Identification of Melioidosis Outbreak by Multilocus Variable Number Tandem Repeat Analysis

Currie, Bart J.; Haslem, Asha; Pearson, Talima; Hornstra, Heidie; Leadem, Benjamin R.; Mayo, Mark; Gal, Daniel; Ward, Linda; Godoy, Daniel; Spratt, Brian G.; Keim, Paul

doi:10.3201/eid1502.081036

Cited by 37 publications

(26 citation statements)

References 26 publications

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“…This finding was not surprising given that MLVA loci are known to evolve rapidly, and multiple mutations have been documented in acute B. pseudomallei infections (11,23). However, despite the MLVA differences of P741 and P811, no remarkable features were noted between the clinical presentation of these two cases, consistent with the intergenic nature of these MLVA loci, which are not expected to impart a selective advantage to the bacterium or to cause more severe disease (10,24). It remains a possibility that the variant MLVA-4 type 402 is present in a lower abundance in the water supply, and therefore insufficient sampling precluded its isolation.…”

Section: Resultssupporting

confidence: 49%

Tracing Melioidosis Back to the Source: Using Whole-Genome Sequencing To Investigate an Outbreak Originating from a Contaminated Domestic Water Supply

et al. 2015

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c Melioidosis, a disease of public health importance in Southeast Asia and northern Australia, is caused by the Gram-negative soil bacillus Burkholderia pseudomallei. Melioidosis is typically acquired through environmental exposure, and case clusters are rare, even in regions where the disease is endemic. B. pseudomallei is classed as a tier 1 select agent by the Centers for Disease Control and Prevention; from a biodefense perspective, source attribution is vital in an outbreak scenario to rule out a deliberate release. Two cases of melioidosis within a 3-month period at a residence in rural northern Australia prompted an investigation to determine the source of exposure. B. pseudomallei isolates from the property's groundwater supply matched the multilocus sequence type of the clinical isolates. Whole-genome sequencing confirmed the water supply as the probable source of infection in both cases, with the clinical isolates differing from the likely infecting environmental strain by just one single nucleotide polymorphism (SNP) each. For the first time, we report a phylogenetic analysis of genomewide insertion/deletion (indel) data, an approach conventionally viewed as problematic due to high mutation rates and homoplasy. Our whole-genome indel analysis was concordant with the SNP phylogeny, and these two combined data sets provided greater resolution and a better fit with our epidemiological chronology of events. Collectively, this investigation represents a highly accurate account of source attribution in a melioidosis outbreak and gives further insight into a frequently overlooked reservoir of B. pseudomallei. Our methods and findings have important implications for outbreak source tracing of this bacterium and other highly recombinogenic pathogens. Melioidosis is an underrecognized disease of significant public health burden in many tropical regions across the globe, especially northern Australia and Southeast Asia, where the greatest number of cases are reported annually (1). Melioidosis is caused by the environmental dwelling Gram-negative bacterium Burkholderia pseudomallei, an opportunistic pathogen that most commonly affects people with underlying disease or risk factors, particularly diabetes and hazardous alcohol use (2). Disease severity varies widely and depends on the strain, host immunity, and inoculum size. The highest case fatality rates exceed 90% in septic shock or untreated septic cases (3). Even when appropriate therapy is administered, mortality ranges from 13% in northern Australia (4, 5) to 50% in Southeast Asia (2). In October 2012, B. pseudomallei was upgraded to a tier 1 select agent by the Centers for Disease Control and Prevention (www.selectagents.gov) owing to fears of a deliberate release coupled with the high mortality rate, lack of a vaccine, intrinsic resistance to standard antimicrobial agents, and protean disease presentations that confound diagnosis, particularly in regions where the disease is not endemic.B. pseudomallei infection primarily occurs via percutaneous inoculati...

