Metagenomic analysis of the abundance and composition of antibiotic resistance genes in hospital wastewater in Benin, Burkina Faso, and Finland

Antibiotic resistance is one of the greatest global threats to human health, but substantial gaps in antibiotic resistance data exist in West African countries. We explored the presence of antibiotic resistance genes (ARGs) in the hospital wastewater (HWW) of nine hospitals in Benin and Burkina Faso and, for comparison, four hospitals in Finland using shotgun metagenomic sequencing. The highest sum of the relative abundance of ARGs in the 68 HWW samples was detected in Benin and the lowest in Finland. HWW resistomes and mobilomes in Benin and Burkina Faso resembled more of each other than those in Finland. Different carbapenemases were detected in varying abundances, especially in HWW from Burkina Faso and Finland. The bla GES genes, the most widespread carbapenemase genes in the Beninese HWW, were also found in water intended for hand-washing and in a puddle at the hospital yard in Benin. mcr were detected in the HWW of all three countries, with mcr-5 being the most common mcr gene. These and other mcr genes were observed in very high relative abundances, even in treated wastewater in Burkina Faso and in a street gutter in Benin. The results provide evidence for public health decision-makers for the dire need to increase wastewater treatment capacity, with particular attention to HWW. Importance The global emergence and increased spread of antibiotic resistance threaten the effectiveness of antibiotics and, thus, the health of the entire population. Therefore, understanding the resistomes in different geographical locations is crucial in the global fight against the antibiotic crisis. However, this information is scarce in many low- and middle-income countries (LMICs), such as those in West Africa. In this study, we describe the resistomes of hospital wastewater in Benin and Burkina Faso and, as a comparison, in Finland. Our results help to understand the hitherto unrevealed resistance in Beninese and Burkinabe hospitals. Furthermore, the results emphasize the importance of wastewater management infrastructure design to minimize exposure events between humans, HWW, and the environment, preventing the circulation of resistant bacteria and ARGs between humans (hospitals and community) and the environment.