Biogeography and genetic diversity of clinical isolates of Burkholderia pseudomallei in Sri Lanka

Abstract

Background Melioidosis is a potentially fatal infectious disease caused by Burkholderia pseudomallei and the disease is endemic in SoutheastAsia and Northern Australia. It has been confirmed as endemic in Sri Lanka. Genomic epidemiology of B. pseudomallei in Sri Lanka is largely unexplored. This study aims to determine the biogeography and genetic diversity of clinical isolates of B. pseudomallei and the phylogenetic and evolutionary relationship of Sri Lankan sequence types (STs) to those found in other endemic regions of Southeast Asia and Oceania. Methods The distribution of variably present genetic markers [Burkholderia intracellular motility A (bimA) gene variants bimABP/bimABM, filamentous hemagglutinin 3 (fhaB3), Yersinia-like fimbrial (YLF) and B. thailandensis-like flagellum and chemotaxis (BTFC) gene clusters and lipopolysaccharide O-antigen type A (LPS type A)] was examined among 310 strains. Multilocus sequence typing (MLST) was done for 84 clinical isolates. The phylogenetic and evolutionary relationship of Sri Lankan STs within Sri Lanka and in relation to those found in other endemic regions of Southeast t Asia and Oceania were studied using e BURST, PHYLOViZ and minimum evolutionary analysis. Results The Sri Lankan B. pseudomallei population contained a large proportion of the rare BTFC Clade (14.5%) and bimABM allele variant (18.5%) with differential geographic distribution. Genotypes fhaB3 and LPSA were found in 80% and 86% respectively. This study reported 43 STs (including 22 novel). e-BURST analysis which include all Sri Lankan STs (71) resulted in four groups, with a large clonal group (group 1) having 46 STs, and 17 singletons. ST1137 was the commonest ST. Several STs were shared with India, Bangladesh and Cambodia. Conclusion This study demonstrates the usefulness of high-resolution molecular typing to locate isolates within the broad geographical boundaries of B. pseudomallei at a global level and reveals that Sri Lankan isolates are intermediate between Southeast Asia and Oceania.

Burkholderia pseudomallei in soil and natural water bodies in rural Sri Lanka: A hidden threat to public health

“…MLST of the eight environmental isolates revealed only three STs, showing a low diversity among the environmental strains as has been noted in Singapore ( 1 ). There were no novel STs, when compared with the international B. pseudomallei database ( https://pubmlst.org/organisms/burkholderia-pseudomallei ) and all three sequence types had been recorded previously in clinical infections in Sri Lankan patients ( 10 ). PHYLOViZ analysis of selected environmental STs from the B. pseudomallei database divided them into two distinct populations, Australian and Southeast Asian.…”

“…It is interesting to note that the Australian population is recognized as the most ancestral population ( 28 ). The reason for the close relationship between B. pseudomallei isolates from Sri Lanka and Australia is unknown but could be related to their original positions in Gondwanaland ( 10 ).…”

“…Multilocus sequence typing (MLST) is a useful epidemiological tool to investigate the biogeographic and phylogenetic features of B. pseudomallei and has been used widely to identify the population genetics of isolates from a particular geographic area and to analyze their relationship to isolates from other regions (1). Sequence type (ST) data can be further analyzed using phylogenetic tools such as PHYLOVIZ to elucidate the genetic relatedness of B. pseudomallei from distinct locations (10). MLST has also been used to identify the source of outbreaks although the restricted number of genes analyzed may limit discrimination as demonstrated by whole genome sequencing (WGS) of identical STs revealing non-clonality in a case cluster (11).…”

“…Sequence typing of 193 B. pseudomallei clinical isolates from Sri Lanka revealed 71 distinct STs with ST1137, ST1136 and ST1132 being the most frequent. In addition, examination of variably present genetic markers i.e., bimA, fhaB3 , YLF, and BTFC gene clusters and LPS type A among 310 isolates showed a diversity of genotypes, intermediate between Southeast Asia and Oceania ( 10 ).…”

Physicochemical Determinants of Distribution of Sequence Types (ST) of Burkholderia pseudomallei from Small Ruminant Farms in Peninsular Malaysia

“…with the physicochemical attributes of the. In endemic countries, the organism may not be evenly distributed throughout the landscape (Limmathurotsakul et al, 2010;Jayasinghearachchi et al, 2021). This uneven distribution of B. pseudomallei is considered to be due to physical and chemical factors in the environment that have been found to affect microbial populations in the soil (Ngamsang et al, 2015;Chewapreecha et al, 2022).…”