Characterization of enteric pathogens in Harare, Zimbabwe using environmental surveillance and metagenomics

High diarrheal disease burden remains an urgent concern in low- and middle-income countries, greatly affecting children under the age of 5 years and those living with HIV and AIDS. Treatment of infectious diseases has also become increasingly difficult with the rapid rise of antimicrobial resistance (AMR). Environmental surveillance of wastewater can supplement gaps in clinical surveillance as residents on a sewage system contribute to the wastewater, providing simple, composite samples that can improve understanding about both pathogens and AMR in the community. This study evaluated the effectiveness of environmental surveillance with shotgun metagenomics as a tool to characterize a broad range of enteric pathogens, antibiotic resistance genes, and virulence factor genes (VFGs) in wastewater from six neighborhoods in Harare, Zimbabwe. Alpha and beta diversity of the microbial community were similar between high-income and low-income suburbs. Enteric pathogens of high AMR and clinical concern, including Staphylococcus aureus, Pseudomonas aeruginosa, and Salmonella enterica, were detected in all samples. The top VFGs were encoded for delivery, adherence, and motility, functions important in toxin secretion, colonization, and immune modulation. The findings provide a foundation for future studies to explore environmental surveillance and shotgun metagenomics as a public health monitoring tool for enteric diseases.