Genetic diversity, determinants, and dissemination of Burkholderia pseudomallei lineages implicated in melioidosis in northeast Thailand

Abstract

Melioidosis is an often-fatal neglected tropical disease caused by an environmental bacterium Burkholderia pseudomallei. However, our understanding of the disease-causing bacterial lineages, their dissemination, and adaptive mechanisms remains limited. To address this, we conducted a comprehensive genomic analysis of 1,391 B. pseudomallei isolates collected from nine hospitals in northeast Thailand between 2015 and 2018, and contemporaneous isolates from neighbouring countries, representing the most densely sampled collection to date. Our study identified three dominant lineages with unique gene sets enhancing bacterial fitness, indicating lineage-specific adaptation strategies. Crucially, recombination was found to drive lineage-specific gene flow. Transcriptome analyses of representative clinical isolates from each dominant lineage revealed heightened expression of lineage-specific genes in environmental versus infection conditions, notably under nutrient depletion, highlighting environmental persistence as a key factor in the success of dominant lineages. The study also revealed the role of environmental factors - slope of terrain, altitude, direction of rivers, and the northeast monsoons - in shaping B. pseudomallei geographical dispersal. Collectively, our findings highlight persistence in the environment as a pivotal element facilitating B. pseudomallei spread, and as a prelude to exposure and infection, thereby providing useful insights for informing melioidosis prevention and control strategies.

Figure 1

Distribution of B. pseudomallei genomes used in this study (a) Geographical representation of the countries and provinces sampled for the 1,391 B. pseudomallei genomes used in this study. Pie-chart summarises the proportion of dominant lineage 1, 2, and 3 presented at each location with the chart size proportional to the number of the samples collected (b) An unrooted phylogenetic tree colour-coded by dominant lineages (c) Histogram depicting the distribution of clinical B. pseudomallei isolates from the northeast Thailand cohort throughout 2015–2018 sampling period. The shaded blue area represents the period of rainy seasons. (d) Boxplots summarising the pairwised core genome SNP distances among isolates in this study, shown in a logarithmic scale. The distribution is depicted for the entire population and each dominant lineage.

Figure 2

Dissemination patterns in northeast Thailand. (a) Province-to-province transmission patterns influenced by northeast Thailand geographical landscape. Nodes present provinces, denoted by abbreviation and ordered by altitude: U-Udon Thani, K-Khon Kaen, B-Buriram, R - Roi Et, N-Nakhon Phanom, Su-Surin, M-Mukdahan, and Si-Sisaket. Rivers are depicted in blue with major rivers including the Great Mekong River, the Chi River, and the Mun River and their flow direction annotated. (b) Average altitude of provinces in meters above sea level. Error bars present 95% confidence interval. The northwest provinces exhibit higher altitudes, gradually declining towards the southeast. For (a) and (b) solid arrows illustrating transmission directionality explained by altitude differences. Dotted arrows represent transmission directionality influenced by northeast monsoon winds. Grey arrows signify patterns with unclear explanation.

Figure 3

Dominant lineage-specific genes and their Gene Ontology (GO terms). (a) The heatmap represents lineage-specific genes (right) detected in each isolate, aligned with the phylogeny (left). Lineage-specific genes shared across multiple dominant lineages are highlighted in yellow. Lineage-specific genes from lineage 1, 2, 3 are coloured in green, red, and purple, respectively. Additionally, the colour stripes provide information on the lineage and sub-lineage membership (b) Bar plots displays the frequency of GO annotations of lineage-specific genes in each dominant lineage categorised by biological process, molecular function, and cellular compartment. The pie-charts summarise the proportion of lineage-specific genes with assigned GO terms (black).

Figure 4

Transcriptome analysis of representative strains: K96243 (lineage 1), UKMD286 (lineage 2) and UKMH10 (lineage 3) (a to c) Volcano plots demonstrate differential gene expression (DGE) between environmental and infection conditions. Vertical dotted lines represent the statistical cut-off at log two-fold change, while horizontal dotted lines display the statistical cut-off at the adjusted p-value of 0.05 on a negative log scale. Each dot represents a gene, with lineage-1, lineage-2, and lineage-3-specific coloured in green, red, and purple, respectively. (d) Binary expression profile of lineage-1-specific genes across different conditions. A star denotes significant differences in the gene expression profile of lineage-1-specific genes compared the remaining genes of strain K96243.