title: Comparative Genomic Analysis of Escherichia coli O157:H7 Isolated from Super-Shedder and Low-Shedder Cattle.
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.
authors.affiliation: Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, Canada.|Department of Biological Sciences, University of Lethbridge, Lethbridge AB, Canada.
authors.forename: Krysty D
authors.initials: KD
authors.lastname: Munns
authors.affiliation: Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, Canada.
authors.forename: Rahat
authors.initials: R
authors.lastname: Zaheer
authors.affiliation: Department of Biological Sciences, University of Lethbridge, Lethbridge AB, Canada.
authors.forename: Yong
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Agriculture and Forestry, Lethbridge, AB, Canada.
authors.forename: Kim
authors.initials: K
authors.lastname: Stanford
authors.affiliation: Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Lethbridge, AB, Canada.
authors.forename: Chad R
authors.initials: CR
authors.lastname: Laing
authors.affiliation: Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Lethbridge, AB, Canada.
authors.forename: Victor P J
authors.initials: VP
authors.lastname: Gannon
authors.affiliation: Department of Biological Sciences, University of Lethbridge, Lethbridge AB, Canada.
authors.forename: L Brent
authors.initials: LB
authors.lastname: Selinger
authors.affiliation: Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, Canada.
authors.forename: Tim A
authors.initials: TA
authors.lastname: McAllister
mesh_terms: D000818:Animals; D057138:Bacterial Shedding; D015373:Bacterial Typing Techniques / Q000379:methods; D002417:Cattle; D002418:Cattle Diseases / Q000382:microbiology; D015169:Colony Count, Microbial; D004927:Escherichia coli Infections / Q000662:veterinary; D019453:Escherichia coli O157 / Q000145:classification / Q000235:genetics* / Q000502:physiology; D005243:Feces / Q000382:microbiology*; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics / Q000379:methods*; D006863:Hydrogen-Ion Concentration; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods