Pathogen Transmission

A key effort in the Food Safety Lab is to develop a better understanding of the transmission, ecology, and evolution of bacterial pathogens and to translate this knowledge into improved detection methods and control strategies. Current research focuses on both transmission, ecology, and evolution of Listeria monocytogenes and Salmonella, including major efforts on the use of full genome sequencing to understand the evolution of Salmonella and Listeria, including the evolution of clonal groups that show host specificity or distinct virulence characteristics. Projects on the ecology of foodborne pathogens focus on (i) understanding transmission and ecology of Listeria monocytogenes and Salmonella in produce production (pre-harvest) environments; (ii) transmission of Salmonella in dairy farms; and (iii) transmission of Listeria monocytogenes in processing facilities.

Relevant Key Publications:

  • Bolten, S., A.S. Harrand, J. Skeens, and M. Wiedmann. 2022. Nonsynonymous Mutations in fepR Are Associated with Adaptation of Listeria monocytogenes and Other Listeria spp. to Low Concentrations of Benzalkonium Chloride but Do Not Increase Survival of L. monocytogenes and Other Listeria spp. after Exposure to Benzalkonium Chloride Concentrations Recommended for Use in Food Processing Environments. Appl. Environ. Microbiol. 88. doi:10.1128/aem.00486-22.
  • Carlin, C.R., J. Liao, L.K. Hudson, T.L. Peters, T.G. Denes, R.H. Orsi, X. Guo, and M. Wiedmann. 2022. Soil Collected in the Great Smoky Mountains National Park Yielded a Novel Listeria sensu stricto Species, L. swaminathanii. Microbiol. Spectr.. doi:10.1128/spectrum.00442-22.
  • Murphy, S.I., R. Chen, A.M. Belias, W. Chen, L.Q. Zhang, S. Sunil, E. Bulut, Y. Li, M. Wiedmann, and R. Ivanek. 2022. Growth and survival of aerobic and Gram-negative bacteria on fresh spinach in a Chinese supply chain from harvest through distribution and refrigerated storage. Int. J. Food Microbiol. 370. doi:10.1016/j.ijfoodmicro.2022.109639.
  • Cheng, R.A., R.H. Orsi, and M. Wiedmann. 2022. The Number and Type of Chaperone-Usher Fimbriae Reflect Phylogenetic Clade Rather than Host Range in Salmonella. mSystems. doi:10.1128/msystems.00115-22.
  • Belias, A., G. Sullivan, M. Wiedmann, and R. Ivanek. 2022. Factors that contribute to persistent Listeria in food processing facilities and relevant interventions: A rapid review. Food Control 133. doi:10.1016/j.foodcont.2021.108579.
  • Chen, T., R.H. Orsi, R. Chen, M. Gunderson, S. Roof, M. Wiedmann, S.E. Childs-Sanford, and K.J. Cummings. 2022. Characterization of Listeria monocytogenes isolated from wildlife in central New York. Vet. Med. Sci.. doi:10.1002/vms3.758.
  • Carroll, L.M., A.J. Buehler, A. Gaballa, J.D. Siler, K.J. Cummings, R.A. Cheng, and M. Wiedmann. 2021. Monitoring the Microevolution of Salmonella enterica in Healthy Dairy Cattle Populations at the Individual Farm Level Using Whole-Genome Sequencing. Front. Microbiol. 12. doi:10.3389/fmicb.2021.763669.
  • Cheng, R.A., R.H. Orsi, and M. Wiedmann. 2021. Phylogeographic Clustering Suggests that Distinct Clades of Salmonella enterica Serovar Mississippi Are Endemic in Australia, the United Kingdom, and the United States. mSphere 6. doi:10.1128/msphere.00485-21.
  • Liao, J., X. Guo, D.L. Weller, S. Pollak, D.H. Buckley, M. Wiedmann, and O.X. Cordero. 2021. Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution. Nat. Microbiol. 6:1021–1030. doi:10.1038/s41564-021-00935-7.
  • Orsi, R.H., B. Jagadeesan, L. Baert, and M. Wiedmann. 2021. Identification of closely related Listeria monocytogenes isolates with no apparent evidence for a common source or location: A retrospective whole genome sequencing analysis. J. Food Prot. 84:1104–1113. doi:10.4315/JFP-20-417.
