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Mataira G, Francis F, Frazer J, Norton R. A comparison of DNA extraction methods used in the direct molecular detection of Burkholderia pseudomallei from blood. Trans R Soc Trop Med Hyg 2024; 118:629-631. [PMID: 38586993 DOI: 10.1093/trstmh/trae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/25/2024] [Accepted: 03/21/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUND Melioidosis is caused by Burkholderia pseudomallei. Direct molecular detection from unamplified blood remains insensitive. METHODS Three different extraction methods-QIAamp UCP Pathogen Mini Kit, High Pure PCR template and MagNA Pure Pathogen Universal-were trialled using spiked human ethylenediaminetetraacetic acid blood. A type III secretion system 1 (TTSS-1) polymerase chain reaction was used for detection. RESULTS The QIAamp UCP Pathogen Mini Kit performed best, with a limit of detection of 1.5×102 cfu/ml. CONCLUSIONS It is planned to use the QIAamp UCP Pathogen Mini Kit to do a larger study on blood collected from patients with melioidosis.
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Affiliation(s)
- Georgia Mataira
- Pathology Queensland, Townsville University Hospital, Douglas, Townsville, Queensland 4814, Australia
| | - Fleur Francis
- Pathology Queensland, Townsville University Hospital, Douglas, Townsville, Queensland 4814, Australia
| | - Jaimie Frazer
- Pathology Queensland, Townsville University Hospital, Douglas, Townsville, Queensland 4814, Australia
| | - Robert Norton
- Pathology Queensland, Townsville University Hospital, Douglas, Townsville, Queensland 4814, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Australia
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2
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Burtnick MN, Dance DAB, Vongsouvath M, Newton PN, Dittrich S, Sendouangphachanh A, Woods K, Davong V, Kenna DTD, Saiprom N, Sengyee S, Hantrakun V, Wuthiekanun V, Limmathurotsakul D, Chantratita N, Brett PJ. Identification of Burkholderia cepacia strains that express a Burkholderia pseudomallei-like capsular polysaccharide. Microbiol Spectr 2024; 12:e0332123. [PMID: 38299821 PMCID: PMC10913486 DOI: 10.1128/spectrum.03321-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/10/2023] [Indexed: 02/02/2024] Open
Abstract
Burkholderia pseudomallei and Burkholderia cepacia are Gram-negative, soil-dwelling bacteria that are found in a wide variety of environmental niches. While B. pseudomallei is the causative agent of melioidosis in humans and animals, members of the B. cepacia complex typically only cause disease in immunocompromised hosts. In this study, we report the identification of B. cepacia strains isolated from either patients or soil in Laos and Thailand that express a B. pseudomallei-like 6-deoxyheptan capsular polysaccharide (CPS). These B. cepacia strains were initially identified based on their positive reactivity in a latex agglutination assay that uses the CPS-specific monoclonal antibody (mAb) 4B11. Mass spectrometry and recA sequencing confirmed the identity of these isolates as B. cepacia (formerly genomovar I). Total carbohydrates extracted from B. cepacia cell pellets reacted with B. pseudomallei CPS-specific mAbs MCA147, 3C5, and 4C4, but did not react with the B. pseudomallei lipopolysaccharide-specific mAb Pp-PS-W. Whole genome sequencing of the B. cepacia isolates revealed the presence of genes demonstrating significant homology to those comprising the B. pseudomallei CPS biosynthetic gene cluster. Collectively, our results provide compelling evidence that B. cepacia strains expressing the same CPS as B. pseudomallei co-exist in the environment alongside B. pseudomallei. Since CPS is a target that is often used for presumptive identification of B. pseudomallei, it is possible that the occurrence of these unique B. cepacia strains may complicate the diagnosis of melioidosis.IMPORTANCEBurkholderia pseudomallei, the etiologic agent of melioidosis, is an important cause of morbidity and mortality in tropical and subtropical regions worldwide. The 6-deoxyheptan capsular polysaccharide (CPS) expressed by this bacterial pathogen is a promising target antigen that is useful for rapidly diagnosing melioidosis. Using assays incorporating CPS-specific monoclonal antibodies, we identified both clinical and environmental isolates of Burkholderia cepacia that express the same CPS antigen as B. pseudomallei. Because of this, it is important that staff working in melioidosis-endemic areas are aware that these strains co-exist in the same niches as B. pseudomallei and do not solely rely on CPS-based assays such as latex-agglutination, AMD Plus Rapid Tests, or immunofluorescence tests for the definitive identification of B. pseudomallei isolates.
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Affiliation(s)
- Mary N. Burtnick
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - David A. B. Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Paul N. Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Sabine Dittrich
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Deggendorf Institut of Technology, European Campus Rottal Inn, Pfarrkirchen, Germany
| | - Amphone Sendouangphachanh
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Kate Woods
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Viengmon Davong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Dervla T. D. Kenna
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health Microbiology Division, Specialised Microbiology & Laboratories Directorate, UK Health Security Agency, London, United Kingdom
| | - Natnaree Saiprom
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sineenart Sengyee
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Viriya Hantrakun
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Direk Limmathurotsakul
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Paul J. Brett
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Yadav PK, Paul M, Singh S, Kumar S, Ponmariappan S, Thavaselvam D. Development of a Novel Internally Controlled HrpB1 Gene-Based Real-Time qPCR Assay for Detection of Burkholderia pseudomallei. Mol Diagn Ther 2024; 28:101-112. [PMID: 38085447 DOI: 10.1007/s40291-023-00686-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2023] [Indexed: 01/14/2024]
Abstract
BACKGROUND Melioidosis, caused by category B bioterrorism agent Burkholderia pseudomallei, is a seasonal disease of tropical and subtropical regions with a high mortality rate. An early and culture-independent detection of B. pseudomallei is required for the appropriate disease management and prevention. The present study is designed to identify novel and unique sequences of B. pseudomallei and development of quantitative polymerase chain reaction (qPCR) assay. METHODS A novel B. pseudomallei-specific target sequence was identified by in silico analysis for the qPCR assay development. The specificity of the developed assay was assessed using purified DNA of 65 different bacterial cultures, and the sensitivity was estimated using a cloned target gene. Further, a type III secretion protein HrpB1 (HrpB1) gene-based duplex qPCR assay incorporating suitable extraction and amplification control was developed, and its viability was assessed in different clinical and environmental matrices for the detection of B. pseudomallei. RESULTS In this study, an 80-nucleotide-long B. pseudomallei-specific region within the gene HrpB1 was identified by computational analysis. The developed HrpB1-based qPCR assay was highly specific for B. pseudomallei detection when evaluated with 65 different bacterial cultures. The sensitivity of the qPCR assay with the HrpB1-recombinant plasmid was found to be five copies per qPCR reaction. The assay's detection limit was found to be 5 × 102 CFU/mL for human blood and urine, 5 × 101 CFU/mL in river water, and 2 × 103 CFU/gm in paddy field soil. CONCLUSION The results of the study showed the applicability of a novel HrpB1-based qPCR assay for sensitive and specific detection of B. pseudomallei in diverse clinical and environmental samples.
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Affiliation(s)
- Pranjal Kumar Yadav
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Moumita Paul
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Suchetna Singh
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Sanjay Kumar
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India.
| | - S Ponmariappan
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Duraipandian Thavaselvam
- O/o Director General Life Science (DGLS), Defence Research and Development Organization, Ministry of Defence, SSPL Campus, Timarpur, New Delhi, 110 054, India.
