Skip to content

Research at St Andrews

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles

Research output: Contribution to journalArticle

DOI

Open Access permissions

Open

Author(s)

Tannistha Nandi, Matthew Holden, Xavier Didelot, Kurosh Mehershahi, Justin A Boddey, Ifor Beacham, Ian Peak, John Harting, Primo Baybayan, Yan Guo, Susana Wang, Lee Chee How, Bernice Sim, Angela Essex-Lopresti, Mitali Sarkar-Tyson, Michelle Nelson, Sophie Smither, Catherine Ong, Lay Tin Aw, Chua Hui Hoon & 6 others Stephen Michell, David J Studholme, Richard Titball, Swaine L Chen, Julian Parkhill, Patrick Tan

School/Research organisations

Abstract

Burkholderia pseudomallei (Bp) is the causative agent of the infectious disease melioidosis. To investigate population diversity, recombination, and horizontal gene transfer in closely related Bp isolates, we performed whole-genome sequencing (WGS) on 106 clinical, animal, and environmental strains from a restricted Asian locale. Whole-genome phylogenies resolved multiple genomic clades of Bp, largely congruent with multilocus sequence typing (MLST). We discovered widespread recombination in the Bp core genome, involving hundreds of regions associated with multiple haplotypes. Highly recombinant regions exhibited functional enrichments that may contribute to virulence. We observed clade-specific patterns of recombination and accessory gene exchange, and provide evidence that this is likely due to ongoing recombination between clade members. Reciprocally, interclade exchanges were rarely observed, suggesting mechanisms restricting gene flow between clades. Interrogation of accessory elements revealed that each clade harbored a distinct complement of restriction-modification (RM) systems, predicted to cause clade-specific patterns of DNA methylation. Using methylome sequencing, we confirmed that representative strains from separate clades indeed exhibit distinct methylation profiles. Finally, using an E. coli system, we demonstrate that Bp RM systems can inhibit uptake of non-self DNA. Our data suggest that RM systems borne on mobile elements, besides preventing foreign DNA invasion, may also contribute to limiting exchanges of genetic material between individuals of the same species. Genomic clades may thus represent functional units of genetic isolation in Bp, modulating intraspecies genetic diversity.
Close

Details

Original languageEnglish
Pages (from-to)129-141
JournalGenome Research
Volume25
Issue number1
Early online date18 Sep 2014
DOIs
StatePublished - Jan 2015

Discover related content
Find related publications, people, projects and more using interactive charts.

View graph of relations

Related by author

  1. The microevolution and epidemiology of Staphylococcus aureus colonization during atopic eczema disease flare

    Harkins, C. P., Pettigrew, K. A., Oravcová, K., Gardner, J., Hearn, R. M. R., Rice, D., Mather, A. E., Parkhill, J., Brown, S. J., Proby, C. M. & Holden, M. T. G. 23 Sep 2017 In : Journal of Investigative Dermatology. 138, 2, p. 336-343

    Research output: Contribution to journalArticle

  2. Pseudomonas aeruginosa intensive care unit outbreak: winnowing of transmissions with molecular and genomic typing

    Parcell, B. J., Oravcova, K., Pinheiro, M., Holden, M. T. G., Phillips, G., Turton, J. F. & Gillespie, S. H. 8 Dec 2017 In : Journal of Hospital Infection. In press

    Research output: Contribution to journalArticle

  3. Haem-iron plays a key role in the regulation of the Ess/type VII secretion system of Staphylococcus aureus RN6390

    Casabona, M. G., Kneuper, H., Alferes de Lima, D., Harkins, C. P., Zoltner, M., Hjerde, E., Holden, M. T. G. & Palmer, T. 24 Nov 2017 In : Microbiology. Latest Article

    Research output: Contribution to journalArticle

  4. Functional analysis of the EsaB component of the Staphylococcus aureus Type VII secretion system

    Casabona, M. G., Buchanan, G., Zoltner, M., Harkins, C. P., Holden, M. T. G. & Palmer, T. 22 Nov 2017 In : Microbiology. Latest Article, 13 p.

    Research output: Contribution to journalArticle

  5. The genetic diversity of Staphylococcus aureus colonisation in atopic eczema disease flare

    Harkins, C. P., Pettigrew, K. A., Oravcova, K., Gardner, J., Hearn, R., Rice, D., Mather, A. E., Parkhill, J., Brown, S. J., Proby, C. M. & Holden, M. T. Oct 2017 In : Journal of Investigative Dermatology. 137, 10, p. S258-S258 1 p.

    Research output: Contribution to journalAbstract

Related by journal

  1. A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy

    Noorani, A., Bornschein, J., Lynch, A. G., Secrier, M., Achilleos, A., Eldridge, M., Bower, L., Weaver, J. M. J., Crawte, J., Ong, C-A., Shannon, N., MacRae, S., Grehan, N., Nutzinger, B., O'Donovan, M., Hardwick, R., Tavaré, S., Fitzgerald, R. C. & on behalf of the Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium 1 Jun 2017 In : Genome Research. 27, 6, p. 902-912 11 p.

    Research output: Contribution to journalArticle

  2. DNA methylation changes induced by long and short photoperiods in Nasonia

    Pegoraro, M., Bafna, A., Davies, N. J., Shuker, D. M. & Tauber, E. 1 Feb 2016 In : Genome Research. 26, 2, p. 203-210 8 p.

    Research output: Contribution to journalArticle

  3. Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland

    Reuter, S., Török, E. M., Holden, M. T., Reynolds, R., Raven, K. E., Blane, B., Donker, T., Bentley, S. D., Aanensen, D. M., Grundmann, H., Feil, E. J., Spratt, B. G., Parkhill, J. & Peacock, S. J. Feb 2016 In : Genome Research. 26, 2, p. 263-270

    Research output: Contribution to journalArticle

  4. Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection

    Harris, S. R., Robinson, C., Steward, K. F., Webb, K. S., Paillot, R., Parkhill, J., Holden, M. T. G. & Waller, A. S. Sep 2015 In : Genome Research. 25, 9, p. 1360-1371

    Research output: Contribution to journalArticle

  5. Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

    Ju, Y. S. , Tubio, J. M. C. , Mifsud, W. , Fu, B. , Davies, H. R. , Ramakrishna, M. , Li, Y. , Yates, L. , Gundem, G. , Tarpey, P. S. , Behjati, S. , Papaemmanuil, E. , Martin, S. , Fullam, A. , Gerstung, M. , Nangalia, J. , Green, A. R. , Caldas, C. , Borg, Å. , Tutt, A. & 29 others Michael Lee, M. T., Van'T Veer, L. J., Tan, B. K. T., Aparicio, S., Span, P. N., Martens, J. W. M., Knappskog, S., Vincent-Salomon, A., Børresen-Dale, A. L., Eyfjörd, J. E., Flanagan, A. M., Foster, C., Neal, D. E., Cooper, C., Eeles, R., Lakhani, S. R., Desmedt, C., Thomas, G., Richardson, A. L., Purdie, C. A., Thompson, A. M., McDermott, U., Yang, F., Nik-Zainal, S., Campbell, P. J., Stratton, M. R., ICGC Prostate Cancer Working Group, ICGC Bone Cancer Working Group & ICGC Breast Cancer Working Group 1 Jun 2015 In : Genome Research. 25, 6, p. 814-824 11 p.

    Research output: Contribution to journalArticle

ID: 159052448