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Taitt CR, Leski TA, Compton JR, Chen A, Berk KL, Dorsey RW, Sozhamannan S, Dutt DL, Vora GJ. Impact of template denaturation prior to whole genome amplification on gene detection in high GC-content species, Burkholderia mallei and B. pseudomallei. BMC Res Notes 2024; 17:70. [PMID: 38475810 DOI: 10.1186/s13104-024-06717-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/13/2024] [Indexed: 03/14/2024] Open
Abstract
OBJECTIVE In this study, we sought to determine the types and prevalence of antimicrobial resistance determinants (ARDs) in Burkholderia spp. strains using the Antimicrobial Resistance Determinant Microarray (ARDM). RESULTS Whole genome amplicons from 22 B. mallei (BM) and 37 B. pseudomallei (BP) isolates were tested for > 500 ARDs using ARDM v.3.1. ARDM detected the following Burkholderia spp.-derived genes, aac(6), blaBP/MBL-3, blaABPS, penA-BP, and qacE, in both BM and BP while blaBP/MBL-1, macB, blaOXA-42/43 and penA-BC were observed in BP only. The method of denaturing template for whole genome amplification greatly affected the numbers and types of genes detected by the ARDM. BlaTEM was detected in nearly a third of BM and BP amplicons derived from thermally, but not chemically denatured templates. BlaTEM results were confirmed by PCR, with 81% concordance between methods. Sequences from 414-nt PCR amplicons (13 preparations) were 100% identical to the Klebsiella pneumoniae reference gene. Although blaTEM sequences have been observed in B. glumae, B. cepacia, and other undefined Burkholderia strains, this is the first report of such sequences in BM/BP/B. thailandensis (BT) clade. These results highlight the importance of sample preparation in achieving adequate genome coverage in methods requiring untargeted amplification before analysis.
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Affiliation(s)
- Chris R Taitt
- Nova Research Inc., Alexandria, VA, 22308, USA
- Center for Biomolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA
| | - Tomasz A Leski
- Center for Biomolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA
| | - Jaimee R Compton
- Center for Biomolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA
| | - Amy Chen
- Karle's Fellow, US Naval Research Laboratory, Washington, DC, USA
| | - Kimberly L Berk
- US Army Combat Capabilities Development Command-Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Robert W Dorsey
- US Army Combat Capabilities Development Command-Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Shanmuga Sozhamannan
- Defense Biological Product Assurance Office, Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Frederick, MD, USA
- Joint Research and Development, Inc., Stafford, VA, USA
| | - Dianne L Dutt
- Defense Threat Reduction Agency, Joint Science and Technology Office, Ft. Belvoir, VA, USA
| | - Gary J Vora
- Center for Biomolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA.
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Meumann EM, Limmathurotsakul D, Dunachie SJ, Wiersinga WJ, Currie BJ. Burkholderia pseudomallei and melioidosis. Nat Rev Microbiol 2024; 22:155-169. [PMID: 37794173 DOI: 10.1038/s41579-023-00972-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2023] [Indexed: 10/06/2023]
Abstract
Burkholderia pseudomallei, the causative agent of melioidosis, is found in soil and water of tropical and subtropical regions globally. Modelled estimates of the global burden predict that melioidosis remains vastly under-reported, and a call has been made for it to be recognized as a neglected tropical disease by the World Health Organization. Severe weather events and environmental disturbance are associated with increased case numbers, and it is anticipated that, in some regions, cases will increase in association with climate change. Genomic epidemiological investigations have confirmed B. pseudomallei endemicity in newly recognized regions, including the southern United States. Melioidosis follows environmental exposure to B. pseudomallei and is associated with comorbidities that affect the immune response, such as diabetes, and with socioeconomic disadvantage. Several vaccine candidates are ready for phase I clinical trials. In this Review, we explore the global burden, epidemiology and pathophysiology of B. pseudomallei as well as current diagnostics, treatment recommendations and preventive measures, highlighting research needs and priorities.
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Affiliation(s)
- Ella M Meumann
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Northern Territory, Australia.
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- NDM Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- NDM Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Willem J Wiersinga
- Division of Infectious Diseases, Center for Experimental Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Northern Territory, Australia
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3
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Seng R, Chomkatekaew C, Tandhavanant S, Saiprom N, Phunpang R, Thaipadungpanit J, Batty EM, Day NPJ, Chantratita W, West TE, Thomson NR, Parkhill J, Chewapreecha C, Chantratita N. Genetic diversity, determinants, and dissemination of Burkholderia pseudomallei lineages implicated in melioidosis in northeast Thailand. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543359. [PMID: 38106061 PMCID: PMC10723255 DOI: 10.1101/2023.06.02.543359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Melioidosis is an often-fatal neglected tropical disease caused by an environmental bacterium Burkholderia pseudomallei. However, our understanding of the disease-causing bacterial lineages, their dissemination, and adaptive mechanisms remains limited. To address this, we conducted a comprehensive genomic analysis of 1,391 B. pseudomallei isolates collected from nine hospitals in northeast Thailand between 2015 and 2018, and contemporaneous isolates from neighbouring countries, representing the most densely sampled collection to date. Our study identified three dominant lineages with unique gene sets enhancing bacterial fitness, indicating lineage-specific adaptation strategies. Crucially, recombination was found to drive lineage-specific gene flow. Transcriptome analyses of representative clinical isolates from each dominant lineage revealed heightened expression of lineage-specific genes in environmental versus infection conditions, notably under nutrient depletion, highlighting environmental persistence as a key factor in the success of dominant lineages. The study also revealed the role of environmental factors - slope of terrain, altitude, direction of rivers, and the northeast monsoons - in shaping B. pseudomallei geographical dispersal. Collectively, our findings highlight persistence in the environment as a pivotal element facilitating B. pseudomallei spread, and as a prelude to exposure and infection, thereby providing useful insights for informing melioidosis prevention and control strategies.
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Affiliation(s)
- Rathanin Seng
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chalita Chomkatekaew
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Veterinary Medicine, University of Cambridge, UK
| | - Sarunporn Tandhavanant
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Natnaree Saiprom
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rungnapa Phunpang
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Janjira Thaipadungpanit
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Elizabeth M Batty
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas PJ Day
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - T. Eoin West
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | | | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, UK
| | - Claire Chewapreecha
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Previous Affiliations: Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut University of Technology Thonburi, Bangkok, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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4
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Zhang JX, Xu JH, Yuan B, Wang XD, Mao XH, Wang JL, Zhang XLL, Yuan Y. Detection of Burkholderia pseudomallei with CRISPR-Cas12a based on specific sequence tags. Front Public Health 2023; 11:1153352. [PMID: 37250090 PMCID: PMC10211466 DOI: 10.3389/fpubh.2023.1153352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/07/2023] [Indexed: 05/31/2023] Open
Abstract
Melioidosis is a bacterial infection caused by Burkholderia pseudomallei (B. pseudomallei), posing a significant threat to public health. Rapid and accurate detection of B. pseudomallei is crucial for preventing and controlling melioidosis. However, identifying B. pseudomallei is challenging due to its high similarity to other species in the same genus. To address this issue, this study proposed a dual-target method that can specifically identify B. pseudomallei in less than 40 min. We analyzed 1722 B. pseudomallei genomes to construct large-scale pan-genomes and selected specific sequence tags in their core genomes that effectively distinguish B. pseudomallei from its closely related species. Specifically, we selected two specific tags, LC1 and LC2, which we combined with the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated proteins (Cas12a) system and recombinase polymerase amplification (RPA) pre-amplification. Our analysis showed that the dual-target RPA-CRISPR/Cas12a assay has a sensitivity of approximately 0.2 copies/reaction and 10 fg genomic DNA for LC1, and 2 copies/reaction and 20 fg genomic DNA for LC2. Additionally, our method can accurately and rapidly detect B. pseudomallei in human blood and moist soil samples using the specific sequence tags mentioned above. In conclusion, the dual-target RPA-CRISPR/Cas12a method is a valuable tool for the rapid and accurate identification of B. pseudomallei in clinical and environmental samples, aiding in the prevention and control of melioidosis.
