Duplications drive diversity inBordetella pertussison an underestimated scale

Abstract

Bacterial genetic diversity is often described using solely base pair changes despite a wide variety of other mutation types likely being major contributors. Tandem duplications of genomic loci are thought to be widespread among bacteria but due to their often intractable size and instability, comprehensive studies of the range and genome dynamics of these mutations are rare. We define a methodology to investigate duplications in bacterial genomes based on read depth of genome sequence data as a proxy for copy number. We demonstrate the approach with Bordetella pertussis, whose insertion sequence element-rich genome provides extensive scope for duplications to occur. Analysis of genome sequence data for 2430 B. pertussis isolates identified 272 putative duplications, of which 94% were located at 11 hotspot loci. We demonstrate limited phylogenetic connection for the occurrence of duplications, suggesting unstable and sporadic characteristics. Genome instability was further described in-vitro using long read sequencing via the Nanopore platform. Clonally derived laboratory cultures produced heterogenous populations containing multiple structural variants. Short read data was used to predict 272 duplications, whilst long reads generated on the Nanopore platform enabled the in-depth study of the genome dynamics of tandem duplications in B. pertussis. Our work reveals the unrecognised and dynamic genetic diversity of B. pertussis and, as the complexity of the B. pertussis genome is not unique, highlights the need for a holistic and fundamental understanding of bacterial genetics.

Genomic surveillance and improved molecular typing ofBordetella pertussisusing wgMLST

“…An allele-based approach to strain characterization cannot resolve chromosome structure variation, which provides a significant source of genomic diversity among circulating B. pertussis (14,15,43). Genomes of B. pertussis clinical isolates exhibit frequent rearrangement, most often as large inversions, but more recently also amplifications (28,44). It remains unclear whether such structural forms of genomic variation yield phenotypes, such as varied transmission or clinical disease presentation, but observed patterns among circulating isolates compared to common reference strains suggests they are under selection (45).…”

A Mutation Upstream of the rplN-rpsD Ribosomal Operon Downregulates Bordetella pertussis Virulence Factor Production without Compromising Bacterial Survival within Human Macrophages

“…Nonetheless, the genome of B. pertussis harbors numerous copies (up to ∼240 copies) of the IS 481 insertion element, and recombination events between them generate a highly variable chromosomal architecture of the clinical isolates ( 12 , 13 ). It remains to be determined whether this fluidity of genome organization and occasional duplication of portions of the genome enhance bacterial fitness and enable the bacterium to dynamically adapt to the selective pressure of the environment within host airways ( 11 , 13 – 16 ).…”