IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-60782-6.html
   My bibliography  Save this article

In-host evolution of Yersinia enterocolitica during a chronic human infection

Author

Listed:
  • Cyril Savin

    (Yersinia Research Unit
    Yersinia National Reference Laboratory
    WHO Collaborating Research and Reference Centre for Plague FRA-146)

  • Pierre Lê-Bury

    (Yersinia Research Unit
    WHO Collaborating Research and Reference Centre for Plague FRA-146
    Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT/UMRS1184))

  • Julien Guglielmini

    (Biostatistics and Bioinformatics Hub)

  • Thibaut Douché

    (Mass Spectrometry for Biology Unit)

  • Guillem Mas Fiol

    (Yersinia Research Unit
    WHO Collaborating Research and Reference Centre for Plague FRA-146)

  • Rodolphe Buzelé

    (CHRU de Tours
    CHRU de Tours
    CH Yves Le Foll)

  • Cécile Brun

    (CHRU de Tours)

  • Frédéric Bastides

    (CHRU de Tours)

  • Maud François

    (CHRU de Tours)

  • Béatrice Birmelé

    (CHRU de Tours)

  • Laura Guichard

    (Yersinia Research Unit
    Yersinia National Reference Laboratory)

  • Julien Madej

    (Yersinia Research Unit
    Yersinia National Reference Laboratory)

  • Rémi Beau

    (Yersinia Research Unit
    Yersinia National Reference Laboratory)

  • Nicolas Cabanel

    (Yersinia Research Unit
    Yersinia National Reference Laboratory)

  • Laurent Dortet

    (Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT/UMRS1184)
    Service de Bactériologie-Hygiène
    Centre National de Référence Associé de la Résistance aux Antibiotiques)

  • Mariette Matondo

    (Mass Spectrometry for Biology Unit)

  • Olivier Dussurget

    (Yersinia Research Unit
    WHO Collaborating Research and Reference Centre for Plague FRA-146)

  • Elisabeth Carniel

    (Yersinia Research Unit
    Yersinia National Reference Laboratory)

  • Philippe Lanotte

    (CHRU de Tours
    UMR1282)

  • Javier Pizarro-Cerdá

    (Yersinia Research Unit
    Yersinia National Reference Laboratory
    WHO Collaborating Research and Reference Centre for Plague FRA-146)

Abstract

Bacteria exhibit remarkable adaptability in response to selective pressures encountered during infection and antibiotic treatment. We characterize four Yersinia enterocolitica clonal isolates from successive bacteremia episodes that evolved within an elderly patient over 14 years. Their common evolution is characterized by a genome size reduction resulting in the loss of about a hundred genes and a so far undescribed deletion in the DNA gyrase gene gyrA conferring quinolone resistance. Third-generation cephalosporin resistance of the last isolate correlates with a truncation of OmpF in synergy with an increased production of BlaA and AmpC β-lactamases. A strong proteome remodeling of the isolates reveals a perturbed stringent response, as well as impaired metabolism which substantiate their severe growth defects in vitro, accounting for antibiotics tolerance and possibly therapeutic failure. This study documents previously unreported genetic and phenotypic changes associated with in-host adaptation of a pathogenic Yersinia species under antibiotic pressure.

