Research Project: Detection, Quantification and Characterization Technologies for Foodborne Pathogens

Location: Characterization and Interventions for Foodborne Pathogens

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

Combination of serial plating and long-read sequencing to detect and quantify live Shiga-toxin producing Escherichia coli - (Peer Reviewed Journal)
Counihan, K.L., Tilman, S. 2026. Combination of serial plating and long-read sequencing to detect and quantify live Shiga-toxin producing Escherichia coli. Pathogens. https://doi.org/10.3390/pathogens15060573.

Genetic variations and accelerated growth at low temperatures in a Listeria monocytogenes isolate - (Peer Reviewed Journal)
Counihan, K.L., Amarasekara, N., Gurtler, J., Fan, X. 2026. Genetic variations and accelerated growth at low temperatures in a Listeria monocytogenes isolate. American Society for Microbiology. https://doi.org/10.1128/spectrum.03786-25.

Correlation of Elastic Light Scatter pattern analysis of clinical and shellfish strains of Vibrio parahaemolyticus from New Zealand with virulence characteristics - (Peer Reviewed Journal)
Guo, X., Bari, S., Zhang, Y., Robinson, J., Patsekin, V., Fletcher, G., Vidovic, S., Gehring, A.G., Lindsay, J.A., On, S. 2025. Correlation of Elastic Light Scatter pattern analysis of clinical and shellfish strains of Vibrio parahaemolyticus from New Zealand with virulence characteristics. Applied and Environmental Microbiology. https://doi.org/10.1016/j.ijfoodmicro.2025.111579.

A modified most probable number (MPN) assay to quantify Salmonella in raw and ready to cook chicken products - (Peer Reviewed Journal)
He, Y., Capobianco Jr, J.A., Dykes, G.E., Armstrong, C.M., Chen, C., Counihan, K.L., Lee, J., Reed, S.A., Tilman, S.M. 2025. A modified most probable number (MPN) assay to quantify Salmonella in raw and ready to cook chicken products. Journal of Visualized Experiments. Article e67910. https://doi.org/10.3791/67910.

Assessment of cluster analysis of elastic light scatter profiles for the identification of foodborne bacteria - (Peer Reviewed Journal)
Bari, S., Zhang, Y., Patsekin, V., Robinson, J., Rajwa, B., Gehring, A.G., Lindsay, J.A., Kulasiri, D., On, S. 2025. Assessment of cluster analysis of elastic light scatter profiles for the identification of foodborne bacteria. Systematic and Applied Microbiology. 48(5). https://doi.org/10.1016/j.syapm.2025.126641.

Prevalence, risk factors, and human health implications of Salmonella enterica and Campylobacter spp. in Vermont backyard poultry - (Peer Reviewed Journal)
Patch, C., Larsen, K., Armstrong, C.M., Kanrar, S., Michaelides, A., Chakraborty, P., Harper, K., Devlin, V., Martin, L., Lunna, A., Blackwell, H., Nguyen, S.C., Penny, A., Etter, A. 2025. Prevalence, risk factors, and human health implications of Salmonella enterica and Campylobacter spp. in Vermont backyard poultry. Zoonoses and Public Health. http://doi.org/10.1111/zph.70004.

Transcriptomic analysis of Campylobacter jejuni following exposure to gaseous chlorine dioxide reveals an oxidative stress response - (Peer Reviewed Journal)
Dykes, G., He, Y., Jin, Z.T., Fan, X., Lee, J., Reed, S., Capobianco Jr, J.A. 2025. Transcriptomic analysis of Campylobacter jejuni following exposure to gaseous chlorine dioxide reveals an oxidative stress response. International Journal of Molecular Sciences. https://doi.org/10.3390/ijms26073254.

Enumeration of Escherichia coli in ground beef and identification with long-read sequencing - (Abstract Only)

Multiplexed detection of Salmonella, Escherichia coli, Campylobacter and Listeria in raw poultry - (Peer Reviewed Journal)
Capobianco Jr, J.A., Armstrong, C.M., Chen, C., He, Y., Counihan, K.L., Lee, J., Dykes, G.E., Johnson, K.M., Tilman, S.M., Koppenhofer, H.L., Atencia, J., Martinos, S. 2025. Multiplexed detection of Salmonella, Escherichia coli, Campylobacter and Listeria in raw poultry. Foods. https://doi.org/10.3390/foods14071137.

