Kerry K Cooper

Interests

Research

Food Safety,Foodborne pathogens,Salmonella,Campylobacter,Escherichia coli,Listeria,Genomics,Transcriptomics,Metabolomics,Outbreak source tracking,Bioinformatics,Microbiome,Foodborne epidemiology,Whole genome sequencing,Bacterial pathogenesis

Teaching

Veterinary Microbiology,Medical Microbiology,Food Safety,Food Microbiology,Bioinformatics,Microbial Genetics,Microbial Genomics

Courses

Scholarly Contributions

Chapters

• Cooper, K. K., & Songer, J. G. (2016). Necrotic Enteritis of Poultry. In Clostridial Diseases of Animals(pp 123-137). wiley. doi:10.1002/9781118728291.ch10
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  Necrotic enteritis (NE) produced by Clostridium perfringens is the most severe clostridial enteric disease of poultry, and it is estimated that worldwide NE costs the poultry industry 2 billion dollars per year. The disease occurs in two forms: acute and chronic. The acute form is associated with loss due to increased mortality rates at around 3-4 weeks of age, but it is the chronic or subclinical form that results in severe economic loss due to reduced weight gain and less efficient feed conversion. The subclinical form causes the greatest production loss, as it often goes undetected. This chapter discusses the epidemology, etiology and pathogenesis, host response, predisposing factors, clinical signs, gross changes, and microscopic changes of the disease. The development of direct PCR screening, DNA sequencing, and real-time PCR assays directly from the intestinal tract of birds without cultivation may significantly speed up the diagnostic process.
• 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

Journals/Publications

• Bosquez, J. M., Parker, C. T., Pascoe, B., & Cooper, K. K. (2025). Growth rates and metabolic traits differ by diarrhoeal manifestation in Campylobacter jejuni strains. Journal of Medical Microbiology, 74(Issue 8). doi:10.1099/jmm.0.002053
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  Introduction. Campylobacter jejuni is the leading cause of bacterial gastroenteritis worldwide. Infections with C. jejuni can result in two different diarrhoeal manifestations in humans: watery diarrhoea or bloody/inflammatory diarrhoea. Hypothesis/Gap Statement. Currently, little is known about C. jejuni and/or host factors associated with the elicitation of these two distinct diarrhoeal manifestations. We hypothesize that these factors may include growth and metabolic trait differences between C. jejuni strains associated with watery diarrhoea and bloody/inflammatory diarrhoea. Aim. Using C. jejuni strains with a defined diarrhoeal manifestation in the neonatal piglet model, we aimed to assess differences in temperature-dependent growth rates, motility, biofilm production and carbon utilization between diarrhoeal manifestation groups. Methodology. Strains were initially assessed for 192 different carbon sources using phenotypic microarrays followed by specific carbon utilization, growth, motility and biofilm assays at 37 and/or 42 °C. Results. We found that at 37 °C, watery diarrhoea-associated C. jejuni strains grew significantly faster compared with bloody/ inflammatory diarrhoea-associated C. jejuni strains. However, there was no significant growth difference at 42 °C between the groups, due to bloody/inflammatory diarrhoea-associated strains growing faster at 42 °C compared with 37 °C. Additionally, at 37 °C, we found that l-fucose utilization was significantly higher among watery diarrhoea-associated strains, while l-glutamine utilization was significantly higher among bloody/inflammatory diarrhoea-associated strains. Conclusion. The results indicate there are distinct metabolic adaptations between watery and/or bloody/inflammatory diarrhoea-associated C. jejuni strains particularly at 37 °C, which may be one of the factors associated with differing diarrhoeal manifestations.
• Brown, K. P., Austhof, E., McFadden, C. M., Scranton, C., Sun, X., Vujkovic-Cviji, I., Rodriguez, D., Falk, L., Heslin, K. M., Arani, G., Obergh, V., Bessey, K., & Cooper, K. (2025). Determining the incidence, risk factors and biological drivers of irritable bowel syndrome (IBS) as part of the constellation of postacute sequelae of SARS-CoV-2 infection (PASC) outcomes in the Arizona CoVHORT-GI: a longitudinal cohort study. BMJ Open, 15(Issue 1). doi:10.1136/bmjopen-2024-095093
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  Introduction Postacute sequelae of SARS-CoV-2 infection (PASC) are extensive. Also known as long COVID, primary outcomes reported are neurologic, cardiac and respiratory in nature. However, several studies have also reported an increase in gastrointestinal (GI) symptoms and syndromes following COVID-19. This study of PASC will include extensive analyses of GI symptoms, determine if people with pre-existing irritable bowel syndrome (IBS) are at higher risk of developing PASC generally or PASC-GI, and which biomarkers are impacted and to what degree. This R01 study is being funded by the National Institute of Diabetes and Digestive and Kidney Diseases (1R01DK135483-01) from 2023 to 2028. Methods and analyses This study combines a longitudinal epidemiologic cohort study and in-depth, novel biologic analyses. In collaboration with a preexisting study, the Arizona CoVID-19 Cohort (CoVHORT)GI will recruit participants based on the history of COVID infection(s), new or ongoing GI symptoms 3–6 months postinfection, and pre-existing or incident IBS diagnosis to represent five study groups for comparison and analyses. A subset (n=1000) of those recruited will submit both stool and blood samples. Both samples will undergo a novel method to quantitate humoral and mucosal immune responses to host-derived faecal communities in conjunction with magnetic bead-based separation and high-depth shotgun microbial sequencing. Stool samples will also undergo traditional microbiome analyses (diversity and abundance) and faecal calprotectin assays. Additional serum analyses will aim to determine if a proteomics-based signature exists that differentiates a unique biomarker compositional signature discriminating PASC-GI versus no PASC. All laboratory data will be linked with in-depth epidemiologic data on demographics, symptoms and chronic conditions.
• Cooper, K. K., Mourkas, E., Schiaffino, F., Parker, C. T., Pinedo Vasquez, T. N., Garcia Bardales, P. F., Yori, P. P., Olortegui, M. P., Villanueva, K. M., Cachique, L. R., Delgado, H. S., Hitchings, M. D., Huynh, S., Sheppard, S. K., Pascoe, B., & Kosek, M. N. (2025). Sharing of cmeRABC alleles between C. coli and C. jejuni associated with extensive drug resistance in Campylobacter isolates from infants and poultry in the Peruvian Amazon. mBio, 16(Issue 2). doi:10.1128/mbio.02054-24
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  Campylobacter is a serious health threat because of the rapid progressive evolution of antimicrobial resistance and efficient transmission from zoonotic as well as human sources. Resistance to fluoroquinolones and macrolides is particularly concerning as this compromises the two most effective oral antibiotic agents currently available for human campylobacteriosis. Here, we report on the prevalence and worldwide distribution of the operon cmeRABC, which encodes an efflux pump conferring high levels of combined resistance to fluoroquinolones and macrolides in Campylobacter strains isolated from poultry (n = 75) and children (n = 177). These mutations were found to be highly prevalent in isolates from poultry (62.7%) and children (29.4%) in Iquitos, Peru. We investigated the population structure of genes in the cmeRABC operon and identified a potential genetic bottleneck for the cmeA and cmeB genes. While most cmeB alleles segregate by species, alleles associated with high resistance to fluoroquinolones and macrolides were found in both Campylobacter jejuni and Campylobacter coli. We inferred that the likely ancestry of these alleles was from C. jejuni and was later acquired by C. coli through recombination. Publicly accessible global genomic data from 16,120 Campylobacter genomes identified these mutations in approximately 6% of C. jejuni and C. coli isolates globally, with higher prevalence in samples from poultry in many countries, including Peru. Our findings suggest that these extensively drug-resistant Campylobacter strains originated from C. jejuni in poultry. IMPORTANCE Antimicrobial resistance in Campylobacter is a growing public health concern, driven by the rapid evolution and zoonotic transmission of resistant strains. This study focuses on mutations in the cmeABC efflux pump, which confer high resistance to fluoroquinolones and macrolides, the two most effective oral antibiotics for human campylobacteriosis. By analyzing genomes from poultry and children in Iquitos, Peru, as well as global genomic data sets, we identified a significant prevalence of these resistance-associated mutations, particularly in poultry and children. Our findings suggest that these mutations originated in Campylobacter jejuni and spread to C. coli through recombination. Globally, these mutations are found in approximately 6% of isolates, with higher prevalence in poultry in multiple countries. This research underscores the critical role of genomic epidemiology in understanding the origins, evolution, and dissemination of antimicrobial resistance and highlights the need to address poultry as a reservoir for resistant Campylobacter.
• Goforth, M., Cooper, M. A., Oliver, A., Pinzon, J., Skots, M., Obergh, V., Suslow, T., Flores, G. E., Huynh, S., Parker, C. T., Mackelprang, R., & Cooper, K. K. (2023).

