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ARS Home Nutrition, Food Safety/Quality People & Locations







Kimberly L Cook

(Kim)                                                                (PhD)
                        Nutrition, Food Safety/Quality

                        




                        
                        National Program Leader
                        Phone: (240) 459-4181
                        
                        
                        Fax: (Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            **National Program Leader For:**
                                Identification, Genomic Characterization, and Metabolic Modeling of Foodborne Pathogens in the Meat Production Continuum
                                            Accession Number: 435565
                                        Reducing Pathogen Contamination Risks and Improving Quality Attributes of Eggs and Egg Products through Housing System Management and Egg Handling Practices
                                            Accession Number: 438593
                                        Intestinal Microbial Ecology and Non-Antibiotic Strategies to Limit Shiga Toxin-Producing Escherichia coli (STEC) and Antimicrobial Resistance Transmission in Food Animals
                                            Accession Number: 438679
                                        Reduction of Foodborne Pathogens and Antimicrobial Resistance in Poultry Production Environments
                                            Accession Number: 438928
                                        Prevention and Mitigation of Pathogen Transmission from Cattle and Swine to Food, Water, and Environment
                                            Accession Number: 439046
                                        Multi-hurdle Approaches for Controlling Foodborne Pathogens in Poultry
                                            Accession Number: 439695
                                        Immunological and Practical Approaches to Manipulate the Ecological Niches and Reduce Foodborne Pathogens in Poultry
                                            Accession Number: 439780
                                        Evaluation of Genetic and Management Factors to Reduce Foodborne Pathogens and Antimicrobial Resistance in Dairy Cattle
                                            Accession Number: 440225
                                        Alternatives to Antibiotics and Genomics of Antimicrobial Resistance to Control Foodborne Pathogens in Poultry
                                            Accession Number: 440256
                                        Ecological Factors that Enable Colonization, Retention, and Dispersal of Foodborne Pathogens and Intervention Strategies to Control the Pathogens and Antimicrobial Resistance in Cattle and Swine
                                            Accession Number: 440314
                                        Holistic Tactics to Advance the Microbiological Safety and Quality of the Red Meat Continuum
                                            Accession Number: 440930
                                        Analysis of Genetic Factors that Increase Foodborne Pathogen Fitness, Virulence, and Antimicrobial Resistance Transfer, to Identify Interventions against Salmonella and Campylobacter in Food Animals
                                            Accession Number: 440948
                                        Intervention Strategies to Control Salmonella and Campylobacter During Poultry Processing
                                            Accession Number: 442616**Publications**
                                                (Clicking on the reprint icon
                                                    Reprint Icon
                                                    will take you to the publication reprint.)An analysis of culture-based methods used for the detection and isolation of Salmonella spp., Escherichia coli, and Enterococcus spp. from surface water: a systematic review
                                                        

- (Peer Reviewed Journal)Mcconn, B.R., Kraft, A.L., Durso, L.M., Ibekwe, A.M., Frye, J.G., Wells, J., Tobey, E.M., Ritchie, S.M., Williams, C.F., Cook, K.L., Sharma, M. 2024. An analysis of culture-based methods used for the detection and isolation of Salmonella spp., Escherichia coli, and Enterococcus spp. from surface water: a systematic review. Science of the Total Environment. https://doi.org/10.1016/j.scitotenv.2024.172190.A comparison of methods to detect low levels of Salmonella enterica in surface waters to support antimicrobial resistance surveillance efforts performed in multiple laboratories
                                                        

- (Peer Reviewed Journal)Kraft, A., Wells, J., Frye, J.G., Ibekwe, A.M., Durso, L.M., Hiott, L.M., East, C.L., Mcconn, B., Franklin, A.M., Boczek, L.A., Garland, J.L., Kabrera, C., Mcdermott, P., Ottesen, A.R., Zheng, J., Cook, K.L., Sharma, M. 2023. A comparison of methods to detect low levels of Salmonella enterica in surface waters to support antimicrobial resistance surveillance efforts performed in multiple laboratories  . Science of the Total Environment. https://doi.org/10.1016/j.scitotenv.2023.167189.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.Litter commensal bacteria can limit the horizontal gene transfer of antimicrobial resistance to Salmonella in chickens.

- (Peer Reviewed Journal)Oladeinde, A.A., Abdo, Z., Zwirzitz, B., Woyda, R., Lakin, S.M., Press, M.O., Cook, K.L., Cox Jr, N.A., Thomas, J.C., Looft, T.P., Rothrock Jr, M.J., Zock, G.S., Plumblee Lawrence, J.R., Cudnik, D., Ritz, C. 2022. Litter commensal bacteria can limit the horizontal gene transfer of antimicrobial resistance to Salmonella in chickens. Applied and Environmental Microbiology.88(9). https://doi.org/10.1128/aem.02517-21One Health Enteric Package: Expanded and standardized metadata for enteric genomic epidemiology in the US (GenFS Metadata workgroup)

- (Abstract Only)Horizontal gene transfer is the main driver of antimicrobial
resistance in broiler chicks infected with Salmonella enterica
Serovar Heidelberg
                                                        

- (Peer Reviewed Journal)Oladeinde, A.A., Abdo, Z., Press, M.O., Cook, K.L., Cox Jr, N.A., Zwirtzitz, B., Woyda, R., Lakin, S.M., Thomas Iv, J.C., Looft, T.P., Cosby, D.E., Hinton Jr, A., Guard, J.Y., Line, J.E., Rothrock Jr, M.J., Berrang, M.E., Herrington, K., Zock, G.S., Plumblee Lawrence, J.R., Cudnik, D., House, S.L., Ingram, K.D., Lariscy, L., Wagner, R., Aggrey, S.E., Chai, L., Ritz, C. 2021. Horizontal gene transfer is the main driver of antimicrobial resistance in broiler chicks infected with Salmonella enterica Serovar Heidelberg. mSystems. 6(4):e00729-21. https://doi.org/10.1128/mSystems.00729-21.Do long-term conservation pasture management practices influence microbial diversity and antimicrobial resistant genes in runoff
                                                        

- (Peer Reviewed Journal)Yang, Y., Ashworth, A.J., Durso, L.M., Savin, M., Debruyan, J., Cook, K.L., Moore Jr., P.A., Owens, P.R. 2021. Do long-term conservation pasture management practices influence microbial diversity and antimicrobial resistant genes in runoff. Frontiers in Microbiology. 12. Article 617066. https://doi.org/10.3389/fmicb.2021.617066.Antimicrobial resistant gene prevalence in soils due to animal manure deposition and long-term pasture management
                                                        

- (Peer Reviewed Journal)Yang, Y., Ashworth, A.J., Debruyn, J., Durso, L.M., Savin, M., Cook, K.L., Moore Jr., P.A., Owens, P.R. 2020. Antimicrobial resistant gene prevalence in soils due to animal manure deposition and long-term pasture management. PeerJ. 8:e10258. https://doi.org/10.7717/peerj.10258.Persistence of antibiotic resistant pathogens and commensal bacteria in “no antibiotic ever” production broiler house litter

- (Abstract Only)Reused poultry litter microbiome with competitive exclusion potential against Salmonella Heidelberg
                                                        

- (Peer Reviewed Journal)Bucher, M., Zwirzitz, B., Oladeinde, A.A., Cook, K.L., Plymel, C., Zock, G., Aggrey, S., Ritz, C., Looft, T.P., Lipp, E., Agga, G.E., Sistani, K.R. 2020. Reused poultry litter microbiome with competitive exclusion potential against Salmonella Heidelberg. Journal of Environmental Quality. 49(4):869-881. https://doi.org/10.1002/jeq2.20081.Multiple E. coli sequence types contribute to the acquisition of IncI1 plasmids in Salmonella Heidelberg

- (Abstract Only)Does built-up litter competitively exclude Salmonella: What have we learned from Salmonella Heidelberg?

