RefSeq-corrected transcriptomic and RNA-interaction integration maps medium-associated vancomycin response rewiring in Staphylococcus aureus

Background Staphylococcus aureus is a major cause of bone, joint and orthopaedic implant-associated infections, providing clinical motivation for understanding adaptive antibiotic-response states. However, the present study is a secondary analysis of public in vitro transcriptomic and RNA-interaction datasets rather than an infection-model or clinical-specimen study. Vancomycin remains important for serious MRSA infections, but adaptive responses to vancomycin may vary across environmental and evolutionary states. Here, we used a framework integrating RefSeq-harmonized transcriptomics and RNA–RNA interaction evidence to examine vancomycin response rewiring. Materials and methods In this secondary analysis, we performed a processed-expression reanalysis of public S. aureus transcriptomic and RNA-interaction datasets, using GSE149213 as the discovery dataset for medium-stratified vancomycin response modeling across cation-adjusted Mueller-Hinton broth (CA-MHB) and Roswell Park Memorial Institute medium supplemented with 10% lysogeny broth (RPMI + 10% LB) in wild-type, media-adapted control and analytically pooled vancomycin-evolved lineages/populations. Candidate identities were harmonized using USA300HOU RefSeq locus-tag annotations, clean GSE254530 was used for conservative cross-dataset assessment, and published RNase III-CLASH data were used to evaluate candidate-associated RNA-interaction evidence. Results In the exploratory GSE149213 processed-expression contrast analysis, analytically pooled vancomycin-evolved lineages/populations retained broad acute responses, with the strongest response-rewiring burden corresponding to the EVO-WT response shift in RPMI + 10% LB; EVO-MAC response shifts were much more limited. RefSeq locus-tag harmonization retained a predefined nine-locus candidate panel for evidence ranking. Conservative GSE254530 assessment provided strict cross-dataset differential-expression support for pyrR only, while glnA was uniquely mapped but not differentially expressed and the remaining seven candidates lacked conservative clean-feature mappings. RNase III-CLASH integration highlighted carbamoyl-P synthase, dihydroorotase and glnA as top-ranked candidate-associated CLASH hotspots. Module-level processed-expression analysis further localized evolved response shifts to RPMI-associated redox/stress, cell-wall/envelope and proteolysis/stress/virulence programs, with translation/ribosome showing a contrasting negative trend. Conclusion This study provides a RefSeq-corrected, evidence-ranked processed-expression map of vancomycin response rewiring in S. aureus . Although the findings remain hypothesis-generating rather than causal, they define prioritized candidate loci, candidate-associated RNA-interaction edges and functional modules for future experimental testing in matched in vitro systems and biologically relevant infection models, including bone- and implant-associated models.