A Conserved Persistence-Associated Functional State Core beneath Phenotypic Diversity in Pseudomonas aeruginosa Small-Colony Variants

Small-colony variants (SCVs) and rugose small-colony variants (RSCVs) of Pseudomonas aeruginosa are associatedwith chronic infection, biofilm formation, antibiotic tolerance, and extensive phenotypic heterogeneity. Whether areproducible molecular state persists beneath this morphological diversity is less clear. We performed a public-data-onlysecondary analysis of independent P. aeruginosa SCV/RSCV transcriptomic datasets, centered on GSE147921 andGSE293895, with GSE34141 used for study-level triangulation, and integrated these results with exploratory quantitativeanalysis of published wild-type/RSCV microscopy. Cross-study genome-wide effect correlations were weak, arguingagainst a universal global SCV transcriptome. Nevertheless, a restricted replicated signature was detectable: a frozentop-100 discovery signature separated independent RSCVs from wild type (exact permutation p=0.0476), with strongersignal at smaller signature sizes. A stringent cross-dataset core contained 260 directionally concordant genes; requiringadditional consistency across SCV24 versus two revertant branches and an independent SCV lineage retained 155genes (59.6%), comprising 91 upregulated and 64 downregulated genes. The strict up-core was strongly enriched forextracellular-matrix genes (odds ratio [OR] 18.7, Fisher p=4.93×10^-7) and iron-acquisition genes (OR 21.8,p=1.16×10^-5). Independently defined alginate/biofilm transcription increased in both primary datasets, whereas motilityand quorum/PQS programs decreased. Published-image reanalysis did not identify a conserved intracellular high-densitystructure and did not show consistent RSCV-specific high-density morphology across matched figure regions (2/4comparisons in the same direction; sign-test p=0.6875). These results support a model in which SCV identity is betterdescribed by a restricted persistence-associated functional state than by uniform morphology or global acute-virulenceactivation. The analysis does not establish increased in vivo virulence, biofilm biomass, or a physical intracellular core. Keywords: Pseudomonas aeruginosa; small-colony variant; RSCV; biofilm; extracellular matrix; iron acquisition;transcriptomics; persistence; phenotypic heterogeneity; public data