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. 2020 Jan 23;9(4):e01207-19. doi: 10.1128/MRA.01207-19

Complete Genome Sequence of Bordetella bronchiseptica Strain KM22

Tracy L Nicholson a,✉, Darrell O Bayles a, Sarah M Shore a
Editor: David Raskob
PMCID: PMC6979298  PMID: 31974149

Bordetella bronchiseptica isolate KM22 has been used in experimental infections of swine as a model of clinical B. bronchiseptica infection and to study host-to-host transmission. The draft genome sequence of KM22 was reported in 2014. Here, we report the complete genome sequence of KM22.

ABSTRACT

Bordetella bronchiseptica isolate KM22 has been used in experimental infections of swine as a model of clinical B. bronchiseptica infection and to study host-to-host transmission. The draft genome sequence of KM22 was reported in 2014. Here, we report the complete genome sequence of KM22.

ANNOUNCEMENT

Bordetella bronchiseptica is a small, coccoid-shaped Gram-negative motile bacterium with a size of about 0.2 to 0.5 μm by 0.5 to 2 μm and is one of 15 species within the genus (http://www.bacterio.net/). Bordetella pertussis, Bordetella parapertussis, and Bordetella bronchiseptica are referred to as the classical Bordetella species due to their close genetic relatedness and their ability to colonize the respiratory tract of mammals, contributing to mild to severe respiratory disease (1). Previous studies focusing on the evolution of Bordetella species demonstrated that B. pertussis and B. parapertussis evolved independently from different lineages of a B. bronchiseptica-like ancestor (1–4); as a result, B. pertussis and B. parapertussis represent two of the many examples of human pathogens that evolved from zoonotic sources (5, 6). In addition to their close genetic relatedness, classical Bordetella species harbor many of the same virulence factors, which are similarly regulated (2, 4, 7). Despite these similarities, the classical Bordetella species differ in traits such as host specificity, disease severity, and duration of infection. B. pertussis infects only humans and lacks an animal reservoir and the ability to survive in the environment (8, 9). B. bronchiseptica infects a variety of animals, often establishing chronic infections that range from lethal pneumonia to asymptomatic carriage, and is capable of surviving in the environment (10, 11).

B. bronchiseptica strain KM22 was originally isolated in Hungary in 1993 from a swine herd with atrophic rhinitis. Based on multilocus sequence type (MLST) analysis, KM22 is sequence type 7 (ST7), in clonal complex 1 of an MLST-based Bordetella phylogeny (3) and harbors a ribotype (12) and pertactin repeat region variant (13) shared with the majority of isolates obtained from swine. KM22 has been successfully used by our laboratory to develop a reproducible swine respiratory disease model reflective of clinical B. bronchiseptica infections within swine herds and host-to-host transmission (14–25). The draft genome sequence of KM22 was previously reported (26). We began to employ transcriptomic and proteomic techniques to fully investigate the mechanisms used by KM22 in response to environmental changes and stress. The need to obtain a complete and closed genome sequence for furthering these studies became clear.

Whole-genome sequencing was performed using both the Pacific Biosciences (PacBio) and Illumina Genome Analyzer IIx (GAIIx) platforms. For DNA extraction, a single colony was inoculated into Stainer-Scholte (SS) broth (27) and cultivated at 37°C with shaking at 250 rpm for 36 h. The High Pure template preparation kit (Roche Applied Science, Indianapolis, IN) was used to extract total genomic DNA from the sample, which was subsequently used to prepare both the PacBio and the Illumina libraries. Library preparation for PacBio sequencing was performed following the PacBio 20-kb insert library preparation protocol (https://www.pacb.com/wp-content/uploads/Procedure-Checklist-20-kb-Template-Preparation-Using-BluePippin-Size-Selection-System.pdf). The 20-kb library was sequenced with a PacBio RS II platform using two single-molecule real-time (SMRT) cells, resulting in 283,436 total reads and an average read length of 7,600 bp. Reads were subsequently assessed for quality using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).

Whole-genome assemblies were generated using PacBio SMRT Analysis v. 2.3.0 and Canu v. 1.5 (28) software. The average PacBio coverage for the assembled genome was 475×. Assembling the PacBio data resulted in a fully sequenced closed circular chromosome, which was subsequently oriented to start at the dnaA gene and trimmed by removing any overlapping sequence. The genome was then polished and error corrected using the Broad Institute’s Pilon v. 1.18 software (29) along with the Illumina GAIIx 3,474,442 paired-end sequencing reads, which were previously used for the draft assembly (26). Default parameters were used for all software. The closed KM22 genome was then annotated using NCBI’s Prokaryotic Genome Annotation Pipeline (PGAP) (30). The complete genome of KM22 consists of 5,205,646 bp with a G+C content of 68.2%, a total of 4,827 predicted protein coding sequences (CDSs), 9 rRNA operons, 1 transfer-messenger RNA (tmRNA), 3 noncoding RNAs (ncRNAs), and 56 tRNAs.

Data availability.

