Studies have demonstrated that people with CF with pancreatic insufficiency (PI) have fecal dysbioses. Evidence suggests the causes of these dysbioses are multifactorial, and that important drivers include antibiotic exposure, dietary intake, and CF gastrointestinal tract dysfunction, including nutrient malabsorption. In this pilot study, we tested whether initiation of the CFTR modulator treatments ivacaftor (in a cohort of pancreatic sufficient (PS) people with CF and an R117H CFTR variant) or lumacaftor/ivacaftor (in a cohort of PI people with CF and an F508del variant) changed fecal measures of malabsorption or fecal microbiomes. While we identified no statistically significant fecal changes with either treatment, we detected trends in the PI cohort when initiating lumacaftor/ivacaftor towards decreased fecal fat content and towards fecal microbiomes that more closely resembled the fecal microbiota of people without PI. While these findings support a model in which nutrient malabsorption resulting from CF-induced PI drives fecal dysbiosis, they must be validated in future, larger studies of fecal microbiome and malabsorption outcomes with highly effective CFTR modulator therapies.

Background: Invasive methods requiring general anaesthesia are needed to sample the lung microbiota in young children who do not expectorate. This poses substantial challenges to longitudinal study of paediatric airway microbiota. Non-invasive upper airway sampling is an alternative method for monitoring airway microbiota; however, there are limited data describing the relationship of such results with lung microbiota in young children. In this study, we compared the upper and lower airway microbiota in young children to determine whether non-invasive upper airway sampling procedures provide a reliable measure of either lung microbiota or clinically defined differences.Results: The microbiota in oropharyngeal (OP) swabs, nasopharyngeal (NP) swabs and bronchoalveolar lavage (BAL) from 78 children (median age 2.2 years) with and without lung disease were characterised using 16S rRNA gene sequencing. Permutational multivariate analysis of variance (PERMANOVA) detected significant differences between the microbiota in BAL and those in both OP swabs (p = 0.0001, Pseudo-F = 12.2, df = 1) and NP swabs (p = 0.0001; Pseudo-F = 21.9, df = 1) with the NP and BAL microbiota more different than the OP and BAL, as indicated by a higher Pseudo-F value. The microbiota in combined OP and NP data (upper airways) provided a more comprehensive representation of BAL microbiota, but significant differences between the upper airway and BAL microbiota remained, albeit with a considerably smaller Pseudo-F (PERMANOVA p = 0.0001; Pseudo-F = 4.9, df = 1). Despite this overall difference, paired BAL and upper airway (OP and NP) microbiota were >50 % similar among 69 % of children. Furthermore, canonical analysis of principal coordinates (CAP analysis) detected significant differences between the microbiota from clinically defined groups when analysing either BAL (eigenvalues >0.8; misclassification rate 26.5 %) or the combined OP and NP data (eigenvalues >0.8; misclassification rate 12.2 %).Conclusions: Upper airway sampling provided an imperfect, but reliable, representation of the BAL microbiota for most children in this study. We recommend inclusion of both OP and NP specimens when non-invasive upper airway sampling is needed to assess airway microbiota in young children who do not expectorate. The results of the CAP analysis suggest lower and upper airway microbiota profiles may differentiate children with chronic suppurative lung disease from those with persistent bacterial bronchitis; however, further research is needed to confirm this observation.

Objectives:The STaph Aureus Resistance -treat or observe trial (STAR-too) evaluates microbiologic effectiveness of an eradication protocol (Rx) compared to observation (Obs.) in subjects with newly + MRSA cultures.The study was stopped early by the Data Monitoring Committee (DMC) due to efficacy.Methods: Subjects were eligible if they were: within the first 6 months of their first MRSA positive culture, age 4-45 years, and had not received MRSA active antibiotics 4 weeks prior.Due to poor enrollment, the protocol was amended to allow patients with a recent + MRSA clinical isolate but negative at screening.The eradication protocol was: oral trimethoprim-sulfamethoxazole (or minocycline) plus rifampin and chlorhexidine mouthwash for two weeks, nasal mupirocin and chlorhexidine body wipes for five days, and environmental decontamination for 21 days.The primary endpoint was MRSA culture status at day 28.Results: Among 42 patients (45% female, mean age 12.3±6.8years, baseline FEV 1 % predicted 98.7±18.7)randomized at the time of the DMC review, 39 had evaluable culture results.Seventeen (81%) were MRSA negative in the Rx arm and 4 (22%) in the Obs.arm at day 28 (diff.: 59%, 95% CI: 28-76%).Among 27 MRSA positive at screening, 8 (67%) were MRSA neg. in the Rx arm compared to 2 (13%) in the Obs.arm (diff.: 53%, 95% CI: 16-75%) at day 28.Exacerbation rate up to day 28 was reduced in the Rx arm vs. Obs.arm [rate ratio 0.40 (0.08, 1.52)]. Conclusion:This MRSA eradication protocol for newly acquired MRSA demonstrated microbiologic efficacy with a large treatment effect.No safety concerns were raised.Final primary efficacy data will be presented.CFF TDN.

Objectives: Advances in genome sequencing have made it feasible to sequence multiple genomes of the same lineage of bacterial pathogens as they evolve in their human hosts.Nonetheless, only little is known about how evolution processes compare between genotypic different lineages of the same pathogenic species when they evolve within their human hosts.Methods: Here, we analyze the genomes of 474 isolates of P. aeruginosa sampled from 34 young Danish CF patients.Our phylogenetic analysis reveals the patients to be infected by 53 different clone types of P. aeruginosa, and for 36 of the clone types we sequenced multiple longitudinal isolates, enabling us to decipher the within-host evolutionary history of each of these lineages.Results: We found the 36 lineages to exhibit mutational convergence in 56 pathoadaptive genes (genes mutated in >5 clone types), in which the host environment imposed a selection for mutations.The pathoadaptive genes were related to motility, antibiotic resistance, remodeling of regulatory networks, biofilm formation, and extracellular virulence factors.Furthermore, our results show that mutation of downstream transcriptional regulators was contingent upon the mutation of upstream regulators in the same regulatory network. Conclusion:In conclusion, we have identified adaptive trajectories generic to P. aeruginosa in the CF environment, and elucidated how early mutations predict later evolutionary events.Knowledge of pathoadaptive mutations and evolutionary contingency may help prediction of bacterial persistence and development of future therapeutic targets against the infection.