Research Project: Reduction of Foodborne Pathogens and Antimicrobial Resistance in Poultry Production Environments

Location: Egg and Poultry Production Safety Research Unit

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

Survival of Antimicrobial Resistant Salmonella Heidelberg Inoculated into Microcosms of Fresh Wood Shavings for Broiler Litter - (Peer Reviewed Journal)

A Novel Slope-Matrix-Graph Algorithm to Analyze Compositional Microbiome Data - (Peer Reviewed Journal)
Zhang, M., Li, X., Oladeinde, A.A., Rothrock Jr, M.J., Pokoo-Aikins, A., Zock, G. 2024. A Novel Slope-Matrix-Graph Algorithm to Analyze Compositional Microbiome Data . Microorganisms. https://doi.org/10.3390/microorganisms12091866.

Salmonella Biomapping of a Commercial Broiler Hatchery - (Peer Reviewed Journal)
Rothrock Jr, M.J., Al Hakeem, W., Oladeinde, A.A., Looft, T.P., Li, X., Guard, J. 2024. Salmonella Biomapping of a Commercial Broiler Hatchery. Journal of Food Protection. //doi.org/10.1016/j.jfp.2024.100347.

16S amplicon-based microbiome biomapping of a commercial broiler hatchery - (Peer Reviewed Journal)
Rothrock Jr, M.J., Zwirzitz, B., Al Hakeem, W., Oladeinde, A.A., Guard, J.Y., Li, X. 2024. 16S amplicon-based microbiome biomapping of a commercial broiler hatchery. Animal Microbiome. https://doi.org/10.1186/s42523-024-00334-3.

Exploring Pathogen Presence Prediction in Pastured Poultry Farms through Transformer-Based Models and Attention Mechanism Explainability - (Peer Reviewed Journal)
Ram Das, A., Pillai, N., Nanduri, B., Rothrock Jr, M.J., Ramkumar, M. 2024. Exploring Pathogen Presence Prediction in Pastured Poultry Farms through Transformer-Based Models and Attention Mechanism Explainability. Microorganisms. https://doi.org/10.3390/microorganisms12071274.

Microbiome analyses of poultry feeds: Part II: Comparison of different poultry feeds. - (Peer Reviewed Journal)
Olson, E.G., Dittoe, D.K., Micciche, A.C., Stock, D.A., Rubinelli, P.M., Rothrock Jr, M.J., Ricke, S.C. 2024. Microbiome analyses of poultry feeds: Part II: Comparison of different poultry feeds. Journal of Environmental Science and Health. https://doi.org/10.1080/03601234.2024.2361596.

Deciphering selective pressures: comparative genomics and phylogenetic analyses of four virulence factors in Listeria monocytogenes isolates linked to chicken consumption in the United States. - (Abstract Only)
Li, X., Oladeinde, A.A., Rothrock Jr, M.J., Ishii, S., Shen, C. 2024. Deciphering selective pressures: comparative genomics and phylogenetic analyses of four virulence factors in Listeria monocytogenes isolates linked to chicken consumption in the United States. Poultry Science Association Meeting Abstract. PSA Annual Meeting.

A metagenomics perspective to evaluate probiotics combating Salmonella Infantis in poultry settings – a case study - (Abstract Only)
Li, X., Oladeinde, A.A., Rothrock Jr, M.J., Aggrey, S.E., Hamaoka, T., Abdo, Z., Buhr, R.J., Pokoo-Aikins, A. 2024. A metagenomics perspective to evaluate probiotics combating Salmonella Infantis in poultry settings – a case study. American Society for Microbiology. ASM Microbe: 2024.

Microbial profile of broiler carcasses processed at a university scale mobile poultry processing unit - (Peer Reviewed Journal)
Stearns, R., Bowen, K., Taylor, R.L., Moritz, J., Matak, K., Tou, J., Freshour, A., Jaczynski, J., Boltz, T., Li, X., Shen, C. 2024. Microbial profile of broiler carcasses processed at a university scale mobile poultry processing unit. Poultry Science. https://doi.org/10.1016/j.psj.2024.103576.

Alternative Additives for Organic and Natural Ready-to-Eat Meats to Control Spoilage and Maintain Shelf Life: Current Perspectives in the United States - (Peer Reviewed Journal)
Bodie, A.R., Wythe, L.A., Dittoe, D.K., Rothrock Jr, M.J., Obryan, C.A., Ricke, S.C. 2024. Alternative Additives for Organic and Natural Ready-to-Eat Meats to Control Spoilage and Maintain Shelf Life: Current Perspectives in the United States. Foods. https://doi.org/10.3390/foods13030464.

