Tracing the environmental footprint of theBurkholderia pseudomalleilipopolysaccharide genotypes in the tropical “Top End” of the Northern Territory, Australia

Abstract

The Tier 1 select agentBurkholderia pseudomalleiis an environmental bacterium that causes melioidosis, a high mortality disease. Variably present genetic markers used to elucidate strain origin, relatedness and virulence inB. pseudomalleiinclude theBurkholderiaintracellular motility factor A (bimA) and filamentous hemagglutinin 3 (fhaB3) gene variants. Three lipopolysaccharide (LPS) O-antigen types inB. pseudomalleihave 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 clinicalB. pseudomalleiisolates 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 minoritybimAgenotypebimABmhas 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-basedB. pseudomalleiLPS types, and their relationships to regional and global dispersal of melioidosis, require global collaborations with further analysis of larger clinically and geospatially-linked datasets.Author SummaryBurkholderia pseudomalleiis a pathogenic soil bacterium that causes the disease melioidosis, which occurs in many tropical regions globally and in recent years has emerged in non-tropical regions. Melioidosis has been predicted to affect 165,000 people every year resulting in an estimated 89,000 deaths. Person to person transmission is rare with most cases linked to exposure to the bacterium from the environment. The genetic background ofB. pseudomalleihas been well studied and variably present genes have been linked to distinct melioidosis disease states and geographic regions, however we still need a stronger understanding of the association of genes with geography. Three lipopolysaccharide types exist inB. pseudomalleiand the prevalence of the lipopolysaccharide genes vary between melioidosis endemic regions, but it is unknown if the lipopolysaccharide genes can be used as geographical markers in a single melioidosis-endemic region. In this study, we used a combination of whole-genome sequencing, statistics and geographical mapping to elucidate if the three lipopolysaccharide genes can be used as geographical markers within the Northern Territory, Australia. We show that the three LPS types have distinct but overlapping geographical footprints within a single melioidosis region and can be used as geographic markers alongside a number of other important variably presentB. pseudomalleigenes.

Genomic diversity of resistant and virulent factors of Burkholderia pseudomallei clinical strains recovered from Guangdong using whole genome sequencing

“…BimA is typically found in B. pseudomallei across Asia and has been linked with pneumonia (Sarovich et al, 2014). We did not find any BimA variant, i.e., BimA Bm, which has only been reported in Australian and Indian isolates and is associated with neurological disease (Mukhopadhyay et al, 2011;Sarovich et al, 2014;Webb et al, 2019). Until now, no BimA Bm variant has been observed in clinical and environmental isolates from Southeast Asia, which could explain the low incidence of encephalomyelitis in this region (Sarovich et al, 2014).…”

Human Melioidosis

“…This method is based on the premise that there are three LPS types which may confer differing severities of disease and may also have distinct epidemiologies (341)(342)(343). The use of LPS typing in an Australian setting revealed a distinct geographical relationship and correlated with MLST (344). Further international analysis is required to better understand the future utility of LPS typing both from epidemiological and clinical perspectives.…”

Opportunistic pathogens and large microbial diversity detected in source-to-distribution drinking water of three remote communities in Northern Australia

“…Both these genetic markers are more common in B . pseudomalllei from remote NT and bimA- Bm is also more widespread in Southeast Asia [62]. The bimA- Bm gene has been associated with neurological disease [61].…”