title: Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.
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.
authors.affiliation: Genome Institute of Singapore, Singapore, 138672, Republic of Singapore;
authors.forename: Tannistha
authors.initials: T
authors.lastname: Nandi
authors.forename: Matthew T G
authors.initials: MT
authors.lastname: Holden
authors.affiliation: The Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, United Kingdom;
authors.forename: Mathew T G
authors.initials: MT
authors.lastname: Holden
authors.affiliation: Department of Infectious Disease Epidemiology, Imperial College London, W2 1PG, United Kingdom;
authors.forename: Xavier
authors.initials: X
authors.lastname: Didelot
authors.affiliation: Department of Medicine, National University of Singapore, Singapore, 119074 Republic of Singapore;
authors.forename: Kurosh
authors.initials: K
authors.lastname: Mehershahi
authors.affiliation: Institute for Glycomics, Griffith University (Gold Coast Campus), Southport, Queensland, QLD 4222, Australia;
authors.forename: Justin A
authors.initials: JA
authors.lastname: Boddey
authors.affiliation: Institute for Glycomics, Griffith University (Gold Coast Campus), Southport, Queensland, QLD 4222, Australia;
authors.forename: Ifor
authors.initials: I
authors.lastname: Beacham
authors.affiliation: Institute for Glycomics, Griffith University (Gold Coast Campus), Southport, Queensland, QLD 4222, Australia;
authors.forename: Ian
authors.initials: I
authors.lastname: Peak
authors.affiliation: Pacific Biosciences, Menlo Park, California 94025, USA;
authors.forename: John
authors.initials: J
authors.lastname: Harting
authors.affiliation: Pacific Biosciences, Menlo Park, California 94025, USA;
authors.forename: Primo
authors.initials: P
authors.lastname: Baybayan
authors.affiliation: Pacific Biosciences, Menlo Park, California 94025, USA;
authors.forename: Yan
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Pacific Biosciences, Menlo Park, California 94025, USA;
authors.forename: Susana
authors.initials: S
authors.lastname: Wang
authors.affiliation: Pacific Biosciences, Menlo Park, California 94025, USA;
authors.forename: Lee Chee
authors.initials: LC
authors.lastname: How
authors.affiliation: Genome Institute of Singapore, Singapore, 138672, Republic of Singapore;
authors.forename: Bernice
authors.initials: B
authors.lastname: Sim
authors.affiliation: Defence Science and Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, United Kingdom;
authors.forename: Angela
authors.initials: A
authors.lastname: Essex-Lopresti
authors.affiliation: Defence Science and Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, United Kingdom;
authors.forename: Mitali
authors.initials: M
authors.lastname: Sarkar-Tyson
authors.affiliation: Defence Science and Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, United Kingdom;
authors.forename: Michelle
authors.initials: M
authors.lastname: Nelson
authors.affiliation: Defence Science and Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, United Kingdom;
authors.forename: Sophie
authors.initials: S
authors.lastname: Smither
authors.affiliation: Defense Medical and Environmental Research Institute, DSO National Laboratories, Singapore, 117510, Republic of Singapore;
authors.forename: Catherine
authors.initials: C
authors.lastname: Ong
authors.affiliation: Defense Medical and Environmental Research Institute, DSO National Laboratories, Singapore, 117510, Republic of Singapore;
authors.forename: Lay Tin
authors.initials: LT
authors.lastname: Aw
authors.affiliation: Genome Institute of Singapore, Singapore, 138672, Republic of Singapore;
authors.forename: Chua Hui
authors.initials: CH
authors.lastname: Hoon
authors.affiliation: Biosciences, University of Exeter, Exeter, EX4 4QD, United Kingdom;
authors.forename: Stephen
authors.initials: S
authors.lastname: Michell
authors.affiliation: Biosciences, University of Exeter, Exeter, EX4 4QD, United Kingdom;
authors.forename: David J
authors.initials: DJ
authors.lastname: Studholme
authors.affiliation: Biosciences, University of Exeter, Exeter, EX4 4QD, United Kingdom; Faculty of Infectious and Tropical Diseases, Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, WC1E 7HT, United Kingdom;
authors.forename: Richard
authors.initials: R
authors.lastname: Titball
authors.affiliation: Genome Institute of Singapore, Singapore, 138672, Republic of Singapore; Department of Medicine, National University of Singapore, Singapore, 119074 Republic of Singapore;
authors.forename: Swaine L
authors.initials: SL
authors.lastname: Chen
authors.affiliation: The Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, United Kingdom;
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: Genome Institute of Singapore, Singapore, 138672, Republic of Singapore; Duke-NUS Graduate Medical School Singapore, Singapore, 169857, Republic of Singapore; Cancer Science Institute of Singapore, National University of Singapore, 117599, Republic of Singapore tanbop@gis.a-star.edu.sg.
authors.forename: Patrick
authors.initials: P
authors.lastname: Tan
mesh_terms: D000818:Animals; D016957:Burkholderia pseudomallei / Q000235:genetics*; D017931:DNA Primers; D004269:DNA, Bacterial / Q000235:genetics; D044127:Epigenesis, Genetic; D004926:Escherichia coli / Q000235:genetics; D005260:Female; D017353:Gene Deletion; D056726:Genetic Association Studies; D016680:Genome, Bacterial; D023281:Genomics; D006239:Haplotypes; D006801:Humans; D008554:Melioidosis / Q000382:microbiology; D051379:Mice; D008807:Mice, Inbred BALB C; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial