Comparative Omics Analysis of Historic and Recent Isolates of Bordetella pertussis and Effects of Genome Rearrangements on Evolution

Abstract

Despite high vaccination coverage, pertussis is increasing in many industrialized countries, including the Czech Republic. To better understand Bordetella pertussis resurgence, we analyzed historic strains and recent clinical isolates by using a comparative omics approach. Whole-genome sequencing showed that historic and recent isolates of B. pertussis have substantial variation in genome organization and form separate phylogenetic clusters. Subsequent RNA sequence analysis and liquid chromatography with mass tandem spectrometry analyses showed that these variations translated into discretely separated transcriptomic and proteomic profiles. When compared with historic strains, recent isolates showed increased expression of flagellar genes and genes involved in lipopolysaccharide biosynthesis and decreased expression of polysaccharide capsule genes. Compared with reference strain Tohama I, all strains had increased expression and production of the type III secretion system apparatus. We detected the potential link between observed effects and insertion sequence element–induced changes in gene context only for a few genes.

Comparative genomics of Bordetella pertussis isolates from New Zealand, a country with an uncommonly high incidence of whooping cough

“…The benefits of closed genome sequences for comparative genomics are demonstrated by the ability to group isolates not only by allelic profile, but also by genomic arrangement type. With a growing number of closed genome sequences to which the arrangement of future isolates can be compared, along with evidence that differences in genomic arrangement may influence the phenotypic behaviour of isolates [15], the ability to easily produce closed genome sequences is becoming increasingly useful. Finally, we were able to use the closed genome sequences to predict pertactin deficiency; in light of globally increasing antigen deficiency, this ability, particularly in the absence of live B. pertussis cells, could be especially beneficial in adding to our understanding of this ongoing trend.…”

“…A final genomic phenomenon, which has become apparent over the last decade, is the existence of a large number of different genome arrangements in circulating B. pertussis isolates. There is some evidence, such as the work of Dienstbier et al [15], that different genomic arrangements have different transcriptomic profiles. Isolates with different genomic arrangements may therefore also vary phenotypically.…”

“…There is some evidence, such as the work of Dienstbier et al . [15], that different genomic arrangements have different transcriptomic profiles. Isolates with different genomic arrangements may therefore also vary phenotypically.…”

Pathogenicity and virulence of Bordetella pertussis and its adaptation to its strictly human host

“…A recent comparison of the genomes of 469 US strains showed 107 unique chromosome structures [ 275 ], with little diversity at the sequence level, indicating that structural rearrangement is also an important source of variability between strains. Chromosomal rearrangements can affect gene expression and may influence the phenotype, as shown in a recent study [ 276 ]. Adaptation of B. pertussis by genome rearrangement is only just beginning to be understood and its true significance will have to be evaluated through in vitro and in vivo experiments.…”

JMM Profile: Bordetella pertussis and whooping cough (pertussis): still a significant cause of infant morbidity and mortality, but vaccine-preventable

“…B. pertussis strains not expressing pertactin and more rarely not expressing PT and FHA [6,7]. The species shows low genetic diversity by gene content, but long-read whole-genome sequencing technologies have revealed previously unrecognised diversity caused through rearrangements which can affect the expression of virulence factors [8,9].…”