Comprehensive Genome Sequencing of Nontyphoidal Salmonellae

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Goals

The nontyphoidal Salmonella are the leading cause of bacterial food borne illness in humans, making these pathogens an immediate biomedical, public health, and biodefense concern. Genome comparisons of Salmonella serovars sequenced to date reveal that extant sequences do not encompass the gene diversity present at the subspecies level. The goal of this project is to understand the pathogenic and antimicrobial resistance properties of Salmonella enterica by sequencing, annotating, and analyzing Salmonella enterica subsp. enterica serovars of public health importance, including those that may be used by terrorists as agents for deliberate release. The strains chosen for genomic analysis were selected based on an extensive examination of their potential to provide information needed for examining pathogenicity, transmission, origin, ecology, evolution, and dissemination of antibiotic resistance. Nine strains will be sequenced to closure, among which are four strains exhibiting multiple-drug resistance (MDR), as such strains are extant among human clinical isolates and pose an added threat of higher morbidity and mortality. An additional eight strains will be sequenced to draft coverage, providing valuable information into the genomic diversity of several clinically relevant serovars. This project will contribute to the development of better diagnostic and therapeutic capabilities for public health responders and the military, improving national bio-preparedness. In addition, this work will provide a genetic "background" that will facilitate bioforensics investigations in the event of an attack using Salmonella.

Serovar/Strain Selection

Following consultation with the Salmonella community, 17 strains of nontyphoidal Salmonella were selected for genome sequencing. The strains encompass a wide genomic diversity, as assessed by a variety of molecular and phylogenetic analyses, and were chosen for their suitability to broadly represent the genus. Nine strains will be sequenced to closure, with the remaining strains sequenced to draft level (8X) coverage. In several cases, paired analysis of antibiotic-resistant and susceptible strains of a serotype will be completed; in each of these cases, the multi-drug resistant (MDR) strain will be sequenced to closure with the susceptible strain sequenced to draft level coverage.