ARS | Publication request: Phylogenetic Classification of Escherichia coli O157:H7 Isolates of Human and Bovine Origin Using a Novel Set of Nucleotide Polymorphisms

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: February 20, 2009
Publication Date: May 1, 2009
Citation: Clawson, M.L., Keen, J.E., Smith, T.P., Durso, L.M., McDaneld, T.G., Mandrell, R.E., Davis, M.A., Bono, J.L. 2009. Phylogenetic Classification of Escherichia coli O157:H7 Isolates of Human and Bovine Origin Using a Novel Set of Nucleotide Polymorphisms [abstract]. American Society for Microbiology. Abstract No. Z-006. p. 612. 2009 CDROM.

Technical Abstract: Background Cattle are a reservoir of Shiga toxin-producing Escherichia coli O157:H7 (STEC O157), and are known to harbor subtypes not typically found in clinically-ill humans. Consequently, nucleotide polymorphisms previously discovered via isolates originating from human outbreaks may be restricted in their ability to distinguish STEC O157 genetic subtypes present in cattle. The objectives of this study were to: 1) identify nucleotide polymorphisms in a diverse sampling of human and bovine STEC O157 isolates, 2) classify isolates of either bovine or human origin by polymorphism-derived genotypes, and 3) compare the genotype diversity with pulsed-field gel electrophoresis (PFGE), a method currently used for assessing STEC O157:H7 diversity. Results High-throughput 454 sequencing of pooled STEC O157 isolate DNAs from human clinical cases (n=91) and cattle (n=102) identified 16,218 putative polymorphisms. From those, 178 were selected primarily within genomic regions conserved across E. coli serotypes and genotyped in 261 STEC O157 isolates. Forty-two unique genotypes were observed that are tagged by a minimal set of 32 polymorphisms. Phylogenetic trees of the genotypes are divided into clades that represent isolates of cattle origin, or cattle and human origin. Although PFGE diversity surpassed genotype diversity overall, ten PFGE patterns each occurred with multiple isolates having different genotypes. Conclusions Deep sequencing of pooled STEC O157 DNAs proved highly effective in polymorphism discovery. A polymorphism set has been identified that characterizes genetic diversity within STEC O157 isolates of bovine origin, and a subset observed in human isolates. The set may complement current techniques used to classify isolates implicated in disease outbreaks.