The whole-genome sequence for Bordetella bronchiseptica isolate KM22 was deposited in DDBJ/ENA/GenBank under the accession number CP022962. The PacBio read data were deposited in the NCBI Sequence Read Archive (SRA) under BioProject accession number PRJNA398562 and SRA study accession number SRP222122 (run numbers SRR10134673 and SRR10134672). Illumina HiSeq short read sequences have been deposited at the European Nucleotide Archive under accession number ERS027415.

ACKNOWLEDGMENTS

We thank the Yale University Center for Genome Analysis for their assistance in producing the PacBio sequence data.

Funding for this research was provided by the USDA Agricultural Research Service. Funding sources did not impact study design, data collection, data analysis, decisions on publication, or preparation of the manuscript.

Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.

REFERENCES

  • 1.Preston A, Parkhill J, Maskell DJ. 2004. The bordetellae: lessons from genomics. Nat Rev Microbiol 2:379–390. doi: 10.1038/nrmicro886. [DOI] [PubMed] [Google Scholar]
  • 2.Parkhill J, Sebaihia M, Preston A, Murphy LD, Thomson N, Harris DE, Holden MTG, Churcher CM, Bentley SD, Mungall KL, Cerdeño-Tárraga AM, Temple L, James K, Harris B, Quail MA, Achtman M, Atkin R, Baker S, Basham D, Bason N, Cherevach I, Chillingworth T, Collins M, Cronin A, Davis P, Doggett J, Feltwell T, Goble A, Hamlin N, Hauser H, Holroyd S, Jagels K, Leather S, Moule S, Norberczak H, O’Neil S, Ormond D, Price C, Rabbinowitsch E, Rutter S, Sanders M, Saunders D, Seeger K, Sharp S, Simmonds M, Skelton J, Squares R, Squares S, Stevens K, Unwin L, Whitehead S, Barrell BG, Maskell DJ. 2003. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat Genet 35:32–40. doi: 10.1038/ng1227. [DOI] [PubMed] [Google Scholar]
  • 3.Diavatopoulos DA, Cummings CA, Schouls LM, Brinig MM, Relman DA, Mooi FR. 2005. Bordetella pertussis, the causative agent of whooping cough, evolved from a distinct, human-associated lineage of B. bronchiseptica. PLoS Pathog 1:e45. doi: 10.1371/journal.ppat.0010045. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.Linz B, Ivanov YV, Preston A, Brinkac L, Parkhill J, Kim M, Harris SR, Goodfield LL, Fry NK, Gorringe AR, Nicholson TL, Register KB, Losada L, Harvill ET. 2016. Acquisition and loss of virulence-associated factors during genome evolution and speciation in three clades of Bordetella species. BMC Genomics 17:767. doi: 10.1186/s12864-016-3112-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Slingenbergh JI, Gilbert M, de Balogh KI, Wint W. 2004. Ecological sources of zoonotic diseases. Rev Sci Tech 23:467–484. doi: 10.20506/rst.23.2.1492. [DOI] [PubMed] [Google Scholar]
  • 6.Taylor LH, Latham SM, Woolhouse ME. 2001. Risk factors for human disease emergence. Philos Trans R Soc Lond B Biol Sci 356:983–989. doi: 10.1098/rstb.2001.0888. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Chen Q, Stibitz S. 2019. The BvgASR virulence regulon of Bordetella pertussis. Curr Opin Microbiol 47:74–81. doi: 10.1016/j.mib.2019.01.002. [DOI] [PubMed] [Google Scholar]
  • 8.Hewlett EL, Burns DL, Cotter PA, Harvill ET, Merkel TJ, Quinn CP, Stibitz ES. 2014. Pertussis pathogenesis—what we know and what we don’t know. J Infect Dis 209:982–985. doi: 10.1093/infdis/jit639. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.Pinto MV, Merkel TJ. 2017. Pertussis disease and transmission and host responses: insights from the baboon model of pertussis. J Infect 74 Suppl 1:S114–S119. doi: 10.1016/S0163-4453(17)30201-3. [DOI] [PubMed] [Google Scholar]
  • 10.Goodnow RA. 1980. Biology of Bordetella bronchiseptica. Microbiol Rev 44:722–738. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Brockmeier SL, Register KB, Nicholson TL, Loving CL, 2019. Bordetellosis, p 767–777. In Zimmerman JJ, Karriker LA, Ramirez A, Schwartz KJ, Stevenson GW, Zhang J (ed), Diseases of swine, 11th ed John Wiley & Sons, Inc, Hoboken, NJ. [Google Scholar]
  • 12.Register KB, Magyar T. 1999. Optimized ribotyping protocol applied to Hungarian Bordetella bronchiseptica isolates: identification of two novel ribotypes. Vet Microbiol 69:277–285. doi: 10.1016/s0378-1135(99)00118-2. [DOI] [PubMed] [Google Scholar]
  • 13.Register KB. 2001. Novel genetic and phenotypic heterogeneity in Bordetella bronchiseptica pertactin. Infect Immun 69:1917–1921. doi: 10.1128/IAI.69.3.1917-1921.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Brockmeier SL. 2004. Prior infection with Bordetella bronchiseptica increases nasal colonization by Haemophilus parasuis in swine. Vet Microbiol 99:75–78. doi: 10.1016/j.vetmic.2003.08.013. [DOI] [PubMed] [Google Scholar]
