New report: Antimicrobial resistance in natural environments: status of GenØk research and future recommendations


Wikmark, O.-G. (2020) Antimicrobial resistance in natural environments: status of GenØk research and future recommendations. GenØk-report, Tromsø, Norway.

At the request of The Norwegian Environment Agency, this report briefly discusses and sums up GenØk’s activities and experiences by screening environmental samples, from sediments, soils, manure and from terrestrial and aquatic animals, for antimicrobial resistant bacteria (ARB) and antimicrobial resistance genes (ARG). The progression from culture based to molecular based methods to direct PCR/sequencing and metagenomic sequencing, discusses and exemplifies the strengths and weaknesses of these different methods. Culture based methods have limitations for in depth comprehensive analysis, and even though direct PCR may help overcome these, full metagenomic sequencing, possibly combined with direct gene sequencing/detection, have emerged as preferred methods for environmental monitoring of antibiotic resistance genes. However, in order to understand the dynamics of ARGs in microbial populations, it is necessary to develop lacking standardization of sampling procedures, methods for how to measure chemical (antibiotic/other drivers) impact, and initiate studies on how to describe genetic context (plasmids etc). There is an emerging indication that biofilm formation and dynamics also play a role in dissemination of ARGs.