2026 Funding

Cooper laboratory part of $104,531 grant from the Center for Produce Safety (CPS) to assess pathogen/indicator loading in Biological Soil Amendment of Animal Origin (BSAAOs), evaluate industry practices at field scale, examine the impact of weather conditions on the persistence, re-growth, and movement of pathogens/indictors within the growing environment, and assess composting and storage conditions associated with pathogen physiological states (especially those that induce a viable but non-culturable state.

2025 Funding

Cooper laboratory and University of Arizona collaborators awarded $96,914 grant from the Arizona Genomic Pathogen Analysis Pipeline to sequence and genomically characterize 1,200 Campylobacter isolates from previously isolated strains as part of a USDA funded 2-year study to understand the transmission dynamics, diversity, and genomic factors/genes associated with cattle colonization.

Cooper laboratory and University of Arizona collaborators awarded $78,516 grant from the Arizona Genomic Pathogen Analysis Pipeline to sequence and genomically characterize 1,000 Salmonella isolates associated with fresh produce production from both Arizona and California to determine what Salmonella serotypes/genotypes are most prevalent in the two growing regions, which serotypes/genotypes are most associated with different vegetable commodities, are strains/serotypes isolated from agricultural environments, domestic animals, and wildlife closely related to those found on actual vegetables, and what genomic factors/genes are associated with colonization of different types of vegetables.

Cooper laboratory part of $93,591 grant from the Arizona Department of Agriculture (AZDA) to develop a targeted DNA enrichment system for improved pathogen detection utilizing different molecular based detection assays.

Cooper laboratory part of $362,490 grant from the Center for Produce Safety (CPS) to identify normal and extreme whether events associated with an increased risk of E. coli O157:H7 transmission from a cattle feedlot to the surrounding environment, and to develop a risk assessment model based on field proximity to animal operation and E. coli O157:H7 transmission via weather.

2024 Funding

Cooper laboratory part of $44,779 grant from BioMade in collaboration with Rice University to help expand an existing comprehensive genetic toolkit for non-model Mycobacteriales, including Gordonia, via the introduction of new Cellulophaga- and Sporosarcina-specific machinery, while retaining its underlying structure and leveraging its extensive catalog of DNA parts and established molecular biology workflows.

Cooper laboratory and University of Arizona collaborators awarded $50,000 grant from the University of Arizona One-Health Initiative to assess water and subsistence foods contamination, pesticide exposures, and toxic metal(loid)s exposures in neonates from rural indigenous areas along the Marañon river in Loreto, Perú.

Cooper laboratory and University of Arizona collaborators awarded $50,000 grant from the University of Arizona One-Health Initiative to quantify the spatial and temporal patterns of pathogens and chemicals in La Pesca, to comprehensively quantify the presence and distribution of targeted pathogens including Salmonella spp., Vibrio spp., C. jejuni, E. coli, enterococci, H. pylori, norovirus, and Giardia across diverse matrices including water, sediment, fish, oysters, shrimp, and domestic avian populations, and assess the microbial community.

2023 Funding

Cooper laboratory and University of Arizona collaborators awarded $112,408 grant from Reckitt Benckiser to determine the impact of toilet bowl disinfectant on restroom hygiene, the impact of different cleaning/disinfecting products on restroom hygiene, and the impact on the reduction of cleaning regime on bacteria on restroom surfaces vs. cleaning/disinfecting.

Cooper laboratory and University of Arizona collaborators awarded $1,284,322 grant from the National Institute of Diabetes and Digestive and Kidney Diseases to estimate the incidence of IBS following SARS-CoV-2 infections compared to non- infected participants, to determine the role of pre-existing IBS on the development and severity of Post-Acute Sequelae of SARS-CoV-2 (PASC), and to establish the mechanisms of IBS following SARS-CoV-2 infections including differences in the fecal microbiome composition and function, the host’s anti-commensal immune response to the fecal microbiome, and targeted/untargeted serum protein biomarkers among SARS-CoV-2 exposed and unexposed, who do and do not develop incident IBS.

Cooper laboratory and University of Arizona collaborators awarded $149,208 grant from the Center for Produce Safety (CPS) as part of a rapid response project to quantify select microbiological indicators and pathogens in flooded fields over time.

