| Title: |
Global evolutionary patterns of Yersinia pestis and its spread into Africa |
| Authors: |
Mas Fiol, Guillem; Lemoine, Frédéric; Mornico, Damien; Bouvier, Guillaume; Andrades Valtueña, Aida; Duchene, Sebastian; Campagne, Pascal; Balière, Charlotte; Kwasiborski, Aurelia; Caro, Valérie; Beau, Rémi; Savin, Cyril; Céspedes, Manuel; Rajerison, Minoarisoa; Shako, Jean-Christophe; Carniel, Elisabeth; Slavin, Philip; Rascovan, Nicolás; Pizarro-Cerdá, Javier |
| Contributors: |
Yersinia; Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047); Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS); Centre collaborateur de l'OMS Yersinia - WHO Collaborating Center Yersinia (CC-OMS / WHO-CC); Institut Pasteur Paris (IP)-Organisation Mondiale de la Santé / World Health Organization Office Genève, Suisse (OMS / WHO)-Université Paris Cité (UPCité); Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB; Institut Pasteur Paris (IP)-Université Paris Cité (UPCité); Paléogénomique microbienne - Microbial paleogenomics; Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité); Bioinformatique structurale - Structural Bioinformatics; Max-Planck-Institut für evolutionäre Anthropologie = Max Planck Institute for Evolutionary Anthropology (MPI-EVA); Max-Planck-Gesellschaft; Dynamiques évolutives des maladies infectieuses / Evolutionary dynamics of infectious diseases; Environnement et Risques infectieux - Environment and Infectious Risks (ERI); Centre National de Référence de la Peste et autres Yersinioses - National Reference Center Plague and Yersinioses (CNR); National Health Institute of Perù Lima (INS); Institut Pasteur de Madagascar; Pasteur Network (Réseau International des Instituts Pasteur); Ministère de la santé publique, hygiène et prévention Kinshasa, RDC; University of Stirling; This work was supported by the French government Agence Nationale de la Recherche - ASTRID program (project ANR-18-ASTR-0004). GMF received a PhD fellowship by the Institut Pasteur and the DGA, as well as from the Université Paris Cité through the EUR G.E.N.E. Doctoral School (project ANR-17-EURE-0013). AAV was supported by the EMBO Scientific Exchange grant (nr. 9482) and the Max Planck Society. NR received funding by the ERC-2020-STG - PaleoMetAmerica – 948800 grant and Investissement d’Avenir grant ANR- 16-CONV- 0005 (INCEPTION program). This work was also supported by the Pasteur Network (Pasteur International Unit ’Plague: Evolution, Spread and Maintenance) and LabEx IBEID (grant ANR-10-LABX-62-IBEID).; We thank François-Xavier Weill, Eduardo Rocha, Julian Parkhill, Sandra Reuter, Kate Baker, and Hendrik Poinar for critical comments during the development of this project; all other members of the Yersinia Unit the Institut Pasteur for helpful discussions throughout the course of this study; Sylvie Brémont for the assistance in the recovery of isolates of old Y. pestis collections. This work stems from the collabo- rative heritage of the historical collection of isolates that have been recovered and sent from diverse sources over the past century by many different actors, to which we are grateful. We would like to acknowledge the GPU lab of the INCEPTION program and the HPC Core Facility of Institut Pasteur for providing access and support to use computing resources.; ANR-18-ASTR-0004,CARTO-PEST,Caractérisation et cartographie de la diversité génétique de Yersinia pestis(2018); ANR-17-EURE-0013,GENE,Génétique et Epigénétique Nouvelle Ecole(2017); ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016); ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010); European Project: 948800,ERC-2020-STG,ERC-2020-STG,PaleoMetAmerica(2020) |
| Source: |
https://hal.science/hal-05132518 ; 2024. |
| Publisher Information: |
CCSD |
| Publication Year: |
2024 |
| Subject Terms: |
[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology |
| Description: |
International audience ; The zoonotic pathogen Yersinia pestis , the etiologic agent of plague, has caused three major pandemics and diversified in different lineages currently established in endemic areas worldwide 1–3 . However, some regions like continental Africa have been poorly covered within the global diversity and epidemiological history of this pathogen 2,4–6 . Here, we report the whole-genome sequences of 1,124 Y. pestis isolates collected from endemic areas worldwide over 116 years, nearly doubling the available genomic data for the species. By integrating population genomics and historical research, we retrace the introduction of multiple Y. pestis lineages into continental Africa, revealing the diversity of the 1.ANT lineage, its historical emergence and its spread to and within Africa since the late 17th century. We identify key mechanisms of genome evolution, including signatures of adaptive evolution present in virulence and biofilm-related genes such as RovA, a master virulence regulator, which likely play a role in the pathogen’s adaptation and endemic persistence. Additionally, our findings reveal an increased trajectory of genome degradation and expansion of IS elements in different lineages. This trend appears especially pronounced in 1.ANT genomes, promoting the remarkable genomic variation within this lineage. Taken together, our findings shed light on the introduction and evolutionary history of plague in Africa and provide a comprehensive framework for understanding the global diversity and genome evolution of Y. pestis , revealing potential factors contributing to its long-term adaptation in endemic areas. |
| Document Type: |
report |
| Language: |
English |
| Relation: |
info:eu-repo/grantAgreement//948800/EU/A microbial perspective of major historical events in the Southern Cone of the Americas/PaleoMetAmerica; BIORXIV: 2024.11.26.625443 |
| DOI: |
10.1101/2024.11.26.625443 |
| Availability: |
https://hal.science/hal-05132518; https://hal.science/hal-05132518v1/document; https://hal.science/hal-05132518v1/file/Mas%20Fiol%20et%20al%202024.pdf; https://doi.org/10.1101/2024.11.26.625443 |
| Rights: |
http://creativecommons.org/licenses/by-nc-nd/ ; info:eu-repo/semantics/OpenAccess |
| Accession Number: |
edsbas.780CE379 |
| Database: |
BASE |