Kerry K Cooper
- Assistant Professor, Animal and Comparative Biomedical Sciences
- Assistant Professor, BIO5 Institute
- Member of the Graduate Faculty
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
Directed ResearchACBS 492 (Spring 2023)
Honors ThesisACBS 498H (Spring 2023)
ResearchMIC 900 (Spring 2023)
ThesisMIC 910 (Spring 2023)
Directed ResearchACBS 492 (Fall 2022)
Honors ThesisACBS 498H (Fall 2022)
Molecular MicrobiologyMIC 350 (Fall 2022)
ResearchMIC 900 (Fall 2022)
ThesisMIC 910 (Fall 2022)
Veterinary MicrobiologyMIC 450 (Fall 2022)
Honors ThesisACBS 498H (Spring 2022)
Independent StudyMIC 599 (Spring 2022)
ResearchMIC 900 (Spring 2022)
Directed ResearchACBS 492 (Fall 2021)
Honors ThesisACBS 498H (Fall 2021)
Honors ThesisPSIO 498H (Fall 2021)
Independent StudyACBS 599 (Fall 2021)
Microbes and SocietyMIC 204 (Fall 2021)
ResearchMIC 900 (Fall 2021)
Veterinary MicrobiologyMIC 450 (Fall 2021)
Veterinary MicrobiologyMIC 550 (Fall 2021)
Independent StudyMIC 599 (Summer I 2021)
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)
- Cooper, K. K., & Songer, J. G. (2016). Necrotic Enteritis of Poultry. In Clostridial Diseases of Animals. John Wiley & Sons, Ltd. doi:10.1002/9781118728291.CH10
- Achtman, M., Van den Broeck, F., Cooper, K. K., Lemey, P., Parker, C. T., & Zhou, Z. (2021). Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature. PLoS Genetics, 17(9), e1009820. doi:10.137/journal.pgen.1009820More infoSalmonella enterica serovar Typhimurium strain ATCC14028s is commercially available from multiple national type culture collections, and has been widely used since 1960 for quality control of growth media and experiments on fitness ("laboratory evolution"). ATCC14028s has been implicated in multiple cross-contaminations in the laboratory, and has also caused multiple laboratory infections and one known attempt at bioterrorism. According to hierarchical clustering of 3002 core gene sequences, ATCC14028s belongs to HierCC cluster HC20_373 in which most internal branch lengths are only one to three SNPs long. Many natural Typhimurium isolates from humans, domesticated animals and the environment also belong to HC20_373, and their core genomes are almost indistinguishable from those of laboratory strains. These natural isolates have infected humans in Ireland and Taiwan for decades, and are common in the British Isles as well as the Americas. The isolation history of some of the natural isolates confirms the conclusion that they do not represent recent contamination by the laboratory strain, and 10% carry plasmids or bacteriophages which have been acquired in nature by HGT from unrelated bacteria. We propose that ATCC14028s has repeatedly escaped from the laboratory environment into nature via laboratory accidents or infections, but the escaped micro-lineages have only a limited life span. As a result, there is a genetic gap separating HC20_373 from its closest natural relatives due to a divergence between them in the late 19th century followed by repeated extinction events of escaped HC20_373.