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Affiliation(s)
- Jia-Xin Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jian-Hao Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bing Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiao-Dong Wang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xu-hu Mao
- Department of Clinical Microbiology and Immunology, The Third Military Medical University, Chongqing, China
| | - Jing-Lin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiang-Li-Lan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuan Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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5
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Wongpalee SP, Thananchai H, Chewapreecha C, Roslund HB, Chomkatekaew C, Tananupak W, Boonklang P, Pakdeerat S, Seng R, Chantratita N, Takarn P, Khamnoi P. Highly specific and sensitive detection of Burkholderia pseudomallei genomic DNA by CRISPR-Cas12a. PLoS Negl Trop Dis 2022; 16:e0010659. [PMID: 36037185 PMCID: PMC9423629 DOI: 10.1371/journal.pntd.0010659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/12/2022] [Indexed: 11/18/2022] Open
Abstract
Detection of Burkholderia pseudomallei, a causative bacterium for melioidosis, remains a challenging undertaking due to long assay time, laboratory requirements, and the lack of specificity and sensitivity of many current assays. In this study, we are presenting a novel method that circumvents those issues by utilizing CRISPR-Cas12a coupled with isothermal amplification to identify B. pseudomallei DNA from clinical isolates. Through in silico search for conserved CRISPR-Cas12a target sites, we engineered the CRISPR-Cas12a to contain a highly specific spacer to B. pseudomallei, named crBP34. The crBP34-based detection assay can detect as few as 40 copies of B. pseudomallei genomic DNA while discriminating against other tested common pathogens. When coupled with a lateral flow dipstick, the assay readout can be simply performed without the loss of sensitivity and does not require expensive equipment. This crBP34-based detection assay provides high sensitivity, specificity and simple detection method for B. pseudomallei DNA. Direct use of this assay on clinical samples may require further optimization as these samples are complexed with high level of human DNA. Melioidosis is a fatal infectious disease caused by a Gram-negative bacterium called Burkholderia pseudomallei. The bacteria can be found in many parts of the world, especially in the tropical and subtropical regions. Infection displays a variety of symptoms such as pneumonia, organ abscess and septicemia. The latter can lead to death within 24–48 hours if not properly diagnosed and treated. Rapid and accurate diagnosis, consequently, are essential for saving patients’ lives. Currently, culturing B. pseudomallei is a gold standard diagnostic method, but the assay turnaround time is 2–4 days, and the result could be of low sensitivity. Other detection methods such as real-time PCR and serological assays are limited by availability of equipment and by low specificity in endemic areas, respectively. For these reasons, in this study we developed a specific, sensitive and rapid detection assay for B. pseudomallei DNA, that is based on CRISPR-Cas12a system. The CRISPR-Cas12a is a protein-RNA complex that recognizes DNA. The RNA can be reprogramed to guide the detection of any DNA of interest, which in our case B. pseudomallei genomic DNA. Our data showed that this assay exhibited a 100% specificity to B. pseudomallei while discriminating against 10 other pathogens and human. The assay can detect B. pseudomallei DNA in less than one hour and does not require sophisticated equipment.
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Affiliation(s)
- Somsakul Pop Wongpalee
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- * E-mail:
| | - Hathairat Thananchai
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Claire Chewapreecha
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Henrik B. Roslund
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Chalita Chomkatekaew
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Warunya Tananupak
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Phumrapee Boonklang
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sukritpong Pakdeerat
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rathanin Seng
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Piyawan Takarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Phadungkiat Khamnoi
- Microbiology Unit, Diagnostic Laboratory, Maharaj Nakorn Chiang Mai Hospital, Chiang Mai, Thailand
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6
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Roe C, Vazquez AJ, Phillips PD, Allender CJ, Bowen RA, Nottingham RD, Doyle A, Wongsuwan G, Wuthiekanun V, Limmathurotsakul D, Peacock S, Keim P, Tuanyok A, Wagner DM, Sahl JW. Multiple phylogenetically-diverse, differentially-virulent Burkholderia pseudomallei isolated from a single soil sample collected in Thailand. PLoS Negl Trop Dis 2022; 16:e0010172. [PMID: 35143500 PMCID: PMC8865643 DOI: 10.1371/journal.pntd.0010172] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 02/23/2022] [Accepted: 01/14/2022] [Indexed: 11/24/2022] Open
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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Affiliation(s)
- Chandler Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Adam J. Vazquez
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul D. Phillips
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Chris J. Allender
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Richard A. Bowen
- Department of Biological Sciences, Colorado State University, Ft. Collins, Colorado, United States of America
| | - Roxanne D. Nottingham
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Adina Doyle
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Gumphol Wongsuwan
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | | | - Sharon Peacock
- Department of Medicine, University of Cambridge, Cambridge, England
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Apichai Tuanyok
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W. Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
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7
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Cummins EA, Hall RJ, McInerney JO, McNally A. Prokaryote pangenomes are dynamic entities. Curr Opin Microbiol 2022; 66:73-78. [PMID: 35104691 DOI: 10.1016/j.mib.2022.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 11/24/2022]
Abstract
Prokaryote pangenomes are influenced heavily by environmental factors and the opportunity for gene gain and loss events. As the field of pangenome analysis has expanded, so has the need to fully understand the complexity of how eco-evolutionary dynamics shape pangenomes. Here, we describe current models of pangenome evolution and discuss their suitability and accuracy. We suggest that pangenomes are dynamic entities under constant flux, highlighting the influence of two-way interactions between pangenome and environment. New classifications of core and accessory genes are also considered, underscoring the need for continuous evaluation of nomenclature in a fast-moving field. We conclude that future models of pangenome evolution should incorporate eco-evolutionary dynamics to fully encompass their dynamic, changeable nature.
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Affiliation(s)
- Elizabeth A Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rebecca J Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - James O McInerney
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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8
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Chewapreecha C, Pensar J, Chattagul S, Pesonen M, Sangphukieo A, Boonklang P, Potisap C, Koosakulnirand S, Feil EJ, Dunachie S, Chantratita N, Limmathurotsakul D, Peacock SJ, Day NPJ, Parkhill J, Thomson NR, Sermswan RW, Corander J. Co-evolutionary Signals Identify Burkholderia pseudomallei Survival Strategies in a Hostile Environment. Mol Biol Evol 2022; 39:6400259. [PMID: 34662416 PMCID: PMC8760936 DOI: 10.1093/molbev/msab306] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The soil bacterium Burkholderia pseudomallei is the causative agent of melioidosis and a significant cause of human morbidity and mortality in many tropical and subtropical countries. The species notoriously survives harsh environmental conditions but the genetic architecture for these adaptations remains unclear. Here we employed a powerful combination of genome-wide epistasis and co-selection studies (2,011 genomes), condition-wide transcriptome analyses (82 diverse conditions), and a gene knockout assay to uncover signals of "co-selection"-that is a combination of genetic markers that have been repeatedly selected together through B. pseudomallei evolution. These enabled us to identify 13,061 mutation pairs under co-selection in distinct genes and noncoding RNA. Genes under co-selection displayed marked expression correlation when B. pseudomallei was subjected to physical stress conditions, highlighting the conditions as one of the major evolutionary driving forces for this bacterium. We identified a putative adhesin (BPSL1661) as a hub of co-selection signals, experimentally confirmed a BPSL1661 role under nutrient deprivation, and explored the functional basis of co-selection gene network surrounding BPSL1661 in facilitating the bacterial survival under nutrient depletion. Our findings suggest that nutrient-limited conditions have been the common selection pressure acting on this species, and allelic variation of BPSL1661 may have promoted B. pseudomallei survival during harsh environmental conditions by facilitating bacterial adherence to different surfaces, cells, or living hosts.
