Defining the phylogenomics of Shigella species: A pathway to diagnostics

Sahl, Jason W. and Morris, Carolyn R. and Emberger, Jennifer and Fraser, Claire M. and Ochieng, John Benjamin and Juma, Jane and Fields, Barry and Breiman, Robert F. and Gilmour, Matthew and Nataro, James P. and Rasko, David A. (2015) Defining the phylogenomics of Shigella species: A pathway to diagnostics. Journal of Clinical Microbiology, 53 (3). pp. 951-960. ISSN 1098-660X

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Abstract

Shigellae cause significant diarrheal disease and mortality in humans, as there are approximately 163 million episodes of shigellosis and 1.1 million deaths annually. While significant strides have been made in the understanding of the pathogenesis, few studies on the genomic content of the Shigella species have been completed. The goal of this study was to characterize the genomic diversity of Shigella species through sequencing of 55 isolates representing members of each of the four Shigella species: S. flexneri, S. sonnei, S. boydii, and S. dysenteriae. Phylogeny inferred from 336 available Shigella and E. coli genomes defined exclusive clades of Shigella; conserved genomic markers were then identified that can identify each clade. Polymerase chain reaction (PCR) assays were developed for each clade-specific marker, which was combined with an amplicon for the conserved Shigella invasion antigen, IpaH3, into a multiplex PCR assay. This assay demonstrated high specificity, correctly identifying 218 of 221 presumptive Shigella isolates, and sensitivity, by not identifying any of 151 diverse E. coli isolates incorrectly as Shigella. This new phylogenomic-based PCR assay represents a valuable tool for rapid typing of uncharacterized Shigella isolates and provides a framework that can be utilized for the identification of novel genomic markers from genomic data.

Item Type:	Article
Publisher’s Statement:	Copyright © 2015, American Society for Microbiology. All Rights Reserved.
ID number or DOI:	10.1128/JCM.03527-14
Keywords:	Shigella; phylogenomics; shigellosis; pathogenesis; genomic diversity; pathogens;
Subjects:	Q Science > QH Natural history > QH426 Genetics Q Science > QR Microbiology
NAU Depositing Author Academic Status:	Faculty/Staff
Department/Unit:	Research Centers > Center for Microbial Genetics and Genomics
Date Deposited:	16 Oct 2015 23:33
URI:	http://openknowledge.nau.edu/id/eprint/845

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