- Crippen, C. S., Zhou, B., Andresen, S., Patry, R. T., Muszyński, A., Parker, C. T., Cooper, K. K., & Szymanski, C. M. (2021). RNA and Sugars, Unique Properties of Bacteriophages Infecting Multidrug Resistant Acinetobacter radioresistens Strain LH6. Viruses, 13(8), 1652. doi:10.3390/v13081652More infoBacteriophages (phages) are predicted to be the most ubiquitous biological entity on earth, and yet, there are still vast knowledge gaps in our understanding of phage diversity and phage-host interactions. Approximately one hundred -infecting DNA viruses have been identified, and in this report, we describe eight more. We isolated two typical dsDNA lytic podoviruses (CAP1-2), five unique dsRNA lytic cystoviruses (CAP3-7), and one dsDNA lysogenic siphovirus (SLAP1), all capable of infecting the multidrug resistant isolate LH6. Using transmission electron microscopy, bacterial mutagenesis, phage infectivity assays, carbohydrate staining, mass-spectrometry, genomic sequencing, and comparative studies, we further characterized these phages. Mutation of the LH6 initiating glycosyltransferase homolog, PglC, necessary for both O-linked glycoprotein and capsular polysaccharide (CPS) biosynthesis, prevented infection by the lytic podovirus CAP1, while mutation of the pilin protein, PilA, prevented infection by CAP3, representing the lytic cystoviruses. Genome sequencing of the three dsRNA segments of the isolated cystoviruses revealed low levels of homology, but conserved synteny with the only other reported cystoviruses that infect species. In , the cystoviruses are known to be enveloped phages surrounding their capsids with the inner membrane from the infected host. To characterize any membrane-associated glycoconjugates in the CAP3 cystovirus, carbohydrate staining was used to identify a low molecular weight lipid-linked glycoconjugate subsequently identified by mutagenesis and mass-spectrometry as bacterial lipooligosaccharide. Together, this study demonstrates the isolation of new -infecting phages and the determination of their cell receptors. Further, we describe the genomes of a new genus of and perform an initial characterization of membrane-associated glycoconjugates.
- Heikema, A. P., Strepis, N., Horst-Kreft, D., Huynh, S., Zomer, A., Kelly, D. J., Cooper, K. K., & Parker, C. T. (2021). Biomolecule sulphation and novel methylations related to Guillain-Barré syndrome-associated serotype HS:19. Microbial genomics, 7(11), 000660. doi:10.1099/mgen.0.000660
- Katiyar, N., Ramadoss, N., Gupta, D., Pakala, S. B., Cooper, K. K., & Basu, C. (2021). Transcriptomic profiling of Paulownia elongata in response to heat stress. Plant Gene, 28, 100330. doi:10.1016/j.plgene.2021.100330
- Luna, E., Parkar, S. G., Kirmiz, N., Hartel, S., Hearn, E., Hossine, M., Kurdian, A., Mendoza, C., Orr, K., Padilla, L., Ramirez, K., Salcedo, P., Serrano, E., Choudhury, B., Paulchakrabarti, M., Parker, C. T., Huynh, S., Cooper, K. K., & Flores, G. E. (2022). Utilization Efficiency of Human Milk Oligosaccharides by Human-Associated Akkermansia Is Strain Dependent. Applied and Environmental Microbiology, 88(1), e0148721. doi:10.1128/AEM.01487-21
- Parker, C. T., Cooper, K. K., Schiaffino, F., Miller, W. G., Huynh, S., Gray, H. K., Olortegui, M. P., Bardales, P. G., Trigoso, D. R., Penataro-Yori, P., & Kosek, M. N. (2021). Genomics characterization of Campylobacter jejuni Adapted to the Guinea Pig (Cavia porcellus) Host. Frontiers in Cellular and Infection Microbiology, 11, 607747. doi:10.3389/fcimb.2021.607747
- Parker, C. T., Huynh, S., Alexander, A., Oliver, A. S., & Cooper, K. K. (2021). Genomic Characterization of Salmonella typhimurium DT104 Strains Associated with Cattle and Beef Products.. Pathogens (Basel, Switzerland), 10(5), 529. doi:10.3390/pathogens10050529More infoSalmonella enterica subsp. enterica serovar Typhimurium DT104, a multidrug-resistant phage type, has emerged globally as a major cause of foodborne outbreaks particularly associated with contaminated beef products. In this study, we sequenced three S. Typhimurium DT104 strains associated with a 2009 outbreak caused by ground beef, including the outbreak source strain and two clinical strains. The goal of the study was to gain a stronger understanding of the genomics and genomic epidemiology of highly clonal S. typhimurium DT104 strains associated with bovine sources. Our study found no single nucleotide polymorphisms (SNPs) between the ground beef source strain and the clinical isolates from the 2009 outbreak. SNP analysis including twelve other S. typhimurium strains from bovine and clinical sources, including both DT104 and non-DT104, determined DT104 strains averaged 55.0 SNPs between strains compared to 474.5 SNPs among non-DT104 strains. Phylogenetic analysis separated the DT104 strains from the non-DT104 strains, but strains did not cluster together based on source of isolation even within the DT104 phage type. Pangenome analysis of the strains confirmed previous studies showing that DT104 strains are missing the genes for the allantoin utilization pathway, but this study confirmed that the genes were part of a deletion event and not substituted or disrupted by the insertion of another genomic element. Additionally, cgMLST analysis revealed that DT104 strains with cattle as the source of isolation were quite diverse as a group and did not cluster together, even among strains from the same country. Expansion of the analysis to 775 S. typhimurium ST19 strains associated with cattle from North America revealed diversity between strains, not limited to just among DT104 strains, which suggests that the cattle environment is favorable for a diverse group of S. typhimurium strains and not just DT104 strains.
