Microbiome complexity and Staphylococcus aureus in chronic rhinosinusitis

Abstract

Objectives/hypothesis: The aim of this study was to compare microbiological culture-based and culture-independent (16S rRNA gene sequencing) methodologies for pathogen identification in chronic rhinosinusitis (CRS) patients. We hypothesized that bacterial culture and DNA sequencing would yield largely concurrent results, although sequencing would detect greater bacterial diversity, and the sinonasal microbiomes of CRS patients would differ in composition and diversity compared with non-CRS controls.

Study design: Cross-sectional observational study.

Methods: Middle meatus swabs from CRS patients collected during endoscopic sinus surgery were analyzed by both clinical culture and broad-range analysis of 16S rRNA gene pyrosequences.

Results: A total of 21 swab samples from 15 CRS patients and five non-CRS controls were analyzed. One CRS patient was also swabbed 3 weeks postoperatively due to evidence of purulence during a clinical visit. All subjects had positive bacterial cultures, with a mean of 2.8 isolates per subject. The most prevalent cultivars were coagulase-negative staphylococci (15/20 specimens, 75%), Staphylococcus aureus (10/20, 50%), and Propionibacterium acnes (6/20, 30%). Among 57,407 pyrosequences generated, the most prevalent were from coagulase-negative staphylococci (21/21 specimens, 100%), Corynebacterium spp (18/21, 85.7%), P acnes (16/21, 76.2%), and S aureus (14/21, 66.7%). Bacterial diversity correlated with recent antibiotic use, asthma, prior sinus surgery, and relative abundance of S aureus.

Conclusions: DNA pyrosequencing revealed greater biodiversity than culture, although in most cases culture results represented a subset of the abundant DNA sequence types. CRS patients were characterized by altered microbial composition (P = .02) and greater abundance of S aureus (P = .03).

Figure 1

Comparison of bacterial culture and 16S rRNA sequencing results in CRS cases and controls. Boxed cells represent genera or species identified by culture. The figure summarizes the distribution of human-commensal and/or airway pathogenic bacterial taxa detected by phylogenetic analysis of pyrosequencing reads, clustered into genus-level groups (because of its potential significance to CRS, Staphylococcus aureus is separated from other staphylococci). Values in the table represent percent abundances of particular taxa for each subject (columns sum to 100%). “Other” refers to bacterial genera not commonly associated with human health or disease and to sequences that could not be assigned to the genus-level of taxonomy. Keys: ^b boxed cells with bold numbers indicate positive result by culture, ^m "mixed anaerobes" by culture not further identified, ^c culture identified Citrobacter freundii, not seen in sequences, ^p culture identified Peptostreptococcus, not seen in sequences, ^* not sent for culture