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4
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Noparatvarakorn C, Jakkul W, Seng R, Tandhavanant S, Ottiwet O, Janon R, Saikong W, Chantratita N. Optimization and prospective evaluation of sensitive real-time PCR assays with an internal control for the diagnosis of melioidosis in Thailand. Microbiol Spectr 2023; 11:e0103923. [PMID: 37819125 PMCID: PMC10715024 DOI: 10.1128/spectrum.01039-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/18/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Melioidosis is a serious infectious disease caused by Burkholderia pseudomallei, an environmental Gram-negative bacterium. Early detection of B. pseudomallei infection is crucial for successful antibiotic treatment and reducing mortality rates associated with melioidosis. Bacteria culture is currently used to identify B. pseudomallei in clinical samples, but the method is slow. Therefore, there is a need for more accurate and sensitive molecular-based diagnostic methods that can detect B. pseudomallei in all sample types, including samples from blood. We developed an optimal DNA extraction method for B. pseudomallei from plasma samples and used an internal control for real-time PCR. We evaluated six PCR target genes and identified the most effective target for the early detection of B. pseudomallei infection in patients. To prevent delays in the treatment of melioidosis that can lead to fatal outcomes, we recommend implementing this new approach for routine early detection of B. pseudomallei in clinical settings.
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Affiliation(s)
- Chawitar Noparatvarakorn
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Wallop Jakkul
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rathanin Seng
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sarunporn Tandhavanant
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Orawan Ottiwet
- Department of Medical Technology and Clinical Pathology, Mukdahan Hospital, Mukdahan, Thailand
| | - Rachan Janon
- Department of Medicine, Mukdahan Hospital, Mukdahan, 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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Somprasong N, Hagen JP, Sahl JW, Webb JR, Hall CM, Currie BJ, Wagner DM, Keim P, Schweizer HP. A conserved active site PenA β-lactamase Ambler motif specific for Burkholderia pseudomallei/B. mallei is likely responsible for intrinsic amoxicillin-clavulanic acid sensitivity and facilitates a simple diagnostic PCR assay for melioidosis. Int J Antimicrob Agents 2023; 61:106714. [PMID: 36640845 DOI: 10.1016/j.ijantimicag.2023.106714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/23/2022] [Accepted: 12/31/2022] [Indexed: 01/13/2023]
Abstract
Burkholderia pseudomallei is a soil- and water-dwelling Gram-negative bacterium that causes melioidosis in humans and animals. Amoxicillin-clavulanic acid (AMC) susceptibility has been hailed as an integral part of the screening algorithm for identification of B. pseudomallei, but the molecular basis for the inherent AMC susceptibility of this bacterium remains undefined. This study showed that B. pseudomallei (and the closely-related B. mallei) wild-type strains are the only Burkholderia spp. that contain a 70STSK73 PenA Ambler motif. This motif was present in >99.5% of 1820 analysed B. pseudomallei strains and 100% of 83 analysed B. mallei strains, and is proposed as the likely cause for their inherent AMC sensitivity. The authors developed a polymerase chain reaction (PCR) assay that specifically amplifies the penA70ST(S/F)K73-containing region from B. pseudomallei and B. mallei, but not from the remaining B. pseudomallei complex species or the 70STFK73 region from the closely-related penB of B. cepacia complex species. The abundance and purity of the 193-bp PCR fragment from putative B. pseudomallei isolates from clinical and environmental samples is likely sufficient for reliable confirmation of the presence of B. pseudomallei. The PCR assay is designed to be especially suited for use in resource-constrained areas. While not further explored in this study, the assay may allow diagnosis of putative B. mallei in culture isolates from animal and human samples.
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Affiliation(s)
- Nawarat Somprasong
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA
| | - Johannah P Hagen
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jessica R Webb
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Carina M Hall
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia; Department of Infectious Diseases and Northern Territory Medical Programme, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - David M Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Herbert P Schweizer
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA.
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Gassiep I, Bauer MJ, Page M, Harris PNA, Norton R. Comparative evaluation of Panther Fusion and real-time PCR for detection of Burkholderia pseudomallei in spiked human blood. Access Microbiol 2022; 4:000333. [PMID: 35693467 PMCID: PMC9175970 DOI: 10.1099/acmi.0.000333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/24/2022] [Indexed: 12/26/2022] Open
Abstract
Introduction. Melioidosis is an infection that most commonly presents with bacteraemia. Culture-based laboratory methods can result in a significant delay to organism identification. Molecular diagnostic techniques have a high sensitivity and rapid time to diagnosis. A decreased time to diagnosis is likely to improve patient outcomes. Aim. To compare the Panther Fusion automated molecular instrument to an in-house method for the detection of Burkholderia pseudomallei directly from spiked human whole-blood samples. Results. The in-house method detected 11/12 (92 %) samples with a B. pseudomallei concentration of 2.5–4.5×102 c.f.u. ml−1. The Panther was less reliable, detecting only 8/14 (75 %) samples with a similar bacterial concentration. The Panther was able to detect 12/12 (100 %) spiked blood culture-positive samples. Conclusion. The direct detection of B. pseudomallei from patient blood on presentation to a healthcare facility will significantly decrease time to diagnosis. We describe an in-house real-time PCR method with the lowest reported limit of detection to date. Due to lower sensitivity, the Panther Fusion would be best used as a diagnostic method directly from a positive blood culture.
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Affiliation(s)
- Ian Gassiep
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
- Department of Infectious Diseases, Mater Hospital Brisbane, South Brisbane, Queensland, Australia
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman’s Hospital, Herston, Queensland, Australia
| | - Michelle J. Bauer
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman’s Hospital, Herston, Queensland, Australia
| | - Melissa Page
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | - Patrick N. A. Harris
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman’s Hospital, Herston, Queensland, Australia
| | - Robert Norton
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Pathology Queensland, Townsville University Hospital, Townsville, Queensland, Australia
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Venkateswaran KS, Parameswaran N, Sarwar J, Plummer A, Santos A, Pillai CA, Bowen S, Granville M, Selvan S, Babu P, Thirunavukkarasu N, Venkateswaran N, Sharma S, Morse SA, Anderson K, Hodge DR, Pillai SP. Validation of a Lateral Flow Test for the Presumptive Identification of the Presence of Burkholderia mallei or Burkholderia pseudomallei in Environmental Samples. Health Secur 2022; 20:154-163. [PMID: 35467945 DOI: 10.1089/hs.2021.0168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We conducted a comprehensive, multiphase laboratory evaluation of InBios Active Melioidosis Detect (AMD) rapid test, a lateral flow immunoassay designed to detect capsular polysaccharides produced by Burkholderia mallei or Burkholderia pseudomallei, used in conjunction with the Omni Array Reader (OAR) for the rapid detection of B mallei or B pseudomallei in environmental (nonclinical) samples at 2 sites. The limit of detection, using reference strains B mallei strain ATCC 23344 and B pseudomallei strain ATCC 11668, was determined to be 103 to 104 CFU/mL. In different phases of the evaluation, inclusivity strains that included geographically diverse strains of B mallei (N = 13) and B pseudomallei (N = 22), geographically diverse phylogenetic near neighbor strains (N = 66), environmental background strains (N = 64), white powder samples (N = 26), and environmental filter extracts (N = 1 pooled sample from 10 filter extracts) were also tested. A total of 1,753 tests were performed, which included positive and negative controls. Visual and OAR results showed that the AMD test detected 92.3% of B mallei and 95.5% of B pseudomallei strains. Of the 66 near-neighbor strains tested, cross-reactivity was observed with only B stabilis 2008724195 and B thailandensis 2003015869. Overall, the specificity and sensitivity were 98.8% and 98.7%, respectively. The results of this evaluation support the use of the AMD test as a rapid, qualitative assay for the presumptive detection of B mallei and B pseudomallei in suspicious environmental samples such as white powders and aerosol samples by first responders and laboratory personnel.