- (Abstract Only)Review of antibiotic resistance, ecology, and dissemination and mitigation in U.S. broiler poultry systems
                                                        

- (Literature Review)Yang, Y., Ashworth, A.J., Cook, K.L., Willett, C., Upadhyay, A., Owens, P.R., Ricke, S.C., DeBruyn, J.M., Moore Jr, P.A. 2019. Review of antibiotic resistance, ecology, and dissemination and mitigation in U.S. broiler poultry systems. Frontiers in Microbiology. 10:2639. https://doi.org/10.3389/fmicb.2019.02639.Research Note: Evaluation of several inoculation procedures for colonization of day-old broiler chicks with Salmonella Heidelberg
                                                        

- (Peer Reviewed Journal)Cox Jr, N.A., Oladeinde, A.A., Cook, K.L., Zock, G.S., Berrang, M.E., Ritz, C.W., Hinton Jr, A. 2020. Research Note: Evaluation of several inoculation procedures for colonization of day-old broiler chicks with Salmonella Heidelberg. Poultry Science. 99(3):1615-1617. https://doi.org/10.1016/j.psj.2019.10.020.Soil bacterial biodiversity is driven by long-term pasture management, poultry litter, and cattle manure inputs
                                                        

- (Peer Reviewed Journal)Yang, Y., Ashworth, A.J., Debruyn, J.M., Willett, C., Durso, L.M., Cook, K.L., Moore Jr, P.A., Owens, P.R. 2019. Soil bacterial biodiversity is driven by long-term pasture management, poultry litter, and cattle manure inputs. PeerJ. 7:e7839. https://doi.org/10.7717/peerj.7839.Horizontal gene transfer and acquired antibiotic resistance in S. Heidelberg following in vitro incubation in broiler ceca
                                                        

- (Peer Reviewed Journal)Oladeinde, A.A., Cook, K.L., Lakin, S., Abdo, Z., Looft, T.P., Herrington, K., Zock, G.S., Plumblee Lawrence, J.R. 2019. Horizontal gene transfer and acquired antibiotic resistance in S. Heidelberg following in vitro incubation in broiler ceca. Applied and Environmental Microbiology. 85(22):e01903-19. https://doi.org/10.1128/AEM.01903-19.A newly developed Escherichia coli isolate panel from a cross section of U.S. animal production systems reveals geographic and commodity-based differences in antibiotic resistance gene carriage
                                                        

- (Peer Reviewed Journal)Ducey, T.F., Durso, L.M., Ibekwe, A.M., Dungan, R.S., Jackson, C.R., Frye, J.G., Castleberry, B., Rashash, D.M., Rothrock Jr, M.J., Boykin, D.L., Whitehead, T.R., Ramos, Z.D., McManus, M.N., Cook, K.L. 2020. A newly developed Escherichia coli isolate panel from a cross section of U.S. animal production systems reveals geographic and commodity-based differences in antibiotic resistance gene carriage. Journal of Hazardous Materials. 382. https://doi.org/10.1016/j.jhazmat.2019.120991.Population analyses reveal preenrichment method and selective enrichment media affect Salmonella serovars detected on broiler carcasses
                                                        

- (Peer Reviewed Journal)Cox Jr, N.A., Berrang, M.E., House, S.L., Medina, D., Cook, K.L., Shariat, N.W. 2019. Population analyses reveal preenrichment method and selective enrichment media affect Salmonella serovars detected on broiler carcasses. Journal of Food Protection. 82(10):1688-1696. https://doi.org/10.4315/0362-028X.JFP-19-166.Pre-enrichment and enrichment influence salmonella serovar populations in broilers

- (Abstract Only)Cox Jr, N.A., Berrang, M.E., House, S.L., Medina, D., Cook, K.L., Shariat, N.W. 2019. Pre-enrichment and enrichment influence salmonella serovar populations in broilers [abstract]. Poultry Science Association Meeting Abstract. 98(1):120.Detection of multiple serotypes of Salmonella on pre-chill chicken carcasses by whole carcass rinse or whole carcass incubation

- (Abstract Only)Detection of multiple serotypes of Salmonella on pre-Chill chicken carcasses by whole carcass rinse or whole carcass incubation

- (Abstract Only)Berrang, M.E., Cox Jr, N.A., Shariat, N., Cook, K.L., Frye, J.G., Meinersmann, R.J. 2019. Detection of multiple serotypes of Salmonella on pre-Chill chicken carcasses by whole carcass rinse or whole carcass incubation [abstract]. International Association for Food Protection Proceedings. 98(1):63.One health and antimicrobial resistance, a United States perspective
                                                        

- (Peer Reviewed Journal)Bright-Pointe, S. A. Beaudoin, K. Bjork, K.L. Cook, L.M. Durso, J. Gilbert, C. Shivley, R. Singh, H. Tate, E.L. Thacker, B. Walters, J. Whichard.  2019.  One Health and antimicrobial resistance, a United States perspective.  Rev. Sci. Tech. Off. Int. Epiz 38:173-184. https://doi.org/10.20506/rst.38.1.2951.Persistence of antibiotic resistance genes in beef cattle backgrounding environment over two years after cessation of operation
                                                        

- (Peer Reviewed Journal)Agga, G.E., Cook, K.L., Netthisinghe, A.M., Gilfillen, R.A., Woosley, P.B., Sistani, K.R. 2019. Persistence of antibiotic resistance genes in beef cattle backgrounding environment over two years after cessation of operation. PLoS One. 12(2):1-19. https://doi.org/10.1371/journal.pone.0212510.Antimicrobial resistance associated with the poultry production environment

- (Abstract Only)Environmental dimension of antibiotic resistance: Assessment of basic science gaps
                                                        

- (Peer Reviewed Journal)Smalla, K., Cook, K.L., Djordjevic, S., Klumper, U., Gillings, M. 2018. Environmental dimension of antibiotic resistance: Assessment of basic science gaps. FEMS Microbiology Ecology. https://doi.org/10.1093/femsec/fiy195.Enrichments of antibiotic resistome following poultry litter soil amendment

- (Abstract Only)Agga, G.E., Fanelli, B., Looft, T.P., Cook, K.L., Durso, L.M., Hasan, N.A., Sistani, K.R. 2018. Enrichments of antibiotic resistome following poultry litter soil amendment. Research Workers in Animal Diseases Conference Proceedings. Poster No. 145.Hotspot mutations and ColE1 plasmids contribute to the fitness of Salmonella Heidelberg in poultry litter
                                                        

- (Peer Reviewed Journal)Oladeinde, A., Cook, K.L., Orlek, A., Zock, G.S., Herrington, K., Plumblee Lawrence, J.R., Hall, M.C., Cox Jr, N.A. 2018. Hotspot mutations and ColE1 plasmids contribute to the fitness of Salmonella Heidelberg in poultry litter. PLoS One. https://doi.org/10.1371/journal.pone.0202286.Managing beef backgrounding residual soil contaminants by alum and biochar amendments
                                                        

- (Peer Reviewed Journal)Netthisinghe, A., Cook, K.L., Gilfillen, R., Woosley, P., Sistani, K.R. 2018. Managing beef backgrounding residual soil contaminants by alum and biochar amendments. Journal of Environmental Quality. https://doi.org/10.2134/jeq2018.02.0088.Transcriptome changes of Escherichia coli, Enterococcus faecalis and Escherichia coli O157:H7 laboratory strains in response to photo-degraded DOM
                                                        

- (Peer Reviewed Journal)Oladeinde, A., Lipp, E., Chen, C., Murihead, R., Glenn, T., Cook, K.L., Molina, M. 2018. Transcriptome changes of Escherichia coli, Enterococcus faecalis and Escherichia coli O157:H7 laboratory strains in response to photo-degraded DOM. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2018.00882.Longitudinal environmental sampling of small organic farms for foodborne pathogens and indicator bacteria as part of the HARVEST Initiative

- (Abstract Only)Co1 plasmids contribute to the fitness of Salmonella Heidelberg in poultry litter

- (Abstract Only)Effect of manure application rate and rainfall timing on the leaching of antibiotic-resistant bacteria and their associated genes

- (Peer Reviewed Journal)Bolster, C.H., Brooks, J.P., Cook, K.L. 2018. Effect of manure application rate and rainfall timing on the leaching of antibiotic-resistant bacteria and their associated genes. Water, Air, and Soil Pollution. https://doi.org/10.1007/s11270-018-3781-6.Antibiotic resistance in agroecosystems: A One Health perspective
                                                        

- (Peer Reviewed Journal)Durso, L.M., Cook, K.L. 2018. Antibiotic resistance in agroecosystems: A One Health perspective. EcoHealth. 14:1-6.Incidence and degree of Salmonella Heidelberg colonization of day old broiler chicks using several methods of inoculation

- (Abstract Only)Oladeinde, A., Cook, K.L., Cox Jr, N.A., Ritz, C., Cosby, D.E., Plumblee Lawrence, J.R., House, S.L., Zock, G.S., Jackson, J. 2018. Incidence and degree of Salmonella Heidelberg colonization of day old broiler chicks using several methods of inoculation . Meeting Abstract. 97(E-Suppl 1):65.Incidence, species and antimicrobial resistance of naturally occurring Campylobacter isolates from quail carcasses sampled in a commercial processing facility
                                                        

- (Peer Reviewed Journal)Cox Jr, N.A., Cosby, D.E., Thippareddi, H., Ritz, C.W., Berrang, M.E., Jackson, J.S., Mize, S.C., Kumar, S., Howard, A.K., Rincon, A.M., Ukidwe, M., Landrum, M., Frye, J.G., Plumblee Lawrence, J.R., Hiott, L.M., Jackson, C.R., Hinton Jr, A., Cook, K.L. 2018. Incidence, species and antimicrobial resistance of naturally occurring Campylobacter isolates from quail carcasses sampled in a commercial processing facility. Journal of Food Safety. 2018:38:e12438. https://doi.org/10.1111/jfs.12438.Use of molecular markers to compare Escherichia coli transport to traditional groundwater tracers in epikarst

- (Peer Reviewed Journal)Bandy, A., Cook, K.L., Fryar, A., Polk, J. 2018. Use of molecular markers to compare Escherichia coli transport to traditional groundwater tracers in epikarst. Journal of Environmental Quality. 47:88-95. doi:10.2134/jeq2017.10.0406.Using the agricultural environment to select better surrogates for foodborne pathogens associated with fresh produce
                                                        

