Molecular analysis of clinical Burkholderia pseudomallei isolates from southwestern coastal region of India, using multi-locus sequence typing

Abstract

BackgroundThe Gram-negative soil dwelling bacterium Burkholderia pseudomallei is the etiological agent of melioidosis. The disease is endemic in most parts of Southeast Asia and northern Australia. Over last few years, there has been an increase in number of melioidosis cases from India; however the disease epidemiology is less clearly understood. Multi-locus sequence typing (MLST) is a powerful genotypic method used to characterize the genetic diversity of B. Pseudomallei both within and across the geographic regions.MethodsIn this study, MLST analysis was performed on 64 B. pseudomallei clinical isolates. These isolates were obtained between 2008–2014 from southwestern coastal region of India. Broad population patterns of Indian B. pseudomallei isolates in context with isolates of Southeast Asia or global collection was determined using in silico phylogenetic tools.ResultsA total of 32 Sequence types (STs) were reported among these isolates of which 17 STs (53%) were found to be novel. ST1368 was found as group founder and the most predominant genotype (n = 11, 17%). Most of the B. pseudomallei isolates reported in this study (or other Indian isolates available in MLST database) clustered in one major group suggesting clonality in Indian isolates; however, there were a few outliers. When analyzed by measure of genetic differentiation (FST) and other phylogenetic tools (e.g. PHYLOViZ), Indian STs were found closer to Southeast Asian isolates than Australian isolates. The phylogenetic analysis further revealed that within Asian clade, Indian isolates grouped more closely with isolates from Sri Lanka, Vietnam, Bangladesh and Thailand.ConclusionsOverall, the results of this study suggest that the Indian B. pseudomallei isolates are closely related with lesser heterogeneity among them and cluster in one major group suggesting clonality of the isolates. However, it appears that there are a few outliers which are distantly related to the majority of Indian STs. Phylogenetic analysis suggest that Indian isolates are closely related to isolates from Southeast Asia, particularly from South Asia.

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

“…Our MLST and phylogenetic analysis demonstrated that B. pseudomallei from Myanmar are genetically diverse and heterogenous, with nine STs identified amongst only sixteen isolates. This finding is consistent with the high levels of genetic and ST diversity in B. pseudomallei from neighbouring countries including India 32 , China 33 and Thailand 34 and in the ancient B. pseudomallei population from the Northern Territory of Australia 35 , 36 . Five of the Myanmar STs had not been previously identified, with four being environmental isolates.…”

Multi locus sequence typing of clinical Burkholderia pseudomallei isolates from Malaysia

“…This uncertainty in the true number of cases and fatalities attributed to melioidosis in Malaysia is related to the lack of awareness of the disease among primary healthcare professionals and the general public. As such, a country-wide survey of B. pseudomallei isolated from melioidosis patients using molecular methods such as sequence typing will be useful to assess the population structure of the organism locally as well as in relation to the worldwide B. pseudomallei population [13,14]. On a broader scope, molecular epidemiology of B. pseudomallei will also provide PLOS NEGLECTED TROPICAL DISEASES insights into the biogeography and factors that influence the distribution of the organism within a particular ecology where such knowledge can assist in public health management during outbreaks [15,16].…”

“…pseudomallei isolated from melioidosis patients using molecular methods such as sequence typing will be useful to assess the population structure of the organism locally as well as in relation to the worldwide B . pseudomallei population [ 13 , 14 ]. On a broader scope, molecular epidemiology of B .…”

Misidentification of Burkholderia pseudomallei, China

“…We conducted multilocus sequence typing as described previously ( 5 ). This isolate belongs to sequence type (ST) 550, corresponding with isolates previously documented in Vietnam in 2005 ( 6 ). The patient in this study had never been to Vietnam, but Guangxi Province borders that country.…”

“…We constructed a phylogenetic tree with 1,000 bootstrap replicates using the unweighted pair group method with arithmetic averages in MEGA X software ( https://www.megasoftware.net ). This tree included isolates from other countries in Asia downloaded from PubMLST ( https://pubmlst.org ); the isolate in this study was most closely related to ST175 from Thailand ( Appendix Figure 2) ( 6 ).…”