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All species MLST databases and published schemes

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

Order by: Organism | Profiles | Isolates

Databases ordered by numbers of organism

Chart shows databases with at least 1000 profiles or isolates.

* Data updated automatically: 2014-10-19.

Organism Website and link to database Sequence types Isolates Applications to date Selected references
Achromobacter spp. http://pubmlst.org/achromobacter 239 * 590 * Isolate characterisation Spilker et al. (2012) J Clin Microbiol 50:3010-5.
Acinetobacter baumannii#1 http://pubmlst.org/abaumannii/ 797 * 679 * Isolate characterisation and population structure analysis Bartual et al. (2005) J Clin Microbiol 43:4382-90.
Acinetobacter baumannii#2 http://www.pasteur.fr/ mlst/Abaumannii.html 633 * 792 * -
Aeromonas spp. http://pubmlst.org/aeromonas/ 328 * 364 * Strain characterization
Anaplasma phagocytophilum http://pubmlst.org/aphagocytophilum/ 112 * 318 * Strain characterization and population structure analysis
Arcobacter spp. http://pubmlst.org/arcobacter/ 439 * 683 * Isolate characterisation and population structure
Aspergillus fumigatus http://pubmlst.org/afumigatus/ 48 * 22 * Isolate characterisation
Bacillus cereus http://pubmlst.org/bcereus/ 988 * 1696 * Population and evolutionary analyses. Priest et al. (2004) J Bacteriol 186:7959-70.
Bacillus licheniformis http://pubmlst.org/blicheniformis/ 27 * 62 * Isolate characterisation and population structure analysis Madslien et al. (2012) BMC Microbiol 12:230.
Bacillus subtilis http://pubmlst.org/bsubtilis/ 100 * 223 * Isolate characterisation and population structure analysis
Batrachochytrium dendrobatidis n/a 10 35 Population and evolutionary analyses.
Bifidobacterium http://www.pasteur.fr/ mlst/Bifidobacterium.html 102 * - -
Bordetella spp. http://pubmlst.org/bordetella/ 81 * 324 * -
Borrelia burgdorferi http://borrelia.mlst.net 576 * 1522 * Isolate characterisation and epidemiological analyses
Brachyspira hampsonii http://pubmlst.org/brachyspira/ 11 * 391 * Strain characterization and population structure analysis
Brachyspira hyodysenteriae http://pubmlst.org/brachyspira/ 116 * 391 * Molecular epidemiology and population structure analyses.
Brachyspira intermedia http://pubmlst.org/brachyspira/ 75 * 391 * Molecular epidemiology and population structure analyses.
Brachyspira pilosicoli http://pubmlst.org/brachyspira/ 124 * 391 * Strain characterization and population structure analysis
Brachyspira spp. http://pubmlst.org/brachyspira/ 36 * 391 * Isolate characterisation and population structure analysis
Burkholderia cepacia complex http://pubmlst.org/bcc/ 889 * 1508 * Isolate characterisation and population structure analyses Baldwin et al. (2005) J Clin Microbiol 43:4665-73.
Burkholderia pseudomallei http://bpseudomallei.mlst.net 1323 * 3758 * Isolate characterisation and species identification.
Campylobacter concisus/curvus http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
124 * 236 * Isolate characterisation and population structure analysis
Campylobacter fetus http://pubmlst.org/cfetus/ 48 * - Isolate characterisation and population structure analyses van Bergen et al. (2005) J Clin Microbiol 43:5888-98.
Campylobacter helveticus http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
8 * 236 * -
Campylobacter hyointestinalis http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
109 * 236 * Isolate characterisation and population structure analysis
Campylobacter insulaenigrae http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
43 * 236 * Isolate characterisation and population structure analysis
Campylobacter jejuni http://pubmlst.org/campylobacter/ 7356 * 30249 * Epidemiological surveillance of food-borne infections, population structure analyses. Dingle et al. (2001) J Clin Microbiol 39:14-23.
