Background

Respiratory tract infections are a major cause of pediatric hospitalization. Post-COVID-19 pandemic, atypical surges and disrupted respiratory pathogen circulation underscore the need for continuous surveillance.

Methods

We retrospectively analyzed respiratory pathogen detection among hospitalized children aged 28 days to 18 years at the largest quaternary hospital in Malaysia from January 2018 to May 2023. The study period was classified into pre-pandemic (2018–2019), pandemic (2020–2021), and post-pandemic (2022–2023) phases. Respiratory pathogens were identified using the FilmArray BioFire® Respiratory Panel 2.1.

Results

Among 20,556 hospitalized children, 7707 (37.5%) underwent BioFire® testing. Overall pathogen positivity remained similar during the pre-pandemic and pandemic periods (50.4% and 50.9%, respectively) and increased to 86.2% post-pandemic. Single-pathogen infections increased from 46.4% to 43.1% to 64.6%, while co-infections rose from 4.0% to 7.9% to 21.6%, respectively. Human rhinovirus/enterovirus and respiratory syncytial virus were consistently detected, whereas adenovirus and influenza viruses increased significantly post-pandemic. Influenza A and B re-emerged after minimal detection during the pandemic, returning to pre-pandemic detection rates. Monthly positivity varied substantially before and during the pandemic but remained consistently high post-pandemic, peaking at 94.4%. Despite increased pathogen detection, pediatric intensive care unit admissions remained low across all periods.

Conclusion

Substantial post-pandemic increases in respiratory pathogen positivity, co-infections, and pathogen diversity were observed among hospitalized children despite stable pediatric intensive care unit admission rates. These findings likely reflect respiratory pathogen re-emergence following relaxation of non-pharmaceutical interventions, altered exposure patterns, and increased BioFire® testing after the COVID-19 pandemic.

Keywords

Co-infection; COVID-19 pandemic; Multiplex PCR; Pediatric intensive care unit; Respiratory pathogen surveillance

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