Staphylococcus aureus and skin infection: a proteomic journey to decipher adaptation strategies

Skin infections caused by methicillin-resistant Staphylococcus aureus (MRSA) pose significant clinical challenges due to their virulence and antibiotic resistance. Understanding the proteome variations of S. aureus during skin infection can reveal critical insights into pathogenic mechanisms and help identify novel targets for therapeutic interventions. This study aimed to characterize the in vitro proteome of S. aureus from infected skin tissues using a 3D skin model.

We focused on two strains of MRSA, ST398 and JE2 (a USA300 isolate), representing different epidemiological contexts. We employed a 3D skin model that mimics human skin, consisting of fibroblasts and keratinocytes, to provide a highly relevant context for human skin infections. These in vitro tissues were infected with 10⁸ CFU/mL of the respective MRSA strains. After 2 days, we washed the tissues with sterile PBS and collected both the bacterial supernatant and the underlying tissues for protein extraction. The extracted proteins were analyzed using shotgun proteomics with a Q-Exactive mass spectrometer. Raw data were processed with Proteome Discoverer using SEQUEST-HT and evaluated by a label-free quantification (LFQ) approach using precursor ion abundances to identify differentially expressed proteins (DEPs).

We identified a total of 2,194 proteins from ST398 and 2,074 proteins from JE2. Analysis of the DEPs revealed that proteins associated with amino acid metabolism, such as those involved in arginine biosynthesis, pyruvate metabolism, and betaine biosynthesis, increased during the infection. We also identified numerous virulence proteins shared by both strains, including acid phosphatase (sapS), autolysin (Atl), leucocidin subunits (hlgA, hlgB), MAP protein, Immunoglobulin G-binding protein A (spa), and ATP-dependent molecular chaperones (clpB and clpC). Additionally, we observed strain-specific responses, with certain proteins being exclusively present in either the JE2 or ST398 strains, reflecting their unique adaptation strategies.

Our study provides a comprehensive proteomic profile of MRSA during skin infection, highlighting both common and unique adaptive mechanisms employed by different strains. These findings offer valuable insights into the pathogenicity of MRSA and identify potential targets for novel therapeutic interventions for better management of skin infections.