Multiple phylogenetically-diverse,differentially-virulent Burkholderia pseudomallei isolated from a single soil sample collected in Thailand |
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| Authors: | Chandler Roe Adam J. Vazquez Paul D. Phillips Chris J. Allender Richard A. Bowen Roxanne D. Nottingham Adina Doyle Gumphol Wongsuwan Vanaporn Wuthiekanun Direk Limmathurotsakul Sharon Peacock Paul Keim Apichai Tuanyok David M. Wagner Jason W. Sahl |
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| Affiliation: | 1. The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America;2. Department of Biological Sciences, Colorado State University, Ft. Collins, Colorado, United States of America;3. Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand;4. Department of Medicine, University of Cambridge, Cambridge, England; National University of Singapore, SINGAPORE |
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| Abstract: | Burkholderia pseudomallei is a soil-dwelling bacterium endemic to Southeast Asia and northern Australia that causes the disease, melioidosis. Although the global genomic diversity of clinical B. pseudomallei isolates has been investigated, there is limited understanding of its genomic diversity across small geographic scales, especially in soil. In this study, we obtained 288 B. pseudomallei isolates from a single soil sample (~100g; intensive site 2, INT2) collected at a depth of 30cm from a site in Ubon Ratchathani Province, Thailand. We sequenced the genomes of 169 of these isolates that represent 7 distinct sequence types (STs), including a new ST (ST1820), based on multi-locus sequence typing (MLST) analysis. A core genome SNP phylogeny demonstrated that all identified STs share a recent common ancestor that diverged an estimated 796–1260 years ago. A pan-genomics analysis demonstrated recombination between clades and intra-MLST phylogenetic and gene differences. To identify potential differential virulence between STs, groups of BALB/c mice (5 mice/isolate) were challenged via subcutaneous injection (500 CFUs) with 30 INT2 isolates representing 5 different STs; over the 21-day experiment, eight isolates killed all mice, 2 isolates killed an intermediate number of mice (1–2), and 20 isolates killed no mice. Although the virulence results were largely stratified by ST, one virulent isolate and six attenuated isolates were from the same ST (ST1005), suggesting that variably conserved genomic regions may contribute to virulence. Genomes from the animal-challenged isolates were subjected to a bacterial genome-wide association study to identify genomic regions associated with differential virulence. One associated region is a unique variant of Hcp1, a component of the type VI secretion system, which may result in attenuation. The results of this study have implications for comprehensive sampling strategies, environmental exposure risk assessment, and understanding recombination and differential virulence in B. pseudomallei. |
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