- 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
- Bian, X., Garber, J. M., Cooper, K. K., Huynh, S., Mills, M. K., Rafala, D., Nasrin, D., Kotloff, K. L., Parker, C. T., Tennant, S. M., Miller, W. G., Szymanski, C. M., & Jones, J. P. (2020). Campylobacter Abundance in Breastfed Infants and Identification of a New Species in the Global Enterics Multicenter Study. mSphere, 5(1), e00735-19. doi:10.1128/mSphere.00735-19More infoABSTRACT Campylobacter jejuni is 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 Campylobacter infection in infants in sub-Saharan Africa and South Asia, we examined fecal microbial compositions, bacterial isolates, and their carbohydrate metabolic pathways in Campylobacter-positive infants IMPORTANCECampylobacter is the primary cause of bacterial diarrhea in the United States and can lead to the development of the postinfectious autoimmune neuropathy known as Guillain-Barre syndrome. Also, drug-resistant campylobacters are becoming a serious concern both locally and abroad. In low- and middle-income countries (LMICs), infection with Campylobacter is linked to high rates of morbidity, growth stunting, and mortality in children, and breastfeeding is important for infant nutrition, development, and protection against infectious diseases. In this study, we examined the relationship between breastfeeding and Campylobacter infection and demonstrate the increased selection for C. jejuni and C. coli strains unable to metabolize fucose. We also identify a new Campylobacter species coinfecting these infants with a high prevalence in five of the seven countries in sub-Saharan Africa and South Asia examined. These findings indicate that more detailed studies are needed in LMICs to understand the Campylobacter infection process in order to devise a strategy for eliminating this pathogenic microbe.
- 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.
- Ravishankar, S., Pinoargote, G., Flores, G. E., & Cooper, K. K. (2018). Effects on survival and bacterial community composition of the aquaculture water and gastrointestinal tract of shrimp (Litopenaeus vannamei) exposed to probiotic treatments after an induced infection of acute hepatopancreatic necrosis disease. Aquaculture Research, 49(10), 3270-3288. doi:10.1111/are.13791
- 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.
- Joshee, N., Gupta, D., Cooper, K. K., Chaires, M., & Basu, C. (2017). RNA-seq analysis of the salt stress-induced transcripts in fast-growing bioenergy tree, Paulownia elongata. Journal of Plant Interactions, 12(1), 128-136. doi:10.1080/17429145.2017.1298851More infoABSTRACTPaulowina elongata is a fast-growing tree species is grown in different climates and types of soils. Environmental adaptability as well as high-yielding biomass make the P. elongata species an ideal candidate for biofuel production. High soil salinity is known to inhibit plant growth dramatically or leads to plant death. The purpose of this study was to characterize the salt-induced changes in the transcriptome of P. elongata. Transcriptome differences in response to salt stress were determined by RNA sequencing (RNA-seq) using next generation sequencing and bioinformatics analysis. A total of 645 genes were found to have significant altered expression in response to salt stress. Expression levels of a selective subset of these genes were chosen and confirmed using quantitative real-time PCR. To the best of our knowledge, this is the first report of salt-induced transcriptome analysis in P. elongata. The current study indicates that differential expression of a select group of genes of P. elongata...
