Tracing the environmental footprint of the Burkholderia pseudomallei lipopolysaccharide genotypes in the tropical “Top End” of the Northern Territory, Australia

Abstract

The Tier 1 select agent Burkholderia pseudomallei is an environmental bacterium that causes melioidosis, a high mortality disease. Variably present genetic markers used to elucidate strain origin, relatedness and virulence in B . pseudomallei include the Burkholderia intracellular motility factor A ( bimA ) and filamentous hemagglutinin 3 ( fhaB3 ) gene variants. Three lipopolysaccharide (LPS) O-antigen types in B . pseudomallei have been described, which vary in proportion between Australian and Asian isolates. However, it remains unknown if these LPS types can be used as genetic markers for geospatial analysis within a contiguous melioidosis-endemic region. Using a combination of whole-genome sequencing (WGS), statistical analysis and geographical mapping, we examined if the LPS types can be used as geographical markers in the Northern Territory, Australia. The clinical isolates revealed that LPS A prevalence was highest in the Darwin and surrounds (n = 660; 96% being LPS A and 4% LPS B) and LPS B in the Katherine and Katherine remote and East Arnhem regions (n = 79; 60% being LPS A and 40% LPS B). Bivariate logistics regression of 999 clinical B . pseudomallei isolates revealed that the odds of getting a clinical isolate with LPS B was highest in East Arnhem in comparison to Darwin and surrounds (OR 19.5, 95% CI 9.1–42.0; p <0.001). This geospatial correlation was subsequently confirmed by geographically mapping the LPS type from 340 environmental Top End strains. We also found that in the Top End, the minority bimA genotype bimA Bm has a similar remote region geographical footprint to that of LPS B. In addition, correlation of LPS type with multi-locus sequence typing (MLST) was strong, and where multiple LPS types were identified within a single sequence type, WGS confirmed homoplasy of the MLST loci. The clinical, sero-diagnostic and vaccine implications of geographically-based B . pseudomallei LPS types, and their relationships to regional and global dispersal of melioidosis, require global collaborations with further analysis of larger clinically and geospatially-linked datasets.

Multi locus sequence typing of clinical Burkholderia pseudomallei isolates from Malaysia

“…All the isolates were also B . pseudomallei BimA allele variant ( bimA Bp ), a further linkage to Southeast Asia [ 23 ]. All B .…”

Myanmar Burkholderia pseudomallei strains are genetically diverse and originate from Asia with phylogenetic evidence of reintroductions from neighbouring countries

“…Our phylogenetic analysis demonstrated that, despite the ST56 genomes being of Asian origin, the Myanmar ST56s are genetically distinct from those from Bangladesh and Vietnam (separated by 5,688 to 12,103 SNPs-indels) and did not all share a common ancestor, clustering in three phylogenetic locations. This represents another instance of ST homoplasy, which with increasing whole genome analyses is being recognised increasingly and which highlights the limitations of MLST, with unrecognised ST homoplasy suggesting incorrect associations between B. pseudomallei genotypes that confounds analysis of melioidosis epidemiology 39 – 42 . The genetic distance of ST56 genomes from the Australasian node suggests that ST56 may have spread from Vietnam to Myanmar and then from Myanmar on towards Bangladesh, but additional ST56 isolates are needed to confirm this hypothesis.…”

“…Burkholderia intracellular motility factor A (BimA) is responsible for actin-based motility of B. pseudomallei 47 and all Myanmar isolates contained the more common bimA Bp , which is typically identified across Asia and has been associated with pneumonia 48 . bimA Bm has only been identified in Australian and Indian isolates and is associated with neurological melioidosis 39 , 48 – 50 . Filamentous hemagglutinin (fha) is a surface protein that functions as an adhesin 51 .…”

An Evolutionary Arms Race Between Burkholderia pseudomallei and Host Immune System: What Do We Know?

“…Their variations have been seen at the genomic, epigenetic, transcriptomic and proteomic levels. Although genome data for human population from melioidois endemic areas is still scarce, genome data for B.pseudomallei has been accumulating ( Holden et al, 2004 ; Hayden et al, 2012 ; Price et al, 2013 , 2016 ; Sahl et al, 2013 , 2016 ; Daligault et al, 2014 ; Bugrysheva et al, 2015 ; Chen et al, 2015 ; Hsueh et al, 2015 ; Johnson et al, 2015a , b ; McRobb et al, 2015 ; Nandi et al, 2015 ; Sidjabat et al, 2015 ; Song et al, 2015 ; Spring-Pearson et al, 2015 ; Viberg et al, 2015 ; Chapple et al, 2016 ; Aziz et al, 2017 ; Chewapreecha et al, 2017 , 2019 ; Podnecky et al, 2017 ; Viberg et al, 2017 ; Webb et al, 2019 ). When combined with spatial and temporal information, this allows further exploration of allelic variants and a shift in allele frequency over space and time.…”