Anthropic Effects on Aquatic Microbial Communities and their Resistomes

The increase in antibiotic resistant bacteria has raised global concern regarding the future effectiveness of antibiotics and the impact that resistance will have on human health. Human activities, which influence microbial communities and environmental resistomes, can inadvertently generate additional risks. In this work, we analyzed microbial communities and the resistome in samples collected at three city hospitals and three sites along the Bogotá River, a vital freshwater supply for the extended metropolitan area of Bogotá. Water parameters indicated an increase in contamination and the presence of antibiotics and other commonly used drugs as the river passed through the city. Community profiles done by 16S rRNA gene analysis and whole metagenome sequencing revealed diverse microbial communities that varied among sites and years sampled, but tended to separate river samples upstream of the city from more contaminated hospital and downstream river samples. Antibiotic resistance genes (ARGs), identified in the metagenomes, were more abundant in the more contaminated water samples from hospitals and the sites downstream of the city. Clinically relevant antibiotic resistant pathogens were also recovered from these sites. We found evidence of mobile genetic elements localized next to ARGs in assembled metagenomic contigs, suggesting the possibility of mobilizing resistance markers in these aquatic microbial populations. This study shows that anthropic activities alter microbial communities and bring together microorganisms of varied origins where interactions can affect both abundance and the possible spread of ARGs in water ecosystems that are fundamental to human welfare.