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Affiliation(s)
- Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Parasites and Microbes Programme, Wellcome Sanger Insitute, Hinxton, United Kingdom
- Bioinformatics & Systems Biology Program, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Corresponding authors: E-mails: ; ;
| | - Johan Pensar
- Department of Mathematics, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
| | - Supaksorn Chattagul
- Melioidosis Research Center, Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Maiju Pesonen
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Apiwat Sangphukieo
- Bioinformatics & Systems Biology Program, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Phumrapee Boonklang
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chotima Potisap
- Melioidosis Research Center, Khon Kaen University, Khon Kaen, Thailand
| | - Sirikamon Koosakulnirand
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Edward J Feil
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Susanna Dunachie
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Narisara Chantratita
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nick P J Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas R Thomson
- Parasites and Microbes Programme, Wellcome Sanger Insitute, Hinxton, United Kingdom
| | - Rasana W Sermswan
- Melioidosis Research Center, Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Corresponding authors: E-mails: ; ;
| | - Jukka Corander
- Parasites and Microbes Programme, Wellcome Sanger Insitute, Hinxton, United Kingdom
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Corresponding authors: E-mails: ; ;
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9
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Caicedo-Montoya C, Manzo-Ruiz M, Ríos-Estepa R. Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds. Front Microbiol 2021; 12:677558. [PMID: 34659136 PMCID: PMC8510958 DOI: 10.3389/fmicb.2021.677558] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/30/2021] [Indexed: 01/07/2023] Open
Abstract
Species of the genus Streptomyces are known for their ability to produce multiple secondary metabolites; their genomes have been extensively explored to discover new bioactive compounds. The richness of genomic data currently available allows filtering for high quality genomes, which in turn permits reliable comparative genomics studies and an improved prediction of biosynthetic gene clusters (BGCs) through genome mining approaches. In this work, we used 121 genome sequences of the genus Streptomyces in a comparative genomics study with the aim of estimating the genomic diversity by protein domains content, sequence similarity of proteins and conservation of Intergenic Regions (IGRs). We also searched for BGCs but prioritizing those with potential antibiotic activity. Our analysis revealed that the pan-genome of the genus Streptomyces is clearly open, with a high quantity of unique gene families across the different species and that the IGRs are rarely conserved. We also described the phylogenetic relationships of the analyzed genomes using multiple markers, obtaining a trustworthy tree whose relationships were further validated by Average Nucleotide Identity (ANI) calculations. Finally, 33 biosynthetic gene clusters were detected to have potential antibiotic activity and a predicted mode of action, which might serve up as a guide to formulation of related experimental studies.
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Affiliation(s)
- Carlos Caicedo-Montoya
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Monserrat Manzo-Ruiz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rigoberto Ríos-Estepa
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Medellín, Colombia
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10
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Floridia-Yapur N, Rusman F, Diosque P, Tomasini N. Genome data vs MLST for exploring intraspecific evolutionary history in bacteria: Much is not always better. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 93:104990. [PMID: 34224899 DOI: 10.1016/j.meegid.2021.104990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Genome-based phylogeny has been proposed to be more accurate than phylogeny based in a few genes as MLST-based phylogeny. However, much is not always better. Here we analyzed 368 complete genomes corresponding to 9 bacterial species in order to address intraspecific phylogeny. The studied species were: Burkholderia pseudomallei, Campylobacter jejuni, Chlamydia trachomatis, Helicobacter pylori, Klebsiella pneumoniae, Listeria monocytogenes, Salmonella enterica, Staphylococcus aureus and Streptococcus pyogenes. The intra-specific phylogenies were inferred using the complete genome sequences of different strains of these species and their MLST schemes. A supermatrix approach was used to infer maximum likelihood phylogenies in both cases. The phylogenetic incongruence between the supermatrix-based genome or MLST tree and individual trees (constructed from genome fragments or MLST genes, respectively) was analyzed. In supermatrix-based trees for genomes, most branches showed a high branch support; however, a high number of branches also showed high percentage of topologically incongruent individual trees. Interestingly, genome and MLST trees showed similar levels of incongruence in the phylogeny for each bacteria specie. Both genome and MLST approaches showed that C. trachomatis and S. aureus have a tree-like evolutionary history (low levels of internal incongruence). Instead, B. pseudomallei and S. pyogenes show high levels of incongruence (network-like evolutionary story) probably caused by HGT (horizontal gene transfer). Concluding, our analysis showed that: high branch supports obtained in genome phylogenies could be an artifact probably caused by data size; MLST is valid to address intraspecific phylogenetic structure; and, each species has its own evolutionary history, which could be affected by HGT to different extents.
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Affiliation(s)
- Noelia Floridia-Yapur
- Instituto de Patología Experimental (IPE), UNSa-CONICET, Av. Bolivia 5150, Salta, Argentina
| | - Fanny Rusman
- Instituto de Patología Experimental (IPE), UNSa-CONICET, Av. Bolivia 5150, Salta, Argentina
| | - Patricio Diosque
- Instituto de Patología Experimental (IPE), UNSa-CONICET, Av. Bolivia 5150, Salta, Argentina
| | - Nicolás Tomasini
- Instituto de Patología Experimental (IPE), UNSa-CONICET, Av. Bolivia 5150, Salta, Argentina.
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11
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Peng Z, Dottorini T, Hu Y, Li M, Yan S, Fanning S, Baker M, Xu J, Li F. Comparative Genomic Analysis of the Foodborne Pathogen Burkholderia gladioli pv. cocovenenans Harboring a Bongkrekic Acid Biosynthesis Gene Cluster. Front Microbiol 2021; 12:628538. [PMID: 34079526 PMCID: PMC8166232 DOI: 10.3389/fmicb.2021.628538] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
The environmental bacterium Burkholderia gladioli pv. cocovenenans (B. cocovenenans) has been linked to fatal food poisoning cases in Asia and Africa. Bongkrekic acid (BA), a mitochondrial toxin produced by B. cocovenenans, is thought to be responsible for these outbreaks. While there are over 80 species in the Burkholderia genus, B. cocovenenans is the only pathovar capable of producing BA and causing human death. However, the genomic features of B. gladioli and the evolution of the BA biosynthesis gene cluster, bon, in B. cocovenenans remain elusive. In this study, 239 whole genome sequences (WGSs) of B. gladioli, isolated from 12 countries collected over 100 years, were used to analyze the intra-species genomic diversity and phylogenetic relationships of B. gladioli and to explore the origin and evolution of the bon gene cluster. Our results showed that the genome-wide average nucleotide identity (ANI) values were above 97.29% for pairs of B. gladioli genomes. Thirty-six of the 239 (15.06%) B. gladioli genomes, isolated from corn, rice, fruits, soil, and patients from Asia, Europe, North America, and South America, contained the bon gene cluster and formed three clades within the phylogenetic tree. Pan- and core-genome analysis suggested that the BA biosynthesis genes were recently acquired. Comparative genome analysis of the bon gene cluster showed that complex recombination events contributed to this toxin biosynthesis gene cluster's evolution and formation. This study suggests that a better understanding of the genomic diversity and evolution of this lethal foodborne pathovar will potentially contribute to B. cocovenenans food poisoning outbreak prevention.
