Prevalence of opportunistic pathogens and anti-microbial resistance in urban aquaculture ponds

Abstract

Bacterial antimicrobial resistance (AMR) has emerged as a significant concern worldwide. The microbial community profile and potential AMR level in aquaculture ponds are often undervalued and attract less attention than other aquatic environments. We used amplicon and metagenomic shotgun sequencing to study microbial communities and AMR in six freshwater polyculture ponds in rural and urban areas of Bangladesh. Amplicon sequencing revealed different community structures between rural and urban ponds, with urban ponds having a higher bacterial diversity and opportunistic pathogens including Streptococcus, Staphylococcus, and Corynebacterium. Despite proteobacterial dominance, Firmicutes was the most interactive in the community network, especially in the urban ponds. Metagenomes showed that drug resistance was the most common type of AMR found, while metal resistance was only observed in urban ponds. AMR and metal resistance genes were found mainly in beta and gamma-proteobacteria in urban ponds, while AMR was found primarily in alpha-proteobacteria in rural ponds. We identified potential pathogens with a high profile of AMR and metal resistance in urban aquaculture ponds. As these ponds provide a significant source of protein for humans, our results raise significant concerns for the environmental sustainability of this food source and the dissemination of AMR into the food chain. Environmental ImplicationsAntimicrobial resistance (AMR) and microbial metal resistance pose constant threats to environmental sustainability and human health. Aquaculture is one of the major protein sources for humans. This research investigates the microbial communities, AMR, and metal resistance in rural and urban ponds in Bangladesh. The goal is to understand how industrial pollution and anthropogenic activities impact the mobility of microbes, AMR, metal resistance, and toxin genes. The study aims to identify and evaluate the potential environmental and human health risks and the necessary steps to mitigate environmental threats and thereby promote the sustainable development of the blue economy.