  • Carlin, C.R., J. Liao, D. Weller, X. Guo, R. Orsi, and M. Wiedmann. 2021. Listeria cossartiae sp. Nov., Listeria immobilis sp. nov., Listeria portnoyi sp. nov. and Listeria rustica sp. nov., isolated from agricultural water and natural environments. Int. J. Syst. Evol. Microbiol. 71. doi:10.1099/ijsem.0.004795.
  • Carroll, L.M., R.A. Cheng, M. Wiedmann, and J. Kovac. 2021. Keeping up with the Bacillus cereus group: taxonomy through the genomics era and beyond. Crit. Rev. Food Sci. Nutr.. doi:10.1080/10408398.2021.1916735.
  • Harrand, A.S., V. Guariglia-Oropeza, J. Skeens, D. Kent, and M. Wiedmanna. 2021. Nature versus Nurture: Assessing the Impact of Strain Diversity and Pregrowth Conditions on Salmonella enterica, Escherichia coli, and Listeria Species Growth and Survival on elected Produce Items. Appl. Environ. Microbiol. 87:1–18. doi:10.1128/AEM.01925-20.
  • Liao, J., P. Bergholz, and M. Wiedmann. 2021. Adjacent Terrestrial Landscapes Impact the Biogeographical Pattern of Soil Escherichia coli Strains in Produce Fields by Modifying the Importance of Environmental Selection and Dispersal. Appl. Environ. Microbiol. 87:1–17. doi:10.1128/AEM.02516-20.
  • Cheng, R.A., and M. Wiedmann. 2021. Recent Advances in Our Understanding of the Diversity and Roles of Chaperone-Usher Fimbriae in Facilitating Salmonella Host and Tissue Tropism. Front. Cell. Infect. Microbiol. 10. doi:10.3389/fcimb.2020.628043.
  • Gaballa, A., R.A. Cheng, A.S. Harrand, A.R. Cohn, and M. Wiedmann. 2021. The Majority of Typhoid Toxin-Positive Salmonella Serovars Encode ArtB, an Alternate Binding Subunit . mSphere 6. doi:10.1128/msphere.01255-20.
  • Belias, A., L.K. Strawn, M. Wiedmann, and D. Weller. 2021. Small produce farm environments can harbor diverse Listeria monocytogenes and Listeria spp. populations. J. Food Prot. 84:113–121. doi:10.4315/JFP-20-179.
  • Sullivan, G., X. Guo, J.I. Tokman, S. Roof, A. Trmcic, R.C. Baker, S. Tang, P. Markwell, M. Wiedmann, and J. Kovac. 2020. Extended enrichment procedures can be used to define false-negative probabilities for cultural gold standard methods for salmonella detection, facilitating comparisons between gold standard and alternative methods. J. Food Prot. 83:1030–1037. doi:10.4315/0362-028X.JFP-19-422.
  • Liao, J., R.H. Orsi, L.M. Carroll, J. Kovac, H. Ou, H. Zhang, and M. Wiedmann. 2019. Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica. BMC Evol. Biol. 19. doi:10.1186/s12862-019-1457-5.
  • Tang, S., R.H. Orsi, H. Luo, C. Ge, G. Zhang, R.C. Baker, A. Stevenson, and M. Wiedmann. 2019. Assessment and comparison of molecular subtyping and characterization methods for Salmonella. Front. Microbiol. 10. doi:10.3389/fmicb.2019.01591.
  • Carlin, C.R., S.S. Lau, R.A. Cheng, A.J. Buehler, Z. Kassaify, and M. Wiedmann. 2020. Validation using diverse, difficult-to-detect Salmonella strains and a dark chocolate matrix highlights the critical role of strain selection for evaluation of simplified, rapid PCR-based methods offering next-day time to results. J. Food Prot. 83:1374–1386. doi:10.4315/JFP-20-066.
  • Harrand, A.S., B. Jagadeesan, L. Baert, M. Wiedmann, and R.H. Orsi. 2020. Evolution of Listeria monocytogenes in a food processing plant involves limited single-nucleotide substitutions but considerable diversification by gain and loss of prophages. Appl. Environ. Microbiol. 86. doi:10.1128/AEM.02493-19.
  • Carroll, L.M., M. Wiedmann, and J. Kovac. 2020. Proposal of a taxonomic nomenclature for the Bacillus cereus group which reconciles genomic definitions of bacterial species with clinical and industrial phenotypes. MBio 11. doi:10.1128/mBio.00034-20.
