Multidrug-resistant bacteria and microbial communities in a river estuary with fragmented suburban waste management

Highlights: • Riverine microbiomes and in situ water quality impacted by local waste management. • Multidrug-resistant and AMR ESBL-producing bacteria prevailed near sewage treatment plant (STP) outfall. • STP discharge was the major fragmentation agent for the studied river. • MinION sequencing data highly correlated with qPCR and microbial culturing quantification. • Dissolved oxygen, Bacteroides and Prevotella (sequencing) and E. coli (probe rodA) are reliable faecal and AMR indicators. River systems in developing and emerging countries are often fragmented relative to land and waste management in their catchment. The impact of inconsistent waste management and releases is a major challenge in water quality management. To examine how anthropogenic activities and estuarine effects impact water quality, we characterised water conditions, in-situ microbiomes, profiles of faecal pollution indicator, pathogenic and antibiotic resistant bacteria in the River Melayu, Southern Malaysia. Overall, upstream sampling locations were distinguished from those closer to the coastline by physicochemical parameters and bacterial communities. The abundances of bacterial DNA, total E. coli marker genes, culturable bacteria as well as antibiotic resistance ESBL-producing bacteria were elevated at upstream sampling locations especially near discharge of a wastewater oxidation pond. Furthermore, 85.7% of E. faecalis was multidrug-resistant (MDR), whereas 100% of E. cloacae, E. coli, K. pneumoniae were MDR. Overall, this work demonstrates how pollution in river estuaries does not monotonically change from inland towards the coast but varies according to local waste releases and tidal mixing. We also show that surrogate markers, such dissolved oxygen, Bacteroides and Prevotella abundances, and the rodA qPCR assay for total E. coli, can identify locations on a river that deserve immediate attention to mitigate AMR spread through improved waste management.