Persistence and evolution of Pseudomonas aeruginosa following initiation of highly effective modulator therapy in cystic fibrosis

Abstract

Today, more than 90% of people with cystic fibrosis (pwCF) are eligible for the highly effective cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy called elexacaftor/tezacaftor/ivacaftor (ETI) and its use is widespread. Given the drastic respiratory symptom improvement experienced by many post-ETI, clinical studies are already underway to reduce the number of respiratory therapies, including antibiotic regimens, that pwCF historically relied on to combat lung disease progression. Early studies suggest that bacterial burden in the lungs is reduced post-ETI, yet it is unknown how chronic Pseudomonas aeruginosa populations are impacted by ETI. We found that pwCF remain infected throughout their upper and lower respiratory tract with their same strain of P. aeruginosa post-ETI, and these strains continue to evolve in response to the newly CFTR-corrected airway. Our work underscores the continued importance of CF airway microbiology in the new era of highly effective CFTR modulator therapy.

Importance: The highly effective cystic fibrosis transmembrane conductance regulator modulator therapy Elexakaftor/Tezacaftor/Ivacaftor (ETI) has changed cystic fibrosis (CF) disease for many people with cystic fibrosis. While respiratory symptoms are improved by ETI, we found that people with CF remain infected with Pseudomonas aeruginosa. How these persistent and evolving bacterial populations will impact the clinical manifestations of CF in the coming years remains to be seen, but the role and potentially changing face of infection in CF should not be discounted in the era of highly effective modulator therapy.

Keywords: Pseudomonas aeruginosa; cystic fibrosis; evolution; lung infection; pathogenesis; respiratory pathogens.

Fig 1

Clonal populations of P. aeruginosa persist throughout the respiratory tract of adults with CF following initiation of highly effective modulator therapy. (A) Total bacterial load is lower in most participants’ post-ETI samples compared to pre-ETI. *P < 0.05 (mixed effects linear regression). (B) Relative abundance of Pseudomonas spp. is reduced post-ETI, but remains detectable in all but one study participant. *P < 0.05 (mixed effects linear regression). (C) The same P. aeruginosa clones present pre-ETI persist post-ETI. Core genome phylogeny of metagenome-assembled P. aeruginosa genomes from seven individuals. The reference strains PAO1 and PA14 are included as representatives of Clade I and Clade II P. aeruginosa strains, respectively. Colored shading indicates instances where a single study participant’s P. aeruginosa does not form a monophyletic clade. Dates are the year and month the sample was collected. (D) Richness and evenness of genetic variants in P. aeruginosa populations is unchanged post-ETI. Top = single nucleotide polymorphism (SNP) richness. Bottom = Pieleou’s evenness. n.s. = not significant (P > 0.05 by mixed effects linear regression).

Fig 2

(A) Most post-ETI variants were not previously detected pre-ETI. Red = proportion of post-ETI variants that were never detected pre-ETI in each study participant. Teal = proportion of post-ETI variants that were also present in pre-ETI populations. The numbers above each bar are the counts of unique post-ETI variants, including those in intergenic regions. (B) Functional categories of newly evolved variants differ from variants that had evolved pre-ETI. Bars show the proportion of post-ETI variants that are assigned to each functional category (COG) by eggNOG. For each participant, left bar (pre) =post-ETI variants that were previously detected pre-ETI. Right bar = post-ETI variants that were newly evolved post-ETI (new). The numbers above each bar are the counts of unique post-ETI variants within coding regions of genes that were either present pre-ETI or newly evolved post-ETI. Bolded labels with asterisks on the COG category labels indicate categories that significantly differed within at least one study participant (Fisher’s exact test, P < 0.05). Bolded labels with asterisks on participant labels indicate individuals whose COG categories were significantly different (Fisher’s exact test, P < 0.05). (C) Lollipop diagram of genes that were mutated post-ETI, but not pre-ETI, in three or more study participants. Colors of variants indicate the study participant in which each mutation was detected.