Genomic islands from five strains of Burkholderia pseudomallei

Abstract

Background: Burkholderia pseudomallei is the etiologic agent of melioidosis, a significant cause of morbidity and mortality where this infection is endemic. Genomic differences among strains of B. pseudomallei are predicted to be one of the major causes of the diverse clinical manifestations observed among patients with melioidosis. The purpose of this study was to examine the role of genomic islands (GIs) as sources of genomic diversity in this species.

Results: We found that genomic islands (GIs) vary greatly among B. pseudomallei strains. We identified 71 distinct GIs from the genome sequences of five reference strains of B. pseudomallei: K96243, 1710b, 1106a, MSHR668, and MSHR305. The genomic positions of these GIs are not random, as many of them are associated with tRNA gene loci. In particular, the 3' end sequences of tRNA genes are predicted to be involved in the integration of GIs. We propose the term "tRNA-mediated site-specific recombination" (tRNA-SSR) for this mechanism. In addition, we provide a GI nomenclature that is based upon integration hotspots identified here or previously described.

Conclusion: Our data suggest that acquisition of GIs is one of the major sources of genomic diversity within B. pseudomallei and the molecular mechanisms that facilitate horizontally-acquired GIs are common across multiple strains of B. pseudomallei. The differential presence of the 71 GIs across multiple strains demonstrates the importance of these mobile elements for shaping the genetic composition of individual strains and populations within this bacterial species.

Figure 1

Genomic locations of 71 GIs on chromosomes 1 and 2 in B. pseudomallei. GIs identified from strains 1710b, 1106a, MSHR668, and MSHR305 (inside of lines) are compared to the original 16 GIs identified from strain K96243 [11] (outside of lines). The genomic location of two mutually exclusive genomic regions, BTFC (B. thailandensis-like flagella and chemotaxis gene cluster) and YLF (Yersinia-like fimbrial gene cluster), [12] is also indicated.

Figure 2

Site-specific recombination (SSR) at tRNA-Pro in B. mallei causes a 3' end repeat 26 bp downstream of the recombination site. This site contains insertion element IS407A, which is common in B. mallei genomes. This suggested that IS407A was present in other mobile genetic elements when they were originally introduced to B. mallei genomes and the recombination event was associated with tRNA-Pro.

Figure 3

Predicted site-specific recombination (SSR) events at tRNA-Arg (CGA) in B. pseudomallei K96243 and B. thailandensis E264 and the relative genomic region in B. mallei ATCC23344. (a) An extra recombinant tRNA-Ser (CGA) was created in the genomes of these two bacterial strains by SSR; parallel dash lines indicate identical regions of the tRNA genes. (b) Nucleotide sequences of the tRNA-Arg and the recombinant tRNA-Ser; the predicted SSR-recognition site of tRNA-Arg in strains K96243 and E264 is underlined, and the identical regions between these two tRNA genes are highlighted in blue.

Figure 4

Site-specific recombination at the mutS gene of B. pseudomallei MSHR305. This event caused a short direct repeat 15 bp downstream of GI8c. GI8c is a putative prophage of MSHR305.

Figure 5

Prevalence of GIs with four predicted functions in five reference B. pseudomallei strains. Interestingly, strains MSHR668 and MSHR305 from Australia contain a high number of GIs associated with metabolism.

Figure 6

Distribution (presence) of GI genes within diverse B. pseudomallei populations. (a) Presence of fhaB gene clusters. (b) Presence of bpaA gene. We note that most B. pseudomallei strains contained either two clusters of the fhaB gene, clusters I and III, or cluster III alone. In addition, the bpaA gene was found only in clinical isolates of B. pseudomallei from Australia.