Microbiome analyses of poultry feeds: Part I. Comparison of five different DNA extraction methods - (Peer Reviewed Journal)
Olson, E.G., Dittoe, D.K., Micciche, A.C., Stock, D.A., Rubinelli, P.M., Rothrock Jr, M.J., Ricke, S.C. 2024. Microbiome analyses of poultry feeds: Part I. Comparison of five different DNA extraction methods. Journal of Environmental Science and Health. https://doi.org/10.1080/03601234.2024.2353002.

Machine learning algorithms predict Listeria prevalence and Campylobacter species on pastured poultry farms based on management practices and farm environment variables - (Abstract Only)
Li, X., Rothrock Jr, M.J., Oladeinde, A.A. 2024. Machine learning algorithms predict Listeria prevalence and Campylobacter species on pastured poultry farms based on management practices and farm environment variables. International Poultry Scientific Forum. IPSF:2024.

Comparison of metagenomic sequencing methods using Salmonella Heidelberg infected broilers - (Abstract Only)
Li, X., Oladeinde, A.A., Rothrock Jr, M.J. 2023. Comparison of metagenomic sequencing methods using Salmonella Heidelberg infected broilers. International Poultry Scientific Forum. IPSF:2024.

Relationship of the Poultry Microbiome to Pathogen Colonization, Farm Management, Poultry Production, and Foodborne Illness Risk Assessmen - (Peer Reviewed Journal)
Xu, X., Rothrock Jr, M.J., Dev Kumar, G., Mishra, A. 2023. Relationship of the Poultry Microbiome to Pathogen Colonization, Farm Management, Poultry Production, and Foodborne Illness Risk Assessmen. Journal of Food Protection. https://doi.org/10.1016/j.jfp.2023.100169.

Virulence factors and antimicrobial resistance profiles of Campylobacter isolates recovered from consecutively reused broiler litter - (Peer Reviewed Journal)
Woyda, R., Oladeinde, A.A., Endale, D.M., Strickland, T.C., Plumblee Lawrence, J.R., Abdo, Z. 2023. Virulence factors and antimicrobial resistance profiles of Campylobacter isolates recovered from consecutively reused broiler litter. Microbiology Spectrum. 11(6):1-18.

Listeria Occurrence in Conventional and Alternative Egg Production Systems - (Peer Reviewed Journal)
Ricke, S.C., Obryan, C.A., Rothrock Jr, M.J. 2023. Listeria Occurrence in Conventional and Alternative Egg Production Systems. Microorganisms. https://doi.org/10.3390/microorganisms11092164.

Predicting Foodborne Pathogens and Probiotics Taxa within poultry-related microbiomes using a machine learning approach - (Peer Reviewed Journal)
Ayoola, M., Pillai, N., Nanduri, B., Rothrock Jr, M.J., Ramkumar, M. 2023. Predicting Foodborne Pathogens and Probiotics Taxa within poultry-related microbiomes using a machine learning approach. Animal Microbiome. https://doi.org/10.1186/s42523-023-00260-w.

Detecting broiler chickens on litter floor with the YOLOv5-CBAM deep learning model - (Peer Reviewed Journal)
Guo, Y., Aggrey, S.E., Oladeinde, A.A., Qiao, Y., Chai, L. 2023. Detecting broiler chickens on litter floor with the YOLOv5-CBAM deep learning model. Artificial Intelligence in Agriculture. 9:36-45.

Assessing the risk of seasonal effects of Campylobacter contaminated broiler meat prepared in-home in the United States - (Peer Reviewed Journal)
Xu, X., Rothrock Jr, M.J., Dev Kumar, G., Mishra, A. 2023. Assessing the risk of seasonal effects of Campylobacter contaminated broiler meat prepared in-home in the United States. Foods. https://doi.org/10.3390/feeds12132559.

Towards Optimal Microbiome to Inhibit Multidrug Resistance - (Proceedings)
Pillai, N., Nanduri, B., Rothrock Jr, M.J., Chen, Z., Ramkumar, M. 2023. Towards Optimal Microbiome to Inhibit Multidrug Resistance. IEEE/ACM Transactions on Computational Biology and Bioinformatics. https://doi.org/10.1109/CIBCB56990.2023.10264914.

Internal organ colonization by Salmonella Enteritidis in layer pullets infected at two different ages during rearing in cage-free housing - (Abstract Only)
Gast, R.K., Jones, D.R., Guraya, R., Garcia, J.S., Karcher, D.M. 2023. Internal organ colonization by Salmonella Enteritidis in layer pullets infected at two different ages during rearing in cage-free housing. Poultry Science Association Meeting Abstract. 102 (E.Suppl.1):135.

