Abstract
We compared the bacterial microbiomes lodged in the bronchial tree, oropharynx and nose of patients with early stage cystic fibrosis (CF) not using chronic antibiotics, determining their relationships with lung function and exacerbation frequency. CF patients were enrolled in a cohort study during stability and were checked regularly over the following 9 months. Upper respiratory samples (sputum [S], oropharyngeal swab [OP] and nasal washing [N]) were collected at the first visit and every 3 months. 16S rRNA gene amplification and sequencing was performed and analyzed with QIIME. Seventeen CF patients were enrolled (16.6 SD 9.6 years). Alpha-diversity of bacterial communities between samples was significantly higher in S than in OP (Shannon index median 4.6 [IQR: 4.1–4.9] vs. 3.7 [IQR: 3-1-4.1], p = 0.003/Chao 1 richness estimator median 97.75 [IQR: 85.1–110.9] vs. 43.9 [IQR: 31.7–59.9], p = 0.003) and beta-diversity analysis also showed significant differences in the microbial composition of both respiratory compartments (Adonis test of Bray Curtis dissimilarity matrix, p = 0.001). Dominant taxa were found at baseline in five patients (29.4%), who showed lower forced expiratory volume in the first second (FEV1%, mean 74.8 [SD 19] vs. 97.2 [SD 17.8], p = 0.035, Student t test). The Staphylococcus genus had low RAs in most samples (median 0.26% [IQR 0.01–0.69%]), but patients with RA > 0.26% of Staphylococcus in bronchial secretions suffered more exacerbations during follow-up (median 2 [IQR 1–2.25] vs. 0 [0–1], p = 0.026. Mann–Whitney U test), due to S. aureus in more than a half of the cases, microorganism that often persists as bronchial colonized in these patients (9/10 [90%] vs. 2/7 [28.6%], p = 0.034, Fisher’s exact test). In conclusion, the bronchial microbiome had significantly higher diversity than the microbial flora lodged in the oropharynx in early stage CF. Although the RA of the Staphylococcus genus was low in bronchial secretions and did not reach a dominance pattern, slight overrepresentations of this genus was associated with higher exacerbation frequencies in these patients.
Highlights
Cystic fibrosis (CF) is a chronic respiratory disease characterized by defective mucociliary clearance and recurrent infections by various potentially pathogenic microorganisms (PPMs) such as Pseudomonas aeruginosa, Staphylococcus aureus, Haemophilus influenzae, Stenotrophomonas maltophila, Achromobacter xylosoxidans and the Burkholderia cepacia complex, some of which evolve into chronic colonization (Guss et al, 2011; Sibley et al, 2011)
S. aureus was recovered from S cultures during the study in more than a half of the participants, but all samples were negative for P. aeruginosa and other common cystic fibrosis (CF) colonizers
In spite that the relative abundances (RAs) of the Staphylococcus genus was low in bronchial secretions and did not reach 1% in most patients, participants with RAs above 0.26% suffered more exacerbations, in most cases due to S. aureus, that often persists as chronic colonizer in the bronchial tree, confirming the clinical meaningfulness of small overrepresentations of the Staphylococcus genus, even at low RAs
Summary
Cystic fibrosis (CF) is a chronic respiratory disease characterized by defective mucociliary clearance and recurrent infections by various potentially pathogenic microorganisms (PPMs) such as Pseudomonas aeruginosa, Staphylococcus aureus, Haemophilus influenzae, Stenotrophomonas maltophila, Achromobacter xylosoxidans and the Burkholderia cepacia complex, some of which evolve into chronic colonization (Guss et al, 2011; Sibley et al, 2011). Culture-independent approaches have recently been introduced in the analysis of the respiratory microbiology in CF and have demonstrated that sputum (S) and oropharyngeal (OP) cultures only identify a fraction of the microbial flora lodged in the bronchial tree and the oropharynx, missing a wide range of bacteria, which include anaerobic genera as Prevotella, Veillonella, Fusobacterium, and Streptococcus, that required specific cultures (Guss et al, 2011; Sibley et al, 2011; Fodor et al, 2012; Carmody et al, 2018) The diversity of this respiratory microbiome has a clinical meaning in CF, because its decline, mainly due to the progressive loss of anaerobic flora and its partial substitution by PPMs that increase their relative abundance, has been related to the lung function impairment commonly found in the disease (Delhaes et al, 2012; Fodor et al, 2012; Flight et al, 2015; Carmody et al, 2018). The relationships between the microbial composition of these upper airway sites and their clinical meaningfulness in early stages of the disease are mostly unknown
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