Molecular Epidemiology of Foodborne Zoonotic Pathogens at the Rodent-Agriculture Interface

Abstract

Wild mammals are reservoirs for a growing number of emerging infectious zoonotic diseases. In particular, wild rodents are well-known reservoirs and vectors for a wide range of viruses and bacteria that cause illness in humans, including foodborne pathogens. It is critical to understand the role that rodents play in emerging zoonotic disease because they are commonly associated with humans, especially as pests throughout our agricultural production systems. Although numerous studies document a link between rodent pests on farms and outbreaks of foodborne pathogens (e.g., E. coli O157, Salmonella, etc.) in Europe and Asia, comparatively little research has focused on the rodent-agricultural interface in the United States. Knowing this, the functional role that rodent pests serve in the amplification and transmission of zoonotic foodborne pathogens is poorly understood in the United States. Given this knowledge gap, my dissertation research is novel in that it will provide a new and unexplored dimension of the rodent-Ag interface in one of the most agriculturally productive regions in the United States, the Midwest. My objective is to test the hypothesis that peridomestic rodents, inhabiting food animal farms, are reservoirs and amplifiers of zoonotic foodborne pathogens and antibiotic resistant bacteria that threaten food production systems and public health initiatives.We used a robust combination of mammalogy field methods, cutting-edge next generation sequencing, and traditional microbiological techniques to discover rodent-borne pathogens circulating on food animal farms. We collected rodents from food animal farms in MN and WI, identified the rodent species, and conduct metagenomic surveillance of putative foodborne pathogens from rodent feces. With the completion of this goal we were be able to describe rodent species diversity in different food animal farms and characterized the metagenomic bacterial community of rodent feces with passive screening for presence of putative zoonotic foodborne pathogens. We then phenotypically characterized rodent fecal isolates including antibiotic resistant Escherichia coli and Shiga-toxin producing E. coli (STEC) using traditional microbiological and molecular methods. We applied whole genome sequencing (WGS) to confirm their virulence traits (e.g., virulence genes, sequence types, serotypes, plasmid) and antibiotic resistance. We utilized a robust combination of comparative genomics and phylogenetic methods to analyze the resulting WGS data. Additional phylogenetic analyses were conducted in the context of relevant human and food animal pathogens of clinical origin gathered from publicly available databases. Successful completion of this goal enabled us to describe the molecular epidemiology of rodent associated zoonotic foodborne pathogens and how closely related or distant the rodent isolates were from human or animal origin (i.e., based on phylogenetic evolutionary relationships). Data generated from my dissertation research has filled an important knowledge gap regarding connections between the rodent-Ag interface and food safety in the two Midwestern states. Furthermore, we provided baseline data on the potential foodborne pathogens and AMR carried by rodents, which can be effectively used to inform public health officials, epidemiologists and farmers in order to improve rodent-associated biosecurity and protect our food supply.