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Affiliation(s)
- Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Yue Hu
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Menghan Li
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Shaofei Yan
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Séamus Fanning
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Jin Xu
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
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12
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Gassiep I, Burnard D, Bauer MJ, Norton RE, Harris PN. Diagnosis of melioidosis: the role of molecular techniques. Future Microbiol 2021; 16:271-288. [PMID: 33595347 DOI: 10.2217/fmb-2020-0202] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Melioidosis is an emerging infectious disease with an estimated global burden of 4.64 million disability-adjusted life years per year. A major determinant related to poor disease outcomes is delay to diagnosis due to the fact that identification of the causative agent Burkholderia pseudomallei may be challenging. Over the last 25 years, advances in molecular diagnostic techniques have resulted in the potential for rapid and accurate organism detection and identification direct from clinical samples. While these methods are not yet routine in clinical practice, laboratory diagnosis of infectious diseases is transitioning to culture-independent techniques. This review article aims to evaluate molecular methods for melioidosis diagnosis direct from clinical samples and discuss current and future utility and limitations.
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Affiliation(s)
- Ian Gassiep
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Queensland, 4029, Australia.,Department of Infectious Diseases, Mater Hospital Brisbane, South Brisbane, Queensland, 4101, Australia
| | - Delaney Burnard
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Queensland, 4029, Australia
| | - Michelle J Bauer
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Queensland, 4029, Australia
| | - Robert E Norton
- Pathology Queensland, Townsville University Hospital, Townsville, Queensland, 4814, Australia
| | - Patrick N Harris
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Queensland, 4029, Australia.,Pathology Queensland, Royal Brisbane & Women's Hospital, Herston, Queensland, 4029, Australia
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13
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Ghazali AK, Eng SA, Khoo JS, Teoh S, Hoh CC, Nathan S. Whole-genome comparative analysis of Malaysian Burkholderia pseudomallei clinical isolates. Microb Genom 2021; 7. [PMID: 33565959 PMCID: PMC8208702 DOI: 10.1099/mgen.0.000527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Burkholderia pseudomallei, a soil-dwelling Gram-negative bacterium, is the causative agent of the endemic tropical disease melioidosis. Clinical manifestations of B. pseudomallei infection range from acute or chronic localized infection in a single organ to fulminant septicaemia in multiple organs. The diverse clinical manifestations are attributed to various factors, including the genome plasticity across B. pseudomallei strains. We previously characterized B. pseudomallei strains isolated in Malaysia and noted different levels of virulence in model hosts. We hypothesized that the difference in virulence might be a result of variance at the genome level. In this study, we sequenced and assembled four Malaysian clinical B. pseudomallei isolates, UKMR15, UKMPMC2000, UKMD286 and UKMH10. Phylogenomic analysis showed that Malaysian subclades emerged from the Asian subclade, suggesting that the Malaysian strains originated from the Asian region. Interestingly, the low-virulence strain, UKMH10, was the most distantly related compared to the other Malaysian isolates. Genomic island (GI) prediction analysis identified a new island of 23 kb, GI9c, which is present in B. pseudomallei and Burkholderia mallei, but not Burkholderia thailandensis. Genes encoding known B. pseudomallei virulence factors were present across all four genomes, but comparative analysis of the total gene content across the Malaysian strains identified 104 genes that are absent in UKMH10. We propose that these genes may encode novel virulence factors, which may explain the reduced virulence of this strain. Further investigation on the identity and role of these 104 proteins may aid in understanding B. pseudomallei pathogenicity to guide the design of new therapeutics for treating melioidosis.
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Affiliation(s)
- Ahmad-Kamal Ghazali
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Su-Anne Eng
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Jia-Shiun Khoo
- Codon Genomics S/B, 26, Jalan Dutamas 7, Taman Dutamas Balakong, Selangor, Malaysia
| | - Seddon Teoh
- Codon Genomics S/B, 26, Jalan Dutamas 7, Taman Dutamas Balakong, Selangor, Malaysia
| | - Chee-Choong Hoh
- Codon Genomics S/B, 26, Jalan Dutamas 7, Taman Dutamas Balakong, Selangor, Malaysia
| | - Sheila Nathan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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14
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Chomkatekaew C, Boonklang P, Sangphukieo A, Chewapreecha C. An Evolutionary Arms Race Between Burkholderia pseudomallei and Host Immune System: What Do We Know? Front Microbiol 2021; 11:612568. [PMID: 33552023 PMCID: PMC7858667 DOI: 10.3389/fmicb.2020.612568] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
A better understanding of co-evolution between pathogens and hosts holds promise for better prevention and control strategies. This review will explore the interactions between Burkholderia pseudomallei, an environmental and opportunistic pathogen, and the human host immune system. B. pseudomallei causes "Melioidosis," a rapidly fatal tropical infectious disease predicted to affect 165,000 cases annually worldwide, of which 89,000 are fatal. Genetic heterogeneities were reported in both B. pseudomallei and human host population, some of which may, at least in part, contribute to inter-individual differences in disease susceptibility. Here, we review (i) a multi-host-pathogen characteristic of the interaction; (ii) selection pressures acting on B. pseudomallei and human genomes with the former being driven by bacterial adaptation across ranges of ecological niches while the latter are driven by human encounter of broad ranges of pathogens; (iii) the mechanisms that generate genetic diversity in bacterial and host population particularly in sequences encoding proteins functioning in host-pathogen interaction; (iv) reported genetic and structural variations of proteins or molecules observed in B. pseudomallei-human host interactions and their implications in infection outcomes. Together, these predict bacterial and host evolutionary trajectory which continues to generate genetic diversity in bacterium and operates host immune selection at the molecular level.
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Affiliation(s)
| | | | - Apiwat Sangphukieo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Wellcome Sanger Institute, Hinxton, United Kingdom
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15
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Detection and differentiation of Burkholderia species with pathogenic potential in environmental soil samples. PLoS One 2021; 16:e0245175. [PMID: 33411797 PMCID: PMC7790303 DOI: 10.1371/journal.pone.0245175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/22/2020] [Indexed: 01/12/2023] Open
Abstract
The Burkholderia pseudomallei phylogenetic cluster includes B. pseudomallei, B. mallei, B. thailandensis, B. oklahomensis, B. humptydooensis and B. singularis. Regarded as the only pathogenic members of this group, B. pseudomallei and B. mallei cause the diseases melioidosis and glanders, respectively. Additionally, variant strains of B. pseudomallei and B. thailandensis exist that include the geographically restricted B. pseudomallei that express a B. mallei-like BimA protein (BPBM), and B. thailandensis that express a B. pseudomallei-like capsular polysaccharide (BTCV). To establish a PCR-based assay for the detection of pathogenic Burkholderia species or their variants, five PCR primers were designed to amplify species-specific sequences within the bimA (Burkholderiaintracellular motility A) gene. Our multiplex PCR assay could distinguish pathogenic B. pseudomallei and BPBM from the non-pathogenic B. thailandensis and the BTCV strains. A second singleplex PCR successfully discriminated the BTCV from B. thailandensis. Apart from B. humptydooensis, specificity testing against other Burkholderia spp., as well as other Gram-negative and Gram-positive bacteria produced a negative result. The detection limit of the multiplex PCR in soil samples artificially spiked with known quantities of B. pseudomallei and B. thailandensis were 5 and 6 CFU/g soil, respectively. Furthermore, comparison between standard bacterial culture and the multiplex PCR to detect B. pseudomallei from 34 soil samples, collected from an endemic area of melioidosis, showed high sensitivity and specificity. This robust, sensitive, and specific PCR assay will be a useful tool for epidemiological study of B. pseudomallei and closely related members with pathogenic potential in soil.
