Global and regional dissemination and evolution of Burkholderia pseudomallei

Abstract

The environmental bacterium Burkholderia pseudomallei causes an estimated 165,000 cases of human melioidosis per year worldwide and is also classified as a biothreat agent. We used whole genome sequences of 469 B. pseudomallei isolates from 30 countries collected over 79 years to explore its geographic transmission. Our data point to Australia as an early reservoir, with transmission to Southeast Asia followed by onward transmission to South Asia and East Asia. Repeated reintroductions were observed within the Malay Peninsula and between countries bordered by the Mekong River. Our data support an African origin of the Central and South American isolates with introduction of B. pseudomallei into the Americas between 1650 and 1850, providing a temporal link with the slave trade. We also identified geographically distinct genes/variants in Australasian or Southeast Asian isolates alone, with virulence-associated genes being among those over-represented. This provides a potential explanation for clinical manifestations of melioidosis that are geographically restricted.

Figure 1. The phylogeny and pan-genome of B. pseudomallei

Differences in level of bacterial diversity across different geographical origins: Australasia (green), Asia (yellow, cyan, and magenta for (a) and yellow for (b and c)), Africa (blue), America (red), and Europe (star). (a) A core SNP-based maximum likelihood phylogeny of 469 genomes with geographical origins highlighted. The tree was rooted on B. pseudomallei MSHR5619, the most genetically distant isolate based on pairwise SNP distance (see methods and Supplementary Figure 10). The outer ring represents population clusters based on BAPS hierarchical clustering (Group 1 – 19). Apart from Group 15, which is paraphyletic and marked by two black arrows, other groups each form a monophyletic branch. (b) Pan-genome accumulation curve representing rates of new gene discovery in isolates collected from different geographical origins. The order of new genome added was permutated 1,000 times to accommodate possible assortment. (c) Summary of core and accessory genomes of isolates grouped by geographical origins.

Figure 2. Timeline of trans-continental and sub-regional spread of B. pseudomallei

(a) Estimated time when the most recent common ancestor (MRCA) of each cluster emerged. Time (black dots) and 95% highest posterior density (horizontal line) were estimated by BEAST for those clusters with temporal signals. Estimations were performed separately for chromosome I (solid lines), and II (dotted lines). Overlapping estimations between the two chromosomes provide further confidence in the time interval in which the MRCA emerged. The estimation for chromosome I of group 4 did not reach a credible effective sample size and was excluded. (b) Transatlantic slave trade routes and sampling locations of African and American isolates. Each dot represents the geographical origin of isolates used for the time estimation with the size proportional to the number of isolates. (c) The geographical landscape and isolates used to determine sub-regional connectivity. Isolates representing six Southeast Asian countries were plotted on the map, highlighting the geographical proximity of the Mekong group, and the Malay group. The number of isolates from each country was annotated.

Figure 3. Region-specific genetic signatures

Functional categories of genes (COG) localised in region-specific loci. One-sided Fisher’s exact test was used to search for terms that showed significant departure from random expectation in the reference genome. Asterisks highlight terms with heightened frequency following Bonferroni correction for multiple testing. *denotes terms with p-value <10^-9, while ** denotes terms with p-value <2.2x10^-16.