- Yahara, K., Wimalarathna, H. M., Taboada, E. N., Sproston, E. L., Sheppard, S. K., Pascoe, B., Parker, C. T., Murray, S., Meric, G., Mccarthy, N. D., Maiden, M. C., Jolley, K. A., Huynh, S., Hitchings, M. D., Didelot, X., Cooper, K. K., Cody, A. J., & Carrillo, C. D. (2017). Local genes for local bacteria: Evidence of allopatry in the genomes of transatlantic Campylobacter populations.. Molecular ecology, 26(17), 4497-4508. doi:10.1111/mec.14176More infoThe genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distance and genetic distance, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance with past human migration, whereas in Mycobacterium tuberculosis it is the lack of recombination that causes allopatric clusters. In Campylobacter, analyses of genomic data and molecular typing have been successful in determining the reservoir host species, but not geographical origin. We investigated biogeographical variation in highly recombining genes to determine the extent of clustering between genomes from geographically distinct Campylobacter populations. Whole-genome sequences from 294 Campylobacter isolates from North America and the UK were analysed. Isolates from within the same country shared more recently recombined DNA than isolates from different countries. Using 15 UK/American closely matched pairs of isolates that shared ancestors, we identify regions that have frequently and recently recombined to test their correlation with geographical origin. The seven genes that demonstrated the greatest clustering by geography were used in an attribution model to infer geographical origin which was tested using a further 383 UK clinical isolates to detect signatures of recent foreign travel. Patient records indicated that in 46 cases, travel abroad had occurred
- Parker, C. T., Miller, W. G., Huynh, S., Gorski, L., & Cooper, K. K. (2015). Complete Genome Sequences of Two Outbreak Strains of Salmonella enterica subsp. enterica Serovar Thompson Associated with Cilantro.. Genome announcements, 3(6). doi:10.1128/genomea.01365-15More infoSalmonella enterica subsp. enterica serovar Thompson strains RM1984 (CADPH-99A2334) and RM1986 (CADPH-99A2345) are associated with a 1999 outbreak in contaminated cilantro. We report here the complete genome sequences and annotation of these two S. Thompson strains. These genomes are distinct and provide additional data for our understanding of S. enterica.
- Parker, C. T., Miller, W. G., Huynh, S., Heikema, A. P., & Cooper, K. K. (2015). Complete Genome Sequences of Campylobacter jejuni Strains RM3196 (233.94) and RM3197 (308.95) Isolated from Patients with Guillain-Barré Syndrome.. Genome announcements, 3(6). doi:10.1128/genomea.01312-15More infoInfections with Campylobacter jejuni subsp. jejuni are a leading cause of foodborne gastroenteritis and the most prevalent infection preceding Guillain-Barré syndrome (GBS). This study describes the genomes of C. jejuni subsp. jejuni HS:41 strains RM3196 (233.94) and RM3197 (308.95) that were isolated from patients with GBS in Cape Town, South Africa.
- Ahmed, S., Parker, C. T., Mandrell, R. E., Louie, J. W., Korlach, J., Huynh, S., Cooper, K. K., Clark, T. A., Chain, P. S., Carter, M. Q., & Ahmed, S. A. (2014). Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7.. BMC genomics, 15(1), 17. doi:10.1186/1471-2164-15-17More infoAlthough serotype O157:H7 is the predominant enterohemorrhagic Escherichia coli (EHEC), outbreaks of non-O157 EHEC that cause severe foodborne illness, including hemolytic uremic syndrome have increased worldwide. In fact, non-O157 serotypes are now estimated to cause over half of all the Shiga toxin-producing Escherichia coli (STEC) cases, and outbreaks of non-O157 EHEC infections are frequently associated with serotypes O26, O45, O103, O111, O121, and O145. Currently, there are no complete genomes for O145 in public databases..We determined the complete genome sequences of two O145 strains (EcO145), one linked to a US lettuce-associated outbreak (RM13514) and one to a Belgium ice-cream-associated outbreak (RM13516). Both strains contain one chromosome and two large plasmids, with genome sizes of 5,737,294 bp for RM13514 and 5,559,008 bp for RM13516. Comparative analysis of the two EcO145 genomes revealed a large core (5,173 genes) and a considerable amount of strain-specific genes. Additionally, the two EcO145 genomes display distinct chromosomal architecture, virulence gene profile, phylogenetic origin of Stx2a prophage, and methylation profile (methylome). Comparative analysis of EcO145 genomes to other completely sequenced STEC and other E. coli and Shigella genomes revealed that, unlike any other known non-O157 EHEC strain, EcO145 ascended from a common lineage with EcO157/EcO55. This evolutionary relationship was further supported by the pangenome analysis of the 10 EHEC str ains. Of the 4,192 EHEC core genes, EcO145 shares more genes with EcO157 than with the any other non-O157 EHEC strains..Our data provide evidence that EcO145 and EcO157 evolved from a common lineage, but ultimately each serotype evolves via a lineage-independent nature to EHEC by acquisition of the core set of EHEC virulence factors, including the genes encoding Shiga toxin and the large virulence plasmid. The large variation between the two EcO145 genomes suggests a distinctive evolutionary path between the two outbreak strains. The distinct methylome between the two EcO145 strains is likely due to the presence of a BsuBI/PstI methyltransferase gene cassette in the Stx2a prophage of the strain RM13514, suggesting a role of horizontal gene transfer-mediated epigenetic alteration in the evolution of individual EHEC strains.
