Impact of gastrointestinal multiplex PCR on the diagnosis, clinical correlation, and antimicrobial stewardship in pediatric acute gastroenteritis

Introduction Acute gastroenteritis (AGE) is a major cause of childhood morbidity and mortality worldwide, yet pathogen identification often remains elusive. Gastrointestinal (GI) multiplex polymerase chain reaction (PCR) enables simultaneous detection of multiple enteropathogens with greater accuracy and faster turnaround than conventional methods. This study aimed to assess the diagnostic and clinical impact of GI multiplex PCR testing on pediatric gastroenteritis at a tertiary care hospital in Saudi Arabia. Methods A retrospective observational study was conducted at King Abdullah Specialized Children's Hospital, Riyadh, including all children aged ≤14 years admitted with gastroenteritis who underwent GI multiplex PCR testing between January 2022 and December 2024. Clinical data, laboratory results, and management outcomes were retrieved from electronic medical records. Stool samples were analyzed using the BioFire FilmArray GI panel, with stool culture and ova/parasite testing performed as indicated. Results A total of 276 children were included, with infants aged 1–23 months comprising the largest subgroup (43.5%). GI multiplex PCR was positive in 90.9% of cases, with single-pathogen detections in 56.2% and co-detections in 34.8%. The most common pathogens were Salmonella (22.1%), Rotavirus A (18.1%), Norovirus (17.4%), and Clostridium difficile (17.0%). Antibiotic use differed by pathogen type, being lower in viral infections (27.4%) and higher in bacterial infections (45.3%). Following PCR results, antibiotics were initiated in 41.3% of bacterial cases and discontinued in 39.4% of viral cases. Detection of bacterial pathogens and abnormal white blood cell count were independently associated with antibiotic use. Inflammatory markers, particularly ESR, were higher in bacterial infections, while length of hospital stay did not differ significantly by pathogen type. Conclusion GI multiplex PCR demonstrated high diagnostic yield and was associated with differences in antibiotic use according to pathogen type, suggesting a potential role in informing targeted therapy and antimicrobial stewardship in pediatric AGE. However, interpretation requires clinical correlation, particularly in cases of co-detection and pathogens with known asymptomatic carriage. Conventional stool culture remains complementary for bacterial isolation and susceptibility testing.