Independently modulated genes in Streptococcus pneumoniae TIGR4 reveal transcriptional rewiring in antibiotic-adapted and antibiotic-sensitive strains

Abstract Streptococcus pneumoniae remains a major pathogen, and increasing antimicrobial resistance complicates disease control. To investigate transcriptional programs associated with antibiotic stress and adaptation, we applied independent component analysis (ICA) to a compendium of 718 RNA-seq datasets from the TIGR4 strain. ICA identified 60 independently modulated gene sets (iModulons), 30 of which significantly overlapped with known regulons. iModulon activity profiles distinguished adaptation-associated and antibiotic-induced transcriptional responses across multiple antibiotic conditions. The CiaRH iModulon recapitulated key features of the known CiaRH regulon despite the absence of ciaR/H mutant transcriptomes. Vancomycin-responsive activation of the CiaRH iModulon was observed in both TIGR4 and serotype 19F strains in nutrient-rich medium and independently reproduced in TIGR4 cultured under chemically defined conditions. However, most iModulon responses differed between TIGR4 and serotype 19F, suggesting these findings may not generalize across pneumococcal strains. These findings demonstrate that iModulon analysis provides a scalable and interpretable framework for characterizing transcriptional rewiring associated with antibiotic stress and adaptation in S. pneumoniae TIGR4.