Enteric pathogen dynamics in onsite sanitation systems: A systematic review and meta-analysis on prevalence,...

Excreta-related diseases remain a major global health concern, particularly in low- and middle-income countries (LMICs) where onsite sanitation systems (OSS) are prevalent. While OSS interrupt fecal pathogen transmission, pathogen dynamics and inactivation within them remain poorly understood. This systematic review and meta-analysis synthesize evidence on the prevalence, distribution, concentration, and inactivation of fecal indicator bacteria and enteric pathogens in OSS containment. Following PRISMA guidelines, 16 studies on pathogen prevalence and concentration and 19 on inactivation were included. Most prevalence studies focused on pit latrines (64.3%), with helminths being the most studied pathogens (68.8%). In septic tanks, pathogens showed vertical stratification; helminths were mainly found in bottom sludge (62.5%) and viruses were more prevalent in the liquid (45.3%), consistent with size-dependent settling. In contrast, pit latrines showed more uniform pathogen distribution across the top, middle, and bottom zones. Pathogen concentrations were negatively correlated with fecal sludge age (R = -0.50), temperature (R = -0.46), pH (R = -0.36), and septic tank length-to-width ratio (R = -0.52) and positively correlated with organic matter (R = 0.49) and user-to volume ratio (R = 0.45). A Bayesian multilayer perceptron model accurately predicted bacterial log reductions (R² = 91.45%, RMSE = 0.643), estimating that a 3-log reduction in stored fecal sludge requires a median of 5 days (95%CI:4-10 days) in dry systems and 12 days (95%CI:10-18 days) in wet systems. Bacteria were the only pathogens evaluated due to limited data. Future research should link pathogen dynamics to OSS design, operation, and microbial communities, and in-situ decay studies should be conducted.