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Chewapreecha C, Mather AE, Harris SR, Hunt M, Holden MTG, Chaichana C, Wuthiekanun V, Dougan G, Day NPJ, Limmathurotsakul D, Parkhill J, Peacock SJ. Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei. Commun Biol 2019; 2:428. [PMID: 31799430 PMCID: PMC6874650 DOI: 10.1038/s42003-019-0678-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 11/04/2019] [Indexed: 01/09/2023] Open
Abstract
The environmental bacterium Burkholderia pseudomallei causes melioidosis, an important endemic human disease in tropical and sub-tropical countries. This bacterium occupies broad ecological niches including soil, contaminated water, single-cell microbes, plants and infection in a range of animal species. Here, we performed genome-wide association studies for genetic determinants of environmental and human adaptation using a combined dataset of 1,010 whole genome sequences of B. pseudomallei from Northeast Thailand and Australia, representing two major disease hotspots. With these data, we identified 47 genes from 26 distinct loci associated with clinical or environmental isolates from Thailand and replicated 12 genes in an independent Australian cohort. We next outlined the selective pressures on the genetic loci (dN/dS) and the frequency at which they had been gained or lost throughout their evolutionary history, reflecting the bacterial adaptability to a wide range of ecological niches. Finally, we highlighted loci likely implicated in human disease.
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Affiliation(s)
- Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
- Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, 10150 Thailand
- Wellcome Sanger Institute, Hinxton, CB10 1SA UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ UK
| | - Alison E. Mather
- Quadram Institute Bioscience, Norwich, NR4 7UQ UK
- Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| | | | - Martin Hunt
- Wellcome Sanger Institute, Hinxton, CB10 1SA UK
| | | | - Chutima Chaichana
- Department of Mathematics, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok, 10140 Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ UK
| | - Nicholas P. J. Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF UK
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES UK
| | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ UK
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