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

Location: Meat Safety and Quality

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

Genome structural variation in Escherichia coli O157:H7 - (Peer Reviewed Journal)
Fitzgerald, S., Lupolova, N., Shaaban, S., Dallman, T.J., Greig, D.Q., Allison, L., Tongue, S.C., Evans, J., Henry, M.K., McNeilly, T., Bono, J.L., Gally, D.L. 2021. Genome structural variation in Escherichia coli O157:H7. Microbial Genomics. 7(11). Article 000682. https://doi.org/10.1099/mgen.0.000682.

Characterisation of early positive mcr-1 resistance gene and plasmidome in Escherichia coli pathogenic strains associated with variable phylogroups under colistin selection - (Peer Reviewed Journal)
Macori, G., Nguyen, S.V., Naithani, A., Hurley, D., Bai, L., El Garach, F., Woehrlé, F., Miossec, C., Roques, B., O'Gaora, P., Bono, J.L., Fanning, S. 2021. Characterisation of early positive mcr-1 resistance gene and plasmidome in Escherichia coli pathogenic strains associated with variable phylogroups under colistin selection. Antibiotics. 10. Article 1041. https://doi.org/10.3390/antibiotics10091041.

Prophage-dependent recombination drives genome structural variation and phenotypic heterogeneity in Escherichia coil O157:H7 - (Pre-print Publication)
Fitzgerald, S.F., Lupolova, N., Shaaban, S., Dallman, T.J., Greig, D., Allison, L., Tongue, S.C., Evans, J., Henry, M.K., McNeilly, T.N., Bono, J.L., Gally, D.L. 2020. Prophage-dependent recombination drives genome structural variation and phenotypic heterogeneity in Escherichia coil O157:H7. bioRxiv. 407981. https://doi.org/10.1101/2020.12.02.407981.

Consecutive treatments with a multicomponent sanitizer inactivate biofilms formed by Escherichia coli O157:H7 and Salmonella enterica and remove biofilm matrix - (Peer Reviewed Journal)
Wang, R., Zhou, Y., Kalchayanand, N., Harhay, D.M., Wheeler, T.L. 2021. Consecutive treatments with a multicomponent sanitizer inactivate biofilms formed by Escherichia coli O157:H7 and Salmonella enterica and remove biofilm matrix. Journal of Food Protection. 84(3):408-417. https://doi.org/10.4315/JFP-20-321.

Rapid estimation of Salmonella enterica contamination level in ground beef – application of the time-to-positivity method using a combination of molecular detection and direct plating - (Peer Reviewed Journal)
Harhay, D.M., Weinroth, M.D., Bono, J.L., Harhay, G.P., Bosilevac, J.M. 2021. Rapid estimation of Salmonella enterica contamination level in ground beef – application of the time-to-positivity method using a combination of molecular detection and direct plating. Food Microbiology. 93. Article 103615. https://doi.org/10.1016/j.fm.2020.103615.

Changes in a closed feedlot Escherchia coli O157:H7 population over 22 years - (Abstract Only)
Weinroth, M., Clawson, M., Arthur, T., Wells, J., Harhay, D., Bono, J. 2020. Changes in a closed feedlot Escherchia coli O157:H7 population over 22 years. [Abstract]. International Association for Food Protection Conference, Cleveland, Ohio, August 2-5 2020. Virtual. Journal of Food Protection. 83(Supplement A):P2-198.

Pathogenomes of atypical non-Shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive phylogenomic analysis using closed genomes - (Peer Reviewed Journal)
Nyong, E.C., Zaia, S.R., Allue-Guardia, A., Rodriguez, A.L., Irion-Byrd, Z., Koenig, S.S.K., Feng, P., Bono, J.L., Eppinger, M. 2020. Pathogenomes of atypical non-Shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive phylogenomic analysis using closed genomes. Frontiers in Microbiology. 11:619. https://doi.org/10.3389/fmicb.2020.00619.

Prophage variation and rearrangements in E. coli O157 and implications for zoonotic threat - (Abstract Only)

Genomic-based identification of environmental and clinical Listeria monocytogenes strains associated with an abortion outbreak in beef heifers - (Peer Reviewed Journal)
Whitman, K.J., Bono, J.L., Clawson, M.L., Loy, J.D., Bosilevac, J.M., Arthur, T.M., Ondrak, J.D. 2020. Genomic-based identification of environmental and clinical Listeria monocytogenes strains associated with an abortion outbreak in beef heifers. BMC Veterinary Research. 16:70. https://doi.org/10.1186/s12917-020-2276-z.

Effectiveness and functional mechanism of a multicomponent sanitizer against biofilms formed by Escherichia coli O157:H7 and five Salmonella serotypes prevalent in the meat industry - (Peer Reviewed Journal)
Wang, R., Zhou, Y., Kalchayanand, N., Harhay, D.M., Wheeler, T.L. 2020. Effectiveness and functional mechanism of a multicomponent sanitizer against biofilms formed by Escherichia coli O157:H7 and five Salmonella serotypes prevalent in the meat industry. Journal of Food Protection. 83(4):568-575. https://doi.org/10.4315/0362-028X.JFP-19-393.

