Metagenome-Wide Analysis of Rural and Urban Surface Waters and Sediments in Bangladesh Identifies Human Waste as a Driver of Antibiotic Resistance

Abstract

Low- and middle-income countries (LMICs) have higher burdens of multidrug-resistant infections than high-income countries, and there is thus an urgent need to elucidate the drivers of the spread of antibiotic-resistant bacteria in LMICs. Here, we study the diversity and abundance of antibiotic resistance genes in surface water and sediments from rural and urban settings in Bangladesh.

The Diversity and Ubiquity of Antibiotic Resistance Genes in Finfish Culture Ponds in Bangladesh

“…Of all environmental factors assessed in our study (fish species farmed in the ponds, pond location, and season/sampling timepoint), only Upazila correlated with microbial diversity. This supports previous work indicating that geography influences the microbiota composition of aquaculture ponds in Bangladesh (McInnes et al, 2021) and Malawi (McMurtrie et al, 2022). This is also true in freshwater lakes (Yang et al, 2019) and open oceans (Sehnal et al, 2021) where geography is correlated with aquatic microbial diversity.…”

“…The most abundant antibiotic drug resistance class was aminoglycosides (as well as sulphonamides) and found to occur across all the farm sites analysed. These findings correspond with a study by McInnes et al (2021) where ARGs encoding resistance to sulphonamides, macrolides, and aminoglycosides were the most common antibiotic resistance classes found in rural Bangladeshi surface waters, including ponds. Overall, although there was a weak correlation between microbial composition and location (Upazila), the ARG content was similar in all ponds sampled within the Mymensingh Division of Bangladesh.…”

“…Proteobacteria were also the most common bacterial phylum found in aquaculture earthen finfish ponds in Malawi (McMurtrie et al, 2022) and China (Liu et al, 2020; Qin et al, 2016). In another study characterising pond microbiomes across districts in Bangladesh (Mymensingh, Shariatpur, and Dhaka), Cyanobacteria were the most common phylum, however, Proteobacteria were the most highly abundant bacteria phyla in five of seven water samples in the Dhaka district (McInnes et al, 2021). Of all environmental factors assessed in our study (fish species farmed in the ponds, pond location, and season/sampling timepoint), only Upazila correlated with microbial diversity.…”

“…Taxonomic identification of sequences allows the linkage of ARGs with taxa of interest such as pathogens and mobile genetic elements whilst maintaining important metrics such as ARG abundance within a metagenome. Metagenomic studies in Bangladesh have linked the abundance of ARGs in rivers and fish ponds with bacteria from the human gut suggesting untreated wastewater as a source of AMR (McInnes et al, 2021) and applied metagenomic data for AMR surveillance (Majeed et al, 2021). ARG prevalence and composition have also been shown to be associated with geography and feed type in fish ponds in Bangladesh (Lassen et al, 2021).…”

Antimicrobial Resistance Development Pathways in Surface Waters and Public Health Implications

“…Anthropogenic activities play an important role in selection pressure. Antimicrobial resistance was found to be highest in urban areas compared to rural areas [ 22 ]. Antibiotic resistance also varies from country to country due to the large quantities of antibiotics consumed by individuals, indicating the selective pressure that antibiotic use exerts on resistance.…”