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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: 2018-12-15.

Organism Website and link to database Sequence types Isolates Applications to date Selected references
Streptococcus pneumoniae https://pubmlst.org/spneumoniae/ 14319 * 40580 * 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/ 14019 * 47948 * 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/ 9464 * 71708 * 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 7994 * 6492 * Examination of the evolution of virulence. Wirth et al. (2006) Mol Microbiol 60:1136-51.
Staphylococcus aureus https://pubmlst.org/saureus 5102 * 33943 * Identification of predominant epidemic MRSA isolates, species evolution, population analyses
Salmonella enterica http://mlst.warwick.ac.uk/mlst/dbs/Senterica 4742 * 6286 * -
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.
Klebsiella pneumoniae http://bigsdb.web.pasteur.fr/klebsiella/ 3482 * 5068 * Isolate characterisation and epidemiological analyses
Helicobacter pylori https://pubmlst.org/helicobacter/ 3381 * 2258 * 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/ 3182 * 6654 * Population and evolutionary analyses. Curran et al. (2004) J Clin Microbiol 42:5644-9.
Bacillus cereus https://pubmlst.org/bcereus/ 2164 * 2465 * Population and evolutionary analyses. Priest et al. (2004) J Bacteriol 186:7959-70.
Haemophilus influenzae https://pubmlst.org/hinfluenzae/ 2054 * 3806 * Isolate characterisation and population structure analysis Meats et al. (2003) J Clin Microbiol 41:1623-36.
Vibrio parahaemolyticus https://pubmlst.org/vparahaemolyticus/ 2010 * 2893 * -
Acinetobacter baumannii#1 https://pubmlst.org/abaumannii/ 1867 * 4032 * Isolate characterisation and population structure analysis Bartual et al. (2005) J Clin Microbiol 43:4382-90.
Burkholderia pseudomallei https://pubmlst.org/bpseudomallei 1696 * 5829 * Isolate characterisation and species identification. Godoy et al. (2003) J Clin Microbiol 41:2068-79.
Burkholderia cepacia complex https://pubmlst.org/bcc/ 1540 * 2844 * Isolate characterisation and population structure analyses Baldwin et al. (2005) J Clin Microbiol 43:4665-73.
Enterococcus faecium https://pubmlst.org/efaecium/ 1497 * 3294 * Strain characterization and population structure analysis
Listeria monocytogenes http://bigsdb.web.pasteur.fr/listeria/ 1437 * 3593 * -
Streptococcus agalactiae https://pubmlst.org/sagalactiae/ 1324 * 4579 * Identification of clones associated with neonatal infections. Jones et al. (2003) J Clin Microbiol 41:2530-6.
Staphylococcus pseudintermedius https://pubmlst.org/spseudintermedius/ 1322 * 1485 * Strain characterization and population structure analysis Solyman et al. (2013) J Clin Microbiol 51:306-10.
Acinetobacter baumannii#2 https://pubmlst.org/abaumannii/ 1299 * 4032 * -
Streptococcus suis https://pubmlst.org/ssuis 1132 * 2085 * Population characterisation and population structure analysis
Enterobacter cloacae https://pubmlst.org/ecloacae/ 1113 * - Strain characterization and population structure analysis
Streptococcus pyogenes https://pubmlst.org/spyogenes 1090 * 3938 * Identification of relationships between emm-type and clonal complex Enright et al. (2001) Infect Immun 69:2416-27.
Streptococcus uberis https://pubmlst.org/suberis/ 994 * 1179 * - Coffey et al. (2006) Appl Environ Microbiol 72:1420-8.
Escherichia coli#2 http://bigsdb.web.pasteur.fr/ecoli/ 921 * 1122 * -
Enterococcus faecalis https://pubmlst.org/efaecalis/ 904 * 1833 * Isolate characterisation and population structure analysis
Mycobacteria spp. http://pubmlst.org/mycobacteria 839 * 9425 * Strain characterisation
Candida tropicalis https://pubmlst.org/ctropicalis/ 833 * 984 * Isolate characterisation and epidemiological analyses Tavanti et al. (2005) J Clin Microbiol 43:5593-600.
Staphylococcus epidermidis https://pubmlst.org/sepidermidis/ 820 * 1315 * Isolate characterisation and population structure analysis Thomas et al. (2007) J Clin Microbiol 45:616-9.
