Comparative genomics of isolates from New Zealand, a country with an uncommonly high incidence of whooping cough.

Whooping cough, the respiratory disease caused by , has undergone a wide-spread resurgence over the last several decades. Previously, we developed a pipeline to assemble the repetitive genome into closed sequences using hybrid nanopore and Illumina sequencing. Here, this sequencing pipeline was used to conduct a more high-throughput, longitudinal screen of 66 strains isolated between 1982 and 2018 in New Zealand.