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United States Department of Agriculture

Agricultural Research Service

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

Location: Meats Safety & Quality Research

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

Evaluation of Salmonella biofilm cell transfer from contact surfaces to beef products - (Abstract Only)
Wang, R., King, D.A., Harhay, D.M., Arthur, T.M. 2016. Evaluation of Salmonella biofilm cell transfer from contact surfaces to beef products. [Abstract] International Association for Food Protection. Supp. A(79):102. P1-64.

Mobilome differences between Salmonella enterica serovars Anatum and Typhimurium isolated from cattle and humans and potential impact on virulence - (Abstract Only)
Nguyen, S.V., Bono, J.L., Smith, T.P.L., Kelley, C.M., Wang, R., Harhay, G.P., Harhay, D.M. 2016. Mobilome differences between Salmonella enterica serovars Anatum and Typhimurium isolated from cattle and humans and potential impact on virulence. [Abstract] In proceedings: 60th Wind River Conference on Procaryotic Biology, 2016 June 1-5. Estes Park, Colorado. p. 67.

Diagnostic accuracy of rectoanal mucosal swab of feedlot cattle for detection and enumeration of Salmonella enterica Reprint Icon - (Peer Reviewed Journal)
Agga, G.E., Arthur, T.M., Schmidt, J.W., Wang, R., Harhay, D.M. 2016. Diagnostic accuracy of rectoanal mucosal swab of feedlot cattle for detection and enumeration of Salmonella enterica. Journal of Food Protection. 79(4):531-537. doi:10.4315/0362-028X.JFP-15-409.

Complete closed genome sequences of Salmonella enterica subsp. enterica serotypes Anatum, Montevideo, Typhimurium and Newport, isolated from beef, cattle, and humans Reprint Icon - (Peer Reviewed Journal)
Harhay, D.M., Bono, J.L., Smith, T.P., Fields, P.I., Dinsmore, B.A., Santovenia, M., Kelley, C.M., Wang, R., Harhay, G.P. 2016. Complete closed genome sequences of Salmonella enterica subsp. enterica serotypes Anatum, Montevideo, Typhimurium and Newport, isolated from beef, cattle, and humans. Genome Announcements. 4(1):e01683-15. doi:10.1128/genomeA.01683-15.

Comparison of O-antigen gene cluster from E. coli O157 from human and non-human strains - (Abstract Only)
Silva, N., Castillo, C., Bono, J.L. 2015. Comparison of O-antigen gene cluster from E. coli O157 from human and non-human strains. [abstract] Biomicroworld Proceedings. Session:7, code 609. Available: http://www.formatex.info/biomicroworld2015/acceptedabstracts.php

Pharmacokinetics and pharmacodynamics of gamithromycin in pulmonary epithelial lining fluid in naturally occurring bovine respiratory disease in multisource commingled feedlot cattle Reprint Icon - (Peer Reviewed Journal)
Dedonder, K.D, Apley, M.D., Li, M., Gehring, R., Harhay, D.M., Lubbers, B.V., White, B.J., Capik, S.F., Kukanich, B., Riviere, J.E., Tessman, R.K. 2015. Pharmacokinetics and pharmacodynamics of gamithromycin in pulmonary epithelial lining fluid in naturally occurring bovine respiratory disease in multisource commingled feedlot cattle. Journal of Veterinary Pharmacology and Therapeutics. doi:10.1111/jvp.12267.

Canonical single nucleotide polymorphisms (SNPs) for high-resolution subtyping of Shiga-toxin producing Escherichia coli (STEC) O157:H7 Reprint Icon - (Peer Reviewed Journal)
Griffing, S.M., Maccannell, D.R., Schmidtke, A.J., Freeman, M.M., Hyytia-Trees, E., Gerner-Smidt, P., Ribot, E.M., Bono, J.L. 2015. Canonical single nucleotide polymorphisms (SNPs) for high-resolution subtyping of Shiga-toxin producing Escherichia coli (STEC) O157:H7. PLoS One. 10(7):e0131967. DOI:10.137/journal.pone.0131967.

