Description of Research Interests

• Bacterial population genetics and genomics
• Bioinformatics
• Biostatistics
• Epidemiology
• Mycology
• Microbiomes, Salmonella, Listeria, and spoilage organisms

Selected Recent Publications

Bergholz, T., H.C. den Bakker, L. Katz, B. Silk, K. Jackson, Z. Kucerova, L. Joseph, M. Turnsek, L. Gladney, J. Halpin, K. Xavier, J. Gossack, T. Ward, M. Frace, and C. Tarr. 2015. Evolutionary relationships of outbreak-associated Listeria monocytogenes strains of serotypes 1/2a and 1/2b determined by whole genome sequencing. Appl. Environ. Microbiol., 82(3):928-38

 Deng, X., H.C. den Bakker, R.D. Hendriksen. 2016. Genomic Epidemiology: WholeGenome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens. Annu Rev Food Sci Technol. 7: 353-74.

Elder, J.R., M. Bugarel, H.C. den Bakker, G.H. Loneragan and K.K. Nightingale.. 2016. Interrogation of single nucleotide polymorphisms in gnd provides a novel method for molecular serogrouping of clinically important Shiga toxin producing Escherichia coli (STEC) targeted by regulation in the United States, including the "big six" non-O157 STEC and STEC O157. J. Microbiol. Methods. 16 (129): 85-93.

Ison S., S. Delannoy, M. Bugarel, T. Nagaraja, D. Renter, H.C. den Bakker, K.K Nightingale, P. Fach, and G.H. Loneragan. 2015. Targeted amplicon sequencing for SNP genotyping of attaching and effacing Escherichia coli O26:H11 cattle strains using a high-throughput library preparation technique. Appl. Environ. Microbiol., doi:10.1128/AEM.03182-15.

Ohta N, Norman KN, Norby B, Lawhon SD, Vinasco J, den Bakker H, Loneragan GH, Scott HM. 2017. Population dynamics of enteric Salmonella in response to antimicrobial use in beef feedlot cattle. Sci Rep. 7:14310. doi: 10.1038/s41598-017-14751-9.

Rodriguez-Rivera, L.D., B.M. Bowen, H.C. den Bakker, G.E. Duhamel and M. Wiedmann. 2015. Functional characterization of the cytolethal distending toxin (Typhoid toxin) in non-typhoidal Salmonella serovars. Gut Pathogens 7:19.

 Stasiewicz, M.J., H.F. Oliver, M. Wiedmann, H.C. den Bakker. 2015. Whole genome sequencing allows for improved identification of persistent Listeria monocytogenes in food associated environments. Appl. Environ. Microbiol., 81(17): 6024-37.  

Stasiewicz, M.J., H.C. den Bakker, M. Wiedmann. 2015. Genomics tools in microbial food safety. Current Opinion in Food Science, 4: 105–10.

Tang, S., R.H. Orsi, H.C. den Bakker, M. Wiedmann, K.J. Boor, T.M. Bergholz. 2015. Transcriptomic analysis of Listeria monocytogenes Adaptation to Growth on Vacuum-Packed Cold Smoked Salmon. Appl. Environ. Microbiol., 81(19):6812-24.

Webb, H.E., M. Bugarel, H.C. den Bakker, K.K. Nightingale, S.A. Granier, H.M. Scott, G.H. Loneragan. 2016. Carbapenem-Resistant Bacteria Recovered from Faeces of Dairy Cattle in the High Plains Region of the USA. PLoS ONE. 11(1): e0147363.

Webb H.E., S.A. Granier, M. Marault, Y. Millemann, H.C. den Bakker, K.K. Nightingale, M. Bugarel, S.A. Ison, H.M. Scott, G.H. Loneragan. 2015. Dissemination of the mcr-1 colistin resistance gene (correspondence). Lancet Infect. Dis., doi:10.1016/S14733099(15)00538-1.