Chronic Staphylococcus aureus Lung Infection Correlates With Proteogenomic and Metabolic Adaptations Leading to an Increased Intracellular Persistence

Abstract

Background Chronic lung infection in cystic fibrosis (CF) patients by Staphylococcus aureus is a well-established epidemiological fact. Indeed, S. aureus is the most commonly identified pathogen in the lungs of CF patients. Improving our understanding of the mechanisms associated with the persistence of S. aureus is therefore an important issue. Methods We selected pairs of sequential S. aureus isolates from 3 patients with CF and from 1 patient with non-CF chronic lung disease. We used a combination of genomic, proteomic, and metabolomic approaches with functional assays for in-depth characterization of S. aureus long-term persistence. Results In this study, we show that late S. aureus isolates from CF patients have an increased ability for intracellular survival in CF bronchial epithelial-F508del cells compared to ancestral early isolates. Importantly, the increased ability to persist intracellularly was confirmed for S. aureus isolates within the own-patient F508del epithelial cells. An increased ability to form biofilm was also demonstrated. Furthermore, we identified the underlying genetic modifications that induce altered protein expression profiles and notable metabolic changes. These modifications affect several metabolic pathways and virulence regulators that could constitute therapeutic targets. Conclusions Our results strongly suggest that the intracellular environment might constitute an important niche of persistence and relapse necessitating adapted antibiotic treatments.

Activity of Antibiotics against Staphylococcus aureus in an In Vitro Model of Biofilms in the Context of Cystic Fibrosis: Influence of the Culture Medium

“…S. aureus is well-known to form biofilms that contribute to its capacity to cause chronic infections, including in CF patients (4,(10)(11)(12). Until now, many studies have mainly concentrated on the activity of antibiotics against Pseudomonas aeruginosa biofilms, because they are the most prevalent in the adult CF population (6).…”

Pulmonary Pathogens Adapt to Immune Signaling Metabolites in the Airway

“…These high fumC-expressing host-adapted strains also displayed abundant biofilm formation, suggesting that by consuming fumarate they not only limited the development of immune memory, as described above, but also improved community lifestyle. In addition to increasing fumC, other metabolic changes seen in S. aureus isolates from a completely different study stemmed from several non-synonymous mutations in other metabolic genes, particularly loci involved in amino acid and carbohydrate metabolism (117). This host-adapted strain from long-standing infection in CF also exhibited increased biofilm formation, changes that correlated with acquisition of stop codon mutations in the master regulator agr (117).…”

“…In addition to increasing fumC, other metabolic changes seen in S. aureus isolates from a completely different study stemmed from several non-synonymous mutations in other metabolic genes, particularly loci involved in amino acid and carbohydrate metabolism (117). This host-adapted strain from long-standing infection in CF also exhibited increased biofilm formation, changes that correlated with acquisition of stop codon mutations in the master regulator agr (117). The progressive acquisition of mutations in metabolic genes and upregulation of fumC observed in S. aureus isolates suggest a continual adaptation to the metabolites produced by immune and epithelial cells, changes that also favor biofilm development.…”

Consequences of Metabolic Interactions during Staphylococcus aureus Infection

“…The bacterial metabolic requirements at a mucosal site may differ substantially from those once the bacteria have reached the bloodstream. 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].…”

“…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.…”