1例老年感染血流及腹腔分离O1群非产毒霍乱弧菌全基因组特征

Whole-genome characteristics of non-toxigenic Vibrio cholerae O1 isolated from blood and ascites of 1 old patient with infections

    摘要
  • 摘要:
    目的 分析1例患者同时从血液及腹腔中分离到的O1群霍乱弧菌非产毒株(HL01和HL02)的基因组特征。
    方法 2024年7月，在南昌大学第一附属医院感染科病房的1例老年患者的血液和腹水中分离出霍乱弧菌菌株(HL01、HL02)。使用全自动药敏分析仪测定菌株的抗菌药物敏感性，使用二代基因测序获得菌株的完整基因组序列，使用BLAST在线比对与综合抗生素抗性数据库、耐药基因预测数据库Resfinder等数据库进行比对分析，明确菌株携带的耐药基因、毒力基因等。基于基因组单核苷酸多样性，使用jolytree构建系统发育树，中值法定根。使用fastANI分别计算HL01和HL02与这146个基因组的核苷酸进行基因组相似性比对。
    结果 两株均为O1群非产毒霍乱弧菌，多位点序列分型(MLST)为ST167型，携带了多个毒力相关基因，该菌对头孢唑林和多黏菌素耐药。结合基因组进化关系发现，菌株间携带耐药基因和耐药质粒的情况呈现出一定聚集性。菌株HL01和HL02的传统ST型为ST167, cgMLST型为与cgMLST-960最接近的新型别，两株菌基因组高度同源。系统发育树表明两株霍乱弧菌与从水生环境中分离的霍乱弧菌菌株密切相关。
    结论 HL01和HL02虽不携带ctxAB毒力基因，但存在多种毒力因子致病，因此需对肠道外分离的O1/O139霍乱弧菌进行持续监测，全基因组分析是必要的。

     

    Abstract:
    OBJECTIVE To analyze the genomic characteristics of non-toxigenic Vibrio cholerae O1 (HL01 and HL02) isolated simultaneously from the blood and abdominal cavity of a patient.
    METHODS In Jul. 2024, Vibrio cholerae strains (HL01 and HL02) were isolated from the blood and ascites of an elderly patient in the Infectious Diseases Ward of the First Affiliated Hospital of Nanchang University. The antimicrobial susceptibility of the strains was determined with an automated susceptibility analyzer. The complete genomic sequences of the strains were obtained through next-generation gene sequencing. Online BLAST alignment was performed with comprehensive antibiotic resistance database, resistance gene prediction database Resfinder and other databases to identify the resistance genes and virulence genes carried by the strains. Based on genomic single-nucleotide diversity, a phylogenetic tree was constructed with Jolytree, with the median method used for rooting. FastANI was employed to calculate the genomic similarity by comparing the nucleotides of HL01 and HL02 with those of 146 genomes.
    RESULTS Both strains were identified as non-toxigenic Vibrio cholerae O1, with multilocus sequence typing (MLST) classified as ST167. They carried multiple virulence-related genes and exhibited resistance to cefazolin and polymyxin. Based on genomic evolutionary relationships, it was found that the presence of resistance genes and resistance plasmids among the strains showed a certain degree of clustering. The traditional ST type of strains HL01 and HL02 was ST167, and their cgMLST type was a novel type closest to cgMLST-960. The genomes of the two strains were highly homologous. The phylogenetic tree indicated a close relationship between the two Vibrio cholerae strains and those isolated from aquatic environment.
    CONCLUSIONS Although HL01 and HL02 do not carry the ctxAB virulence gene, they possess multiple virulence factors that can cause disease. Therefore, continuous monitoring of O1/O139 Vibrio cholerae isolated from extraintestinal sites is necessary, and whole-genome analysis is essential.

     

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