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.

长读长测序（Long read sequencing）有望为复杂基因组构建单重叠群组装（single contig assemblies），例如引发百日咳的病原菌——百日咳鲍特菌（Bordetella pertussis）的高度重复基因组。百日咳鲍特菌基因组中存在数百个插入序列元件（Insertion Sequence element）拷贝，这使得采用短于1000bp的测序读长无法实现全基因组解析。本研究针对英国2012年暴发疫情中的多株百日咳鲍特菌开展了纳米孔长读长测序（nanopore long read sequencing），成功为每株菌株构建了闭合式单重叠群组装。这些闭合基因组实现了对广泛存在的菌株间基因组重排的可视化与验证，而此类重排此前仅通过脉冲场凝胶电泳分型（Pulsed Field Gel Electrophoresis typing）得到预测。未来，长读长测序或可帮助我们解析这一复现性病原体中亲缘关系密切的菌株间的表型差异。