Journal article
Genetic Concordance of Staphylococcus aureus From Oropharyngeal and Sputum Cultures in People With Cystic Fibrosis
Pediatric pulmonology, Vol.60(1), p.e27475
01/2025
DOI: 10.1002/ppul.27475
PMCID: PMC11715147
PMID: 39785222
Appears in UI Libraries Support Open Access
Abstract
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.
Details
- Title: Subtitle
- Genetic Concordance of Staphylococcus aureus From Oropharyngeal and Sputum Cultures in People With Cystic Fibrosis
- Creators
- Christian F Zirbes - University of IowaAndries Feder - Children's Hospital of PhiladelphiaAnthony J Pamatmat - University of IowaAlyssa R Bartels - University of Iowa, Stead Family Department of PediatricsNicholas J Pitcher - University of IowaAlexis L Rozen - University of IowaMary Teresi - University of IowaJustin Krogh - University of IowaMargaret Regan - University of IowaErin A Arnold - University of IowaJared J Hill - University of Iowa, Orthopedics and RehabilitationLindsey D Reinhardt - University of IowaCarlos L Oberto - University of IowaLinda Boyken - University of Iowa, PathologyValérie C Reeb - University of Iowa, Hygienic Laboratory - BdcAhmed M Moustafa - Children's Hospital of PhiladelphiaPaul J Planet - Children's Hospital of PhiladelphiaAnthony J Fischer - University of Iowa, Pulmonary Medicine
- Resource Type
- Journal article
- Publication Details
- Pediatric pulmonology, Vol.60(1), p.e27475
- DOI
- 10.1002/ppul.27475
- PMID
- 39785222
- PMCID
- PMC11715147
- NLM abbreviation
- Pediatr Pulmonol
- ISSN
- 1099-0496
- eISSN
- 1099-0496
- Publisher
- Wiley; HOBOKEN
- Grant note
- This research was supported by NHLBI K08 HL136927 (AJF), University of Iowa CTSA UL1TR002537. Cystic Fibrosis Foundation FISCHE20A0-KB, FISCHE21GO, and CFF Research and Development Program STOLTZ19R0 CDC Advanced Molecular Detection, Epidemiology and Laboratory Capacity Cooperative Agreement (VR). NIAID 1R01AI137526-01 (PJP). NSF supported high performance through Award#1925590 (American Museum of Natural History/PJP).
- Language
- English
- Date published
- 01/2025
- Academic Unit
- Pulmonary Medicine; Stead Family Department of Pediatrics; Hygienic Laboratory - Bdc; Pathology; Orthopedics and Rehabilitation
- Record Identifier
- 9984772372502771
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