{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,19]],"date-time":"2026-06-19T23:16:57Z","timestamp":1781911017347,"version":"3.54.5"},"reference-count":62,"publisher":"Microbiology Society","issue":"11","license":[{"start":{"date-parts":[[2025,11,14]],"date-time":"2025-11-14T00:00:00Z","timestamp":1763078400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"French Government\u2019s Investissement d\u2019Avenir grants","award":["ANR-10-LABX-62-IBEID"],"award-info":[{"award-number":["ANR-10-LABX-62-IBEID"]}]},{"name":"Spanish \u201cMinisterio de Econom\u00eda y Competitividad\u201d and \u201cInstituto de Salud Carlos III\u201d","award":["FIS PI18\/00703"],"award-info":[{"award-number":["FIS PI18\/00703"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,14]]},"abstract":"<jats:p>\n                    Pathogens adapting to the human host and to vaccination-induced immunity may follow parallel evolutionary paths.\n                    <jats:italic>Bordetella parapertussis<\/jats:italic>\n                    (\n                    <jats:italic>Bpp<\/jats:italic>\n                    ) contributes significantly to the burden of whooping cough (pertussis) and shares vaccine antigens with\n                    <jats:italic>Bordetella pertussis (Bp)<\/jats:italic>\n                    ; both pathogens are phylogenetically related and ecological competitors.\n                    <jats:italic>Bp<\/jats:italic>\n                    vaccine antigen-coding genes have accumulated variation, including pertactin (PRN) disruptions, after the introduction of acellular vaccines in the 1990s. We aimed to evaluate evolutionary parallelisms in\n                    <jats:italic>Bpp<\/jats:italic>\n                    , even though pertussis vaccines were designed against\n                    <jats:italic>Bp<\/jats:italic>\n                    . We sequenced 242\n                    <jats:italic>Bpp<\/jats:italic>\n                    isolates collected in France, the USA and Spain between 1937 and 2019, spanning pre-vaccine and two vaccines eras. We investigated the temporal evolution of\n                    <jats:italic>Bpp<\/jats:italic>\n                    sublineages using a Bayesian approach based on whole-genome SNPs and performed comparative genomic analyses focusing on antigen and virulence gene loci. The most recent common ancestor of all sequenced\n                    <jats:italic>Bpp<\/jats:italic>\n                    isolates was estimated around the year 1877, making it one of the youngest human pathogens, and the\n                    <jats:italic>Bpp<\/jats:italic>\n                    evolutionary rate we estimated (2.12\u00d710\n                    <jats:sup>\u22127<\/jats:sup>\n                    substitutions per site per year) was remarkably similar to the one previously reported for\n                    <jats:italic>Bp<\/jats:italic>\n                    (2.24\u00d710\n                    <jats:sup>\u22127<\/jats:sup>\n                    ). PRN antigen deficiency in\n                    <jats:italic>Bpp<\/jats:italic>\n                    was driven by 18 disruptive mutations, including deletion\n                    <jats:italic>prn<\/jats:italic>\n                    :\u0394G-1895 estimated to have occurred around 1998 and observed in 73.8 % (149\/202) of post-2007\n                    <jats:italic>Bpp<\/jats:italic>\n                    isolates. In addition, we detected two early (year ~1900) mutations in the\n                    <jats:italic>bvg<\/jats:italic>\n                    A-\n                    <jats:italic>fhaB<\/jats:italic>\n                    intergenic region, which controls multiple virulence factors including the filamentous haemagglutinin antigen. Gene clusters for pertussis toxin and fimbriae showed a surprising lack of gene decay. Our findings suggest early adaptation of\n                    <jats:italic>Bpp<\/jats:italic>\n                    to humans through modulation of the\n                    <jats:italic>bvgAS<\/jats:italic>\n                    regulon, and a rapid adaptation through the loss of PRN expression, representing a late evolutionary parallelism concomitant with acellular vaccination against whooping cough.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001544","type":"journal-article","created":{"date-parts":[[2025,11,14]],"date-time":"2025-11-14T18:16:11Z","timestamp":1763144171000},"source":"Crossref","is-referenced-by-count":1,"title":["No innocent bystanders: pertussis vaccination and evolutionary parallelisms between Bordetella parapertussis and Bordetella pertussis"],"prefix":"10.1099","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5947-6383","authenticated-orcid":false,"given":"Val\u00e9rie","family":"Bouchez","sequence":"first","affiliation":[{"name":"National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, Paris, France"},{"name":"Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3073-5046","authenticated-orcid":false,"given":"Albert","family":"Moreno-Mingorance","sequence":"additional","affiliation":[{"name":"CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain"},{"name":"Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4827-9824","authenticated-orcid":false,"given":"Alba","family":"Mir-Cros","sequence":"additional","affiliation":[{"name":"CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain"},{"name":"Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annie","family":"Landier","sequence":"additional","affiliation":[{"name":"National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, Paris, France"},{"name":"Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathalie","family":"Armatys","sequence":"additional","affiliation":[{"name":"National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, Paris, France"},{"name":"Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5440-7012","authenticated-orcid":false,"given":"Sophie","family":"Guillot","sequence":"additional","affiliation":[{"name":"National Reference Center for Whooping Cough and Other Bordetella Infections, Institut Pasteur, Paris, France"},{"name":"Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Teresa","family":"Mart\u00edn-G\u00f3mez","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, Hospital Universitari Vall d'Hebron, Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9608-2404","authenticated-orcid":false,"given":"Carla","family":"Rodrigues","sequence":"additional","affiliation":[{"name":"National Reference Center for Whooping Cough and Other 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