- (Peer Reviewed Journal)Cook, K.L., Givan, E., Mayton, H., Parekh, R.R., Taylor, R., Walker, S. 2017. Using the agricultural environment to select better surrogates for foodborne pathogens associated with fresh produce. International Journal of Food Microbiology. 262/80-88. doi: 10.1016/j.ijfoodmicro.2017.09.017.Effect of cessation of beef cattle pasture-feedlot type backgrounding operation on the persistence of antibiotic resistance genes in the environment

- (Abstract Only)Agga, G.E., Cook, K.L., Netthisinghe, A.M., Parekh, R.R. 2017. Effect of cessation of beef cattle pasture-feedlot type backgrounding operation on the persistence of antibiotic resistance genes in the environment. Meeting Abstract. p. 97.Antibiotic resistance genes persist longer in soils with subsurface banded poultry litter

- (Abstract Only)Poultry litter environment selects for the development of antibiotic resistance (AR) in Salmonella Heidelberg via conjugative IncX plasmids

- (Abstract Only)Evaluation of a single-stage carbon oxidation-nitrification process for treating high TAN effluent from anaerobic digestion of poultry rendering wastewater

- (Abstract Only)Lovanh, N.C., Loughrin, J.H., Cook, K.L., Silva, P.J., Sistani, K.R. 2017. Evaluation of a single-stage carbon oxidation-nitrification process for treating high TAN effluent from anaerobic digestion of poultry rendering wastewater. ASABE Annual International Meeting. Paper No. 1327.Plasmid mediated colistin resistance in food animal intestinal contents detected by selective enrichment

- (Abstract Only)Bacterial and archaeal ammonia oxidizers respond differently to long-term tillage and fertilizer management at a continuous maize site
                                                        

- (Peer Reviewed Journal)Segal, L.M., Miller, D.N., McGhee, R., Loecke, T.D., Cook, K.L., Shapiro, C.A., Drijber, R.A. 2017. Bacterial and archaeal ammonia oxidizers respond differently to long-term tillage and fertilizer management at a continuous maize site. Soil and Tillage Research. 168:110-117.Prevalence of mcr-1 in U.S. food-animal cecal contents

- (Peer Reviewed Journal)Meinersmann, R.J., Ladely, S.R., Plumblee Lawrence, J.R., Cook, K.L., Thacker, E.L. 2017. Prevalence of mcr-1 in U.S. food-animal cecal contents. Antimicrobial Agents and Chemotherapy. 61(2):e02244-16.Complete sequence of a colistin resistance gene (mcr-1) bearing isolate of Escherichia coli from the United States

- (Peer Reviewed Journal)Meinersmann, R.J., Ladely, S.R., Bono, J.L., Plumblee Lawrence, J.R., Hall, M.C., Genzlinger, L.L., Cook, K.L. 2016. Complete sequence of a colistin resistance gene (mcr-1) bearing isolate of Escherichia coli from the United States. Genome Announcements. 4(6):1283-16.Composting swine manure from high rise finishing facilities

- (Trade Journal)Ritchey, E., Cook, K.L. 2016. Composting swine manure from high rise finishing facilities. University of Kentucky Cooperative Extension Bulletin. 5:14. Available: http://uknowledge.uky.edu/pss_reports/8/.Colistin resistance mcr-1 gene bearing Escherichia coli from the United States

- (Peer Reviewed Journal)Meinersmann, R.J., Ladely, S.R., Plumblee Lawrence, J.R., Hall, M.C., Simpson, S.A., Ballard, L.L., Scheffler, B.E., Genzlinger, L.L., Cook, K.L. 2016. Colistin resistance mcr-1 gene bearing Escherichia coli from the United States. Genome Announcements. 4(5):898-16.Using the Agricultural Environment to Find Better Surrogates for Foodborne Pathogens

- (Abstract Only)Methane generation during swine manure windrows: a case study

- (Proceedings)Lovanh, N.C., Loughrin, J.H., Cook, K.L., Silva, P.J., Sistani, K.R. 2016. Methane generation during swine manure windrows: a case study. Florida Section - Air and Waste Management Association Annual Conference. 1121.Evaluating antibiotic resistance genes in soils with applied manures

- (Abstract Only)Cook, K.L., Netthisinghe, A., Parekh, R.R., Gilfillen, R. 2016. Evaluating antibiotic resistance genes in soils with applied manures. International Association for Food Protection. July 31-August 3, 2016. St. Louis, MO.Management Can Reduce Mobility of Escherichia coli compared to traditional groundwater tracers within karst terrains

- (Abstract Only)Bandy, A., Cook, K.L., Gilfillen, R., Polk, J., Macko, S. 2016. Management Can Reduce Mobility of Escherichia coli compared to traditional groundwater tracers within karst terrains. Karst Water Environment Symposium. January 27-20, 2016. San Juan, Puerto Rico.How should we be determining background and baseline antibiotic resistance levels in agroecosystem research?

- (Peer Reviewed Journal)Rothrock Jr, M.J., Keen, P., Cook, K.L., Durso, L.M., Franklin, A.M., Dungan, R.S. 2016. How should we be determining background and baseline antibiotic resistance levels in agroecosystem research? Journal of Environmental Quality. 45:420-431.Characterization of Potential Surrogates for Produce Pathogens

- (Abstract Only)Mayton, H., Cook, K.L., Walker, S. 2015. Characterization of Potential Surrogates for Produce Pathogens. University of California, UCLA Water Resources Group.  December 2-4, 2015. Los Angeles, CA.Management Can Reduce Contamination Potential of Beef Backgrounding

- (Trade Journal)Netthisinghe, A., Cook, K.L., Gilfillen, R., Woosley, P. 2015. Management Can Reduce Contamination Potential of Beef Backgrounding. Crop Science Newsletter. 60(11):16-17.Elucidating the potential for transfer of antibiotic resistance genes trhough agro-ecosystems

- (Abstract Only)Cook, K.L., Jechalke, S., Wolters, B., Smalla. 2015. Elucidating the potential for transfer of antibiotic resistance genes trhough agro-ecosystems. 2015 ASA-CSSA-SSSA Annual Meeting. November 15-18, 2015. Minneapolis, Minnesota.Proposed chemical mechanismsManagement practices impacts soil nutrients and bacterial populations in backgrounding beef
feedlot

- (Proceedings)Netthisinghe, A., Sistani, K.R., Cook, K.L., Gilfillen, R., Rice, C. 2015. Proposed chemical mechanismsManagement practices impacts soil nutrients and bacterial populations in backgrounding beef feedlot . Meeting Proceedings. http://proceedings.esri.com/library/userconf/proc15/index.html.Field scale manure born animal waste management : GIS application

- (Proceedings)Netthisinghe, A., Sistani, K.R., Cook, K.L., Gilfillen, R., Rice, C. 2015. Field scale manure born animal waste management : GIS application . ESRI Conference Proceedings. 24:239.Approaches to assess the effects and risks of veterinary antibiotics applied with manure to soil

- (Book / Chapter)Sven, J., Cook, K.L., Kornelia, S. 2015. Approaches to assess the effects and risks of veterinary antibiotics applied with manure to soil. Antibiotic Resistant Bacteria - An Open Challenge, Prof. Maria Cristina Ossiprandi (Ed.), InTech, DOI: 10.5772/61871.Soil Microbiology, Ecology, and Biochemistry

- (Review Article)Cook, K.L. 2015. Soil Microbiology, Ecology, and Biochemistry. Fourth Edition. Soil Science Society of America Journal. 79:1821.Management practices affect soil nutrients and bacterial populations in backgrounding beef feedlot

- (Peer Reviewed Journal)Netthisinghe, A., Cook, K.L., Gilfillen, R., Sistani, K.R., Woosley, P. 2015. Management practices affect soil nutrients and bacterial populations in backgrounding beef feedlot. Journal of Environmental Quality. 44(6):1892-1902.Escherichia coli strain diversity: Selecting isolates for use as pathogen surrogates

- (Abstract Only)Cook, K.L., Givan, E., Taylor, R. 2015. Escherichia coli strain diversity: Selecting isolates for use as pathogen surrogates. Federation of European Microbiological Societies, 6th Congress of European Microbiology. June 7-11, 2015. Maastricht, Netherlands.Antibiotic resistance gene concentrations in agroecosystems following beef manure or poultry litter deposition

- (Abstract Only)Cook, K.L., Netthisinghe, A., Gilfillen, R. 2015. Antibiotic resistance gene concentrations in agroecosystems following beef manure or poultry litter deposition. 3rd International Symposium on the Environmental Dimension of Antibiotic Resistance. May 17-21, 2015. Wernigerode, Germany.The effectiveness of flocculants on inorganic and metallic species removal during aerobic digestion of wastewater from poultry processing plant