- Ahmed, S., Parker, C. T., Mandrell, R. E., Louie, J. W., Korlach, J., Huynh, S., Cooper, K. K., Clark, T. A., Chain, P. S., Carter, M. Q., & Ahmed, S. A. (2014). Complete Genome Sequences of Two Escherichia coli O145:H28 Outbreak Strains of Food Origin.. Genome announcements, 2(3). doi:10.1128/genomea.00482-14More infoEscherichia coli O145:H28 strain RM12581 was isolated from bagged romaine lettuce during a 2010 U.S. lettuce-associated outbreak. E. coli O145:H28 strain RM12761 was isolated from ice cream during a 2007 ice cream-associated outbreak in Belgium. Here we report the complete genome sequences and annotation of both strains.
- Cooper, M. A., Zuccolo, A., Joens, L. A., Cooper, M. A., & Cooper, K. K. (2013). Re-sequencing of a virulent strain of Campylobacter jejuni NCTC11168 reveals potential virulence factors.. Research in microbiology, 164(1), 6-11. doi:10.1016/j.resmic.2012.10.002More infoIn vitro passage of Campylobacter jejuni strains results in phenotypic changes and a general loss of virulence, as is the case with the genome-sequenced strain C. jejuni NCTC11168. Re-sequencing of a virulent strain of NCTC11168 identified 41 SNPs or indels involving 20 genes, four intergenic regions and three pseudogenes. The genes include six motility genes, two chemotaxis genes, three hypothetical genes and a capsule biosynthesis gene, which might have a critical role in C. jejuni virulence. Additionally, we found an insertion in both Cj0676 and Cj1470c, pseudogenes in avirulent NCTC11168, but functional proteins in virulent NCTC11168.
- Songer, J. G., Cooper, K. K., & Bueschel, D. M. (2013). Presence of Clostridium perfringens in retail chicken livers.. Anaerobe, 21, 67-8. doi:10.1016/j.anaerobe.2013.03.013More infoChicken livers sold at grocery stores in Tucson, AZ, USA were examined for the presence of Clostridium perfringens. Results showed that 69.6% of sampled retail chicken livers were culture positive for C. perfringens. Genotyping of the isolates showed that all the isolates were type A, but were negative for the enterotoxin gene (cpe).
- Uzal, F. A., Songer, J. G., & Cooper, K. K. (2013). Diagnosing clostridial enteric disease in poultry.. Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc, 25(3), 314-27. doi:10.1177/1040638713483468More infoThe world's poultry industry has grown into a multibillion-dollar business, the success of which hinges on healthy intestinal tracts, which result in effective feed conversion. Enteric disease in poultry can have devastating economic effects on producers, due to high mortality rates and poor feed efficiency. Clostridia are considered to be among the most important agents of enteric disease in poultry. Diagnosis of enteric diseases produced by clostridia is usually challenging, mainly because many clostridial species can be normal inhabitants of the gut, making it difficult to determine their role in virulence. The most common clostridial enteric disease in poultry is necrotic enteritis, caused by Clostridium perfringens, which typically occurs in broiler chickens but has also been diagnosed in various avian species including turkeys, waterfowl, and ostriches. Diagnosis is based on clinical and pathological findings. Negative culture and toxin detection results may be used to rule out this disease, but isolation of C. perfringens and/or detection of its alpha toxin are of little value to confirm the disease because both are often found in the intestine of healthy birds. Ulcerative enteritis, caused by Clostridium colinum, is the other major clostridial enteric disease of poultry. Diagnosis of ulcerative enteritis is by documentation of typical pathological findings, coupled with isolation of C. colinum from the intestine of affected birds. Other clostridial enteric diseases include infections produced by Clostridium difficile, Clostridium fallax, and Clostridium baratii.
