Yang Chao, Qiu Hongling, Svensson Sarah L, Ni Chengpei, Gao Song, Jia Zhizhou, Wen Huiqi, Xie Li, Xu Wenxuan, Qin Yujiao, Lin Shuzhu, Wang Jiancheng, Zhang Yiquan, Li Yinghui, Jiang Min, Shi Xiaolu, Hu Qinghua, Zhou Zhemin, Chao Yanjie, Yang Ruifu, Cui Yujun, Martinez-Urtaza Jaime, Wang Hui, Falush Daniel
The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
Nat Ecol Evol. 2025 Aug 27. doi: 10.1038/s41559-025-02827-z.
While spontaneous mutation and gene acquisition are well-established drivers of pathogen adaptation, the role of gene loss remains underexplored. Here we investigated the emergence and diversification of the pandemic clone of Vibrio parahaemolyticus through large-scale phylogenomic analysis of 8,684 global isolates. The pandemic clone rapidly acquired multiple marker genes and genomic islands, subsequently diverging into successive sublineages mediating independent waves of cross-country transmission, as also observed in Vibrio cholerae. Wave succession in the last two decades was driven by loss of putrescine utilization (Puu) genes, conferring phenotypic advantages for environmental adaptation (enhanced biofilm formation) and human transmission (increased cell adhesion and intestinal colonization and reduced virulence), consistent with the virulence trade-off hypothesis. We identified Puu-gene loss in several bacterial genera, with effects on biofilm and adhesion replicated in V. cholerae and Escherichia coli, suggesting convergent evolution and universal phenotypic effects. Our results highlight the indispensable role of gene loss in bacterial pathogen adaptation.
虽然自发突变和基因获得是病原体适应的既定驱动因素，但基因丢失的作用仍未得到充分探索。在这里，我们通过对8684株全球分离株进行大规模系统发育基因组分析，研究了副溶血性弧菌大流行克隆的出现和多样化。大流行克隆迅速获得了多个标记基因和基因组岛，随后分化为连续的亚谱系，介导了独立的跨国传播浪潮，霍乱弧菌也有类似情况。过去二十年中的浪潮演替是由腐胺利用（Puu）基因的丢失驱动的，这赋予了环境适应（增强生物膜形成）和人际传播（增加细胞粘附和肠道定植以及降低毒力）的表型优势，这与毒力权衡假说一致。我们在几个细菌属中发现了Puu基因的丢失，其对生物膜和粘附的影响在霍乱弧菌和大肠杆菌中得到了重现，表明存在趋同进化和普遍的表型效应。我们的结果突出了基因丢失在细菌病原体适应中的不可或缺的作用。