WGS accurately predicts antimicrobial resistance in Escherichia coli Reprint Icon - (Peer Reviewed Journal)
Tyson, G.H., McDermott, P., Li, C., Chen, Y., Tadesse, D.A., Mukherjee, S., Bodeis-Jones, S., Kabera, C., Gaines, S.A., Loneragan, G.H., Edrington, T.S., Torrence, M., Harhay, D.M., Zhao, S. 2015. WGS accurately predicts antimicrobial resistance in Escherichia coli. Journal of Antimicrobial Chemotherapy. July 2015:1-7.

Sequence of colonization determines the composition of mixed biofilms by Escherichia coli O157:H7 and O111:H8 strains Reprint Icon - (Peer Reviewed Journal)
Wang, R., Kalchayanand, N., Bono, J.L. 2015. Sequence of colonization determines the composition of mixed biofilms by Escherichia coli O157:H7 and O111:H8 strains. Journal of Food Protection. 78(8):1554-1559. DOI: 10.4315/0362-028X.JFP-15-009.

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 Only)
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.

Comparison of whole genome sequences from human and non-human Escherichia coli O26 strains Reprint Icon - (Peer Reviewed Journal)
Norman, K.N., Clawson, M.L., Strockbine, N.N., Mandrell, R.E., Johnson, R., Ziebell, K., Zhao, S., Fratamico, P.M., Stones, R., Allard, M., Bono, J.L. 2015. Comparison of whole genome sequences from human and non-human Escherichia coli O26 strains. Frontiers in Cellular and Infection Microbiology. 5(21). DOI: 10.3389/fcimb.2015.00021.

Genomic comparison of Salmonella enterica serotypes commonly associated with cattle and beef – Analysis of variation in virulence potential - (Abstract Only)
Harhay, D.M., Bono, J.L., Wang, R., Smith, T.P., Harhay, G.P., Kalbfleisch, T., Wheeler, T.L. 2015. Genomic comparison of Salmonella enterica serotypes commonly associated with cattle and beef – Analysis of variation in virulence potential. [Abstract]. Beef Industry Safety Summit. http://www.bifsco.org/2015researchsessionabstracts.aspx.

Examination of the relationship between Salmonella contamination in pre-harvest environments and contamination of bovine peripheral lymph nodes - (Abstract Only)
Harhay, D.M. 2014. Examination of the relationship between Salmonella contamination in pre-harvest environments and contamination of bovine peripheral lymph nodes [abstract]. Recent Advances in Microbial Control (RAMC) 2014. p. 21.

Salmonella spp. in lymph nodes of fed and cull cattle: Relative assessment of risk to ground beef Reprint Icon - (Peer Reviewed Journal)
Li, M., Malladi, S., Hurd, S., Goldsmith, T.J., Harhay, D.M., Loneragan, G. 2015. Salmonella spp. in lymph nodes of fed and cull cattle: Relative assessment of risk to ground beef. Food Control. 50:423-434.

Prevalence of Escherichia coli 0157:H7 and Salmonella in camel, cattle, goat and sheep harvested for meat in Riyadh Reprint Icon - (Peer Reviewed Journal)
Bosilevac, J.M., Gassem, M.A., Al Sheddy, I.A., Almaiman, S.A., Al-Mohizea, I., Alowaimer, A., Koohmaraie, M. 2015. Prevalence of Escherichia coli 0157:H7 and Salmonella in camel, cattle, goat and sheep harvested for meat in Riyadh. Journal of Food Protection. 78(1):89-96.

Biofilm formation and sanitizer resistance of Escherichia coli 0157:H7 strains isolated from "High Event Period" meat contamination Reprint Icon - (Peer Reviewed Journal)
Wang, R., Kalchayanand, N., King, D.A., Luedtke, B.E., Bosilevac, J.M., Arthur, T.M. 2014. Biofilm formation and sanitizer resistance of Escherichia coli 0157:H7 strains isolated from "High Event Period" meat contamination. Journal of Food Protection. 77(11):1982-1987.

Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems - (Other)
Franz, E., Delaquis, P., Stefano, M., Beutin, L., Gobius, K., Rasko, D., Bono, J.L., French, N., Osek, J., Lindstedt, B., Muniesa, M., Manning, S., LeJeune, J., Callaway, T.R., Beatson, S., Eppinger, M., Dallman, T., Forbes, K., Aarts, H., Pearl, D., Strachan, N.J. 2014. Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems. International Journal of Food Microbiology. 187:57-72.

