Incidence and aetiology of diarrhoeal disease among children under five years in the post-rotavirus vaccine introduction era in Manhiça District, Mozambique

Background Diarrhoea remains a major cause of death in children under five, despite the global decline in hospitalisations following the widespread introduction of rotavirus vaccines . As rotavirus-associated disease declines, it is important to identify other diarrhoea associated pathogens, although post-vaccine data remain limited in Mozambique. This study aimed to estimate the incidence and determine the aetiology of Moderate-to-Severe Diarrhoea (MSD) and Less Severe Diarrhoea (LSD) among children under five, post-rotavirus vaccine introduction in Manhiça District, a rural setting in Mozambique. Methods We estimated the incidence of diarrhoea using data from the morbidity surveillance and pathogen-attributable fractions based on analysis of stool specimens collected in a case–control study. Results The overall incidence of MSD was 5.6 cases per 1,000 child-years at risk (CYAR), with the highest rate observed among infants aged 0–11 months (15.5 per 1,000 CYAR) with a declining trend over time. LSD incidence was approximately 20 times higher than MSD incidence (119.7 per 1,000 CYAR), peaking among children aged 12–23 months (232.9 per 1,000 CYAR). Rotavirus remained the leading cause of both MSD and LSD among infants aged 0–11 months, while other important pathogens associated with LSD in this age group included sapovirus and Cryptosporidium spp. Among children aged 12–23 months, enteroaggregative Escherichia coli and adenovirus 40/41 were the major contributors to MSD. Conclusions Our findings highlight that rotavirus remains an important diarrhoea aetiology among infants and demonstrate changes on diarrhoea aetiologies post-rotavirus vaccine introduction; reinforcing the need for continued surveillance to better inform control and prevention strategies.