title: Lineage and genogroup-defining single nucleotide polymorphisms of Escherichia coli O157:H7.
abstract: Escherichia coli O157:H7 is a zoonotic human pathogen for which cattle are an important reservoir host. Using both previously published and new sequencing data, a 48-locus single nucleotide polymorphism (SNP)-based typing panel was developed that redundantly identified 11 genogroups that span six of the eight lineages recently described for E. coli O157:H7 (J. L. Bono, T. P. Smith, J. E. Keen, G. P. Harhay, T. G. McDaneld, R. E. Mandrell, W. K. Jung, T. E. Besser, P. Gerner-Smidt, M. Bielaszewska, H. Karch, M. L. Clawson, Mol. Biol. Evol. 29:2047-2062, 2012) and additionally defined subgroups within four of those lineages. This assay was applied to 530 isolates from human and bovine sources. The SNP-based lineage groups were concordant with previously identified E. coli O157:H7 genotypes identified by other methods and were strongly associated with carriage of specific Stx genes. Two SNP lineages (Ia and Vb) were disproportionately represented among cattle isolates, and three others (IIa, Ib, and IIb) were disproportionately represented among human clinical isolates. This 48-plex SNP assay efficiently and economically identifies biologically relevant lineages within E. coli O157:H7.
authors.affiliation: Department of Veterinary Microbiology and Pathology, Washington State University College of Veterinary Medicine, Pullman, Washington, USA.
authors.forename: Woo Kyung
authors.initials: WK
authors.lastname: Jung
authors.forename: James L
authors.initials: JL
authors.lastname: Bono
authors.forename: Michael L
authors.initials: ML
authors.lastname: Clawson
authors.forename: Shana R
authors.initials: SR
authors.lastname: Leopold
authors.forename: Smriti
authors.initials: S
authors.lastname: Shringi
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Besser
mesh_terms: D000818:Animals; D015373:Bacterial Typing Techniques; D002417:Cattle / Q000382:microbiology; D002418:Cattle Diseases / Q000382:microbiology; D004927:Escherichia coli Infections / Q000382:microbiology; D019453:Escherichia coli O157 / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D005798:Genes, Bacterial; D005838:Genotype; D006801:Humans; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D022622:Shiga Toxin 1 / Q000235:genetics
chemical_list: D022622:Shiga Toxin 1