Shiga toxin sub-type 2a increases the efficiency of Escherichia coli O157 transmission between animals and restricts epithelial regeneration in bovine enteroids - (Peer Reviewed Journal)
Fitzgerald, S.F., Beckett, A.E., Palarea-Albaladejo, J., McAteer, S., Shaaban, S., Morgan, J., Ahmad, N.I., Young, R., Mabbott, N.A., Morrison, L., Bono, J.L., Gally, D.L., McNeilly, T.N. 2019. Shiga toxin sub-type 2a increases the efficiency of Escherichia coli O157 transmission between animals and restricts epithelial regeneration in bovine enteroids. PLoS Pathogens. 15(10):e1008003. https://doi.org/10.1371/journal.ppat.1008003.

Cropland amendment with beef cattle manure minimally affects antimicrobial resistance - (Peer Reviewed Journal)
Miller, E., Spiehs, M., Arthur, T.M., Woodbury, B., Cortus, E., Chatterjee, A., Rahman, S., Schmidt, J.W. 2019. Cropland amendment with beef cattle manure minimally affects antimicrobial resistance. Journal of Environmental Quality. 48:1683-1693. https://doi.org/10.2134/jeq2019.02.0042.

Closed genome sequence of Escherichia coli K-12 group strain C600 - (Peer Reviewed Journal)
Allue-Guardia, A., Nyong, E.C., Koenig, S.S.K., Vargas, S.M., Bono, J.L., Eppinger, M. 2019. Closed genome sequence of Escherichia coli K-12 group strain C600. Microbiology Resource Announcements. 8:e1052-18. https://doi.org/10.1128/MRA.01052-18.

Complete genome sequences of four Salmonella enterica strains (including those of serotypes Montevideo, Mbandaka, and Lubbock) isolated from peripheral lymph nodes of healthy cattle - (Peer Reviewed Journal)
Bugarel, M., Cook, P.W., Den Bakker, H.C., Harhay, D.M., Nightingale, K.K., Loneragan, G.H. 2019. Complete genome sequences of four Salmonella enterica strains (including those of serotypes Montevideo, Mbandaka, and Lubbock) isolated from peripheral lymph nodes of healthy cattle. Microbiology Resource Announcements. 8(2):e01450-18. https://doi.org/10.1128/MRA.01450-18.

Complete closed genome sequences of three Salmonella enterica subsp. enterica Serovar Dublin strains isolated from cattle at harvest - (Peer Reviewed Journal)
Harhay, D.M., Smith, T.P.L., Harhay, G.P., Loneragan, G.H., Webb, H.E., Bugarel, M., Haley, B.J., Kim, S.W., Van Kessel, J.S. 2018. Complete closed genome sequences of three Salmonella enterica subsp. enterica Serovar Dublin strains isolated from cattle at harvest. Microbiology Resource Announcements. 7:e01334-18. https://doi.org/10.1128/MRA.01334-18.

Phylogeographic analysis reveals multiple international transmission events have driven the global emergence of Escherichia coli O157:H7 - (Peer Reviewed Journal)
Franz, E., Rotariu, O., Lopes, B.S., MacRae, M., Bono, J.L., Laing, C., Gannon, V., Söderlund, R., van Hoek, A., Friesema, I., French, N.P., George, T., Biggs, P.J., Jaros, P., Rivas, M., Chinen, I., Campos, J., Jernberg, C., Gobius, K., Mellor, G.E., Chandry, P., Perez-Reche, F., Forbes, K.J., Strachan, N. 2019. Phylogeographic analysis reveals multiple international transmission events have driven the global emergence of Escherichia coli O157:H7. Clinical Infectious Diseases. 69(3):428-437. https://doi.org/10.1093/cid/ciy919.

Closed genome and comparative phylogenetic analysis of the clinical multidrug resistant Shigella sonnei strain 866 - (Peer Reviewed Journal)
Allue-Guardia, A., Koenig, S.S.K., Quiros, P., Muniesa, M., Bono, J.L., Eppinger, M. 2018. Closed genome and comparative phylogenetic analysis of the clinical multidrug resistant Shigella sonnei strain 866. Genome Biology and Evolution. 10(9):2241-2247. https://doi.org/10.1093/gbe/evy168.

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.

Whole-genome sequence analysis of CTX-M containing Escherichia coli isolates from retail meats and cattle in the United States - (Peer Reviewed Journal)
Tadesse, D.A., Li, C., Mukherjee, S., Hsu, C., Bodeis Jones, S., Gaines, S.A., Kabera, C., Loneragan, G.H., Torrence, M., Harhay, D.M., McDermott, P.F., Zhao, S. 2018. Whole-genome sequence analysis of CTX-M containing Escherichia coli isolates from retail meats and cattle in the United States. Microbial Drug Resistance. 24(7):939-948. https://doi.org/10.1089/mdr.2018.0206.

Genetic context of antimicrobial-resistant Escherichia coli at the livestock-wildlife interface - (Abstract Only)
Chandler, J.C., Blouin, N.A., Bono, J.L., Franklin, A.B., Goodridge, L.D., Root, J., Shriner, S., Bisha, B. 2018. Genetic context of antimicrobial-resistant Escherichia coli at the livestock-wildlife interface. Journal of Food Protection. 81 (Supplement A): P2-228.

Identification of a new Shiga toxin-producing Escherichia coli O26:H11 stx2 single nucleotide polymorphism clonal complex in the United States - (Abstract Only)
Bono, J., Strockbine, N. 2018. Identification of a new Shiga toxin-producing Escherichia coli O26:H11 stx2 single nucleotide polymorphism clonal complex in the United States. Journal of Food Protection. 81 (Supplement A): P2-229.

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 - (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. https://doi.org/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 - (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 - (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 - (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.