Escherichia coli cgMLST

Name	E. coli cgMLST
Version	1.0
Seed Genome	K-12 (NC_000913.3, 08-AUG-2016)
Genus	Escherichia
Species	coli
Locus Count	2,513
Complex Type Distance	10
Complex Type Count	64,669
Last Change	Jul 3, 2025, 8:19 AM
Curator	This Escherichia coli core genome MLST scheme uses exactly the same loci and reference gene sequences as the EnteroBase (http://enterobase.warwick.ac.uk) Escherichia/Shigella cgMLST v1 scheme. However, the SeqSphere+ allele calling procedure is slightly different and our allele numbering is independent from and not compatible with the EnteroBase allele nomenclature.
Publications	Zhou Z, Alikhan NF, Mohamed K, Fan Y, and . The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity. Genome Res. 2020, 30: 138-152 [PubMed 31809257]
	Senthakumaran T, Brandal LT, Lindstedt BA, Jørgensen SB, Charnock C, and Tunsjø HS. Implications of stx loss for clinical diagnostics of Shiga toxin-producing Escherichia coli. Eur. J. Clin. Microbiol. Infect. Dis. 2018, 37: 2361-2370 [PubMed 30267169]
	Weber RE, Pietsch M, Frühauf A, Pfeifer Y, Martin M, Luft D, Gatermann S, Pfennigwerth N, Kaase M, Werner G, and Fuchs S. IS26-Mediated Transfer of blaNDM-1 as the Main Route of Resistance Transmission During a Polyclonal, Multispecies Outbreak in a German Hospital. Front Microbiol. 2019, 10: 2817 [PubMed 31921015]