LAUSR

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. Description Genomic analyses of Bordetella pertussis reveal spatial structure, rate of geographic spread, and fitness shifts in response to vaccine changes. Immunity-induced pathogen evolution Population immunity is thought to drive pathogen evolutionary dynamics, but this can be hard to measure. Considering the switch from whole-cell vaccines to acellular vaccines (ACVs) as a natural experiment, Lefrancq et al. analyzed the diversity of B. pertussis genome isolates from five continents to infer local changes in strain fitness after ACV introduction. Their analysis provides evidence that ACVs have led to the increased fitness of strains lacking the virulence factor pertactin and may have implications for understanding asymptomatic B. pertussis infection.