  • Liao, J., R.H. Orsi, L.M. Carroll, and M. Wiedmann. 2020. Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial-resistant Salmonella enterica. Environ. Microbiol. 22:2811–2828. doi:10.1111/1462-2920.15014.
  • Belias, A.M., A. Sbodio, P. Truchado, D. Weller, J. Pinzon, M. Skots, A. Allende, D. Munther, T. Suslow, M. Wiedmann, and R. Ivanek. 2020. Effect of weather on the die-off of escherichia coli and attenuated salmonella enterica serovar typhimurium on preharvest leafy greens following irrigation with contaminated water. Appl. Environ. Microbiol. 86. doi:10.1128/AEM.00899-20.
  • Sullivan, G., and M. Wiedmann. 2020. Detection and prevalence of Listeria in U.S. Produce packinghouses and fresh-cut facilities. J. Food Prot. 83:1656–1666. doi:10.4315/JFP-20-094.
  • Carroll, L.M., and M. Wiedmann. 2020. Cereulide synthetase acquisition and loss events within the evolutionary history of group iii Bacillus cereus sensu lato facilitate the transition between emetic and diarrheal foodborne pathogens. MBio 11:1–16. doi:10.1128/mBio.01263-20.
  • Chen, R., J. Skeens, R.H. Orsi, M. Wiedmann, and V. Guariglia-Oropeza. 2020. Pre-growth conditions and strain diversity affect nisin treatment efficacy against Listeria monocytogenes on cold-smoked salmon. Int. J. Food Microbiol. 333. doi:10.1016/j.ijfoodmicro.2020.108793.
  • Harrand, A.S., L.K. Strawn, P.M. Illas-Ortiz, M. Wiedmann, and D.L. Weller. 2020. Listeria monocytogenes Prevalence Varies More within Fields Than between Fields or over Time on Conventionally Farmed New York Produce Fields. J. Food Prot. 83:1958–1966. doi:10.4315/JFP-20-120.
  • Carroll, L.M., A. Gaballa, C. Guldimann, G. Sullivan, L.O. Henderson, and M. Wiedmann. 2019. Identification of novel mobilized colistin resistance gene mcr-9 in a multidrug-resistant, colistin-susceptible salmonella enterica serotype typhimurium isolate. MBio 10. doi:10.1128/mBio.00853-19.
  • Weller, D.L., J. Kovac, D.J. Kent, S. Roof, J.I. Tokman, E. Mudrak, and M. Wiedmann. 2019. A conceptual framework for developing recommendations for no-harvest buffers around in-field feces. J. Food Prot. 82:1052–1060. doi:10.4315/0362-028X.JFP-18-414.
  • Carroll, L.M., M. Wiedmann, M. Mukherjee, D.C. Nicholas, L.A. Mingle, N.B. Dumas, J.A. Cole, and J. Kovac. 2019. Characterization of emetic and diarrheal Bacillus cereus strains from a 2016 foodborne outbreak using whole-genome sequencing: Addressing the microbiological, epidemiological, and bioinformatic challenges. Front. Microbiol. 10. doi:10.3389/fmicb.2019.00144.

  • Buehler, A.J., M. Wiedmann, Z. Kassaify, and R.A. Cheng. 2019. Evaluation of inva diversity among Salmonella species suggests why some commercially available rapid detection kits may fail to detect multiple Salmonella subspecies and species. J. Food Prot. 82:710–717. doi:10.4315/0362-028X.JFP-18-525.
  • Jagadeesan, B., L. Baert, M. Wiedmann, and R.H. Orsi. 2019. Comparative analysis of tools and approaches for source tracking Listeria monocytogenes in a food facility using whole-genome sequence data. Front. Microbiol. 10. doi:10.3389/fmicb.2019.00947.
  • Simmons, C.K., and M. Wiedmann. 2018. Identification and classification of sampling sites for pathogen environmental monitoring programs for Listeria monocytogenes: Results from an expert elicitation. Food Microbiol. 75:2–17. doi:10.1016/j.fm.2017.07.005.
  • Hoelzer, K., A.I. Moreno Switt, M. Wiedmann, and K.J. Boor. 2018. Emerging needs and opportunities in foodborne disease detection and prevention: From tools to people. Food Microbiol. 75:65–71. doi:10.1016/j.fm.2017.07.006.
  • Zoellner, C., K. Ceres, K. Ghezzi-Kopel, M. Wiedmann, and R. Ivanek. 2018. Design Elements of Listeria Environmental Monitoring Programs in Food Processing Facilities: A Scoping Review of Research and Guidance Materials. Compr. Rev. Food Sci. Food Saf. 17:1156–1171. doi:10.1111/1541-4337.12366.
