol 167:609-18.
Trichomonas vaginalis https://pubmlst.org/tvaginalis/ 60 * 68 * -
Staphylococcus hominis https://pubmlst.org/shominis 57 * 126 * Isolate characterisation and population structure analysis
Photobacterium damselae https://pubmlst.org/pdamselae/ 56 * 78 * Isolate characterisation and population structure analysis
Carnobacterium maltaromaticum https://pubmlst.org/cmaltaromaticum 56 * 71 * Strain characterization and population structure analysis
Mannheimia haemolytica https://pubmlst.org/mhaemolytica/ 51 * 147 * Isolate characterisation
Aspergillus fumigatus https://pubmlst.org/afumigatus/ 48 * 22 * Isolate characterisation
Bacillus licheniformis https://pubmlst.org/blicheniformis/ 47 * 73 * Isolate characterisation and population structure analysis Madslien et al. (2012) BMC Microbiol 12:230.
Streptococcus canis https://pubmlst.org/scanis/ 46 * 209 * Strain characterization and population structure analysis Pinho et al. (2013) J Clin Microbiol 51:1099-109.
Riemerella anatipestifer https://pubmlst.org/ranatipestifer/ 44 * 184 * Isolate characterisation and populations structure analysis
Campylobacter insulaenigrae https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
43 * 582 * Isolate characterisation and population structure analysis
Staphylococcus lugdunensis http://bigsdb.web.pasteur.fr/staphlugdunensis/ 42 * 109 * -
Rhodococcus spp. https://pubmlst.org/rhodococcus 39 * 65 * Isolate characterisation and population structure analysis
Bartonella henselae https://pubmlst.org/bhenselae 36 * 437 * Isolate characterisation and population structure analysis
Brachyspira spp. https://pubmlst.org/brachyspira/ 36 * 815 * Isolate characterisation and population structure analysis
Ornithobacterium rhinotracheale https://pubmlst.org/orhinotracheale/ 35 * 164 * Isolate characterisation and population structure analysis Thieme et al. (2016) PLoS One 11:e0148158.
Melissococcus plutonius https://pubmlst.org/mplutonius/ 35 * 379 * Isolate characterisation and population structure analysis
Mycoplasma iowae https://pubmlst.org/miowae/ 35 * 47 * Isolate characterisation and population structure analysis Ghanem et al. (2016) Vet Microbiol 195:2-8.
Mycoplasma agalactiae https://pubmlst.org/magalactiae/ 35 * 137 * Isolate characterisation and population structure analysis McAuliffe et al. (2011) J Med Microbiol 60:803-11.
Pencillium marneffei http://mlstdb.hku.hk:14206/MLST_index.html 35 44 -
Mycoplasma pneumoniae https://pubmlst.org/mpneumoniae/ 34 * 436 * Isolate characterisation and population structure Brown et al. (2015) J Clin Microbiol 53:3195-203.
Mycoplasma hominis http://pubmlst.org/mhominis 32 * 66 * Isolate characterisation Boujemaa et al. (2018) Sci Rep 8:14854.
Yersinia ruckeri https://pubmlst.org/yruckeri/ 30 * 103 * Population and evolutionary analyses.
Mycobacterium abscessus https://pubmlst.org/mabscessus/ 26 * - Isolate characterisation and population structure analyses
Lactobacillus salivarius https://pubmlst.org/lsalivarius/ 25 * 33 * Population and evolutionary analyses. Raftis et al. (2011) Appl Environ Microbiol 77:954-65.
Paenibacillus larvae https://pubmlst.org/plarvae 24 * 394 * Isolate characterisation and population structure analysis
Piscirickettsia salmonis http://pubmlst.org/psalmonis 24 * 43 * Isolate characterisation and population structure analysis
Bartonella washoensis http://pubmlst.org/bwashoensis 21 * 21 * Isolate characterisation
Brachyspira hampsonii https://pubmlst.org/brachyspira/ 20 * 815 * Strain characterization and population structure analysis
Helicobacter cinaedi https://pubmlst.org/hcinaedi 19 * 69 * Molecular epidemiology and population structure analysis
Edwardsiella spp. http://pubmlst.org/edwardsiella/ 18 * 62 * Isolate characterisation and population structure analysis
Pediococcus pentosaceus https://pubmlst.org/ppentosaceus/ 17 * 31 * Strain characterization and population structure analysis
Campylobacter sputorum https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
16 * 582 * Isolate characterisation and population structure analysis
Saprolegnia parasitica http://pubmlst.org/sparasitica 15 * 82 * Isolate characterisation and population structure
Bartonella bacilliformis https://pubmlst.org/bbacilliformis/ 14 * 64 * Isolate characterisation and population structure analysis Chaloner et al. (2011) PLoS Negl Trop Dis 5:e1248.
Mycobacterium massiliense https://pubmlst.org/mabscessus/ 12 * - Isolate characterisation and population structure analyses
Candidatus Liberibacter solanacearum https://pubmlst.org/liberibacter/ 10 * 10 * Isolate characterisation and population structure analysis Haapalainen et al. (2018) Phytopathology 108:925-934.
Vibrio tapetis https://pubmlst.org/vtapetis/ 10 * 30 * Isolate characterisation and populaton structure
Batrachochytrium dendrobatidis n/a 10 35 Population and evolutionary analyses.
Campylobacter helveticus https://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
9 * 582 * -
Clostridium septicum https://pubmlst.org/csepticum/ 8 * - Isolate characterisation and evolutionary analyses
Mycoplasma flocculare http://pubmlst.org/mflocculare 8 * 8 * Isolate characterisation
Salmonella typhi n/a 4 26 Estimation of age and time of emergence of S. typhi.
Kudoa septempunctata https://pubmlst.org/kseptempunctata/ 3 * 104 * Isolate characterisation