Adaptive evolution and global spread of macrolide-resistant Bordetella pertussis during the post-pandemic pertussis resurgence

Pertussis resurgence following the COVID-19 pandemic remains poorly understood. Here, we integrate global surveillance data with 8,117 Bordetella pertussis genomes from 35 countries to investigate the role of pathogen evolution. We identify substantial shifts in B. pertussis populations in China and Australia, alongside marked changes in multiple European countries. In China, resurgence is driven by the rapid expansion of a single macrolide- resistant clone, MR-MT28. Elsewhere, resurgence involves diverse, pre-pandemic polyphyletic strains. Australia and Europe show convergent antigenic changes, including a decline in pertactin-deficient strains, a rise in prn2 alleles, and rising macrolide resistance.

Notably, we detect post-pandemic international dissemination of MR-MT28 across four continents, with non-Chinese isolates belonging predominantly to a pertactin-deficient subclone. These findings reveal convergent and region-specific strain replacement, antigenic evolution and macrolide resistance, highlighting the key role of adaptive evolution in the global pertussis resurgence. The emergence and global spread of MR-MT28 underscore the urgent need for coordinated global surveillance.