  Bacterial Diversity Shifts of Commercial Tree Fruit Carpospheres at Different Harvest Points Across Multiple Growing Seasons

  . PLoS One. doi:10.2139/ssrn.4462305
• Goforth, M., Obergh, V., Park, R., Porchas, M., Crosby, K., Jifon, J., Ravishankar, S., Brierley, P., Leskovar, D. I., Turini, T. A., Schultheis, J. R., Coolong, T., Miller, R., Koiwa, H., Patil, B. S., Cooper, M. A., Huynh, S., Parker, C. T., Guan, W., & Cooper, K. K. (2023).

  Bacterial diversity and composition on the rinds of specific melon cultivars and hybrids from across different growing regions in the United States

  . PLoS One. doi:10.1101/2023.10.23.563553
• Mourkas, E., Valdebenito, J. O., Marsh, H., Hitchings, M. D., Cooper, K. K., Parker, C. T., Székely, T., Johansson, H., Ellström, P., Pascoe, B., Waldenström, J., & Sheppard, S. K. (2023).

  Urbanization spreads antimicrobial resistant enteric pathogens in wild bird microbiomes

  . PNAS. doi:10.1101/2023.07.11.548564
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  Abstract Human behaviour is dramatically changing global ecology. Nowhere is this more apparent than in urbanization, where novel high human density habitats are disrupting long established ecotones. Resultant changes to the transitional areas between organisms, especially enhanced contact between humans and wild animals, provides new opportunities for the spread of zoonotic pathogens, posing a serious threat to global public health. Here, by studying the multi-host enteric pathogen Campylobacter jejuni isolated from the gut of 30 bird species in 8 countries, we investigated how proximity to urbanization influenced the spread of antimicrobial resistant (AMR) strains. Generalized linear models compared multiple behavioural and ecological traits and confirmed a positive correlation between proximity to urbanization and the number of C. jejuni genotypes and AMR genes in wild bird hosts. Wild birds from highly urban areas harboured up to four times more C. jejuni genotypes and six times more AMR genes. This is consistent with increased frequency of transition events. Quantifying zoonotic transmission and gene pool spread is essential for quantitative one health surveillance and control measures against future zoonosis emergences.
• Parker, C. T., Kathariou, S., Miller, W. G., Huynh, S., Pascoe, B., & Cooper, K. K. (2025). American black bear (Ursus americanus) as a potential host for Campylobacter jejuni. PLOS ONE, 20(Issue 9). doi:10.1371/journal.pone.0331559
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  The Gram-negative bacterium Campylobacter jejuni is part of the commensal gut microbiota of numerous animal species and a leading cause of bacterial foodborne illness in humans. Most complete genomes of C. jejuni are from strains isolated from human clinical, poultry, and ruminant samples. Here, we characterized and compared the genomes of C. jejuni that were isolated from American black bears in three states in the southeastern United States from 2014 to 2016. Despite the limited sample size (n = 9), the isolates displayed substantial genotypic variability, including eight distinct sequence types (STs) and variable gene content encoding surface glycan structures such as capsular polysaccharides (CPS) and lipooligosaccharides (LOS). Phylogenetic analysis identified several C. jejuni host generalist strains among the isolates from bears that clustered with isolates from domestic poultry, cattle, and environmental sources. Three isolates (SKBC94, SKBC3, SKBC5) clustered with wildlife-associated strains, exhibiting mutations or deletions in loci associated with cytolethal distending toxin production and oxidative stress resistance, potentially influencing host-specific colonization. Additionally, strains SKBC3 and SKBC5 harbored distinct Entner-Doudoroff (E-D) loci, suggesting a potential evolutionary fitness advantage. This study provides the first evidence of C. jejuni colonization in American black bears, highlighting their potential role as reservoirs for diverse C. jejuni lineages from both anthropogenic and environmental sources. Further research is needed to determine the prevalence and host specificity of C. jejuni strains in black bears and their potential implications for public and wildlife health.
• Goforth, M., Cooper, M., Oliver, A., Pinzon, J., Skots, M., Obergh, V., Suslow, T., Flores, G., Huynh, S., Parker, C., Mackelprang, R., & Cooper, K. (2024). Bacterial community shifts of commercial apples, oranges, and peaches at different harvest points across multiple growing seasons. PLoS ONE, 19(4). doi:10.1371/journal.pone.0297453
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  Assessing the microbes present on tree fruit carpospheres as the fruit enters postharvest processing could have useful applications, as these microbes could have a major influence on spoilage, food safety, verification of packing process controls, or other aspects of processing. The goal of this study was to establish a baseline profile of bacterial communities associated with apple (pome fruit), peach (stone fruit), and Navel orange (citrus fruit) at harvest. We found that commercial peaches had the greatest bacterial richness followed by oranges then apples. Time of harvest significantly changed bacterial diversity in oranges and peaches, but not apples. Shifts in diversity varied by fruit type, where 70% of the variability in beta diversity on the apple carposphere was driven by the gain and loss of species (i.e., nestedness). The peach and orange carposphere bacterial community shifts were driven by nearly an even split between turnover (species replacement) and nestedness. We identified a small core microbiome for apples across and between growing seasons that included only Methylobacteriaceae and Sphingomonadaceae among the samples, while peaches had a larger core microbiome composed of five bacterial families: Bacillaceae, Geodermtophilaceae, Nocardioidaceae, Micrococcaeceae, and Trueperaceae. There was a relatively diverse core microbiome for oranges that shared all the families present on apples and peaches, except for Trueperaceae, but also included an additional nine bacterial families not shared including Oxalobacteraceae, Cytophagaceae, and Comamonadaceae. Overall, our findings illustrate the important temporal dynamics of bacterial communities found on major commercial tree fruit, but also the core bacterial families that constantly remain with both implications being important entering postharvest packing and processing.
• Goforth, M., Obergh, V., Park, R., Porchas, M., Brierley, P., Turni, T., Patil, B., Ravishankar, S., Huynh, S., Parker, C., & Cooper, K. (2024). Bacterial diversity of cantaloupes and soil from Arizona and California commercial fields at the point of harvest. PLoS ONE, 19(9). doi:10.1371/journal.pone.0307477
