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

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.

Consequences of Metabolic Interactions during Staphylococcus aureus Infection

“…A study of S. aureus strains from children with atopic dermatitis and chronic staphylococcal skin infection did not reveal many strains with agr mutation, and the expression of toxins was highly variable, as was their induction of cytokines [3]. Surveys of clinical strains from a variety of sites indicate that there are relatively few loss-of-function SNPs in major virulence genes, as might be expected, but many strains had accrued mutations or changes in the levels of expression of metabolic genes [3,[10][11][12].…”

“…Such adaptive changes may be genetic and correlate with the accumulation of single nucleotide polymorphisms (SNPs) in strains harvested over time from sites of chronic infection [3,10,11]. Over the course of infection, clinical isolates of S. aureus often have altered expression of toxins [12] that is associated with mutations in central regulatory genes such as the agr, sar and codY loci [11,13,14]. Perhaps more commonly, adaptive change is at the level of transcriptional regulation, enabling the microorganisms to rapidly adapt to different metabolic modes, as reflected by planktonic versus sessile/biofilm lifestyles.…”

Crosstalk Between Staphylococcus aureus and Innate Immunity: Focus on Immunometabolism

“…Such molecules constitute a new avenue for cellular signaling that the host and/or pathogen could leverage to their benefit during infection. These systems become even more complex in the context of polymicrobial infections, a common occurrence with P. aeruginosa and S. aureus in the lungs of CF patients (111)(112)(113). With the additional layering of another organism, the potential number of molecules and interactions increases exponentially.…”

Polymicrobial Interactions in the Cystic Fibrosis Airway Microbiome Impact the Antimicrobial Susceptibility of Pseudomonas aeruginosa

“…A recent study has shed some light on the potential reason for the disparity in these studies. Sixty-four S. aureus clinical isolates from CF patients were tested for their ability to interact with P. aeruginosa and ranged from highly sensitive to completely tolerant to P. aeruginosa [156]. Many studies have now reported that long-term co-adaption of these two pathogens results in a more commensal, cooperative relationship [154,157,158].…”