Comparison of targeted next-generation sequencing and conventional tests for pathogen detection in community-acquired and severe community-acquired pneumonia: a retrospective cohort study

Background Community-acquired pneumonia (CAP) and severe community-acquired pneumonia (sCAP) impose a significant burden on the healthcare system. As a more severe form of CAP, sCAP is associated with a higher mortality rate, and patients frequently require intensive care. Identifying clinical biomarkers to distinguish CAP from sCAP is expected to improve pneumonia management and patient outcomes. Targeted next-generation sequencing (tNGS) has considerable potential for pathogen detection and distinguishing microbial profile differences between CAP and sCAP. Methods In this retrospective cohort study, we analyzed 380 bronchoalveolar lavage fluid (BALF) samples from patients diagnosed with CAP or sCAP who underwent both conventional tests (CTs) and tNGS to identify and compare the pathogen species and clinical consistency. Results The results were as follows: tNGS demonstrated a significantly higher clinical consistency rate with the final diagnosis (83.02%) than CTs (38.37%), with a statistically significant difference ( p < 0.05). Among the analyses, the most prevalent combination of pathogen co-infection was mixed infection, with bacterial-viral co-infection being the most common, accounting for 40.7% of cases. Diverse microbial profiles were present in 72.94% (62/85) of patients with sCAP. Significant differences in the composition of diverse microbial profiles were observed between patients with CAP and those with sCAP ( p = 0.001). Resistance genes were detected in 31 patients, of whom 35.48% (11/31) were consistent with CTs. Conclusion Targeted next-generation sequencing demonstrated superior performance as a sensitive auxiliary diagnostic tool, which resulted in an increased pathogen identification rate and higher clinical diagnostic consistency. Although tNGS provides more comprehensive detection of etiological agents, clinical interpretation, diagnosis, and prediction require careful integration with conventional tests. The distinct clinical features, pathogen profiles, and pathogen composition between patients with CAP and those with sCAP highlight the need for a comprehensive diagnostic approach in pneumonia management.