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Affiliation(s)
- Kodumudi S Venkateswaran
- Kodumudi S. Venkateswaran, PhD, is Chief Executive Officer, Omni Array Biotechnology, Rockville, MD
| | | | - Jawad Sarwar
- Jawad Sarwar, MS, is Scientists, Omni Array Biotechnology, Rockville, MD
| | - Andrea Plummer
- Andrea Plummer is Microbiologists, Tetracore, Inc., Rockville, MD
| | - Alan Santos
- Alan Santos is Microbiologists, Tetracore, Inc., Rockville, MD
| | - Christine A Pillai
- Christine A. Pillai is a Oak Ridge Institute for Science and Education Fellow Research Scientist, Molecular Methods Development Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD
| | - Samantha Bowen
- Samantha Bowen, MS is Project Managers, Science and Technology Directorate, US Department of Homeland Security, Washington, DC
| | - Maria Granville
- Maria Granville is Project Managers, Science and Technology Directorate, US Department of Homeland Security, Washington, DC
| | - Senthamil Selvan
- Senthamil Selvan, PhD, is Vice President, Omni Array Biotechnology, Rockville, MD
| | - Prasanti Babu
- Prasanti Babu, MS, is a Research Associate, Omni Array Biotechnology, Rockville, MD
| | - Nagarajan Thirunavukkarasu
- Nagarajan Thirunavukkarasu, PhD, is a Microbiologist, Molecular Methods Development Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD
| | | | - Shashi Sharma
- Shashi Sharma, PhD, is Principal Investigator, Molecular Methods Development Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD
| | - Stephen A Morse
- Stephen A. Morse, MSPH, PhD, is Senior Scientist, IHRC, Inc., Atlanta, GA
| | - Kevin Anderson
- Kevin Anderson, PhD, is Program Manager, Science and Technology Directorate, US Department of Homeland Security, Washington, DC
| | - David R Hodge
- David R. Hodge, PhD, is Program Manager, Science and Technology Directorate, US Department of Homeland Security, Washington, DC
| | - Segaran P Pillai
- Segaran P. Pillai, PhD, FAAM, SM(NRCM), SM(ASCP), is Director, Office of Laboratory Safety, Office of the Commissioner, US Food and Drug Administration, Silver Spring, MD
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8
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Li J, Zhong Q, Shang MY, Li M, Jiang YS, Zou JJ, Ma SS, Huang Q, Lu WP. Preliminary Evaluation of Rapid Visual Identification of Burkholderia pseudomallei Using a Newly Developed Lateral Flow Strip-Based Recombinase Polymerase Amplification (LF-RPA) System. Front Cell Infect Microbiol 2022; 11:804737. [PMID: 35118011 PMCID: PMC8804217 DOI: 10.3389/fcimb.2021.804737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/20/2021] [Indexed: 12/23/2022] Open
Abstract
Burkholderia pseudomallei is an important infectious disease pathogen that can cause melioidosis. Melioidosis is mainly prevalent in Thailand, northern Australia and southern China and has become a global public health problem. Early identification of B. pseudomallei is of great significance for the diagnosis and prognosis of melioidosis. In this study, a simple and visual device combined with lateral flow strip-based recombinase polymerase amplification (LF-RPA) was developed, and the utility of the LF-RPA assay for identifying B. pseudomallei was evaluated. In order to screen out the optimal primer probe, a total of 16 pairs of specific primers targeting the orf2 gene of B. pseudomallei type III secretion system (T3SS) cluster genes were designed for screening, and F1/R3 was selected as an optimal set of primers for the identification of B. pseudomallei, and parameters for LF-RPA were optimized. The LF-RPA can be amplified at 30-45°C and complete the entire reaction in 5-30 min. This reaction does not cross-amplify the DNA of other non-B. pseudomallei species. The limit of detection (LOD) of this assay for B. pseudomallei genomic DNA was as low as 30 femtograms (fg), which was comparable to the results of real-time PCR. Moreover, 21 clinical B. pseudomallei isolates identified by 16S rRNA gene sequencing were retrospectively confirmed by the newly developed LF-RPA system. Our results showed that the newly developed LF-RPA system has a simple and short time of operation and has good application prospect in the identification of B. pseudomallei.
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Affiliation(s)
- Jin Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Laboratory Medicine, Ministry of Education (M.O.E.) Key Laboratory of Laboratory Medicine Diagnostics, Chongqing Medical University, Chongqing, China
| | - Qiu Zhong
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Mei-Yun Shang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Min Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yuan-Su Jiang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Jia-Jun Zou
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Shan-Shan Ma
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- *Correspondence: Wei-Ping Lu, ; Qing Huang,
| | - Wei-Ping Lu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- *Correspondence: Wei-Ping Lu, ; Qing Huang,
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9
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Jayasinghearachchi HS, Corea EM, Jayaratne KI, Fonseka RA, Muthugama TA, Masakorala J, Ramasinghe RYC, De Silva AD. Biogeography and genetic diversity of clinical isolates of Burkholderia pseudomallei in Sri Lanka. PLoS Negl Trop Dis 2021; 15:e0009917. [PMID: 34851950 PMCID: PMC8824316 DOI: 10.1371/journal.pntd.0009917] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 02/08/2022] [Accepted: 10/16/2021] [Indexed: 11/19/2022] Open
Abstract
Background Melioidosis is a potentially fatal infectious disease caused by Burkholderia pseudomallei and the disease is endemic in Southeast Asia and Northern Australia. It has been confirmed as endemic in Sri Lanka. Genomic epidemiology of B. pseudomallei in Sri Lanka is largely unexplored. This study aims to determine the biogeography and genetic diversity of clinical isolates of B. pseudomallei and the phylogenetic and evolutionary relationship of Sri Lankan sequence types (STs) to those found in other endemic regions of Southeast Asia and Oceania. Methods The distribution of variably present genetic markers [Burkholderia intracellular motility A (bimA) gene variants bimABP/bimABM, filamentous hemagglutinin 3 (fhaB3), Yersinia-like fimbrial (YLF) and B. thailandensis-like flagellum and chemotaxis (BTFC) gene clusters and lipopolysaccharide O-antigen type A (LPS type A)] was examined among 310 strains. Multilocus sequence typing (MLST) was done for 84 clinical isolates. The phylogenetic and evolutionary relationship of Sri Lankan STs within Sri Lanka and in relation to those found in other endemic regions of Southeast Asia and Oceania were studied using e BURST, PHYLOViZ and minimum evolutionary analysis. Results The Sri Lankan B. pseudomallei population contained a large proportion of the rare BTFC clade (14.5%) and bimABM allele variant (18.5%) with differential geographic distribution. Genotypes fhaB3 and LPSA were found in 80% and 86% respectively. This study reported 43 STs (including 22 novel). e-BURST analysis which include all Sri Lankan STs (71) resulted in four groups, with a large clonal group (group 1) having 46 STs, and 17 singletons. ST1137 was the commonest ST. Several STs were shared with India, Bangladesh and Cambodia. Conclusion This study demonstrates the usefulness of high-resolution molecular typing to locate isolates within the broad geographical boundaries of B. pseudomallei at a global level and reveals that Sri Lankan isolates are intermediate between Southeast Asia and Oceania. Burkholderia pseudomallei is an important cause of community acquired pneumonia, septicemia and abscesses in Sri Lanka. The risk of infection is increased after flooding following heavy rainfall. Risk groups include rice farmers and rural populations engaged in subsistence cultivation in home gardens. Nationwide surveillance has been carried out since 2006 and the state public health system offers free diagnostics and free antibiotic therapy. The incidence of melioidosis in Sri Lanka has increased in tandem with increased awareness among clinicians. This study reports the genetic diversity among Sri Lankan B. pseudomallei clinical isolates and shows that some variably present genes are regionally distributed. The population is intermediate between Southeast Asia and Oceania. This may reflect its past geological history.
