(477) Longitudinal population genetics of Pseudomonas aeruginosa isolated from the sinuses, throat, and sputum of adults with cystic fibrosis

Background: Chronic rhinosinusitis (CRS) is a prominent manifestation of cystic fibrosis (CF) in the upper respiratory tract (URT) and a growing body of literature demonstrates similarities and interplay between CRS and lower respiratory tract (LRT) disease in CF. The unified airway hypothesis is a conceptual framework that proposes treatment of URT symptoms can improve LRT disease and vice versa. Several studies support a model in which bacteria inhaled from the environment first colonize the URT, with the URT subsequently seeding bacteria into the LRT. Furthermore, our laboratory recently found that sinus exacerbation increases the odds of a pulmonary exacerbation before the next study visit, suggesting a link between sinus and lung disease progression in CF. The present study tests the overall hypothesis that P. aeruginosa populations in the URT are representative of those in the LRT, which would suggest the URT is a source of P. aeruginosa seeding the LRT. We also sought to identify how highly-effective modulator therapy (HEMT; elexacaftor/tezacaftor/ivacaftor, commercially available as Trikafta or Kaftrio) may impact evolution and persistence of P. aeruginosa populations.

Methods: We enrolled 39 adults with CF CRS in a prospective, observational study of P. aeruginosa respiratory populations. Respiratory samples (sinonasal or throat swabs, sputum) were cultured on Pseudomonas Isolation Agar (PIA), DNA extracted from mixed populations of cultured bacteria, and sequenced on an Illumina NextSeq 2000. At least one sinus, throat, and/or sputum PIA population (putatively P. aeruginosa) was sequenced from 37 of 39 participants. Sample collection was completed in June 2021 and includes samples collected before and after FDA approval and widespread use of HEMT. Sequenced PIA populations were assembled into representative metagenome-assembled genomes (MAGs). SprayNPray was used to identify P. aeruginosa bins from the sinuses, throat, and sputum MAGs. Maximum likelihood phylogenetic trees were constructed to determine the genetic relatedness of P. aeruginosa within each participant over time (i.e. whether URT and LRT populations derived from the same clone) and between study participants (i.e. shared strains). Mutation frequencies were tracked with breseq.

Results: Most study participants (32 of 37 with sequenced PIA populations) began HEMT during our study. Of the 32 participants that began HEMT, at least one sinus PIA population was sequenced from 27 (84%) participants, throat from 18 (56%), and sputum from 23 (72%) participants prior to initiation of HEMT. Following initiation of HEMT, at least one population was cultured from 20 of 32 participants (63%): at least one sinus population was sequenced from 8 (25%) participants, throat from 16 (50%), and sputum from 9 (28%) of 32 participants. Preliminary analysis suggests URT P. aeruginosa populations are clonally related to those present in the LRT (sputum and/or throat).

Conclusions: As HEMT becomes more widespread and people with CF are no longer able to produce sputum, the URT may be an important site for for microbiological surveillance. Our preliminary results suggest that people with CF harbor clonal P. aeruginosa populations throughout their URT and LRT. Ongoing efforts are aimed at comparing genetic diversity of P. aeruginosa populations in URT and LRT pre- and post-HEMT as an indicator of changing selective pressures in the airways. Additionally, we aim to determine whether P. aeruginosa migrates from the URT into the LRT.

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