Investigation of bacterial communities and antibiotic-resistant bacteria in the aquatic environments from Kathmandu, Nepal

The discharge of municipal and industrial wastewaters often influences bacterial community composition and the prevalence of antibiotic resistance in the receiving river ecosystems. To identify key influencing factors, we analyzed bacterial communities and antibiotic resistance markers across pharmaceutical wastewater, municipal wastewater, and river water samples collected from Kathmandu, Nepal. Our results revealed that the dominant bacterial taxa in the rivers were more closely shared with municipal wastewater than with pharmaceutical wastewater. Prevotella was dominant in both municipal wastewater and river samples, whereas Acinetobacter was more commonly found in pharmaceutical wastewater. The neutral community model indicated that stochastic processes governed the assembly of bacterial communities in municipal wastewater and rivers, whereas deterministic factors played a more significant role in shaping the communities in pharmaceutical wastewater. pH and chloride concentration were the primary factors shaping the bacterial community in pharmaceutical wastewater, whereas chemical oxygen demand and nitrate levels had a greater influence on the bacterial composition in municipal wastewater. Culture and PCR-based approaches revealed that E. coli and K. pneumoniae were the major extended-spectrum β-lactamase (ESBL)- and carbapenemase-producers. bla _CTX-M, sul1 and qnrS genes were frequently found in E. coli , whereas bla _SHV along with sul1 and sul2 , were primarily associated with K. pneumoniae . Additionally, around 60 % of the ESBL-producing bacteria carried the intI1 gene. Our study highlights the diversity and assembly dynamics of bacterial communities, the presence of circulating pathogens, and resistance markers in wastewaters and river systems of Nepal, which are crucial for ensuring public health protection.