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  Across the United States, melons are a high demand crop reaching a net production of 2.7 million tons in 2020 with an economic value of $915 million dollars. The goal of this study was to characterize the bacterial diversity of cantaloupe rinds and soil from commercial melon fields at the point of harvest from two major production regions, Arizona, and California. Cantaloupes and composite soil samples were collected from three different commercial production fields, including Imperial Valley, CA, Central Valley, CA, and Yuma Valley, AZ, at the point of harvest over a three-month period, and 16S rRNA gene amplicon sequencing was used to assess bacterial diversity and community structure. The Shannon Diversity Index showed higher diversity among soil compared to the cantaloupe rind regardless of the sampling location. Regional diversity of soil differed significantly, whereas there was no difference in diversity on cantaloupe surfaces. Bray-Curtis Principal Coordinate Analysis (PCoA) dissimilarity distance matrix found the samples clustered by soil and melon individually, and then clustered tighter by region for the soil samples compared to the cantaloupe samples. Taxonomic analysis found total families among the regions to be 52 for the soil samples and 12 among cantaloupes from all three locations, but composition and abundance did vary between the three locations. Core microbiome analysis identified two taxa shared among soil and cantaloupe which were Bacillaceae and Micrococcaceae. This study lays the foundation for characterizing the cantaloupe microbiome at the point of harvest that provides the cantaloupe industry with those bacterial families that are potentially present entering post-harvest processing, which could assist in improving cantaloupe safety, shelf-life, cantaloupe quality and other critical aspects of cantaloupe post-harvest practices.
• Goforth, M., Obergh, V., Park, R., Porchas, M., Crosby, K., Jifon, J., Ravishankar, S., Brierley, P., Leskovar, D., Turini, T., Schultheis, J., Coolong, T., Miller, R., Koiwa, H., Patil, B., Cooper, M., Huynh, S., Parker, C., Guan, W., & Cooper, K. (2024). Bacterial diversity and composition on the rinds of specific melon cultivars and hybrids from across different growing regions in the United States. PLoS ONE, 19(4). doi:10.1371/journal.pone.0293861
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  The goal of this study was to characterize the bacterial diversity on different melon varieties grown in different regions of the US, and determine the influence that region, rind netting, and variety of melon has on the composition of the melon microbiome. Assessing the bacterial diversity of the microbiome on the melon rind can identify antagonistic and protagonistic bacteria for foodborne pathogens and spoilage organisms to improve melon safety, prolong shelf-life, and/or improve overall plant health. Bacterial community composition of melons (n = 603) grown in seven locations over a four-year period were used for 16S rRNA gene amplicon sequencing and analysis to identify bacterial diversity and constituents. Statistically significant differences in alpha diversity based on the rind netting and growing region (p < 0.01) were found among the melon samples. Principal Coordinate Analysis based on the Bray-Curtis dissimilarity distance matrix found that the melon bacterial communities clustered more by region rather than melon variety (R2 value: 0.09 & R2 value: 0.02 respectively). Taxonomic profiling among the growing regions found Enterobacteriaceae, Bacillaceae, Microbacteriaceae, and Pseudomonadaceae present on the different melon rinds at an abundance of ≥ 0.1%, but no specific core microbiome was found for netted melons. However, a core of Pseudomonadaceae, Bacillaceae, and Exiguobacteraceae were found for non-netted melons. The results of this study indicate that bacterial diversity is driven more by the region that the melons were grown in compared to rind netting or melon type. Establishing the foundation for regional differences could improve melon safety, shelf-life, and quality as well as the consumers’ health.
• Mourkas, E., Valdebenito, J., Marsh, H., Hitchings, M., Cooper, K., Parker, C., Johansson, H., Pascoe, B., Sheppard, S., Ellström, P., Székely, T., & Waldenström, J. (2024). Proximity to humans is associated with antimicrobial-resistant enteric pathogens in wild bird microbiomes. Current Biology, 34(17). doi:10.1016/j.cub.2024.07.059
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  Humans are radically altering global ecology, and one of the most apparent human-induced effects is urbanization, where high-density human habitats disrupt long-established ecotones. Changes to these transitional areas between organisms, especially enhanced contact among humans and wild animals, provide new opportunities for the spread of zoonotic pathogens. This poses a serious threat to global public health, but little is known about how habitat disruption impacts cross-species pathogen spread. Here, we investigated variation in the zoonotic enteric pathogen Campylobacter jejuni. The ubiquity of C. jejuni in wild bird gut microbiomes makes it an ideal organism for understanding how host behavior and ecology influence pathogen transition and spread. We analyzed 700 C. jejuni isolate genomes from 30 bird species in eight countries using a scalable generalized linear model approach. Comparing multiple behavioral and ecological traits showed that proximity to human habitation promotes lineage diversity and is associated with antimicrobial-resistant (AMR) strains in natural populations. Specifically, wild birds from urban areas harbored up to three times more C. jejuni genotypes and AMR genes. This study provides novel methodology and much-needed quantitative evidence linking urbanization to gene pool spread and zoonoses.
• Pascoe, B., Futcher, G., Pensar, J., Bayliss, S., Mourkas, E., Calland, J., Hitchings, M., Joseph, L., Lane, C., Greenlee, T., Arning, N., Wilson, D., Jolley, K., Corander, J., Maiden, M., Parker, C., Cooper, K., Rose, E., Hiett, K., , Bruce, B., et al. (2024). Machine learning to attribute the source of Campylobacter infections in the United States: A retrospective analysis of national surveillance data. Journal of Infection, 89(5). doi:10.1016/j.jinf.2024.106265
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  Objectives: Integrating pathogen genomic surveillance with bioinformatics can enhance public health responses by identifying risk and guiding interventions. This study focusses on the two predominant Campylobacter species, which are commonly found in the gut of birds and mammals and often infect humans via contaminated food. Rising incidence and antimicrobial resistance (AMR) are a global concern, and there is an urgent need to quantify the main routes to human infection. Methods: During routine US national surveillance (2009–2019), 8856 Campylobacter genomes from human infections and 16,703 from possible sources were sequenced. Using machine learning and probabilistic models, we target genetic variation associated with host adaptation to attribute the source of human infections and estimate the importance of different disease reservoirs. Results: Poultry was identified as the primary source of human infections, responsible for an estimated 68% of cases, followed by cattle (28%), and only a small contribution from wild birds (3%) and pork sources (1%). There was also evidence of an increase in multidrug resistance, particularly among isolates attributed to chickens. Conclusions: National surveillance and source attribution can guide policy, and our study suggests that interventions targeting poultry will yield the greatest reductions in campylobacteriosis and spread of AMR in the US. Data availability: All sequence reads were uploaded and shared on NCBI's Sequence Read Archive (SRA) associated with BioProjects; PRJNA239251 (CDC / PulseNet surveillance), PRJNA287430 (FSIS surveillance), PRJNA292668 & PRJNA292664 (NARMS) and PRJNA258022 (FDA surveillance). Publicly available genomes, including reference genomes and isolates sampled worldwide from wild birds are associated with BioProject accessions: PRJNA176480, PRJNA177352, PRJNA342755, PRJNA345429, PRJNA312235, PRJNA415188, PRJNA524300, PRJNA528879, PRJNA529798, PRJNA575343, PRJNA524315 and PRJNA689604. Contiguous assemblies of all genome sequences compared are available at Mendeley data (assembled C. coli genomes doi: 10.17632/gxswjvxyh3.1; assembled C. jejuni genomes doi: 10.17632/6ngsz3dtbd.1) and individual project and accession numbers can be found in Supplementary tables S1 and S2, which also includes pubMLST identifiers for assembled genomes. Figshare (10.6084/m9.figshare.20279928). Interactive phylogenies are hosted on microreact separately for C. jejuni (https://microreact.org/project/pascoe-us-cjejuni) and C. coli (https://microreact.org/project/pascoe-us-ccoli).
