A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments

The environment is an important component in the emergence and transmission of antimicrobial resistance (AMR). Despite that, little effort has been made to monitor AMR outside of clinical and veterinary settings. Partially, this is caused by a lack of comprehensive reference data for the vast majority of environments. To enable monitoring to detect deviations from the normal background resistance levels in the environment, it is necessary to establish a baseline of AMR in a variety of settings. In an attempt to establish this baseline level, we here performed a comprehensive literature survey, identifying 150 scientific papers containing relevant qPCR data on antimicrobial resistance genes (ARGs) in environments associated with potential routes for AMR dissemination. The collected data included 1594 samples distributed across 30 different countries and 12 sample types, in a time span from 2001 to 2020. We found that for most ARGs, the typically reported abundances in human impacted environments fell in an interval from 10-5 to 10-3 copies per 16S rRNA, roughly corresponding to one ARG copy in a thousand bacteria. Altogether these data represent a comprehensive overview of the occurrence and levels of ARGs in different environments, providing background data for risk assessment models within current and future AMR monitoring frameworks.

Automated summary

The environment plays a crucial role in the emergence and spread of antimicrobial resistance (AMR), yet monitoring efforts outside of clinical and veterinary settings have been limited. This is partly due to a lack of comprehensive reference data for most environments. To establish a baseline of AMR in various settings, a literature survey was conducted, identifying 150 papers with relevant qPCR data on antimicrobial resistance genes (ARGs) in environments associated with potential routes for AMR dissemination. The collected data, spanning from 2001 to 2020 and representing 1594 samples from 30 countries and 12 sample types, revealed that the abundances of most ARGs in human impacted environments fell within a range of 10-5 to 10-3 copies per 16S rRNA, approximately one ARG copy in a thousand bacteria. Overall, these findings provide a comprehensive overview of ARG occurrence and levels in different environments, contributing to the development of risk assessment models in AMR monitoring frameworks.