Variability of enteric pathogen infections by season and meteorological conditions in a low-income, urban setting in Mozambique

Enteric pathogen transmission is influenced by seasonality and meteorological conditions, yet these relationships are not well understood. We investigated the relationships between (1) season, (2) heavy rainfall events, and (3) temperature and enteric pathogen infections among 12-month-old children in a low-income, urban setting. We analyzed household data and stool samples from 630 participants enrolled in the PAASIM Study in Beira, Mozambique collected between February 2022 and November 2023. We applied generalized estimating equations with robust standard errors to determine the association between season and weather predictors and enteric pathogen prevalence (modified Poisson (PR) for binary outcomes and linear regression ({beta}) for continuous outcomes). During the rainy season, compared to the dry season, we found a 34% lower prevalence of protozoan infections [aPR: 0.66; 95% CI: (0.51, 0.86)], an 11% lower prevalence of co-infections [aPR: 0.89; 95% CI: (0.78, 1.00)], and lower total number of concurrent infections per individual [a{beta}: -0.17; 95% CI: (-0.38, 0.04)], but no meaningful difference in prevalence of bacterial infections [aPR: 0.97; 95% CI: (0.89, 1.06)] or viral infections [aPR: 0.98; 95% CI: (0.79, 1.22)]. We also saw some associations between rainy season and individual pathogen infections, including a higher prevalence of enteroaggregative E. coli (EAEC) [aPR: 1.13; 95% CI: (0.96, 1.33)], enterotoxigenic E. coli (ETEC) [aPR: 1.48; 95% CI: (0.88, 2.47], and norovirus infections [aPR: 1.48; 95% CI: (0.93, 2.37)] and a lower prevalence of diffusely adherent E. coli (DAEC) [aPR: 0.91; 95% CI: (0.83, 1.00)], atypical enteropathogenic E. coli (aEPEC) [aPR: 0.88; 95% CI: (0.74, 1.05)], and Cryptosporidium [aPR: 0.40; 95% CI: (0.27, 0.60)] during the rainy season. Following heavy rainfall events (1-week lag), there was a 30% higher prevalence of protozoan infections [aPR: 1.30; 95% CI: (1.06, 1.59)], a 22% higher prevalence of viral infections [aPR: 1.22; 95% CI: (0.95, 1.57)], and a 10% higher prevalence of co-infections [aPR: 1.09; 95% CI: (0.99, 1.21)], but no meaningful difference in prevalence for bacterial infections [aPR: 1.01; 95% CI: (0.92, 1.10)] and no difference in the total number of infections [a{beta}: -0.04; 95% CI: (-0.22, 0.14)]. Temperatures above the median (1-week lag), compared to below the median, were associated with a 35% lower prevalence of protozoan infections [aPR: 0.65; 95% CI: (0.49, 0.86)] and a 14% lower prevalence of co-infections [aPR: 0.86; 95% CI: (0.76, 0.97)], but we did not find evidence of a difference in bacterial infections [aPR: 0.98; 95% CI: (0.89, 1.07)], viral infections [aPR: 0.94; 95% CI: (0.74, 1.19)], or the total number of infections [a{beta}: -0.13; 95% CI: (-0.33, 0.07)] by temperature. Our results contrast many previous studies that have predominately shown a higher risk of bacterial infections and a lower risk of viral infection during periods with higher temperatures and precipitation but align with previous research suggesting a higher prevalence of some enteric infections following heavy rainfall events. Both long-term seasonal trends in enteric infections as well as the more immediate effects of extreme weather events, such as heavy rainfall events, are therefore important for designing interventions.