- Law, B. F., Zekarias, B., Theoret, J. R., Roland, K. L., Law, B. F., Joens, L. A., Curtiss, R., & Cooper, K. K. (2012). The Campylobacter jejuni Dps homologue is important for in vitro biofilm formation and cecal colonization of poultry and may serve as a protective antigen for vaccination.. Clinical and vaccine immunology : CVI, 19(9), 1426-31. doi:10.1128/cvi.00151-12More infoIn this work, we investigated the Campylobacter jejuni dps (DNA binding protein from starved cells) gene for a role in biofilm formation and cecal colonization in poultry. In vitro biofilm formation assays were conducted with stationary-phase cells in cell culture plates under microaerophilic conditions. These studies demonstrated a significant (>50%) reduction in biofilm formation by the C. jejuni dps mutant compared to that by the wild-type strain. Studies in poultry also demonstrated the importance of the dps gene in host colonization by C. jejuni. Real-time PCR analysis of mRNA extracted from the cecal contents of poultry infected with wild-type C. jejuni indicated that the dps gene is upregulated 20-fold during poultry colonization. Cecal colonization was greater than 5 log CFU lower in chicks infected with the dps mutant than chicks infected with the wild-type C. jejuni strain. Moreover, the dps mutant failed to colonize 75% of the chicks following challenge with 10(5) CFU. Preliminary studies were conducted in chicks by parenteral vaccination with a recombinant Dps protein or through oral vaccination with a recombinant attenuated Salmonella enterica strain synthesizing the C. jejuni Dps protein. No reduction in C. jejuni was noted in chicks vaccinated with the parenteral recombinant protein, whereas, a 2.5-log-unit reduction of C. jejuni was achieved in chicks vaccinated with the attenuated Salmonella vector after homologous challenge. Taken together, this work demonstrated the importance of Dps for biofilm formation and poultry colonization, and the study also provides a basis for continued work using the Dps protein as a vaccine antigen when delivered through a Salmonella vaccine vector.
- Songer, J. G., Moore, K. L., Glock, R. D., Coursodon, C. F., & Cooper, K. K. (2012). TpeL-producing strains of Clostridium perfringens type A are highly virulent for broiler chicks.. Anaerobe, 18(1), 117-21. doi:10.1016/j.anaerobe.2011.10.001More infoClostridium perfringens type A and type C are causative agents of necrotic enteritis (NE) in poultry. TpeL, a recently-described novel member of the family of large clostridial cytotoxins, was found in C. perfringens type C. Others have since reported TpeL in type A isolates from NE outbreaks, suggesting that it may contribute to the pathogenesis of NE. The virulence of TpeL-positive and -negative C. perfringens strains from cases of NE was examined by challenge of broiler chicks. Gross lesions typical of NE were observed in all challenged birds, and those inoculated with TpeL(pos) strains had higher average macroscopic lesion scores than those inoculated with a TpeL(neg) strain. Infection with TpeL(pos) strains may yield disease with a more rapid course and higher case fatality rate. Thus, TpeL may potentiate the effect of other virulence attributes of NE strains of C. perfringens. However, TpeL(pos) and Tpel(neg) strains compared here were not isogenic, and definitive results await the production and testing of specific TpeL mutants.
