Whole Genome Sequencing Reveals Genetic Concordance of Staphylococcus aureus from Oropharynx and Sputum in Cystic Fibrosis. Staphylococcus aureus

Rationale: Patients with cystic fibrosis (CF) may not expectorate sputum because of young age or after receiving 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 infecting the lungs.Objective: To determine whether oropharyngeal and sputum isolates of S. aureus are genetically distinct in patients with CF.Methods: We obtained historical S. aureus isolates from patients who intermittently expectorated sputum in 2018 and 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 less than 60 SNPs or the isolates were not disturbed by clade breaker analysis.Results: 36 subjects had S. aureus in less than 1 oropharyngeal swab and less than 1 sputum 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 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 genetically matching isolates cultured from sputum.