title: 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 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.
authors.affiliation: University of Maryland School of Medicine, Institute for Genome Sciences, Department of Microbiology and Immunology, Baltimore, Maryland, USA Translational Genomics Research Institute, Flagstaff, Arizona, USA Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA.
authors.forename: Jason W
authors.initials: JW
authors.lastname: Sahl
authors.affiliation: University of Maryland School of Medicine, Institute for Genome Sciences, Department of Microbiology and Immunology, Baltimore, Maryland, USA.
authors.forename: Carolyn R
authors.initials: CR
authors.lastname: Morris
authors.affiliation: University of Maryland School of Medicine, Institute for Genome Sciences, Department of Microbiology and Immunology, Baltimore, Maryland, USA.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Emberger
authors.affiliation: University of Maryland School of Medicine, Institute for Genome Sciences, Department of Microbiology and Immunology, Baltimore, Maryland, USA.
authors.forename: Claire M
authors.initials: CM
authors.lastname: Fraser
authors.affiliation: KEMRI-CDC Kisumu, Kisumu, Kenya.
authors.forename: John Benjamin
authors.initials: JB
authors.lastname: Ochieng
authors.affiliation: KEMRI-CDC Kisumu, Kisumu, Kenya.
authors.forename: Jane
authors.initials: J
authors.lastname: Juma
authors.affiliation: CDC Kenya, KEMRI Headquarters, Nairobi, Kenya.
authors.forename: Barry
authors.initials: B
authors.lastname: Fields
authors.affiliation: CDC Kenya, KEMRI Headquarters, Nairobi, Kenya.
authors.forename: Robert F
authors.initials: RF
authors.lastname: Breiman
authors.affiliation: National Microbiology, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
authors.forename: Matthew
authors.initials: M
authors.lastname: Gilmour
authors.affiliation: Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA.
authors.forename: James P
authors.initials: JP
authors.lastname: Nataro
authors.affiliation: University of Maryland School of Medicine, Institute for Genome Sciences, Department of Microbiology and Immunology, Baltimore, Maryland, USA drasko@som.umaryland.edu.
authors.forename: David A
authors.initials: DA
authors.lastname: Rasko
mesh_terms: D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004405:Dysentery, Bacillary / Q000175:diagnosis* / Q000382:microbiology; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D010802:Phylogeny; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D012760:Shigella / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*
chemical_list: D004269:DNA, Bacterial