Distribution of Burkholderia pseudomallei in Northern Australia, a Land of Diversity

Abstract

dBurkholderia pseudomallei is a Gram-negative soil bacillus that is the etiological agent of melioidosis and a biothreat agent. Little is known about the biogeography of this bacterium in Australia, despite its hyperendemicity in the northern region of this continent. The population structure of 953 Australian B. pseudomallei strains representing 779 and 174 isolates of clinical and environmental origins, respectively, was analyzed using multilocus sequence typing (MLST). Bayesian population structure and network SplitsTree analyses were performed on concatenated MLST loci, and sequence type (ST) diversity and evenness were examined using Simpson's and Pielou's indices and a multivariate dissimilarity matrix. Bayesian analysis found two B. pseudomallei populations in Australia that were geographically distinct; isolates from the Northern Territory were grouped mainly into the first population, whereas the majority of isolates from Queensland were grouped in a second population. Differences in ST evenness were observed between sampling areas, confirming that B. pseudomallei is widespread and established across northern Australia, with a large number of fragmented habitats. ST analysis showed that B. pseudomallei populations diversified as the sampling area increased. This observation was in contrast to smaller sampling areas where a few STs predominated, suggesting that B. pseudomallei populations are ecologically established and not frequently dispersed. Interestingly, there was no identifiable ST bias between clinical and environmental isolates, suggesting the potential for all culturable B. pseudomallei isolates to cause disease. Our findings have important implications for understanding the ecology of B. pseudomallei in Australia and for potential source attribution of this bacterium in the event of unexpected cases of melioidosis.

Unprecedented Melioidosis Cases in Northern Australia Caused by an Asian Burkholderia pseudomallei Strain Identified by Using Large-Scale Comparative Genomics

“…S2 in the supplemental material) (7,33). The ST genome phylogenies used both SNP and insertion-deletion (indel) variants to improve the epidemiological associations, as we described elsewhere (5). Recombinogenic SNPs were also identified using the default parameters in Gubbins (see Fig.…”

“…Maximum parsimony trees were generated from relevant SPANDx .nex outputs using PAUP* 4.0b10 (37). For within-ST genomic comparisons, SNP and small indel variants were combined for increased resolution and improved epidemiological signal (5). For the 455-genome phylogeny, bootstrapping using 100 replicates was performed to determine the robustness of the relevant branches.…”

“…On a per-allele basis, recombination is estimated to occur between 18 and 30 times more frequently than mutation (4). This extensive lateral gene transfer can confound population analyses, particularly those that are based on studying limited geographic regions (e.g., the Northern Territory, Australia [5]) due to high rates of homoplasy observed among genetic variants. In contrast, genomic analyses of B. pseudomallei populations on a continental scale have revealed a clear separation of B. pseudomallei isolates between Asia and Australia (4,6,7).…”

Burkholderia pseudomallei Genotype Distribution in the Northern Territory, Australia

“…In particular, there are no shared environmental STs between the Northern Territory and Queensland. 9,10 Confirmation of population structure at increasingly fine scales suggests that the bacterium has limited dispersal ability. Limited dispersal is unexpected, because the species can be carried by agricultural animals and is relatively resistant to environmental stress.…”

“…The rate of new STs being recovered in Darwin and surrounds in response to increased sampling effort is levelling off, suggesting that only a limited number of environmental strains are yet to be discovered in this specific region. 10 Melioidosis also occurs in remote indigenous communities on the offshore islands of the Top End, but none of our most common STs have yet been found in environmental strains from any of these islands.…”