Profiling the nasopharyngeal Microbiome in patients with community-acquired pneumonia caused by Streptococcus pneumoniae: diagnostic challenges and ecological insights

Abstract

Community-acquired pneumonia (CAP) is a significant health threat for adults. Although conjugate vaccines have reduced pneumococcal CAP incidence in children, Streptococcus pneumoniae-related CAP remains prevalent among older adults. The nasopharynx acts as a reservoir for S. pneumoniae, yet the interplay between this pathogen and the nasopharyngeal microbiome during and after pneumonia remains poorly understood. This study included 61 adult patients diagnosed with pneumococcal CAP and 61 matched healthy controls. An S. pneumoniae-specific PCR, urine antigen tests and bacterial cultures were performed. Nasopharyngeal swabs collected at admission and three months post-infection were analyzed for microbiome dynamics through 16 S rRNA gene amplicon sequencing. 16 S rRNA gene amplicon sequencing revealed Streptococcus spp. in the majority of all nasopharyngeal samples during infection compared to the other diagnostic test performed. While overall bacterial biomass did not differ between groups, patients exhibited higher alpha diversity (p = 0.012) and lower microbiome stability post-infection. Beta diversity analysis distinguished infection from healthy status (p = 0.002). Taxonomic analysis showed similar core microbiota across groups, but Streptococcus spp. was significantly more abundant during infection, particularly in those patients with viral co-infections. Notably, unique significant bacterial interactions were identified both during and after infection, as well as in healthy states. A negative correlation was observed between Corynebacterium and Streptococcus spp. in infected patients, suggesting a potential antagonistic interaction between these taxa. The nasopharyngeal microbiome in patients with pneumococcal CAP demonstrates persistent disruption post-infection, characterized by lower resilience three months after acute illness. Additionally, we identified specific bacterial interplays during and after infection that differed from those in healthy donors. These bacterial dynamics might play critical roles in pathogen colonization resistance and infection prevention. Thus, our findings highlight the need for further investigation into microbial interactions and potential microbiome-based therapies for respiratory infections, particularly in vulnerable populations.

Keywords: Streptococcus pneumoniae; Community acquired pneumonia (CAP); Microbial interactions; Microbiome; Nasopharynx; Resilience; Viral infection.

Fig. 1

Bacterial biomass of nasopharyngeal swab samples. Scatter dot plot depict the quantitative analysis of bacterial biomass measured by qPCR, represented as 16 S rRNA gene copies per sample. Statistical significance was assessed using pairwise comparisons with the Wilcoxon test, with p-values < 0.01 indicating significant differences

Fig. 2

Diversity measurements between nasopharyngeal samples from S. pneumoniae CAP patients and healthy controls. (A) Box plots showing different indices for alpha diversity measurements of nasopharyngeal swab samples from Streptococcus pneumoniae CAP patients and healthy subjects. Comparisons are made between different sample collection time points and healthy controls. P-values from pairwise comparisons are derived using the Mann-Whitney U-test. (B-C-D) Bray Curtis distances were calculated to assess for the comparison of microbiome diversities between groups (beta diversity). Sample distances were plotted as non-metric multidimensional scaling (NMDS) plot. P-values from pairwise comparisons are determined using PERMANOVA and the permutation test for beta dispersion (betadisper). * indicates p < 0.05

Fig. 3

Taxonomic composition of nasopharyngeal bacterial communities in S. pneumoniae CAP patients and healthy controls. (A) Mean relative abundances (RA) of the 20 most abundant genera are illustrated for each group. (B) Violin plot showing the median RA of the five most representative bacterial genera across the three study groups, with ANCOMBC statistical significance indicated. (C) Mean relative abundance of the top 10 bacterial taxa in each pneumococcal CAP sample group, classified according to the abundance of Streptococcus spp. (Strep.): Group 1 (Strep. > 50% RA), Group 2 (Strep. 50%-5% RA), and Group 3 (Strep. <5% RA)

Fig. 4

Network visualization of Pearson Correlation Coefficients (PCC) among bacterial taxa in nasopharyngeal samples. The network diagram illustrates Pearson correlation coefficients (PCC > 0.1) for bacterial taxa with a mean relative abundance greater than 1% in nasopharyngeal swab samples from both S. pneumoniae CAP patients and healthy controls. Positive PCCs are depicted in red, while negative PCCs are shown in blue. Significant positive and negative associations are represented by thick lines, while non-significant associations are shown with thin lines. A positive bacterial association suggests that both bacteria are likely to be present together in a sample, while a negative correlation indicates that if one bacterium is present, the other might be absent

Fig. 5

Bacterial taxonomic profiling of patients´ nasopharyngeal swabs collected during infection and grouped based on the presence or absence of a viral co-infection