Culture independent multiplex amplicon and metagenomic sequencing of B. pertussis

Whooping cough (pertussis) has re-emerged despite high vaccine coverage in Australia and many other countries worldwide, partly attributable to genetic adaptation of the causative organism, Bordetella pertussis, to vaccines. Therefore, genomic surveillance has become essential to monitor circulating strains for these changes. However, increasing uptake of PCR for diagnosis of pertussis has affected availability of cultured isolates for typing. In this study, we evaluated the use of targeted multiplex PCR (mPCR) amplicon sequencing and shotgun metagenomic sequencing for culture independent typing of B. pertussis directly in respiratory swabs.