Tonight, I watched Sarah Cameron from the University of Bath in the UK present at London Calling 2024 on “100 years of Bordetella pertussis evolution in the UK. I had watched a similar session and wanted to learn more. Cameron noted that in 2001, the whole-cell vaccine from 1957 was replaced with an acellular vaccine (ACV) with 4-5 antigens from this bacterium. However, since the introduction of the ACV, immunity has waned, and new cases have been identified, including an ongoing outbreak in the UK. The organism has several repetitive regions, about ~1 kb and>240 copies. This study aimed to sequence 198 strains isolated between 1920-2020, including 87 strains from the pre-vaccine era. Cameron explained that the primary mechanism of variation is the loss and gain of sequences. Cameron sequenced all the strains with the V14 chemistry with the Rapid Barcoding Kit v14 24. They used Super Accurate Basecalling (SUP) with Dorado duplex. Genome assemblies were assessed with BUSCO >95%. The pangenome analysis of B. pertussis isolated in the UK identified a region of ~24 kb that is different in the whole vaccine era (“ROD D“). The growth of the isolates with this region is different. B. pertussis with ROD D seems to grow faster and be from the pre-vaccine/whole cell vaccine era. Has this region been lost in newer strains? Currently, Cameron is working on deleting this region from strains that have it and transforming isolates that don’t have it to assess its function. Cameron assembled single contig high-quality genomes with Flye and then used ggCaller to analyze the pangenome. I noticed they used Dorado and duplex. I will try some of their methods for Comamonas.
