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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety & Quality Research » Research » Publications at this Location » Publication #315666

Research Project: Exploring Genomic Differences and Ecological Reservoirs To Control Foodborne Pathogens

Location: Meat Safety & Quality Research

Title: Comparative analysis of twenty-four complete aenome aequences of Salmonella enterica Serotypes Anatum, Montevideo, Typhimurium and Newport isolated from ground beef or asymptomatic cattle on farm or at harvest

Author
item Harhay, Dayna
item Bono, James - Jim
item Smith, Timothy - Tim
item Kalbfleisch, T - University Of Louisville
item Kelley, C - University Of Louisville
item Wang, Rong
item Harhay, Gregory

Submitted to: American Society for Microbiology General Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 3/31/2015
Publication Date: 5/1/2015
Citation: Harhay, D.M., Bono, J.L., Smith, T.P., Kalbfleisch, T., Kelley, C., Wang, R., Harhay, G.P. 2015. Comparative analysis of twenty-four complete aenome aequences of Salmonella enterica Serotypes Anatum, Montevideo, Typhimurium and Newport isolated from ground beef or asymptomatic cattle on farm or at harvest [abstract]. American Society for Microbiology 115th General Meeting. Poster No. 397, Session 029.

Interpretive Summary:

Technical Abstract: Salmonella enterica subsp. enterica are a versatile group of bacteria with a wide range of variation in virulence potential. Complete S. enterica genome sequences available to date are primarily of strains isolated from humans or of serotypes that commonly cause human disease. To facilitate genomic comparisons of Salmonella from different ends of the virulence spectrum, we sequenced and de novo assembled complete genome sequences of twenty-four S. enterica strains, six each of serotypes Anatum, Montevideo, Typhimurium and Newport, isolated from ground beef or asymptomatic cattle on farm or at harvest. Genomic DNA was sequenced using Pacific Bioscience RS technology with C1 chemistry. Error corrected sequence reads (14 – 28 fold coverage per genome) were assembled using the Celera assembler version 7, which produced a single large contig for each isolate (on average 4.9 Mbp) that was validated and improved using Quiver. For all isolates, a self/self dot plot of the consensus sequence was used to identify overlap between the ends of the contig, consistent with a circular chromosome. Duplicated sequence was removed to generate a circularized sequence. The origin of replication was approximated using OriFinder and a new, linear model of the chromosome generated using this origin position. A local instance of Do-It-Yourself Annotator (DIYA) was used to annotate each circularized chromosome. Annotated sequence files were uploaded to geneious© v 7.1 and the EDGAR server (https://edgar.computational.bio.uni-giessen.de) for alignment and comparative analyses. Phylogenetic tree construction, core genome, and pan genome analyses were performed. Data were further mind for potential functional differences using Blast2GO, as well as for CRISPR regions and phage content. Comparative analyses revealed core genome elements that differentiate between serotypes, but also variable regions within serotype, likely under lineage-specific selective pressure. These included differences in Salmonella pathogenicity island gene content, fimbral gene clusters, two component systems, and metabolic pathways, including allantoin metabolism, PTS components, purine degradation, iron uptake and heavy-metal resistance. The differences observed and possible effects on niche specificity will be discussed.