• Schiaffino, F., Colston, J., Paredes Olortegui, M., Mourkas, E., Pascoe, B., Lima, A., Mason, C., Ahmed, T., Kang, G., Mduma, E., Samie, A., Zaidi, A., Liu, J., Cooper, K., Houpt, E., Parker, C., Lee, G., Kosek, M., & Peñataro Yori, P. (2024). The epidemiology and impact of persistent Campylobacter infections on childhood growth among children 0–24 months of age in resource-limited settings. eClinicalMedicine, 76. doi:10.1016/j.eclinm.2024.102841
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  Background: Campylobacter is the leading cause of bacterial gastroenteritis worldwide. It is generally associated with an acute gastrointestinal infection causing a self-limiting diarrheal episode. However, there is evidence that persistent/recurrent carriage of Campylobacter also occurs. In hyperendemic settings the epidemiology and consequences of persistent Campylobacter enteric infections is poorly studied. Methods: Risk factors for and growth consequences of persistent Campylobacter infections detected by polymerase chain reaction (qPCR) were evaluated with data from the MAL-ED birth cohort study in children 0–24 months of age between November 2009 and February 2012. A persistent Campylobacter infection was defined as three or more consecutive Campylobacter positive monthly stools. Findings: Across all study sites, 45.5% (781/1715) of children experienced at least one persistent Campylobacter episode. The average cumulative duration of days in which children with persistent Campylobacter were positive for Campylobacter spp. was 150 days (inter-quartile range: 28–236 days). Children who experienced a persistent Campylobacter episode had an attained 24-month length-for-age (LAZ) score that was 0.23 (95% (CI): −0.31, −0.15) less than children without a persistent Campylobacter episode. Among children who had at least one episode of Campylobacter over a 3-month or 9-month window, persistent episodes were not significantly associated with poorer 3-month weight gain (−28.7 g, 95% CI: −63.4 g, 6.0 g) but were associated with poorer 9-month linear growth (−0.134 cm 95% CI: −0.246, −0.022) compared to children with an episode that resolved within 31 days. Interpretation: Persistent/recurrent Campylobacter infection is common among children and has a measurable negative impact on linear growth in early childhood. Funding: Funding for this study was provided by the Bill and Melinda Gates Foundation (OPP1066146 and OPP1152146), the National Institutes of Health United States (R01AI158576 and R21AI163801 to MNK and CTP; K43TW012298 to FS; K01AI168493 to JMC; GOL was supported by K01AI145080. This research was also supported in part by USDA-ARS CRIS project 2030-42000-055-00D. The funders had no role in study design, study implementation, data analysis, or interpretation of the results.
• Schiaffino, F., Parker, C., Garcia Bardales, P., Huynh, S., Villanueva, K., Mourkas, E., Pascoe, B., Yori, P., Olortegui, M., Houpt, E., Liu, J., Cooper, K., & Kosek, M. (2024). Novel rpsK / rpsD primer-probe assay improves detection of Campylobacter jejuni and Campylobacter coli in human stool. PLoS Neglected Tropical Diseases, 18(3). doi:10.1371/journal.pntd.0012018
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  Campylobacter causes bacterial enteritis, dysentery, and growth faltering in children in low-and middle-income countries (LMICs). Campylobacter spp. are fastidious organisms, and their detection often relies on culture independent diagnostic technologies, especially in LMICs. Campylobacter jejuni and Campylobacter coli are most often the infectious agents and in high income settings together account for 95% of Campylobacter infections. Several other Campylobacter species have been detected in LMIC children at an increased prevalence relative to high income settings. After doing extensive whole genome sequencing of isolates of C. jejuni and C. coli in Peru, we observed heterogeneity in the binding sites for the main species-specific PCR assay (cadF) and designed an alternative rpsKD-based qPCR assay to detect both C. jejuni and C. coli. The rpsKD-based qPCR assay identified 23% more C.jejuni/C.coli samples than the cadF assay among 47 Campylobacter genus positive cadF negative samples verified to have C. jejuni and or C. coli with shotgun metage-nomics. This assay can be expected to be useful in diagnostic studies of enteric infectious diseases and be useful in revising the attribution estimates of Campylobacter in LMICs.
• Schiaffino, F., Parker, C., Paredes Olortegui, M., Pascoe, B., Manzanares Villanueva, K., Garcia Bardales, P., Mourkas, E., Huynh, S., Romaina Cachique, L., Gray, H., Salvatierra, G., Silva Delgado, H., Sheppard, S., Cooper, K., Kosek, M., & Peñataro Yori, P. (2024). Genomic resistant determinants of multidrug-resistant Campylobacter spp. isolates in Peru. Journal of Global Antimicrobial Resistance, 36. doi:10.1016/j.jgar.2024.01.009
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  Objectives: Antimicrobial resistant (AMR) Campylobacter is a global health threat; however, there is limited information on genomic determinants of resistance in low- and middle-income countries. We evaluated genomic determinants of AMR using a collection of whole genome sequenced Campylobacter jejuni and C. coli isolates from Iquitos, Peru. Methods: Campylobacter isolates from two paediatric cohort studies enriched with isolates that demonstrated resistance to ciprofloxacin and azithromycin were sequenced and mined for AMR determinants. Results: The gyrA mutation leading to the Thr86Ile amino acid change was the only gyrA mutation associated with fluoroquinolone resistance identified. The A2075G mutation in 23S rRNA was present, but three other 23S rRNA mutations previously associated with macrolide resistance were not identified. A resistant-enhancing variant of the cmeABC efflux pump genotype (RE-cmeABC) was identified in 36.1% (35/97) of C. jejuni genomes and 17.9% (12/67) of C. coli genomes. Mutations identified in the CmeR-binding site, an inverted repeat sequence in the cmeABC promoter region that increases expression of the operon, were identified in 24/97 C. jejuni and 14/67 C. coli genomes. The presence of these variants, in addition to RE-cmeABC, was noted in 18 of the 24 C. jejuni and 9 of the 14 C. coli genomes. Conclusions: Both RE-cmeABC and mutations in the CmeR-binding site were strongly associated with the MDR phenotype in C. jejuni and C. coli. This is the first report of RE-cmeABC in Peru and suggests it is a major driver of resistance to the principal therapies used to treat human campylobacteriosis in this setting.
• Gabbert, A. D., Mydosh, J. L., Talukdar, P. K., Gloss, L. M., McDermott, J., Cooper, K. K., Clair, G., & Konkel, M. E. (2023).

