Defining the Phylogenomics of Shigella Species: a Pathway to Diagnostics

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 theShigellaspecies have been completed. The goal of this study was to characterize the genomic diversity ofShigellaspecies through sequencing of 55 isolates representing members of each of the fourShigellaspecies:S. flexneri,S. sonnei,S. boydii, andS. dysenteriae. Phylogeny inferred from 336 availableShigellaandEscherichia coligenomes defined exclusive clades ofShigella; conserved genomic markers that can identify each clade were then identified. PCR assays were developed for each clade-specific marker, which was combined with an amplicon for the conservedShigellainvasion antigen, IpaH3, into a multiplex PCR assay. This assay demonstrated high specificity, correctly identifying 218 of 221 presumptiveShigellaisolates, and sensitivity, by not identifying any of 151 diverseE. coliisolates incorrectly asShigella. This new phylogenomics-based PCR assay represents a valuable tool for rapid typing of uncharacterizedShigellaisolates and provides a framework that can be utilized for the identification of novel genomic markers from genomic data.