Nasopharyngeal microbiota profiles and lytA-PCR status in adult pneumococcal pneumonia: distinct microbial communities and diagnostic implications.

Abstract

Background: Streptococcus pneumoniae is a leading cause of community-acquired pneumonia (CAP) in adults, yet microbiological diagnosis remains challenging. Quantitative lytA-PCR on nasopharyngeal samples has improved diagnostic yield; however, a substantial proportion of patients with confirmed pneumococcal pneumonia (PPn) remain lytA-negative. We hypothesized that nasopharyngeal microbiota profiles differ according to lytA-PCR status on nasopharynx and may reflect distinct pathogenetic pathways.

Methods: We conducted a prospective, observational study including adults hospitalized with confirmed PPn. Nasopharyngeal samples were collected before initiation of antimicrobial therapy for lytA-PCR quantification and 16S rRNA gene sequencing. Patients were stratified according to nasopharyngeal lytA-PCR status. Microbiota diversity and composition were analysed at the genus and amplicon sequence variant (ASV) levels. Differential abundance was assessed using ALDEx2, and associations between pneumococcal load and Streptococcus ASVs were explored.

Results: Among 38 patients, 24 (63%) were lytA-positive and 14 (37%) lytA-negative in nasopharyngeal samples. Alpha-diversity did not differ between groups. However, beta-diversity analysis at the ASV level revealed significant compositional differences according to lytA status. Streptococcus spp. were significantly enriched in lytA-positive patients, whereas Corynebacterium and Dolosigranulum were more abundant in lytA-negative patients. Specific Streptococcus ASVs, consistent with S. pneumoniae, were enriched in lytA-positive samples and correlated with pneumococcal load.

Conclusions: Among adults with pneumococcal pneumonia, nasopharyngeal lytA-PCR identified two distinct patterns of nasopharyngeal microbiota composition. These findings support the coexistence of colonization-driven and invasion-driven disease pathways and highlight the added value of integrating microbiota profiling with molecular diagnostics to better understand pneumococcal disease pathogenesis in adults.