  • Goodman, L.B., M.R. Lawton, R.J. Franklin-Guild, R.R. Anderson, L. Schaan, A.J. Thachil, M. Wiedmann, C.B. Miller, S.D. Alcaine, and J. Kovac. 2017. Lactococcus petauri sp. nov., isolated from an abscess of a sugar glider. Int. J. Syst. Evol. Microbiol. 67:4397–4404. doi:10.1099/ijsem.0.002303.
  • Liao, J., M. Wiedmann, and J. Kovac. 2017. Genetic stability and evolution of the sigB allele, used for Listeria sensu stricto subtyping and phylogenetic inference. Appl. Environ. Microbiol. 83. doi:10.1128/AEM.00306-17.
  • Kovac, J., K.J. Cummings, L.D. Rodriguez-Rivera, L.M. Carroll, A. Thachil, and M. Wiedmann. 2017. Temporal genomic phylogeny reconstruction indicates a geospatial transmission path of Salmonella cerro in the United States and a clade-specific loss of hydrogen sulfide production. Front. Microbiol. 8. doi:10.3389/fmicb.2017.00737.
  • Weller, D.L., J. Kovac, S. Roof, D.J. Kent, J.I. Tokman, B. Kowalcyk, D. Oryang, R. Ivanek, A. Aceituno, C. Sroka, and M. Wiedmann. 2017. on lettuce under field conditions encountered in the Northeastern United States. J. Food Prot. 80:1214–1221. doi:10.4315/0362-028X.JFP-16-419.
  • Etter, A.J., S.R. Hammons, S. Roof, C. Simmons, T. Wu, P.W. Cook, A. Katubig, M.J. Stasiewicz, E. Wright, S. Warchocki, J. Hollingworth, H.S. Thesmar, S.A. Ibrahim, M. Wiedmann, and H.F. Oliver. 2017. Enhanced sanitation standard operating procedures have limited impact on Listeria monocytogenes prevalence in retail delis. J. Food Prot. 80:1903–1912. doi:10.4315/0362-028X.JFP-17-112.
  • Weller, D.L., J. Kovac, D.J. Kent, S. Roof, J.I. Tokman, E. Mudrak, B. Kowalcyk, D. Oryang, A. Aceituno, and M. Wiedmann. 2017. Escherichia coli transfer from simulated wildlife feces to lettuce during foliar irrigation: A field study in the Northeastern United States. Food Microbiol. 68:24–33. doi:10.1016/j.fm.2017.06.009.
  • Carroll, L.M., M. Wiedmann, H. den Bakker, J. Siler, S. Warchocki, D. Kent, S. Lyalina, M. Davis, W. Sischo, T. Besser, L.D. Warnick, and R. V. Pereira. 2017. Whole-genome sequencing of drugresistant Salmonella enterica isolates from dairy cattle and humans in New York and Washington States reveals source and geographic associations. Appl. Environ. Microbiol. 83. doi:10.1128/AEM.00140-17.
  • Carroll, L.M., J. Kovac, R.A. Miller, and M. Wiedmann. 2017. Rapid, high-throughput identification of anthrax-causing and emetic Bacillus cereus group genome assemblies via BTyper, a computational tool for virulencebased classification of Bacillus cereus group isolates by using nucleotide sequencing data. Appl. Environ. Microbiol. 83. doi:10.1128/AEM.01096-17.
  • Ho, A., P. Pennell-Huth, A. Newman, S. Zansky, and M. Wiedmann. 2018. Foodborne Illness Outbreak Investigation Training Needs: A Survey among State Public Health Staff in the Northeast and Mid-Atlantic United States. J. Public Heal. Manag. Pract. 24:34–40. doi:10.1097/PHH.0000000000000539.
  • Orsi, R. H. and M. Wiedmann. 2016. Characteristics and distribution of Listeria spp., including Listeria species newly described since 2009. Appl. Micro & Biotech. doi:10.1007/s00253-016-7552-2.
  • Strawn, L. K., Y. T. Gröhn, S. Warchocki, R. W. Worobo, E. A. Bihn, and M. Wiedmann. 2013. Risk Factors Associated with Salmonella and Listeria monocytogenes Contamination of Produce Fields. Appl. Environ. Micro. 79:7618-7627.
