Gastrointestinal pathogens detected by a multiplex PCR panel in a tertiary care center in Riyadh, Saudi Arabia...

Multiplex polymerase chain reaction (PCR) assays have transformed the diagnosis of infectious gastroenteritis by enabling rapid, simultaneous detection of multiple enteric pathogens. However, contemporary data describing pathogen distribution, age-specific patterns, co-infection, and seasonality in Saudi Arabia remain limited. This study aimed to characterize the epidemiology of gastrointestinal pathogens detected by multiplex PCR in a tertiary care center in Riyadh, Saudi Arabia.

We conducted a retrospective analysis of stool specimens tested using a multiplex gastrointestinal PCR panel at King Abdulaziz Medical City, Riyadh, between January 2023 and December 2024. Demographic data, detected pathogens, co-infection status, and timing of testing were analyzed. Repeat samples from the same patient within 30 days were excluded. Descriptive analyses assessed pathogen distribution by age group and season, and multivariable logistic regression was used to identify factors independently associated with co-infection.

Of 9,122 stool specimens processed, 2,866 positive tests from 2,189 unique patients remained after excluding 30-day repeat samples. Positivity was 31.4%, higher in pediatrics than adult patients (36.5% vs. 28.0%, p < 0.001). The most frequently detected pathogens were Clostridioides difficile toxin A/B, enteropathogenic Escherichia coli, enteroaggregative E. coli, norovirus, and Salmonella spp. Co-infections occurred in 30.8% of positive samples, more commonly in pediatric patients. In multivariable analysis, children under 2 years had significantly higher adjusted odds of co-infection compared with adults aged 18-64 years, and source of sample was independently associated with co-infection.

Multiplex PCR testing revealed a diverse, age-dependent spectrum of gastrointestinal pathogens with a substantial burden of co-infections. These findings highlight the importance of age-specific interpretation and careful clinical correlation of multiplex PCR results.