  • 15.Brockmeier SL, Lager KM. 2002. Experimental airborne transmission of porcine reproductive and respiratory syndrome virus and Bordetella bronchiseptica. Vet Microbiol 89:267–275. doi: 10.1016/s0378-1135(02)00204-3. [DOI] [PubMed] [Google Scholar]
  • 16.Brockmeier SL, Loving CL, Nicholson TL, Palmer MV. 2008. Coinfection of pigs with porcine respiratory coronavirus and Bordetella bronchiseptica. Vet Microbiol 128:36–47. doi: 10.1016/j.vetmic.2007.09.025. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17.Brockmeier SL, Palmer MV, Bolin SR. 2000. Effects of intranasal inoculation of porcine reproductive and respiratory syndrome virus, Bordetella bronchiseptica, or a combination of both organisms in pigs. Am J Vet Res 61:892–899. doi: 10.2460/ajvr.2000.61.892. [DOI] [PubMed] [Google Scholar]
  • 18.Brockmeier SL, Palmer MV, Bolin SR, Rimler RB. 2001. Effects of intranasal inoculation with Bordetella bronchiseptica, porcine reproductive and respiratory syndrome virus, or a combination of both organisms on subsequent infection with Pasteurella multocida in pigs. Am J Vet Res 62:521–525. doi: 10.2460/ajvr.2001.62.521. [DOI] [PubMed] [Google Scholar]
  • 19.Brockmeier SL, Register KB. 2007. Expression of the dermonecrotic toxin by Bordetella bronchiseptica is not necessary for predisposing to infection with toxigenic Pasteurella multocida. Vet Microbiol 125:284–289. doi: 10.1016/j.vetmic.2007.05.022. [DOI] [PubMed] [Google Scholar]
  • 20.Brockmeier SL, Register KB, Magyar T, Lax AJ, Pullinger GD, Kunkle RA. 2002. Role of the dermonecrotic toxin of Bordetella bronchiseptica in the pathogenesis of respiratory disease in swine. Infect Immun 70:481–490. doi: 10.1128/iai.70.2.481-490.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.Loving CL, Brockmeier SL, Vincent AL, Palmer MV, Sacco RE, Nicholson TL. 2010. Influenza virus coinfection with Bordetella bronchiseptica enhances bacterial colonization and host responses exacerbating pulmonary lesions. Microb Pathog 49:237–245. doi: 10.1016/j.micpath.2010.06.004. [DOI] [PubMed] [Google Scholar]
  • 22.Nicholson TL, Brockmeier SL, Loving CL. 2009. Contribution of Bordetella bronchiseptica filamentous hemagglutinin and pertactin to respiratory disease in swine. Infect Immun 77:2136–2146. doi: 10.1128/IAI.01379-08. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 23.Nicholson TL, Brockmeier SL, Loving CL, Register KB, Kehrli ME Jr, Shore SM. 2014. The Bordetella bronchiseptica type III secretion system is required for persistence and disease severity but not transmission in swine. Infect Immun 82:1092–1103. doi: 10.1128/IAI.01115-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 24.Nicholson TL, Brockmeier SL, Loving CL, Register KB, Kehrli ME Jr, Stibitz SE, Shore SM. 2012. Phenotypic modulation of the virulent Bvg phase is not required for pathogenesis and transmission of Bordetella bronchiseptica in swine. Infect Immun 80:1025–1036. doi: 10.1128/IAI.06016-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 25.Nicholson TL, Brockmeier SL, Sukumar N, Paharik AE, Lister JL, Horswill AR, Kehrli ME Jr, Loving CL, Shore SM, Deora R. 2017. The Bordetella Bps polysaccharide is required for biofilm formation and enhances survival in the lower respiratory tract of swine. Infect Immun 85:e00261-17. doi: 10.1128/IAI.00261-17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 26.Nicholson TL, Shore SM, Bayles DO, Register KB, Kingsley RA. 2014. Draft genome sequence of the Bordetella bronchiseptica swine isolate KM22. Genome Announc 2:e00670-14. doi: 10.1128/genomeA.00670-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27.Stainer DW, Scholte MJ. 1970. A simple chemically defined medium for the production of phase I Bordetella pertussis. J Gen Microbiol 63:211–220. doi: 10.1099/00221287-63-2-211. [DOI] [PubMed] [Google Scholar]
  • 28.Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736. doi: 10.1101/gr.215087.116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 29.Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963. doi: 10.1371/journal.pone.0112963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 30.Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 44:6614–6624. doi: 10.1093/nar/gkw569. [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The whole-genome sequence for Bordetella bronchiseptica isolate KM22 was deposited in DDBJ/ENA/GenBank under the accession number CP022962. The PacBio read data were deposited in the NCBI Sequence Read Archive (SRA) under BioProject accession number PRJNA398562 and SRA study accession number SRP222122 (run numbers SRR10134673 and SRR10134672). Illumina HiSeq short read sequences have been deposited at the European Nucleotide Archive under accession number ERS027415.

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