  • den Bakker, H., C. Desjardins, A. Griggs, J. Peters, Q. Zeng, S. Young, C. Kodira, C. Yandava, T. Hepburn, B. Haas, B. Birren, and M. Wiedmann. 2013. Evolutionary Dynamics of the Accessory Genome of Listeria monocytogenes. PLoS ONE 8(6): e67511. doi:10.1371/journal.pone.0067511.
  • Strawn, L. K., E. D. Fortes, E. A. Bihn, K. K. Nightingale, Y. T. Gröhn, R. W. Worobo, M. Wiedmann, and P. W. Bergholz. 2013. Landscape and meteorological factors affecting prevalence of three foodborne pathogens in fruit and vegetable farms. Appl. Environ. Micro. 79:588-600.
  • Moreno Switt, A. I., H. C. den Bakker, C. A. Cummings, L. D. Rodriguez-Rivera, G. Govoni, M. L Ranieri, L. Degoricija, S. Brown; K. Hoelzer; J. E. Peters, E. Bolchacova; Manohar R Furtado; and M. Wiedmann.  2012. Identification and Characterization of Novel Salmonella Mobile Elements Involved in the Dissemination of Pathogenic Genes. PLoS ONE 7(7): e41247. doi:10.1371/journal.pone.0041247.
  • den Bakker, H. A. Moreno Switt, C. Cummings, K. Hoelzer, L. Degoricija, L. Rodriguez-Rivera, E. Wright, R. Fang, M. Davis, T. Root, D. Schoonmaker-Bopp, K. Musser, E. Villamil, H. Waechter, L. Kornstein, M. Furtado, and M. Wiedmann. 2011. A whole genome SNP based approach to trace and identify outbreaks linked to a common Salmonella enterica subsp. enterica serovar Montevideo Pulsed Field Gel Electrophoresis type. Appl. Environ. Micro. 77:8648-55.
  • Den Bakker, H.C., AI Moreno Switt, G Govoni, CA Cummings, ML Ranieri, L Degoricija, K Hoelzer, L.D. Rodriguez-Rivera, S. Brown, E. Bolchacova, M.R. Furtado and M. Wiedmann. 2011. Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica. BMC Genomics 12(1):425.
  • Hoelzer, K., B. D. Sauders, M. D. Sanchez, P. T. Olsen, M. M. Pickett, K. J. Mangione, D. H. Rice, J. Corby, S. Stich, E. D. Fortes, S. E. Roof, Y. T. Grohn, M. Wiedmann, and H. F. Oliver. 2011. Prevalence, distribution, and diversity of Listeria monocytogenes in retail environments, focusing on small establishments and establishments with a history of failed inspections.  J. Food Prot. 74: 1083-1095.
  • den Bakker, H. C., C. A. Cummings, V. Ferreira, P. Vatta, R. H. Orsi, L. Degoricija, M. Barker, O. Petrauskene, M. R. Furtado, and M. Wiedmann. 2010. Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss. BMC Genomics 2010 Dec 2;11:688.
  • Orsi, R. H., H. C. den Bakker, and M. Wiedmann. 2011. Listeria monocytogenes lineages: genomics, evolution, ecology and phenotypic characteristics. International Journal of Medical Microbiology 301: 79–96.
  • Den Bakker, H. C., B. N. Bundrant, E. D. Fortes, R. H. Orsi, and M. Wiedmann. 2010. A population and phylogenetic approach to understand the evolution of virulence in the genus Listeria. Appl. Environ. Micro. 76:6085-6100.
  • Cummings, K. J., L. D. Warnick, M. Elton, L.D. Rodriguez–Rivera, J.D. Siler, E.M. Wright, Y.T. Gröhn, and M. Wiedmann. 2010.  Salmonella enterica serotype Cerro among dairy cattle in New York: an emerging pathogen? Foodb. Path. Dis. 7:659-665.
  • Soyer, Y., R. Orsi, L. Rodriguez Rivera, Q. Sun, and M. Wiedmann. 2009.  Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes. BMC Evol. Biol 9 (1):264.
  • Soyer, Y., A. Moreno Switt, M.A. Davis, J. Maurer, P.L. McDonough, D. J. Schoonmaker-Bopp, N. B. Dumas, T. Root, L.D. Warnick, Y.T. Grohn, and M. Wiedmann. 2009. Salmonella 4,5,12:i:-: an emerging Salmonella serotype that represents multiple distinct clones. J. Clin. Microbiol. 47: 3546–3556.