Metagenomic analysis of antimicrobial resistance genes in wastewaters in Benin and Burkina Faso indicates a serious health risk from untreated hospital wastewaters in low-income countries

Antimicrobial resistance (AMR) is one of the greatest global threats to human health, but substantial gaps in AMR data exist in West African countries. To obtain in-depth data, we explored the presence of antimicrobial resistance genes (ARGs) in the hospital wastewaters (HWW) of nine hospitals in Benin and Burkina Faso and, for comparison, of four hospitals in Finland. The highest total relative abundance of ARGs in HWWs was observed in Benin and the lowest in Finland. HWW resistomes were more similar to each other in Benin and Burkina Faso than in Finland. Different clinically relevant carbapenemases were detected in varying abundances, especially in HWWs from Burkina Faso and Finland. The most widespread carbapenemase gene in the Beninese hospitals, blaGES, was also found in water used for handwashing. blaNDM was present in the HWW of one Beninese hospital and was also detected in the stools of a hospitalized patient. Mobile colistin ARGs were detected in the HWWs of all the three studied countries, with mcr-5 variants being the most common. These and other mcr genes were observed in very high abundance in treated wastewater released into rivers in Burkina Faso. In Benin, only little is done to treat wastewaters, including HWWs. The results provide evidence for public health decision-makers in Benin and Burkina Faso for the dire need to increase wastewater treatment capacity, with particular attention to HWWs.