Sequence diversity of the Pseudomonas aeruginosa population in loci that undergo microevolution during chronic cystic fibrosis airways colonization. Sequence diversity in P. aeruginosa microevolution hotspots

534 unrelated Pseudomonas aeruginosa isolates from inanimate habitats, patients with cystic fibrosis (CF) and other human infections were sequenced in 19 genes that had been identified previously as the hot spots of genomic within-host evolution in serial isolates from 12 CF lungs. Amplicon sequencing confirmed a significantly higher sequence diversity of the 19 loci in P. aeruginosa isolates from CF patients than in those from other habitats but this overrepresentation was mainly due to the larger share of synonymous substitutions. All 19 loci were under stronger purifying selection Correspondingly, non-synonymous substitutions were either rare or benign in some loci. Other loci, however, showed an accumulation of non-neutral coding variants. The strongest skew towards the CF lung habitat was seen for amino acid sequence variants in AlgG that clustered in the carbohydrate-binding/sugar hydrolysis domain. The master regulators of quorum sensing lasR and rhlR were frequent targets for coding variants in isolates from human infections, from chronic as well as from acute infections. Unique variants in lasR showed strong evidence of positive selection.The sequencing of the candidate loci in isolates from other several CF clinics, other human infections and the environment thus revealed that coding variants in a subset of the examined loci are indeed characteristic for the adaptation of P. aeruginosa to the CF airways. For other loci, however, whereas the elevated mutation rate in others is more indicative for infections of a human habitats (lasR, rhlR) or global diversifying selection (pelA).