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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety & Quality Research » Research » Research Project #430418

Research Project: Genomic and Metagenomic Differences in Foodborne Pathogens and Determination of Ecological Niches and Reservoirs

Location: Meat Safety & Quality Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Complete, closed genome sequences of three Salmonella enterica subsp. enterica Serovar Dublin isolated from cattle at Harvest - (Peer Reviewed Journal)

Comparative genomics of Salmonella enterica serovar Montevideo reveals lineage-specific gene differences that may influence ecological niche association - (Peer Reviewed Journal)
Nguyen, S.V., Harhay, D.M., Bono, J.L., Smith, T.P.L., Fields, P.I., Dinsmore, B.A., Santovina, M., Wang, R., Bosilevac, J.M., Harhay, G.P. 2018. Comparative genomics of Salmonella enterica serovar Montevideo reveals lineage-specific gene differences that may influence ecological niche association. Microbial Genomics. 4:1-17. https://doi.org/10.1099/mgen.0.000202.

Rapid detection and classification of Salmonella enterica shedding in feedlot cattle utilizing Roka Bioscience Atlas Salmonella detection assay for the analysis of rectoanal mucosal swabs Reprint Icon - (Peer Reviewed Journal)
Chaney, W.E, Agga, G.E., Nguyen, S.V., Arthur, T.M., Bosilevac, J.M., Dreyling, E., Rishi, A., Brichta-Harhay, D. 2017. Rapid detection and classification of Salmonella enterica shedding in feedlot cattle utilizing Roka Bioscience Atlas Salmonella detection assay for the analysis of rectoanal mucosal swabs. Journal of Food Protection. 80(10):1760-1767. https://doi.org/10.4315/0362-028X.JFP-17-124.

Whole genome sequencing may not be adequate to determine genome relatedness for surveillance and outbreak investigation of foodborne pathogens - (Abstract Only)
Bono, J.L., Arthur, T.M., Harhay, G.P., Smith, T.P. 2017. Whole genome sequencing may not be adequate to determine genome relatedness for surveillance and outbreak investigation of foodborne pathogens. [Abstract]. 12th Annual Sequencing, Finish, and Analysis in the Future Meeting, PS-2.32. Available: http://www.lanl.gov/conferences/sequencing-finishing-analysis-future/index.php.

Complete genome sequence of the thermotolerant foodborne pathogen Salmonella enterica serovar Senftenberg ATCC 43845 and phylogenetic analysis of loci encoding thermotolerance - (Abstract Only)
Nguyen, S.V., Bono, J.L., Smith, T.P., Harhay, G.P., Harhay, D.M. 2017. Complete genome sequence of the thermotolerant foodborne pathogen Salmonella enterica Serovar Senftenberg ATCC 43845 and phylogenetic analysis of Loci encoding thermotolerance . [Abstract] International Association for Food Protection Proceedings. Session T2-09. Available at: https://iafp.confex.com/iafp/2017/webprogram/authork.html.

Evolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic E. coli O157 by long-read sequencing - (Abstract Only)
Shaaban, S., Dallman, T., McAteer, S., Cowley, L., Jenkins, C., Bono, J.L., Gally, D. 2017. Evolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic E. coli O157 by long-read sequencing. [Abstract]. Microbiology Society Annual Conference 2017, Edinburgh, UK. No. 561.

Genome sequence of the thermotolerant foodborne pathogen Salmonella enterica serovar Senftenberg ATCC 43845 and phylogenetic analysis of Loci encoding increased protein quality control mechanisms - (Peer Reviewed Journal)
Nguyen, S.V., Harhay, G.P., Bono, J.L., Smith, T.P., Harhay, D.M. 2017. Genome sequence of the thermotolerant foodborne pathogen Salmonella enterica serovar Senftenberg ATCC 43845 and phylogenetic analysis of Loci encoding increased protein quality control mechanisms. mSystems 2:e00190-16. doi:10.1128/mSystems.00190-16.

Effect of in-feed Chlortetracycline prophylaxis in beef cattle on levels of 10 antimicrobial resistance genes - (Abstract Only)
Miller, E.W., Agga, G.E., Vikram, A., Arthur, T.M., Schmidt, J.W. 2017. Effect of in-feed Chlortetracycline prophylaxis in beef cattle on levels of 10 antimicrobial resistance genes. [Abstract]. American Society for Microbiology Meeting. p.43, no.13.

Evolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic Escherichia coli O157 by long-read sequencing - (Peer Reviewed Journal)
Shaaban, S., Cowley, L., McAteer, S., Jenkins, C., Dallman, T., Bono, J.L., Gally, D. 2016. Evolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic Escherichia coli O157 by long-read sequencing. Microbial Genomics. doi:10.1099/mgen.0.000096.

Complete, closed genome sequences of 10 Salmonella enterica subsp. enterica serovar Typhimurium strains isolated from human and bovine sources Reprint Icon - (Peer Reviewed Journal)
Nguyen, S.V., Harhay, D.M., Bono, J.L., Smith, T.P.L., Fields, P.I., Dinsmore, B.A., Santovenia, M., Kelley, C.M., Wang, R., Bosilevac, J.M., Harhay, G.P. 2016. Complete, closed genome sequences of 10 Salmonella enterica subsp. enterica serovar Typhimurium strains isolated from human and bovine sources. Genome Announcements. 4(6):e01212-16. doi:10.1128/genomeA.01212-16.

Short-term evolution of Shiga toxin-producing Escherichia coli O157:H7 between two food-borne outbreaks Reprint Icon - (Peer Reviewed Journal)
Cowley, L.A., Dallman, T.J., Fitzgerald, S., Irvine, N., Rooney, P.J., McAteer, S., Day, M., Perry, N.T., Bono, J.L., Jenkins, C., Gally, D. 2016. Short-term evolution of Shiga toxin-producing Escherichia coli O157 between two food-borne outbreaks. Microbial Genomics. doi:10.1099/mgen.0.000084.

Complete and closed genome sequences of 10 Salmonella enterica subsp. enterica serovar Anatum isolated from human and bovine sources Reprint Icon - (Peer Reviewed Journal)
Nguyen, S.V., Harhay, D.M., Bono, J.L., Smith, T.P.L., Fields, P.I., Dinsmore, B.A., Santovenia, M., Kelley, C.M., Wang, R., Bosilevac, J.M., Harhay, G.P. 2016. Complete and closed genome sequences of 10 Salmonella enterica subsp. enterica serovar Anatum isolated from human and bovine sources. Genome Announcements. Vol. 4(3): e00447-16. doi: 10.1128/genomeA.00447-16.