Kerry K Cooper
- Assistant Professor, Animal and Comparative Biomedical Sciences
- Assistant Professor, BIO5 Institute
Dr. Cooper attended Sterling College on a basketball scholarship, where in 1998 he obtained his B.S. in Biology. He spent the next 3 years working as a Environmental Health Specialist at the Navajo County Health Department, focusing on foodborne outbreak investigations, food establishment inspections, and environmental health complaints. In 2001, he entered the Pathobiology Ph.D. program in the Veterinary Science and Microbiology Department at the University of Arizona. At the U of A, he conducted his doctorate research with Dr. Glenn Songer, where he focused on the pathogenesis of necrotic enteritis in poultry. After earning his Ph.D. in 2007, he spent four years as a post-doctoral fellow also at the U of A in Dr. Lynn Joens's laboratory. His post-doctoral research focused on the genomics, epidemiology and pathogenesis of the foodborne pathogen Campylobacter jejuni. In 2011, he moved to the Produce Safety and Microbiology Unit of the United States Department of Agriculture, Agricultural Research Service in Albany, CA for a second post-doctoral fellowship, where his research focused on the comparative genomics of Shiga toxin producing Escherichia coli. In 2013, Dr. Cooper became an Assistant Professor at California State University, Northridge (CSUN) in Northridge, CA, where his research laboratory specialized in various aspects of food microbiology, particularly focussing on the genomics, epidemiology and pathogenesis of bacterial foodborne pathogens. In 2017, Dr. Cooper moved back to the University of Arizona, where he is now an Assistant Professor of Food Safety and Epidemiology in the School of Animal and Comparative Biomedical Sciences, and continues his research on the genomics, epidemiology and pathogenesis of bacterial foodborne pathogens, produce safety, and microbiome of various fruits and vegetables.
- Ph.D. Pathobiology
- The University of Arizona, Tucson, Arizona, United States
- Necrotic Enteritis in Broiler Chickens: Studies in Disease Reproduction and Pathogenesis
- B.S. Biology
- Sterling College, Sterling, Kansas, United States
- The University of Arizona, Tucson, Arizona (2017 - Ongoing)
- California State University, Northridge, Northridge, California (2013 - 2017)
- USDA, ARS, Produce Safety and Microbiology (2011 - 2013)
- The University of Arizona, Tucson, Arizona (2007 - 2011)
- The University of Arizona, Tucson, Arizona (2001 - 2007)
Veterinary Microbiology,Medical Microbiology,Food Safety,Food Microbiology,Bioinformatics,Microbial Genetics,Microbial Genomics
Food Safety,Foodborne pathogens,Salmonella,Campylobacter,Escherichia coli,Listeria,Genomics,Transcriptomics,Metabolomics,Outbreak source tracking,Bioinformatics,Microbiome,Foodborne epidemiology,Whole genome sequencing,Bacterial pathogenesis
Careers in MicrobiologyMIC 195G (Spring 2021)
Directed RsrchMCB 392 (Spring 2021)
Honors ThesisPSIO 498H (Spring 2021)
Independent StudyMIC 499 (Spring 2021)
ResearchMIC 900 (Spring 2021)
Independent StudyMIC 499 (Fall 2020)
Internship in Applied BiosciABS 593A (Fall 2020)
ResearchMIC 900 (Fall 2020)
Veterinary MicrobiologyMIC 450 (Fall 2020)
Veterinary MicrobiologyMIC 550 (Fall 2020)
Internship in Applied BiosciABS 593A (Summer I 2020)
Careers in MicrobiologyMIC 195G (Spring 2020)
Directed ResearchACBS 492 (Spring 2020)
Honors Independent StudyACBS 499H (Spring 2020)
Independent StudyACBS 499 (Spring 2020)
Directed ResearchACBS 492 (Fall 2019)
Honors Independent StudyACBS 499H (Fall 2019)
Veterinary MicrobiologyMIC 450 (Fall 2019)
Veterinary MicrobiologyMIC 550 (Fall 2019)
Careers in MicrobiologyMIC 195G (Spring 2019)
Independent StudyACBS 399 (Spring 2019)
Veterinary MicrobiologyMIC 450 (Fall 2018)
Veterinary MicrobiologyMIC 550 (Fall 2018)