Effect of direct-fed microbial supplementation on the presence of Salmonella enterica in bovine peripheral lymph nodes - (Abstract Only)
Harhay, D.M., Loneragan, G.H., Arthur, T.M., Bosilevac, J.M., Kalchayanand, N., Schmidt, J.W., Wang, R., Wheeler, T.L., Kolath, B., Theunick, D., Riemann, M., Schaefer, D., Brown, T. 2014. Effect of direct-fed microbial supplementation on the presence of Salmonella enterica in bovine peripheral lymph nodes. [Abstract]. International Association for Food Protection. Supp. A(77):211-212. P3-65.

Examination of predictors of Salmonella enterica contamination in cattle feedlot environments - (Abstract Only)
Harhay, D.M., Arthur, T.M., Schmidt, J.W., Wang, R., Kalchayanand, N., Bosilevac, J.M., Edrington, T.S., Loneragan, G., Wheeler, T.L. 2014. Examination of predictors of Salmonella enterica contamination in cattle feedlot environments. [Abstract] Beef Industray Safety Summit. Available: www.bifsco.org/attendees.aspx.

Lineage and genogroup-defining single nucleotide polymorphisms of Escherichia coli 0157:H7 Reprint Icon - (Peer Reviewed Journal)
Jung, W.K., Bono, J.L., Clawson, M.L., Leopold, S.R., Shringi, S., Besser, T.E. 2013. Lineage and genogroup-defining single nucleotide polymorphisms of Escherichia coli 0157:H7. Applied and Environmental Microbiology. 79(22):7036-7041.

Substantial within-Animal Diversity of Salmonella Isolates from Lymph Nodes, Feces, and Hides of Cattle at Slaughter Reprint Icon - (Peer Reviewed Journal)
Gragg, S.E., Loneragan, G.H., Nightingale, K.K., Harhay, D.M., Ruiz, H., Elder, J.R., Garcia, L.G., Miller, M.F., Echeverry, A., Porras, R., Brashears, M. 2013. Substantial within-Animal Diversity of Salmonella Isolates from Lymph Nodes, Feces, and Hides of Cattle at Slaughter. Applied and Environmental Microbiology. 79(15):4744-4750.

Phylogenetic classification of Escherichia coli O26 strains from human, animals, and environmental origins using nucleotide polymorphisms - (Abstract Only)
Norman, K.N., Clawson, M.L., Strockbine, N.A., Mandrell, R.E., Johnson, R., Ziebell, K., Zhao, S., Fratamico, P.M., Stones, R., Allard, M., Bono, J.L. 2013. Phylogenetic classification of Escherichia coli O26 strains from human, animals, and environmental origins using nucleotide polymorphisms. American Society for Microbiology General Meeting. Poster No. 484 p. 40.

Longitudinal concentrations of antibiotic resistant Escherichia coli in feces do not correspond to the patterns of antibiotic use at a cattle feedlot - (Abstract Only)
Schmidt, J.W. 2013. Longitudinal concentrations of antibiotic resistant Escherichia coli in feces do not correspond to the patterns of antibiotic use at a cattle feedlot. American Society for Microbiology Annual Meeting. Poster No. 15 p. 101.

Salmonella virulence, genomics and interactions with the immune system - (Proceedings)
Harhay, D.M., Smith, T.P., Harhay, G.P., Bono, J.L., Bosilevac, J.M. 2013. Salmonella virulence, genomics and interactions with the immune system. Meeting Abstract. The Beef Industry Safety Summit, March 13-15, 2013, Dallas Texas, FLASHDRIVE.

Salmonella in lymph nodes of cull and fed cattle at harvest - (Abstract Only)
Webb, H.E., Harhay, D.M., Gragg, S.E., Brashears, M.M., Nightingale, K.K., Arthur, T.M., Bosilevac, J.M., Kalchayanand, N., Schmidt, J.W., Wang, R., Lonergan, G.H. 2013. Salmonella in lymph nodes of cull and fed cattle at harvest. IN: Proceedings of The Beef Industry Summit 2013, March 13-15, 2013, Dallas Texas, 2013 FLASHDRIVE.