- Cooper, M. A., Law, B., Zuccolo, A., Law, B., Joens, L. A., Cooper, M. A., & Cooper, K. K. (2011). Complete genome sequence of Campylobacter jejuni strain S3.. Journal of bacteriology, 193(6), 1491-2. doi:10.1128/jb.01475-10More infoCampylobacter jejuni is one of the leading causes of bacterial gastroenteritis in the world; however, there is only one complete genome sequence of a poultry strain to date. Here we report the complete genome sequence and annotation of the second poultry strain, C. jejuni strain S3. This strain has been shown to be nonmotile, to be a poor invader in vitro, and to be a poor colonizer of poultry after minimal in vitro passage.
- Theoret, J. R., Joens, L. A., Glock, R. D., & Cooper, K. K. (2011). A Campylobacter jejuni Dps homolog has a role in intracellular survival and in the development of campylobacterosis in neonate piglets.. Foodborne pathogens and disease, 8(12), 1263-8. doi:10.1089/fpd.2011.0892More infoIron acquisition is an absolute requirement by most microorganisms for host survival. In this work, we investigated the Campylobacter jejuni iron binding Dps protein for a potential role in virulence. In vitro assays using J774A.1 macrophage-like cells demonstrated a 2.5 log reduction in C. jejuni survival of the Dps mutant and a reduction of four logs in invasion of HEp-2 epithelial cells compared to the wild-type strain. To examine the role of the dps gene in host pathogenesis, the piglet model was used in C. jejuni challenge studies. In vivo inoculation studies of newborn piglets with wild-type C. jejuni demonstrated an 11-fold upregulation of the dps gene and intestinal lesion production typical of campylobacteriosis in humans. In contrast, piglets inoculated with the dps mutant were not colonized and remained normal throughout the study period. Mucosal lesion production was restored in piglets inoculated with the complemented Dps mutant strain. Based on these results, we conclude that the C. jejuni Dps homolog is a virulence factor in the production of campylobacteriosis, and warrants further investigation.
- Songer, J. G., & Cooper, K. K. (2010). Virulence of Clostridium perfringens in an experimental model of poultry necrotic enteritis.. Veterinary microbiology, 142(3-4), 323-8. doi:10.1016/j.vetmic.2009.09.065More infoPoultry necrotic enteritis (NE) has, over recent decades, been prevented and treated by addition of antimicrobials to poultry feed. Recent bans of antimicrobial growth promoters in feed, as well as other factors, have led to a slow, worldwide re-emergence of NE. Understanding of pathogenesis of NE has been hampered by lack of a consistent and effective experimental model in which virulence of strains can be reliably evaluated, with an endpoint yielding lesions comparable to those seen in acute NE in the field. The overall objective of this work was to develop an experimental approach that would allow consistent production of a full range of clinical signs and lesions of the disease, and to do so without use of coccidia as inciting agents. In addition, we assessed the virulence of strains of Clostridium perfringens from field cases of NE. Broiler chicks fed a commercial chick starter for 7 days post-hatch were switched to a high protein feed mixed 50:50 with fishmeal for an additional 7 days. On day 14, feed was withheld for 20 h, and birds were then offered feed mixed with C. perfringens (3 parts culture to 4 parts feed) twice daily on 4 consecutive days. On average, >75% of challenged birds developed typical gross lesions when inoculated with type A strains from field cases of NE. In addition, in vivo passage apparently increases strain virulence. Virulence varies from strain-to-strain; NetB-producing strains were virulent, as were some NetB non-producing strains.
