High prevalence of colistin resistance genes in German municipal wastewater

Highlights: • Bacterial resistance against the antibiotic colistin is of global concern. • We screened German municipal wastewater for genotypic colistin resistance. • Metagenomics revealed low prevalences of mcr-1. • However, we found high prevalences of other mcr gene variants like mcr-3 and mcr-7. -- Abstract: Bacterial resistance against the last-resort antibiotic colistin is of increasing concern on a global scale. Wastewater is suspected to be one of the pathways by which resistant bacteria and the respective genes are disseminated. We employed a metagenomics approach to detect and quantify colistin resistance genes in raw municipal wastewater sampled at 9 locations all over Germany (14 samples in total, collected in 2016/2017). Our data support the findings of earlier studies according to which the prevalence of the colistin resistance gene mcr-1 is still low. However, we were able to demonstrate that the total prevalence of colistin resistance genes is dramatically underestimated if the focus is put on that specific gene alone. In comparison to mcr-1, other gene variants like mcr-3 and mcr-7 proved to be 10 to 100 times more abundant in samples of untreated wastewater. The average relative abundances expressed as copies per 16S rRNA gene copies were 2.3×10^–3 for mcr-3, 2.2×10^–4 for mcr-4, 3.0×10^–4 for mcr-5, and 4.4×10^–4 for mcr-7. While these four gene variants were ubiquitous in all 14 samples, mcr-1 was detected only once at a relative abundance of 1.4×10^–5. Our results suggest a high risk of increasing incidence of colistin resistance as large amounts of mcr genes are continuously disseminated to diverse microbial communities via the wastewater path.