Defining the phylogenomics of Shigella species: a pathway to diagnostics

Jason W Sahl, Carolyn R Morris, Jennifer Emberger, Claire M Fraser, John Benjamin Ochieng, Jane Juma, Barry Fields, Robert F Breiman, Matthew Gilmour, James P Nataro, David A Rasko

Research output: Contribution to journalArticlepeer-review

59 Citations (Scopus)


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 Escherichia coli genomes defined exclusive clades of Shigella; 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 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 phylogenomics-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.

Original languageEnglish
Pages (from-to)951-960
Number of pages10
JournalJournal of Clinical Microbiology
Issue number3
Early online date19 Feb 2015
Publication statusPublished - Mar 2015


  • Cluster Analysis
  • DNA, Bacterial/chemistry
  • Dysentery, Bacillary/diagnosis
  • Genetic Variation
  • Genome, Bacterial
  • Humans
  • Multiplex Polymerase Chain Reaction/methods
  • Phylogeny
  • Sensitivity and Specificity
  • Sequence Analysis, DNA
  • Shigella/classification

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