Metagenomic insights into AMR distributions in freshwaters and soils

Abstract: Antimicrobial resistance (AMR) is rapidly becoming a public health issue, as more and more infectious bacteria become resistant to our known antibiotics. Suggested reasons for the proliferation of these strains are misuse and overuse of antimicrobials, especially on an industrial level, in agriculture, livestock and aquaculture. These resistances are not unique for pathogenic bacteria but originates in nature where complicated systems of microbes interact with each other. Freshwater environments hold special interest as they provide drinking water, have unique biodiversity, and provide other ecosystem services. Soil environments have the most diverse microbial communities and are often the source of new discoveries in microbial functions and AMR interactions. Since the vast majority of microbes can’t be maintained in pure culture or replicated in the laboratory setting, metagenomic methods have proven to be vital for understanding the diversity and occurrence of AMR in the environment that would otherwise have remained unexplored and unaccounted for. By producing metagenomic pipelines that utilize parallel computing to handle vast amounts of data, a catalogue of AMR in 390 samples mainly from Scandinavia was created from two datasets. One of the datasets had been previously processed and published, while the other was managed from raw reads to metagenomic assembled bins. This revealed a difference in the distribution of resistance mechanisms that microbes utilize to achieve AMR based on lifestyle and that AMR can be found in most taxa as well as in any freshwater and soil environments.