Overview of Research Program

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

Publications

(2017-present)

Pal A, Mann A, den Bakker HC. 2024. Analysis of microbial composition of edible insect products available for human consumption within the United States using traditional microbiological methods and whole genome sequencing. J Food Prot. 87(6):100277. doi: 10.1016/j.jfp.2024.100277. Epub 2024 Apr 12. PMID: 38615992

Gędas A, Draszanowska A, den Bakker H, Diez-Gonzalez F, Simões M, Olszewska MA.2023. Prevention of surface colonization and anti-biofilm effect of selected phytochemicals against Listeria innocua strain. Colloids Surf B Biointerfaces. 228:113391. doi: 10.1016/j.colsurfb.2023.113391.

Novoa Rama E, Bailey M, Kumar S, Leone C, den Bakker HC, Thippareddi H, Singh M. 2023.  Characterizing the gut microbiome of broilers raised under conventional and no antibiotics ever practices. Poult Sci. 102(8):102832. doi: 10.1016/j.psj.2023.102832.

Townsend A, den Bakker HC, Mann A, Murphy CM, Strawn LK, Dunn LL. 2023. 16S microbiome analysis of microbial communities in distribution centers handling fresh produce. Front Microbiol. 14:1041936. doi: 10.3389/fmicb.2023.1041936.

He Y, Xu T, Li S, Mann DA, Britton B, Oliver HF, den Bakker HC, Deng X. 2022. Integrative assessment of reduced Listeria monocytogenes susceptibility to benzalkonium chloride in produce processing environments. Appl Environ Microbiol. 13:e0126922. doi: 10.1128/aem.01269-22.  

Hudson LK, Chaggar HK, Schamp CN, Claxton ML, Bryan DW, Peters TL, Song Y, Carlin CR, den Bakker HC, Denes TG. 2022. Phenotypic characterization and analysis of complete genomes of two distinct strains of the proposed species "L. swaminathanii". Sci Rep. 12(1):9137. doi: 10.1038/s41598-022-13119-y. PMID: 35650389; PMCID: PMC9159981. 

Reed A, Olszewska MA, Mann A, Novoa Rama E, Thippareddi H, Singh M, den Bakker HC. 2022. Draft genome sequences of two lactobacillus johnsonii and three Ligilactobacillus salivarius strains isolated from intestinal microbiomes of chickens. Microbiol Resour Announc. 11(2):e0092521. doi: 10.1128/mra.00925-21. Epub 2022 Feb 3. PMID: 35112897; PMCID: PMC8812308. 

Den Bakker HC, Katz L. 2021. Sepia, a taxonomy oriented read classifier in Rust. Journal of Open Source Software, 6(68), 3839. https://doi.org/10.21105/joss.03839.

Den Bakker M, den Bakker HC, Diez-Gonzalez F. 2021. Heat inactivation of Listeria monocytogenes on pecans, macadamia nuts, and sunflower seeds. Microbiol. Spect. 9: e01134-21. https://doi.org/10.1128/Spectrum.01134-21.

Hudson LK, Orellana LAG, Bryan DW, Moore A, Munafo JP, den Bakker HC, Denes TG. 2022. Phylogeny of the Bacillus altitudinis complex and characterization of a newly isolated strain with antilisterial activity. J Food Prot. 84(8):1321-1332. doi: 10.4315/JFP-20-498.

Hudson LK, Peters TL, Bryan DW, Song Y, den Bakker HC, Denes TG. 2021. Complete Genome sequences of three Listeria monocytogenes bacteriophage propagation strains. Microbiol Resour Announc. 10(1):e01159-20. doi: 10.1128/MRA.01159-20.

Levent G, Schlochtermeier A, Ives SE, Norman KN, Lawhon SD, Loneragan GH, Anderson RC, Vinasco J, Den Bakker HC, Scott HM. 2021. High-resolution genomic comparisons within Salmonella enterica serotypes derived from beef feedlot cattle: parsing the roles of cattle source, pen, animal, sample type and production period. Appl Environ Microbiol. Apr 16:AEM.00485-21. doi: 10.1128/AEM.00485-21.

Peters TL, Hudson LK, Bryan DW, Song Y, den Bakker HC, Kucerova Z, Denes TG. 2021. Complete genome sequence of a serotype 7 Listeria monocytogenes strain, FSL R9-0915. Microbiol Resour Announc. 2021 Jan 7;10(1):e01158-20. doi: 10.1128/MRA.01158-20.

