The latest generation of cystic fibrosis transmembrane conductance regulator-targeted modulator therapy, Elexacaftor/Tezacaftor/Ivacaftor (ETI), has significantly improved the clinical outcomes of persons with cystic fibrosis (pwCF) but does not appear to completely eliminate CF respiratory microbial colonization. Here, we analyzed over 4,200 publicly available respiratory microbiomes spanning pre- and post-ETI treatment periods and further stratified by age and type of sample. Our analyses reveal that despite reshaping of community composition by ETI, classical CF pathogens such as Pseudomonas and Staphylococcus spp. persist in sputum and sinonasal samples, while Streptococcus spp. drastically increase in prevalence and relative abundance post-ETI treatment. Obligate anaerobes such as Prevotella spp., Fusobacterium spp., Porphyromonas spp., and Veillonella spp. were readily detected post-ETI. We observed changes in the sputum samples from pwCF post-ETI, with an increase in the relative abundance of Streptococcus spp. and prevalence of Prevotella and a decline in Pseudomonas spp. Analysis of co-occurrence networks revealed mostly positive correlations between the different genera pre- and post-ETI; however, these correlations were reduced in number following ETI treatment, suggesting a disruption of community connectivity. To test one of the hypotheses raised by the computational analyses, we experimentally investigated the relationship between Streptococcus sanguinis and Prevotella melaninogenica in a CF sputum-like medium. Our data suggest that S. sanguinis uses reactive nitrogen species, and likely other factors, to antagonize P. melaninogenica, while Pseudomonas aeruginosa protects P. melaninogenica in CF-like culture conditions. Our findings implicate polymicrobial interactions, rather than individual species abundance, in determining microbial persistence and adaptation within the CF airway post-ETI.IMPORTANCEThe introduction of the latest cystic fibrosis transmembrane conductance regulator (CFTR)-targeted Elexacaftor/Tezacaftor/Ivacaftor (ETI) therapy represents a major therapeutic advance for persons with cystic fibrosis (pwCF); however, this therapy does not completely negate respiratory infections and colonization. We leverage large-scale publicly available microbiome data to demonstrate that while ETI therapy alters the respiratory microbial landscape, canonically prevalent and abundant CF pathogens persist in many pwCF and likely maintain ecological relevance through adaptive interactions with other taxa. Our in vitro findings also reveal that Streptococcus sanguinis can antagonize Prevotella melaninogenica, and that Pseudomonas aeruginosa can provide selective protection to quell this antagonism. These insights highlight the need to consider microbial interactions and community dynamics when evaluating long-term responses to CFTR modulators.
Hafi et al. (Fri,) studied this question.