Standardization of In vitro Method of Biofilm Formation by Clinical Isolates of Pseudomonas aeruginosa and Elucidating Its Biofilm-Specific Proteins Through LC-Orbitrap HRMS-Based Peptidomics.

Abstract

Introduction: Pseudomonas aeruginosa biofilms drive chronic infections, yet heterogeneous matrix composition hinders standardized in vitro classification of clinical isolates. This study aimed to develop a reproducible biofilm formation protocol using a defined supplement mix and elucidate proteomic signatures across biofilm categories to enable risk stratification and targeted therapies.

Methods: 139 clinical P. aeruginosa isolates were tested in BHI broth supplemented with 0.5% each glucose, mannose, NaCl, and arginine. Biofilm formation was quantified via TCP assay (ODcut=0.344 at 570 nm), validated by confocal (ConA-TRITC), SEM, protein/eDNA quantification (Bradford, phenol-chloroform), SDS-PAGE, and LC-Orbitrap HRMS peptidomics (549 proteins; PRIDE PXD057726). Antimicrobial susceptibility followed CLSI guidelines.

Results: Supplement mix increased biofilm OD 26.9% (1.28±0.12 vs. 0.95±0.13; P<0.001), reclassifying isolates: HBF 38.8% (n=54), MBF 46.0% (n=64), WBF 13.7% (n=19), NBF 1.4% (n=2), resistance: ceftazidime 43.9%, meropenem 43.2%, imipenem 33.1%; 12.9% MDR. HBF matrices showed the highest protein levels (1.38±0.37 mg/mL); peptidomics revealed 12 shared proteins, 26 in PAO1/HBF/MBF, and 16 HBF-unique (ribosomal RpsA-RpsQ/RplA-RplY; stress YidC/KatA/ClpB/DnaJ; metabolic Edd/Pgk/PckA/ArcA).

Discussion: Distinct signatures indicate anoxic adaptations (HupB, AtpA-G) that drive HBF robustness, linking matrix heterogeneity(GeNei, India) to infection persistence beyond mere polysaccharide dominance. HBF matrices exhibited anoxic adaptation (HupB, AtpA-G), with YidC insertase facilitating membrane protein biogenesis under stress, supporting metabolic speciation for biofilm-specific diagnostics, therapies, and isolate risk stratification.

Conclusion: This protocol enables biofilm categorization and reveals metabolic speciation targets for diagnostics and therapies against MDR P. aeruginosa biofilms.