Identification and genomic characterization of Sphingomonas paucimobilis CL001
10.13200/j.cnki.cjb.004734
- VernacularTitle:少动鞘氨醇单胞菌（Sphingomonas paucimobilis）CL001的鉴定及基因组特征
- Author:
Xin ZHANG
- Publication Type:Journal Article
- Keywords:
Sphingomonas paucimobilis;
Microbiological contamination in cell cultures;
Species identification;
Whole genome sequencing(WGS);
Objectionable microorganism
- From:
Chinese Journal of Biologicals
2026;39(07):788-797+806
- CountryChina
- Language:Chinese
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Abstract:
Objective To conduct species-level identification of the laboratory-isolated contaminant strain CL001 and perform preliminary genomic characterization, providing a basis for subsequent contaminant source tracing.Methods Precise identification and preliminary genomic characterization of strain CL001 were performed through morphological observation,biochemical tests, 16S rRNA gene sequencing, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry(MALDI-TOF MS), and whole genome sequencing(WGS).Results The strain was identified as a non-fermenting Gramnegative bacterium(NFGNB) with biochemical characteristics consistent with the genus Sphingomonas. The highest sequence similarity of the 16S rRNA gene was found with the type strains of Sphingomonas paucimobilis and Facivitalis istanbulensis(2025). MALDI-TOF MS reported the strain as S.paucimobilis. WGS showed that the strain forms a phylogenetic branch with S. paucimobilis, with both average nucleotide identity(ANI) and digital DNA-DNA hybridization(dDDH) values above the species-level threshold, while those with other closely related species such as F.istanbulensis were below the species-level threshold. Antimicrobial susceptibility testing revealed drug resistance. Database annotation via Cluster of Orthologous Groups of proteins(COG) and Kyoto Encyclopedia of Genes and Genomes(KEGG) identified 2 858 and 2 258 functional genes, respectively. Comprehensive Antibiotic Resistance Database(CARD) predicted the acquisition of the distant-related resistance gene adeF(identity 43. 4%), and Virulence Factors Database(VFDB) predicted the virulence gene acpXL(identity81. 3%).Conclusion Through polyphasic identification involving phenotypic(morphology, biochemistry, MALDI-TOF MS),16S rRNA gene, and WGS analyses, contaminant strain CL001 was identified as S.paucimobilis, the most common human opportunistic pathogen among Sphingomonas spp., which is identified as an objectionable microorganism designated by the Chinese Pharmacopoeia(VolumeⅣ, 2025 edition) for non-sterile aqueous-based products. The strain′s genomic sequence and functional gene annotations(including virulence factors) have been submitted to the NCBI database, obtaining GenBank accession number: GCA＿050971725.1. This strain can be utilized for subsequent contamination source tracing and quality control.