Forghani F, Li S, Zhang S, Mann DA, Deng X, den Bakker HC, Diez-Gonzalez F. 2020. Salmonella enterica and Escherichia coli in wheat flour: detection and serotyping by a quasimetagenomic approach assisted by magnetic capture, multiple-displacement amplification, and real-time sequencing. Appl Environ Microbiol. 86(13):e00097-20. doi: 10.1128/AEM.00097-20.

Burnett J., Wu S.T., den Bakker H.C., Cook P.W., Veenhuizen D.R., Hammons S.R., Singh M. & Oliver H.F., Listeria monocytogenes is prevalent in retail produce environments but Salmonella enterica is rare, Food Control (2020), doi:  https://doi.org/10.1016/j.foodcont.2020.107173 .

Katz L, Griswold T, Morrison SS, Caravas JA, Zhang S, den Bakker HC, Deng X, Carleton HA. 2019. Mashtree: a rapid comparison of whole genome sequence files. J Open So Soft 4(44), 1762 DOI: 10.21105/joss.01762

Ohta N, Norby B, Loneragan GH, Vinasco J, den Bakker HC, Lawhon SD, Norman KN, Scott HM. 2019. Quantitative dynamics of Salmonella and E. coli in feces of feedlot cattle treated with ceftiofur and chlortetracycline. PLoS ONE 14(12): e0225697. https://doi.org/10.1371/journal.pone.0225697

Zhang S, Den-Bakker HC, Li S, Chen J, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. 2019. SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. Appl Environ Microbiol. doi: 10.1128/AEM.01746-19. [Epub ahead of print]

Bradley P, den Bakker HC, Rocha EPC,  McVean G, Iqbal Z. 2019. Ultrafast search of all deposited bacterial and viral genomic data. Nature Biotechnol. 37:152–159.

Bugarel M, Cook PW, den Bakker HC, Harhay D, Nightingale KK, Loneragan GH. 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. Microbiol Resour Announc. 10;8 pii: e01450-18. doi: 10.1128/MRA.01450-18.

Zhang S, Li S, Gu W, den Bakker H, Boxrud D, Taylor A, Roe C, Driebe E, Engelthaler DM, Allard M, Brown E, McDermott P, Zhao S, Bruce BB, Trees E, Fields PI, Deng X. 2019. Zoonotic source attribution of Salmonella enterica serotype Typhimurium using genomic surveillance data, United States. Emerg Infect Dis. 25:82-91.

Forghani F, den Bakker M, Futral AN, Diez-Gonzalez F. 2018. Long-term survival and thermal death kinetics of enterohemorrhagic Escherichia coli serogroups O26, O103, O111 and O157 in wheat flour. Appl Environ Microbiol. 84. pii: e00283-18. doi: 10.1128/AEM.00283-18.

Erickson MC, Liao JY, Payton AS, Cook PW, Den Bakker HC, Bautista J, Pérez JCD. 2018. Pre-harvest internalization and surface survival of Salmonella and Escherichia coliO157:H7 sprayed onto different lettuce cultivars under field and growth chamber conditions. Int J Food Microbiol. 291:197-204.

Erickson, M.C., J-Y. Liao, A.S. Payton, P.W. Cook, H.C. Den Bakker, J. Bautista, and J.C. Diaz-Perez. 2018.  Fate of enteric pathogens in different spinach cultivars cultivated in growth chamber and field systems.  Food Quality and Safety 2:221-228.

Ahlstrom, C.A., C.S. Manuel, H.C. Den Bakker, M. Wiedmann, and K.K. Nightingale. 2018. Molecular ecology of Listeria spp., Salmonella, Escherichia coli O157:H7 and non-O157 Shiga toxin-producing E. coli in pristine natural environments in Northern Colorado. J. Appl. Microbiol. 124:511-521.

Toledo V, den Bakker HC, Hormazábal JC, González-Rocha G, Bello-Toledo H, Toro M, Moreno-Switt AI. 2018. Genomic diversity of Listeria monocytogenes isolated from clinical and non-clinical samples in Chile. Genes (Basel). 9(8). pii: E396. doi: 10.3390/genes9080396.

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.