title: Comparative accessory gene fingerprinting of surface water Escherichia coli reveals genetically diverse naturalized population.
abstract: OBJECTIVE
  To utilize comparative accessory gene fingerprinting to discriminate between naturalized and faecal Escherichia coli, with particular emphasis on strains from phylogroup B1.
  
  
  RESULTS
  Fourteen accessory genes that were potentially ecotype-specific were selected on the basis of comparative genomic DNA sequence analysis between faecal and environmental strains and also using a literature-based strategy. PCR assays were designed for each gene, and used to screen 107 faecal strains from various hosts and 106 environmental strains from surface water and sediment. While none of the 14 accessory genes were ecotype-specific, six of the genes were ecotype-enriched. Specifically, toxin-antitoxin system genes were more abundant among faecal strains, whereas genes involved in iron acquisition, complement resistance/surface exclusion, and biofilm formation were more abundant among environmental strains. These six genes were used to form composite fingerprints which revealed the presence of several ecotype-specific and -enriched fingerprints. Notably, some of the environmental strain-specific or -enriched fingerprints consisted of strains putatively belonging to clade ET-1, which has been previously recognized as a naturalized subpopulation.
  
  
  CONCLUSIONS
  Unlike single genes which did not reliably distinguish between faecal and naturalized phylogroup B1 E. coli strains, composite fingerprints of ecotype-enriched accessory genes may offer a novel method for distinguishing between these two populations.
  
  
  CONCLUSIONS
  Accessory gene fingerprinting may have important practical implications for improving the specificity of methods that are widely used for quantifying and identifying the sources of faecal contamination in surface water.
authors: Alberta Agriculture and Rural Development, Lethbridge, AB, Canada.
authors: L D
authors: LD
authors: Tymensen
authors: Umwelt-und Ingenieurtechnik GmbH, Dresden, Germany.
authors: F
authors: F
authors: Pyrdok
authors: Alberta Agriculture and Rural Development, Lethbridge, AB, Canada.
authors: D
authors: D
authors: Coles
authors: Alberta Environment and Sustainable Resource Development, Calgary, AB, Canada.
authors: W
authors: W
authors: Koning
authors: Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
authors: T A
authors: TA
authors: McAllister
authors: Alberta Agriculture and Rural Development, Lethbridge, AB, Canada.
authors: C C
authors: CC
authors: Jokinen
authors: Molecular Research LP, Shallowater, TX, USA.
authors: S E
authors: SE
authors: Dowd
authors: Department of Public Health Sciences, University of Alberta, Edmonton, AB, Canada.
authors: N F
authors: NF
authors: Neumann
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods*; D016172:DNA Fingerprinting / Q000379:methods*; D004926:Escherichia coli / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism; D005243:Feces / Q000382:microbiology; D005618:Fresh Water / Q000382:microbiology*; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction
chemical_list: D029968:Escherichia coli Proteins
keywords: E. coli; enteric bacteria; environmental/recreational water; indicators; water quality