Enteric pathogens associated with diarrhea in children under five years of age in Yogyakarta, Indonesia (2017–2018): a hospital-based surveillance study

Diarrhea is a major public health problem globally and remains an important cause of death and malnutrition in children under five years of age. In Indonesia, the burden of pediatric diarrhea remains substantial, yet most previous etiologic studies have focused on single pathogens, limiting understanding of the broader spectrum of enteric coinfections. This study aimed to identify the causes of diarrhea in hospitalized children under five years of age in Indonesia. Children aged < 5 years who were admitted to two participating hospitals in Yogyakarta with a diagnosis of diarrhea were prospectively recruited through active diarrhea surveillance between 2017 and 2018. Stool samples were collected during the first 48 h of admission and stored at -20 °C. Of 325 enrolled children, 171 stool samples (53%; 79 in 2017 and 92 in 2018) were randomly selected from eligible cases (acute, persistent, watery, or bloody diarrhea) by quarter, based on sufficient specimen availability. Multipathogen detection was performed using TaqMan Array Cards (TACs) at the Wellcome Trust Research Laboratory, Vellore, India. Targets with a cycle threshold (Ct) value < 40 were considered positive. Of the 325 hospitalized children, 171 (53%) underwent TAC testing (79 in 2017 and 92 in 2018). Rotavirus was the most frequently detected enteropathogen, accounting for 39% of TAC-tested samples in 2017 and 37% in 2018. Other commonly detected pathogens included adenovirus 40/41 (28% in 2017 and 3% in 2018), enteroaggregative Escherichia coli (EAEC) (27% and 28%, respectively), and norovirus GII (11% and 10%, respectively). The majority of rotavirus-positive samples had at least one additional pathogen detected (81% in 2017 and 74% in 2018), with bacterial pathogens being the most common coinfecting agents. Multiple pathogens detected in the same sample were recorded individually; however, co-infections were not analyzed as a separate category. Therefore, the potential contribution of co-infection to disease severity could not be fully assessed and should be considered a limitation of the study. Rotavirus remains the leading cause of hospitalization due to diarrhea in children under five years of age in Yogyakarta, Indonesia. These findings support continued monitoring of rotavirus vaccine impact and highlight the need for multi-pathogen surveillance to guide clinical management, antimicrobial stewardship, and immunization policy. Clinical trial number: not applicable.