Campylobacter lanienae http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
69 * 236 * Isolate characterisation and population structure analysis
Campylobacter lari http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
18 * 236 * -
Campylobacter sputorum http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
16 * 236 * Isolate characterisation and population structure analysis
Campylobacter upsaliensis http://pubmlst.org/campylobacter/
(Isolate database contains other non-jejuni/coli Campylobacter species and the number of isolates reported reflect all of these together)
155 * 236 * -
Candida albicans http://calbicans.mlst.net 2545 * 2446 * Isolate characterisation and identification of nosocomial outbreaks.
Candida glabrata http://cglabrata.mlst.net 68 * 212 * Isolate characterisation and population structure analyses
Candida krusei http://pubmlst.org/ckrusei/ 186 * 243 * Isolate characterisation and population structure analyses Jacobsen et al. (2007) J Clin Microbiol 45:317-23.
Candida tropicalis http://pubmlst.org/ctropicalis/ 407 * 560 * Isolate characterisation and epidemiological analyses Tavanti et al. (2005) J Clin Microbiol 43:5593-600.
Carnobacterium maltaromaticum http://pubmlst.org/cmaltaromaticum 39 * 50 * Strain characterization and population structure analysis
Chlamydiales spp. http://pubmlst.org/chlamydiales/ 90 * 384 * Isolate characterisation and population structure analysis Pannekoek et al. (2008) BMC Microbiol 8:42.
Citrobacter freundii http://pubmlst.org/cfreundii 8 * 36 * Isolate characterisation and population structure analysis Bai et al. (2012) PLoS One 7:e33054.
Clonorchis sinensis http://pubmlst.org/csinensis/ 254 * 256 * Strain characterization and population structure analysis
Clostridium botulinum http://pubmlst.org/cbotulinum/ 83 * 261 * Isolate characterisation and evolutionary analyses
Clostridium difficile http://pubmlst.org/cdifficile 278 * 1472 * Isolate characterisation and population structure analysis Griffiths et al. (2010) J Clin Microbiol 48:770-8.
Clostridium difficile#2 http://www.pasteur.fr/ mlst/Cdifficile2.html 70 * 539 * -
Clostridium septicum http://pubmlst.org/csepticum/ 8 * - Isolate characterisation and evolutionary analyses
Corynebacterium diphtheriae http://pubmlst.org/cdiphtheriae/ 340 * - -
Cronobacter spp. http://pubmlst.org/cronobacter/ 313 * 1005 * -
Cryptococcus neoformans http://cneoformans.mlst.net 53 * 261 * Isolate characterisation and population structure analysis
Enterobacter cloacae http://pubmlst.org/ecloacae/ 261 * - Strain characterization and population structure analysis
Enterococcus faecalis http://efaecalis.mlst.net 605 * 1201 * -
Enterococcus faecium http://efaecium.mlst.net 927 * 2234 * Isolate characterisation and epidemiological analyses.
Escherichia coli#1 http://mlst.warwick.ac.uk/mlst/dbs/Ecoli 4236 * 6492 * Examination of the evolution of virulence. Wirth et al. (2006) Mol Microbiol 60:1136-51.
Escherichia coli#2 http://www.pasteur.fr/ mlst/EColi.html 637 * 449 * -
Flavobacterium psychrophilum http://pubmlst.org/fpsychrophilum/ 166 * 994 * Strain characterization and population structure analysis
Haemophilus influenzae http://haemophilus.mlst.net 1395 * 2291 * Epidemiological surveillance.
Haemophilus parasuis http://pubmlst.org/hparasuis/ 148 * 166 * Population and evolutionary analyses.
Helicobacter cinaedi http://pubmlst.org/hcinaedi 18 * 68 * Molecular epidemiology and population structure analysis
Helicobacter pylori http://pubmlst.org/helicobacter/ 2900 * 1993 * Tracking the patterns of human migration. Wirth et al. (2004) Proc Natl Acad Sci U S A 101:4746-51.