- (Abstract Only)Lovanh, N.C., Loughrin, J.H., Cook, K.L., Sistani, K.R., Silva, P.J. 2015. The effectiveness of flocculants on inorganic and metallic species removal during aerobic digestion of wastewater from poultry processing plant. American Chemical Society Annual Meeting Symposium Proceedings. Paper #152123798.Strain diversity in the fecal indicator Escherichia coli: implications for its use as a produce pathogen surrogate

- (Proceedings)Cook, K.L., Givan, E., Taylor, R. 2015. Strain diversity in the fecal indicator Escherichia coli: implications for its use as a produce pathogen surrogate. Kentucky Water Resources Research Institute Symposium. 49-50.Environmental E.coli isolate characterization and selection as improved indicators for pathogens associated with produce contamination

- (Abstract Only)Cook, K.L., Givan, E., Taylor, R. 2015. Environmental E.coli isolate characterization and selection as improved indicators for pathogens associated with produce contamination. 2015 Kentucky Public Health Association Conference. April 14-16, 2015. Owensboro, Kentucky.Composting swine slurry to reduce indicators and antibiotic resistance genes

- (Proceedings)Cook, K.L., Bolster, C.H., Sistani, K.R. 2015. Composting swine slurry to reduce indicators and antibiotic resistance genes. Waste to Worth Conference. March 30-Aril 3, 2015. Seattle, Washington.Effect of turning frequency and season on composting materials from swine high-rise facilities

- (Peer Reviewed Journal)Cook, K.L., Ritchey, E.L., Loughrin, J.H., Haley, M.A., Sistani, K.R., Bolster, C.H. 2015. Effect of turning frequency and season on composting materials from swine high-rise facilities. Waste Management. 39:86-95.The effectiveness of flocculants on inorganic and metallic species removal during aerobic digestion of wastewater from poultry processing plant

- (Abstract Only)Lovanh, N.C., Loughrin, J.H., Cook, K.L., Sistani, K.R., Silva, P.J. 2015. The effectiveness of flocculants on inorganic and metallic species removal during aerobic digestion of wastewater from poultry processing plant. American Chemical Society National Meeting. Abstract.Turning schedules influence final composition of composted swine manure

- (Abstract Only)Ritchey, E., Cook, K.L., Sistani, K.R., Simmons, J.R. 2014. Turning schedules influence final composition of composted swine manure. ASA-CSSA-SSSA Annual Meeting Abstracts. November 3-5, 2014. Long Beach, California.Use of stable isotope-labeled Escherichia coli as a tracer in karst aquifers

- (Abstract Only)Bandy, A., Cook, K.L., Macko, S., Fryar, A. 2014. Use of stable isotope-labeled Escherichia coli as a tracer in karst aquifers. Geological Society of America Annual Meeting. October 19-22, 2014. Vancouver, Canada.Detection of pathogens, indicators, and antibiotic resistance genes following land application of poultry litter

- (Popular Publication)Cook, K.L. 2014. Detection of pathogens, indicators, and antibiotic resistance genes following land application of poultry litter. CSA News. 59:39.Antibiotic resistance gene concentrations in soils from cattle feedlot:  A three year study

- (Abstract Only)Cook, K.L., Netthisinghe, A., Gilfillen, R. 2014. Antibiotic resistance gene concentrations in soils from cattle feedlot:  A three year study. ASA-CSSA-SSSA Annual Meeting Abstracts. November 3-5,2014. Long Beach, California.Effect of windrow management on ammonia and nitrous oxide emissions from swine manure composting

- (Peer Reviewed Journal)Lovanh, N.C., Loughrin, J.H., Cook, K.L., Silva, P.J., Oh, B. 2014. Effect of windrow management on ammonia and nitrous oxide emissions from swine manure composting. International Journal of Agricultural and Biosystems Engineering. 8(6):369-373.Effect of manure application rate and timing on the leaching potential of antibiotic resistant bacteria.

- (Abstract Only)Bolster, C.H., Cook, K.L., Brooks, J.P. 2014. Effect of manure application rate and timing on the leaching potential of antibiotic resistant bacteria.. ASA-CSSA-SSSA Annual Meeting Abstracts. Abastract.Impacts of antibiotic use in agriculture: what are the benefits and risks?

- (Peer Reviewed Journal)Durso, L.M., Cook, K.L. 2014. Impacts of antibiotic use in agriculture: what are the benefits and risks? Current Opinion in Microbiology. 19:37-44. DOI: 10.1016/J.MIB.2014.05.019.Nutrient source and tillage impacts on tall fescue production and soil properties

- (Peer Reviewed Journal)Netthisinghe, A., Woosley, P., Gilfillen, R., Cook, K.L., Sistani, K.R. 2014. Nutrient source and tillage impacts on tall fescue production and soil properties. Agronomy Journal. 106:1427–1437.Detection of pathogens, indicators and antibiotic resistance genes following land application of poultry litter

- (Peer Reviewed Journal)Cook, K.L., Netthisinghe, A.M., Gilfillen, R.A. 2014. Detection of pathogens, indicators and antibiotic resistance genes following land application of poultry litter. Journal of Environmental Quality. 43:1546-1558.Effect of windrow management on ammonia and nitrous oxide emissions from swine manure composting

- (Proceedings)Lovanh, N.C., Loughrin, J.H., Cook, K.L., Silva, P.J., Oh, B. 2014. Effect of windrow management on ammonia and nitrous oxide emissions from swine manure composting. CAEE 2014 : International Conference on Agricultural and Environmental Engineering. 65-69.Pathogens, indicators and antibiotic resistance genes in soils with land applied poultry litter

- (Abstract Only)Cook, K.L., Gilfillen, R.A., Netthisinghe, A.P., Woosley, P. 2014. Pathogens, indicators and antibiotic resistance genes in soils with land applied poultry litter. International Association for Food Protection Proceedings. August 3-4, 2014. Indianapolis, Indiana.Soil micro nutrients in backgrounding beef feedlot site

- (Abstract Only)Netthisinghe, A., Gilfillen, R., Cook, K.L., Sistani, K.R. 2014. Soil micro nutrients in backgrounding beef feedlot site. American Society of Agronomy Branch Meeting. Abstract.The use of organic soil amendments for winter wheat production in Kentucky

- (Proceedings)Ritchey, E.L., Cook, K.L., Gray, J.L. 2013. The use of organic soil amendments for winter wheat production in Kentucky. North Central Extension Industry Soil Fertility Conference Proceedings. on-line at http://www.ipni.net/ipniweb/conference/ncisfc.nsf. 29:69-76.Improvement of anaerobic digester performance by wastewater recirculation through an aerated membrane.

- (Peer Reviewed Journal)Loughrin, J.H., Lovanh, N.C., Cook, K.L. 2013. Improvement of anaerobic digester performance by wastewater recirculation through an aerated membrane. Transactions of the ASABE. 56(5):1675-1681.Affect of soil amendments and manure application on nitrifiers and denitrifiers

- (Abstract Only)Cook, K.L., Sistani, K.R. 2013. Affect of soil amendments and manure application on nitrifiers and denitrifiers. ASA-CSSA-SSSA Annual Meeting Abstracts. Abstract.Robust, cross-laboratory validated PCR methods to track antibiotic resistance in agricultural settings

- (Abstract Only)Cook, K.L., Moorman, T.B., Durso, L.M. 2013. Robust, cross-laboratory validated PCR methods to track antibiotic resistance in agricultural settings. ASA-CSSA-SSSA Annual Meeting Abstracts. Abstract.Sensitivity of mycobacterium avium subsp paratuberculosis, escherichia coli and salmonella enterica serotype typhimurium to low pH, high organic acids and ensiling

- (Peer Reviewed Journal)Cook, K.L., Flis, S.A., Ballard, C.S. 2013. Sensitivity of mycobacterium avium subsp paratuberculosis, escherichia coli and salmonella enterica serotype typhimurium to low pH, high organic acids and ensiling. Journal of Applied Microbiology. 115:334-345. doi:10.1111/jam.12243.Mycobacterium avium subsp paratuberculosis cells are surprisingly resistant to ensiling process.

- (Research Technical Update)Cook, K.L., Flis, S.A., Ballard, C.S. 2013. Mycobacterium avium subsp paratuberculosis cells are surprisingly resistant to ensiling process. Paratuberculosis Newsletter. March 2013 p7-8.Relationship of soil nutrient content from poultry litter and dairy manure on microbial survival in fescue soils

- (Abstract Only)Gilfillen, R., Cook, K.L., Netthisinghe, A., Woosley, P., Cundiff, G. 2013. Relationship of soil nutrient content from poultry litter and dairy manure on microbial survival in fescue soils. American Society of Agronomy Branch Meeting. Abstrat.Soil nutrient dynamics in small beef cattle backgrounding feedlot on karst environment

- (Abstract Only)Netthisinghe, A., Gilfillen, R., Cook, K.L., Sistani, K.R. 2013. Soil nutrient dynamics in small beef cattle backgrounding feedlot on karst environment. American Society of Agronomy Branch Meeting. abstract.Effects of Poultry litter and dairy manure applications on forage yield and quality in conventional and no-till established tall fescue (Scheonourous phoenix [Scop.] Holub) sward.