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Affiliation(s)
- Himali S. Jayasinghearachchi
- Institute for Combinatorial Advance Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
- * E-mail: (ASJ); (ADDeS)
| | - Enoka M. Corea
- Department of Medical Microbiology and Immunology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Kumari I. Jayaratne
- Biomedical Laboratory 2, Faculty of Medicine, General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
| | - Regina A. Fonseka
- Department of Medical Microbiology and Immunology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Thilini A. Muthugama
- Biomedical Laboratory 2, Faculty of Medicine, General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
| | - Jayanthi Masakorala
- Department of Medical Microbiology and Immunology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Ravija YC. Ramasinghe
- Biomedical Laboratory 2, Faculty of Medicine, General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
| | - Aruna D. De Silva
- Biomedical Laboratory 2, Faculty of Medicine, General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
- Department of Para-Clinical Sciences, Faculty of Medicine, General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
- * E-mail: (ASJ); (ADDeS)
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10
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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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11
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Adapting Microarray Gene Expression Signatures for Early Melioidosis Diagnosis. J Clin Microbiol 2020; 58:JCM.01906-19. [PMID: 32350042 DOI: 10.1128/jcm.01906-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/17/2020] [Indexed: 12/24/2022] Open
Abstract
Melioidosis is caused by Burkholderia pseudomallei and is predominantly seen in tropical regions. The clinical signs and symptoms of the disease are nonspecific and often result in misdiagnosis, failure of treatment, and poor clinical outcome. Septicemia with septic shock is the most common cause of death, with mortality rates above 40%. Bacterial culture is the gold standard for diagnosis, but it has low sensitivity and takes days to produce definitive results. Early laboratory diagnosis can help guide physicians to provide treatment specific to B. pseudomallei In our study, we adapted host gene expression signatures obtained from microarray data of B. pseudomallei-infected cases to develop a real-time PCR diagnostic test using two differentially expressed genes, AIM2 (absent in melanoma 2) and FAM26F (family with sequence similarity 26, member F). We tested blood from 33 patients with B. pseudomallei infections and 29 patients with other bacterial infections to validate the test and determine cutoff values for use in a cascading diagnostic algorithm. Differentiation of septicemic melioidosis from other sepsis cases had a sensitivity of 82%, specificity of 93%, and negative and positive predictive values (NPV and PPV) of 82% and 93%, respectively. Separation of cases likely to be melioidosis from those unlikely to be melioidosis in nonbacteremic situations showed a sensitivity of 40%, specificity of 54%, and NPV and PPV of 44% and 50%, respectively. We suggest that our AIM2 and FAM26F expression combination algorithm could be beneficial for early melioidosis diagnosis, offering a result within 24 h of admission.
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12
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Choi JY, Hii KC, Bailey ES, Chuang JY, Tang WY, Yuen Wong EK, Ti T, Pau KS, Berita A, Saihidi I, Ting J, Chua TT, Toh TH, AuCoin DP, DeShazer D, Gray GC. Burkholderia pseudomallei Detection among Hospitalized Patients, Sarawak. Am J Trop Med Hyg 2020; 102:388-391. [PMID: 31769397 DOI: 10.4269/ajtmh.19-0625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Burkholderia pseudomallei infections are prevalent in Southeast Asia and northern Australia and often misdiagnosed. Diagnostics are often neither sensitive nor rapid, contributing up to 50% mortality rate. In this 2018 pilot study, we enrolled 100 patients aged 6 months-79 years from Kapit Hospital in Sarawak, Malaysia, with symptoms of B. pseudomallei infection. We used three different methods for the detection of B. pseudomallei: a real-time polymerase chain reaction (PCR) assay, a rapid lateral flow immunoassay, and the standard-of-care bacterial culture-the gold standard. Among the 100 participants, 24 (24%) were positive for B. pseudomallei by one or more of the detection methods. Comparing the two individual diagnostic methods against the gold standard-bacterial culture-of any positive test, there was low sensitivity for each test (25-44%) but high specificity (93-98%). It seems clear that more sensitive diagnostics or a sensitive screening diagnostic followed by specific confirmatory diagnostic is needed for this disease.
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Affiliation(s)
- Jessica Y Choi
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina.,Duke Global Health Institute, Duke University, Durham, North Carolina
| | - King Ching Hii
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Emily S Bailey
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina.,Duke Global Health Institute, Duke University, Durham, North Carolina
| | - Jia Yun Chuang
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Wei Yieng Tang
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | | | - Tiana Ti
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Kat Siong Pau
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Antoinette Berita
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Izreena Saihidi
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Jakie Ting
- Faculty of Medicine, SEGi University, Kota Damansara, Malaysia.,Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia
| | - Tiing-Tiing Chua
- Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia
| | - Teck-Hock Toh
- Faculty of Medicine, SEGi University, Kota Damansara, Malaysia.,Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia
| | | | - David DeShazer
- US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, Maryland
| | - Gregory C Gray
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore.,Duke Global Health Institute, Duke University, Durham, North Carolina.,Global Health Research Center, Duke-Kunshan University, Kunshan, China.,Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina
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13
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Whole-genome sequencing of Burkholderia pseudomallei from an urban melioidosis hot spot reveals a fine-scale population structure and localised spatial clustering in the environment. Sci Rep 2020; 10:5443. [PMID: 32214186 PMCID: PMC7096523 DOI: 10.1038/s41598-020-62300-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/17/2019] [Indexed: 11/12/2022] Open
Abstract
Melioidosis is a severe disease caused by the environmental bacterium Burkholderia pseudomallei that affects both humans and animals throughout northern Australia, Southeast Asia and increasingly globally. While there is a considerable degree of genetic diversity amongst isolates, B. pseudomallei has a robust global biogeographic structure and genetic populations are spatially clustered in the environment. We examined the distribution and local spread of B. pseudomallei in Darwin, Northern Territory, Australia, which has the highest recorded urban incidence of melioidosis globally. We sampled soil and land runoff throughout the city centre and performed whole-genome sequencing (WGS) on B. pseudomallei isolates. By combining phylogenetic analyses, Bayesian clustering and spatial hot spot analysis our results demonstrate that some sequence types (STs) are widespread in the urban Darwin environment, while others are highly spatially clustered over a small geographic scale. This clustering matches the spatial distribution of clinical cases for one ST. Results also demonstrate a greater overall isolate diversity recovered from drains compared to park soils, further supporting the role drains may play in dispersal of B. pseudomallei STs in the environment. Collectively, knowledge gained from this study will allow for better understanding of B. pseudomallei phylogeography and melioidosis source attribution, particularly on a local level.
