Pseudomonas aeruginosa adaptation and diversification in the non-cystic fibrosis bronchiectasis lung

Abstract

To characterise Pseudomonas aeruginosa populations during chronic lung infections of non-cystic fibrosis bronchiectasis patients, we used whole-genome sequencing to 1) assess the diversity of P. aeruginosa and the prevalence of multilineage infections; 2) seek evidence for cross-infection or common source acquisition; and 3) characterise P. aeruginosa adaptations.189 isolates, obtained from the sputa of 91 patients attending 16 adult bronchiectasis centres in the UK, were whole-genome sequenced.Bronchiectasis isolates were representative of the wider P. aeruginosa population. Of 24 patients from whom multiple isolates were examined, there were seven examples of multilineage infections, probably arising from multiple infection events. The number of nucleotide variants between genomes of isolates from different patients was in some cases similar to the variations observed between isolates from individual patients, implying the possible occurrence of cross-infection or common source acquisition.Our data indicate that during infections of bronchiectasis patients, P. aeruginosa populations adapt by accumulating loss-of-function mutations, leading to changes in phenotypes including different modes of iron acquisition and variations in biofilm-associated polysaccharides. The within-population diversification suggests that larger scale longitudinal surveillance studies will be required to capture cross-infection or common source acquisition events at an early stage.

FIGURE 1

Evidence for multilineage co-infections in seven patients. A core genome single nucleotide polymorphism phylogeny is shown for the subset of 99 isolates, confirming that all but one isolate (B113) clusters into one of two major groups. Each bronchiectasis centre is represented by a different colour. Arrows sharing the same colour indicate isolates that were obtained from the same patient. The three isolates from the same patient 92 sample are numbered 1–3.

FIGURE 2

Example pairwise comparisons between isolates sharing the same clonal lineage that were isolated from more than one patient attending the same centre. The number of single nucleotide polymorphism variations are indicated, with the number of small insertion and deletion variations shown in brackets. Full details are shown in online supplementary table S3. The five examples where isolates shared <200 variant sites are highlighted in green. All isolates of ST-244 from patients attending centre 4 were compared, with similarity graded according to variant sites.

FIGURE 3

Examples of alignment of genomes of bronchiectasis strains with that of reference strain Pseudomonas aeruginosa PAO1. Sequences identified as present (dark grey) or absent (white) in the genome of PAO1 are indicated. a) Isolates of the same lineage (ST-253) from the same patient. From innermost to outermost: C95, C97, C98, C99 and C96. A deletion present in isolate C96 only is highlighted (arrow). b) Pairs of isolates (from innermost to outermost: C6 and C7; and C156 and C159) that both share the same clonal lineage but are from different patients attending the same hospital. Isolates C6 and C7 share a large deletion and isolates C156 and C159 share a smaller overlapping deletion (online supplementary table S4), as indicated (arrow). c) Isolates of different lineages from the same patient. From innermost to outermost: A77, A80 and A85 (all ST-175); and A78, A81 and A82 (all ST-17). A large deletion present in the ST-17 isolates is indicated by an arrow. The figures were generated using the BLAST Ring Image Generator [19].