Rotavirus Leads Childhood Diarrhea Hospitalizations in Yogyakarta Surveillance Study

Diarrhea remains one of the world’s most stubborn killers of young children, and a new hospital-based surveillance study from Yogyakarta, Indonesia, offers a detailed molecular portrait of what is actually driving severe cases in this part of Southeast Asia. The research, published in BMC Pediatrics, prospectively enrolled children under five years of age who were admitted to two participating hospitals in Yogyakarta with a diagnosis of diarrhea between 2017 and 2018. Using a multipathogen molecular detection platform, the team found that rotavirus was the most frequently detected enteropathogen, present in 39 percent of tested samples in 2017 and 37 percent in 2018, confirming that this virus remains the leading cause of diarrhea-related hospitalization among young children in the region.

The study was conducted through active diarrhea surveillance, meaning that research staff systematically identified and recruited eligible children as they were admitted, rather than relying on retrospective records. A total of 325 hospitalized children under five were enrolled during the two-year period. Stool samples were collected within the first 48 hours of admission and stored at minus 20 degrees Celsius to preserve the genetic material of any pathogens present. From this larger cohort, 171 stool samples, representing 53 percent of enrolled cases, were randomly selected for full multipathogen testing, with 79 samples from 2017 and 92 from 2018. Selection was done by quarter and based on sufficient specimen availability, covering children with acute, persistent, watery, or bloody diarrhea.

The molecular engine of the study was the TaqMan Array Card, a compact real-time PCR platform that can probe a single stool sample for a large panel of enteric pathogens simultaneously. The laboratory work was carried out at the Wellcome Trust Research Laboratory in Vellore, India, a center with extensive experience in multipathogen diarrheal surveillance across low- and middle-income countries. The TaqMan Array Card approach relies on targeted amplification of pathogen-specific genetic sequences, with each target producing a measurable fluorescent signal as the reaction proceeds. A cycle threshold value below 40 was considered positive, a conventional cutoff that balances analytical sensitivity against the risk of detecting insignificant amounts of genetic material.

This technology matters because traditional diagnostics, such as culture for bacteria or enzyme immunoassays for viruses, typically identify only one pathogen at a time and can miss coinfections entirely. Most previous etiologic studies of pediatric diarrhea in Indonesia focused on single pathogens, which limited understanding of the broader spectrum of enteric coinfections. By screening for many viruses, bacteria, and parasites in parallel, the TaqMan Array Card revealed a microbial landscape far more complex than single-pathogen testing would suggest, capturing the full range of agents circulating in this hospitalized population.

Beyond rotavirus, the surveillance identified several other major contributors to childhood diarrheal disease in Yogyakarta. Adenovirus 40/41, the enteric adenovirus types most classically associated with pediatric gastroenteritis, was detected in 28 percent of tested samples in 2017 but only 3 percent in 2018, a striking year-to-year swing that underscores how dramatically the circulation of individual pathogens can fluctuate across seasons. Enteroaggregative Escherichia coli, or EAEC, a diarrheagenic strain of bacteria named for its characteristic stacked-brick pattern of aggregation on intestinal cells, was detected at nearly identical rates in both years, 27 percent in 2017 and 28 percent in 2018, making it the most consistently detected bacterial pathogen in the cohort.

Norovirus GII, the genogroup responsible for the majority of human norovirus outbreaks worldwide, was detected in 11 percent of samples in 2017 and 10 percent in 2018, adding another viral agent to the list of common culprits. The stability of EAEC and norovirus GII detection across both years contrasts sharply with the volatility of adenovirus 40/41, illustrating why sustained, multiyear surveillance is essential for understanding the true etiology of pediatric diarrhea. Pathogens that appear dominant in one season may recede the next, while others maintain a steady presence year after year.

One of the most consequential findings of the study concerns coinfection. Among samples in which rotavirus was detected, the overwhelming majority carried at least one additional pathogen, with coinfection present in 81 percent of rotavirus-positive samples in 2017 and 74 percent in 2018. Bacterial pathogens were the most common coinfecting agents in these rotavirus-positive samples. This pattern suggests that children hospitalized with severe diarrhea in Yogyakarta are frequently carrying multiple enteric pathogens at once, a reality that single-pathogen diagnostics would completely miss and one that complicates the interpretation of which agent is actually responsible for the illness.

The authors were careful to note an important limitation in how coinfections were handled analytically. Multiple pathogens detected in the same sample were recorded individually, but coinfections were not analyzed as a separate category. As a result, the potential contribution of coinfection to disease severity could not be fully assessed. This is a significant caveat for the field, because the mere detection of a pathogen’s genetic material does not prove it is causing disease, and when several agents are present simultaneously, attributing clinical severity to any single one becomes genuinely difficult. Future studies with larger sample sizes and dedicated coinfection analysis will be needed to untangle these relationships.

The detection of bacterial pathogens such as EAEC also carries direct implications for clinical practice and antimicrobial stewardship. Diarrheagenic E. coli strains, including EAEC and enteropathogenic E. coli, are typically managed with supportive care rather than antibiotics in young children, and knowing the local spectrum of bacterial pathogens helps clinicians avoid unnecessary antimicrobial use. The study’s findings support the need for multipathogen surveillance to guide clinical management, antimicrobial stewardship, and immunization policy, giving health authorities a clearer evidence base for deciding when laboratory testing is warranted and which pathogens deserve targeted intervention.

For rotavirus specifically, the findings arrive at a moment when vaccine impact monitoring remains a global priority. Rotavirus vaccines have dramatically reduced severe diarrheal disease in many countries, but the persistence of rotavirus as the leading detected pathogen among hospitalized children in Yogyakarta highlights the continued importance of tracking vaccine performance and coverage in Indonesia. The study’s conclusions emphasize that rotavirus remains the leading cause of hospitalization due to diarrhea in children under five in the region, and that continued monitoring of rotavirus vaccine impact is essential. As Indonesia works toward the Sustainable Development Goals related to child health, studies like this one provide the granular, pathogen-level evidence needed to direct resources where they will save the most lives.

Subject of Research: Enteric pathogens associated with diarrhea in hospitalized children under five in Yogyakarta, Indonesia

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

Article References: Nirwati, H., Giri, S., Mulyani, N. S., Erlin Mulyadi, A. W., Palupi-Baroto, R., Anggraini, D., Wahab, A., & Soenarto, Y. (2026). Enteric pathogens associated with diarrhea in children under five years of age in Yogyakarta, Indonesia (2017–2018): a hospital-based surveillance study. BMC Pediatrics. https://doi.org/10.1186/s12887-026-07875-3

Image Credits: AI Generated

DOI: 10.1186/s12887-026-07875-3

Keywords: rotavirus, diarrhea, children under five, Yogyakarta, Indonesia, coinfection, TaqMan Array Card, enteroaggregative E. coli, norovirus, adenovirus 40/41, pediatric hospitalization, multipathogen surveillance