Quantification of Salmonella in raw poultry using droplet digital PCR with a whole cell, enrichment-free approach - (Peer Reviewed Journal)
Armstrong, C.M., Chen, C., Xie, Y., Atencia, J., Pierre, S., He, Y., Lee, J., Dykes, G.E., Johnson, K.M., Froment, B., Martinos, S., Capobianco Jr, J.A. 2025. Quantification of Salmonella in raw poultry using droplet digital PCR with a whole cell, enrichment-free approach. Journal of Food Protection. https://doi.org/10.1016/j.jfp.2025.100498.

Differentiation of Salmonella serotypes in meat using long-read sequencing - (Abstract Only)

Detection of live Escherichia coli with long-read sequencing - (Peer Reviewed Journal)
Counihan, K.L., Tilman, S.M., Chen, C., He, Y. 2025. Detection of live Escherichia coli with long-read sequencing. International Journal of Molecular Sciences. https://doi.org/10.3390/ijms26052228.

Rapid detection of Salmonella Typhimurium in egg biofilms on three different surfaces using long-read sequencing - (Peer Reviewed Journal)
Bermudez-Aguirre, L.D., Tilman, S.M., Niemira, B.A., Counihan, K.L., Uknalis, J. 2025. Rapid detection of Salmonella Typhimurium in egg biofilms on three different surfaces using long-read sequencing. Microorganisms. https://doi.org/10.3390/.

Rapid and accurate detection of huanglongbing in citrus by elasticity testing using a piezoelectric finger - (Peer Reviewed Journal)
Rao, P., Huang, S., Armstrong, C.M., Capobianco Jr, J.A., Duan, Y., Shih, W., Shih, W. 2025. Rapid and accurate detection of huanglongbing in citrus by elasticity testing using a piezoelectric finger. Analytical Methods. https://doi.org/10.1039/d4ay01952k.

Comparative genomic analysis of food-originated plasmids identified in Campylobacter jejuni and C. coli - (Peer Reviewed Journal)
He, Y., Dykes, G.E., Kanrar, S., Liu, Y., Gunther, N.W., Counihan, K.L., Lee, J., Capobianco Jr, J.A. 2025. Comparative genomic analysis of food-originated plasmids identified in Campylobacter jejuni and C. coli. Microorganisms. https://doi.org/10.3390/microorganisms13010206.

Investigations into Nanopore-based sequencing for portable detection of foodborne pathogens: Simulation, detection limit, and quantification - (Abstract Only)

Investigating the quantification capabilities of a nanopore-based sequencing platform for food safety application via external standards of lambda DNA and lambda spiked beef - (Peer Reviewed Journal)
Harper, S.A., Counihan, K.L., Kanrar, S., Paoli, G., Tilman, S.M., Gehring, A.G. 2024. Investigating the quantification capabilities of a nanopore-based sequencing platform for food safety application via external standards of lambda DNA and lambda spiked beef. Foods. https://doi.org/10.3390/foods13203304.

High-throughput homogenous assay for the direct detection of Listeria monocytogenes DNA - (Peer Reviewed Journal)
Armstrong, C.M., Capobianco Jr, J.A., Nguyen, S.C., Guragain, M., Liu, Y. 2024. High-throughput homogenous assay for the direct detection of Listeria monocytogenes DNA. Scientific Reports. 14:7026. https://doi.org/10.1038/s41598-024-56911-8.

Detection of Escherichia coli O157:H7 in ground beef using long-read sequencing - (Peer Reviewed Journal)
Counihan, K.L., Kanrar, S., Tilman, S.M., Capobianco Jr, J.A., Armstrong, C.M., Gehring, A.G. 2024. Detection of Escherichia coli O157:H7 in ground beef using long-read sequencing. Foods. 13(6):828. https://doi.org/10.3390/foods13060828.

