not-yet-known not-yet-known not-yet-known unknown Background: People with cystic fibrosis (CF) may not expectorate sputum at young ages or while on CFTR modulators. While oropharyngeal swabs are commonly used to test for lower airway pathogens, it is unknown whether Staphylococcus aureus isolated from the oropharynx represents the strain that infects the lungs. Our goal was to determine whether oropharyngeal and sputum isolates of S. aureus are genetically distinct in a cohort of patients with CF. Methods: We obtained historical S. aureus isolates from patients who intermittently expectorated sputum in 2018 and we prospectively cultured S. aureus from oropharyngeal swabs and sputum from subjects with CF between August 2020 - February 2022. We performed short-read whole genome sequencing, determined sequence type, and performed phylogenetic analysis using S. aureus core genome single nucleotide polymorphisms (SNPs). We assigned isolates from a patient to the same strain if they had the same sequence type and differed by ≤ 60 SNPs or the isolates were not disturbed by clade breaker analysis. Results: 36 subjects had S. aureus in ≥1 oropharyngeal swab and ≥1 sputum sample in 2018. In the prospective collection, 31 subjects had synchronous oropharyngeal swab and sputum collections. Although polyclonal infections were detected, sputum and oropharyngeal isolates of S. aureus typically matched the same strain within study subjects, both over the span of 2018 (31/36 patients), and when collected simultaneously from 2020-2022 (29/31 patients). Conclusions: In patients with CF who intermittently produce sputum, oropharyngeal swabs identify S. aureus with genetic and phenotypic similarity to those cultured from sputum.

Introduction: Cystic Fibrosis Foundation guidelines recommend people with CF perform daily airway clearance. This can be difficult for patients to complete, as some find it time consuming or uncomfortable. Data comparing airway clearance methods are limited. We surveyed patients and families to understand which methods are preferred and identify obstacles performing airway clearance. Methods: We designed a REDCap survey and enrolled participants in 2021. Respondents reported information on airway clearance usage, time commitment, and medication use. They rated airway clearance methods for effectiveness, comfort, time commitment, importance, and compatibility with other treatments. Analysis included descriptive statistics and clustering. Results: 60 respondents started and 52 completed the survey. The median patient age was 20 years. Respondents experienced a median of four airway clearance methods in their lifetime, including chest wall oscillation (vest, 92%), manual chest physical therapy (CPT, 88%), huff coughing (77%), and exercise (75%). Past 30-day use was highest for exercise (62%) and vest (57%). Time commitment was generally less than 2 hours daily. Of those eligible for CFTR modulators, 53% reported decreased time commitment to airway clearance after starting treatment. On a scale of 0-100, respondents rated CFTR modulators as their most important treatment (median 99.5), followed by exercise (88). Discussion: Patients and caregivers are familiar with several methods of airway clearance for CF. They report distinct strengths and limitations of each method. Exercise and vest are the most common methods of airway clearance. Use of CFTR modulators may reduce patient-reported time commitment to airway clearance.

Rationale: Methicillin resistant Staphylococcus aureus (MRSA) is prevalent and consequential in cystic fibrosis (CF). Whole genome sequencing (WGS) could reveal genomic differences in MRSA associated with poorer outcomes or detect MRSA transmission. Objectives: To identify MRSA genes associated with low lung function and identify potential MRSA transmission in CF. Methods: We collected 97 MRSA isolates from 74 individuals with CF from 2017 and performed short-read WGS. We determined sequence type (ST) and the phylogenetic relationship between isolates. We aligned accessory genes from 25 reference genomes to genome assemblies. We classified the MRSA by accessory gene content and correlated the accessory genome to clinical outcomes. Results: The most prevalent ST were ST5 (N=55), ST105 (N=14), and ST8 (N=14). Closely related MRSA strains were shared by family members with CF, but rarely between unrelated individuals. Three distinct clusters of MRSA were identified by accessory genome content. The first included ST5 and ST105 strains and was common among older patients with lower FEV1. The second cluster included ST8, which was generally identified in younger patients. Sputum density of MRSA and Pseudomonas aeruginosa was higher in cultures from patients with ST5/ST105 compared to patients with ST8 at similar ages. Conclusions: In this CF cohort, we identified MRSA subtypes that predominate at different ages and differ by accessory gene content. ST5 and ST105 represented the most prevalent cluster of MRSA. ST8 MRSA was more common in younger patients and thus has the potential to rise in prevalence as these patients age.