Ultra-long nanopore reads uniquely demonstrate genome plasticity in Bordetella pertussis

Jonathan and his team research genome plasticity (via homologous recombination within genome) in Bordetella pertussis, the causative agent of whooping cough.

SVs in bacteria ‘happen much more frequently than SNPs’. Many bacteria (including B. pertussis) are very repetitive – mostly via insertion sequences that can replicate themselves.

Jonathan: Nanopore sequencing is ‘an excellent way’ of studying genome plasticity.

Very large duplicated regions can be identified via long-read sequencing of the full tandem array or sequencing of the unique junctions between repeat and genomic context.

Isolate UK54: short reads suggested 4 x 16 kb duplications; nanopore sequencing revealed dynamic population with 1, 4 and 5 copies of tandem array, sequenced end-to-end in single reads.

Isolate UK76: short reads found 2 copies of 300 kb locus; nanopore sequencing of junctions found ‘an extremely heterogeneous population’ featuring at least 20 different duplications at that locus + more mutations across the genome.

Jonathan: this genome plasticity is likely seen in many strains, ‘so if you work on a funny bacteria with a funny, repetitive genome, please get in touch’.