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16
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Vezina B, Petit GA, Martin JL, Halili MA. Prediction of Burkholderia pseudomallei DsbA substrates identifies potential virulence factors and vaccine targets. PLoS One 2020; 15:e0241306. [PMID: 33216758 PMCID: PMC7678975 DOI: 10.1371/journal.pone.0241306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/12/2020] [Indexed: 11/19/2022] Open
Abstract
Identification of bacterial virulence factors is critical for understanding disease pathogenesis, drug discovery and vaccine development. In this study we used two approaches to predict virulence factors of Burkholderia pseudomallei, the Gram-negative bacterium that causes melioidosis. B. pseudomallei is naturally antibiotic resistant and there are no clinically available melioidosis vaccines. To identify B. pseudomallei protein targets for drug discovery and vaccine development, we chose to search for substrates of the B. pseudomallei periplasmic disulfide bond forming protein A (DsbA). DsbA introduces disulfide bonds into extra-cytoplasmic proteins and is essential for virulence in many Gram-negative organism, including B. pseudomallei. The first approach to identify B. pseudomallei DsbA virulence factor substrates was a large-scale genomic analysis of 511 unique B. pseudomallei disease-associated strains. This yielded 4,496 core gene products, of which we hypothesise 263 are DsbA substrates. Manual curation and database screening of the 263 mature proteins yielded 81 associated with disease pathogenesis or virulence. These were screened for structural homologues to predict potential B-cell epitopes. In the second approach, we searched the B. pseudomallei genome for homologues of the more than 90 known DsbA substrates in other bacteria. Using this approach, we identified 15 putative B. pseudomallei DsbA virulence factor substrates, with two of these previously identified in the genomic approach, bringing the total number of putative DsbA virulence factor substrates to 94. The two putative B. pseudomallei virulence factors identified by both methods are homologues of PenI family β-lactamase and a molecular chaperone. These two proteins could serve as high priority targets for future B. pseudomallei virulence factor characterization.
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Affiliation(s)
- Ben Vezina
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Guillaume A. Petit
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Jennifer L. Martin
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
- Vice-Chancellor’s Unit, University of Wollongong, Wollongong, New South Wales, Australia
| | - Maria A. Halili
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
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17
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Webb JR, Win MM, Zin KN, Win KKN, Wah TT, Ashley EA, Smithuis F, Swe MMM, Mayo M, Currie BJ, Dance DAB. Myanmar Burkholderia pseudomallei strains are genetically diverse and originate from Asia with phylogenetic evidence of reintroductions from neighbouring countries. Sci Rep 2020; 10:16260. [PMID: 33004984 PMCID: PMC7530998 DOI: 10.1038/s41598-020-73545-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/11/2020] [Indexed: 02/08/2023] Open
Abstract
Melioidosis was first identified in Myanmar in 1911 but for the last century it has remained largely unreported there. Burkholderia pseudomallei was first isolated from the environment of Myanmar in 2016, confirming continuing endemicity. Recent genomic studies showed that B. pseudomallei originated in Australia and spread to Asia, with phylogenetic evidence of repeated reintroduction of B. pseudomallei across countries bordered by the Mekong River and the Malay Peninsula. We present the first whole-genome sequences of B. pseudomallei isolates from Myanmar: nine clinical and seven environmental isolates. We used large-scale comparative genomics to assess the genetic diversity, phylogeography and potential origins of B. pseudomallei in Myanmar. Global phylogenetics demonstrated that Myanmar isolates group in two distantly related clades that reside in a more ancestral Asian clade with high amounts of genetic diversity. The diversity of B. pseudomallei from Myanmar and divergence within our global phylogeny suggest that the original introduction of B. pseudomallei to Myanmar was not a recent event. Our study provides new insights into global patterns of B. pseudomallei dissemination, most notably the dynamic nature of movement of B. pseudomallei within densely populated Southeast Asia. The role of anthropogenic influences in both ancient and more recent dissemination of B. pseudomallei to Myanmar and elsewhere in Southeast Asia and globally requires further study.
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Affiliation(s)
- Jessica R Webb
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.
| | - Mo Mo Win
- Department of Medical Research, Yangon, Myanmar
| | - Khwar Nyo Zin
- Microbiology Laboratory, Yangon General Hospital, Yangon, Myanmar
| | | | | | - Elizabeth A Ashley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Myanmar-Oxford Clinical Research Unit, Yangon, Myanmar
| | - Frank Smithuis
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Myanmar-Oxford Clinical Research Unit, Yangon, Myanmar
| | - Myo Maung Maung Swe
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Department of Infectious Diseases and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, NT, Australia
| | - David A B Dance
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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18
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Abstract
The causative agent of melioidosis, Burkholderia pseudomallei, a tier 1 select agent, is endemic in Southeast Asia and northern Australia, with increased incidence associated with high levels of rainfall. Increasing reports of this condition have occurred worldwide, with estimates of up to 165,000 cases and 89,000 deaths per year. The ecological niche of the organism has yet to be clearly defined, although the organism is associated with soil and water. The culture of appropriate clinical material remains the mainstay of laboratory diagnosis. Identification is best done by phenotypic methods, although mass spectrometric methods have been described. Serology has a limited diagnostic role. Direct molecular and antigen detection methods have limited availability and sensitivity. Clinical presentations of melioidosis range from acute bacteremic pneumonia to disseminated visceral abscesses and localized infections. Transmission is by direct inoculation, inhalation, or ingestion. Risk factors for melioidosis include male sex, diabetes mellitus, alcohol abuse, and immunosuppression. The organism is well adapted to intracellular survival, with numerous virulence mechanisms. Immunity likely requires innate and adaptive responses. The principles of management of this condition are drainage and debridement of infected material and appropriate antimicrobial therapy. Global mortality rates vary between 9% and 70%. Research into vaccine development is ongoing.
