|Clawson, Michael - Mike|
|KEEN, JAMES - University Of Nebraska|
|Smith, Timothy - Tim|
|DAVIS, MARGARET - Washington State University|
|Bono, James - Jim|
Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/22/2009
Publication Date: 5/22/2009
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 Strains of Human and Bovine Origin Using a Novel Set of Nucleotide Polymorphisms. Genome Biology [serial online]. 10:R56. Available: http://genomebiology.com/2009/10/5/R56.
Interpretive Summary: Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) are a major source of diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome and cause an estimated 73,480 illnesses each year in the United States. Cattle are a reservoir of STEC O157:H7 and are known to harbor subtypes not typically found in clinically-ill humans. To find genetic variation that might explain why some STEC O157 are not found in humans, a diverse collection of STEC O157 isolates originating from both human clinical cases and cattle were subjected to high-throughput sequencing. The genomes of 193 isolates were sequenced and over 16,000 putative nucleotide polymorphisms were identified. Of those, 178 polymorphisms were genotyped in a larger set of 261 isolates. The polymorphisms classify STEC O157 into 42 distinct genetic subtypes that appear unequally in isolates of cattle or human origin, as many of the subtypes were observed exclusively in isolates originating from cattle. It is not clear why STEC O157 with certain genetic subtypes are not typically found in humans. Of the 178 polymorphisms characterized in this study, only 32 are required to detect all 42 genetic subtypes. This system of genetic subtyping may eventually replace Pulsed-Field Gel Electrophoresis as the preferred method for assessing STEC O157 diversity.
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.