- (Abstract Only)Woosley, P.B., Netthisinghe, A., Gilfillen, R., Cook, K.L., Sandor, D.S. 2013. Effects of Poultry litter and dairy manure applications on forage yield and quality in conventional and no-till established tall fescue (Scheonourous phoenix [Scop.] Holub) sward.. American Society of Agronomy Branch Meeting. abstract.Influence of swine manure application method on concentrations of methanogens and denitrifiers in agricultural soils

- (Proceedings)Cook, K.L., Sistani, K.R. 2013. Influence of swine manure application method on concentrations of methanogens and denitrifiers in agricultural soils. Meeting Abstract. online. http://www.extension.org/67590Microbial populations associated with agricultural wastewaters and wastewater treatment

- (Abstract Only)Cook, K.L., Loughrin, J.H., Sistani, K.R. 2013. Microbial populations associated with agricultural wastewaters and wastewater treatment. Water Research. Abstract.Soil nutrients, bacteria populations, and veterinary pharmaceuticals across a backgrounding beef feedlot

- (Peer Reviewed Journal)Netthisinghe, A.P., Cook, K.L., Rice, C., Gilfillen, R.A., Sistani, K.R. 2013. Soil nutrients, bacteria populations, and veterinary pharmaceuticals across a backgrounding beef feedlot. Journal of Environmental Quality. 42:532–544; DOI:10.2134.Recirculating waste through a silicone membrane in an aerobic chamber improves biogas quality and wastewater malodors

- (Peer Reviewed Journal)Loughrin, J.H., Cook, K.L., Lovanh, N.C. 2012. Recirculating waste through a silicone membrane in an aerobic chamber improves biogas quality and wastewater malodors. Transactions of the ASABE. 55(5):1229-1237.Microbial pathogen and indicator survival in fescue soils with livestock amendments

- (Abstract Only)Cook, K.L., Gilfillen, R.A., Netthisinghe, A.P., Woosley, P. 2012. Microbial pathogen and indicator survival in fescue soils with livestock amendments. ASA-CSSA-SSSA Annual Meeting Abstracts. Abstract.Ammonia emission from swine manure windrows: a case study of biomass reduction vs. potential nutrient loss

- (Abstract Only)Lovanh, N.C., Loughrin, J.H., Cook, K.L., Silva, P.J., Ritchey, E. 2012. Ammonia emission from swine manure windrows: a case study of biomass reduction vs. potential nutrient loss. ASABE Annual International Meeting. Abstract Only.Seasonal variation in heat fluxes, predicted emissions of malodorants, and wastewater quality of an anaerobic swine waste lagoon

- (Peer Reviewed Journal)Loughrin, J.H., Quintanar, A.I., Cook, K.L., Lovanh, N.C., Mahmood, R., Bexerra-Acosta, E. 2012. Seasonal variation in heat fluxes, predicted emissions of malodorants, and wastewater quality of an anaerobic swine waste lagoon. Water, Air, and Soil Pollution. 223:3611–3618.Johnes disease: Troughs as a hidden source

- (Research Technical Update)Cook, K.L., Bolster, C.H. 2012. Johnes disease: Troughs as a hidden source. Natural Resources Research Update (NRRU). NRRU only.A microbial approach to understanding the production of ammonia in poultry litter

- (Research Technical Update)Cook, K.L., Rothrock Jr, M.J., Lovanh, N.C., Sistani, K.R. 2012. A microbial approach to understanding the production of ammonia in poultry litter. Natural Resources Research Update (NRRU). NRRU only.Development of in-house methods for high-throughput DNA extraction

- (Proceedings)Cook, K.L., Hill, L. 2012. Development of in-house methods for high-throughput DNA extraction. Kentucky Water Resources Research Institute Symposium. 25-26.Impact of growth conditions on transport behavior of E. coli

- (Peer Reviewed Journal)Marcus, I.M., Bolster, C.H., Cook, K.L., Opot, S.R., Walker, S.L. 2012. Impact of growth conditions on transport behavior of E. coli. Journal of Environmental Monitoring. 14:984-991.Amending poultry litter to reduce ammonia producing bacteria

- (Research Technical Update)Cook, K.L., Rothrock Jr, M.J., Lovanh, N.C., Sistani, K.R. 2012. Amending poultry litter to reduce ammonia producing bacteria. Natural Resources Research Update (NRRU). Technical update.Comparison of nutrient source and forage quality as it relates to microbial survival in fescue soils.

- (Abstract Only)Gilfillen, B., Cook, K.L., Netthisinghe, A., Woosley, P., Condiff, G. 2012. Comparison of nutrient source and forage quality as it relates to microbial survival in fescue soils.. American Society of Agronomy Branch Meeting. Abstract only.Turning schedules effect nutrient content of composted swine manure

- (Abstract Only)Ritchey, E., Cook, K.L., Loughrin, J.H., Sistani, K.R. 2012. Turning schedules effect nutrient content of composted swine manure. American Society of Agronomy Branch Meeting. Abstract.Utilization of poultry litter for pesticide bioremediation

- (Book / Chapter)Lovanh, N.C., Ruiz-Aguilar, G., Rothrock Jr, M.J., Cook, K.L. 2012. Utilization of poultry litter for pesticide bioremediation. Applied Research in Animal Manure Management: Challenges and Opportunities beyond the Adverse Environmental Impacts. 11:285-296.Spatial variation in selected veterinary drugs across a cattle feedlot transect from barn to retention basin

- (Abstract Only)Atmospheric emissions of nitrous oxide, methane, and carbon dioxide from different nitrogen fertilizers

- (Peer Reviewed Journal)Sistani, K.R., Jn-Baptiste, M., Lovanh, N.C., Cook, K.L. 2011. Atmospheric emissions of nitrous oxide, methane, and carbon dioxide from different nitrogen fertilizers. Journal of Environmental Quality. 40:1797–1805.Escherichia coli diversity in livestock manures and agriculturally impacted stream waters

- (Peer Reviewed Journal)Cook, K.L., Bolster, C.H., Ayers, K.A., Reynolds, D.N. 2011. Escherichia coli diversity in livestock manures and agriculturally impacted stream waters. Current Microbiology. 63(5):439–449.Effect of volumetric water content and crimson clover (Trifolium incarnatum) growth on the survival of Escherichia Coli O157:H7 in a soil matrix

- (Abstract Only)Cook, K.L., Rothrock Jr, M.J., Frantz, J., Burnett, S. 2012. Effect of volumetric water content and crimson clover (Trifolium incarnatum) growth on the survival of Escherichia Coli O157:H7 in a soil matrix. ASA-CSSA-SSSA Annual Meeting Abstracts. Abstract.Atmospheric Emissions of N2O, CH4, and CO2 from Different Nitrogen Fertilizers

- (Abstract Only)Sistani, K.R., Jn-Baptiste, M., Lovanh, N.C., Cook, K.L. 2011. Atmospheric Emissions of N2O, CH4, and CO2 from Different Nitrogen Fertilizers. ASA-CSSA-SSSA Annual Meeting Abstracts. Abstract Only.Effect of volumetric water content and crimson clover (Trifolium incarnatum) growthon the survival of Escherichia coli O157:H7 in a soil matrix

- (Abstract Only)Rothrock Jr, M.J., Frantz, J., Burnett, S., Cook, K.L. 2011. Effect of volumetric water content and crimson clover (Trifolium incarnatum) growthon the survival of Escherichia coli O157:H7 in a soil matrix. ASA-CSSA-SSSA Annual Meeting Abstracts. p. 1.Soil nutrients, bacterial communities, and veterinary pharmaceuticals in beef cattle backgrounding confinement on karst environment

- (Abstract Only)Netthisinghe, A., Cook, K.L., Rice, C., Sistani, K.R., Gilfillen, R., Nino De Guzman, G.T. 2011. Soil nutrients, bacterial communities, and veterinary pharmaceuticals in beef cattle backgrounding confinement on karst environment. ASA-CSSA-SSSA Annual Meeting Abstracts. Abstract.Effect of volumetric water content and crimson clover (trifolium incarnatum)growth on the survival of escherichia coli o157:h7 in a soil matrix

- (Abstract Only)Rothrock Jr, M.J., Frantz, J., Bumett, S., Cook, K.L. 2011. Effect of volumetric water content and crimson clover (trifolium incarnatum)growth on the survival of escherichia coli o157:h7 in a soil matrix [abstract]. ASA-CSSA-SSSA Annual Meeting Abstracts.Impact of amendments on microbial communities associated with nitrogen mineralization in poultry litter

- (Abstract Only)Cook, K.L., Rothrock Jr, M.J., Warren, J.G., Gilfillen, R., Netthisinghe, A., Sistani, K.R. 2011. Impact of amendments on microbial communities associated with nitrogen mineralization in poultry litter. ASA-CSSA-SSSA Annual Meeting Abstracts. Abstract.Remediation of swine slurry odor and methane using a partitioning bioreactor

- (Abstract Only)Cook, K.L., Loughrin, J.H., Lovanh, N.C. 2011. Remediation of swine slurry odor and methane using a partitioning bioreactor. Conference on Gastrointestinal Function. Abstract Only.Ammonium and skatole biodegradation by swine waste microflora in a flow-through  bioreactor

- (Abstract Only)Lovanh, N.C., Cook, K.L., Loughrin, J.H. 2011. Ammonium and skatole biodegradation by swine waste microflora in a flow-through  bioreactor. ASABE Annual International Meeting. Abstract.Skatole biodegradation via isolates from swine manure

- (Proceedings)Lovanh, N.C., Cook, K.L., Rothrock Jr, M.J. 2011. Skatole biodegradation via isolates from swine manure. Bioremediation and Sustainable Environmental Technologies. Abstract.Genotypic diversity of escherichia coli isolates from environmental sources and the influence on transport behavior

- (Proceedings)Cook, K.L., Bolster, C.H., Ayers, K., Reynolds, D. 2011. Genotypic diversity of escherichia coli isolates from environmental sources and the influence on transport behavior. Kentucky Water Resources Research Institute Symposium. 53-55.  http://www.uky.edu/WaterResources/2011_Proceedings.pdfEvaluation of amendments to manage nitrogen loss and microbiological quality in poultry litter.