Tanshinone IIA-loaded nanoparticles and neural stem cell combination therapy improves gut homeostasis and recovery in a pig ishemic stroke model - (Peer Reviewed Journal)
Jeon, J.H., Kaiser, E.E., Water, E.S., Yang, X., Lourenco, J.M., Fagan, M.M., Schuelin, K.M., Sneed, S.E., Shin, S.K., Kinder, H.A., Kumar, A., Platt, S., Anh, J., Duberstein, K.J., Rothrock Jr, M.J., Callaway, T.R., Xie, J., West, F.D., Park, H. 2023. Tanshinone IIA-loaded nanoparticles and neural stem cell combination therapy improves gut homeostasis and recovery in a pig ishemic stroke model. Nature Scientific Reports. https://doi.org/10.1038/s41598-023-29282-9.

Temporal dynamics of the cecal and litter microbiome of chickens raised in two separate broiler houses - (Peer Reviewed Journal)
Zwirzitz, B., Oladeinde, A.A., Johnson, J., Zock, G., Milfort, M.C., Fuller, L.A., Ghareeb, A., Foutz, J., Teran, J., Woyda, R., Abdoa, Z., Looft, T., Plumblee Lawrence, J.R., Aggrey, S.E. 2023. Temporal dynamics of the cecal and litter microbiome of chickens raised in two separate broiler houses. Frontiers in Physiology. https://doi.org/10.3389/fphys.2023.1083192.

Serotype screening of salmonella enterica subspecies I by intergenic sequence ribotyping (ISR): Critical updates - (Peer Reviewed Journal)
Guard, J.Y., Jones, D.R., Gast, R.K., Garcia, J.S., Rothrock Jr, M.J. 2022. Serotype screening of salmonella enterica subspecies I by intergenic sequence ribotyping (ISR): Critical updates. Microorganisms. 11(1):97. https://doi.org/10.3390/microorganisms11010097.

Chicken production and human clinical Escherichia coli isolates differ in their carriage of antimicrobial resistance and virulence factors - (Peer Reviewed Journal)
Woyda, R., Oladeinde, A., Abdo, Z. 2023. Chicken production and human clinical Escherichia coli isolates differ in their carriage of antimicrobial resistance and virulence factors. Applied and Environmental Microbiology. https://doi.org/10.1128/aem.01167-22.

Environmental conditions shape the gut microbiome of broiler chicken - (Abstract Only)

Monitoring behaviors of broiler chickens at different ages with deep learning - (Peer Reviewed Journal)
Guo, Y., Aggrey, S.E., Wang, P., Oladeinde, A.A., Chai, L. 2022. Monitoring behaviors of broiler chickens at different ages with deep learning. Animals. https://doi.org/10.3390/ani12233390.

Management and environmental factors influence the prevalence and abundance of food-borne pathogens and commensal bacteria in peanut hull-based broiler litter - (Peer Reviewed Journal)
Oladeinde, A., Babafela, A., Woyda, R., Abdo, Z., Endale, D., Strickland, T., Plumblee Lawrence, J.R., Cudnik, D., House, S.L., Cook, K.L. 2022. Management and environmental factors influence the prevalence and abundance of food-borne pathogens and commensal bacteria in peanut hull-based broiler litter. Poultry Science. https://doi.org/10.1016/j.psj.2022.102313.

An ensemble learning approach to identify pastured poultry farm practice variables and soil constituents that promote Salmonella prevalence - (Peer Reviewed Journal)
Pillai, N., Ayoola, M.B., Nanduri, B., Rothrock Jr, M.J., Ramkumar, M. 2022. An ensemble learning approach to identify pastured poultry farm practice variables and soil constituents that promote Salmonella prevalence. Heliyon. 8(11):e11331. https://doi.org/10.1016/j.heliyon.2022.e11331.

Preharvest Environmental and Management Drivers of Multidrug Resistance in Major Bacterial Zoonotic Pathogens in Pastured Poultry Flocks - (Peer Reviewed Journal)
Ayoola, M.B., Pillai, N., Nanduri, B., Rothrock Jr, M.J., Ramkumar, M. 2022. Preharvest Environmental and Management Drivers of Multidrug Resistance in Major Bacterial Zoonotic Pathogens in Pastured Poultry Flocks. Microorganisms. v. 10 (9). https://doi.org/10.3390/microorganisms10091703.

Comparison between LASSO and RT methods for prediction of generic E. coli concentration in pastured poultry farms - (Peer Reviewed Journal)
Xu, K., Rothrock Jr, M.J., Reeves, J., Dev Kumar, G., Mishra, A. 2022. Comparison between LASSO and RT methods for prediction of generic E. coli concentration in pastured poultry farms. Food Research International. v.161, p.111860. https://doi.org/10.1016/j.foodres.2022.111860.

Using E. coli populations to predict foodborne pathogens in pastured poultry farms. - (Peer Reviewed Journal)
Xu, X., Rothrock Jr, M.J., Reeves, J., Mishra, A. 2022. Using E. coli populations to predict foodborne pathogens in pastured poultry farms. Food Microbiology. https://doi.org/10.1016/j.fm.2022.104092.

