Genomic characterization and niche adaptive analysis of Pseudomonas promysalinigenes W2469: the first clinical isolate from a human bile specimen

Background Pseudomonas promysalinigenes is a newly described bacterial species renowned for producing promysalin, a species-selective lipopeptide antibiotic. All previously reported strains of this species are derived from environmental niches such as plant rhizospheres, and no clinical infection cases associated with this bacterium have been documented to date. Thus, the clinical microbiology relevance, genomic features, and adaptive potential of P. promysalinigenes remain largely unexplored, and current reference databases have limited coverage of this rare species. Methods A bacterial strain designated W2469 was isolated from the bile specimen of a patient with acute suppurative cholecystitis and cholecystolithiasis. Conventional phenotypic and molecular identification matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), VITEK 2 biochemical assay, 16S ribosomal RNA (rRNA), and whole-genome sequencing (WGS) was performed. Bioinformatics analyses, including average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), core genome single-nucleotide polymorphism (cgSNP), pan-genome analysis, and functional annotation against COG, KEGG, CAZy, VFDB, and CARD databases, were conducted to characterize the strain. Results Conventional methods yielded consistent misidentification of the strain, while WGS definitively assigned it to P. promysalinigenes (ANI = 98.8%, dDDH = 91.1% against the type strain RW10S1). The strain exhibited a narrow-spectrum resistance phenotype, with resistance to aztreonam and ticarcillin/clavulanic acid, intermediate susceptibility to meropenem, and susceptibility to most clinically used antibiotics. Genomic annotation identified 25 antimicrobial resistance genes and 139 niche adaptation-related factors, most of which are low-identity homologs (80%) of canonical reference sequences. Pan-genome analysis identified 571 clinical-specific genes associated with host adaptation, with complete loss of the environmental promysalin biosynthetic gene cluster. Conclusion This study provides the first documentation of P. promysalinigenes as a clinical isolate from human bile, expanding the known ecological niche of this species to the clinical setting. Conventional methods are prone to misidentifying this rare species, and WGS is critical for accurate taxonomic identification. Importantly, the strain exhibits clear adaptive phenotypes despite low sequence identity to known functional elements, highlighting profound knowledge gaps in the genomic diversity and uncharacterized adaptive mechanisms of this rare Pseudomonas species. This work provides a foundational genomic resource for future investigations into this emerging opportunistic pathogen.