The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients

Abstract

Bacterial infections of the lungs of cystic fibrosis (CF) patients cause major complications in the treatment of this common genetic disease. Burkholderia cenocepacia infection is particularly problematic since this organism has high levels of antibiotic resistance, making it difficult to eradicate; the resulting chronic infections are associated with severe declines in lung function and increased mortality rates. B. cenocepacia strain J2315 was isolated from a CF patient and is a member of the epidemic ET12 lineage that originated in Canada or the United Kingdom and spread to Europe. The 8.06-Mb genome of this highly transmissible pathogen comprises three circular chromosomes and a plasmid and encodes a broad array of functions typical of this metabolically versatile genus, as well as numerous virulence and drug resistance functions. Although B. cenocepacia strains can be isolated from soil and can be pathogenic to both plants and man, J2315 is representative of a lineage of B. cenocepacia rarely isolated from the environment and which spreads between CF patients. Comparative analysis revealed that ca. 21% of the genome is unique in comparison to other strains of B. cenocepacia, highlighting the genomic plasticity of this species. Pseudogenes in virulence determinants suggest that the pathogenic response of J2315 may have been recently selected to promote persistence in the CF lung. The J2315 genome contains evidence that its unique and highly adapted genetic content has played a significant role in its success as an epidemic CF pathogen.

FIG. 1.

Schematic circular diagrams of the B. cenocepacia J2315 genome. The circular diagrams for chromosomes 1 (A) and 2 (B) are drawn to scale, whereas those for chromosome 3 (C) and plasmid pBCJ2315 (D) are not drawn to scale. Black circles representing these replicons are drawn to scale. The key for the three chromosomal circular diagrams (A, B, and C; outside to inside), with scale in Mb, is as follows. Annotated CDSs are colored according to the predicted function represented on a pair of concentric circles, representing both coding strands. CDSs in genomic island regions are indicated in green, and other RODs defined by pairwise genome comparisons with other BCC are indicated in red. CDSs with matches identified by reciprocal FASTA with other Burkholderia species—B. cenocepacia HI2424, B. cenocepacia AU1054, B. contaminans 383, B. ambifaria AMMD, B. vietnamiensis G4, B. xenovorans LB400, B. pseudomallei K96243, and B. thailandensis E264—are indicated in dark blue. Orthologues shared with Ralstonia solanacearum GMI1000 are indicated in purple. For the G+C content plot, the GC bias (G−C/G+C) is indicated as >1% in khaki and <1% in purple. (D) The key for the circular diagram for plasmid pBCJ2315 is as described for the chromosomes but lacks the orthologue matches. Color coding for CDS functions: dark blue for pathogenicity/adaptation, black for energy metabolism, red for information transfer, dark green for surface associated, cyan for degradation of large molecules, magenta for degradation of small molecules, yellow for central/intermediary metabolism, pale green for unknown, pale blue for regulators, orange for conserved hypothetical, brown for pseudogenes, pink for phage and IS elements, and gray for miscellaneous.

FIG. 2.

Relative distribution of CDSs belonging to different functional classes on the three chromosomes of B. cenocepacia J2315. Figures for the distribution of the functional classes on a chromosome are expressed as a ratio of the number of CDSs of a class per replicon against the total number CDSs for that class in the genome, normalized per number of CDS on that replicon.

FIG. 3.

Comparison of the distribution of B. cenocepacia J2315 orthologs. Orthologs were identified in the Burkholderiaceae genomes B. cenocepacia HI2424, B. cenocepacia AU1054, B. contaminans 383, B. ambifaria AMMD, B. vietnamiensis G4, B. xenovorans LB400, B. pseudomallei K96243, and B. thailandensis E264 and in Ralstonia solanacearum GMI1000. Orthologs were identified by best reciprocal FASTA with an identity cutoff of 30% and a length of match cutoff of 80%. The percentages of matches for individual J2315 chromosomes and the total genome are plotted.