Whole genome sequences, de novo assembly, and annotation of antibiotic resistant Campylobacter jejuni strains S27, S33, and S36 newly isolated from chicken meat - (Peer Reviewed Journal)
He, Y., Kanrar, S., Reed, S., Lee, J., Capobianco Jr, J.A. 2024. Whole genome sequences, de novo assembly, and annotation of antibiotic resistant Campylobacter jejuni strains S27, S33, and S36 newly isolated from chicken meat. Microorganisms. 12(1):159. https://doi.org/10.3390/microorganisms12010159.

Magnetic capture device for large volume sample analysis - (Peer Reviewed Journal)
Armstrong, C.M., Capobianco Jr, J.A., Lee, J. 2024. Magnetic capture device for large volume sample analysis. PLOS ONE. https://doi.org/10.1371/journal.pone.0297806.

Detection and isolation of Campylobacter spp. from raw meat - (Peer Reviewed Journal)
He, Y., Capobianco Jr, J.A., Armstrong, C.M., Chen, C., Counihan, K.L., Lee, J., Reed, S.A., Tilman, S.M. 2024. Detection and isolation of Campylobacter spp. from raw meat. The Journal of Visualized Experiments (JoVE). http://dx.doi.org/10.3791/66462.

Evaluation of long-read sequencing simulators to assess real-world applications for food safety - (Peer Reviewed Journal)
Counihan, K.L., Kanrar, S., Tilman, S.M., Gehring, A.G. 2023. Evaluation of long-read sequencing simulators to assess real-world applications for food safety. Foods. 13(1):16. https://doi.org/10.3390/foods13010016.

High-yield and high-throuhput delamination of multilayer MXene via high-pressure homogenization - (Peer Reviewed Journal)
Inman, C.A., Shevchuk, K., Anayee, M., Hammill, B., Lee, J., Saraf, M., Shuck, C., Armstrong, C.M., He, Y., Jin, Z.T., Shekhirev, M., Capobianco Jr, J.A., Gogotsi1, Y. 2023. High-yield and high-throuhput delamination of multilayer MXene via high-pressure homogenization. Chemical Engineering Journal. 475:146089. https://doi.org/10.1016/j.cej.2023.146089.

Complete genome sequence of Campylobacter jejuni BSD5, a multidrug-resistant isolate from a poultry processing facility in the United States - (Peer Reviewed Journal)
He, Y., Reed, S.A., Gunther, N.W., Armstrong, C.M., Capobianco Jr, J.A. 2023. Complete genome sequence of Campylobacter jejuni BSD5, a multidrug-resistant isolate from a poultry processing facility in the United States. Microbiology Resource Announcements. 12(6). https://doi.org/10.1128/mra.00284-23.

Use of a commercial tissue dissociation system to detect Salmonella-contaminated poultry products - (Peer Reviewed Journal)
Armstrong, C.M., He, Y., Chen, C., Counihan, K.L., Lee, J., Reed, S.A., Capobianco Jr, J.A. 2023. Use of a commercial tissue dissociation system to detect Salmonella-contaminated poultry products. Analytical and Bioanalytical Chemistry. https://doi.org/10.1007/s00216-023-04668-w.

Enhancing detection of Listeria monocytogenes in food products using an enzyme - (Peer Reviewed Journal)
Felton, S., Armstrong, C.M., Chen, C., He, Y., Lee, J., Reed, S.A., Akula, N., Walker, S., Berger, B., Capobianco Jr, J.A. 2022. Enhancing detection of Listeria monocytogenes in food products using an enzyme. Food Control. https://doi.org/10.1016/j.foodcont.2022.109445.

Complete genome sequences of multidrug-resistant Campylobacter coli strains YH501, YH503, and YH504 from retail chicken - (Peer Reviewed Journal)
He, Y., Reed, S.A., Yan, X., Zhang, D., Strobaugh Jr, T.P., Capobianco Jr, J.A., Gehring, A.G. 2022. Complete genome sequences of multidrug-resistant Campylobacter coli strains YH501, YH503, and YH504 from retail chicken. Microbiology Resource Announcements. Available online: https://www.researchgate.net/journal/Microbiology-Resource-Announcements-2576-098X. https://doi.org/10.1128%2Fmra.00237-22.