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Tracing melioidosis back to the source: using whole-genome sequencing to investigate an outbreak originating from a contaminated domestic water supply

McRobb, Evan and Sarovich, Derek S. and Price, Erin P. and Kaestli, Mirjam and Mayo, Mark and Keim, Paul and Currie, Bart J. (2015) Tracing melioidosis back to the source: using whole-genome sequencing to investigate an outbreak originating from a contaminated domestic water supply. Journal of Clinical Microbiology, 53 (4). pp. 1144-1148. ISSN 1098-660X


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Publisher’s or external URL: http://dx.doi.org/10.1128/JCM.03453-14


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.

Item Type: Article
Publisher’s Statement: Copyright © 2015, American Society for Microbiology. All Rights Reserved.
ID number or DOI: 10.1128/JCM.03453-14
Subjects: Q Science > QH Natural history > QH426 Genetics
NAU Depositing Author Academic Status: Faculty/Staff
Department/Unit: Research Centers > Center for Microbial Genetics and Genomics
Date Deposited: 18 Oct 2015 19:23
URI: http://openknowledge.nau.edu/id/eprint/843

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