Skip to main content
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

2017 Annual Report

4. Accomplishments
1. Levels of antimicrobial resistance in meats from animals produced with and without antibiotics. Meats produced from animals "raised without antibiotics" (RWA) are perceived to harbor lower levels of antimicrobial resistance than meats from animals produced with no restrictions on antimicrobial use ("Conventional"). Additionally, risk-benefit modeling requires concentrations of antimicrobial resistant bacteria and antimicrobial resistance genes. ARS scientists in Clay Center, Nebraska determined prevalence and concentrations of antimicrobial resistant bacteria and the levels of 10 antimicrobial resistance genes in ground beef and pork chops from animals either raised without antibiotics or conventionally. Generally, levels of antimicrobial resistance were similar between meats from animals raised with and without antimicrobials. These results demonstrate that conventional beef and pork products do not pose a greater risk of exposure to antimicrobial resistance than RWA products.

2. Computer modeling to predict the zoonotic potential of E. coli O157 cattle isolates. Conventional genome sequence-based analyses predict that the majority of E. coli O157 strains from cattle can cause infections in humans, especially if they belong to one of two established groups. ARS scientist in Clay Center, Nebraska, with collaborators in Scotland used genome sequence with computer modeling to successfully predict the human infection potential of cattle E. coli O157 isolates. Only a small subset of strains (<10%) from the bovine reservoir are likely to cause human disease. This finding has potentially important implications for public health as herds infected only with these virulent strains could be targeted for control.

Review Publications
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.

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.

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.

Lupolova, N., Dallman, T.J., Matthews, L., Bono, J.L., Gally, D.L. 2016. Support vector machine applied to predict the zoonotic potential of E. coli O157 cattle isolates. Proceedings of the National Academy of Sciences. 113(40):11312-11317. doi:10.1073/pnas.1606567113.

Miller, W.G., Yee, E., Lopes, B.S., Chapman, M.H., Huynh, S., Bono, J.L., Parker, C., Strachan, N., Forbes, K.J. 2017. Comparative genomic analysis identifies a Campylobacter clade deficient in selenium metabolism. Genome Biology and Evolution. doi: 10.1093/gbe/evx093.

Miller, W.G., Yee, E., Bono, J.L. 2017. Complete genome sequence of the Campylobacter helveticus type strain ATCC 51209T. Genome Announcements. 5(21): e00398-17.

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.

Miller, W.G., Yee, E., Revez, J., Bono, J.L., Rossi, M. 2017. Complete genome sequence of the Campylobacter cuniculorum type strain LMG 24588. Genome Announcements. 5:e00543-17.