Urban waste piles are reservoirs for human pathogenic bacteria with high levels of multidrug resistance against last resort antibiotics: a comprehensive temporal and geographic field analysis

Abstract

Inadequate waste management and poor sanitation practices in Low- and Middle-Income Countries (LMICs) leads to waste accumulation in urban and peri-urban residential areas. This increases human exposure to hazardous waste, including plastics, which can harbour pathogenic bacteria. Although lab-based studies demonstrate how plastic pollution can increase the persistence and dissemination of dangerous pathogens, empirical data on pathogen association with plastic in real-world settings are limited. We conducted a year-long spatiotemporal sampling survey in a densely populated informal settlement in Malawi, quantifying enteric bacterial pathogens including ESBL-producing E. coli, Klebsiella pneumoniae, Salmonella spp., Shigella spp., and Vibrio cholerae. Culture-based screening and molecular approaches were used to quantify the presence of each pathogen, together with the distribution and frequency of resistance to antibiotics. Our data indicate that these pathogens commonly associate with urban waste materials. Elevated levels of these pathogens precede typical infection outbreaks, suggesting that urban waste piles may be an important source of community transmission. Notably, many pathogens displayed increased levels of AMR, including against several ‘last resort’ antibiotics. These findings highlight urban waste piles as potential hotspots for the dissemination of infectious diseases and AMR and underscores the need for urgent waste management interventions to mitigate public health risks.