  The Missing Pieces: The Role of Secretion Systems in Campylobacter jejuni Virulence

  . Biomolecules, 13(1), 135. doi:10.3390/biom13010135
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  Campylobacter jejuni is likely the most common bacterial cause of gastroenteritis worldwide, responsible for millions of cases of inflammatory diarrhea characterized by severe abdominal cramps and blood in the stool. Further, C. jejuni infections are associated with post-infection sequelae in developed countries and malnutrition and growth-stunting in low- and middle-income countries. Despite the increasing prevalence of the disease, campylobacteriosis, and the recognition that this pathogen is a serious health threat, our understanding of C. jejuni pathogenesis remains incomplete. In this review, we focus on the Campylobacter secretion systems proposed to contribute to host-cell interactions and survival in the host. Moreover, we have applied a genomics approach to defining the structural and mechanistic features of C. jejuni type III, IV, and VI secretion systems. Special attention is focused on the flagellar type III secretion system and the prediction of putative effectors, given that the proteins exported via this system are essential for host cell invasion and the inflammatory response. We conclude that C. jejuni does not possess a type IV secretion system and relies on the type III and type VI secretion systems to establish a niche and potentiate disease.
• Yori, P. P., Olórtegui, M. P., Schiaffino, F., Colston, J. M., Vasquez, T. P., Bardales, P. F., Lopez, V. S., Paredes, L. F., Perez, K., Curico, G., Flynn, T., Zhang, J., Asayag, C. R., Sánchez, G. M., Delgado, H. S., Morales, M. C., Casanova, W., Jiu, B., Oberhelman, R. A., , Escate, C. M., et al. (2023).

  Etiology of acute febrile illness in the peruvian amazon as determined by modular formatted quantitative PCR: a protocol for RIVERA, a health facility-based case-control study

  . BMC Public Health, 23(1), 674. doi:10.1186/s12889-023-15619-6
• Yori, P. P., Olórtegui, M. P., Schiaffino, F., Perez, K., Huansi, G. C., Flynn, T., Zhang, J., Asayag, C. R., Sánchez, G. M., Delgado, H. S., Morales, M. C., Casanova, W., Jiu, B., Escate, C. M., Silver, R., Henao, O., Cooper, K. K., Liu, J., Houpt, E. R., , Kosek, M., et al. (2023).

  Etiology of Acute Febrile Illness in the Peruvian Amazon as determined by modular formatted quantitative PCR: A Protocol for RIVERA, a Health Facility-Based Case-Control Study

  . Res Sq, 31, re.3.rs-2635774. doi:10.21203/rs.3.rs-2635774/v1
• Austhof, E., Bell, M. L., Riddle, M. S., Catalfamo, C. J., McFadden, C., Cooper, K. K., Walter, E. S., Jacobs, E. T., & Pogreba-Brown, K. (2022).

  Persisting gastrointestinal symptoms and post-infectious irritable bowel syndrome following SARS-CoV-2 infection: results from the Arizona CoVHORT

  . Epidemiol Infect, 150, e136. doi:10.1017/s0950268822001200
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  Abstract In this study, we aimed to examine the association between gastrointestinal (GI) symptom presence during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the prevalence of GI symptoms and the development of post-infectious irritable bowel syndrome (PI-IBS). We used data from a prospective cohort and logistic regression to examine the association between GI symptom status during confirmed SARS-CoV-2 infection and prevalence of persistent GI symptoms at ≥45 days. We also report the incidence of PI-IBS following SARS-CoV-2 infection. Of the 1475 participants in this study, 33.8% ( n = 499) had GI symptoms during acute infection. Cases with acute GI symptoms had an odds of persisting GI symptoms 4 times higher than cases without acute GI symptoms (odds ratio (OR) 4.29, 95% confidence interval (CI) 2.45–7.53); symptoms lasted on average 8 months following infection. Of those with persisting GI symptoms, 67% sought care for their symptoms and incident PI-IBS occurred in 3.0% ( n = 15) of participants. Those with acute GI symptoms after SARS-CoV-2 infection are likely to have similar persistent symptoms 45 days and greater. These data indicate that attention to a potential increase in related healthcare needs is warranted.
• Bardales, P. F., Schiaffino, F., Huynh, S., Olórtegui, M. P., Yori, P. P., Vasquez, T. P., Villanueva, K. M., Huansi, G. E., Lopez, W. V., Cooper, K. K., Parker, C. T., & Kosek, M. (2022).

  “Candidatus Campylobacter infans” detection is not associated with diarrhea in children under the age of 2 in Peru

  . PLoS Negl Trop Dis, 16(10), e0010869. doi:10.1371/journal.pntd.0010869
• Cooper, K. K., Sen, A., Goforth, M., & Anakk, S. (2022). Deletion of Constitutive Androstane Receptor Led to Intestinal Alterations and Increased Imidacloprid in Murine Liver. Journal of the Endocrine Society, 6(12). doi:10.1210/jendso/bvac145
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  Imidacloprid (IMI) is the most frequently detected neonicotinoid pesticide in the environment. Despite typically low toxicity in vertebrates, IMI exposure is associated with liver and gastrointestinal toxicity. The mechanism underlying IMI toxicity in mammals is unclear. Pesticide exposure frequently activates xenobiotic nuclear receptors, such as the constitutive androstane receptor (CAR), to induce detoxification phase I and phase II genes. This study examined the role of CAR in mediating IMI off-target toxicity. Female Car-/- and wild-type (WT) mice were orally administered imidacloprid (50 mg/kg, twice daily) for 21 days, following which serum, liver, and intestinal tissues were collected. Liver tissue analysis indicated mild inflammation and induction of detoxification gene Cyp2b10 in IMI-exposed WT mice. The absence of CAR increased hepatic IMI accumulation. Microbiome analysis of ileal samples revealed IMI altered microbial diversity in a genotype-specific manner, with increased α-diversity in Car-/- mice while decreased α-diversity in WT mice. We observed Car-/- mice exhibit intestinal alterations with decreased CYP-P450 expression, blunted villi height, and increased small intestine length and weight independent of IMI exposure. Our results suggest that IMI is not overtly toxic. However, the absence of xenobiotic nuclear receptor CAR allows increased accumulation of IMI in the liver and disrupts the villi structure and Cyp gene expression in the intestine.
• Luna, E., Parkar, S. G., Kirmiz, N., Hartel, S., Hearn, E., Hossine, M., Kurdian, A., Mendoza, C. 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

  . Appl Environ Microbiol, 88(1), e0148721. doi:10.1128/AEM.01487-21
• Parker, C. T., Schiaffino, F., Huynh, S., Olórtegui, M. P., Yori, P. P., Bardales, P. F., Vasquez, T. P., Huansi, G. E., Villanueva, K. M., Lopez, W. V., Cooper, K. K., & Kosek, M. (2022).

