Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China.
Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China.
Mol Genet Genomics. 2019 Apr;294(2):417-430. doi: 10.1007/s00438-018-1514-6. Epub 2018 Nov 28.
Vibriocholerae, which is autochthonous to estuaries worldwide, can cause human cholera that is still pandemic in developing countries. A number of V. cholerae isolates of clinical and environmental origin worldwide have been subjected to genome sequencing to address their phylogenesis and bacterial pathogenesis, however, little genome information is available for V. cholerae isolates derived from estuaries, particularly in China. In this study, we determined the complete genome sequence of V. cholerae CHN108B (non-O1/O139 serogroup) isolated from the Yangtze River Estuary, China and performed comparative genome analysis between CHN108B and other eight representative V. cholerae isolates. The 4,168,545-bp V. cholerae CHN108B genome (47.2% G+C) consists of two circular chromosomes with 3,691 predicted protein-encoding genes. It has 110 strain-specific genes, the highest number among the eight representative V. cholerae whole genomes from serogroup O1: there are seven clinical isolates linked to cholera pandemics (1937-2010) and one environmental isolate from Brazil. Various mobile genetic elements (such as insertion sequences, prophages, integrative and conjugative elements, and super-integrons) were identified in the nine V. cholerae genomes of clinical and environmental origin, indicating that the bacterium undergoes extensive genetic recombination via lateral gene transfer. Comparative genomics also revealed different virulence and antimicrobial resistance gene patterns among the V. cholerae isolates, suggesting some potential virulence factors and the rising development of resistance among pathogenic V. cholerae. Additionally, draft genome sequences of multiple V. cholerae isolates recovered from the Yangtze River Estuary were also determined, and comparative genomics revealed many genes involved in specific metabolism pathways, which are likely shaped by the unique estuary environment. These results provide additional evidence of V. cholerae genome plasticity and will facilitate better understanding of the genome evolution and pathogenesis of this severe water-borne pathogen worldwide.
霍乱弧菌是世界范围内港湾地区的本土物种，可以引起人类霍乱，这种疾病在发展中国家仍然流行。为了研究其系统发育和细菌发病机制，全世界许多临床和环境来源的霍乱弧菌分离株都已经进行了基因组测序，然而，来自港湾地区的霍乱弧菌分离株，特别是中国港湾地区的霍乱弧菌分离株，其基因组信息却很少。在本研究中，我们测定了来自中国长江口的霍乱弧菌 CHN108B（非 O1/O139 血清群）的全基因组序列，并对 CHN108B 与其他 8 个有代表性的霍乱弧菌分离株进行了比较基因组分析。该 4168545bp 的霍乱弧菌 CHN108B 基因组（47.2%G+C）由两个圆形染色体组成，包含 3691 个预测的蛋白编码基因。它有 110 个菌株特异性基因，在 8 个 O1 血清群的有代表性的霍乱弧菌全基因组中是数量最多的：其中有 7 个临床分离株与霍乱大流行（1937-2010 年）有关，还有一个来自巴西的环境分离株。在这 9 个来自临床和环境的霍乱弧菌基因组中，发现了各种移动遗传元件（如插入序列、噬菌体、整合和共轭元件以及超级整合子），表明该细菌通过水平基因转移经历了广泛的遗传重组。比较基因组学还揭示了这些霍乱弧菌分离株之间不同的毒力和抗微生物药物耐药性基因模式，表明一些潜在的毒力因子和致病性霍乱弧菌中抗药性的上升发展。此外，还测定了从长江口采集的多个霍乱弧菌分离株的草图基因组序列，比较基因组学揭示了许多涉及特定代谢途径的基因，这些基因可能是由独特的港湾环境塑造的。这些结果为霍乱弧菌基因组可塑性提供了更多证据，并将有助于更好地了解这种严重的水源性病原体在全球的基因组进化和发病机制。
