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.

Fig 1

Schematic diagram of SNP genotypes of E. coli O157:H7 isolates from cattle and humans to illustrate relative phylogenetic positions (not drawn to scale). Numbers on branches identify the SNP loci that support each bifurcation as shown in Table S2 in the supplemental material. The numbers (percentages) of each of the SNP-defined lineages isolated from cattle and human sources are indicated in the table. Boxed tabulations identify lineages significantly associated with cattle (bovine-biased lineages; solid lines) or human (clinical lineages; dashed lines) sources.