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14
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Peng Y, Zheng X, Kan B, Li W, Zhang W, Jiang T, Lu J, Qin A. Rapid detection of Burkholderia pseudomallei with a lateral flow recombinase polymerase amplification assay. PLoS One 2019; 14:e0213416. [PMID: 31283772 PMCID: PMC6613700 DOI: 10.1371/journal.pone.0213416] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/17/2019] [Indexed: 02/06/2023] Open
Abstract
Melioidosis is a severe infectious disease caused by gram-negative, facultative intracellular pathogen Burkholderia pseudomallei (B. pseudomallei). Although cases are increasing reported from other parts of the world, it is an illness of tropical and subtropical climates primarily found in southeast Asia and northern Australia. Because of a 40% mortality rate, this life-threatening disease poses a public health risk in endemic area. Early detection of B. pseudomallei infection is vital for prognosis of a melioidosis patient. In this study, a novel isothermal recombinase polymerase amplification combined with lateral flow dipstick (LF-RPA) assay was established for rapid detection of B. pseudomallei. A set of primer-probe targeting orf2 gene within the putative type III secretion system (T3SS) cluster genes was generated and parameters for the LF-RPA assay were optimized. Result can be easy visualized in 30 minutes with the limit of detection (LOD) as low as 20 femtogram (fg) (ca. 25.6 copies) of B. pseudomallei genomic DNA without a specific equipment. The assay is highly specific as no cross amplification was observed with Burkholderia mallei, members of the Burkholderia cepacia-complex and 35 non-B. pseudomallei bacteria species. Moreover, isolates from patients in Hainan (N = 19), Guangdong (N = 1), Guangxi (N = 3) province of China as well as in Australia (N = 3) and Thailand (N = 1) were retrospectively confirmed by the newly developed method. LODs for B. pseudomallei-spiked soil and blood samples were 2.1×103 CFU/g and 4.2×103 CFU/ml respectively. The sensitivity of the LF-RPA assay was comparable to TaqMan Real-Time PCR (TaqMan PCR). In addition, the LF-RPA assay exhibited a better tolerance to inhibitors in blood than TaqMan PCR. Our results showed that the LF-RPA assay is an alternative to existing PCR-based methods for detection of B. pseudomallei with a potentiality of early accurate diagnosis of melioidosis at point of care or in-field use.
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Affiliation(s)
- Yao Peng
- Department of Pestis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Xiao Zheng
- Department of Pestis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Biao Kan
- Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Wei Li
- Department of Pestis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Wen Zhang
- Department of Bioinformatics, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Taozhen Jiang
- Department of Preservation Center for Standard Strain, China Institute of Veterinary Drug Control, Beijing, China
| | - Jinxing Lu
- Department of Hospital Antibiotics Resistance, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Aiping Qin
- State Key Laboratory of Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
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15
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Mohd Ali MR, Lih Huey L, Foo PC, Goay YX, Ismail AS, Mustaffa KMF, Aziah I, Kia Kien P, Harun A, Ismail N, Yean Yean C. Duplex TaqMan Hydrolysis Probe-Based Molecular Assay for Simultaneous Detection and Differentiation of Burkholderia pseudomallei and Leptospira spp. DNA. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9451791. [PMID: 31355287 PMCID: PMC6633960 DOI: 10.1155/2019/9451791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 11/18/2022]
Abstract
Melioidosis and leptospirosis, caused by two different bacteria, Burkholderia pseudomallei and Leptospira spp., are potentially fatal infections that share a very similar spectrum of clinical features and cause significant mortality and morbidity in humans and livestock. Early detection is important for better clinical consequences. To our knowledge, there is no diagnostic tool available to simultaneously detect and differentiate melioidosis and leptospirosis in humans and animals. In this study, we described a duplex TaqMan probe-based qPCR for the detection of B. pseudomallei and Leptospira spp. DNA. The performance of the assay was evaluated on 20 B. pseudomallei isolates, 23 Leptospira strains, and 39 other microorganisms, as well as two sets of serially diluted reference strains. The duplex qPCR assay was able to detect 0.02 pg (~ 4 copies) Leptospira spp. DNA and 0.2 pg (~ 25.6 copies) B. pseudomallei DNA. No undesired amplification was observed in other microorganisms. In conclusion, the duplex qPCR assay was sensitive and specific for the detection of B. pseudomallei & Leptospira spp. DNA and is suitable for further analytical and clinical evaluation.
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Affiliation(s)
- Mohammad Ridhuan Mohd Ali
- Bacteriology Unit, Infectious Disease Research Centre, Institute for Medical Research, Ministry of Health Malaysia, National Institutes of Health Complex, Bandar Setia Alam, 40170 Shah Alam, Selangor, Malaysia
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Lee Lih Huey
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Phiaw Chong Foo
- Acarology Unit, Infectious Disease Research Centre, Institute for Medical Research, Ministry of Health Malaysia, National Institutes of Health Complex, Bandar Setia Alam, 40170 Shah Alam, Selangor, Malaysia
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Yuan Xin Goay
- INTI International College Penang, Lebuh Bukit Jambul, Bukit Jambul, 11900 Bayan Lepas, Pulau Pinang, Malaysia
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Asmaliza S. Ismail
- Research Policy & Planning Division, National Institutes of Health, Ministry of Health Malaysia, Bandar Setia Alam, 40170 Shah Alam, Selangor, Malaysia
| | - Khairul Mohd Fadzli Mustaffa
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Ismail Aziah
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Phua Kia Kien
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Azian Harun
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
- Hospital Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Nabilah Ismail
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
- Hospital Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Chan Yean Yean
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
- Hospital Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
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16
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Lipid A Remodeling Is a Pathoadaptive Mechanism That Impacts Lipopolysaccharide Recognition and Intracellular Survival of Burkholderia pseudomallei. Infect Immun 2018; 86:IAI.00360-18. [PMID: 30037795 PMCID: PMC6204721 DOI: 10.1128/iai.00360-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/13/2018] [Indexed: 12/13/2022] Open
Abstract
Burkholderia pseudomallei causes the severe disease melioidosis. The bacterium subverts the host immune system and replicates inside cells, and host mortality results primarily from sepsis-related complications. Burkholderia pseudomallei causes the severe disease melioidosis. The bacterium subverts the host immune system and replicates inside cells, and host mortality results primarily from sepsis-related complications. Lipopolysaccharide (LPS) is a major virulence factor and mediator of sepsis that many pathogens capable of intracellular growth modify to reduce their immunological “footprint.” The binding strength of B. pseudomallei LPS for human LPS binding protein (hLBP) was measured using surface plasmon resonance. The structures of lipid A isolated from B. pseudomallei under different temperatures were analyzed by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), and the gene expression of two lipid A remodeling genes, lpxO and pagL, was investigated. The LPS was characterized for its ability to trigger tumor necrosis factor alpha (TNF-α) release and to activate caspase-11-triggered pyroptosis by introduction of LPS into the cytosol. Lipid A from long-term chronic-infection isolates was isolated and characterized by MALDI-TOF MS and also by the ability to trigger caspase-11-mediated cell death. Lipid A from B. pseudomallei 1026b lpxO and pagL mutants were characterized by positive- and negative-mode MALDI-TOF MS to ultimately identify their role in lipid A structural modifications. Replication of lpxO and pagL mutants and their complements within macrophages showed that lipid A remodeling can effect growth in host cells and activation of caspase-11-mediated cytotoxicity.