  Shotgun metagenomics of fecal samples from children in Peru reveals frequent complex co-infections with multiple Campylobacter species

  . PLoS Negl Trop Dis, 16(10), e0010815. doi:10.1371/journal.pntd.0010815
• 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.1009820
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  Salmonella 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.
• Achtman, M., van den Broeck, F., Cooper, K. K., Lemey, P., Parker, C. T., Zhou, Z., Huynh, S., Gorski, L., Liang, A. S., Guerbidjian, O., Chiou, C. S., Delappe, N., Claus, H., Weill, F. X., Brown, D., Litrup, E., Torpdahl, M., Smith, A. M., & Turnball, J. D. (2021). Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature. PLoS Genetics, 17(Issue 9). doi:10.1371/journal.pgen.1009820
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  Salmonella 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/v13081652
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  Bacteriophages (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.
• 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(Issue 8). doi:10.3390/v13081652
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  Bacteriophages (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 Acinetobacter-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 Acinetobacter radioresistens 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 Pseudomonas species. In Pseudomonas, 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 Acinetobacter-infecting phages and the determination of their cell receptors. Further, we describe the genomes of a new genus of Cystoviruses 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
• 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 campylobacter jejuni serotype hs:19. Microbial Genomics, 7(Issue 11). doi:10.1099/mgen.0.000660
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  Campylobacter jejuni strains that produce sialylated lipooligosaccharides (LOS) can cause the immune-mediated disease Guillain-Barré syndrome (GBS). The risk of GBS after infection with C. jejuni Penner serotype HS:19 is estimated to be at least six times higher than the average risk. Aside from LOS biosynthesis genes, genomic characteristics that promote an increased risk for GBS following C. jejuni HS:19 infection, remain uncharacterized. We hypothesized that strains with the HS:19 serotype have unique genomic features that explain the increased risk for GBS. We performed genome sequencing, alignments, single nucleotide polymorphisms' analysis and methylome characterization on a subset, and pan-genome analysis on a large number of genomes to compare HS:19 with non-HS:19 C. jejuni genome sequences. Comparison of 36 C. jejuni HS:19 with 874 C. jejuni non-HS:19 genome sequences led to the identification of three single genes and ten clusters containing contiguous genes that were significantly associated with C. jejuni HS:19. One gene cluster of seven genes, localized downstream of the capsular biosynthesis locus, was related to sulphation of biomolecules. This cluster also encoded the campylobacter sialyl transferase Cst-I. Interestingly, sulphated bacterial biomolecules such as polysaccharides can promote immune responses and, therefore, (in the presence of sialic acid) may play a role in the development of GBS. Additional gene clusters included those involved in persistence-mediated pathogenicity and gene clusters involved in restriction-modification systems. Furthermore, characterization of methylomes of two HS:19 strains exhibited novel methylation patterns (5′-CATG-3 and 5′-m6AGTNNNNNNRTTG-3) that could differentially effect gene-expression patterns of C. jejuni HS:19 strains. Our study provides novel insight into specific genetic features and possible virulence factors of C. jejuni associated with the HS:19 serotype that may explain the increased risk of GBS.
• 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
• Katiyar, N., Ramadoss, N., Gupta, D., Pakala, S. B., Cooper, K., & Basu, C. (2021). Transcriptomic profiling of Paulownia elongata in response to heat stress. Plant Gene, 28(Issue). doi:10.1016/j.plgene.2021.100330
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  Rising global temperatures have caused a substantial loss in crop productivity throughout the world. Understanding the fundamental mechanisms underlying tolerance to heat stress in plants has become increasingly relevant, particularly as global warming continues to rise. The goal of our study was to identify and analyze heat stress-induced transcriptomic changes in Paulownia elongata plants. Paulownia elongata are fast growing trees known for their ability to grow in a wide range of temperatures. However, the genes responsible for its thermotolerance have not yet been identified and studied in detail. In our study, we used RNA-sequencing (RNA-seq) to analyze changes in gene expression at the transcriptomic level after inducing heat stress and identified 4,435 genes as differentially expressed. Most of the genes found to be upregulated play a critical role in protein binding, unfolding, retention, and transport, suggesting that heat tolerance in plants can be achieved by protecting native proteins. The genes and pathways identified in this study can serve as valuable targets in heat tolerance studies and development of heat tolerant plants. To the best of our knowledge, this is the first in-depth report of heat-induced transcriptome analysis in P. elongata.
• 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). Genomic Characterization of Campylobacter jejuni Adapted to the Guinea Pig (Cavia porcellus) Host. Frontiers in Cellular and Infection Microbiology, 11(Issue). doi:10.3389/fcimb.2021.607747
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  Campylobacter jejuni is the leading bacterial cause of gastroenteritis worldwide with excessive incidence in low-and middle-income countries (LMIC). During a survey for C. jejuni from putative animal hosts in a town in the Peruvian Amazon, we were able to isolate and whole genome sequence two C. jejuni strains from domesticated guinea pigs (Cavia porcellus). The C. jejuni isolated from guinea pigs had a novel multilocus sequence type that shared some alleles with other C. jejuni collected from guinea pigs. Average nucleotide identity and phylogenetic analysis with a collection of C. jejuni subsp. jejuni and C. jejuni subsp. doylei suggest that the guinea pig isolates are distinct. Genomic comparisons demonstrated gene gain and loss that could be associated with guinea pig host specialization related to guinea pig diet, anatomy, and physiology including the deletion of genes involved with selenium metabolism, including genes encoding the selenocysteine insertion machinery and selenocysteine-containing proteins.
• 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/pathogens10050529
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  Salmonella 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.
• 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, 10(Issue 5). doi:10.3390/pathogens10050529
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  Salmonella 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).
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  The 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.
• Arias, D. B., 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(Issue 10). doi:10.1099/mgen.0.000432
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  The cyanobacterium Nostoc punctiforme can form lipid droplets (LDs), internal inclusions containing triacylglycerols, carotenoids and alkanes. LDs are enriched for a 17 carbon-long alkane in N. punctiforme, and it has been shown that the overexpression of the aar and ado 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 N. punctiforme 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).
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  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 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.00735-19
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  ABSTRACT 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.
• Cooper, K. K., Bian, X., Garber, J. M., 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). Campylobacter Abundance in Breastfed Infants and Identification of a New Species in the Global Enterics Multicenter Study. mSphere, 5(1). doi:10.1128/msphere.00735-19
• 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.
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  Campylobacter 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.
• 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(Issue 8). doi:10.1371/journal.pntd.0008533
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  Campylobacter 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 campylobacterio-sis 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).
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  The 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.
• 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(Issue 5). doi:10.1128/msphere.00631-19
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  The Gram-negative bacterium Cupriavidus gilardii 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 C. gilardii 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 C. gilardii strains sequenced to date. The intrinsic resistome of C. gilardii did not include the colistin resistance gene mcr-5, which was in a transposon present only in one strain. The intrinsic resistome of C. gilardii was comprised of (i) many multidrug efflux pumps, such as a homolog of the Pseudomonas aeruginosa 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-N-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 C. gilardii to multiple antibiotics and its ability to become resistant to an increasing number of drugs during therapy.
• Oliver, A., Kay, M., & Cooper, K. K. (2018). Comparative genomics of cocci-shaped Sporosarcina strains with diverse spatial isolation. BMC Genomics, 19(Issue 1). doi:10.1186/s12864-018-4635-8
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  Background: Cocci-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. Results: For this study, we sequenced 28 genomes of cocci-shaped Sporosarcina strains isolated from 13 different locations around the world. We generated the first six complete genomes and methylomes utilizing PacBio sequencing, and an additional 22 draft genomes using Illumina sequencing. Genomic analysis revealed that cocci-shaped Sporosarcina strains contained an average genome of 3.3 Mb comprised of 3222 CDS, 54 tRNAs and 6 rRNAs, while only two strains contained plasmids. The cocci-shaped Sporosarcina genome on average contained 2.3 prophages and 15.6 IS elements, while methylome analysis supported the diversity of these strains as only one of 31 methylation motifs were shared under identical growth conditions. Analysis with a 90% identity cut-off revealed 221 core genes or ~7% of the genome, while a 30% identity cut-off generated a pan-genome of 8610 genes. The phylogenetic relationship of the cocci-shaped Sporosarcina strains based on either core genes, accessory genes or spore-related genes consistently resulted in the 29 strains being divided into eight clades. Conclusions: This study begins to unravel the phylogenetic relationship of cocci-shaped Sporosarcina strains, and the comparative genomics of these strains supports identification of several new species.
• Oliver, A., Kay, M., & Cooper, K. K. (2018). Comparative genomics of cocci-shaped Sporosarcina strains with diverse spatial isolation. BMC genomics, 19(1), 310.
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  Cocci-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.00801-18
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  Produce 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.
• 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(Issue 1). doi:10.1128/mra.00807-18
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  Produce 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.
• Pinoargote, G., Flores, G., Cooper, K., & Ravishankar, S. (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(Issue 10). doi:10.1111/are.13791
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  Acute hepatopancreatic necrosis disease (AHPND) is a devastating condition impacting marine shrimp production worldwide. The objective of this study was to evaluate the effects of four probiotic formulations on Pacific white shrimp (Litopenaeus vannamei) infected with pathogenic Vibrio parahaemolyticus causing AHPND. In addition, bacterial community composition analyses of shrimp gastrointestinal tract (GIT) and aquaculture water before and after infection were conducted by sequencing variable region 4 of the 16S rRNA gene on the Illumina MiSeq platform. Treatments included: (1) Lactobacillus casei (P1), (2) L. casei and Rhodopseudomonas palustris (P2), (3) L. casei, Saccharomyces cerevisiae and R. palustris (P3), and (4) a commercial probiotic EM® (EM), which showed shrimp survival of 11.7%, 26.7%, 36.7% and 73.3% respectively. Treatments causing lower survival showed greater relative abundance (>60%) of family Vibrionaceae in the GIT compared to treatments with higher survival. Diversity indices from GIT samples revealed that treatments showing higher survival had higher Shannon index values (4.69 ± 0.133), compared with those of treatments with lower survival (0.17 ± 0.004). Diversity indices from water samples did not show significant differences after infection (Shannon index 4.64 ± 0.53). The results showed that probiotics could effectively mitigate AHPND while maintaining diverse microbial composition in shrimp GIT, thus maintaining sustainability in the shrimp aquaculture industry.
• 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 12 Dry-Heat-Resistant Bacillus Strains Isolated from the Cleanrooms Where the Viking Spacecraft Were Assembled

