Enhancing upper respiratory tract infection detection: exploring qPCR negative respiratory samples using targeted...

Area of Science:

• Medical Microbiology
• Infectious Diseases
• Genomics

Background:

• Respiratory infections pose a recurring public health challenge.
• Rapid and accurate pathogen identification is essential for timely and effective treatment.

Purpose of the Study:

• To compare the diagnostic performance of targeted next-generation sequencing (tNGS) against quantitative real-time PCR (qPCR).
• To identify prevalent pathogens and co-infections in respiratory tract samples.

Main Methods:

• Collected 574 respiratory samples (nasopharyngeal and oropharyngeal swabs) between November 15 and December 15, 2023.
• Utilized qPCR for initial screening, followed by tNGS for samples with unfavorable results.
• Analyzed pathogen detection rates, identified specific microbial agents, and investigated co-infections and antibiotic resistance genes.

Main Results:

• qPCR identified pathogens in 64.1% of samples; tNGS detected pathogens in 81.1% of the remaining samples.
• Identified 58 different pathogens, with H3N2, Streptococcus pneumoniae, Staphylococcus aureus, and Candida albicans being most frequent.
• Observed 102 cases of mixed infections, frequently involving H3N2, Human betaherpesvirus 7, and S. aureus. Antibiotic resistance genes were detected in 20 cases.

Conclusions:

• tNGS demonstrates higher sensitivity than qPCR for respiratory pathogen detection.
• tNGS is crucial for identifying prevalent and significant pathogens like H3N2, S. pneumoniae, and S. aureus.
• Integration of tNGS into routine clinical diagnostics is recommended, pending further research for guideline development.