Epidemiological tracking and population assignment of the non-clonal bacterium, burkholderia pseudomallei

J Dale; Erin P Price; H Hornstra; J D Busch; M Mayo; D Godoy; V Wuthiekanun; A Baker; J T Foster; D M Wagner; A Tuanyok; J Warner; B G Spratt; S J Peacock; B J Currie; P Keim; T Pearson

doi:10.1371/journal.pntd.0001381

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Epidemiological tracking and population assignment of the non-clonal bacterium, burkholderia pseudomallei

Journal article

Open access

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Epidemiological tracking and population assignment of the non-clonal bacterium, burkholderia pseudomallei

J Dale, Erin P Price, H Hornstra, J D Busch, M Mayo, D Godoy, V Wuthiekanun, A Baker, J T Foster, D M Wagner, …

PLoS Neglected Tropical Diseases, Vol.5(12), e1381

2011

DOI: https://doi.org/10.1371/journal.pntd.0001381

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Abstract

Rapid assignment of bacterial pathogens into predefined populations is an important first step for epidemiological tracking. For clonal species, a single allele can theoretically define a population. For non-clonal species such as Burkholderia pseudomallei, however, shared allelic states between distantly related isolates make it more difficult to identify population defining characteristics. Two distinct B. pseudomallei populations have been previously identified using multilocus sequence typing (MLST). These populations correlate with the major foci of endemicity (Australia and Southeast Asia). Here, we use multiple Bayesian approaches to evaluate the compositional robustness of these populations, and provide assignment results for MLST sequence types (STs). Our goal was to provide a reference for assigning STs to an established population without the need for further computational analyses. We also provide allele frequency results for each population to enable estimation of population assignment even when novel STs are discovered. The ability for humans and potentially contaminated goods to move rapidly across the globe complicates the task of identifying the source of an infection or outbreak. Population genetic dynamics of B. pseudomallei are particularly complicated relative to other bacterial pathogens, but the work here provides the ability for broad scale population assignment. As there is currently no independent empirical measure of successful population assignment, we provide comprehensive analytical details of our comparisons to enable the reader to evaluate the robustness of population designations and assignments as they pertain to individual research questions. Finer scale subdivision and verification of current population compositions will likely be possible with genotyping data that more comprehensively samples the genome. The approach used here may be valuable for other non-clonal pathogens that lack simple group-defining genetic characteristics and provides a rapid reference for epidemiologists wishing to track the origin of infection without the need to compile population data and learn population assignment algorithms. © 2011 Dale et al.

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Title: Epidemiological tracking and population assignment of the non-clonal bacterium, burkholderia pseudomallei
Authors: J Dale (Author) - Northern Arizona University, United States
Erin P Price (Author) - Northern Arizona University, United States
H Hornstra (Author) - Northern Arizona University, United States
J D Busch (Author) - Northern Arizona University, United States
M Mayo (Author) - Royal Darwin Hospital
D Godoy (Author) - Imperial College London, United Kingdom
V Wuthiekanun (Author) - Mahidol University, Thailand
A Baker (Author) - James Cook University
J T Foster (Author) - Northern Arizona University, United States
D M Wagner (Author) - Northern Arizona University, United States
A Tuanyok (Author) - Northern Arizona University, United States
J Warner (Author) - James Cook University
B G Spratt (Author) - Imperial College London, United Kingdom
S J Peacock (Author) - University of Cambridge, United Kingdom
B J Currie (Author) - Royal Darwin Hospital
P Keim (Author) - Northern Arizona University, United States
T Pearson (Author) - Northern Arizona University, United States
Publication details: PLoS Neglected Tropical Diseases, Vol.5(12), e1381
Publisher: Public Library of Science
Date published: 2011
DOI: 10.1371/journal.pntd.0001381
ISSN: 1935-2727
Copyright note: Copyright © 2011 Dale et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Organisation Unit: University of the Sunshine Coast, Queensland; Centre for Bioinnovation
Language: English
Record Identifier: 99450931502621
Output Type: Journal article

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