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Section: Resultssupporting

confidence: 49%

Tracing Melioidosis Back to the Source: Using Whole-Genome Sequencing To Investigate an Outbreak Originating from a Contaminated Domestic Water Supply

et al. 2015

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“…No MLST data were obtained from isolate 3 because of technical reasons, but isolates 2 and 3 shared the same MLVA-4 pattern suggesting an identical ST for these isolates. 10 Although such an identical MLV-4 type indicates a likely geographical or epidemiological link, no such link was found, with these two patients from locations around 50 km apart. All other isolates showed different MLVA-4 patterns.…”

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“…8 Molecular diversity was assessed by multilocus sequence typing (MLST) 9 and multilocus VNTR (variable number tandem repeat) analysis (MLVA-4). 10 Details of molecular results are shown in Table 1 and Figure 1 . The MLST analysis resulted in six different sequence types (STs) from six B. pseudomallei isolates.…”

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Molecular Characterization of Clinical Burkholderia pseudomallei Isolates from India

Mukhopadhyay¹,

Kaestli²,

Vandana³

et al. 2011

The American Society of Tropical Medicine and Hygiene

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“…Ribotyping, BOX primer PCR, or pulsed-field gel electrophoresis (PFGE) have also been used to study the population structure of B. pseudomallei (8)(9)(10); however, these approaches either suffered from reduced resolution and low reproducibility or are labor-intensive. Multilocus variable-number tandem-repeat analysis (MLVA) has previously been used to study the fine-scale genetic diversity of epidemiologically linked B. pseudomallei isolates (11), but this method suffers from homoplasy issues across more distantly related isolates. Recently developed approaches, such as genomic island and 16S to 23S rRNA gene internal transcribed spacer analysis are useful for certain circumstances but, like MLVA, can be confounded by a high rate of lateral gene transfer (12,13).…”

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Distribution of Burkholderia pseudomallei in Northern Australia, a Land of Diversity

McRobb

Kaestli

Price

et al. 2014

Appl Environ Microbiol

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dBurkholderia pseudomallei is a Gram-negative soil bacillus that is the etiological agent of melioidosis and a biothreat agent. Little is known about the biogeography of this bacterium in Australia, despite its hyperendemicity in the northern region of this continent. The population structure of 953 Australian B. pseudomallei strains representing 779 and 174 isolates of clinical and environmental origins, respectively, was analyzed using multilocus sequence typing (MLST). Bayesian population structure and network SplitsTree analyses were performed on concatenated MLST loci, and sequence type (ST) diversity and evenness were examined using Simpson's and Pielou's indices and a multivariate dissimilarity matrix. Bayesian analysis found two B. pseudomallei populations in Australia that were geographically distinct; isolates from the Northern Territory were grouped mainly into the first population, whereas the majority of isolates from Queensland were grouped in a second population. Differences in ST evenness were observed between sampling areas, confirming that B. pseudomallei is widespread and established across northern Australia, with a large number of fragmented habitats. ST analysis showed that B. pseudomallei populations diversified as the sampling area increased. This observation was in contrast to smaller sampling areas where a few STs predominated, suggesting that B. pseudomallei populations are ecologically established and not frequently dispersed. Interestingly, there was no identifiable ST bias between clinical and environmental isolates, suggesting the potential for all culturable B. pseudomallei isolates to cause disease. Our findings have important implications for understanding the ecology of B. pseudomallei in Australia and for potential source attribution of this bacterium in the event of unexpected cases of melioidosis.

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Identification of Melioidosis Outbreak by Multilocus Variable Number Tandem Repeat Analysis

Cited by 37 publications

References 26 publications

Tracing Melioidosis Back to the Source: Using Whole-Genome Sequencing To Investigate an Outbreak Originating from a Contaminated Domestic Water Supply

Tracing Melioidosis Back to the Source: Using Whole-Genome Sequencing To Investigate an Outbreak Originating from a Contaminated Domestic Water Supply

Molecular Characterization of Clinical Burkholderia pseudomallei Isolates from India

Distribution of Burkholderia pseudomallei in Northern Australia, a Land of Diversity

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