title: Escherichia coli O157:H7 strains harbor at least three distinct sequence types of Shiga toxin 2a-converting phages.
abstract: BACKGROUND
  Shiga toxin-producing Escherichia coli O157:H7 is a foodborne pathogen that causes severe human diseases including hemolytic uremic syndrome (HUS). The virulence factor that mediates HUS, Shiga toxin (Stx), is encoded within the genome of a lambdoid prophage. Although draft sequences are publicly available for a large number of E. coli O157:H7 strains, the high sequence similarity of stx-converting bacteriophages with other lambdoid prophages poses challenges to accurately assess the organization and plasticity among stx-converting phages due to assembly difficulties.
  
  
  METHODS
  To further explore genome plasticity of stx-converting prophages, we enriched phage DNA from 45 ciprofloxacin-induced cultures for subsequent 454 pyrosequencing to facilitate assembly of the complete phage genomes. In total, 22 stx2a-converting phage genomes were closed.
  
  
  RESULTS
  Comparison of the genomes distinguished nine distinct phage sequence types (PSTs) delineated by variation in obtained sequences, such as single nucleotide polymorphisms (SNPs) and insertion sequence element prevalence and location. These nine PSTs formed three distinct clusters, designated as PST1, PST2 and PST3. The PST2 cluster, identified in two clade 8 strains, was related to stx2a-converting phages previously identified in non-O157 Shiga-toxin producing E. coli (STEC) strains associated with a high incidence of HUS. The PST1 cluster contained phages related to those from E. coli O157:H7 strain Sakai (lineage I, clade 1), and PST3 contained a single phage that was distinct from the rest but most related to the phage from E. coli O157:H7 strain EC4115 (lineage I/II, clade 8). Five strains carried identical stx2a-converting phages (PST1-1) integrated at the same chromosomal locus, but these strains produced different levels of Stx2.
  
  
  CONCLUSIONS
  The stx2a-converting phages of E. coli O157:H7 can be categorized into at least three phage types. Diversification within a phage type is mainly driven by IS629 and by a small number of SNPs. Polymorphisms between phage genomes may help explain differences in Stx2a production between strains, however our data indicates that genes encoded external to the phage affect toxin production as well.
authors.affiliation: Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA.
authors.forename: Shuang
authors.initials: S
authors.lastname: Yin
authors.affiliation: Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, 78249, USA.
authors.forename: Brigida
authors.initials: B
authors.lastname: Rusconi
authors.affiliation: Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, 78249, USA.
authors.forename: Fatemeh
authors.initials: F
authors.lastname: Sanjar
authors.affiliation: Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA.
authors.forename: Kakolie
authors.initials: K
authors.lastname: Goswami
authors.affiliation: Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA.
authors.forename: Lingzi
authors.initials: L
authors.lastname: Xiaoli
authors.affiliation: Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, 78249, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Eppinger
authors.affiliation: Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA. egd100@psu.edu.|Center of Molecular Immunology and Infectious Disease, The Pennsylvania State University, University Park, PA, 16802, USA. egd100@psu.edu.|427 Food Science Building, The Pennsylvania State University, University Park, PA, 16802, USA. egd100@psu.edu.
authors.forename: Edward G
authors.initials: EG
authors.lastname: Dudley
mesh_terms: D001435:Bacteriophages / Q000235:genetics*; D002939:Ciprofloxacin / Q000494:pharmacology; D019453:Escherichia coli O157 / Q000235:genetics* / Q000472:pathogenicity; D016678:Genome; D006463:Hemolytic-Uremic Syndrome / Q000235:genetics* / Q000382:microbiology; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D022641:Shiga Toxin 2 / Q000235:genetics*
chemical_list: D022641:Shiga Toxin 2; D002939:Ciprofloxacin