Bronchial microbiome of severe COPD patients colonised by Pseudomonas aeruginosa

Abstract

The bronchial microbiome in severe COPD during stability and exacerbation in patients chronically colonised by Pseudomonas aeruginosa (PA), has not been defined. Our objective was to determine the characteristics of the bronchial microbiome of severe COPD patients colonised and not colonised by P. aeruginosa and its changes during exacerbation. COPD patients with severe disease and frequent exacerbations were categorised according to chronic colonisation by P. aeruginosa. Sputum samples were obtained in stability and exacerbation, cultured, and analysed by 16S rRNA gene amplification and pyrosequencing. Sixteen patients were included, 5 of them showing chronic colonisation by P. aeruginosa. Pseudomonas genus had significantly higher relative abundance in stable colonised patients (p = 0.019), but no significant differences in biodiversity parameters were found between the two groups (Shannon, 3 (2-4) vs 3 (2-3), p = 0.699; Chao1, 124 (77-159) vs 140 (115-163), p = 0.364). In PA-colonised patients bronchial microbiome changed to a microbiome similar to non-PA-colonised patients during exacerbations. An increase in the relative abundance over 20 % during exacerbation was found for Streptococcus, Pseudomonas, Moraxella, Haemophilus, Neisseria, Achromobacter and Corynebacterium genera, which include recognised potentially pathogenic microorganisms, in 13 patients colonised and not colonised by P. aeruginosa with paired samples. These increases were not identified by culture in 5 out of 13 participants (38.5 %). Stable COPD patients with severe disease and PA-colonised showed a similar biodiversity to non-PA-colonised patients, with a higher relative abundance of Pseudomonas genus in bronchial secretions. Exacerbation in severe COPD patients showed the same microbial pattern, independently of previous colonisation by P. aeruginosa.

Fig. 1

Relative abundance of Pseudomonas genus a under stability and b during exacerbation in PA-colonised and non-PA-colonised patients. Solid line represents the mean and dashed line the median

Fig. 2

Principal coordinate analysis with Bray–Curtis dissimilarity index. a Samples from stability and b samples of exacerbation. Red dots represent colonised patients, and blue dots non-PA-colonised patients

Fig. 3

Cluster dendrogram with Bray–Curtis dissimilarity index. Samples were combined depending on their clinical situation and clustered with the Bray–Curtis index, which takes values between 0 and 1 (0 meaning that samples share all the genera and 1 meaning samples do not share any). PS colonised by P. aeruginosa under stability; PE colonised by P. aeruginosa during exacerbation; S non-colonised by P. aeruginosa under stability; E non-colonised by P. aeruginosa during exacerbation)

Fig. 4

Heat map showing the most abundant genera in the four groups of samples. Columns represent the groups and rows the genera whose relative abundance is >1 % in at least one sample. The relative abundance of each genus is represented by the colour key

Fig. 5

Percentage of change in the relative abundance of genera. Only genera with a percentage of change over 20 % in at least one patient are represented. a Percentage of variability in the genera observed in consecutive samples recovered in stable situation (n = 2); b Percentage of variability in exacerbation in patients colonised by P. aeruginosa using the baseline stability sample as the reference (n = 5); c Percentage of variability in exacerbation in non-PA-colonised patients (n = 7). Dark blue: Neisseria; orange: Achromobacter; purple: Streptococcus; light blue: Pseudomonas; green: Moraxella; pink: Haemophilus; grey: Corynebacterium