Genotypic and Phenotypic Diversity of Staphylococcus aureus Isolates from Cystic Fibrosis Patient Lung Infections and Their Interactions with Pseudomonas aeruginosa

• Type of Material: Article
• Authors: Eryn E. Bernardy, Emory University; Robert A. Petit, Emory University; Vishnu Raghuram, Emory University; Ashley M. Alexander, Emory University; Timothy Read, Emory University; Joanna Goldberg, Emory University
• Language: English
• Date: 2020-05-01
• Publisher: American Society for Microbiology
• Publication Version: Final Published Version
• Copyright Statement: © 2020 Bernardy et al.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1128/mBio.00735-20
• Title of Journal or Parent Work: mBio
• Volume: 11
• Issue: 3
• Start Page: 1
• End Page: 18
• Grant/Funding Information: We also thank the NIH IRACDA Fellowships in Research and Science Teaching (FIRST) program at Emory for financial support to E.E.B. (project number 5K12GM000680-19).; Children’s Healthcare of Atlanta. Bacterial isolates were obtained from the Cystic Fibrosis Biospecimen Registry, which is supported in part by the CF Discovery Core of the CF@LANTA RDP Center; This work was supported, in part, by a Pediatric Research Alliance pilot project (00068914 to J.B.G. and T.D.R.) from the Center for Cystic Fibrosis and Airways Disease Research (CF-AIR); Center for Cystic Fibrosis and Airways Disease Research, components of the Children’s CF Center of Excellence at Emory University, and Children’s Healthcare of Atlanta.
• Keywords: phylogenetic analysis; Slime production; Antimicrobial resistance; Hydrogen peroxide; Science & Technology; Sequence; Microbiology; Identification; Children; Pseudornonas aeruginosa; Virulence; Metchillin resistant; cystic fibrosis; Life Sciences & Biomedicine; interspecies competition; Small colony variants; ICA locus; Staphylococcus aureus
• Research Categories: Health Sciences, Immunology; Biology, Microbiology; Health Sciences, Epidemiology

Abstract

Staphylococcus aureus has recently overtaken Pseudomonas aeruginosa as the most commonly recognized bacterial pathogen that infects the respiratory tracts of individuals with the genetic disease cystic fibrosis (CF) in the United States. Most studies of S. aureus in CF patient lung infections have focused on a few isolates, often exclusively laboratory-adapted strains, and how they are killed by P. aeruginosa. Less is known about the diversity of S. aureus CF patient lung isolates in terms of both their virulence and their interaction with P. aeruginosa. To begin to address this gap, we recently sequenced 64 clinical S. aureus isolates and a reference isolate, JE2. Here, we analyzed the antibiotic resistance genotypes, sequence types, clonal complexes, spa types, agr types, and presence/absence of other known virulence factor genes of these isolates. We hypothesized that virulence phenotypes of S. aureus, namely, toxin production and the mucoid phenotype, would be lost in these isolates due to adaptation in the CF patient lung. In contrast to these expectations, we found that most isolates can lyse both rabbit and sheep blood (67.7%) and produce polysaccharide (69.2%), suggesting that these phenotypes were not lost during adaptation to the CF lung. We also identified three distinct phenotypic groups of S. aureus based on their survival in the presence of nonmucoid P. aeruginosa laboratory strain PAO1 and its mucoid derivative. Altogether, our work provides greater insight into the diversity of S. aureus isolates from CF patients, specifically the distribution of important virulence factors and their interaction with P. aeruginosa, all of which have implications in patient health. IMPORTANCE Staphylococcus aureus is now the most frequently detected recognized pathogen in the lungs of individuals who have cystic fibrosis (CF) in the United States, followed closely by Pseudomonas aeruginosa. When these pathogens are found to coinfect the CF lung, patients have a significantly worse prognosis. While P. aeruginosa has been rigorously studied in the context of bacterial pathogenesis in CF, less is known about S. aureus. Here, we present an in-depth study of 64 S. aureus clinical isolates from CF patients, for which we investigated genetic diversity utilizing whole-genome sequencing, virulence phenotypes, and interactions with P. aeruginosa. We found that S. aureus isolated from CF lungs are phylogenetically diverse; most retain known virulence factors and vary in their interactions with P. aeruginosa (i.e., they range from being highly sensitive to P. aeruginosa to completely tolerant to it). Deepening our understanding of how S. aureus responds to its environment and other microbes in the CF lung will enable future development of effective treatments and preventative measures against these formidable infections.