Genetic Adaptation of Pseudomonas aeruginosa to the Airways of Cystic Fibrosis Patients Is Catalyzed by Hypermutation

Abstract

) it was shown that Pseudomonas aeruginosa undergoes intense genetic adaptation during chronic respiratory infection (CRI) in cystic fibrosis (CF) patients. We used the same collection of isolates to explore the role of hypermutation in this process, since one of the hallmarks of CRI is the high prevalence of DNA mismatch repair (MMR) system-deficient mutator strains. The presence of mutations in 34 genes (many of them positively linked to adaptation in CF patients) in the study collection of 90 P. aeruginosa isolates obtained longitudinally from 29 CF patients was not homogeneous; on the contrary, mutations were significantly concentrated in the mutator lineages, which represented 17% of the isolates (87% MMR deficient). While sequential nonmutator lineages acquired a median of only 0.25 mutation per year of infection, mutator lineages accumulated more than 3 mutations per year. On the whole-genome scale, data for the first fully sequenced late CF isolate, which was also shown to be an MMR-deficient mutator, also support these findings. Moreover, for the first time the predicted amplification of mutator populations due to hitchhiking with adaptive mutations in the course of natural human infections is clearly documented. Interestingly, increased accumulation of mutations in mutator lineages was not a consequence of overrepresentation of mutations in genes involved in antimicrobial resistance, the only adaptive trait linked so far to hypermutation in CF patients, demonstrating that hypermutation also plays a major role in P. aeruginosa genome evolution and adaptation during CRI.Chronic respiratory infection (CRI) with Pseudomonas aeruginosa is the main driver of morbidity and mortality in cystic fibrosis (CF) patients (4, 15). The establishment of P. aeruginosa CRI is mediated by a complex adaptive process that includes physiological changes produced by the activation of specific regulatory pathways, including the induction of the biofilm mode of growth or the differential expression of virulence genes (39), and genetic changes leading to selection of an important number of adaptive mutations required for long-term persistence (19,27,34).Although CF patients with CRI are generally infected by a single P. aeruginosa strain that in most cases persists throughout the patient's life (32), one of the hallmarks of such infections is the emergence and fixation over time of multiple phenotypic variants of the underlying clonal populations (24), a process known as adaptive radiation (30). Many of the selected phenotypes have been clearly linked to adaptation to the lung environment that favors lifelong persistence of CRI (27). Indeed, once the adaptation stage is reached and the CRI is fully established, eradication is generally no longer possible. At this point, with resignation, the therapeutic goals change from attempting to cure the infection to slowing the decline of lung function and improving the patient's quality of life.The intense genetic adaptation process that takes place during the establishment of CRI has r...

Low oxygen induces the type III secretion system in Pseudomonas aeruginosa via modulation of the small RNAs rsmZ and rsmY

“…The physiological relevance of these findings during infection remains to be elucidated, as typically strains isolated from CF patients infected long-term with P. aeruginosa are type III-defective due to mutation of regulatory genes during chronic/late infection (Mena et al, 2008;Smith et al, 2006), while stationary phase growth in artificial sputum media correlates with reduced T3SS production (Fung et al, 2010). Therefore, while the T3SS-inducing conditions of limiting oxygen may exist throughout chronic infection, it is possible that activation of the T3SS under these conditions may be restricted to early chronic infection.…”

Resistance suppression by high-intensity, short-duration aminoglycoside exposure against hypermutable and non-hypermutablePseudomonas aeruginosa

“…We also used the isogenic hypermutable P. aeruginosa PAODmutS strain that was constructed from the PAO1 WT reference strain by Mena et al 30 via deletion of the mutS gene. All susceptibility and time-kill studies were performed in CAMHB (containing 20-25 mg/L Ca 2+ and 10 -12.5 mg/L Mg…”

Chronic pulmonary pseudomonal infection in patients with cystic fibrosis: A model for early phase symbiotic evolution

“…Based on microbiological studies, the traditional interpretation of Pa associated with chronic airway infected CF patients has been dominated by such concepts as ''multi-resistance'' or ''pan-resistance'' to antimicrobial agents and a gain of ''biofilm or cell-associated virulence'' (Bragonzi et al, 2009;Cigana et al, 2011;Head & Yu, 2004;Hogardt & Heesemann, 2010;Lee et al, 2006). However, this is paradoxically unsupported by the in vitro properties of CF Pa isolates in which accumulation of mutations in virulence regulators, as well as virulence genes and drug resistant determinants, have been attributed to a ''hyper-mutable'' state (Bragonzi et al, 2009;Cigana et al, 2011;Hoiby et al, 2010;Smith et al, 2006;Livermore, 2002;Mena et al, 2008;Oliver & Mena, 2010). This analysis focuses on the evolution of pseudomonal syntrophy during niche specialization in response to polarized airway epithelia in the CF host.…”