- (Peer Reviewed Journal)Cook, K.L., Rothrock Jr, M.J., Eiteman, M.A., Lovanh, N.C., Sistani, K.R. 2011. Evaluation of amendments to manage nitrogen loss and microbiological quality in poultry litter. Journal of Environmental Management. 92:1760-1766.Effect of Litter Amendments on Microbial and Nitrogen Dynamics in  Poultry Houses

- (Abstract Only)Cook, K.L., Rothrock Jr, M.J., Parekh, R.R., Warren, J.G., Lovanh, N.C., Sistani, K.R. 2011. Effect of Litter Amendments on Microbial and Nitrogen Dynamics in  Poultry Houses. Poultry International Exposition. Meeting - No page numbers.Flooding event impacts soil pH, Ca, and P concentration distribution in a cattle backgrounding site on karst topography.

- (Abstract Only)Netthisinghe, A., Gilfillen, R., Cook, K.L., Sistani, K.R. 2011. Flooding event impacts soil pH, Ca, and P concentration distribution in a cattle backgrounding site on karst topography.. Meeting Abstract. Abstract Only.Acidification delays the microbial mineralization of organic N forms in poultry litter

- (Popular Publication)Rothrock Jr, M.J., Cook, K.L., Warren, J.G., Eiteman, M.A., Sistani, K.R. 2010. Acidification delays the microbial mineralization of organic N forms in poultry litter. CSA News. 55(10):11-13.Survival of the causative agent of Johne’s disease (Mycobacterium avium subsp paratuberculosis) in biofilms on trough materials

- (Other)Cook, K.L., Bolster, C.H., Britt, J. 2010. Survival of the causative agent of Johne’s disease (Mycobacterium avium subsp. paratuberculosis) in biofilms on trough materials. Paratuberculosis Newsletter. p.35.Microbial mineralization of organic nitrogen forms in poultry litters

- (Peer Reviewed Journal)Rothrock Jr, M.J., Cook, K.L., Warren, J.G., Eiteman, M.A., Sistani, K.R. 2010. Microbial mineralization of organic nitrogen forms in poultry litters. Journal of Environmental Quality. 39:1848-1857.Spatial Variation in Microbial Populations Across a Cattle Feedlot Transect from Barn to Retention Basin

- (Abstract Only)Cook, K.L., Netthisinghe, A., Gilfillen, B. 2010. Spatial Variation in Microbial Populations Across a Cattle Feedlot Transect from Barn to Retention Basin. ASA-CSSA-SSSA Annual Meeting Abstracts. Abstract only.Correlating Transport Behavior with Cell Properties for Eight Porcine Escherichia coli Isolates

- (Peer Reviewed Journal)Bolster, C.H., Cook, K.L., Marcus, I.M., Haznedaroglu, B.Z., Walker, S.L. 2010. Correlating Transport Behavior with Cell Properties for Eight Porcine Escherichia coli Isolates. Environmental Science and Technology. 44(13):5008–5014.Strain level differences in Escherichia coli transport, cell surface and adhesion characteristics

- (Abstract Only)Ayers, K., Cook, K.L., Parekh, R.R., Bolster, C.H., Reynolds, D. 2010. Strain level differences in Escherichia coli transport, cell surface and adhesion characteristics. American Society for Microbiology Branch Meeting. 1:15.Correlating attachment behavior with cell properties for eight Porcine Escherichia coli Isolates

- (Abstract Only)Bolster, C.H., Cook, K.L., Marcus, I.M., Haznedaroglu, B.Z., Walker, S.L. 2010. Correlating attachment behavior with cell properties for eight Porcine Escherichia coli Isolates. ASA-CSSA-SSSA Annual Meeting Abstracts.Survival of the Causative Agent of Johne’s Disease (Mycobacterium avium subsp. paratuberculosis) in Biofilms on Trough Materials

- (Research Technical Update)Cook, K.L. 2010. Survival of the Causative Agent of Johne’s Disease (Mycobacterium avium subsp. paratuberculosis) in Biofilms on Trough Materials. Natural Resources Research Update (NRRU). Update #1.Survivability of Mycobacterium avium subsp paratuberculosis in grass silage after fermentation and exposure to low pH and high organic acids

- (Abstract Only)Flis, S.A., Cook, K.L., Ballard, C.S. 2010. Survivability of Mycobacterium avium subsp paratuberculosis in grass silage after fermentation and exposure to low pH and high organic acids. American Dairy Science Association Proceedings. Abstract only.Strain level differences in E. coli transport, cell surface and adhesion characteristics

- (Abstract Only)Cook, K.L., Bolster, C.H., Walker, S., Ayers, K., Marcus, I. 2010. Strain level differences in E. coli transport, cell surface and adhesion characteristics. Microbial Ecology International Symposium. Abstract only.Quantification of the Sensitivity of Mycobacterium avium subsp paratuberculosis and Salmonella enterica subsp enterica to Low pH and High Organic Acids using Propidium Monoazide and Quantitative PCR

- (Abstract Only)Cook, K.L., Flis, S.A., Ballard, C.S. 2010. Quantification of the Sensitivity of Mycobacterium avium subsp paratuberculosis and Salmonella enterica subsp enterica to Low pH and High Organic Acids using Propidium Monoazide and Quantitative PCR. American Society for Microbiology.Utilization of Poultry Litter to Enhance Fungal Activity and Microbial Dynamics in the Presence of Pesticide Mixture: Implication on Pesticide Bioremediation

- (Proceedings)Lovanh, N.C., Ruiz-Aguilar, G., Rothrock Jr, M.J., Cook, K.L. 2010. Utilization of Poultry Litter to Enhance Fungal Activity and Microbial Dynamics in the Presence of Pesticide Mixture: Implication on Pesticide Bioremediation. Residuals and Biosolids Conference. Abstract presented at proceeding.Effect of Watering Trough Chlorination on Persistence of Mycobacterium avium subsp. Paratuberculosi

- (Peer Reviewed Journal)Cook, K.L., Bolster, C.H., Britt, J., Rothrock Jr, M.J. 2010. Effect of Watering Trough Chlorination on Persistence of Mycobacterium avium subsp. Paratuberculosi. Bovine Practitioner Journal. 44(1):69-76.Properties and Transport Behavior among 12 Different Environmental Escherichia coli

- (Abstract Only)Bolster, C.H., Cook, K.L. 2010. Properties and Transport Behavior among 12 Different Environmental Escherichia coli. Environmental Protection Agency. EPA meeting AbstractInfluence of seasonal changes on the microbial community in an anaerobic swine waste treatment lagoon

- (Abstract Only)Cook, K.L., Rothrock Jr, M.J., Lovanh, N.C., Sorrell, J. 2009. Influence of seasonal changes on the microbial community in an anaerobic swine waste treatment lagoon. ASA-CSSA-SSSA Annual Meeting Abstracts.Survival of Mycobacterium avium subsp. paratuberculosis in Biofilms on Livestock Watering Trough Materials

- (Peer Reviewed Journal)Cook, K.L., Britt, J., Bolster, C.H. 2010. Survival of Mycobacterium avium subsp. paratuberculosis in Biofilms on Livestock Watering Trough Materials. Veterinary Microbiology. 141(1):103-109.Spatial and Temporal Changes in the Microbial Community in an Anaerobic Swine Waste Treatment Lagoon

- (Peer Reviewed Journal)Cook, K.L., Rothrock Jr, M.J., Sorrell, J., Lovanh, N.C., Loughrin, J.H. 2010. Spatial and Temporal Changes in the Microbial Community in an Anaerobic Swine Waste Treatment Lagoon. Anaerobe. 16:74-82.The Role of Inter-strain Variability on the Sorption Behavior of Escherichia coli to Aquifer Sediments

