Whole genome DNA sequence analysis of Salmonella Enterica subspecies isolated from environmental soil and fecal samples in Western North Carolina

WCU Author/Contributor (non-WCU co-authors, if there are any, appear on document)
David Austin Russell (Creator)
Western Carolina University (WCU )
Web Site: http://library.wcu.edu/
Mark Wilson

Abstract: Foodborne bacterial pathogens like Salmonella genera remain of interest to regulatory agencieslike the FDA and CDC. As a foodborne pathogen, capable of causing serious illness in bothhuman and non-human animals, the CDC has listed Salmonella spp. as potential bioterrorismagents. From a forensic perspective, accurate and rapid identification of Salmonella subspecies isessential for successful investigation of foodborne outbreaks or suspected biocrimes. Massivelyparallel sequencing (MPS) provides investigators with a streamlined, cost-effective method torapidly sequence the whole bacterial genome. To study the genetic variation of naturallyoccurring Salmonella spp., environmental samples were collected from areas around freshwaterlakes, rivers and ponds in the Piedmont and mountains of western North Carolina. NineteenSalmonella isolates were sequenced using the Illumina MiSeq producing high quality sequencedata that were submitted to NCBI in an effort to build a comprehensive database containingwhole genome sequences of bacterial pathogens. Distance–based phylogenetic trees were createdusing the sequence information. This method was shown to be susceptible to the quality of thegiven sequence data. kSNP, a SNP analysis program to create phylogenetic trees, was shown toproduce trees of similar quality without the influences of sequence quality as found in distance-based trees. Ultimately, the databases generated from MPS data can serve as a repository of phylogenetic information and population data to most effectively answer questions germane tobacterial forensics, such as identifying the source of a foodborne outbreak

Additional Information

Language: English
Date: 2015
Bacterial forensics, GenomeTrackr, Illumina, Massively parallel sequencing, NCBI, Salmonella Enterica
Salmonella -- North Carolina, Western
Salmonella -- North Carolina -- Piedmont Triad
Environmental sampling -- North Carolina -- Piedmont Triad
Environmental sampling -- North Carolina, Western
Nucleotide sequence -- Data processing

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