Suggested Citation

  • Cyril Savin & Pierre Lê-Bury & Julien Guglielmini & Thibaut Douché & Guillem Mas Fiol & Rodolphe Buzelé & Cécile Brun & Frédéric Bastides & Maud François & Béatrice Birmelé & Laura Guichard & Julien M, 2025. "In-host evolution of Yersinia enterocolitica during a chronic human infection," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-60782-6
    DOI: 10.1038/s41467-025-60782-6
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-60782-6
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-60782-6?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Alpha Kabinet Keita & Fara R. Koundouno & Martin Faye & Ariane Düx & Julia Hinzmann & Haby Diallo & Ahidjo Ayouba & Frederic Le Marcis & Barré Soropogui & Kékoura Ifono & Moussa M. Diagne & Mamadou S., 2021. "Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks," Nature, Nature, vol. 597(7877), pages 539-543, September.
    2. Xiongqi Ding & Catherine Robbe-Masselot & Xiali Fu & Renaud Léonard & Benjamin Marsac & Charlene J. G. Dauriat & Agathe Lepissier & Héloïse Rytter & Elodie Ramond & Marion Dupuis & Daniel Euphrasie & , 2023. "Airway environment drives the selection of quorum sensing mutants and promote Staphylococcus aureus chronic lifestyle," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    3. Guillaume Gautreau & Adelme Bazin & Mathieu Gachet & Rémi Planel & Laura Burlot & Mathieu Dubois & Amandine Perrin & Claudine Médigue & Alexandra Calteau & Stéphane Cruveiller & Catherine Matias & Chr, 2020. "PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph," PLOS Computational Biology, Public Library of Science, vol. 16(3), pages 1-27, March.
    4. Vanina Dengler Haunreiter & Mathilde Boumasmoud & Nicola Häffner & Dennis Wipfli & Nadja Leimer & Carole Rachmühl & Denise Kühnert & Yvonne Achermann & Reinhard Zbinden & Stefano Benussi & Clement Vul, 2019. "In-host evolution of Staphylococcus epidermidis in a pacemaker-associated endocarditis resulting in increased antibiotic tolerance," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    5. Zhi-xue Cheng & Chang Guo & Zhuang-gui Chen & Tian-ci Yang & Jian-ying Zhang & Jie Wang & Jia-xin Zhu & Dan Li & Tian-tuo Zhang & Hui Li & Bo Peng & Xuan-xian Peng, 2019. "Glycine, serine and threonine metabolism confounds efficacy of complement-mediated killing," Nature Communications, Nature, vol. 10(1), pages 1-17, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Liu, Fangzhou & Xue, Dong & Yu, Xinghu & Zhao, Zhihong & Lin, Shiying & Zhuang, Songlin & del Genio, Charo I. & Boccaletti, Stefano & Gao, Huijun, 2025. "Flexible mitigation of epidemics by transport management," Chaos, Solitons & Fractals, Elsevier, vol. 194(C).
    2. Mostafa Bentahir & Mamadou Diouldé Barry & Kekoura Koulemou & Jean-Luc Gala, 2022. "Providing On-Site Laboratory and Biosafety Just-In-Time Training Inside a Box-Based Laboratory during the West Africa Ebola Outbreak: Supporting Better Preparedness for Future Health Emergencies," IJERPH, MDPI, vol. 19(18), pages 1-13, September.
    3. Lucie Semenec & Amy K. Cain & Catherine J. Dawson & Qi Liu & Hue Dinh & Hannah Lott & Anahit Penesyan & Ram Maharjan & Francesca L. Short & Karl A. Hassan & Ian T. Paulsen, 2023. "Cross-protection and cross-feeding between Klebsiella pneumoniae and Acinetobacter baumannii promotes their co-existence," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    4. Guilhem Royer & Olivier Clermont & Julie Marin & Bénédicte Condamine & Sara Dion & François Blanquart & Marco Galardini & Erick Denamur, 2023. "Epistatic interactions between the high pathogenicity island and other iron uptake systems shape Escherichia coli extra-intestinal virulence," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    5. S. A. Riesle-Sbarbaro & G. Wibbelt & A. Düx & V. Kouakou & M. Bokelmann & K. Hansen-Kant & N. Kirchoff & M. Laue & N. Kromarek & A. Lander & U. Vogel & A. Wahlbrink & D. M. Wozniak & D. P. Scott & J. , 2024. "Selective replication and vertical transmission of Ebola virus in experimentally infected Angolan free-tailed bats," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    6. Michael J. Tisza & Derek D. N. Smith & Andrew E. Clark & Jung-Ho Youn & Pavel P. Khil & John P. Dekker, 2023. "Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    7. Joseph Akoi Boré & Joseph W. S. Timothy & Tom Tipton & Ifono Kekoura & Yper Hall & Grace Hood & Stephanie Longet & Kimberly Fornace & Millimono S. Lucien & Sarah Katarina Fehling & Beatrice K. Koivogu, 2024. "Serological evidence of zoonotic filovirus exposure among bushmeat hunters in Guinea," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    8. Erica J. Zheng & Ian W. Andrews & Alexandra T. Grote & Abigail L. Manson & Miguel A. Alcantar & Ashlee M. Earl & James J. Collins, 2022. "Modulating the evolutionary trajectory of tolerance using antibiotics with different metabolic dependencies," Nature Communications, Nature, vol. 13(1), pages 1-11, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-60782-6. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.