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17
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Rapid design and fielding of four diagnostic technologies in Sierra Leone, Thailand, Peru, and Australia: Successes and challenges faced introducing these biosensors. SENSING AND BIO-SENSING RESEARCH 2018. [DOI: 10.1016/j.sbsr.2018.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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18
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Melioidosis: An Australian Perspective. Trop Med Infect Dis 2018; 3:tropicalmed3010027. [PMID: 30274424 PMCID: PMC6136632 DOI: 10.3390/tropicalmed3010027] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/21/2018] [Accepted: 02/22/2018] [Indexed: 12/16/2022] Open
Abstract
Burkholderia pseudomallei is endemic in northern Australia, with cases of melioidosis most commonly occurring during the wet season in individuals with diabetes, hazardous alcohol use, and chronic kidney disease. Pneumonia is the most common presentation and the majority of patients are bacteraemic—however, infection may involve almost any organ, with the skin and soft tissues, genitourinary system, visceral organs, and bone and joints affected most commonly. Central nervous system involvement is rarer, but has a high attributable mortality. Increased awareness of the disease amongst healthcare providers, ready access to appropriate antibiotic therapy and high-quality intensive care services has resulted in a sharp decline in the case fatality rate over the last 20 years. Further improvement in clinical outcomes will require a greater understanding of the disease′s pathophysiology, its optimal management, and more effective strategies for its prevention.
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19
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Abstract
Burkholderia pseudomallei is a Gram-negative environmental bacterium and the aetiological agent of melioidosis, a life-threatening infection that is estimated to account for ∼89,000 deaths per year worldwide. Diabetes mellitus is a major risk factor for melioidosis, and the global diabetes pandemic could increase the number of fatalities caused by melioidosis. Melioidosis is endemic across tropical areas, especially in southeast Asia and northern Australia. Disease manifestations can range from acute septicaemia to chronic infection, as the facultative intracellular lifestyle and virulence factors of B. pseudomallei promote survival and persistence of the pathogen within a broad range of cells, and the bacteria can manipulate the host's immune responses and signalling pathways to escape surveillance. The majority of patients present with sepsis, but specific clinical presentations and their severity vary depending on the route of bacterial entry (skin penetration, inhalation or ingestion), host immune function and bacterial strain and load. Diagnosis is based on clinical and epidemiological features as well as bacterial culture. Treatment requires long-term intravenous and oral antibiotic courses. Delays in treatment due to difficulties in clinical recognition and laboratory diagnosis often lead to poor outcomes and mortality can exceed 40% in some regions. Research into B. pseudomallei is increasing, owing to the biothreat potential of this pathogen and increasing awareness of the disease and its burden; however, better diagnostic tests are needed to improve early confirmation of diagnosis, which would enable better therapeutic efficacy and survival.
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Affiliation(s)
- W Joost Wiersinga
- Department of Medicine, Division of Infectious Diseases, Academic Medical Center, Meibergdreef 9, Rm. G2-132, 1105 AZ Amsterdam, The Netherlands
- Centre for Experimental and Molecular Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Harjeet S Virk
- Centre for Experimental and Molecular Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Alfredo G Torres
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Bart J Currie
- Menzies School of Health Research, Charles Darwin University and Royal Darwin Hospital, Darwin, Australia
| | - Sharon J Peacock
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - David A B Dance
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Lao-Oxford-Mahosot Hospital Wellcome Trust Research Unit, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Direk Limmathurotsakul
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Department of Tropical Hygiene and Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
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20
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TESTAMENTI VINCENTIUSARCA, ISKANDRIATI DIAH, WAHYUDI ARISTRI, PAMUNGKAS JOKO. Detection of Antibody to Burkholderia pseudomallei in Captive and Wild Macaques in West Java and Bali, Indonesia. MICROBIOLOGY INDONESIA 2018. [DOI: 10.5454/mi.12.1.4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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21
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Peddayelachagiri BV, Paul S, Gogoi M, Sripathy MH, Batra HV. Evaluation of fimC and bdha based duplex PCR for specific identification and differentiation of Burkholderia pseudomallei from near-neighbor Burkholderia species. Int J Med Microbiol 2017; 308:271-278. [PMID: 29273310 DOI: 10.1016/j.ijmm.2017.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/18/2017] [Accepted: 11/19/2017] [Indexed: 11/16/2022] Open
Abstract
Assays for the rapid detection and accurate differentiation of Burkholderia pseudomallei from near-neighbor species are urgently needed in melioidosis endemic regions due to the high associated mortality and biowarfare importance of the pathogen. PCR-based methods have revolutionized this field due to the accuracy, sensitivity, and specificity that are achievable in a rapid way. In this study, a compound molecular detection system, consisting of a duplex PCR assay, was developed for the specific identification of Burkholderia pseudomallei and differentiation from other Burkholderia species. For accurate identification of B. pseudomallei, we deciphered and adopted a novel gene termed putative fimbrial chaperone (fimC). d-beta hydroxybutyrate dehydrogenase (bdha), reported previously by our group for sequence-based differentiation of B. pseudomallei from other Burkholderia species, was employed as a genus-specific target. Enforcement of an internal amplification control in the PCR format ruled out possible false negative results in the assay. Thus, the developed PCR assay was highly specific (100%) in its detection features, and a clear detection sensitivity of 10 pg/μl for purified gDNA and 3 × 103 CFU/ml for B. pseudomallei spiked urine was recorded. Successful identification of B. pseudomallei from an experimental mouse model at both the genus and species level revealed the accurate diagnostic efficiency of the duplex PCR method.
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Affiliation(s)
| | - Soumya Paul
- Microbiology Division, Defence Food Research Laboratory, Mysore 570 011, Karnataka, India
| | - Madhurjya Gogoi
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Murali H Sripathy
- Microbiology Division, Defence Food Research Laboratory, Mysore 570 011, Karnataka, India.
