The Cooper laboratory research focuses on utilizing different -omic tools, phenotype assays, and animal models to address the genomics, pathogenesis and epidemiology of various bacterial foodborne pathogens including Campylobacter jejuni, Salmonella, Listeria, and Shiga toxin-producing Escherichia coli.

Cooper Laboratory Research Focus:

• Comparative genomics, transcriptomics, and epigenetics of various pathogenic bacteria, particularly Shiga toxin-producing Escherichia coli (STEC), Campylobacter, and Salmonella.
• SNP analysis and developing other tools to improve source tracking of foodborne pathogens during outbreaks.
• Studying the evolution of numerous bacterial foodborne pathogens in various agricultural environments.
• Utilizing various -omics tools to identify host-specific genes, virulence genes, fitness genes and conserved genes.
• Investigating the pathogenesis of Campylobacter and other foodborne pathogens.
• Development and improvement of animal models for various bacteriological diseases, and innovation of effective vaccines against various bacteriological diseases.
• Development of rapid and effective detection and surveillance techniques for foodborne pathogens.
• Exploring the microbiomes and metagenomics of different agricultural environments, and the impact foodborne pathogens have on the communities.
• Role antibiotic resistant bacteria in various environments have on human health.

Postdoctoral Research Projects:

Jared Smith, Ph.D.

Animal operations adjacent to land used for fresh produce production are a known risk for transmission of Escherichia coli O157:H7, particularly cattle operations have been suspected as the contaminating source during outbreaks. Weather has been suggested, but not proven, to influence the transmission of foodborne pathogens to the wider environment surrounding cattle operations. The goal of his research project is to assess how specific weather conditions influence transmission of E. coli O157:H7 from animal operations to adjacent lands and then develop a weather-based risk assessment model of E. coli O157:H7 transmission for field proximity to animal operations. This project will result in critical industry guidance about weather factors to account for environmental assessments during the pre-harvest stage of production for farms near cattle operations.

Graduate Student Research Projects:

Caroline Scranton – 4^th year doctorate student

Caroline joined the lab as an undergraduate student in 2021. She holds a B.S. in microbiology (2022) from the University of Arizona and is currently a PhD candidate in her fourth year of her graduate program. Her PhD research focuses on Long Covid and chronic gastrointestinal diseases, particularly irritable bowel syndrome (IBS), looking at the gut microbiome and immune response in individuals with these conditions. She specializes in bioinformatics and has worked on a multitude of other projects exploring the household microbiome, the soil microbiome, and more.

Dominic Rodriguez, M.S. – 1^st year doctorate student

Dominic joined the lab as a graduate student in 2023. He holds a B.S. in biology and an M.S. in microbiology from the University of Arizona. As the leading cause of bacterial gastroenteritis worldwide, Campylobacter jejuni and its interactions with host metabolites are largely unknown. His research aims to characterize the effects of short-chain fatty acids (SFCAs), produced by bacteria in the gut, on C. jejunivirulence across10 strains that cause bloody, inflammatory, or watery diarrhea. Specifically, his research aims to determine whether SFCAs play a significant role in influencingC. jejunigeneration times, attachment, and invasion of host cells.

Loujine Salib, – 1^st year graduate student

Loujine joined the lab as an undergraduate Honor’s thesis student in 2024 as part of a collaboration with Dr. Margarethe Cooper. Loujine’s research

Studies have shown a direct link between the industry practices of using Biological Soil Amendments of Animal Origin (BSAAOs) and increased pathogen prevalence in the farm environment. Furthermore, repeated observations have highlighted how storage and application strategies at the field level, coupled with environmental conditions, potentially exacerbate in-use amplification during or after a crop production cycle. To address this critical need, this proposal aims to fill the current knowledge gaps concerning the identification and resolution of microbial issues in on-farm practices surrounding the use and storage of BSAAOs. To achieve these goals, we propose a series of four objectives. First, we will work with producers to conduct assessments of finished inputs at appropriate volumes to assess pathogen/indicator loading. This will include testing final finished and cured compost, as well as thermal-treated and pelletized manures to determine the baseline microbial load. Next, we will evaluate industry practices at field scale (e.g., stockpiling, temperature/moisture conditions, timing of incorporation/irrigation) that may cause pathogen/indicator persistence or re-growth. These assessments will provide actionable insights into how storage and application practices influence microbial risks and inform improvements in management strategies. Additionally, we will examine the impact of weather conditions (e.g., drought, soil moisture, seasonality, temperature, precipitation) on the persistence, re-growth, and movement of pathogens/indicators within the growing environment. Understanding the influence of weather variability will be critical to developing robust risk mitigation strategies and recommendations. Finally, the study will assess composting and storage conditions associated with pathogen physiological state, particularly conditions that may induce a viable but non-culturable (VBNC) state. This research will uncover critical traits that influence microbial behavior and persistence in diverse agricultural environments. By integrating these efforts, the study will evaluate post-delivery grower management practices and environmental conditions to determine risk reduction strategies that support industry decision-making. This work aims to equip leafy green producers with science-based best practices for the use and application of BSAAOs at the field scale, reducing food safety risks and fostering confidence in fresh produce safety.

