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Whole-genome sequencing of Burkholderia pseudomallei from an urban melioidosis hot spot reveals a fine-scale population structure and localised spatial clustering in the environment.
Sci Rep. 2020 03 25; 10(1):5443.SR

Abstract

Melioidosis is a severe disease caused by the environmental bacterium Burkholderia pseudomallei that affects both humans and animals throughout northern Australia, Southeast Asia and increasingly globally. While there is a considerable degree of genetic diversity amongst isolates, B. pseudomallei has a robust global biogeographic structure and genetic populations are spatially clustered in the environment. We examined the distribution and local spread of B. pseudomallei in Darwin, Northern Territory, Australia, which has the highest recorded urban incidence of melioidosis globally. We sampled soil and land runoff throughout the city centre and performed whole-genome sequencing (WGS) on B. pseudomallei isolates. By combining phylogenetic analyses, Bayesian clustering and spatial hot spot analysis our results demonstrate that some sequence types (STs) are widespread in the urban Darwin environment, while others are highly spatially clustered over a small geographic scale. This clustering matches the spatial distribution of clinical cases for one ST. Results also demonstrate a greater overall isolate diversity recovered from drains compared to park soils, further supporting the role drains may play in dispersal of B. pseudomallei STs in the environment. Collectively, knowledge gained from this study will allow for better understanding of B. pseudomallei phylogeography and melioidosis source attribution, particularly on a local level.

Authors+Show Affiliations

Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, 0811, Australia.Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, 0811, Australia.Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, 0811, Australia.Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, 0811, Australia.Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, 0811, Australia.Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, 0811, Australia.Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, 0811, Australia. Royal Darwin Hospital and Northern Territory Medical Program, Darwin, Northern Territory, 0811, Australia.Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, 0811, Australia. mirjam.kaestli@menzies.edu.au. Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, 0811, Australia. mirjam.kaestli@menzies.edu.au.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32214186

Citation

Rachlin, Audrey, et al. "Whole-genome Sequencing of Burkholderia Pseudomallei From an Urban Melioidosis Hot Spot Reveals a Fine-scale Population Structure and Localised Spatial Clustering in the Environment." Scientific Reports, vol. 10, no. 1, 2020, p. 5443.
Rachlin A, Mayo M, Webb JR, et al. Whole-genome sequencing of Burkholderia pseudomallei from an urban melioidosis hot spot reveals a fine-scale population structure and localised spatial clustering in the environment. Sci Rep. 2020;10(1):5443.
Rachlin, A., Mayo, M., Webb, J. R., Kleinecke, M., Rigas, V., Harrington, G., Currie, B. J., & Kaestli, M. (2020). Whole-genome sequencing of Burkholderia pseudomallei from an urban melioidosis hot spot reveals a fine-scale population structure and localised spatial clustering in the environment. Scientific Reports, 10(1), 5443. https://doi.org/10.1038/s41598-020-62300-8
Rachlin A, et al. Whole-genome Sequencing of Burkholderia Pseudomallei From an Urban Melioidosis Hot Spot Reveals a Fine-scale Population Structure and Localised Spatial Clustering in the Environment. Sci Rep. 2020 03 25;10(1):5443. PubMed PMID: 32214186.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Whole-genome sequencing of Burkholderia pseudomallei from an urban melioidosis hot spot reveals a fine-scale population structure and localised spatial clustering in the environment. AU - Rachlin,Audrey, AU - Mayo,Mark, AU - Webb,Jessica R, AU - Kleinecke,Mariana, AU - Rigas,Vanessa, AU - Harrington,Glenda, AU - Currie,Bart J, AU - Kaestli,Mirjam, Y1 - 2020/03/25/ PY - 2019/10/23/received PY - 2019/12/17/accepted PY - 2020/3/28/entrez PY - 2020/3/28/pubmed PY - 2020/12/17/medline SP - 5443 EP - 5443 JF - Scientific reports JO - Sci Rep VL - 10 IS - 1 N2 - Melioidosis is a severe disease caused by the environmental bacterium Burkholderia pseudomallei that affects both humans and animals throughout northern Australia, Southeast Asia and increasingly globally. While there is a considerable degree of genetic diversity amongst isolates, B. pseudomallei has a robust global biogeographic structure and genetic populations are spatially clustered in the environment. We examined the distribution and local spread of B. pseudomallei in Darwin, Northern Territory, Australia, which has the highest recorded urban incidence of melioidosis globally. We sampled soil and land runoff throughout the city centre and performed whole-genome sequencing (WGS) on B. pseudomallei isolates. By combining phylogenetic analyses, Bayesian clustering and spatial hot spot analysis our results demonstrate that some sequence types (STs) are widespread in the urban Darwin environment, while others are highly spatially clustered over a small geographic scale. This clustering matches the spatial distribution of clinical cases for one ST. Results also demonstrate a greater overall isolate diversity recovered from drains compared to park soils, further supporting the role drains may play in dispersal of B. pseudomallei STs in the environment. Collectively, knowledge gained from this study will allow for better understanding of B. pseudomallei phylogeography and melioidosis source attribution, particularly on a local level. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/32214186/Whole_genome_sequencing_of_Burkholderia_pseudomallei_from_an_urban_melioidosis_hot_spot_reveals_a_fine_scale_population_structure_and_localised_spatial_clustering_in_the_environment_ L2 - https://doi.org/10.1038/s41598-020-62300-8 DB - PRIME DP - Unbound Medicine ER -