The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement

Despite high pertussis vaccine coverage, reported cases of whooping cough (pertussis) have increased over the last decade in the United States and other developed countries. Although is well known for its limited gene sequence variation, recent advances in long-read sequencing technology have begun...

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Published in:	Journal of bacteriology Vol. 199; no. 8; p. E00806
Main Authors:	Weigand, Michael R, Peng, Yanhui, Loparev, Vladimir, Batra, Dhwani, Bowden, Katherine E, Burroughs, Mark, Cassiday, Pamela K, Davis, Jamie K, Johnson, Taccara, Juieng, Phalasy, Knipe, Kristen, Mathis, Marsenia H, Pruitt, Andrea M, Rowe, Lori, Sheth, Mili, Tondella, M Lucia, Williams, Margaret M
Format:	Journal Article
Language:	English
Published:	United States American Society for Microbiology 15-04-2017
Subjects:	Bacteriology Bordetella pertussis Chromosomes, Bacterial - genetics Conserved Sequence Evolution Evolution, Molecular Gene Expression Profiling Gene Expression Regulation, Bacterial - genetics Gene Order - genetics Genes, Bacterial - genetics Genetic Linkage Genetic Variation - genetics Genome, Bacterial Genomes Gram-negative bacteria Phylogeny Vaccines Whooping cough whooping cough genomics Bordetella pertussis evolution pertussis rearrangement
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Summary:	Despite high pertussis vaccine coverage, reported cases of whooping cough (pertussis) have increased over the last decade in the United States and other developed countries. Although is well known for its limited gene sequence variation, recent advances in long-read sequencing technology have begun to reveal genomic structural heterogeneity among otherwise indistinguishable isolates, even within geographically or temporally defined epidemics. We have compared rearrangements among complete genome assemblies from 257 isolates to examine the potential evolution of the chromosomal structure in a pathogen with minimal gene nucleotide sequence diversity. Discrete changes in gene order were identified that differentiated genomes from vaccine reference strains and clinical isolates of various genotypes, frequently along phylogenetic boundaries defined by single nucleotide polymorphisms. The observed rearrangements were primarily large inversions centered on the replication origin or terminus and flanked by IS , a mobile genetic element with >240 copies per genome and previously suspected to mediate rearrangements and deletions by homologous recombination. These data illustrate that structural genome evolution in is not limited to reduction but also includes rearrangement. Therefore, although genomes of clinical isolates are structurally diverse, specific changes in gene order are conserved, perhaps due to positive selection, providing novel information for investigating disease resurgence and molecular epidemiology. Whooping cough, primarily caused by , has resurged in the United States even though the coverage with pertussis-containing vaccines remains high. The rise in reported cases has included increased disease rates among all vaccinated age groups, provoking questions about the pathogen's evolution. The chromosome of includes a large number of repetitive mobile genetic elements that obstruct genome analysis. However, these mobile elements facilitate large rearrangements that alter the order and orientation of essential protein-encoding genes, which otherwise exhibit little nucleotide sequence diversity. By comparing the complete genome assemblies from 257 isolates, we show that specific rearrangements have been conserved throughout recent evolutionary history, perhaps by eliciting changes in gene expression, which may also provide useful information for molecular epidemiology.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Citation Weigand MR, Peng Y, Loparev V, Batra D, Bowden KE, Burroughs M, Cassiday PK, Davis JK, Johnson T, Juieng P, Knipe K, Mathis MH, Pruitt AM, Rowe L, Sheth M, Tondella ML, Williams MM. 2017. The history of Bordetella pertussis genome evolution includes structural rearrangement. J Bacteriol 199:e00806-16. https://doi.org/10.1128/JB.00806-16.
ISSN:	0021-9193 1098-5530
DOI:	10.1128/jb.00806-16