- Trinh, H. T., Theoret, J. R., Stewart, B. A., Songer, J. G., Glock, R. D., & Cooper, K. K. (2010). Virulence for chickens of Clostridium perfringens isolated from poultry and other sources.. Anaerobe, 16(3), 289-92. doi:10.1016/j.anaerobe.2010.02.006More infoClostridium perfringens type A is the most common cause of poultry necrotic enteritis (NE). Of the four "major" toxins, type A strains produce only alpha toxin (CPA), which has long been considered a major factor in pathogenesis of NE. We investigated the virulence for poultry of type A strains from a variety of enteric sources. Newly-hatched CornishxRock chicks were fed a low protein diet for one week, a high protein diet for a second week, and then challenged with log-phase cultures of C. perfringens, mixed 3:4 (v/v) with high protein feed. Strain JGS4143 [genotype A, beta2 positive (cpb2(pos)), from a field case of NE] produced gross lesions compatible with NE in >85% of challenged birds. However, strains JGS1714 (enterotoxigenic genotype A, cpb2(pos), human food poisoning), JGS1936 (genotype A, cpb2(neg), bovine neonatal enteritis), JGS4142 (genotype A, cpb2(pos), bovine jejunal hemorrhage syndrome), JGS1473 (genotype A, cpb2(pos), chicken normal flora), JGS1070 (genotype C, cpb2(pos), porcine hemorrhagic enteritis), JGS1882 (genotype A, cpb2(pos), porcine neonatal enteritis), JGS1120 (ATCC 13124, genotype A, cpb2(neg), gas gangrene), JGS4151 (strain 13, genotype A, cpb2(pos), canine), and JGS4303 (SM101, enterotoxigenic genotype A, cpb2(neg), human food poisoning) failed to produce disease. In vivo passage failed to increase virulence of the non-NE strains. NE strains must have specific poultry-associated virulence attributes, such as the recently identified NetB and other factors, which allow for the development of disease.
- Songer, J. G., & Cooper, K. K. (2009). Necrotic enteritis in chickens: a paradigm of enteric infection by Clostridium perfringens type A.. Anaerobe, 15(1-2), 55-60. doi:10.1016/j.anaerobe.2009.01.006More infoWithdrawal of antimicrobial growth promoters and ionophore coccidiostats has been accompanied by a resurgence in incidence of necrotic enteritis (NE), a severe Clostridium perfringens-induced disease which some consider the most clinically dramatic bacterial enteric disease of poultry. Lesions, in jejunum and ileum, are focal-to-confluent, often with a tightly adhered pseudomembrane, and hemorrhage is uncommon. The key risk factor for development of NE is an intestinal environment that favors growth of the organism. Birds on high energy, protein-rich, wheat- or barley-based diets experience NE at a rate up to ten times greater than do birds on maize-based diets. Specific strains of type A cause NE, although only a few specific virulence attributes are known. The role of alpha toxin (CPA) has been called into question by the finding that an engineered CPA mutant retained full virulence in vivo, although the counterpoint to this is the finding that immunization with CPA toxoids provides substantial protection against NE. A recently described toxin, NetB, seems likely to be involved in pathogenesis of infection by most NE strains. Immunization with CPA, NetB, or other proteins, delivered by conventional means or vectored by recombinant attenuated Salmonella vectors may help the industry deal with NE. Future progress may be based in large part on genomic and proteomic analyses.
- Trinh, H. T., Songer, J. G., & Cooper, K. K. (2009). Immunization with recombinant alpha toxin partially protects broiler chicks against experimental challenge with Clostridium perfringens.. Veterinary microbiology, 133(1-2), 92-7. doi:10.1016/j.vetmic.2008.06.001More infoNecrotic enteritis (NE) in poultry has re-emerged as a concern for poultry producers, due in part to banning, by many countries, of the use of antimicrobial growth promoters in feeds. This re-emergence has led to a search for alternative methods for control of the disease, particularly vaccination. The objective of this work was to determine if vaccination of broiler chicks with recombinant alpha toxin protected against experimental challenge. Broiler chicks were vaccinated subcutaneously at 5 and 15 days of age, followed 10 days later by challenge with Clostridium perfringens. Birds were challenged twice daily on 4 consecutive days by mixing C. perfringens cultures with feed (three parts culture: four parts feed). Non-vaccinated birds challenged with C. perfringens developed NE at the rate of 87.8%, while only 54.9% of vaccinated birds developed lesions. In addition, non-vaccinated birds had lesion scores averaging 2.37, while average scores in vaccinated birds were 1.35. Vaccination produced an antibody response, with post-vaccination anti-alpha toxin IgG (IgY) titers in vaccinated birds more than 5-fold greater than in non-vaccinated birds. After challenge, vaccinated birds had average IgG (IgY) titers>15-fold higher than those in non-vaccinated birds. These results suggest that alpha toxin may serve as an effective immunogen, and, as such, may play a role in pathogenesis.
- 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., Verhougstraete, M., Cooper, K. K., Mclain, J. E., 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.