Indonesia Code river microbiome

Water and sanitation are important factors in the emergence of antimicrobial resistance in low- and middle-income countries. Contaminants such as drug residues, metals and various wastes have shown to foster the spread of antibiotic resistance genes (ARGs) with the help of mobile genetic elements (MGEs) and therefore rivers receiving contamination and effluents from multiple sources are of special interest. We followed both the microbiome and resistome of Code River in Indonesia from the pristine starting point at the Merapi volcano through rural and city areas to the coast of the Indian ocean. We used a SmartChip quantitative PCR with 382 primer pairs for profiling the resistome and 16S rRNA gene amplicon sequencing to determine the bacterial communities. Community structure explained the resistome composition in rural areas, while the city sampling sites had lower bacterial diversity and more ARGs linking with MGEs, suggesting increased mobility potential in response to pressures from human activities. Importantly, the vast majority of ARGs and MGEs did not disseminate to the marine environment. Our work provides information on the impact of different sources on the river health as well as sheds light on how land use contributes to the river resistome and microbiome.