Helicobacter suis http://pubmlst.org/hsuis/ 25 * 29 * Strain characterization and population structure analysis
Klebsiella oxytoca http://pubmlst.org/koxytoca/ 131 * 81 * Isolate characterisation and population structure analysis
Klebsiella pneumoniae http://www.pasteur.fr/ mlst/Kpneumoniae.html 1677 * 1650 * Isolate characterisation and epidemiological analyses
Lactobacillus casei http://www.pasteur.fr/ mlst/Lcasei.html 40 * 53 * Isolate characterisation and population structure analysis
Lactobacillus salivarius http://pubmlst.org/lsalivarius/ 25 * 33 * Population and evolutionary analyses. Raftis et al. (2011) Appl Environ Microbiol 77:954-65.
Laribacter hongkongensis http://mlstdb.hku.hk:14206/MLST_index.html 97 146 -
Leptospira spp. http://leptospira.mlst.net 202 * 365 * Isolate characterisation and epidemiological analyses
Leptospira spp.#2 http://pubmlst.org/leptospira/ 96 * 116 * Strain characterization and population structure analysis Varni et al. (2014) Infect Genet Evol 22:216-22.
Leptospira spp.#3 http://pubmlst.org/leptospira - 116 * Strain characterization and population structure analysis Ahmed et al. (2006) Ann Clin Microbiol Antimicrob 5:28.
Listeria monocytogenes http://www.pasteur.fr/ mlst/Lmono.html 703 * 2586 * -
Mannheimia haemolytica http://pubmlst.org/mhaemolytica/ 36 * 115 * Isolate characterisation
Melissococcus plutonius http://pubmlst.org/mplutonius/ 27 * 352 * Isolate characterisation and population structure analysis
Moraxella catarrhalis http://mlst.warwick.ac.uk/mlst/dbs/Mcatarrhalis 228 * 346 * -
Mycobacterium abscessus http://pubmlst.org/mabscessus/ 26 * - Isolate characterisation and population structure analyses
Mycobacterium massiliense http://pubmlst.org/mabscessus/ 12 * - Isolate characterisation and population structure analyses
Mycoplasma agalactiae http://pubmlst.org/magalactiae/ 18 * 104 * Isolate characterisation and population structure analysis McAuliffe et al. (2011) J Med Microbiol 60:803-11.
Mycoplasma hyorhinis http://pubmlst.org/mhyorhinis/ 29 * 33 * Isolate characterisation and population structure analysis
Neisseria spp. http://pubmlst.org/neisseria/ 11011 * 29369 * Epidemiological surveillance, post-vaccine studies, population and evolutionary analyses. Maiden et al. (1998) Proc Natl Acad Sci U S A 95:3140-5.
Paenibacillus larvae http://pubmlst.org/plarvae 21 * - Isolate characterisation and population structure analysis
Pantoea agglomerans http://www.pasteur.fr/ mlst/Pantoea.html 22 * - -
Pasteurella multocida#1 http://pubmlst.org/pmultocida/ 285 * 562 * Isolate characterisation and population structure analysis
Pasteurella multocida#2 http://pubmlst.org/pmultocida/ 61 * 125 * Evolutionary analyses between isolates from different host species
Pediococcus pentosaceus http://pubmlst.org/ppentosaceus/ 17 * 31 * Strain characterization and population structure analysis
Pencillium marneffei http://mlstdb.hku.hk:14206/MLST_index.html 35 44 -
Plesiomonas shigelloides http://www.pasteur.fr/ mlst/Pshigelloides.html 76 * 77 * Isolate characterisation and population structure analysis
Porphyromonas gingivalis http://pubmlst.org/pgingivalis/ 138 * 144 * Isolate characterisation and population structure analyses Enersen et al. (2006) J Clin Microbiol 44:35-41.
Propionibacterium acnes http://pubmlst.org/pacnes/ 121 * 5 * Isolate characterisation and population structure analyses
Propionibacterium freudenreichii http://www.pasteur.fr/ mlst/Propio-freudenreichii.html 46 * 113 * -
Pseudomonas aeruginosa http://pubmlst.org/paeruginosa/ 1931 * 2428 * Population and evolutionary analyses.
Pseudomonas fluorescens http://pubmlst.org/pfluorescens/ 98 * 103 * Strain characterization and population structure analysis
Salmonella enterica http://mlst.warwick.ac.uk/mlst/dbs/Senterica 1757 * 6286 * -
Salmonella typhi n/a 4 26 Estimation of age and time of emergence of S. typhi.