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Affiliation(s)
- I Gassiep
- Pathology Queensland, Townsville Hospital, Townsville, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - M Armstrong
- Pathology Queensland, Townsville Hospital, Townsville, Queensland, Australia
| | - R Norton
- Pathology Queensland, Townsville Hospital, Townsville, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
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19
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Pearson T, Sahl JW, Hepp CM, Handady K, Hornstra H, Vazquez AJ, Settles E, Mayo M, Kaestli M, Williamson CHD, Price EP, Sarovich DS, Cook JM, Wolken SR, Bowen RA, Tuanyok A, Foster JT, Drees KP, Kidd TJ, Bell SC, Currie BJ, Keim P. Pathogen to commensal? Longitudinal within-host population dynamics, evolution, and adaptation during a chronic >16-year Burkholderia pseudomallei infection. PLoS Pathog 2020; 16:e1008298. [PMID: 32134991 PMCID: PMC7077878 DOI: 10.1371/journal.ppat.1008298] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 03/17/2020] [Accepted: 01/02/2020] [Indexed: 12/14/2022] Open
Abstract
Although acute melioidosis is the most common outcome of Burkholderia pseudomallei infection, we have documented a case, P314, where disease severity lessened with time, and the pathogen evolved towards a commensal relationship with the host. In the current study, we used whole-genome sequencing to monitor this long-term symbiotic relationship to better understand B. pseudomallei persistence in P314’s sputum despite intensive initial therapeutic regimens. We collected and sequenced 118 B. pseudomallei isolates from P314’s airways over a >16-year period, and also sampled the patient’s home environment, recovering six closely related B. pseudomallei isolates from the household water system. Using comparative genomics, we identified 126 SNPs in the core genome of the 124 isolates or 162 SNPs/indels when the accessory genome was included. The core SNPs were used to construct a phylogenetic tree, which demonstrated a close relationship between environmental and clinical isolates and detailed within-host evolutionary patterns. The phylogeny had little homoplasy, consistent with a strictly clonal mode of genetic inheritance. Repeated sampling revealed evidence of genetic diversification, but frequent extinctions left only one successful lineage through the first four years and two lineages after that. Overall, the evolution of this population is nonadaptive and best explained by genetic drift. However, some genetic and phenotypic changes are consistent with in situ adaptation. Using a mouse model, P314 isolates caused greatly reduced morbidity and mortality compared to the environmental isolates. Additionally, potentially adaptive phenotypes emerged and included differences in the O-antigen, capsular polysaccharide, motility, and colony morphology. The >13-year co-existence of two long-lived lineages presents interesting hypotheses that can be tested in future studies to provide additional insights into selective pressures, niche differentiation, and microbial adaptation. This unusual melioidosis case presents a rare example of the evolutionary progression towards commensalism by a highly virulent pathogen within a single human host. Pathogens frequently jump between different hosts, and associated adaptation may lead to the emergence of new infectious agents. Such host-jumping evolution is witnessed through endpoint analyses but these cannot capture genetic changes in lineages that have gone extinct. In this study, we have identified and monitored an example of the evolution of a bacterium often deadly to its mammalian host, in an unprecedented case whereby disease lessened through time and the pathogen became a part of the commensal human flora. We used genomic analyses to characterize more than 16 years of this evolutionary process and the stepwise mutations that control pathogen interactions with the patient. Soon after infection, mutational changes occurred that allowed the bacterium to remain in the airways without causing disease. This shift towards avirulence was determined based on clinical data and virulence testing in an animal model. In addition, mutations occurred that contributed to the persistence of the bacteria in the patient's lungs. Finally, we found evidence for the evolutionary emergence and persistence of two distinct lineages of the bacterium over the last 13 years, presenting interesting questions about niche utilization. Bacteria are ubiquitous in the human body and almost all are beneficial or benign. In this study, we document the evolutionary conversion of a normally deadly bacterium towards a commensal.
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Affiliation(s)
- Talima Pearson
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W. Sahl
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Crystal M. Hepp
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Karthik Handady
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Heidie Hornstra
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Adam J. Vazquez
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Erik Settles
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Mirjam Kaestli
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Charles H. D. Williamson
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Erin P. Price
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Derek S. Sarovich
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - James M. Cook
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Spenser R. Wolken
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Richard A. Bowen
- Department of Biomedical Sciences, Colorado State University, Colorado, United States of America
| | - Apichai Tuanyok
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jeffrey T. Foster
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Kevin P. Drees
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Timothy J. Kidd
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Scott C. Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, and QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Infectious Diseases Department and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Paul Keim
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail:
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French CT, Bulterys PL, Woodward CL, Tatters AO, Ng KR, Miller JF. Virulence from the rhizosphere: ecology and evolution of Burkholderia pseudomallei-complex species. Curr Opin Microbiol 2020; 54:18-32. [PMID: 32028234 DOI: 10.1016/j.mib.2019.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/30/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Christopher T French
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, 609 Charles E. Young Drive East, Los Angeles, CA 90095, United States; Northern Arizona University, Department of Biological Sciences, Pathogen and Microbiome Institute 1395 S Knoles Drive, Flagstaff, AZ 86011, United States.
| | - Philip L Bulterys
- Department of Pathology, Stanford University, Lane Building, L235, 300 Pasteur Drive, Stanford, CA, 94305, United States
| | - Cora L Woodward
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Avery O Tatters
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Ken R Ng
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Jeff F Miller
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States; Molecular Biology Institute, UCLA, 611 Charles E. Young Drive East, Los Angeles, CA 90095, United States; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, 609 Charles E. Young Drive East, Los Angeles, CA 90095, United States
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21
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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] [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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22
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Rachlin A, Kleinecke M, Kaestli M, Mayo M, Webb JR, Rigas V, Shilton C, Benedict S, Dyrting K, Currie BJ. A cluster of melioidosis infections in hatchling saltwater crocodiles ( Crocodylus porosus) resolved using genome-wide comparison of a common north Australian strain of Burkholderia pseudomallei. Microb Genom 2019; 5. [PMID: 31433287 PMCID: PMC6755496 DOI: 10.1099/mgen.0.000288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Burkholderia pseudomallei is a Gram-negative saprophytic bacillus and the aetiological agent of melioidosis, a disease of public-health importance throughout Southeast Asia and northern Australia. Infection can occur in humans and a wide array of animal species, though zoonotic transmission and case clusters are rare. Despite its highly plastic genome and extensive strain diversity, fine-scale investigations into the population structure of B. pseudomallei indicate there is limited geographical dispersal amongst sequence types (STs). In the ‘Top End’ of northern Australia, five STs comprise 90 % of the overall abundance, the most prevalent and widespread of which is ST-109. In May 2016, ST-109 was implicated in two fatal cases of melioidosis in juvenile saltwater crocodiles at a wildlife park near Darwin, Australia. To determine the probable source of infection, we sampled the crocodile enclosures and analysed the phylogenetic relatedness of crocodile and culture-positive ST-109 environmental park isolates against an additional 135 ST-109 B. pseudomallei isolates from the Top End. Collectively, our whole-genome sequencing (WGS) and pathology findings confirmed B. pseudomallei detected in the hatchling incubator as the likely source of infection, with zero SNPs identified between clinical and environmental isolates. Our results also demonstrate little variation across the ST-109 genome, with SNPs in recombinogenic regions and one suspected case of ST homoplasy accounting for nearly all observed diversity. Collectively, this study supports the use of WGS for outbreak source attribution in highly recombinogenic pathogens, and confirms the epidemiological and phylogenetic insights that can be gained from high-resolution sequencing platforms.
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Affiliation(s)
- Audrey Rachlin
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory 0811, Australia
- *Correspondence: Audrey Rachlin,
| | - Mariana Kleinecke
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory 0811, Australia
| | - Mirjam Kaestli
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory 0811, Australia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory 0811, Australia
| | - Mark Mayo
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory 0811, Australia
| | - Jessica R. Webb
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory 0811, Australia
| | - Vanessa Rigas
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory 0811, Australia
| | - Cathy Shilton
- Berrimah Veterinary Laboratory, Department of Primary Industry, Fisheries and Mines, Berrimah Farm, Makagon Road, Berrimah, Northern Territory 0828, Australia
| | - Suresh Benedict
- Berrimah Veterinary Laboratory, Department of Primary Industry, Fisheries and Mines, Berrimah Farm, Makagon Road, Berrimah, Northern Territory 0828, Australia
| | - Kitman Dyrting
- Berrimah Veterinary Laboratory, Department of Primary Industry, Fisheries and Mines, Berrimah Farm, Makagon Road, Berrimah, Northern Territory 0828, Australia
| | - Bart J. Currie
- 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
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23
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Ledenyova ML, Tkachenko GA, Shpak IM. Imperfect and Compound Microsatellites in the Genomes of Burkholderia pseudomallei Strains. Mol Biol 2019. [DOI: 10.1134/s0026893319010084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Bochkareva OO, Moroz EV, Davydov II, Gelfand MS. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics 2018; 19:965. [PMID: 30587126 PMCID: PMC6307245 DOI: 10.1186/s12864-018-5245-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 11/14/2018] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes. RESULTS We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group. CONCLUSIONS This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei.
