Isabelle Gurney
Project
Environmental Metagenomics for Surveillance of Antimicrobial Resistance in HospitalsAntimicrobial resistance is a significant issue for human health. Currently, physicians have one major resource on antimicrobial resistance available to them to use when making decisions about prescribing antimicrobials, which is an antibiogram, or chart that shows the resistance patterns of microorganisms against different antimicrobial compounds. The antibiograms currently used are derived from patient infection data and are only updated yearly. Thus, they are far behind the current state of antimicrobial resistance. Different hospital wards prescribe antimicrobials differently, which changes the selection pressure for antimicrobial resistance between wards, but current antibiograms assembled from hospital-wide data lack spatial resolution to specific wards. This project aims to improve environmental metagenomic analysis methods for detecting and understanding the dynamics of antimicrobial-resistant genes and organisms recovered from the built environment, specifically from floor swabs. Samples will be collected from three rooms in each of 17 different hospital units across 15 months. Each floor sample will undergo genomic sequencing to give us information on how target genomes shift in the context of antimicrobial resistance in different selection environments, through time, and in a patient metapopulation pattern of a tertiary care facility. The 15-month sampling timeframe should allow ample time to optimize sampling and analysis methods while collecting enough data to observe trends. Assuming the sample data reflects patient infection data, over time we expect to see increases in the prevalence of resistance genes in the swab data that correspond to increases in patient antimicrobial-resistant infections. Using this information, we should be able to assemble environmental antibiograms rapidly (~ monthly) containing information on present resistance patterns. This project aims to utilize these methods to complement hospital antimicrobial resistance resources and patient-based antimicrobial resistance monitoring. Bringing hospital resources up to date will assist physicians in prescribing appropriate treatments and help mitigate antimicrobial resistance by reducing ineffective antimicrobial use that can contribute to resistance spread by being present in the environment. We aim to both evaluate the link between antibiotic prescriptions and prevalence on a refined spatial scale (unit to unit within a hospital) and to provide clinicians with additional data on antimicrobial resistance prevalence to guide empiric decision-making when treating patients. One of the aims of this project is to optimize environmental sampling and metagenomics for hospital environments, a methodology that could be adapted to care facilities beyond our study and to other human environments to track antimicrobial resistance or other targets in other contexts.
