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A comprehensive understanding of how Staphylococcus aureus adapts to cause infections in humans can inform development of diagnostic, therapeutic, and preventive approaches. Expression analysis of clinical strain libraries depicts in vitro conditions that differ from those in human infection, but low bacterial burden and the requirement for reverse transcription or nucleic acid amplification complicate such analyses of bacteria causing human infection. We developed methods to evaluate the mRNA transcript signature of S. aureus in pediatric skin and soft tissue infections (SSTI) directly ex vivo Abscess drainage from 47 healthy pediatric patients undergoing drainage of a soft tissue infection was collected, and RNA was extracted from samples from patients with microbiologically confirmed S. aureus abscesses (42% due to methicillin-resistant S. aureus [MRSA]). Using the NanoString platform and primers targeting S. aureus mRNA transcripts encoding surface-expressed or secreted proteins, we measured direct counts of 188 S. aureus mRNA transcripts in abscess drainage. We further evaluated this mRNA signature in murine models of S. aureus SSTI and nasal colonization where the kinetics of the transcriptome could be determined. Heat maps of the S. aureus mRNA signatures from pediatric abscesses demonstrated consistent per-target expression across patients. While there was significant overlap with the profiles from murine SSTI and nasal colonization, important differences were noted, which can inform efforts to develop therapeutic and vaccine approaches.

Analysis of Staphylococcus aureus Transcriptome in Pediatric Soft Tissue Abscesses and Comparison to Murine Infections