- Arias, D. B., Gomez Pinto, K. A., Cooper, K. K., & Summers, M. L. (2020). Transcriptomic analysis of cyanobacterial alkane overproduction reveals stress-related genes and inhibitors of lipid droplet formation. Microbial genomics, 6(10).More infoThe cyanobacterium can form lipid droplets (LDs), internal inclusions containing triacylglycerols, carotenoids and alkanes. LDs are enriched for a 17 carbon-long alkane in , and it has been shown that the overexpression of the and genes results in increased LD and alkane production. To identify transcriptional adaptations associated with increased alkane production, we performed comparative transcriptomic analysis of an alkane overproduction strain. RNA-seq data identified a large number of highly upregulated genes in the overproduction strain, including genes potentially involved in rRNA processing, mycosporine-glycine production and synthesis of non-ribosomal peptides, including nostopeptolide A. Other genes encoding helical carotenoid proteins, stress-induced proteins and those for microviridin synthesis were also upregulated. Construction of strains with several upregulated genes or operons on multi-copy plasmids resulted in reduced alkane accumulation, indicating possible negative regulators of alkane production. A strain containing four genes for microviridin biosynthesis completely lost the ability to synthesize LDs. This strain exhibited wild-type growth and lag phase recovery under standard conditions, and slightly faster growth under high light. The transcriptional changes associated with increased alkane production identified in this work will provide the basis for future experiments designed to use cyanobacteria as a production platform for biofuel or high-value hydrophobic products.
- Bian, X., Garber, J. M., Cooper, K. K., Huynh, S., Jones, J., Mills, M. K., Rafala, D., Nasrin, D., Kotloff, K. L., Parker, C. T., Tennant, S. M., Miller, W. G., & Szymanski, C. M. (2020). Abundance in Breastfed Infants and Identification of a New Species in the Global Enterics Multicenter Study. mSphere, 5(1).More infois a leading cause of bacterial diarrhea worldwide and is associated with high rates of mortality and growth stunting in children inhabiting low- to middle-resource countries. To better understand the impact of breastfeeding on infection in infants in sub-Saharan Africa and South Asia, we examined fecal microbial compositions, bacterial isolates, and their carbohydrate metabolic pathways in -positive infants
- Pascoe, B., Schiaffino, F., Murray, S., Méric, G., Bayliss, S. C., Hitchings, M. D., Mourkas, E., Calland, J. K., Burga, R., Yori, P. P., Jolley, K. A., Cooper, K. K., Parker, C. T., Olortegui, M. P., Kosek, M. N., & Sheppard, S. K. (2020). Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon. PLoS neglected tropical diseases, 14(8), e0008533.More infoCampylobacter is the leading bacterial cause of gastroenteritis worldwide and its incidence is especially high in low- and middle-income countries (LMIC). Disease epidemiology in LMICs is different compared to high income countries like the USA or in Europe. Children in LMICs commonly have repeated and chronic infections even in the absence of symptoms, which can lead to deficits in early childhood development. In this study, we sequenced and characterized C. jejuni (n = 62) from a longitudinal cohort study of children under the age of 5 with and without diarrheal symptoms, and contextualized them within a global C. jejuni genome collection. Epidemiological differences in disease presentation were reflected in the genomes, specifically by the absence of some of the most common global disease-causing lineages. As in many other countries, poultry-associated strains were likely a major source of human infection but almost half of local disease cases (15 of 31) were attributable to genotypes that are rare outside of Peru. Asymptomatic infection was not limited to a single (or few) human adapted lineages but resulted from phylogenetically divergent strains suggesting an important role for host factors in the cryptic epidemiology of campylobacteriosis in LMICs.
