Comparative transcriptomics uncover differential regulatory mechanisms in MRSA and MSSA biofilms through RNA-sequencing

Staphylococcus aureus is an opportunistic pathogen that can form biofilms and is known for its persistence in causing infections. This study aims to characterise the transcriptional mechanisms underlying biofilm formation in both methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) strains. Total RNA was extracted from cells grown under biofilm and planktonic conditions and subjected to RNA sequencing on the Illumina HiSeq 2500. Differential expression analysis was performed using DESeq2 and functional enrichment was assessed through Kyoto Encyclopedia of Genes and Genomes enrichment pathway analyses. Transcriptome analysis identified 2,809 genes in MRSA (612 DEGs: 552 upregulated, 60 downregulated) and 2,744 genes in MSSA (66 DEGs: 29 upregulated, 37 downregulated) expressed genes in MRSA and MSSA biofilm cells, respectively. The genes that are significantly differentially expressed in biofilms (log2 fold change > 1, p-value < 0.05) include 221 genes in MRSA and 12 in MSSA. MRSA biofilms showed a significant upregulation of known genes associated with biofilm formation, including polysaccharide adhesin synthesis (icaADBC), fibronectin-binding (fnbA), extracellular matrix-binding protein (Embp) and surface protein C (sasC). In contrast, the upregulated genes in MSSA biofilms highlight aspects of metabolism (ferredoxin, formate dehydrogenase), transport (aquaporin, ABC transporter) and virulence staphylococcal secretory antigen A (ssaA). MRSA and MSSA exhibit distinct gene expression profiles in their biofilm cells, suggesting that biofilm formation in MRSA and MSSA is strain-specific.