| | - Harsh V Batra
- Microbiology Division, Defence Food Research Laboratory, Mysore 570 011, Karnataka, India
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22
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Tellapragada C, Shaw T, D'Souza A, Eshwara VK, Mukhopadhyay C. Improved detection ofBurkholderia pseudomalleifrom non-blood clinical specimens using enrichment culture and PCR: narrowing diagnostic gap in resource-constrained settings. Trop Med Int Health 2017; 22:866-870. [DOI: 10.1111/tmi.12894] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Tushar Shaw
- Department of Microbiology; Kasturba Medical College; Manipal University; Manipal India
| | - Annet D'Souza
- Department of Microbiology; Kasturba Medical College; Manipal University; Manipal India
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Loss of Methyltransferase Function and Increased Efflux Activity Leads to Doxycycline Resistance in Burkholderia pseudomallei. Antimicrob Agents Chemother 2017; 61:AAC.00268-17. [PMID: 28348161 DOI: 10.1128/aac.00268-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/18/2017] [Indexed: 01/15/2023] Open
Abstract
The soil-dwelling bacterium Burkholderia pseudomallei is the causative agent of the potentially fatal disease melioidosis. The lack of a vaccine toward B. pseudomallei means that melioidosis treatment relies on prolonged antibiotic therapy, which can last up to 6 months in duration or longer. Due to intrinsic resistance, few antibiotics are effective against B. pseudomallei The lengthy treatment regimen required increases the likelihood of resistance development, with subsequent potentially fatal relapse. Doxycycline (DOX) has historically played an important role in the eradication phase of melioidosis treatment. Both primary and acquired DOX resistances have been documented in B. pseudomallei; however, the molecular mechanisms underpinning DOX resistance have remained elusive. Here, we identify and functionally characterize the molecular mechanisms conferring acquired DOX resistance in an isogenic B. pseudomallei pair. Two synergistic mechanisms were identified. The first mutation occurred in a putative S-adenosyl-l-methionine-dependent methyltransferase (encoded by BPSL3085), which we propose leads to altered ribosomal methylation, thereby decreasing DOX binding efficiency. The second mutation altered the function of the efflux pump repressor gene, amrR, resulting in increased expression of the resistance-nodulation-division efflux pump, AmrAB-OprA. Our findings highlight the diverse mechanisms by which B. pseudomallei can become resistant to antibiotics used in melioidosis therapy and the need for resistance monitoring during treatment regimens, especially in patients with prolonged or recrudesced positive cultures for B. pseudomallei.
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24
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Loh TL, Latis S, Crossland G, Patel H. Disseminated melioidosis in the head and neck. BMJ Case Rep 2017; 2017:bcr-2016-218606. [PMID: 28096229 DOI: 10.1136/bcr-2016-218606] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A 35-year-old man was admitted to an intensive care unit with unilateral facial swelling and septic shock after multiple presentations to the emergency department with non-specific unilateral pain over the parotid area. A CT scan of his neck showed diffuse right-sided facial soft tissue infection, mastoid effusion and temporal lobe cerebritis. The upper lobes of his lungs had cannonball lesions that were suggestive of septic lung metastases. Blood cultures and ear canal swabs were positive for Burkholderia pseudomallei The temporal lobe cerebritis eventually developed into an abscess, necessitating a cortical mastoidectomy, craniectomy and temporal lobectomy. After the surgical interventions, antibiotic therapy was continued for a further 6 months. The patient remained well and had no signs of recurrence up to 7 months after the initial presentation.
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Affiliation(s)
- Tze Ling Loh
- Royal Darwin Hospital, Tiwi, Northern Territory, Australia
| | - Sergios Latis
- Royal Darwin Hospital, Tiwi, Northern Territory, Australia
| | | | - Hemi Patel
- Royal Darwin Hospital, Tiwi, Northern Territory, Australia
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25
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Lowe CW, Satterfield BA, Nelson DB, Thiriot JD, Heder MJ, March JK, Drake DS, Lew CS, Bunnell AJ, Moore ES, O'Neill KL, Robison RA. A Quadruplex Real-Time PCR Assay for the Rapid Detection and Differentiation of the Most Relevant Members of the B. pseudomallei Complex: B. mallei, B. pseudomallei, and B. thailandensis. PLoS One 2016; 11:e0164006. [PMID: 27736903 PMCID: PMC5063335 DOI: 10.1371/journal.pone.0164006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 09/19/2016] [Indexed: 11/24/2022] Open
Abstract
The Burkholderia pseudomallei complex classically consisted of B. mallei, B. pseudomallei, and B. thailandensis, but has now expanded to include B. oklahomensis, B. humptydooensis, and three unassigned Burkholderia clades. Methods for detecting and differentiating the B. pseudomallei complex has been the topic of recent research due to phenotypic and genotypic similarities of these species. B. mallei and B. pseudomallei are recognized as CDC Tier 1 select agents, and are the causative agents of glanders and melioidosis, respectively. Although B. thailandensis and B. oklahomensis are generally avirulent, both display similar phenotypic characteristics to that of B. pseudomallei. B. humptydooensis and the Burkholderia clades are genetically similar to the B. pseudomallei complex, and are not associated with disease. Optimal identification of these species remains problematic, and PCR-based methods can resolve issues with B. pseudomallei complex detection and differentiation. Currently, no PCR assay is available that detects the major species of the B. pseudomallei complex. A real-time PCR assay in a multiplex single-tube format was developed to simultaneously detect and differentiate B. mallei, B. pseudomallei, and B. thailandensis, and a common sequence found in B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis. A total of 309 Burkholderia isolates and 5 other bacterial species were evaluated. The assay was 100% sensitive and specific, demonstrated sensitivity beyond culture and GC methods for the isolates tested, and is completed in about an hour with a detection limit between 2.6pg and 48.9pg of gDNA. Bioinformatic analyses also showed the assay is likely 100% specific and sensitive for all 84 fully sequenced B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis strains currently available in GenBank. For these reasons, this assay could be a rapid and sensitive tool in the detection and differentiation for those species of the B. pseudomallei complex with recognized clinical and practical significance.
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Affiliation(s)
- Chinn-Woan Lowe
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Benjamin A. Satterfield
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Daniel B. Nelson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Joseph D. Thiriot
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Michael J. Heder
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Jordon K. March
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - David S. Drake
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Cynthia S. Lew
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Annette J. Bunnell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Emily S. Moore
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Kim L. O'Neill
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Richard A. Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
- * E-mail:
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26
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Hoffmaster AR, AuCoin D, Baccam P, Baggett HC, Baird R, Bhengsri S, Blaney DD, Brett PJ, Brooks TJG, Brown KA, Chantratita N, Cheng AC, Dance DAB, Decuypere S, Defenbaugh D, Gee JE, Houghton R, Jorakate P, Lertmemongkolchai G, Limmathurotsakul D, Merlin TL, Mukhopadhyay C, Norton R, Peacock SJ, Rolim DB, Simpson AJ, Steinmetz I, Stoddard RA, Stokes MM, Sue D, Tuanyok A, Whistler T, Wuthiekanun V, Walke HT. Melioidosis diagnostic workshop, 2013. Emerg Infect Dis 2015; 21. [PMID: 25626057 PMCID: PMC4313648 DOI: 10.3201/eid2102.141045] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Melioidosis is a severe disease that can be difficult to diagnose because of its diverse clinical manifestations and a lack of adequate diagnostic capabilities for suspected cases. There is broad interest in improving detection and diagnosis of this disease not only in melioidosis-endemic regions but also outside these regions because melioidosis may be underreported and poses a potential bioterrorism challenge for public health authorities. Therefore, a workshop of academic, government, and private sector personnel from around the world was convened to discuss the current state of melioidosis diagnostics, diagnostic needs, and future directions.
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27
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Robertson G, Sorenson A, Govan B, Ketheesan N, Houghton R, Chen H, AuCoin D, Dillon M, Norton R. Rapid diagnostics for melioidosis: a comparative study of a novel lateral flow antigen detection assay. J Med Microbiol 2015; 64:845-848. [PMID: 26055557 DOI: 10.1099/jmm.0.000098] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The rapid diagnosis of septicaemic melioidosis will have an impact on reduction of mortality. Currently, this relies almost exclusively upon culture of the causative agent Burkholderia pseudomallei from clinical samples. In acute sepsis, blood is the preferred specimen for culture and therefore should be the target for a rapid diagnostic tool. A lateral flow immunoassay (LFI) for the detection of B. pseudomallei antigen has been developed. This was compared with molecular detection using the targets T3SS1 and IpxO. Forty-five clinical samples of EDTA blood, which were culture-positive, were tested using both modalities. The LFI had a sensitivity of 40 %, whilst molecular detection had a sensitivity of 20 %. The poor performance of molecular detection has been described previously and is largely related to the use of whole-blood specimens collected into blood tubes containing EDTA. Whilst suboptimal, the LFI would be an adjunct in the rapid diagnosis of melioidosis.
