Complete Genome Sequences of Four Different
            <i>Bordetella</i>
            sp. Isolates Causing Human Respiratory Infections

Weigand, Michael R.; Peng, Yanhui; Loparev, Vladimir N.; Batra, Dhwani; Bowden, Katherine E.; Cassiday, Pamela K.; Davis, Jamie K.; Johnson, Taccara; Juieng, Phalasy; Miner, Christine E.; Rowe, Lori A.; Sheth, Mili; Tondella, M. Lucia; Williams, Margaret M.

doi:10.1128/genomea.01080-16

“…U.S. isolates of other Bordetella species were selected from the CDC collection for sequencing across as many years as available, but with additional emphasis on those recovered after 2000 from patients presenting respiratory illness. A few isolates sequenced previously were also included (37,77,78). The present study featured new genome assemblies for 125 B. pertussis, 11 B. bronchiseptica, 60 B. holmesii, 78 B. parapertussis, 2 B. trematum, 1 B. hinzii, and 1 other Bordetella species isolate as outlined in Table S1.…”

Section: Methodsmentioning

confidence: 99%

Conserved Patterns of Symmetric Inversion in the Genome Evolution of Bordetella Respiratory Pathogens

Weigand

¹

,

Peng

²

,

Batra

³

et al. 2019

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Whooping cough (pertussis), primarily caused by Bordetella pertussis, has resurged in the United States, and circulating strains exhibit considerable chromosome structural fluidity in the form of rearrangement and deletion. The genus Bordetella includes additional pathogenic species infecting various animals, some even causing pertussis-like respiratory disease in humans; however, investigation of their genome evolution has been limited. We studied chromosome structure in complete genome sequences from 167 Bordetella species isolates, as well as 469 B. pertussis isolates, to gain a generalized understanding of rearrangement patterns among these related pathogens. Observed changes in gene order primarily resulted from large inversions and were only detected in species with genomes harboring multicopy insertion sequence (IS) elements, most notably B. holmesii and B. parapertussis. While genomes of B. pertussis contain >240 copies of IS481, IS elements appear less numerous in other species and yield less chromosome structural diversity through rearrangement. These data were further used to predict all possible rearrangements between IS element copies present in Bordetella genomes, revealing that only a subset is observed among circulating strains. Therefore, while it appears that rearrangement occurs less frequently in other species than in B. pertussis, these clinically relevant respiratory pathogens likely experience similar mutation of gene order. The resulting chromosome structural fluidity presents both challenges and opportunity for the study of Bordetella respiratory pathogens. IMPORTANCE Bordetella pertussis is the primary agent of whooping cough (pertussis). The Bordetella genus includes additional pathogens of animals and humans, including some that cause pertussis-like respiratory illness. The chromosome of B. pertussis has previously been shown to exhibit considerable structural rearrangement, but insufficient data have prevented comparable investigation in related species. In this study, we analyze chromosome structure variation in several Bordetella species to gain a generalized understanding of rearrangement patterns in this genus. Just as in B. pertussis, we observed inversions in other species that likely result from common mutational processes. We used these data to further predict additional, unobserved inversions, suggesting that specific genome structures may be preferred in each species.

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“…tuberculosis , revealing there was greater genetic diversity in both species than previously thought. This contributes to a growing literature demonstrating that quantifying diversity requires a comprehensive view of mutation types, not just the quantification of DNA base changes and gene gain/loss [7, 31, 43, 50].…”

Section: Discussionmentioning

confidence: 99%

Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in Bordetella pertussis and Mycobacterium tuberculosis

Abrahams

¹

,

Weigand

²

,

Ring

³

et al. 2022

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Bacterial genetic diversity is often described solely using base-pair changes despite a wide variety of other mutation types likely being major contributors. Tandem duplication/amplifications are thought to be widespread among bacteria but due to their often-intractable size and instability, comprehensive studies of these mutations are rare. We define a methodology to investigate amplifications 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 amplifications to occur. Analysis of data for 2430 B. pertussis isolates identified 272 putative amplifications, of which 94 % were located at 11 hotspot loci. We demonstrate limited phylogenetic connection for the occurrence of amplifications, suggesting unstable and sporadic characteristics. Genome instability was further described in vitro using long-read sequencing via the Nanopore platform, which revealed that clonally derived laboratory cultures produced heterogenous populations rapidly. We extended this research to analyse a population of 1000 isolates of another important pathogen, Mycobacterium tuberculosis . We found 590 amplifications in M. tuberculosis , and like B. pertussis , these occurred primarily at hotspots. Genes amplified in B. pertussis include those involved in motility and respiration, whilst in M. tuberuclosis, functions included intracellular growth and regulation of virulence. Using publicly available short-read data we predicted previously unrecognized, large amplifications in B. pertussis and M. tuberculosis . This reveals the unrecognized and dynamic genetic diversity of B. pertussis and M. tuberculosis , highlighting the need for a more holistic understanding of bacterial genetics.

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“…An ad hoc core genome multilocus sequence typing scheme comprising 3,479 core targets was created using the Target-Definer v1.5 from SeqSphere + v8.5.1 (Ridom, Münster, Germany), using strain 12822 ( 14 ) as reference and 35 Bpp query genomes from GenBank ( Table 1 ). Comparison of Bpp 400431-b with all available genomes from GenBank showed 37, 16, and 10 allelic differences to strains 12822, FR6242 ( 1 ), and J456 ( 15 ), respectively.…”

Section: Announcementmentioning

confidence: 99%

Complete genome sequence of Bordetella parapertussis strain 400431-b, isolated from a protracted course of whooping cough in Austria, 2023

Cardoso,

Rouhani,

Cabal Rosel

et al. 2024

Microbiol Resour Announc

0

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Complete Genome Sequences of Four Different Bordetella sp. Isolates Causing Human Respiratory Infections

Cited by 7 publications

References 15 publications

Conserved Patterns of Symmetric Inversion in the Genome Evolution of Bordetella Respiratory Pathogens

Conserved Patterns of Symmetric Inversion in the Genome Evolution of Bordetella Respiratory Pathogens

Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in Bordetella pertussis and Mycobacterium tuberculosis

Complete genome sequence of Bordetella parapertussis strain 400431-b, isolated from a protracted course of whooping cough in Austria, 2023

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