Epidemiology is at the core of our research agenda -- understanding how disease behaves within and between populations:
Disease = disruption of the normal functioning of a system (e.g., illness, dysbiosis, antimicrobial resistance)
Populations = collections of things (e.g., hosts, microbes, ecosystems)
We practice "epidemiology without borders":
Without scientific borders - we utilize methods, theories and concepts from all fields
Without geographical borders - we practice epidemiology across the globe, at all scales
Without cultural borders - we strive to recognize our own cultural constraints and how these influence our practice of epidemiology
Without thought borders - we encourage free thinking, and continuously question the paradigms within which we practice epidemiology
With these concepts at the foundation of our research program, here are some of the specific content areas being investigated:
Antimicrobial resistance is a complex ecological and population genetic phenomenon of microbes, with potentially dire consequences for human and animal health. In the lab, we strive to:
Advance understanding of how antimicrobial resistance develops and persists in both microbial and host populations
Investigate applied, practical measures to effectively mitigate and control antimicrobial resistance
Improve risk assessment of antimicrobial resistance from different spheres in our society (e.g., human hospitals, veterinary medicine, livestock production)
View antimicrobial resistance as both a "natural" and anthropogenically-mediated process
We work with many different types of data, but in all cases our goal is to turn the data into usable and useful information: Examples:
Use of Bayesian Network Analysis for evaluation of disparate, hierarchical microbiome data
Development of bioinformatic pipelines for both metagenomic and WGS analysis
Curation of an antimicrobial resistance database and ontology specifically for metagenomic data
Development of modeling techniques for risk assessment (i.e., identifying associations between antimicrobial use and resistance)
Our group includes veterinarian-scientists whose mission is to preserve and improve herd health by providing evidence-based recommendations regarding herd health issues, including issues related to public health and food safety. Previous and current work includes:
Bovine respiratory disease in beef cattle, impacts of antimicrobial drugs on morbidity, mortality and antimicrobial resistance in Mannheimia haemolytica
WGS analysis of bovine respiratory disease pathogens
Impacts of regulatory changes on antimicrobial use practices and subsequent herd health considerations
Our lab specializes in using metagenomic data to improve our understanding of the ecology of antimicrobial resistance, aka the "resistome" (i.e., all antimicrobial resistance genes within a given sample):
How does the resistome change within and between livestock production systems?
How can we increase the sensitivity and specificity of the metagenomics approach?
How can metagenomic data be used to identify pathogens from a food safety perspective?
Livestock production is an integral part of our world. Contact between livestock and humans can be direct and indirect, occurring through the food chain and the environment. Our lab is particularly interested in how livestock production systems exchange microbes and DNA across environmental interfaces:
What role do wastewater and manure sustainability practices play in this potential transfer?
Do antimicrobial use practices impact the transfer of antimicrobial resistance through environmental routes of exposure?
Food safety is the cornerstone of a healthy society. We investigate comprehensive, systems-based approaches to improving both pre- and post-harvest food safety:
Impact of multiple-hurdle interventions on post-harvest levels of pathogens and antimicrobial resistance
Impact of antimicrobial drugs on antimicrobial resistance in pre-harvest animal pathogens and indicator organisms
The microbiome is crucial to the health of animal, humans and the planet. While we often think of microbiomes in terms of the body (e.g., the "gut microbiome"), non-living environments also contain microbiomes (e.g., the microbiome of the "built environment"). Our lab is interested in understanding how these various microbiomes influence livestock production, food safety and animal/public health.