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United States Department of Agriculture

Agricultural Research Service

Research Project: PREVENTION AND CHARACTERIZATION OF PERSISTENT COLONIZATION BY E. COLI O157:H7 AND OTHER SHIGA TOXIN-PRODUCING E. COLI (STEC) IN CATTLE Title: Polymorphic amplified typing sequences (PATS) strain typing system accurately discriminates a set of temporally and spatially disparate Escherichia coli (O157) isolates associated with human infection

Authors
item Kudva, Indira
item Smole, Sandra -
item Griffin, Robert -
item Garren, Jeonifer -
item Kalia, Nimisha -
item Murray, Megan -
item John, Manohar -
item Timperi, Ralph -
item Calderwood, Stephen -

Submitted to: The Open Microbiology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 3, 2013
Publication Date: October 31, 2013
Repository URL: http://handle.nal.usda.gov/10113/58034
Citation: Kudva, I.T., Smole, S., Griffin, R.W., Garren, J., Kalia, N., Murray, M., John, M., Timperi, R., Calderwood, S.B. 2013. Polymorphic amplified typing sequences (PATS) strain typing system accurately discriminates a set of temporally and spatially disparate Escherichia coli (O157) isolates associated with human infection. The Open Microbiology Journal. 7:123-129.

Interpretive Summary: Pulsed-field gel electrophoresis (PFGE) is routinely used in most laboratories to develop genomic DNA patterns/fingerprints of bacterial pathogens to identify the sources from which these human disease causing organisms enter the food chain. PFGE relies on the genomic DNA banding pattern following digestion/cleavage with restriction enzymes that have rare/few cleavage sites in the O157 genome. But inherent drawbacks in the technique are leading epidemiologists to other genomic DNA fingerprinting methodologies or to variously modifying the existing PFGE protocol. Polymorphic Amplified Typing Sequences (PATS) is a PCR-based bacterial genomic DNA fingerprinting system that relies on specific DNA sequence variations (polymorphisms) at these rare restriction enzyme cleavage sites, and virulence genes in the O157 genome, to differentiate between related and unrelated O157 bacterial isolates. Previously, PATS was used to effectively fingerprint (type) 46 different O157 isolates associated with various outbreaks and human disease. Here, we determined whether PATS could reliably type a geographically diverse collection of 48 O157 isolates in a “blind” study (details of isolates withheld until after completion of PATS to remove user biases and mimic real world outbreak situation). Comparison of the PATS results with those obtained using PFGE revealed that both PATS and PFGE distributed the 48 O157 isolates examined into two major groups with the same set of isolates. PATS complemented PFGE and reliably typed all O157 isolates, matching them to their geographic locations. Hence, PATS could have potential as a tool for rapid and unbiased typing of bacterial isolates.

Technical Abstract: In this study, we determined whether Polymorphic Amplified Typing Sequences (PATS), a PCR-based Escherichia coli O157 (O157) strain typing system, could reliably discriminate/relate a geographically diverse collection of O157 isolates. Comparative analyses of results for this “blind” study (details of isolates withheld until after completion of PATS to obviate biases) with those obtained using pulsed-field gel electrophoresis (PFGE) revealed that both PATS and PFGE distributed the 48 O157 isolates examined into two major clades with the same set of isolates. Interestingly, PATS clustered O157 isolates from the same geographical locations better than PFGE. Hence, PATS could have potential as a tool for rapid and unbiased typing of bacterial isolates.

Last Modified: 11/1/2014
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