Targeting current and future threats: Recent methodological trends in environmental antimicrobial resistance research and their relationship to risk assessment

Authors: Burch, Tucker; NEWTON, RYAN - University Of Wisconsin; KIMBELL, LEE - Marquette University; LAMARTINA, EMILY - University Of Wisconsin; OMALLEY, KASSIDY - Marquette University; THOMSON, SAN MARIE - Marquette University; MARSHALL, CHRIS - Marquette University; MCNAMARA, PATRICK - Marquette University

Submitted to: Environmental Science: Water Research & Technology
Publication Type: Review Article
Publication Acceptance Date: 6/7/2022
Publication Date: 7/26/2022
Citation: Burch, T.R., Newton, R.J., Kimbell, L.K., LaMartina, E.L., O'Malley, K., Thomson, S., Marshall, C., McNamara, P.J. 2022. Targeting current and future threats: Recent methodological trends in environmental antimicrobial resistance research and their relationship to risk assessment. Environmental Science: Water Research & Technology. 8:1787-1802. https://doi.org/10.1039/D2EW00087C.
DOI: https://doi.org/10.1039/D2EW00087C

Interpretive Summary: Antimicrobial resistance is a growing global public health threat stemming from antibiotic use in humans and animals, and it is mediated (in part) by environmental matrices like soil, water, and air. Antimicrobial resistance must be managed based on public health data, but scientists cannot always measure the data they need directly, so risk assessment is required to forecast those public health data based on more readily available microbiological data. Furthermore, two different forms of risk assessment for antimicrobial resistance have developed – one addressing “current threats” that are already known to exist and one addressing new “future threats” that might evolve in the future. Each form requires different underlying microbiological data produced using different methods: “targeted” methods for current threats (e.g., quantitative polymerase chain reaction) and “non-targeted” methods for future threats (e.g., shotgun metagenomics). However, it is unknown how common each method is in practice. We reviewed recent environmental science literature related to antimicrobial resistance (published between 2018 and 2020) to determine how frequently studies used targeted versus non-targeted methods. Our results indicate that most studies we reviewed addressed current threats, and there is a lack of data related to future threats. New studies using non-targeted microbiological methods will be required to fully delineate the risk of AMR in the environment and guide interventions intended to reduce its impact on human and animal health.

Technical Abstract: Antimicrobial resistance (AMR) is a growing global public health threat, and improved environmental surveillance of AMR is required to develop a better understanding of the problem at a global scale. Recent monitoring of the SARS-CoV-2 virus in sewage highlights the importance of tracking genetic indicators in efforts to identify and reduce the spread of diseases and pathogens in the environment. However, precisely what should be monitored to help understand AMR risk has been debated. Some scientists have posed that quantifying the abundance of known genes conferring antibiotic resistance is most important, while others have stated that monitoring for the potential of new genes to arise is most important. The goal of this work was to examine which methods were employed by the most influential papers studying AMR in environmental engineering and agricultural systems, thus providing insight into current methodological trends in the field and their relationship with risk assessment for AMR. We performed a search of recent (2018-2020) literature documenting AMR in five environmental matrices: wastewater, surface water, drinking water, stormwater, and livestock manure. Based on the number of citations, we selected the most influential papers across these matrices (92 papers from 17,809 initial results) and binned them as using targeted methods (e.g., qPCR), non-targeted methods (e.g., shotgun metagenomics), or both. More than 80% of papers employed targeted methods while only 33% employed non-targeted methods. Livestock manure had the lowest proportion of non-targeted methods while drinking water had the highest proportion of non-targeted analysis. Targeted methods are appropriate for assessing removal efficiency of known threats (ARGs) in treatment systems, but long-term studies employing non-targeted analysis will be required to understand how frequently new threats (novel ARGs) arise in each environmental matrix.