20Pseudomonas aeruginosa and Staphylococcus aureus are the most common bacteria 21 that infect the respiratory tract of individuals with the genetic disease cystic fibrosis (CF); in fact, 22S. aureus has recently overtaken P. aeruginosa to become the most common. Substantial 23 research has been performed on the epidemiology of S. aureus in CF; however, there appears 24 to be a gap in knowledge in regard to the pathogenesis of S. aureus in the context of CF lung 25 infections. Most studies have focused on a few S. aureus isolates, often exclusively laboratory 26 adapted strains, and how they are killed by P. aeruginosa. Because of this, little is known about 27 the diversity of S. aureus CF lung isolates in both virulence and interaction with P. aeruginosa. 28To begin to address this gap in knowledge, we recently sequenced 65 clinical S. aureus isolates 29 from the Emory CF Biospecimen Registry and Boston Children's Hospital, including the 30 reference isolate JE2, a USA300 strain. Here, we analyzed antibiotic resistance genotypes, 31 sequence type, clonal complex, spa type, and agr type of these isolates. We hypothesized that 32 major virulence phenotypes of S. aureus that may be associated with CF lung infections, 33 namely toxin production and mucoid phenotype, would be retained in these isolates. To test our 34 hypothesis, we plated on specific agars and found that most isolates can hemolyze both rabbit 35 and sheep blood (67.7%) and produce polysaccharide (69.2%), consistent with virulence 36 retention in CF lung isolates. We also identified three distinct phenotypic groups of S. aureus 37 based on their survival in the presence of nonmucoid P. aeruginosa laboratory strain PAO1 and 38 its mucoid derivative. Altogether, our work provides greater insight into the diversity of S. aureus 39 CF isolates, specifically the distribution of important virulence factors and their interaction with 40 P. aeruginosa, all of which have implications in patient health. 41 42
Author Summary 43Staphylococcus aureus is now the most frequently detected pathogen in the lungs of 44 individuals who have cystic fibrosis (CF), followed closely by Pseudomonas aeruginosa. When 45 these two pathogens are found to coinfect the CF lung, patients have a significantly worse 46 prognosis. While P. aeruginosa has been rigorously studied in the context of bacterial 47 pathogenesis in CF, less is known about S. aureus. Here we present an in-depth study of 64 S. 48 aureus CF clinical isolates where we investigated genetic diversity utilizing whole genome 49 sequencing, virulence phenotypes, and interactions with P. aeruginosa. We have found that S. 50 aureus isolated from the CF lung are phylogenetically diverse, most retain known virulence 51 factors, and they vary in interactions with P. aeruginosa from highly sensitive to completely 52 tolerant. Deepening our understanding of how S. aureus responds to its environment and other 53 microbes in the CF lung will enable future development of effective treatments and preventative 54 measures agains...