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Published on: November 28, 2016
Targeted next-generation sequencing for pathogen detection and epidemiological analysis of pediatric acute
Meng-Yang Cai1, Hua-Wei Yi2, Ya-Qian Cai3
1Laboratory Department of the First Affiliated Hospital of Yangtze University, Jingzhou 434000, China; Laboratory Department of the First People's Hospital of Xiantao City, Xiantao 433000, China.
Insights
Pediatric acute respiratory infections (ARIs) in China show complex multi-pathogen co-infections, with bacteria being more prevalent than viruses. Targeted next-generation sequencing (tNGS) effectively identifies pathogens and informs age-specific, seasonal management strategies.
Area of Science:
- Microbiology
- Pediatrics
- Infectious Diseases
Background:
- Acute respiratory infections (ARIs) are a major global cause of child illness and death.
- Understanding pathogen epidemiology in pediatric ARIs is crucial but remains understudied.
- This study focused on characterizing pathogen profiles and trends in pediatric ARIs in Xiantao, China.
Purpose of the Study:
- To characterize pathogen profiles and co-infection patterns in pediatric ARIs.
- To investigate epidemiological trends of pediatric ARIs using targeted next-generation sequencing (tNGS).
- To assess the utility of tNGS in identifying pathogens and informing clinical decisions.
Main Methods:
- Retrospective analysis of 4,330 children hospitalized with ARIs (May 2022-September 2023).
- Oropharyngeal swab specimens tested by tNGS for 96 pathogens using ultra-multiplex PCR and high-throughput sequencing.
- Analysis included pathogen detection rates, co-infection complexity, pathogen types, age-stratified incidence, and seasonal trends.
Main Results:
- Pathogens detected in 99.3% of cases; 88.7% had multi-pathogen co-infections (dual, triple, quadruple+).
- Bacterial pathogens (57.7%) were more common than viral (35.7%).
- Incidence varied significantly by age and season, with peaks in spring/early summer; pneumonia was the most frequent diagnosis.
Conclusions:
- tNGS offers rapid, comprehensive pathogen identification in pediatric ARIs, revealing complex co-infections.
- Findings emphasize the need for age-specific and seasonal approaches in managing respiratory infections.
- tNGS shows potential for improving clinical decision-making and pediatric outcomes, warranting further study.
Background:
Acute respiratory infections (ARIs) are a leading cause of pediatric morbidity and mortality globally, yet comprehensive pathogen epidemiology in children remains understudied. This study aimed to characterize the pathogen profiles, co-infection patterns, and epidemiological trends of pediatric ARIs in Xiantao, China, using targeted next-generation sequencing (tNGS).
Methods:
A retrospective analysis was conducted on 4,330 children hospitalized with ARIs from May 2022 to September 2023. Oropharyngeal swab specimens were tested by tNGS for 96 pathogens via ultra-multiplex PCR and high-throughput sequencing.
Results:
Pathogens were detected in 99.3 % (4,298/4,330) of cases, with multi-pathogen co-infections in 88.7 % (3811/4298) of samples, including dual (26.1 %), triple (28.2 %), and ≥quadruple pathogens (34.4 %), demonstrating high co-infection complexity. Bacterial pathogens (57.7 %) exceeded viral (35.7 %) and Mycoplasma/ Chlamydial (6.6 %). Age-stratified analysis revealed significant variability in 37 pathogens (p < 0.05), with incidence inversely correlated to age. Seasonal peaks occurred in spring (March-May) and early summer (June), driven first by bacterial then viral agents. Pneumonia (57.8 %, 2,407/4,162) and acute upper respiratory infections (24.1 %, 1,005/4,162) were the most frequent clinical diagnoses.
Conclusions:
tNGS provides rapid, comprehensive pathogen identification in pediatric ARIs while uncovering intricate co-infection patterns. The findings highlight the importance of age-specific and seasonal considerations in managing respiratory infections, and suggest that tNGS has the potential to provide information useful for clinical decision-making, reduce antibiotic misuse, and improve pediatric outcomes-although these advantages await confirmation in future studies.
