As with other pathogens, competitive interactions between Bordetella pertussis strains drive infection risk. Vaccines are thought to perturb strain diversity through shifts in immune pressures; however, this has rarely been measured because of inadequate data and analytical tools. We used 3344 sequences from 23 countries to show that, on average, there are 28.1 transmission chains circulating within a subnational region, with the number of chains strongly associated with host population size. It took 5 to 10 years for B. pertussis to be homogeneously distributed throughout Europe, with the same time frame required for the United States. Increased fitness of pertactin-deficient strains after implementation of acellular vaccines, but reduced fitness otherwise, can explain long-term genotype dynamics. These findings highlight the role of vaccine policy in shifting local diversity of a pathogen that is responsible for 160,000 deaths annually.

Centre for Infectious Disease Control National Institute for Public Health and the Environment 3720 BA Bilthoven Netherlands

Centre for Research and Development Uppsala University Region Gävleborg 80187 Gävle Sweden

Department of Genetics University of Cambridge Cambridge CB2 3EH UK

Department of Infectious Diseases Istituto Superiore di Sanità IT 00161 Rome Italy

Department of Microbiology Immunology and Transplantation Rega Institute KU Leuven 3000 Leuven Belgium

Department of Microbiology National Reference Centre for Bordetella pertussis Universitair Ziekenhuis Brussel Vrije Universiteit Brussel B 1090 Brussels Belgium

Department of Veterinary Medicine University of Cambridge Cambridge CB3 0ES UK

Immunisation and Countermeasures Division Public Health England National Infection Service London NW9 5EQ UK

InFLAMES Research Flagship Center University of Turku FI 20520 Turku Finland

Insitut Pasteur Université Paris Cité Mathematical Modelling of Infectious Diseases Unit UMR2000 CNRS 75015 Paris France

Institut Pasteur Université Paris Cité Biodiversity and Epidemiology of Bacterial Pathogens 75724 Paris France

Molecular Microbiology Laboratory Children's Health Ireland Crumlin D12 N512 Dublin Ireland

National Institute of Public Health Department of Infectious Diseases Epidemiology CZ 10000 Prague Czech Republic

National Institute of Public Health National Reference Laboratory for Pertussis and Diphtheria 100 00 Prague Czech Republic

National Reference Center for Whooping Cough and Other Bordetella Infections 75724 Paris France

Norwegian Institute of Public Health Department of Infectious Disease Control and Vaccine N 0213 Oslo Norway

Respiratory and Vaccine Preventable Bacteria Reference Unit Public Health England National Infection Service London NW9 5EQ UK

Statens Serum Institut Bacteria Parasites and Fungi Infectious Disease Preparedness 2300 Copenhagen Denmark

The Public Health Agency of Sweden Unit for Laboratory Surveillance of Bacterial Pathogens SE 171 82 Solna Sweden

Universitat Autònoma de Barcelona Department of Genetics and Microbiology 08193 Barcelona Spain

Université Paris Cité Department of General Paediatrics and Paediatric Infectious Diseases Necker Enfants Malades Hospital APHP 75015 Paris France

University Hospital Vall d'Hebron Microbiology Department 08035 Barcelona Spain

University of Turku UTU Institute of Biomedicine Research Center for Infections and Immunity FI 20520 Turku Finland

References provided by Crossref.org

Effectiveness of one and two doses of acellular pertussis vaccines against laboratory-confirmed pertussis requiring hospitalisation in infants: Results of the PERTINENT sentinel surveillance system in six EU/EEA countries, December 2015 - December 2019