Cooper laboratory and University of Arizona collaborators awarded $407,697 grant from the Center for Produce Safety (CPS) to determine the die-off or log-reduction of E. coli O157:H7 and generic E. coli surrogates pre-established on leaf surfaces and in soil following agricultural water treatment using commonly used water treatment sanitizers (PAA and Calcium Hypochlorite), conduct in-field evaluations with grower collaborators of water treatment variability or “breakthrough” and use real world collected data to conduct a QMRA for STECs in leafy greens (romaine and spinach).

2022 Funding

Cooper laboratory and University of Arizona collaborators awarded $108,940 from Reckitt Benckiser Pharmaceuticals to characterize the resident biome of household toilets in three different continents to determine which cleaning products and procedures can be used to optimize the microbiome which produces the least odors and disease-causing microorganisms in the different regions of the world.

Cooper laboratory and University of Arizona collaborators awarded $322,942 grant from the Center for Produce Safety (CPS) to investigate two Next Generation Sequencing (NGS) technologies (Illumina and Oxford Nanopore) that offer slightly different approaches for pathogen detection, and identify the benefits and limitations of each, verify the results, and validate the technologies for use by the produce industry.

2021 Funding

Cooper laboratory and University of Arizona collaborators awarded $242,960 grant from the Arizona Department of Agriculture (AZDA) to develop an Arizona-specific microbial index for on-site validation and verification of antimicrobial wash water systems for leafy greens industry in Arizona.

Cooper laboratory and University of Arizona collaborators awarded $240,157 grant from the Arizona Department of Agriculture (AZDA) to study the die-off rates of Escherichia coli O157:H7 strains in soils from Arizona leafy greens fields.

Cooper laboratory and University of Arizona collaborators awarded $3,490,798 grant from the National Institutes of Health to determine whether industrially produced meat products are the principal source of campylobacteriosis and MDR Campylobacter in humans in Peru by identify host segregating features of Campylobacter from zoonotic sources, characterize genomes of strains that cause disease in humans, evaluate the risk of household person-to-person transmission and identify microbial genomic features associated with persistent asymptomatic human carriage, and estimate the burden of campylobacteriosis and human MDR infections attributable to domestic and industrially derived zoonotic sources.

2020 Funding

Cooper laboratory part of $2,771,400 grant from the Centers for Disease Control and Prevention (CDC) to understand the etiology of acute febrile illness (AFI) across diverse contexts in South America and contribute to global strategies that improve etiology-specific disease estimates to inform public health practice and policy.

Cooper laboratory part of $412,610 grant from the Center for Produce Safety (CPS) to evaluate the efficacy of three antimicrobial treatments Peroxyacetic Acid (PAA), Calcium Hypochlorite, and Ultra Violet Light across four produce growing regions in Arizona and Texas to inform produce growers how to better manage their use of antimicrobial agriculture water treatments in the Southwest.

2019 Funding

Cooper laboratory part of $2,197,881 grant from the Fogarty International Center to continue expanding the local workforce of highly trained professionals with public health and infectious diseases research skills to help expand the research capacity of infectious diseases in Iquitos, Peru by offering a collaborative research training program in partnership with the Universidad Nacional de la Amazonia Peruana (UNAP; National University of the Peruvian Amazon).

Cooper laboratory part of $49,960 grant from University of Arizona Research, Discovery and Innovation (RDI) to assess the public health risk of antibiotic-resistant bacteria from daily sewage spills along the Mexico-Arizona border.

2018 Funding

Cooper laboratory part of $88,689 grant from the Center for Produce Safety (CPS) to study the impact of disinfecting irrigation water on pathogens and agricultural microbiomes.

Cooper laboratory part of $24,782 grant from University of Arizona Research, Discovery and Innovation (RDI) to establish an animal model for post-infectious IBS.

2017 Funding

Cooper laboratory part of $4,736,356 grant from United States Department of Agriculture (USDA), National Institute of Food and Agriculture to study the microbiome of different types of melons and determine the prevalence of foodborne pathogens directly in melon fields at point of harvest.