Borrelia spp. https://pubmlst.org/borrelia/ 806 * 2489 * Isolate characterisation and epidemiological analyses
Arcobacter spp. https://pubmlst.org/arcobacter/ 762 * 893 * Isolate characterisation and population structure
Vibrio cholerae https://pubmlst.org/vcholerae/ 742 * 1363 * Strain characterization and population structure analysis
Cronobacter spp. https://pubmlst.org/cronobacter/ 674 * 2650 * -
Moraxella catarrhalis http://mlst.warwick.ac.uk/mlst/dbs/Mcatarrhalis 618 * 346 * -
Corynebacterium diphtheriae https://pubmlst.org/cdiphtheriae/ 586 * 736 * -
Vibrio cholerae#2 http://pubmlst.org/vcholerae 566 * 1363 * Isolate characterisation
Aeromonas spp. https://pubmlst.org/aeromonas/ 559 * 632 * Strain characterization
Clostridium difficile https://pubmlst.org/cdifficile 530 * 1619 * Isolate characterisation and population structure analysis Griffiths et al. (2010) J Clin Microbiol 48:770-8.
Wolbachia https://pubmlst.org/wolbachia/ 501 * 1869 * Isolate characterisation and population structure analyses Baldo et al. (2006) Appl Environ Microbiol 72:7098-110.
Achromobacter spp. https://pubmlst.org/achromobacter 453 * 1022 * Isolate characterisation Spilker et al. (2012) J Clin Microbiol 50:3010-5.
Streptococcus dysgalactiae equisimilis https://pubmlst.org/sdysgalactiae/ 453 * 1431 * Isolate characterisation and population structure analysis McMillan et al. (2010) PLoS One 5:e11741.
Citrobacter freundii https://pubmlst.org/cfreundii 408 * 379 * Isolate characterisation and population structure analysis Bai et al. (2012) PLoS One 7:e33054.
Streptococcus zooepidemicus https://pubmlst.org/szooepidemicus/ 379 * 1426 * Isolate characterisation and population structure analysis
Yersinia pseudotuberculosis http://mlst.warwick.ac.uk/mlst/dbs/Ypseudotuberculosis 374 * 748 * Population and evolutionary analyses.
Vibrio vulnificus https://pubmlst.org/vvulnificus/ 364 * 473 * Isolate characterisation and epidemiological analyses. Bisharat et al. (2005) Emerg Infect Dis 11:30-5.
Haemophilus parasuis https://pubmlst.org/hparasuis/ 359 * 351 * Population and evolutionary analyses.
Pasteurella multocida#1 https://pubmlst.org/pmultocida/ 350 * 562 * Isolate characterisation and population structure analysis
Stenotrophomonas maltophilia https://pubmlst.org/smaltophilia/ 334 * 480 * -
Leptospira spp.#2 https://pubmlst.org/leptospira/ 271 * 1289 * Strain characterization and population structure analysis Varni et al. (2014) Infect Genet Evol 22:216-22.
Leptospira spp. https://pubmlst.org/leptospira/ 265 * 1289 * Isolate characterisation and epidemiological analyses
Clonorchis sinensis https://pubmlst.org/csinensis/ 254 * 256 * Strain characterization and population structure analysis
Chlamydiales spp. https://pubmlst.org/chlamydiales/ 253 * 4396 * Isolate characterisation and population structure analysis Pannekoek et al. (2008) BMC Microbiol 8:42.
Brachyspira hyodysenteriae https://pubmlst.org/brachyspira/ 249 * 695 * Molecular epidemiology and population structure analyses.
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.
Klebsiella oxytoca https://pubmlst.org/koxytoca/ 212 * 144 * Isolate characterisation and population structure analysis
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 * -
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.
Bacillus subtilis https://pubmlst.org/bsubtilis/ 175 * 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
Anaplasma phagocytophilum https://pubmlst.org/aphagocytophilum/ 165 * 443 * Strain characterization and population structure analysis
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 * -
Mycoplasma bovis https://pubmlst.org/mbovis 155 * 400 * Isolate characterisation and population structure analysis Register et al. (2015) Vet Microbiol 175:92-8.
Vibrio spp. https://pubmlst.org/vibrio 149 * 182 * Species identification
Klebsiella aerogenes http://pubmlst.org/kaerogenes/ 146 * 185 * Isolate characterisation and population structure analysis
Leptospira spp.#3 https://pubmlst.org/leptospira 143 * 1289 * Strain characterization and population structure analysis Ahmed et al. (2006) Ann Clin Microbiol Antimicrob 5:28.
Propionibacterium acnes https://pubmlst.org/pacnes/ 139 * 5 * 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
Candida glabrata https://pubmlst.org/cglabrata/ 131 * 850 * Isolate characterisation and population structure analyses Dodgson et al. (2003) J Clin Microbiol 41:5709-17.
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
Streptococcus thermophilus http://bigsdb.web.pasteur.fr/streptococcus/ 125 * 174 * -
Tenacibaculum spp. https://pubmlst.org/tenacibaculum/ 125 * 114 * Isolate characterisation and populations structure analysis
Mycoplasma hyopneumoniae https://pubmlst.org/mhyopneumoniae/ 122 * 265 * Strain characterization and population structure analysis Mayor et al. (2008) Vet Microbiol 127:63-72.
