Microevolution of the major common Pseudomonas aeruginosa clones C and PA14 in cystic fibrosis lungs

Abstract

Clones C and PA14 are the worldwide most abundant clonal complexes in the Pseudomonas aeruginosa population. The microevolution of clones C and PA14 was investigated in serial cystic fibrosis (CF) airway isolates collected over 20 years since the onset of colonization. Intraclonal evolution in CF lungs was resolved by genome sequencing of first, intermediate and late isolates and subsequent multimarker SNP genotyping of the whole strain panel. Mapping of sequence reads onto the P. aeruginosa PA14 reference genome unravelled an intraclonal and interclonal sequence diversity of 0.0035% and 0.68% respectively. Clone PA14 diversified into three branches in the patient's lungs, and the PA14 population acquired 15 nucleotide substitutions and a large deletion during the observation period. The clone C genome remained invariant during the first 3 years in CF lungs; however, 15 years later 947 transitions and 12 transversions were detected in a clone C mutL mutant strain. Key mutations occurred in retS, RNA polymerase, multidrug transporter, virulence and denitrification genes. Late clone C and PA14 persistors in the CF lungs were compromised in growth and cytotoxicity, but their mutation frequency was normal even in mutL mutant clades.

Genomic Variation among Contemporary Pseudomonas aeruginosa Isolates from Chronically Infected Cystic Fibrosis Patients

“…Finally, mutS, which encodes a mismatch repair protein (and which is responsible for the so-called "hypermutator" phenotype in some strains [20,23]), contained a nonsense mutation that truncated the encoded protein in both isolates from patient 7 at residue S813, leading to loss of the last 42 amino acids. To assess whether this truncation had functional consequences, we measured the rate of acquisition of spontaneous rifampin resistance (mainly due to rpoB mutations) for each isolate, as described by Cramer et al (3). The isolates from patients 5 and 6 all displayed negligible spontaneous Rif resistance.…”

“…For example, Cramer et al reported that patient "RN" accrued 15 SNPs over a period of ca. 15 years (no indels were reported [3]). Similarly, in the two longitudinal isolates sequenced by Smith et al (35), 41 SNPs and 27 indels appeared over a 7.5-year period.…”

Transmissible strains ofPseudomonas aeruginosain cystic fibrosis lung infections

“…This unusual strain also appears to have broad pathogenic ability, having been identified in infections of the urinary tract and peritoneal dialysis fluid [112]. Recently, sophisticated approaches, including genome sequencing, were used to study the evolution of both clone C and another abundant P. aeruginosa lineage (PA14), indicating differences between patients [113]. However, it is not clear whether the prevalence of such strain types in CF is attributable to transmissibility or merely a reflection of their environmental abundance.…”

Evolutionary genomics of epidemic and nonepidemic strains of Pseudomonas aeruginosa

“…Evidence from longitudinal studies suggests that a large number of candidate genes can accrue substitutions during adaptation of P. aeruginosa (6)(7)(8)(9). Any given infection involves only a small subset of those substitutions, and most virulence-related phenotypes are not observed uniformly (10), making it difficult to say with confidence which genetic changes are most commonly associated with adaptation to the CF lung.…”