title: Genomic comparison of Escherichia coli serotype O103:H2 isolates with and without verotoxin genes: implications for risk assessment of strains commonly found in ruminant reservoirs.
abstract: BACKGROUND
  Escherichia coli O103:H2 occurs as verotoxigenic E. coli (VTEC) carrying only vtx 1 or vtx 2 or both variants, but also as vtx-negative atypical enteropathogenic E. coli (aEPEC). The majority of E. coli O103:H2 identified from cases of human disease are caused by the VTEC form. If aEPEC strains frequently acquire verotoxin genes and become VTEC, they must be considered a significant public health concern. In this study, we have characterized and compared aEPEC and VTEC isolates of E. coli O103:H2 from Swedish cattle.
  
  
  METHODS
  Fourteen isolates of E. coli O103:H2 with and without verotoxin genes were collected from samples of cattle feces taken during a nationwide cattle prevalence study 2011-2012. Isolates were sequenced with a 2×100 bp setup on a HiSeq2500 instrument producing >100× coverage per isolate. Single-nucleotide polymorphism (SNP) typing was performed using the genome analysis tool kit (GATK). Virulence genes and other regions of interest were detected. Susceptibility to transduction by two verotoxin-encoding phages was investigated for one representative aEPEC O103:H2 isolate.
  
  
  CONCLUSIONS
  This study shows that aEPEC O103:H2 is more commonly found (64%) than VTEC O103:H2 (36%) in the Swedish cattle reservoir. The only verotoxin gene variant identified was vtx 1a . Phylogenetic comparison by SNP analysis indicates that while certain subgroups of aEPEC and VTEC are closely related and have otherwise near identical virulence gene repertoires, they belong to separate lineages. This indicates that the uptake or loss of verotoxin genes is a rare event in the natural cattle environment of these bacteria. However, a representative of a VTEC-like aEPEC O103:H2 subgroup could be stably lysogenized by a vtx-encoding phage in vitro.
authors.affiliation: SLU Global Bioinformatics Centre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.|Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden; robert.soderlund@sva.se.
authors.forename: Robert
authors.initials: R
authors.lastname: Söderlund
authors.affiliation: SLU Global Bioinformatics Centre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
authors.forename: Julie
authors.initials: J
authors.lastname: Hurel
authors.affiliation: Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden.
authors.forename: Tomas
authors.initials: T
authors.lastname: Jinnerot
authors.affiliation: Department of Laboratory Services, Norwegian Veterinary Institute (NVI), Oslo, Norway.
authors.forename: Camilla
authors.initials: C
authors.lastname: Sekse
authors.affiliation: Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden.
authors.forename: Anna
authors.initials: A
authors.lastname: Aspán
authors.affiliation: Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Eriksson
authors.affiliation: SLU Global Bioinformatics Centre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Bongcam-Rudloff
keywords: EHEC; STEC; VTEC; aEPEC; cattle; high-throughput sequencing; next-generation sequencing; zoonosis