Characterization and Genome Analysis of the Delftia lacustris Strain LzhVag01 Isolated from Vaginal Discharge

Abstract

Delftia has been separated from freshwater, sludge, and soil and has emerged as a novel opportunistic pathogen in the female vagina. However, the genomic characteristics, pathogenicity, and biotechnological properties still need to be comprehensively investigated. In this study, a Delftia strain was isolated from the vaginal discharge of a 43-year-old female with histologically confirmed cervical intraepithelial neoplasm (CIN III), followed by whole-genome sequencing. Phylogenetic analysis and average nucleotide identity (ANI) analysis demonstrated that it belongs to Delftia lacustris, named D. lacustris strain LzhVag01. LzhVag01 was sensitive to β-lactams, macrolides, and tetracyclines but exhibited resistance to lincoamines, nitroimidazoles, aminoglycosides, and fluoroquinolones. Its genome is a single, circular chromosome of 6,740,460 bp with an average GC content of 66.59%. Whole-genome analysis identified 16 antibiotic resistance-related genes, which match the antimicrobial susceptibility profile of this strain, and 11 potential virulence genes. These pathogenic factors may contribute to its colonization in the vaginal environment and its adaptation and accelerate the progression of cervical cancer. This study sequenced and characterized the whole-genome of Delftia lacustris isolated from vaginal discharge, which provides investigators and clinicians with valuable insights into this uncommon species.

Fig. 1

Morphological characteristics of LzhVag01. LzhVag01 displayed white colonies on the LB agar plate (a) and gram-negative rods by Gram staining (b). Scale bar = 25 μm

Fig. 2

Phylogenetic relationships of D. lacustris strain LzhVag01 with other type strains of Delftia species based on whole-genome sequences. LzhVag01 was highlighted with a red dot. GenBank accession numbers were listed in parentheses following the species names

Fig. 3

Circular representation of the genome of D. lacustris strain LzhVag01. Counting from the outside toward the center: circle 1 shows the genome size of LzhVag01, each scale represents 5 kb; circle 2 represents GC content; circles 3–4 indicates positive (red) and negative (green) strands genes of the genome; circles 5 displays the ncRNA on positive strands (blue); circles 6 refer to the ncRNA on negative strands (purple); circles 7 represent long segment repeat sequence information within genome (orange)

Fig. 4

Pan-genome analysis of Delftia species. a Flower plot of 17 Delftia species genomes showing the gene content of core genome (flower center) and strain-specific genes (flower petals). b The cumulative curves for the core and pan-genome of Delftia species. The curves showed the downward trend of the core gene families and the upward trend of the pan-gene families with the increase in the number of genomes

Fig. 5

Circular representation of the D. lacustris strain LzhVag01 genome and comparative genomics analysis with other Delftia strains generated by BRIG. Counting from the outside toward the center: circles 1–4 refer to regions of D. acidovorans ANG1 (green), D. tsuruhatensis ULwDis3 (yellow), D. tsuruhatensis strain TR1180 (pink) and D. lacustris strain LzhVag01 (red), where empty regions indicate parts without similar hits between them; circles 5 and 6 represent GC content and GC skew of LzhVag01, respectively

Fig. 6

COG categories of the genes in each strain. COG functional categories are described as follows: A, RNA processing and modification; B, Chromatin structure and dynamics; C, energy production and conversion; D, cell cycle control, cell division, chromosome partitioning; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; J, translation, ribosomal structure, and biogenesis; K, transcription; L, replication, recombination, and repair; M, cell wall/membrane/envelope biogenesis; N, cell motility; O, posttranslational modification, protein turnover, chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolite biosynthesis, transport, and catabolism; R, general function prediction only; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking, secretion, and vesicular transport; V, defense mechanisms; W, Extracellular structures; Z, Cytoskeleton