Christian F. Zirbes, Andries Feder, Anthony J. Pamatmat, Alyssa R. Bartels, Nicholas J. Pitcher, Alexis L. Rozen, Mary Teresi, Justin Krogh, Margaret Regan, Erin A. Arnold, Jared J. Hill, Lindsey D. Reinhardt, Carlos L. Oberto, Linda Boyken, Valérie C. Reeb, Ahmed M. Moustafa, Paul J. Planet, Anthony J. Fischer

People with cystic fibrosis (CF) may not expectorate sputum at young ages or after they receive CFTR modulators. While oropharyngeal swabs are commonly used to test for lower airway pathogens, it is unknown whether Staphylococcus aureus from the oropharynx matches the strain(s) infecting 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. 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 and 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. 36 subjects had S. aureus in ≥ 1 oropharyngeal swab and ≥ 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 typically matched the same strain within study subjects, both over the span of 2018 (31/36 patients) and when collected simultaneously from 2020 to 2022 (29/31 patients). In patients with CF who intermittently produce sputum, oropharyngeal swabs identify S. aureus with genetic and phenotypic similarity to those cultured from sputum.