Genetic Concordance of Staphylococcus aureus from Oropharyngeal and
Sputum Cultures in People with Cystic Fibrosis
- Christian F. Zirbes,
- Andries Feder,
- Anthony J. Pamatmat,
- Alyssa Bartels,
- Nicholas Pitcher,
- Alexis L. Rozen,
- Mary Teresi,
- Justin Krogh,
- Margaret Regan,
- Erin A. Arnold,
- Jared J. Hill,
- Lindsey D. Reinhardt,
- Carlos Oberto,
- Linda Boyken,
- Valerie Reeb,
- Ahmed M. Moustafa,
- Paul Planet,
- Anthony Fischer
Christian F. Zirbes
The University of Iowa Stead Family Department of Pediatrics
Author ProfileAndries Feder
The Children's Hospital of Philadelphia Research Institute
Author ProfileAnthony J. Pamatmat
The University of Iowa Stead Family Department of Pediatrics
Author ProfileAlyssa Bartels
The University of Iowa Stead Family Department of Pediatrics
Author ProfileNicholas Pitcher
The University of Iowa Stead Family Department of Pediatrics
Author ProfileAlexis L. Rozen
The University of Iowa Stead Family Department of Pediatrics
Author ProfileMary Teresi
The University of Iowa Stead Family Department of Pediatrics
Author ProfileJustin Krogh
The University of Iowa Stead Family Department of Pediatrics
Author ProfileMargaret Regan
The University of Iowa Stead Family Department of Pediatrics
Author ProfileErin A. Arnold
The University of Iowa Stead Family Department of Pediatrics
Author ProfileJared J. Hill
The University of Iowa Stead Family Department of Pediatrics
Author ProfileLindsey D. Reinhardt
The University of Iowa Stead Family Department of Pediatrics
Author ProfileCarlos Oberto
The University of Iowa Stead Family Department of Pediatrics
Author ProfileLinda Boyken
The University of Iowa Department of Pathology
Author ProfileValerie Reeb
The University of Iowa State Hygienic Laboratory
Author ProfileAhmed M. Moustafa
The Children's Hospital of Philadelphia Research Institute
Author ProfilePaul Planet
The Children's Hospital of Philadelphia Research Institute
Author ProfileAbstract
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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.28 Aug 2024Submitted to Pediatric Pulmonology 30 Aug 2024Submission Checks Completed
30 Aug 2024Assigned to Editor
30 Aug 2024Review(s) Completed, Editorial Evaluation Pending
25 Sep 2024Reviewer(s) Assigned
16 Nov 2024Editorial Decision: Revise Minor