- Ruiz, C., McCarley, A., Espejo, M. L., Cooper, K. K., & Harmon, D. E. (2019). Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii. mSphere, 4(5).More infoThe Gram-negative bacterium is an emerging multidrug-resistant pathogen found in many environments. However, little is known about this species or its antibiotic resistance mechanisms. We used biochemical tests, antibiotic susceptibility experiments, and whole-genome sequencing to characterize an environmental isolate. Like clinical isolates, this isolate was resistant to meropenem, gentamicin, and other antibiotics. Resistance to these antibiotics appeared to be related to the large number of intrinsic antibiotic resistance genes found in this isolate. As determined by comparative genomics, this resistome was also well conserved in the only two other strains sequenced to date. The intrinsic resistome of did not include the colistin resistance gene , which was in a transposon present only in one strain. The intrinsic resistome of was comprised of (i) many multidrug efflux pumps, such as a homolog of the MexAB-OprM pump that may be involved in resistance to meropenem, other β-lactams, and aminoglycosides; (ii) a novel β-lactamase (OXA-837) that decreases susceptibility to ampicillin but not to other β-lactams tested; (iii) a new aminoglycoside 3--acetyltransferase [AAC(3)-IVb, AacC10] that decreases susceptibility to gentamicin and tobramycin; and (iv) a novel partially conserved aminoglycoside 3"-adenylyltransferase [ANT(3")-Ib, AadA32] that decreases susceptibility to spectinomycin and streptomycin. These findings provide the first mechanistic insight into the intrinsic resistance of to multiple antibiotics and its ability to become resistant to an increasing number of drugs during therapy. is a bacterium that is gaining increasing attention both as an infectious agent and because of its potential use in the detoxification of toxic compounds and other biotechnological applications. In recent years, however, there has been an increasing number of reported infections, some of them fatal, caused by These infections are hard to treat because this bacterium is naturally resistant to many antibiotics, including last-resort antibiotics, such as carbapenems. Moreover, this bacterium often becomes resistant to additional antibiotics during therapy. However, little is known about and its antibiotic resistance mechanisms. The significance of our research is in providing, for the first time, whole-genome information about the natural antibiotic resistance genes found in this bacterium and their conservation among different strains. This information may provide new insights into the appropriate use of antibiotics in combating infections caused by this emerging pathogen.
- Oliver, A., Kay, M., & Cooper, K. K. (2018). Comparative genomics of cocci-shaped Sporosarcina strains with diverse spatial isolation. BMC genomics, 19(1), 310.More infoCocci-shaped Sporosarcina strains are currently one of the few known cocci-shaped spore-forming bacteria, yet we know very little about the genomics. The goal of this study is to utilize comparative genomics to investigate the diversity of cocci-shaped Sporosarcina strains that differ in their geographical isolation and show different nutritional requirements.
- Parker, C. T., Cooper, K. K., Huynh, S., Smith, T. P., Bono, J. L., & Cooley, M. (2018). Genome Sequences of Eight Shiga Toxin-Producing Escherichia coli Strains Isolated from a Produce-Growing Region in California. Microbiology resource announcements, 7(1), e00807-18. doi:10.1128/MRA.00801-18More infoProduce contaminated with Shiga toxin-producing Escherichia coli (STEC) is a continuing source of foodborne illness in the United States. This report documents the complete genome sequences of eight STEC strains isolated from livestock and water samples taken from a major agricultural region for leafy greens in California.
- Seuylemezian, A., Cooper, K. K., Schubert, W., & Vaishampayan, P. (2018). Draft genome sequences of 13 highly dry heat resistant Bacillus strains isolated from the cleanrooms where the Viking spacecraft were assembled.. Genome Announcements, 6(12), e00094-18. doi:10.1128/genomeA.00094-18More infoThe concern for forward contamination of terrestrial microorganisms on spacecraft is evident in the international space community. To mitigate the inadvertent forward contamination, Planetary Protection policy is put forth and maintained by the Committee on Space Research. Spore-forming bacteria are of particular concern because they may withstand the dry heat microbial reduction efforts and could survive harsh interplanetary conditions as inactive spores. Herein we report the draft genome sequences and annotations of 13 bacterial strains isolated from the Manned Spacecraft Operations Building and the Vehicle Assembly Building in Cape Canaveral, Florida where the Viking spacecraft were assembled.