- (Abstract Only)Bolster, C.H., Cook, K.L. 2009. The Role of Inter-strain Variability on the Sorption Behavior of Escherichia coli to Aquifer Sediments. International Conference on Microbial Transport and Survival in Porous Media.Spatial and Temporal Changes in the Microbial Community in an Anaerobic Swine Waste Treatment Lagoon

- (Abstract Only)Cook, K.L., Rothrock Jr, M.J., Lovanh, N.C., Sorrell, J., Loughrin, J.H. 2009. Spatial and Temporal Changes in the Microbial Community in an Anaerobic Swine Waste Treatment Lagoon. Conference on Gastrointestinal Function.Comparative quantification of Campylobacter jejuni from environmental samples using traditional and molecular biological techniques

- (Peer Reviewed Journal)Rothrock Jr, M.J., Cook, K.L., Bolster, C.H. 2009. Comparative quantification of Campylobacter jejuni from environmental samples using traditional and molecular biological techniques. Canadian Journal of Microbiology. 55: 633–641The Transport of Mycobacterium avium subsp. paratuberculosis through Saturated Aquifer Materials

- (Peer Reviewed Journal)Bolster, C.H., Cook, K.L., Haznedaroglu, B.Z., Walker, S.L. 2009. The Transport of Mycobacterium avium subsp. paratuberculosis through Saturated Aquifer Materials. Letters in Applied Microbiology. vol. 48 p 307-312Alum affects ammonia-producing microorganisms in poultry litter

- (Popular Publication)Cook, K.L., Rothrock Jr, M.J., Warren, J.G., Sistani, K.R. 2009. Alum affects ammonia-producing microorganisms in poultry litter. CSA News. 54(1):5.The Effect of Stratification and Seasonal Variability on the Profile of an Anaerobic Swine Waste Treatment Lagoon.

- (Peer Reviewed Journal)Lovanh, N.C., Loughrin, J.H., Cook, K.L., Rothrock Jr, M.J., Sistani, K.R. 2009. The Effect of Stratification and Seasonal Variability on the Profile of an Anaerobic Swine Waste Treatment Lagoon. Bioresource Technology.  100:3706-3712Survival of Mycobacterium avium subsp. paratuberculosis in Biofilms on Livestock Watering Trough Materials

- (Proceedings)Britt, J., Cook, K.L., Rothrock Jr, M.J., Sorrell, J. 2008. Survival of Mycobacterium avium subsp. paratuberculosis in Biofilms on Livestock Watering Trough Materials. American Association of Bovine Practitioners Proceedings.3-Methylindole production is regulated in Clostridium scatologenes ATCC 25775

- (Peer Reviewed Journal)Doerner, K., Cook, K.L., Mason, B. 2009. 3-Methylindole production is regulated in Clostridium scatologenes ATCC 25775. Letters in Applied Microbiology. 48:125-132.Effect of Litter Amendments on Poultry Litter Microbial Communities and the Subsequent Effect on Nitrogen Dynamics

- (Abstract Only)Rothrock Jr, M.J., Cook, K.L., Warren, J.G., Lovanh, N.C., Sistani, K.R. 2008. Effect of Litter Amendments on Poultry Litter Microbial Communities and the Subsequent Effect on Nitrogen Dynamics. ASA-CSSA-SSSA Annual Meeting Abstracts.Evaluation of Mycobacterium avium subsp. paratuberculosis Transport in Saturated Porous Media

- (Abstract Only)Cook, K.L., Bolster, C.H., Walker, S. 2008. Evaluation of Mycobacterium avium subsp. paratuberculosis Transport in Saturated Porous Media. ASA-CSSA-SSSA Annual Meeting Abstracts.Effect of Alum Treatment on the Concentration of Total and Ureolytic Microorganisms in Poultry Litter

- (Peer Reviewed Journal)Cook,K.L., Rothrock Jr,M.J., Warren,J.G., Sistani,K.R., Moore Jr,P.A. 2008. Effect of Alum Treatment on the Concentration of Total and Ureolytic Microorganisms in Poultry Litter. Journal of Environmental Quality. 37:2360-2367The effect of alum addition on microbial communities in poultry litter

- (Peer Reviewed Journal)Rothrock Jr, M.J., Cook, K.L., Warren, J.G., Sistani, K.R. 2008. The effect of alum addition on microbial communities in poultry litter. Poultry Science. 87(8) 1493-1503Comparison of Molecular Methods and Traditional Plate Counting for Detecting Campylobacter Jejuni and Escherichia Coli from Environmental Samples

- (Abstract Only)Rothrock Jr, M.J., Cook, K.L., Bolster, C.H., Sorrell, J. 2008. Comparison of Molecular Methods and Traditional Plate Counting for Detecting Campylobacter Jejuni and Escherichia Coli from Environmental Samples. American Society for Microbiology Annual Meeting.Survival of Mycobacterium avium subsp. paratuberculosis in Biofilms on Livestock Watering Trough Materials

- (Abstract Only)Cook, K.L., Britt, J., Rothrock Jr, M.J., Sorrell, J. 2008. Survival of Mycobacterium avium subsp. paratuberculosis in Biofilms on Livestock Watering Trough Materials. American Society for Microbiology Annual Meeting.Development of a Quantitative Real-Time Polymerase Chain Reaction Assay to Target a Novel Group of Ammonia-Producing Bacteria Found in Poultry Litter

- (Peer Reviewed Journal)Rothrock Jr, M.J., Cook, K.L., Lovanh, N.C., Warren, J.G., Sistani, K.R. 2008. Development of a Quantitative Real-Time Polymerase Chain Reaction Assay to Target a Novel Group of Ammonia-Producing Bacteria Found in Poultry Litter . Poultry Science. 87(6):1058-1067Evaluation of the Sulfate-Reducing Bacterial Population Associated With Stored Swine Slurry

- (Peer Reviewed Journal)Cook, K.L., Whitehead, T.R., Spence, C., Cotta, M.A. 2008. Evaluation of the sulfate-reducing bacterial population associated with stored swine slurry. Anaerobe. 14:172-180.EFFECTS OF LITTER AMENDMENTS ON BACTERIA AND MANURE-BORNE PATHOGENS

- (Proceedings)Cook, K.L. 2008. Effects of litter amendments on bacteria and manure-borne pathogens . Midwest Poultry Federation Proceedings.Spatial Shifts in Microbial Population Structure Within Poultry Litter Associated with Physicochemical Properties

- (Peer Reviewed Journal)Lovanh, N.C., Cook, K.L., Rothrock Jr, M.J., Miles, D.M., Sistani, K.R. 2007. Spatial Shifts in Microbial Population Structure Within Poultry Litter Associated with Physicochemical Properties. Poultry Science. Vol 86 pages 1840-1849Spatial Variability of Ammonia Production in Poultry House: Biological, Chemical, and Physical Effects at Microscale.

- (Proceedings)Lovanh, N.C., Cook, K.L., Rothrock Jr, M.J., Miles, D.M., Sistani, K.R. 2007. Spatial Variability of Ammonia Production in Poultry House: Biological, Chemical, and Physical Effects at Microscale.. International Ammonia Conference in Agriculture.Evaluation of survival of Mycobacterium avium subsp. paratuberculosis (Map) in ciliates isolated from Johne’s positive cow.

- (Abstract Only)Cook, K.L., Janaki, L., Berk, S.G. 2007. Evaluation of survival of Mycobacterium avium subsp. paratuberculosis (Map) in ciliates isolated from Johne’s positive cow.. Annual Johne's Disease Integrate Program Conference.Effect of Stratification on the Profile of an Anaerobic Swine Waste Treatment Lagoon in Kentucky: A Case Study for Designing Alternative Remediation Options.

- (Proceedings)Lovanh, N.C., Loughrin, J.H., Cook, K.L., Rothrock Jr, M.J., Sistani, K.R. 2007. Effect of Stratification on the Profile of an Anaerobic Swine Waste Treatment Lagoon in Kentucky: A Case Study for Designing Alternative Remediation Options.. ASABE Annual International Meeting.Characterization of acetogenic bacteria associated with skatole production in swine lagoon slurry.

- (Abstract Only)Cook, K.L., Loughrin, J.H., Rothrock Jr, M.J. 2007. Characterization of acetogenic bacteria associated with skatole production in swine lagoon slurry.. Conference on Gastrointestinal Function. Microbial Ecology in Health and Disease (2007) V19 pp42Characterization of skatole-producing microbial populations in enriched swine lagoon slurry.

