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Some strains of the Burkholderia cepacia complex, including the ET12 lineage, have been implicated in epidemic spread amongst cystic fibrosis (CF) patients. Suppression-subtractive hybridisation was used to identify genomic regions within strain J2315 (ET12 lineage; genomovar IIIA) that were absent from a non-transmissible genomovar IIIB strain. Sequence data from 15 subtracted clones were used to interrogate the genome sequence of strain J2315 and identify genomic regions incorporating the subtracted sequences. Many of the genomic regions displayed abnormally low GC content and similarity to sequences implicated in gene transfer. The distribution of three subtracted regions amongst members of the B. cepacia complex varied. A large cluster of genes with strong sequence similarity to capsular production genes from Burkholderia mallei and other bacterial pathogens was identified. This genomic island was detected in some but not all representatives of genomovar IIIA, two out of four genomovar I strains, and one of two strains of Burkholderia multivorans, but was not detected in Burkholderia stabilis, Burkholderia vietnamiensis, genomovar VI or Burkholderia. ambifaria. The polysaccharide production gene cluster of strain J2315 carries an IS 407-like sequence within the gene similar to B. mallei wcbO that is lacking in other ET12 isolates. Genes from this cluster are expressed during exponential growth in broth.

Burkholderia cepacia, an important opportunist pathogen, is genetically heterogeneous. The B. cepacia complex has been subdivided into a number of genospecies or genomovars. A flagellin gene PCR-RFLP method was applied to a representative panel of strains of known genomovar. The technique was able to distinguish strains of B. multivorans from other members of the B. cepacia complex on the basis of amplicon size (typical of type I rather than type II flagellins) with the exception of one genomovar I strain. There was considerable variation in RFLP patterns amongst the panel of strains; only two pairs of strains were indistinguishable with both HaeIII and MspI digestion. Where RFLP patterns matched with both enzymes or a single enzyme, matching strains were always in the same genomovar. It was possible to distinguish the UK cystic fibrosis epidemic strain from all other members of the panel, including nine other genomovar III strains. The level of variation suggests that flagellin genotyping is a useful method for discriminating between B. cepacia strains.

Using probes constructed from Ralstonia solanacearum and Burkholderia pseudomallei, putative type III secretion (TTS) genes were identified in Burkholderia cepacia J2315 (genomovar III). A cosmid clone containing DNA with homology to five TTS genes was sub-cloned and regions were sequenced in order to design oligonucleotides for polymerase chain reaction assays. These indicated that two putative TTS genes (bcscQ and bcscV) were present in all members of the B. cepacia complex with the exception of strains from genomovar I. Southern blot assays confirmed this observation, suggesting that the lack of a TTS gene cluster may define a major difference between B. cepacia genomovar I and other members of the B. cepacia complex, including genomovar III. In contrast to TTS gene clusters in other bacteria, a putative gene homologous to the virB1 gene of Brucella suis was located directly downstream of bcscQR.