Bordetella pertussis nanopore sequencing

Long read sequencing offers the potential to construct single contig assemblies for complex genomes, such as the highly repetitive genome of the pathogen which causes whooping cough, Bordetella pertussis. Several hundred Insertion Sequence element copies in the B. pertussis genome have meant that full genome resolution has not been possible using reads shorter than 1000bp. We have conducted nanopore long read sequencing of several B. pertussis strains from the United Kingdom's 2012 outbreak, enabling the construction of closed, single contig assemblies for each. These closed genomes allowed visualisation and confirmation of extensive inter-strain genomic rearrangements, which had previously been predicted by Pulsed Field Gel Electrophoresis typing. Going forwards, long read sequencing may allow us to understand phenotypic differences between closely-related strains in this resurging pathogen.