Whole-genome sequencing confirms that Burkholderia pseudomallei multilocus sequence types common to both Cambodia and Australia are due to homoplasy

Abstract

Burkholderia pseudomallei isolates with shared multilocus sequence types (STs) have not been isolated from different continents. We identified two STs shared between Australia and Cambodia. Whole-genome analysis revealed substantial diversity within STs, correctly identified the Asian or Australian origin, and confirmed that these shared STs were due to homoplasy.

FIG 1

eBURST analysis of 954 Burkholderia pseudomallei isolates from Australia and Cambodia, comprising 245 sequence types (STs). Both ST105 and ST849 (shaded green) contain B. pseudomallei isolates found in Cambodia and Australia. All other STs have been found solely in Australasia or Asia. STs shaded in red indicate an Asian origin and include isolates found in Cambodia, Thailand, China, and Vietnam. STs shaded in blue represent islands in Australasia. All unshaded STs are of Australian origin.

FIG 2

Maximum likelihood phylogenetic analysis of two Cambodian (CAM41 and SHCH2430) and two Australian (MSHR282 and MSHR4004) Burkholderia pseudomallei genomes in comparison to B. pseudomallei reference genomes. A total of 84,839 core genome single-nucleotide polymorphisms were used to construct the phylogeny. Based on multilocus sequence typing (MLST), both MSHR282 and CAM41 isolates are ST105 (red), and isolates MSHR4004 and SHCH2430 are ST849 (blue). However, whole-genome phylogenetic analysis clearly groups these strains based upon geographic origin, i.e., MSHR282 and MSHR4004 group with other Australian isolates, and CAM41 and SHCH2430 group with other Asian strains. Thus, MLST of B. pseudomallei can, in rare cases, be confounded by ST homoplasy. The scale bar represents the average number of nucleotide substitutions per site.