A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions

Abstract

Burkholderia pseudomallei is the etiologic agent of melioidosis. Many disease manifestations are associated with melioidosis, and the mechanisms causing this variation are unknown; genomic differences among strains offer one explanation. We compared the genome sequences of two strains of B. pseudomallei: the original reference strain K96243 from Thailand and strain MSHR305 from Australia. We identified a variable homologous region between the two strains. This region was previously identified in comparisons of the genome of B. pseudomallei strain K96243 with the genome of strain E264 from the closely related B. thailandensis. In that comparison, K96243 was shown to possess a horizontally acquired Yersinia-like fimbrial (YLF) gene cluster. Here, we show that the homologous genomic region in B. pseudomallei strain 305 is similar to that previously identified in B. thailandensis strain E264. We have named this region in B. pseudomallei strain 305 the B. thailandensis-like flagellum and chemotaxis (BTFC) gene cluster. We screened for these different genomic components across additional genome sequences and 571 B. pseudomallei DNA extracts obtained from regions of endemicity. These alternate genomic states define two distinct groups within B. pseudomallei: all strains contained either the BTFC gene cluster (group BTFC) or the YLF gene cluster (group YLF). These two groups have distinct geographic distributions: group BTFC is dominant in Australia, and group YLF is dominant in Thailand and elsewhere. In addition, clinical isolates are more likely to belong to group YLF, whereas environmental isolates are more likely to belong to group BTFC. These groups should be further characterized in an animal model.

FIG. 1.

Genomic diversity between B. pseudomallei strains K96243 and 305 compared to the related region in the genome of B. thailandensis E264. A horizontal gene transfer event caused the ancestral BTFC gene cluster to be replaced by the acquired YLF genes (BPSS0120 to -0123), as observed in strain K96243. The BTFC cluster remains in strain 305 and has 91 to 94% nucleotide similarity to B. thailandensis E264. This diverse region was used to design markers that differentiate B. pseudomallei into two distinct groups: group YLF and group BTFC. Yellow, chemotaxis protein genes; green, flagellum biosynthesis genes; blue, YLF genes; red, matched areas.

FIG. 2.

Multiplex SYBR green real-time PCR assay targeting genes btfc-orf18 (the BTFC gene cluster target) and BPSS0120 (the YLF gene cluster target). This assay divides B. pseudomallei into two distinct groups. Strain 305 was the positive control strain for group BTFC, whereas strain K96243 was the positive control for group YLF. (A) Derivative dissociation curves of two different PCR amplicons for gene btfc-orf18, melted at 80.0°C, and gene BPSS0120, melted at 88.0°C. NTC, no-template control. (B) PCR amplicons of 115 bp and 350 bp resolved by agarose gel electrophoresis for genes btfc-orf18 and BPSS0120, respectively. Lanes 1 to 4 contain strain 305, strain K96243, NTC, and a 100-bp DNA ladder, respectively.

FIG. 3.

Countries of origin for isolates in B. pseudomallei groups BTFC and YLF. Group BTFC strains are dominant in Australia, whereas group YLF strains are dominant in Thailand and elsewhere.