LISTERIA MONOCYTOGENES AND DRAIN MICROBIOMES IN RETAIL DELIS DURING COVID-19 AND AN ASSESSMENT OF MICROBIAL CONTAMINATION IN SENEGALESE PEANUTS

<p>Foodborne illnesses have global impacts and research institutions, government agencies, and the private sector have made significant efforts to understand the causative agents of foodborne illness and to discover new ways to combat them. There are a number of foodborne pathogens of interest (e.g. <i>Escherichia coli</i>, <i>Salmonella </i>spp., <i>Campylobacter</i> spp., and <i>Listeria monocytogenes</i>) and other microorganisms that impact food safety and security on a global scale. Additionally, COVID-19 was declared a global pandemic in March 2020; the pandemic greatly impacted research efforts for more than a year. This dissertation discusses three different studies that highlight my contribution to the efforts to mitigate foodborne illness both domestically and abroad. The chapters of this dissertation describe (i) the impact of COVID-19 on <i>Listeria monocytogenes</i> in retail deli departments, (ii) the microbial consortia inhabiting retail deli drains and drain biofilms, and (iii) microbial contamination of peanuts produced and sold in the Senegalese peanut basin.</p> <p> Chapter 1: Given the diversity of the studies contained in this dissertation, I began with a review of literature for the various chapters discussed here. This chapter begins with an introduction to the COVID-19 pandemic due to its significant effects on the research described here. The review then briefly summarizes the current knowledge of <i>Listeria monocytogenes</i> and its importance in the retail deli environments, as well as the microbial ecology of drains and biofilms in food processing. Additionally, this chapter ends with a summary of the current literature in regard to peanut production, consumption, and concerns associated with foodborne illness derived from peanut consumption.</p> <p> Chapter 2: “<i>Listeria monocytogenes</i> prevalence in retail delicatessen departments decreased during the first year of the COVID-19 pandemic” describes a study investigating <i>L. monocytogenes</i> contamination in retail deli departments during COVID-19 and validating a predictive risk model associated with the enhanced cleaning and sanitation procedures utilized in response to the pandemic. This study was conducted in 44 retail deli departments across seven states in the US. The results showed that <i>L. monocytogenes </i>prevalence decreased from 5.8% positive prior to March 2020 to 4.3% during the pandemic. No <i>L. monocytogenes</i> was found on the scales or trashcans, which were factors previously correlated with high <i>L. monocytogenes </i>prevalence (>10%). The predictive model accurately predicted high <i>L. monocytogenes</i> in 10/17 stores with high prevalence (α < 0.0001, β=0.1186) during the COVID-19 pandemic. Cleaning and sanitation protocols were the factors most highly correlated with high <i>L. monocytogenes</i> prevalence in the conducted survey. These results indicated that the heightened awareness of personal hygiene and cleaning and sanitation due to COVID-19 likely reduced the prevalence of <i>L. monocytogenes</i> in retail delis.</p> <p> Chapter 3: “Characterization of retail delicatessen drains and biofilms using 16S rRNA metataxonomic and shotgun metagenomic sequencing” was a study designed to understand the microbial ecology of retail deli drains and biofilms harvested from deli drains. In this study, 14 biofilms were harvested from drain trenches and environmental sponge samples were collected from the surface of the same drain covers. 16S rRNA gene sequencing was used to characterize the microbiome of the biofilms and sponge samples and shotgun metagenomics analysis was conducted on nine biofilms with ≥10 ng/µL DNA. While <i>Pseudomonas</i> spp. dominated the microbiomes of the biofilms and drain surfaces, the microbial consortia inhabiting each location of the drains was vastly different. Additionally, shotgun metagenomics revealed that pathogenic bacterial species were in low abundance in the biofilms, and rare taxa reside in the same biofilms. Common sanitizer resistance genes (<i>qacE</i><i>1</i>, <i>qacE</i>, and <i>qacL</i>) were observed in the biofilms as well, indicating possible increased tolerance to quaternary ammonium-based sanitizers.</p> Chapter 4: “Microbial contamination patterns in peanuts produced and sold in the Senegalese peanut basin” was a study conducted as part of the USAID Feed the Future Food Safety Innovation Lab (FSIL) in collaboration with the Senegalese Institute of Agricultural Research (ISRA). A survey was conducted of 198 households that produce peanuts in Senegal and 198 peanut samples were collected for microbial analysis. These peanut samples were evaluated for Enterobacteriaceae, coliforms, and total yeast and mold concentrations, then observed populations (log CFU/g) were correlated with survey questions related to producer knowledge of microbial contamination and storage methods utilized by producers. The results indicated that peanuts were heavily contaminated with the fecal indicators Enterobacteriaceae and coliforms (13.0% and 13.6% above detection limit [5.0 log CFU/g], respectively). Only 22.7% and 18.7% of producers reported they had heard of pathogenic bacteria or aflatoxins, respectively, before this study. Additionally, the combination of storage container type and whether the peanuts were store off the ground were predictive of bacterial contamination. This study provides preliminary data to inform future studies which should assess prevalence of pathogenic microorganisms (e.g. <i>Salmonella</i> spp. and <i>E. coli</i>) and evaluate preventive measures to be utilized during harvest and storage to minimize the risk of microbial contamination of peanuts. <br>