Whole genome analysis of a Non-O1, Non-O139 Vibrio cholerae isolate from a bacteremia case in Ho Chi Minh City

Non-O1/non-O139 Vibrio (V.) cholerae (NOVC) has emerged as a potential pathogen in patients with compromised health conditions[1]. We report the whole genome sequencing (WGS) of a rare NOVC sepsis isolate (GenBank Accession: GCF_051906115.1) from an 89-year-old male admitted to the Intensive Care Unit (ICU) with septic shock (lactate 6.61 mmol/L) digestive illness. The patient’s severe underlying cardiovascular comorbidities, including chronic mesenteric ischemia (superior mesenteric artery stenosis), significantly compromised his intestinal barrier, enabling rapid pathogen translocation and systemic infection. WGS identified the isolate as closest to Sequence Type (ST)-1565/ cgST-1986, a lineage circulated in South East Asia[2]. Its NOVC status was confirmed by the absence of the ctxA/B operon and O1/O139 clusters. Core genome single nucleotide polymorphism (SNP) phylogenetic dendrogram (Figure 1A, Supplementary Table 1) revealed clustering within a major monophyletic clade encompassing regional clinical strains and, significantly, all classical O1 and O139 pandemic reference strains. This suggests that our isolate shares a recent evolutionary background with highly virulent V. cholerae lineages, highlighting the broad pathogenic potential within this common ancestral pool.Figure 1: A: Gene circle map of Vibrio cholerae isolate from an 89-year-old male patient with septic shock complicated by digestive disease. B: Phylogenetic dendrogram of Vibrio cholerae strains in this study versus reference strains. J: Translation; A: RNA processing and modification; K: Transcription; L: Replication, recombination and repair; B: Chromatin structure and dynamics; D: Cell cycle control, cell division, chromosome partitioning; Y: Nuclear structure; V: Defense mechanisms; T: Signal transduction mechanisms; M: Cell wall/membrane/envelope biogenesis; N: Cell motility; Z: Cytoskeleton; W: Extracellular structures; U: Intracellular trafficking, secretion, and vesicular transport; O: Posttranslational modification, protein turnover, chaperones; X: Mobilome: prophages, transposons; C: Energy production and conversion; G: Carbohydrate transport and metabolism; E: Amino acid transport and metabolism; F: Nucleotide transport and metabolism; H: Coenzyme transport and metabolism; I: Lipid transport and metabolism; ribosomal structure and biogenesis; P: Inorganic ion transport and metabolism; Q: Secondary metabolites biosynthesis, transport and catabolism; R: General function prediction only; S: Function unknown.The functional analysis, summarized in the Circos map (Figure 1B) and virulence table (Table 1), provides the basis for virulence evaluation. The isolate possessed a potent pathogenic payload, including genes for RTX toxins and hemolysins, factors that facilitate tissue damage and epithelial breach. Crucially, complete Type III (T3SS) and Type VI (T6SS) Secretion Systems were detected. T3SS, known for degrading epithelial barriers, likely drove the widespread tissue damage and subsequent septic shock observed in our patient whose immunity and gut health has been compromised[3]. Further analysis indicated that the gene for the adherence protein MSHA pili (mshA) was structurally truncated, suggesting the isolate relies on alternative or compensatory adhesion mechanisms.Table 1: Virulence factor genes identified in the study.The isolate exhibited intermediate resistance to ciprofloxacin on phenotypic testing (Supplementary Table 2). This reduced susceptibility was supported by WGS detection of the plasmid-mediated quinolone resistance gene QnrVC5 and mutations in parC and parE genes[4,5]. Although resistance genes associated with meropenem and trimethoprim were present, the isolate remained phenotypically susceptible, underscoring the importance of combined genotype and phenotype assessment. In conclusion, our report provides WGS characterization of a highly virulent NOVC isolate linked to severe Intensive Care Unit infection. The presence of T3SS/T6SS and the close phylogenetic relationship to pandemic strains demonstrate that this isolate possesses high pathogenic potential, particularly when combined with patient vulnerability. We emphasize that WGS is essential for rapidly identifying and differentiating such highly virulent NOVC strains for clinical surveillance. Conflict of interest statement The authors declare that they have no conflict of interest. Ethical approval and patient’s consent to participate The research project is approved by Ethics Committee for Biomedical Research of Thong Nhat Hospital pursuant to Decision No. 462/QD-BVTN dated 8 April 2024 by the Director of Thong Nhat Hospital regarding the establishment of the Institutional Review Board (IRB) for Biomedical Research, and Approval Certificate no. 18/2025/CN-BVTN-HDDD signed on 10 March 2025. Participants provided written informed consent prior to taking part in the study. Funding The authors received no extramural funding for the study. Publisher’s note The Publisher of the Journal remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Edited by Pan Y, Lei Y, Zhang Q