Shari (Victoria) Brechbiel, M.S. – Accelerated Masters Student

Victoria joined the lab as an accelerated master’s student in 2025. Her research

Recent metrics changes to the Arizona and California Leafy Greens Marketing Agreement(s) (LGMA) now require growers utilizing surface water for overhead irrigation, to treat their water within 21 days of harvest. For many producers, this is the first time that water quality data may indicate the need for antimicrobial treatment of agricultural water as a corrective action before irrigation can be applied safely. Exacerbating these challenges, growers are faced with a myriad of options related to antimicrobial water treatment with very little guidance on the most appropriate treatment option for their ranch, or the requirements needed for successful implementation. With limited guidance, water treatment decisions are likely to be unsuccessful and expend both excess time and money without the ultimate outcome of eliminating generic E. coli (non-detect per 100mL), and reducing Total Coliform bacteria (< 99 MPN/100mL). Unsuccessful treatments will likely lead to little or no reduction in potential pathogen loading in an agricultural water source and thus little to no reduction in microbiological risk. CPS-funded studies conducted by Dr. Rock characterizing microbial quality of water used to irrigate fresh produce in the Southwest found that foodborne pathogens are present in surface waters (Rock and Gerba, 2014) and that treatment options can be highly variable (Rock, 2019). Grower guidance is needed on antimicrobial agricultural water treatment options available to industry and monitoring strategies to ensure successful treatment and ultimately the protection of public health. Over the course of one growing season, the research team will evaluate the efficacy of three antimicrobial treatments (Peroxyacetic Acid - PAA, Calcium Hypochlorite, and Ultra Violet Light) across four produce growing regions of the Southwest; Yuma, AZ; Maricopa, AZ; Edinburg, TX; and Uvalde, TX. The overall goal of this proposal is to develop scientific data, which will allow produce growers to better manage their use of antimicrobial agriculture water treatments in the Southwest.

Past Graduate Student Research Projects:

Jennifer Bosquez, Ph.D.

Jennifer joined the lab as a graduate student in 2020.Campylobacter jejuniis the leading cause of bacterial gastroenteritis in the world, which is estimated to result in close to 500 million cases per year. Infection with Campylobacter jejuni produces two different diarrheal manifestations: a bloody, inflammatory diarrhea or a watery diarrhea. However, little is known about the underlying genetics, pathogenesis, or host factors involved in the production of either clinical manifestation. Her research aimed to solve the differential pathogenesis seen withC. jejuni strains by investigating the role of one of its two component regulatory systems called RacRS. This two-component regulatory system consistently has SNPs in the racR or racS genes only with strains associated with bloody, inflammatory diarrhea. She created RacRS knockout mutants in a few different strains associated with both clinical manifestation and assessing their phenotypes in vitro through virulence assays compared to the wildtype strains. Ultimately her research aimed to solidify the role that RacRS plays in the production of the different diarrheal manifestations and expand our collective knowledge on the pathogenesis of this important foodborne pathogen.

Madison Goforth, M.S.

Madison joined the lab as an undergraduate in 2019 and completed her B.S. and M.S. in microbiology. Her research interests lie in understanding commensal microbial populations in different environmental regions and communities such as types of soil and agricultural crops and their geography by which they are naturally found in domestic or international locations. Her work focused on the bacterial communities found on melon rinds based on melon type, as well as the region where the melon is grown in the United States. Current knowledge on the melon microbiome was very limited with one published paper about the cantaloupe microbiome in Mexico based on a single farm with additional farm worker microbiomes. The paper highlighted the need for further studies looking into the bacterial communities of different melons grown in varying regions. Understanding the bacterial communities on melons can help producers develop food safety protocols based on type of melon or the region in which the melon is grown. Analyzing protagonistic and antagonistic bacteria in the microbial community can help further develop protocols against foodborne pathogens likeListeria spp.orSalmonella spp. Further outlooks would be establishing roles of certain bacteria in plant and soil health.

Urmi Patel, M.S.

Urmi joined the lab as an undergraduate student in 2021 and completed her B.S. in microbiology at the University of Arizona. Her research addressed leaks regarding the International Outfall Interceptor (IOI) between the Nogales-Sonora border. Issues with structural integrity of the wastewater collection system have resulted in periodic releases of sewage into the Santa Cruz River. Her work focused on identifying antibiotic resistance and virulence genes present in river sediment at different points upstream of the sewage leak. Taxonomic profiles of the river sediment were determined to better understand the microbial composition of the river sediment and potential pathogens introduced via sewage. Ultimately her research aimed to understand the impacts of the sewage leaks on the Santa Cruz River using metagenomics. In addition, samples were analyzed using different metagenomic databases to determine if the results remained consistent for each sample output and between the sequencing technology used (Illumina versus Oxford Nanopore Technologies).