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

Abstract

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.SynopsisMetagenomic analysis of HWWs revealed high abundances of ARGs and their potential transmission to other environments in Benin and Burkina Faso.

Closing the GAP in Antimicrobial Resistance Policy in Benin and Burkina Faso

“…More microbiological research is needed to determine if resistance genes are transmitted across these domains between human and animal species, but the lack of sanitation, and the potential flow of contaminated water, means that resistant infections are spreading. For example, Markkanen et al ( 13 ) identified a worryingly high abundance of AMR genes in hospital water in the region.…”

Advancing antimicrobial resistance monitoring in surface waters with metagenomic and quasimetagenomic methods

“…Important studies have described AMR in water and effluents [3][4][5][26][27][28][29][30][31][32][33][34][35][36], but lack of a consensus set of tools to harmonize methodologies and analyses across multiple groups' efforts (from water collection and laboratory processing to bioinformatic analysis and reporting) leaves us without a ready, common source of information to support local, national and global AMR monitoring of the environment. Metagenomic approaches provide valuable surveillance of species such as Mycobacterium, Mycoplasma and Neisseria (as shown in Figure 11), but for surveillance of NARMS critically important gene targets, metagenomics should be coupled with microbial pre-enrichment using relevant bacterial growth media.…”

Seasonal Patterns in Mobile Colistin Resistance Gene Variants in Wastewater Bioaerosols and Liquid Sludge

“…Since the initial identification of mcr-1, a range of gene variants (mcr-1 to mcr-10) have been discovered in numerous bacteria, including ESKAPE pathogens. 14 The occurrence of these genes on mobile genetic elements such as plasmids has also aided in the dissemination of mcr genes across socioecological borders, with gene variants being detected in humans, livestock, agricultural soils, water, wastewater, and wildlife. 15 Furthermore, an extensive survey using publicly available metagenomic data sets showed a global distribution of mcr genes with differences in the abundance of mcr variants occurring based on time and geographic location.…”