Sinorhizobium spp. http://pubmlst.org/sinorhizobium/ 136 * 550 * -
Staphylococcus aureus http://saureus.mlst.net 2805 * 5292 * Identification of predominant epidemic MRSA isolates, species evolution, population analyses.
Staphylococcus epidermidis http://sepidermidis.mlst.net 562 * 750 * -
Staphylococcus pseudintermedius http://pubmlst.org/spseudintermedius/ 400 * 457 * Strain characterization and population structure analysis Solyman et al. (2013) J Clin Microbiol 51:306-10.
Stenotrophomonas maltophilia http://pubmlst.org/smaltophilia/ 96 * 131 * -
Streptococcus agalactiae http://pubmlst.org/sagalactiae/ 711 * 933 * Identification of clones associated with neonatal infections. Jones et al. (2003) J Clin Microbiol 41:2530-6.
Streptococcus canis http://pubmlst.org/scanis/ 25 * 90 * Strain characterization and population structure analysis Pinho et al. (2013) J Clin Microbiol 51:1099-109.
Streptococcus dysgalactiae equisimilis http://sdse.mlst.net/ 189 * 178 * -
Streptococcus gallolyticus http://pubmlst.org/sgallolyticus/ 90 * 280 * Strain characterization and population structure analysis
Streptococcus oralis http://pubmlst.org/soralis/ 77 * 574 * Isolate characterisation and population structure analyses Do et al. (2009) Microbiology 155:2593-602.
Streptococcus pneumoniae http://pubmlst.org/spneumoniae/ 9839 * 24027 * Identification of antibiotic resistant clones, epidemiological surveillance, population analyses. Enright et al. (1998) Microbiology 144 ( Pt 11):3049-60.
Streptococcus pyogenes http://spyogenes.mlst.net 628 * 2343 * Identification of relationships between emm-type and clonal complex.
Streptococcus suis http://ssuis.mlst.net 618 * 1309 * -
Streptococcus thermophilus http://www.pasteur.fr/ mlst/strepto-thermophilus.html 116 * - -
Streptococcus uberis http://pubmlst.org/suberis/ 639 * 988 * - Coffey et al. (2006) Appl Environ Microbiol 72:1420-8.
Streptococcus zooepidemicus http://pubmlst.org/szooepidemicus/ 324 * 1307 * Isolate characterisation and population structure analysis
Streptomyces spp http://pubmlst.org/streptomyces/ 135 * 150 * Species identification
Taylorella spp. http://pubmlst.org/taylorella/ 50 * 200 * Strain characterization and population structure analysis Duquesne et al. (2013) Vet Microbiol 167:609-18.
Vibrio cholerae http://pubmlst.org/vcholerae/ 177 * 106 * Strain characterization and population structure analysis
Vibrio parahaemolyticus http://pubmlst.org/vparahaemolyticus/ 1123 * 1596 * -
Vibrio spp. http://pubmlst.org/vibrio 149 * 182 * Species identification
Vibrio tapetis http://pubmlst.org/vtapetis/ 10 * 30 * Isolate characterisation and populaton structure
Vibrio vulnificus http://pubmlst.org/vvulnificus/ 284 * 385 * Isolate characterisation and epidemiological analyses. Bisharat et al. (2005) Emerg Infect Dis 11:30-5.
Wolbachia http://pubmlst.org/wolbachia/ 429 * 1663 * Isolate characterisation and population structure analyses Baldo et al. (2006) Appl Environ Microbiol 72:7098-110.
Xylella fastidiosa http://pubmlst.org/xfastidiosa/ 58 * 284 * Isolate characterisation and population structure.
Yersinia pseudotuberculosis http://mlst.warwick.ac.uk/mlst/dbs/Ypseudotuberculosis 123 * 748 * Population and evolutionary analyses.
Yersinia ruckeri http://pubmlst.org/yruckeri/ 30 * 103 * Population and evolutionary analyses.
Yersinia spp. http://pubmlst.org/yersinia/ 169 * 388 * Speciation and isolate characterisation