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Affiliation(s)
- Olga O. Bochkareva
- Kharkevich Institute for Information Transmission Problems, Moscow, Russia
- Center of Life Sciences Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Elena V. Moroz
- Kharkevich Institute for Information Transmission Problems, Moscow, Russia
| | - Iakov I. Davydov
- Department of Ecology and Evolution & Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mikhail S. Gelfand
- Kharkevich Institute for Information Transmission Problems, Moscow, Russia
- Center of Life Sciences Skolkovo Institute of Science and Technology, Moscow, Russia
- Faculty of Computer Science, Higher School of Economics, Moscow, Russia
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25
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Fleshman A, Mullins K, Sahl J, Hepp C, Nieto N, Wiggins K, Hornstra H, Kelly D, Chan TC, Phetsouvanh R, Dittrich S, Panyanivong P, Paris D, Newton P, Richards A, Pearson T. Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity. Microb Genom 2018; 4. [PMID: 30035711 PMCID: PMC6202447 DOI: 10.1099/mgen.0.000199] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Orientia tsutsugamushi, formerly Rickettsia tsutsugamushi, is an obligate intracellular pathogen that causes scrub typhus, an underdiagnosed acute febrile disease with high morbidity. Scrub typhus is transmitted by the larval stage (chigger) of Leptotrombidium mites and is irregularly distributed across endemic regions of Asia, Australia and islands of the western Pacific Ocean. Previous work to understand population genetics in O. tsutsugamushi has been based on sub-genomic sampling methods and whole-genome characterization of two genomes. In this study, we compared 40 genomes from geographically dispersed areas and confirmed patterns of extensive homologous recombination likely driven by transposons, conjugative elements and repetitive sequences. High rates of lateral gene transfer (LGT) among O. tsutsugamushi genomes appear to have effectively eliminated a detectable clonal frame, but not our ability to infer evolutionary relationships and phylogeographical clustering. Pan-genomic comparisons using 31 082 high-quality bacterial genomes from 253 species suggests that genomic duplication in O. tsutsugamushi is almost unparalleled. Unlike other highly recombinant species where the uptake of exogenous DNA largely drives genomic diversity, the pan-genome of O. tsutsugamushi is driven by duplication and divergence. Extensive gene innovation by duplication is most commonly attributed to plants and animals and, in contrast with LGT, is thought to be only a minor evolutionary mechanism for bacteria. The near unprecedented evolutionary characteristics of O. tsutsugamushi, coupled with extensive intra-specific LGT, expand our present understanding of rapid bacterial evolutionary adaptive mechanisms.
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Affiliation(s)
- Amy Fleshman
- 1Northern Arizona University, Flagstaff, AZ, USA
| | | | - Jason Sahl
- 1Northern Arizona University, Flagstaff, AZ, USA
| | - Crystal Hepp
- 1Northern Arizona University, Flagstaff, AZ, USA
| | - Nathan Nieto
- 1Northern Arizona University, Flagstaff, AZ, USA
| | | | | | - Daryl Kelly
- 2Naval Medical Research Center, Silver Spring, MD, USA.,3The Ohio State University, Columbus, OH, USA
| | | | - Rattanaphone Phetsouvanh
- 4Lao-Oxford-Mahosot Hospital-Wellcome Trust, Research Unit, Mahosot Hospital, Vientiane, Vientiane, Lao People's Democratic Republic
| | - Sabine Dittrich
- 5University of Oxford, Centre for Tropical Medicine and Global Health, Oxford, UK.,6Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People's Democratic Republic.,7Foundation of Innovative New Diagnostics, Geneva, Switzerland
| | - Phonepasith Panyanivong
- 6Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Daniel Paris
- 8Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.,9Swiss Tropical and Public Health Institute, Basel, Switzerland.,10University of Basel, Basel, Switzerland
| | - Paul Newton
- 5University of Oxford, Centre for Tropical Medicine and Global Health, Oxford, UK.,6Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Allen Richards
- 2Naval Medical Research Center, Silver Spring, MD, USA.,11Uniformed Services University of the Health Sciences, Bethesda, MD, USA
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26
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Price EP, Currie BJ, Sarovich DS. Genomic Insights Into the Melioidosis Pathogen, Burkholderia pseudomallei. CURRENT TROPICAL MEDICINE REPORTS 2017. [DOI: 10.1007/s40475-017-0111-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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27
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Sarovich DS, Chapple SNJ, Price EP, Mayo M, Holden MTG, Peacock SJ, Currie BJ. Whole-genome sequencing to investigate a non-clonal melioidosis cluster on a remote Australian island. Microb Genom 2017; 3:e000117. [PMID: 29026657 PMCID: PMC5610713 DOI: 10.1099/mgen.0.000117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 04/20/2017] [Indexed: 12/22/2022] Open
Abstract
Melioidosis is a tropical disease caused by the bacterium Burkholderia pseudomallei. Outbreaks are uncommon and can generally be attributed to a single point source and strain. We used whole-genome sequencing to analyse B. pseudomallei isolates collected from an historical 2-year long case cluster that occurred in a remote northern Australian indigenous island community, where infections were previously linked to a contaminated communal water supply. We analysed the genome-wide relatedness of the two most common multilocus sequence types (STs) involved in the outbreak, STs 125 and 126. This analysis showed that although these STs were closely related on a whole-genome level, they demonstrated evidence of multiple recombination events that were unlikely to have occurred over the timeframe of the outbreak. Based on epidemiological and genetic data, we also identified two additional patients not previously associated with this outbreak. Our results confirm the previous hypothesis that a single unchlorinated water source harbouring multiple B. pseudomallei strains was linked to the outbreak, and that increased melioidosis risk in this community was associated with Piper methysticum root (kava) consumption.
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Affiliation(s)
- Derek S Sarovich
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia.,2Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs, Australia
| | - Stephanie N J Chapple
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia.,3Melbourne Medical School, University of Melbourne, Melbourne, Australia
| | - Erin P Price
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia.,2Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs, Australia
| | - Mark Mayo
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - Matthew T G Holden
- 4School of Medicine, Medical and Biological Sciences, University of St Andrews, St Andrews, UK.,5Wellcome Trust Sanger Institute, Cambridge, UK
| | - Sharon J Peacock
- 5Wellcome Trust Sanger Institute, Cambridge, UK.,6Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bart J Currie
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia.,7Department of Infectious Diseases and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Australia
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28
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Abstract
Background The ability to estimate the evolutionary distance between extant genomes plays a crucial role in many phylogenomic studies. Often such estimation is based on the parsimony assumption, implying that the distance between two genomes can be estimated as the rearrangement distance equal the minimal number of genome rearrangements required to transform one genome into the other. However, in reality the parsimony assumption may not always hold, emphasizing the need for estimation that does not rely on the rearrangement distance. The distance that accounts for the actual (rather than minimal) number of rearrangements between two genomes is often referred to as the true evolutionary distance. While there exists a method for the true evolutionary distance estimation, it however assumes that genomes can be broken by rearrangements equally likely at any position in the course of evolution. This assumption, known as the random breakage model, has recently been refuted in favor of the more rigorous fragile breakage model postulating that only certain “fragile” genomic regions are prone to rearrangements. Results We propose a new method for estimating the true evolutionary distance between two genomes under the fragile breakage model. We evaluate the proposed method on simulated genomes, which show its high accuracy. We further apply the proposed method for estimation of evolutionary distances within a set of five yeast genomes and a set of two fish genomes. Conclusions The true evolutionary distances between the five yeast genomes estimated with the proposed method reveals that some pairs of yeast genomes violate the parsimony assumption. The proposed method further demonstrates that the rearrangement distance between the two fish genomes underestimates their evolutionary distance by about 20%. These results demonstrate how drastically the two distances can differ and justify the use of true evolutionary distance in phylogenomic studies.