Streptococcus thermophilus#2 https://pubmlst.org/sthermophilus 119 * 257 * Isolate characterisation and population structure analysis
Dichelobacter nodosus http://pubmlst.org/dnodosus 115 * 172 * Isolate characterisation and population structure analysis
Clostridium botulinum https://pubmlst.org/cbotulinum/ 112 * 276 * Isolate characterisation and evolutionary analyses
Streptococcus gallolyticus https://pubmlst.org/sgallolyticus/ 109 * 364 * Strain characterization and population structure analysis Dumke et al. (2014) J Clin Microbiol 52:2472-8.
Pseudomonas fluorescens https://pubmlst.org/pfluorescens/ 108 * 116 * Strain characterization and population structure analysis
Orientia tsutsugamushi https://pubmlst.org/otsutsugamushi/ 92 * 163 * Population and evolutionary analyses
Mycoplasma synoviae https://pubmlst.org/msynoviae/ 88 * 141 * Isolate characterisation and population structure analysis
Bordetella spp. https://pubmlst.org/bordetella/ 86 * 1637 * -
Xylella fastidiosa https://pubmlst.org/xfastidiosa/ 86 * 293 * Isolate characterisation and population structure.
Brachyspira intermedia https://pubmlst.org/brachyspira/ 83 * 695 * Molecular epidemiology and population structure analyses.
Mycoplasma hyorhinis https://pubmlst.org/mhyorhinis/ 82 * 111 * Isolate characterisation and population structure analysis
Brucella spp. https://pubmlst.org/brucella 81 * 858 * Isolate characterisation and population structure analysis
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 * 672 * Isolate characterisation and population structure analyses Do et al. (2009) Microbiology 155:2593-602.
Pasteurella multocida#2 https://pubmlst.org/pmultocida/ 75 * 125 * Evolutionary analyses between isolates from different host species
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.
Pseudomonas putida http://pubmlst.org/pputida 68 * 106 * Isolate characterisation and population structure analysis
Trichomonas vaginalis https://pubmlst.org/tvaginalis/ 60 * 68 * -
Staphylococcus hominis https://pubmlst.org/shominis 57 * 126 * Isolate characterisation and population structure analysis
Taylorella spp. https://pubmlst.org/taylorella/ 57 * 305 * Strain characterization and population structure analysis Duquesne et al. (2013) Vet Microbiol 167:609-18.
Macrococcus canis https://pubmlst.org/mcanis/ 56 * 25 * Isolate characterisation and population structure
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
Staphylococcus haemolyticus https://pubmlst.org/shaemolyticus/ 48 * 87 * Strain characterisation and population structure analysis
Bacillus licheniformis https://pubmlst.org/blicheniformis/ 47 * 73 * Isolate characterisation and population structure analysis Madslien et al. (2012) BMC Microbiol 12:230.
Treponema pallidum http://pubmlst.org/tpallidum 47 * 681 * Isolate characterisation and population structure analysis Grillová et al. (2018) PLoS One 13:e0200773.
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
Streptococcus canis https://pubmlst.org/scanis/ 38 * 194 * Strain characterization and population structure analysis Pinho et al. (2013) J Clin Microbiol 51:1099-109.
Brachyspira spp. https://pubmlst.org/brachyspira/ 36 * 695 * 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.
Pencillium marneffei http://mlstdb.hku.hk:14206/MLST_index.html 35 44 -
Melissococcus plutonius https://pubmlst.org/mplutonius/ 35 * 379 * Isolate characterisation and population structure analysis
Mycoplasma agalactiae https://pubmlst.org/magalactiae/ 34 * 136 * Isolate characterisation and population structure analysis McAuliffe et al. (2011) J Med Microbiol 60:803-11.
Bartonella henselae https://pubmlst.org/bhenselae 33 * 434 * Isolate characterisation and population structure analysis
Macrococcus caseolyticus https://pubmlst.org/mcaseolyticus/ 33 * 54 * Isolate characterisation and population structure
Mycoplasma pneumoniae https://pubmlst.org/mpneumoniae/ 33 * 436 * Isolate characterisation and population structure Brown et al. (2015) J Clin Microbiol 53:3195-203.
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
Mycoplasma iowae https://pubmlst.org/miowae/ 23 * 47 * Isolate characterisation and population structure analysis Ghanem et al. (2016) Vet Microbiol 195:2-8.
Brachyspira hampsonii https://pubmlst.org/brachyspira/ 20 * 695 * 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
Batrachochytrium dendrobatidis n/a 10 35 Population and evolutionary analyses.
Vibrio tapetis https://pubmlst.org/vtapetis/ 10 * 30 * Isolate characterisation and populaton structure
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
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
Brachyspira pilosicoli https://pubmlst.org/brachyspira/ - 695 * Strain characterization and population structure analysis