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. New Zealand has a higher incidence of whooping cough than many other countries; usually at least twice as many cases per 100000 people as the USA and UK and often even higher, despite similar rates of vaccine uptake. To the best of our knowledge, these strains are the first New Zealand isolates to be sequenced. The analyses here show that, on the whole, genomic trends in New Zealand isolates, such as changing allelic profile in vaccine-related genes and increasing pertactin deficiency, have paralleled those seen elsewhere in the world. At the same time, phylogenetic comparisons of the New Zealand isolates with global isolates suggest that a number of strains are circulating in New Zealand, which cluster separately from other global strains, but which are closely related to each other. The results of this study add to a growing body of knowledge regarding recent changes to the genome, and are the first genetic investigation into isolates from New Zealand.