The core and accessory genomes of Burkholderia pseudomallei: implications for human melioidosis

• Published in: PLoS pathogens Vol. 4; no. 10; p. e1000178
• Main Authors: Sim, Siew Hoon, Yu, Yiting, Lin, Chi Ho, Karuturi, R Krishna M, Wuthiekanun, Vanaporn, Tuanyok, Apichai, Chua, Hui Hoon, Ong, Catherine, Paramalingam, Sivalingam Suppiah, Tan, Gladys, Tang, Lynn, Lau, Gary, Ooi, Eng Eong, Woods, Donald, Feil, Edward, Peacock, Sharon J, Tan, Patrick
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.10.2008; Public Library of Science (PLoS)
• Subjects: Animals; Bacteria; Birds; Burkholderia pseudomallei - genetics; Burkholderia pseudomallei - isolation & purification; Burkholderia pseudomallei - pathogenicity; Cluster Analysis; Dogs; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Gene Frequency; Genes; Genome, Bacterial; Genomes; Genomic Islands; Haplorhini; Humans; INDEL Mutation; Melioidosis - genetics; Melioidosis - microbiology; Melioidosis - veterinary; Microbiology; Microbiology/Environmental Microbiology; Microbiology/Microbial Evolution and Genomics; Oligonucleotide Array Sequence Analysis; Pathogenesis; Phylogeny; Studies; Swine; Virulence Factors - genetics
• ISSN: 1553-7374; 1553-7366; 1553-7374
• DOI: 10.1371/journal.ppat.1000178

Natural isolates of Burkholderia pseudomallei (Bp), the causative agent of melioidosis, can exhibit significant ecological flexibility that is likely reflective of a dynamic genome. Using whole-genome Bp microarrays, we examined patterns of gene presence and absence across 94 South East Asian strains isolated from a variety of clinical, environmental, or animal sources. 86% of the Bp K96243 reference genome was common to all the strains representing the Bp "core genome", comprising genes largely involved in essential functions (eg amino acid metabolism, protein translation). In contrast, 14% of the K96243 genome was variably present across the isolates. This Bp accessory genome encompassed multiple genomic islands (GIs), paralogous genes, and insertions/deletions, including three distinct lipopolysaccharide (LPS)-related gene clusters. Strikingly, strains recovered from cases of human melioidosis clustered on a tree based on accessory gene content, and were significantly more likely to harbor certain GIs compared to animal and environmental isolates. Consistent with the inference that the GIs may contribute to pathogenesis, experimental mutation of BPSS2053, a GI gene, reduced microbial adherence to human epithelial cells. Our results suggest that the Bp accessory genome is likely to play an important role in microbial adaptation and virulence.