Through the looking glass: Genome, phenome, and interactome of salmonella enterica - (Peer Reviewed Journal)
Guard, J.Y. 2022. Through the looking glass: Genome, phenome, and interactome of salmonella enterica. Pathogens. 11(5):581. https://doi.org/10.3390/pathogens11050581.

Transferability of ESBL-encoding IncN and IncI1 plasmids among field strains of different Salmonella serovars and Escherichia coli - (Peer Reviewed Journal)
Dorr, M., Silver, A., Smurlick, D., Arukha, A., Kariyawasam, S., Oladeinde, A.A., Cook, K., Denagamage, T. 2022. Transferability of ESBL-encoding IncN and IncI1 plasmids among field strains of different Salmonella serovars and Escherichia coli. Journal of Global Antimicrobial Resistance. 30:88-95. https://doi.org/10.1016/j.jgar.2022.04.015.

Bacterial sampling from organic farms demonstrates importance of cleaning produce before consumption - (Abstract Only)

Communicating the utility of the microbiome and bioinformatics to small flock poultry producers - (Peer Reviewed Journal)
Ricke, S.C., Dittoe, D.K., Tarcin, A.A., Rothrock Jr, M.J. 2022. Communicating the utility of the microbiome and bioinformatics to small flock poultry producers. Poultry Science. 101(5) https://doi.org/10.1016/j.psj.2022.101788.

Genetic characterization of Salmonella Infantis recovered from comminuted turkey samples collected by the USDA Food Safety and Inspection Service between 2019 and 2021 - (Abstract Only)

The impact of pre-slaughter fasting on the ruminal microbial population of commercial angus steers - (Peer Reviewed Journal)
Welch, C.W., Lourenco, J.M., Seidel, D.S., Krause, T.R., Rothrock Jr, M.J., Pringle, T., Callaway, T.R. 2021. The impact of pre-slaughter fasting on the ruminal microbial population of commercial angus steers. Microorganisms. 9(12):2625. https://doi.org/10.3390/microorganisms9122625.

Determination of bacterial pathogen diversity and prevalence in acidified re-used poultry litter during commercial live production - (Abstract Only)

Campylobacter prevalence differs across and within broiler houses with re-used poultry litter - (Abstract Only)

AT homopolymer strings in salmonella enterica subspecies I contribute to speciation and serovar diversity - (Peer Reviewed Journal)
Guard, J.Y., Rivers, A.R., Vaughn, J.N., Rothrock Jr, M.J., Oladeinde, A.A., Shah, D. 2021. AT homopolymer strings in salmonella enterica subspecies I contribute to speciation and serovar diversity. Microorganisms. 9(10):2075. https://doi.org/10.3390/microorganisms9102075.

Salmonella diversity along the farm-to-fork continuum of pastured poultry flocks in the southeastern United States - (Peer Reviewed Journal)
Rothrock Jr, M.J., Oladeinde, A.A., Guard, J.Y. 2021. Salmonella diversity along the farm-to-fork continuum of pastured poultry flocks in the southeastern United States. Frontiers in Animal Science. 2:761930. https://doi.org/10.3389/fanim.2021.761930.

Genetic characterization of Salmonella Enteritidis recovered from chicken samples collected by the USDA FSIS in Mississippi between 2016 and 2020 - (Abstract Only)
Sanchez-Ingunza, R., Pulido-Landinez, M., Guard, J.Y. 2021. Genetic characterization of Salmonella Enteritidis recovered from chicken samples collected by the USDA FSIS in Mississippi between 2016 and 2020. American Association of Avian Pathologists. https://pheedloop.com/EVESOUDKILPPY/site/sessions/?id=SESVARPD89FKJ87AH.

Antibiotic resistance, antimicrobial residues and bacterial community diversity in pasture-raised poultry, swine and beef cattle manures - (Peer Reviewed Journal)
Rothrock Jr, M.J., Min, B., Castleberry, B., Waldrip, H., Parker, D.B., Brauer, D.K., Pitta, D., Indugu, N. 2021. Antibiotic resistance, antimicrobial residues and bacterial community diversity in pasture-raised poultry, swine and beef cattle manures. Journal of Animal Science. https://doi.org/10.1093/jas/skab144

Genetic characteristics of Salmonella Isolates recovered from reused broiler - (Peer Reviewed Journal)
Woyda, R., Oladeinde, A.A., Endale, D., Strickland, T., Plumblee Lawrence, J.R., Abdo, Z. 2024. Genetic characteristics of Salmonella Isolates recovered from reused broiler. Journal of Food Protection. https://doi.org/10.1016/j.jfp.2024.100236.