We conducted a controlled before-and-after trial to evaluate the impact of an onsite urban sanitation intervention on the prevalence of enteric infection, soil transmitted helminth re-infection, and diarrhea among children in Maputo, Mozambique. A non-governmental organization replaced existing poor-quality latrines with pour-flush toilets with septic tanks serving household clusters. We enrolled children aged 1-48 months at baseline and measured outcomes before and 12 and 24 months after the intervention, with concurrent measurement among children in a comparable control arm. Despite nearly exclusive use, we found no evidence that intervention affected the prevalence of any measured outcome after 12 or 24 months of exposure. Among children born into study sites after intervention, we observed a reduced prevalence of Trichuris and Shigella infection relative to the same age group at baseline (<2 years old). Protection from birth may be important to reduce exposure to and infection with enteric pathogens in this setting.

Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.

Background. Onsite sanitation serves more than 740 million people in urban areas, primarily in low-income countries. Although this critical infrastructure may play an important role in controlling enteric infections in high-burden settings, its health impacts have never been evaluated in a controlled trial. Methods. We conducted a controlled before and after trial to evaluate the impact an onsite urban sanitation intervention on the prevalence of bacterial and protozoan infection (primary outcome), soil transmitted helminth (STH) re-infection, and seven-day period prevalence of diarrhoea among children living in informal neighborhoods of Maputo, Mozambique. A non-governmental organization replaced existing shared latrines in poor condition with engineered pour-flush toilets with septic tanks serving household clusters. We enrolled children aged 1-48 months at baseline and measured outcomes before the intervention and at 12 and 24 months following intervention. We measured outcomes concurrently among children served by the sanitation improvements and those in a comparable control arm served by existing poor sanitation. The trial was registered at ClinicalTrials.gov, number NCT02362932. Findings. At baseline, we enrolled 454 children from 208 intervention clusters and 533 children from 287 control clusters. We enrolled or re-visited 462 intervention and 477 control children 12 months 60 after intervention and 502 intervention and 499 control children 24 months after intervention. Despite nearly exclusive use of the intervention, we found no evidence that engineered onsite sanitation affected the overall prevalence of any measured bacterial or protozoan infection (12-month adjusted prevalence ratio 1.05, 95% CI [0.95-1.16]; 24-month adjusted prevalence ratio 0.99, 95% CI [0.91-1.09]), any STH re-infection (1.11 [0.89-1.38]; 0.95 [0.77-1.17]), or diarrhoea (1.69 [0.89-3.21]; 0.84 [0.47-1.51]) after 12 or 24 months of exposure. Among children born into study sites after the intervention and measured at the 24-month visit, we observed a reduced prevalence of any STH re-infection of 49% (adjusted prevalence ratio 0.51 [95% confidence interval 0.27 - 0.95]), Trichuris of 76% (0.24 [0.10 - 0.60]), and Shigella infection by 51% (0.49 [0.28-0.85]) relative to the same age group at baseline. Interpretation. The intervention did not reduce the overall prevalence of enteric infection and diarrhoea among all enrolled children but may have substantially reduced the prevalence of STHs and Shigella among children born into clusters with sanitary improvements.