Genomic characterization of an unusual bloodstream Weissella viridescens isolate obtained from a Bulgarian intensive care unit patient.

BACKGROUND: The present study aimed to explore the genomic characteristics of an extremely rare clinical Weissella viridescens isolate (designated Wvir453), obtained in 2022 from the blood sample of a Bulgarian 37-year-old critically ill male patient diagnosed with spinal meningeal melanocytoma. METHODS AND RESULTS: Species identification using MALDI-TOF mass spectrometry, antimicrobial susceptibility testing, whole-genome sequencing, pangenomic, phylogenomic, and virulome analyses were performed. The isolate demonstrated high-level intrinsic resistance to glycopeptides, probable resistance to penicillin G and trimethoprim-sulfamethoxazole, and susceptibility to ampicillin, imipenem, clindamycin, tetracycline, ciprofloxacin, and linezolid. The observed genome size (1.73 Mb) and GC content (40.73%) were comparable with the accessible data from sequenced W. viridescens genomes. Phylogenomic analysis indicated that Wvir453 is not closely related to the other sequenced genomes (differed by 1,412 core genome SNPs from the closest one). No antimicrobial resistance-associated determinants were detected. To evaluate the virulence potential of Wvir453 compared to food and probiotic W. viridescens strains, a framework integrating protein language models with deep learning classifiers was applied. The results revealed notable differences in the size of its cloud genome, the total number of putative virulence factors, and the higher predicted virulence scores. CONCLUSIONS: To the best of our knowledge, this is the third documented case of a clinical W. viridescens isolate worldwide and the first for which a genome sequence is publicly available. Therefore, its genome constitutes a valuable resource for fundamental research on rare infectious agents of public health significance, as well as for the safety assessment and development of Weissella-based probiotics.