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Affiliation(s)
- Nikita Alexeev
- Computational Biology Institute at the George Washington University, Ashburn, 20147, VA, USA.
| | - Max A Alekseyev
- Computational Biology Institute at the George Washington University, Ashburn, 20147, VA, USA
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29
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Multitarget Quantitative PCR Improves Detection and Predicts Cultivability of the Pathogen Burkholderia pseudomallei. Appl Environ Microbiol 2017; 83:AEM.03212-16. [PMID: 28188208 PMCID: PMC5377509 DOI: 10.1128/aem.03212-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/01/2017] [Indexed: 11/20/2022] Open
Abstract
Burkholderia pseudomallei is present in the environment in many parts of the world and causes the often-fatal disease melioidosis. The sensitive detection and quantification of B. pseudomallei in the environment are a prerequisite for assessing the risk of infection. We recently reported the direct detection of B. pseudomallei in soil samples using a quantitative PCR (qPCR) targeting a single type three secretion system 1 (TTSS1) gene. Here, we extend the qPCR-based analysis of B. pseudomallei in soil by validating novel qPCR gene targets selected from a comparative genomic analysis. Two hundred soil samples from two rice paddies in northeast Thailand were evaluated, of which 47% (94/200) were B. pseudomallei culture positive. The TTSS1 qPCR and two novel qPCR assays that targeted open reading frames (ORFs) BPSS0087 and BPSS0745 exhibited detection rates of 76.5% (153/200), 34.5% (69/200), and 74.5% (150/200), respectively. The combination of TTSS1 and BPSS0745 qPCR increased the detection rate to 90% (180/200). Combining the results of the three qPCR assays and the BPSS1187 nested PCR previously published, all 200 samples were positive by at least one PCR assay. Samples positive by either TTSS1 (n = 153) or BPSS0745 (n = 150) qPCR were more likely to be direct-culture positive, with odds ratios of 4.0 (95% confidence interval [CI], 1.7 to 9.5; P < 0.001) and 9.0 (95% CI, 3.1 to 26.4; P < 0.001), respectively. High B. pseudomallei genome equivalents correlated with high CFU counts by culture. In conclusion, multitarget qPCR improved the B. pseudomallei detection rate in soil samples and predicted culture positivity. This approach has the potential for use as a sensitive environmental screening method for B. pseudomallei. IMPORTANCE The worldwide environmental distribution of the soil bacterium Burkholderia pseudomallei remains to be determined. So far, most environmental studies have relied on culture-based approaches to detect this pathogen. Since current culture methods are laborious, are time consuming, and have limited sensitivity, culture-independent and more sensitive methods are needed. In this study, we show that a B. pseudomallei-specific qPCR approach can detect significantly higher numbers of B. pseudomallei-positive soil samples from areas where it is endemic compared with that from culture. The use of multiple independent B. pseudomallei-specific qPCR targets further increased the detection rate of B. pseudomallei compared with that from single targets. Samples with a high molecular B. pseudomallei load were more likely to be culture positive. We conclude that our quantitative multitarget approach might be useful in defining areas where there is a risk of B. pseudomallei infections in different parts of the world.
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30
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Chewapreecha C, Holden MTG, Vehkala M, Välimäki N, Yang Z, Harris SR, Mather AE, Tuanyok A, De Smet B, Le Hello S, Bizet C, Mayo M, Wuthiekanun V, Limmathurotsakul D, Phetsouvanh R, Spratt BG, Corander J, Keim P, Dougan G, Dance DAB, Currie BJ, Parkhill J, Peacock SJ. Global and regional dissemination and evolution of Burkholderia pseudomallei. Nat Microbiol 2017; 2:16263. [PMID: 28112723 PMCID: PMC5300093 DOI: 10.1038/nmicrobiol.2016.263] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 12/08/2016] [Indexed: 11/09/2022]
Abstract
The environmental bacterium Burkholderia pseudomallei causes an estimated 165,000 cases of human melioidosis per year worldwide and is also classified as a biothreat agent. We used whole genome sequences of 469 B. pseudomallei isolates from 30 countries collected over 79 years to explore its geographic transmission. Our data point to Australia as an early reservoir, with transmission to Southeast Asia followed by onward transmission to South Asia and East Asia. Repeated reintroductions were observed within the Malay Peninsula and between countries bordered by the Mekong River. Our data support an African origin of the Central and South American isolates with introduction of B. pseudomallei into the Americas between 1650 and 1850, providing a temporal link with the slave trade. We also identified geographically distinct genes/variants in Australasian or Southeast Asian isolates alone, with virulence-associated genes being among those over-represented. This provides a potential explanation for clinical manifestations of melioidosis that are geographically restricted.
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Affiliation(s)
- Claire Chewapreecha
- Department of Medicine, University of Cambridge, UK
- Wellcome Trust Sanger Institute, Cambridge, UK
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Thailand
| | - Matthew T. G. Holden
- Wellcome Trust Sanger Institute, Cambridge, UK
- School of Medicine, University of St Andrew, UK
| | - Minna Vehkala
- Department of Mathematics and Statistics, University of Helsinki, Finland
| | - Niko Välimäki
- Department of Medical and Clinical Genetics, Genome-Scale Biology Research Program, University of Helsinki, Finland
| | - Zhirong Yang
- Department of Mathematics and Statistics, University of Helsinki, Finland
| | | | | | | | - Birgit De Smet
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Belgium
| | - Simon Le Hello
- Department of Infection and Epidemiology, Enteric bacteria pathogen Unit, Institut Pasteur, Paris, France
| | - Chantal Bizet
- Department of Microbiology, Collection of Institut Pasteur, Institut Pasteur, Paris, France
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University and Royal Darwin Hospital, Darwin, Australia
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine & Global Health, University of Oxford, UK
| | - Rattanaphone Phetsouvanh
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot, Vientiane, Lao PDR
| | - Brian G Spratt
- Department of Infectious Disease Epidemiology, Imperial College, UK
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Finland
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, USA
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, UK
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - David A. B. Dance
- Centre for Tropical Medicine & Global Health, University of Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot, Vientiane, Lao PDR
- London School of Hygiene and Tropical Medicine, UK
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University and Royal Darwin Hospital, Darwin, Australia
| | | | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, UK
- Wellcome Trust Sanger Institute, Cambridge, UK
- London School of Hygiene and Tropical Medicine, UK
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The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers. mBio 2016; 7:mBio.00846-16. [PMID: 27651357 PMCID: PMC5030356 DOI: 10.1128/mbio.00846-16] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whole-genome sequence (WGS) data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive to identify the strict core genome that is specific to the target pathogen. As additional genomes are analyzed, the core genome size is reduced and there is erosion of the target-specific regions due to commonality with related species, potentially resulting in the identification of false positives and/or false negatives. A comparative analysis of 1,130 Burkholderia genomes identified unique markers for many named species, including the human pathogens B. pseudomallei and B. mallei. Due to core genome reduction and signature erosion, only 38 targets specific to B. pseudomallei/mallei were identified. By using only public genomes, a larger number of markers were identified, due to undersampling, and this larger number represents the potential for false positives. This analysis has implications for the design of diagnostics for other species where the genomic space of the target and/or closely related species is not well defined.
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