  . Genome Announcements, 6(12). doi:10.1128/genomea.00094-18
• 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.00094-18
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  The 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., Vaishampayan, P., Cooper, K., & Venkateswaran, K. (2018). Draft genome sequences of Acinetobacter and Bacillus strains isolated from spacecraftassociated surfaces. Genome Announcements, 6(Issue 6). doi:10.1128/genomea.01554-17
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  We report here the draft genome sequences of four strains isolated from spacecraft-associated surfaces exhibiting increased resistance to stressors such as UV radiation and exposure to H2O2. The draft genomes of strains 1P01SCT, FO-92T, 50v1, and 2P01AA had sizes of 5,500,894 bp, 4,699,376 bp, 3,174,402 bp, and 4,328,804 bp, respectively.
• 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.00094-18
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  We 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.
• Chaires, M., Gupta, D., Joshee, N., Cooper, K. K., & Basu, C. (2017). RNA-seq analysis of the salt stress-induced transcripts in fast-growing bioenergy tree, Paulownia elongata. Journal of Plant Interactions, 12(Issue 1). doi:10.1080/17429145.2017.1298851
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  Paulowina 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 saltinduced transcriptome analysis in P. elongata. The current study indicates that differential expression of a select group of genes of P. elongata and their possible roles in pathways and mechanisms related to salt tolerance. Functional characterization of these genes will assist in future investigations of salt tolerance in P. elongata, which could be used to enhance biofuel production.
• 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.01234-17
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  Salmonella 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.
• 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(Issue 46). doi:10.1128/genomea.01234-17
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  Salmonella 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:10.1080/17429145.2017.1298851
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  ABSTRACTPaulowina 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...
• Pascoe, B., Méric, G., Yahara, K., Wimaralathna, H., Murray, S. F., Hitchings, M. D., Sproston, E. L., Carrillo, C. D., Taboada, E., Cooper, K. K., Huynh, S., Cody, A. J., Jolley, K. A., Maiden, M. C., McCarthy, N. D., Didelot, X., Parker, C. T., & Sheppard, S. K. (2017).

  Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations

  . Mol Ecol, 26(17), 4497-4508. doi:10.1111/mec.14176
• 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.14176
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  The 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., Huynh, S., Gorski, L., Cooper, K. K., & Miller, W. G. (2015). Complete genome sequences of two outbreak strains of Salmonella enterica subsp. enterica serovar thompson associated with cilantro. Genome Announcements, 3(Issue 6). doi:10.1128/genomea.01365-15
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  Salmonella 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., 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.01365-15
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  Salmonella 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.01312-15
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  Infections 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:10.1186/1471-2164-15-17
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  Although 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.00482-14
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  Escherichia 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, K. K., Mandrell, R. E., Louie, J. W., Korlach, J., Clark, T. A., Parker, C. T., Huynh, S., Chain, P. S., Ahmed, S., & Carter, M. Q. (2014). Comparative genomics of enterohemorrhagic Escherichia coli O145: H28 demonstrates a common evolutionary lineage with Escherichia coli O157: H7. BMC Genomics, 15(Issue 1). doi:10.1186/1471-2164-15-17
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  Background: Although 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. Results: 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. Conclusions: 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. © 2014 Cooper et al.; licensee BioMed Central Ltd.
• Cooper, K. K., Mandrell, R. E., Louie, J. W., Korlach, J., Clark, T. A., Parker, C. T., Huynh, S., Chain, P. S., Ahmed, S., & Carter, M. Q. (2014). Complete genome sequences of two Escherichia coli O145:H28 outbreak strains of food origin. Genome Announcements, 2(Issue 3). doi:10.1128/genomea.00482-14
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  Escherichia 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, K. K., Bueschel, D. M., & Songer, J. G. (2013). Presence of Clostridium perfringens in retail chicken livers. Anaerobe, 21(Issue). doi:10.1016/j.anaerobe.2013.03.013
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  Chicken 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). © 2013 Elsevier Ltd.
• Cooper, K. K., Cooper, M. A., Zuccolo, A., & Joens, L. A. (2013). Re-sequencing of a virulent strain of Campylobacter jejuni NCTC11168 reveals potential virulence factors. Research in Microbiology, 164(Issue 1). doi:10.1016/j.resmic.2012.10.002
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  In 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. © 2012 Institut Pasteur.
• Cooper, K. K., Songer, J. G., & Uzal, F. A. (2013). Diagnosing clostridial enteric disease in poultry. Journal of Veterinary Diagnostic Investigation, 25(Issue 3). doi:10.1177/1040638713483468
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  The 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. © 2013 The Author(s).
• 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.2012.10.002
  More info

  In 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.2013.03.013
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  Chicken 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:10.1177/1040638713483468
  More info

  The 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.
• Coursodon, C. F., Glock, R. D., Moore, K. L., Cooper, K. K., & Songer, J. G. (2012). TpeL-producing strains of Clostridium perfringens type A are highly virulent for broiler chicks. Anaerobe, 18(Issue 1). doi:10.1016/j.anaerobe.2011.10.001
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  Clostridium 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. © 2011 Elsevier Ltd.
• Law, B. F., Cooper, K. K., Theoret, J. R., Zekarias, B., Roland, K. L., Curtiss, R., Joens, L. A., Law, B. F., Cooper, K. K., Theoret, J. R., Zekarias, B., Roland, K. L., Curtiss, R., & Joens, L. A. (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, 19(9), 1426-1431. doi:10.1128/cvi.00151-12
• 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.00151-12
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  In 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.2011.10.001
  More info

  Clostridium 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, K. K., Cooper, M. A., Zuccolo, A., Law, B., & Joens, L. A. (2011). Complete genome sequence of Campylobacter jejuni strain S3. Journal of Bacteriology, 193(Issue 6). doi:10.1128/jb.01475-10
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  Campylobacter 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. Copyright © 2011, American Society for Microbiology. All Rights Reserved.
• 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.01475-10
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  Campylobacter 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., Cooper, K. K., Glock, R. D., & Joens, L. A. (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(Issue 12). doi:10.1089/fpd.2011.0892
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  Iron 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. © 2011 Mary Ann Liebert, Inc.
• 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.2011.0892
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  Iron 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.
• Cooper, K. K., & Songer, J. G. (2010). Virulence of Clostridium perfringens in an experimental model of poultry necrotic enteritis. Veterinary Microbiology, 142(Issue 3-4). doi:10.1016/j.vetmic.2009.09.065
  More info

  Poultry 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. © 2009 Elsevier B.V.
• Cooper, K. K., Theoret, J. R., Stewart, B. A., Trinh, H. T., Glock, R. D., & Songer, J. G. (2010). Virulence for chickens of Clostridium perfringens isolated from poultry and other sources. Anaerobe, 16(Issue 3). doi:10.1016/j.anaerobe.2010.02.006
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  Clostridium 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 Cornish×Rock 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 (cpb2pos), from a field case of NE] produced gross lesions compatible with NE in >85% of challenged birds. However, strains JGS1714 (enterotoxigenic genotype A, cpb2pos, human food poisoning), JGS1936 (genotype A, cpb2neg, bovine neonatal enteritis), JGS4142 (genotype A, cpb2pos, bovine jejunal hemorrhage syndrome), JGS1473 (genotype A, cpb2pos, chicken normal flora), JGS1070 (genotype C, cpb2pos, porcine hemorrhagic enteritis), JGS1882 (genotype A, cpb2pos, porcine neonatal enteritis), JGS1120 (ATCC 13124, genotype A, cpb2neg, gas gangrene), JGS4151 (strain 13, genotype A, cpb2pos, canine), and JGS4303 (SM101, enterotoxigenic genotype A, cpb2neg, 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. © 2010 Elsevier Ltd.
• 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.2009.09.065
  More info

  Poultry 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.2010.02.006
  More info

  Clostridium 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.
• Cooper, K. K., & Songer, J. G. (2009). Necrotic enteritis in chickens: A paradigm of enteric infection by Clostridium perfringens type A. Anaerobe, 15(Issue 1-2). doi:10.1016/j.anaerobe.2009.01.006
  More info

  Withdrawal 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. © 2009 Elsevier Ltd. All rights reserved.
• Cooper, K. K., Trinh, H. T., & Songer, J. G. (2009). Immunization with recombinant alpha toxin partially protects broiler chicks against experimental challenge with Clostridium perfringens. Veterinary Microbiology, 133(Issue 1-2). doi:10.1016/j.vetmic.2008.06.001
  More info

  Necrotic 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. © 2008 Elsevier B.V. All rights reserved.
• 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.2009.01.006
  More info

  Withdrawal 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.2008.06.001
  More info

  Necrotic 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. (2007).

  NECROTIC ENTERITIS IN BROILER CHICKENS: STUDIES IN DISEASE REPRODUCTION AND PATHOGENESIS

  . Doctorate Dissertation.
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  11 1.0 INTRODUCTION 12 1.1 Problem 12 1.2 Overview 12 1.3 Etiology of NE 14 1.4 Historical Aspects 15 1.5 Signs, Lesions, and Diagnosis 20 1.6 Pathogenesis and Host Response 23 1.7 Epidemiology 29 1.8 Treatment and Prevention 36 1.9 Reproduction of NE 41 1.10 Research contributions 44 2.0 PRESENT STUDY 45 2.1 Methods 45 2.2 Results 48 2.3 Conclusions 52

Presentations

• 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.
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  McLain, 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.

Poster Presentations

• 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.