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Title: Lineage and genogroup-defining single nucleotide polymorphisms of Escherichia coli 0157:H7

item JUNG, WOO - Washington State University
item Bono, James - Jim
item Clawson, Michael - Mike
item LEOPOLD, SHANA - University Of Munster
item SHRINGI, SMRITI - Washington State University
item BESSER, THOMAS - Washington State University

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/2/2013
Publication Date: 11/1/2013
Publication URL:
Citation: Jung, W.K., Bono, J.L., Clawson, M.L., Leopold, S.R., Shringi, S., Besser, T.E. 2013. Lineage and genogroup-defining single nucleotide polymorphisms of Escherichia coli 0157:H7. Applied and Environmental Microbiology. 79(22):7036-7041.

Interpretive Summary: Escherichia coli O157:H7 bacteria are genetically diverse and place into major subdivisions, or lineages, that do not all associate with human disease. Cattle are an important reservoir for these bacteria and harbor a wide spectrum of genetic subtypes, including those of lineages that do and do not associate with human disease. In this study, an assay was developed to identify genetic subtypes within and across the major lineages of E. coli O157:H7. A large collection of cattle- or human-isolated E. coli O157:H7 strains was characterized with the assay and several new genetic associations with the cattle reservoir and/or human disease were detected. The assay is based on 48 highly informative single nucleotide polymorphisms and types E. coli O157:H7 genetic subtypes rapidly and economically.

Technical 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 eleven genogroups that span six of the eight lineages recently described for E. coli O157:H7 (Bono JL et al., Mol Biol Evol 29:2047, 2012), and additionally define 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.