Comparative Genomic Analysis of Escherichia coli O157:H7 Isolated from Super-Shedder and Low-Shedder Cattle

PLoS One. 2016 Mar 28;11(3):e0151673. doi: 10.1371/journal.pone.0151673. eCollection 2016.

Abstract

Cattle are the primary reservoir of the foodborne pathogen Escherichia coli O157:H7, with the concentration and frequency of E. coli O157:H7 shedding varying substantially among individual hosts. The term ''super-shedder" has been applied to cattle that shed ≥10(4) cfu E. coli O157:H7/g of feces. Super-shedders have been reported to be responsible for the majority of E. coli O157:H7 shed into the environment. The objective of this study was to determine if there are phenotypic and/or genotypic differences between E. coli O157:H7 isolates obtained from super-shedder compared to low-shedder cattle. From a total of 784 isolates, four were selected from low-shedder steers and six isolates from super-shedder steers (4.01-8.45 log cfu/g feces) for whole genome sequencing. Isolates were phage and clade typed, screened for substrate utilization, pH sensitivity, virulence gene profiles and Stx bacteriophage insertion (SBI) sites. A range of 89-2473 total single nucleotide polymorphisms (SNPs) were identified when sequenced strains were compared to E. coli O157:H7 strain Sakai. More non-synonymous SNP mutations were observed in low-shedder isolates. Pan-genomic and SNPs comparisons did not identify genetic segregation between super-shedder or low-shedder isolates. All super-shedder isolates and 3 of 4 of low-shedder isolates were typed as phage type 14a, SBI cluster 3 and SNP clade 2. Super-shedder isolates displayed increased utilization of galactitol, thymidine and 3-O-β-D-galactopyranosyl-D-arabinose when compared to low-shedder isolates, but no differences in SNPs were observed in genes encoding for proteins involved in the metabolism of these substrates. While genetic traits specific to super-shedder isolates were not identified in this study, differences in the level of gene expression or genes of unknown function may still contribute to some strains of E. coli O157:H7 reaching high densities within bovine feces.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bacterial Shedding*
  • Bacterial Typing Techniques / methods
  • Cattle
  • Cattle Diseases / microbiology
  • Colony Count, Microbial
  • Escherichia coli Infections / veterinary
  • Escherichia coli O157 / classification
  • Escherichia coli O157 / genetics*
  • Escherichia coli O157 / physiology
  • Feces / microbiology*
  • Genome, Bacterial / genetics
  • Genomics / methods*
  • Hydrogen-Ion Concentration
  • Phylogeny
  • Polymorphism, Single Nucleotide
  • Sequence Analysis, DNA / methods

Grants and funding

Funded by Genome Alberta to TAM and LBS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.