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EcMLST specifications


Unique identifier OMICS_29584
Alternative name E. coli Multilocus Sequence Typing
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 1.2
Maintained Yes


  • Bacteria
    • Escherichia coli


  • person_outline Weihong Qi

Publication for E. coli Multilocus Sequence Typing

EcMLST citations


Genetic Relatedness and Novel Sequence Types of Non O157 Shiga Toxin Producing Escherichia coli Strains Isolated in Argentina

PMCID: 5003923
PMID: 27625995
DOI: 10.3389/fcimb.2016.00093

[…] scheme were assigned to clonal groups (CGs) (Qi et al., ).On the other hand, a population snapshot was generated from the STs identified and STs from closely related STEC strains downloaded from the EcMLST database (accessed October 10, 2015), based on BURST algorithm, using the eBURSTv3 software (Feil et al., ), available at The input data used by eBURST are the STs and t […]


Molecular Characterization of Shigella sonnei: An Increasingly Prevalent Etiologic Agent of Shigellosis in Guizhou Province, Southwest of China

PLoS One
PMCID: 4873039
PMID: 27195892
DOI: 10.1371/journal.pone.0156020

[…] ST76 and ST116 were previously reported, while four STs including ST122, ST123, ST140 and ST141 were novel. The allele number for each loci and the designation of ST are listed in and shared in the EcMLST website. The most common STs are ST76 (N = 43) and ST116 (N = 25), accounting for 92.1%. ST76 contained the most number of isolates, represented by 42 isolates of phase II from different years […]


Utility of Whole Genome Sequencing of Escherichia coli O157 for Outbreak Detection and Epidemiological Surveillance

J Clin Microbiol
PMCID: 4609728
PMID: 26354815
DOI: 10.1128/JCM.01066-15

[…] ies. For MLST, the database consisted of the alleles of 15 housekeeping genes (arcA, aroE, aspC, clpX, cyaA, dnaG, fadD, grpE, icdA, lysP, mdh, mtlD, mutS, rpoS, uidA), which were downloaded from the EcMLST website (; for stx subtyping, the database consisted of 600-bp sequences (342 bp of the C-terminal part of subunit A and 258 bp of the N-terminal part of s […]


A Novel Escherichia coli O157:H7 Clone Causing a Major Hemolytic Uremic Syndrome Outbreak in China

PLoS One
PMCID: 3338595
PMID: 22558360
DOI: 10.1371/journal.pone.0036144
call_split See protocol

[…] lpX, cyaA, dnaG, fadD, grpE, icdA, lysP, mdh, mtlD, mutS, rpoS, uidA). A detailed protocol of the MLST procedure, including allelic type and sequence type (ST) assignment methods, can be found at the EcMLST website ( MEGA 4.0 was used to construct phylogenetic trees and eBURST was used to cluster STs into clonal complexes which consist of STs differing by one of the […]


Characterisation of atypical enteropathogenic E. coli strains of clinical origin

BMC Microbiol
PMCID: 2700815
PMID: 19490652
DOI: 10.1186/1471-2180-9-117
call_split See protocol

[…] olated from humans or cattle in Australia and New Zealand, together with four archetypal aEPEC and eight A/E E. coli control strains were subjected to MLST analysis using the methods described on the EcMLST website Briefly, seven housekeeping genes (aspC, clpX, fadD, icdA, lysP, mdh and uidA) were amplified with AmpliTaq Gold in 50 μl reaction volumes. PCR products (5 […]


Shiga Toxin–producing Escherichia coli Strains Negative for Locus of Enterocyte Effacement

PMCID: 2681110
PMID: 19239748
DOI: 10.3201/eid1502.080631
call_split See protocol

[…] erved housekeeping genes: aspC, clpX, fadD, icdA, lysP, mdh, and uidA. A detailed protocol of the MLST procedure, including allelic type and sequence type (ST) assignment methods, can be found at the EcMLST Web site ( Sequences were concatenated for phylogenetic analyses. A neighbor-joining tree was constructed by using the Kimura 2-parameter model of nucleotide substitution […]


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EcMLST institution(s)
Microbial Evolution Laboratory, National Food Safety and Toxicology Center, Michigan State University, East Lansing, MI, USA
EcMLST funding source(s)
Supported by the NIAID, NIH, DHHS, under Contract # N01-AI-30058.

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