- (Peer Reviewed Journal)Cook, K.L., Rothrock Jr, M.J., Loughrin, J.H., Doerner, K. Characterization of skatole-producing microbial populations in enriched swine lagoon slurry.Federation of European Microbiological Societies Microbiology Letters. 60:329-340Optimization of Methods for Obtaining, Extracting and Detecting Mycobacterium avium subsp. paratuberculosis in Environmental Samples using Quantitative, Real-Time PCR

- (Peer Reviewed Journal)Cook, K.L., Britt, J. 2006. Optimization of Methods for Obtaining, Extracting and Detecting Mycobacterium avium subsp. paratuberculosis in Environmental Samples using Quantitative, Real-Time PCR. Journal of Microbiological Methods. V29:154-160SURVIVAL OF CAMPYLOBACTER JEJUNI AND ESCHERICHIA COLI IN GROUNDWATER DURING PROLONGED STARVATION AT LOW TEMPERATURES

- (Peer Reviewed Journal)Cook, K.L., Bolster, C.H. Survival of Campylobacter Jejuni and Escherichia Coli in Groundwater During Prolonged Starvation at Low Temperatures. Journal of Applied Microbiology. 103 (2007) 573-583Effect of Alum Amendment on the Bacterial and Fungal Populations in Poultry Litter

- (Abstract Only)Rothrock Jr, M.J., Warren, J.G., Cook, K.L., Sistani, K.R. 2006. Effect of Alum Amendment on the Bacterial and Fungal Populations in Poultry Litter . ASA-CSSA-SSSA Annual Meeting Abstracts.Quantification of a Novel Group of Ammonia Producing Bacteria Found in Poultry Litter by Quantitative Real-Time PCR

- (Abstract Only)Rothrock Jr, M.J., Cook, K.L., Lovanh, N.C., Warren, J.G., Sistani, K.R. 2006. Quantification of a Novel Group of Ammonia Producing Bacteria Found in Poultry Litter by Quantitative Real-Time PCR	 . ASA-CSSA-SSSA Annual Meeting Abstracts.Survival and Transport of Campylobacter Jejuni from Poultry Litter

- (Abstract Only)Cook, K.L., Bolster, C.H., Rothrock Jr, M.J., Warren, J.G., Sistani, K.R. 2006. Survival and Transport of Campylobacter Jejuni from Poultry Litter. ASA-CSSA-SSSA Annual Meeting Abstracts.EFFECT OF BROILER LITTER PHYSICAL, CHEMICAL, AND SPATIAL CHARACTERISTICS ON THE MICROBIAL POPULATION EVALUATED USING MOLECULAR TECHNIQUES

- (Abstract Only)Cook, K.L., Lovanh, N.C., Rothrock Jr, M.J., Miles, D.M., Sistani, K.R. 2006. Effect of broiler litter physical, chemical, and spatial characteristics on the microbial population evaluated using molecular techniques. ASA-CSSA-SSSA Annual Meeting Abstracts.Characterization of skatole-producing microbial populations in enriched swine lagoon slurry.

- (Abstract Only)Rothrock Jr, M.J., Cook, K.L., Loughrin, J.H., Doerner, K. 2006. Characterization of skatole-producing microbial populations in enriched swine lagoon slurry.. American Society for Microbiology Branch Meeting.DETECTION OF BOVINE MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS IN CLINICAL AND ENVIRONMENTAL SAMPLES FROM AN INFECTED ANIMAL

- (Abstract Only)Cook, K.L., Britt, J., Berk, S. 2006. Detection of bovine mycobacterium avium subsp. paratuberculosis in clinical and environmental samples from an infected animal. American Association of Bovine Practitioners Proceedings.CHARACTERIZATION OF MICROBIAL POPULATIONS IN SWINE LAGOON SLURRIES ENRICHED FOR SKATOLE PRODUCTION

- (Abstract Only)Cook, K.L., Loughrin, J.H., Rothrock Jr, M.J. 2006. Characterization of microbial populations in swine lagoon slurries enriched for skatole production. American Society for Microbiology Annual Meeting. ISBN 1-55581-389-5 Pg A127SURVIVAL OF CAMPYLOBACTER JEJUNI AND ESCHERICHIA COLI IN GROUNDWATER DURING PROLONGED EXPOSURE TO LOW TEMPERATURES

- (Abstract Only)Cook, K.L., Bolster, C.H. 2006. Survival of campylobacter jejuni and escherichia coli in groundwater during prolonged exposure to low temperatures. American Society for Microbiology. (ISBN 1-55581-389-5)TARGETING MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS IN THE ENVIRONMENT

- (Abstract Only)Cook, K.L. 2006. Targeting mycobacterium avium subsp. paratuberculosis in the environment. American Society for Microbiology.(ISBN 1-55581-389-5)INTERACTIONS BETWEEN MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS AND PROTOZOA ISOLATED FROM A WATERING TROUGH OF A COW WITH JOHNE'S DISEASE

- (Abstract Only)Janaki, L., Cook, K.L., Berk, S.G. Interactions between mycobacterium avium subsp. paratuberculosis and protozoa isolated from a watering trough of a cow with johne's disease. American Society for Microbiology. CDROMCHARACTERIZATION OF SKATOLE-PRODUCING MICROBIAL POPULATIONS IN ENRICHED SWINE LAGOON SLURRY

- (Proceedings)Cook, K.L., Loughrin, J.H. 2006. Characterization of Skatole-Producing Microbial Populations in Enriched Swine Lagoon Slurry. Proceedings of the Workshop on Agricultural Air Quality: State of the Science. pp 547-551Comparison of Escerichia coli and Camplobacter jejuni transport in saturated porous media

- (Peer Reviewed Journal)Bolster, C.H., Walker, S.L., Cook, K.L. 2006. Comparison of Escerichia coli and Camplobacter jejuni Transport in Saturated Porous Media. Journal of Environmental Quality. 35:1018-1025 (2006)IS ESCHERICHAIA COLI A GOOD INDICATOR OF THE TRANSPORT OF CAMPYLOBACTER JEJUNI IN GROUND WATER ENVIRONMENTS

- (Abstract Only)Bolster, C.H., Cook, K.L. 2006. Is escherichaia coli a good indicator of the transport of campylobacter jejuni in ground water environments. ASABE Annual International Meeting.DETECTION OF MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS (MAP) IN THE ENVIRONMENT

- (Abstract Only)Cook, K.L. 2005. Detection of mycobacterium avium subsp. paratuberculosis (map) in the environment. American Society for Microbiology Branch Meeting.EFFECT OF MICROBIAL SPECIES RICHNESS ON COMMUNITY STABILITY AND COMMUNITY FUNCTION IN A MODEL PLANT-BASED WASTEWATER PROCESSING SYSTEM

- (Peer Reviewed Journal)Cook, K.L., Garland, J.L., Layton, A.C., Dionisi, H.M., Levine, L.F., Sayler, G.S. 2007. Effect of microbial species richness on community stability and community function in a model plant-based wastewater processing system. Microbial Ecology. 52:725-737.EVALUATION OF MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS SURVIVAL IN THE ENVIRONMENT

- (Abstract Only)Cook, K.L., Britt, J., Pike, A. Evaluation of mycobacterium avium subsp. paratuberculosis survival in the environment. Conference on Gastrointestinal Function.  Abstract CD-ROMTHE WESTERN KENTUCKY UNIVERSITY JOHNE’S ERADICATION PROJECT

- (Proceedings)Britt, J., Pike, A., Cook, K.L. The Western Kentucky University Johne’s Eradication Project. pgs 25-30DETECTION OF SULFATE REDUCING BACTERIA IN STORED SWINE MANURE USING QUANTITATIVE, REAL-TIME PCR ANALYSIS

- (Abstract Only)Cook, K.L., Whitehead, T.R., Cotta, M.A. 2004. Detection of sulfate reducing bacteria in stored swine manure using quantitative, real-time pcr analysis [abstract]. Microbial Ecology International Symposium. Paper No. 226.IDENTIFICATION OF SULFATE-REDUCING BACTERIA FROM STORED SWINE MANURE BY PURE CULTURE ISOLATION AND DIRECT DSRA PCR

- (Abstract Only)Whitehead, T.R., Cook, K.L., Cotta, M.A. 2004. Identification of sulfate-reducing bacteria from stored swine manure by pure culture isolation and direct dsra pcr [abstract]. Microbial Ecology International Symposium. Paper No. 228.PURE CULTURE AND PCR ANALYSES OF SULFATE-REDUCING BACTERIA FROM SWINE FECES AND STORED SWINE MANURE

- (Abstract Only)Whitehead, T.R., Cook, K.L., Cotta, M.A. 2004. Pure culture and pcr analyses of sulfate-reducing bacteria from swine feces and stored swine manure [abstract]. Reproduction Nutrition Development. 44(1):S32.VARIABILITY IN THE CONCENTRATION OF SULFATE-REDUCING BACTERIA IN SWINE MANURE AND FECES AS DETERMINED USING A REAL-TIME PCR ASSAY

- (Abstract Only)Cook, K.L., Cotta, M.A., Whitehead, T.R. 2004. Variability in the concentration of sulfate-reducing bacteria in swine manure and feces as determined using a real-time PCR assay [abstract]. Reproduction Nutrition Development. 44(1):S6.DEVELOPMENT OF A REAL-TIME PCR ASSAY FOR DETECTION OF SULFATE-REDUCING BACTERIA IN STORED SWINE MANURE AND SWINE FECES

- (Abstract Only)Cook, K.L., Whitehead, T.R., Cotta, M.A. 2004. Development of a real-time PCR assay for detection of sulfate-reducing bacteria in stored swine manure and swine feces [abstract]. American Society for Microbiology. Paper No. Q-093.
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