Wastewater-based surveillance (WBS) has become a useful public health tool as an early warning system revealing emergence/re-emergence of pathogenic diseases and spread of antimicrobial resistance (AMR). WBS is crucial in development of rapid response and increasing public health awareness to curb dangers associated with disease emergence and antibiotic resistance. In this study, we characterized bacterial pathogens detected in wastewater, their composition, relative abundance and associated antibiotic resistant genes (ARGs) from different sewerage sites covering distinct epidemiological (socio-economic) population zones within Nairobi – the busiest East African city of Kenya representing a low- and middle-income country (LMIC). We show detection, abundance, spatio-temporal surveillance profiles of pathogens of interest and demonstrate WBS’s utility as an early warning system to inform public health response.
Arcobacter disease-causing bacteria associated with gastroenteritis (stomach flu) and persistent diarrhoea was the most abundant pathogen detected, depicting its significance in public health challenges in the city of Nairobi. The ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp) group of pathogenic bacteria associated with multidrug resistance and linked to several clinical infections were detected across all the sampled time points and sites. This study also investigated the presence/abundance of ARGs and detected several (n>600) antibiotic resistance gene (ARGs) sequences linked to many pathogenic bacteria capable of rendering more than thirty classes of antibiotics ineffective.
Detection of pathogenic bacteria, and associated ARGs they harbour in wastewater samples from the Nairobi City population contributes to the global surveillance efforts needed for prediction, monitoring and reporting of harmful microorganisms in the context of One Health. The current effort demonstrates the utility of wastewater surveillance as an early warning system to inform public health response and mitigate potential outbreaks through timely interventions.