Influence of therapeutic ceftiofur treatments of feedlot cattle on fecal and hide prevalences of commensal Escherichia coli resistant to expanded-spectrum cephalosporins, and molecular characterization of resistant isolates Reprint Icon - (Peer Reviewed Journal)
Schmidt, J.W., Griffin, D., Kuehn, L.A., Harhay, D.M. 2013. Influence of therapeutic ceftiofur treatments of feedlot cattle on fecal and hide prevalences of commensal Escherichia coli resistant to expanded-spectrum cephalosporins, and molecular characterization of resistant isolates. Applied and Environmental Microbiology. 79(7):2273-2283.

Cross-sectional study examining Salmonella enterica carriage in subiliac lymph nodes of cull and feedlot cattle at harvest Reprint Icon - (Peer Reviewed Journal)
Gragg, S.E., Loneragan, G.H., Brashears, M.M., Arthur, T.M., Bosilevac, J.M., Kalchayanand, N., Wang, R., Schmidt, J.W., Brooks, J., Shackelford, S.D., Wheeler, T.L., Brown, T.R., Edrington, T.S., Harhay, D.M. 2013. Cross-sectional study examining Salmonella enterica carriage in subiliac lymph nodes of cull and feedlot cattle at harvest. Foodborne Pathogens and Disease. 10(4):368-374.

Dual-serotype biofilm formation by Shiga toxin-producing Escherichia coli 0157:H7 and 026:H11 strains - (Peer Reviewed Journal)
SWang, R., Kalchayanand, N., Schmidt, J.W., Bosilevac, J.M., Bono, J.L. 2012. Dual-serotype biofilm formation by Shiga toxin-producing Escherichia coli 0157:H7 and 026:H11 strains. Applied and Environmental Microbiology. 78(17):6341-6344.

Association of nucleotide polymorphisms within the O-antigen gene cluster of Escherichia coli O26, O45, O103, O111, O121, and O145 with serogroups and genetic subtypes Reprint Icon - (Peer Reviewed Journal)
Norman, K.N., Strockbine, N.A., Bono, J.L. 2012. Association of nucleotide polymorphisms within the O-antigen gene cluster of Escherichia coli O26, O45, O103, O111, O121, and O145 with serogroups and genetic subtypes. Applied and Environmental Microbiology. 78(18):6689-6703.

Biofilm formation by Shiga toxin–producing Escherichia coli O157:H7 and non-O157 strains and their tolerance to sanitizers commonly used in the food processing environment Reprint Icon - (Peer Reviewed Journal)
Wang, R., Bono, J.L., Kalchayanand, N., Shackelford, S.D., Harhay, D.M. 2012. Biofilm formation by Shiga toxin–producing Escherichia coli O157:H7 and non-O157 strains and their tolerance to sanitizers commonly used in the food processing environment. Journal of Food Protection. 75(8):1418-1428.

Prevalence of lactose fermenting coliforms resistant to third generation cephalosporins in cattle feedlot throughout a production cycle and molecular characterization of resistant isolates - (Abstract Only)
Schmidt, J.W., Kuehn, L.A., Griffin, D., Harhay, D.M. 2012. Prevalence of lactose fermenting coliforms resistant to third generation cephalosporins in cattle feedlot throughout a production cycle and molecular characterization of resistant isolates [abstract]. International Association for Food Protection. p. 148-149. Abstract No. P2-95.

Phylogeny of Shiga toxin-producing Escherichia coli O157 isolated from cattle and clinically ill humans Reprint Icon - (Peer Reviewed Journal)
Bono, J.L., Smith, T.P., Keen, J.E., Harhay, G.P., McDaneld, T.G., Mandrell, R.E., Jung, W., Besser, T.E., Gerner-Smidt, P., Bielaszewska, M., Karch, H., Clawson, M.L. 2012. Phylogeny of Shiga toxin-producing Escherichia coli O157 isolated from cattle and clinically ill humans. Molecular Biology and Evolution. 29(8):2047-2062. doi: 10.1093/molbev/mss072.

Biofilm formation by foodborne pathogens and their resistance to sanitization - (Abstract Only)
Wang, R., Bono, J.L., Kalchayanand, N., Shackelford, S.D., Harhay, D.M. 2012. Biofilm formation by foodborne pathogens and their resistance to sanitization. [Abstract]. Americian Society for Microbiology, 112th General Meeting. Poster No 2154, session 170.

Last Modified: 2/23/2016
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