Lower airway microbiota and decreasing lung function in young Brazilian cystic fibrosis patients with pulmonary Staphylococcus and Pseudomonas infection

Abstract

Cystic fibrosis (CF) is a genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator gene that leads to respiratory complications and mortality. Studies have shown shifts in the respiratory microbiota during disease progression in individuals with CF. In addition, CF patients experience short cycles of acute intermittent aggravations of symptoms called pulmonary exacerbations, which may be characterized by a decrease in lung function and weight loss. The resident microbiota become imbalanced, promoting biofilm formation, and reducing the effectiveness of therapy. The aim of this study was to monitor patients aged 8-23 years with CF to evaluate their lower respiratory microbiota using 16S rRNA sequencing. The most predominant pathogens observed in microbiota, Staphylococcus (Staph) and Pseudomonas (Pseud) were correlated with clinical variables, and the in vitro capacity of biofilm formation for these pathogens was tested. A group of 34 patients was followed up for 84 days, and 306 sputum samples were collected and sequenced. Clustering of microbiota by predominant pathogen showed that children with more Staph had reduced forced expiratory volume in one second (FEV1) and forced vital capacity (FVC) compared to children with Pseud. Furthermore, the patients' clinical condition was consistent with the results of pulmonary function. More patients with pulmonary exacerbation were observed in the Staph group than in the Pseud group, as confirmed by lower body mass index and pulmonary function. Additionally, prediction of bacterial functional profiles identified genes encoding key enzymes involved in virulence pathways in the Pseud group. Importantly, this study is the first Brazilian study to assess the lower respiratory microbiota in a significant group of young CF patients. In this sense, the data collected for this study on the microbiota of children in Brazil with CF provide a valuable contribution to the knowledge in the field.

Fig 1. Flowchart of samples analyzed in the study.

Fig 2. Beta diversity of bacterial community, represented by PCA plot.

Dots with the same color mean samples of the same group, n = 20 per group.

Fig 3. Comparison between pathogens showing decreased forced vital capacity and forced expiratory volume in patients in the Staph group.

Forced vital capacity = FVC; forced expiratory volume in one second = FVE. Bars represent the average of the air volume, (**) means significant difference among treatments by Mann-Whitney test (P <0.05), n = 20 per group.

Fig 4. Pearson’s correlation showing significant correlations (P < 0.05) between microbiota and clinical variables in the Staph group.

Asterisks represent significant correlations. The bar in the right shows the correlation type, with positive in blue and negative in red. A positive correlation means that two variables in the matrix increased, n = 20.

Fig 5. Non-metric Multidimensional Scaling (NMDS) plot showing significant correlations (P < 0.05) between microbiota and clinical variables in the Staph group.

The ellipses encompass different groups, with the Staph group in green and Pseud group in orange. Taxa are shown in black and clinical variables in red and blue vectors (red means significant). The direction of the vectors FEV and FVC indicates an inverse relationship with bacteria present in high quantities in the Staph group, n = 20 per group.