- Seuylemezian, A., Valshampayan, P., Cooper, K. K., & Venkateswaran, K. (2018). Draft Genome Sequences of Acinetobacter and Bacillus Strains Isolated from Spacecraft Associated Surfaces. Genome Announcements, 6(6), e01554-17. doi:10.1128/genomeA.00094-18More infoWe report here the draft genomes of four strains isolated from spacecraft associated surfaces exhibiting increased resistances to stressors such as UV radiation and exposure to H2O2. The draft genomes of strains 1P01SCT, FO-92T, 50v1, and 2P01AA had genome sizes of 5,500,894 bp, 4,699,376 bp, 3,174,402 bp, and 4,328,804 bp, respectively.
- Gorski, L., Huynh, S., Cooper, K. K., & Parker, C. T. (2017). Complete Genomic Sequences of Two Salmonella enterica subsp. enterica Serogroup C2 (O:6,8) Strains from Central California. Genome Announcements, 5(46), e01234-17. doi:10.1128/genomeA.01234-17More infoSalmonella enterica subsp. enterica strains RM11060, serotype 6,8:d:-, and RM11065, serotype 6,8:-:e,n,z15, were isolated from environmental samples collected in central California in 2009. We report the complete genome sequences of these two strains. These genomic sequences are distinct and will provide additional data to our understanding of S. enterica genomics.
- Cooper, K. K. (2020, July). Illuminating the role of whole genome sequencing in produce safety. Center for Produce Safety Research Symposium Webinar Series. Webinar - due to COVID-19 pandemic: Center for Produce Safety (CPS).
- Cooper, K. K. (2019, March). Comparative microbial genomics: applying next generation sequencing to resolve pathogenesis and epidemiology of foodborne pathogens. Ecosystem Genomics Seminar Series. Drachman Hall: BIO5.
- Cooper, K. K. (2019, September). Comparative genomics of Campylobacter jejuni strains producing different diarrheal pathotypes. Campylobacter, Helicobacter and Related Organisms (CHRO) Meeting. Belfast, Northern Ireland: Campylobacter, Helicobacter and Related Organisms (CHRO).
- Pogreba Brown, K. M., Pogreba Brown, K. M., Verhougstraete, M., Verhougstraete, M., Cooper, K. K., Cooper, K. K., Mclain, J. E., & Mclain, J. E. (2019, November). Breaking down scientific silos: using One Health to address the World’s wicked problems. TENWEST Impact Festival. Tucson, Arizona.More infoMcLain, J.E. K. Cooper, K. Pogreba-Brown, and M. Verhougstraete. Breaking down scientific silos: using One Health to address the World’s wicked problems. Tucson, Arizona, October 14, 2019.
- Pogreba Brown, K. M., Verhougstraete, M., Cooper, K. K., & Mclain, J. E. (2019, November). Breaking down scientific silos: using One Health to address the World’s wicked problems. TENWEST Impact Festival. Tucson, Arizona.More infoMcLain, J.E. K. Cooper, K. Pogreba-Brown, and M. Verhougstraete. Breaking down scientific silos: using One Health to address the World’s wicked problems. Tucson, Arizona, October 14, 2019.
- Cooper, K. K. (2018, April). Comparative microbial genomics: applying next generation sequencing as a critical food safety tool and beyond. Soil, Water and Environmental Sciences Colloquium.
- Cooper, K. K., Cooper, K. K., Pinzon, J., Pinzon, J., Cooper, M. A., Cooper, M. A., Skots, M., Skots, M., Flores, G. E., Flores, G. E., Mackelprang, R., Mackelprang, R., Suslow, T. V., & Suslow, T. V. (2019, July). Characterization of tree fruit bacterial communities during harvest. International Food Protection Association Annual Meeting,. Louisville, KY: International Food Protection Association.
- Cooper, K. K., Pinzon, J., Cooper, M. A., Skots, M., Flores, G. E., Mackelprang, R., & Suslow, T. V. (2018, September). Characterization of Tree Fruit Bacterial Communities during Harvest. Lake Arrowhead Microbial Genomics Conference. Lake Arrowhead, CA.
- Cooper, K. K., Pinzon, J., Cooper, M. A., Skots, M., Suslow, T. V., Flores, G. E., & Mackelprang, R. (2018, July). Characterization of Tree Fruit Bacterial Communities during Harvest. USDA NIFA "Improving Food Safety" Meeting. Salt Lake City, UT: United State Department of Agriculture, National Institute of Food and Agriculture.