Evidence map›Paper›PMID 40866534›Full record

ArticleNature ecology & evolution2026

Wave succession in the pandemic clone of Vibrio parahaemolyticus driven by gene loss.

Chao Yang, Hongling Qiu, Sarah L Svensson, Chengpei Ni, Song Gao, Zhizhou Jia, Huiqi Wen, Li Xie, Wenxuan Xu, Yujiao Qin and 14 more

Abstract read
PubMed Publisher
In one paragraph

Article in Nature ecology & evolution, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

24 authors.

Chao Yang *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. cyang@siii.cas.cn.ORCID http://orcid.org/0000-0003-0626-0586
Hongling Qiu *State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Sarah L Svensson *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.ORCID http://orcid.org/0000-0002-3183-6084
Chengpei Ni *The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, China.
Song GaoThe Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, China.
Zhizhou JiaThe 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.
Huiqi WenThe 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.
Li XieThe 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.
Wenxuan XuThe 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.
Yujiao QinThe 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.
Shuzhu LinThe 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.
Jiancheng WangThe 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.
Yiquan ZhangDepartment of Clinical Laboratory, Nantong Third People's Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, China.
Yinghui LiShenzhen Center for Disease Control and Prevention, Shenzhen, China.
Min JiangShenzhen Center for Disease Control and Prevention, Shenzhen, China.
Xiaolu ShiShenzhen Center for Disease Control and Prevention, Shenzhen, China.
Qinghua HuShenzhen Center for Disease Control and Prevention, Shenzhen, China.
Zhemin ZhouKey Laboratory of Alkene-Carbon Fibers-Based Technology & Application for Detection of Major Infectious Diseases, Cancer Institute, Suzhou Medical College, Soochow University, Suzhou, China.ORCID http://orcid.org/0000-0001-9783-0366
Yanjie ChaoThe 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.ORCID http://orcid.org/0000-0002-5735-7954
Ruifu YangState Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, China.ORCID http://orcid.org/0000-0003-3219-7269
Yujun CuiState Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, China.ORCID http://orcid.org/0000-0001-7236-2412
Jaime Martinez-UrtazaDepartment of Genetics and Microbiology, Facultat de Biociències, Universitat Autònoma de Barcelona, Barcelona, Spain. Jaime.Martinez.Urtaza@uab.cat.ORCID http://orcid.org/0000-0001-6219-0418
Hui WangState Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China. huiwang@shsmu.edu.cn.ORCID http://orcid.org/0000-0003-2791-8981
Daniel FalushThe 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. daniel.falush@siii.cas.cn.ORCID http://orcid.org/0000-0002-2956-0795

Funding

National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund) 32270003
6 · The paper itself

Abstract

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.

Indexed as

Gene DeletionVibrio InfectionsVibrio parahaemolyticusBiofilmsHumansPandemicsPhylogenyVirulence

Identifiers

PMID40866534

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.