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Affiliation(s)
- Gemma Robertson
- Pathology Queensland, The Townsville Hospital, Townsville, Queensland, Australia
| | - Alanna Sorenson
- Australian Institute of Tropical Health and Medicine, James Cook University, Douglas, Townsville, Queensland, Australia
| | - Brenda Govan
- Australian Institute of Tropical Health and Medicine, James Cook University, Douglas, Townsville, Queensland, Australia
| | - Natkunam Ketheesan
- Australian Institute of Tropical Health and Medicine, James Cook University, Douglas, Townsville, Queensland, Australia
| | | | | | - David AuCoin
- Department of Microbiology and Immunology, University of Nevada School of Medicine, Reno, Nevada, USA
| | - Michael Dillon
- Department of Microbiology and Immunology, University of Nevada School of Medicine, Reno, Nevada, USA
| | - Robert Norton
- Pathology Queensland, The Townsville Hospital, Townsville, Queensland, Australia
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28
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Kaestli M, Harrington G, Mayo M, Chatfield MD, Harrington I, Hill A, Munksgaard N, Gibb K, Currie BJ. What drives the occurrence of the melioidosis bacterium Burkholderia pseudomallei in domestic gardens? PLoS Negl Trop Dis 2015; 9:e0003635. [PMID: 25803046 PMCID: PMC4372393 DOI: 10.1371/journal.pntd.0003635] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/20/2015] [Indexed: 11/19/2022] Open
Abstract
Melioidosis is an often fatal infectious disease affecting humans and animals in tropical regions and is caused by the saprophytic environmental bacterium Burkholderia pseudomallei. Domestic gardens are not only a common source of exposure to soil and thus to B. pseudomallei, but they also have been found to contain more B. pseudomallei than other environments. In this study we addressed whether anthropogenic manipulations common to gardens such as irrigation or fertilizers change the occurrence of B. pseudomallei. We conducted a soil microcosm experiment with a range of fertilizers and soil types as well as a longitudinal interventional study over three years on an experimental fertilized field site in an area naturally positive for B. pseudomallei. Irrigation was the only consistent treatment to increase B. pseudomallei occurrence over time. The effects of fertilizers upon these bacteria depended on soil texture, physicochemical soil properties and biotic factors. Nitrates and urea increased B. pseudomallei load in sand while phosphates had a positive effect in clay. The high buffering and cation exchange capacities of organic material found in a commercial potting mix led to a marked increase in soil salinity with no survival of B. pseudomallei after four weeks in the potting mix sampled. Imported grasses were also associated with B. pseudomallei occurrence in a multivariate model. With increasing population density in endemic areas these findings inform the identification of areas in the anthropogenic environment with increased risk of exposure to B. pseudomallei.
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Affiliation(s)
- Mirjam Kaestli
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- * E-mail:
| | - Glenda Harrington
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Mark D. Chatfield
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Ian Harrington
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Audrey Hill
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Niels Munksgaard
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
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29
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Sarovich DS, Price EP, Webb JR, Ward LM, Voutsinos MY, Tuanyok A, Mayo M, Kaestli M, Currie BJ. Variable virulence factors in Burkholderia pseudomallei (melioidosis) associated with human disease. PLoS One 2014; 9:e91682. [PMID: 24618705 PMCID: PMC3950250 DOI: 10.1371/journal.pone.0091682] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 02/14/2014] [Indexed: 11/18/2022] Open
Abstract
Burkholderia pseudomallei is a Gram-negative environmental bacterium that causes melioidosis, a potentially life-threatening infectious disease affecting mammals, including humans. Melioidosis symptoms are both protean and diverse, ranging from mild, localized skin infections to more severe and often fatal presentations including pneumonia, septic shock with multiple internal abscesses and occasionally neurological involvement. Several ubiquitous virulence determinants in B. pseudomallei have already been discovered. However, the molecular basis for differential pathogenesis has, until now, remained elusive. Using clinical data from 556 Australian melioidosis cases spanning more than 20 years, we identified a Burkholderia mallei-like actin polymerization bimA(Bm) gene that is strongly associated with neurological disease. We also report that a filamentous hemagglutinin gene, fhaB3, is associated with positive blood cultures but is negatively correlated with localized skin lesions without sepsis. We show, for the first time, that variably present virulence factors play an important role in the pathogenesis of melioidosis. Collectively, our study provides a framework for assessing other non-ubiquitous bacterial virulence factors and their association with disease, such as candidate loci identified from large-scale microbial genome-wide association studies.
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Affiliation(s)
- Derek S. Sarovich
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Erin P. Price
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Jessica R. Webb
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Linda M. Ward
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Marcos Y. Voutsinos
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Apichai Tuanyok
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, University of Hawai’i, Honolulu, Hawai’i, 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
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Infectious Diseases Department, Royal Darwin Hospital, Darwin, Northern Territory, Australia
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30
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Reliability of automated biochemical identification of Burkholderia pseudomallei is regionally dependent. J Clin Microbiol 2013; 51:3076-8. [PMID: 23784129 DOI: 10.1128/jcm.01290-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Misidentifications of Burkholderia pseudomallei as Burkholderia cepacia by Vitek 2 have occurred. Multidimensional scaling ordination of biochemical profiles of 217 Malaysian and Australian B. pseudomallei isolates found clustering of misidentified B. pseudomallei isolates from Malaysian Borneo. Specificity of B. pseudomallei identification in Vitek 2 and potentially other automated identification systems is regionally dependent.
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31
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Cheng AC, Currie BJ, Dance DAB, Funnell SGP, Limmathurotsakul D, Simpson AJH, Peacock SJ. Clinical definitions of melioidosis. Am J Trop Med Hyg 2013; 88:411-413. [PMID: 23468355 PMCID: PMC3592517 DOI: 10.4269/ajtmh.12-0555] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Clinical definitions of melioidosis and inhalation-acquired melioidosis (Burkholderia pseudomallei infection) are described together with the evidence used to develop these definitions. Such definitions support accurate public health reporting, preparedness planning for deliberate B. pseudomallei release, design of experimental models, and categorization of naturally acquired melioidosis.
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Affiliation(s)
| | | | | | | | | | | | - Sharon J. Peacock
- *Address correspondence to Sharon J. Peacock, Department of Medicine, University of Cambridge, Box 157, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, United Kingdom. E-mail:
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32
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Puah SM, Puthucheary SD, Chua KH. Potential immunogenic polypeptides of Burkholderia pseudomallei identified by shotgun expression library and evaluation of their efficacy for serodiagnosis of melioidosis. Int J Med Sci 2013; 10:539-47. [PMID: 23532805 PMCID: PMC3607239 DOI: 10.7150/ijms.5516] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 03/06/2013] [Indexed: 11/25/2022] Open
Abstract
The search for novel immunogenic polypeptides to improve the accuracy and reliability of serologic diagnostic methods for Burkholderia pseudomallei infection is ongoing. We employed a rapid and efficient approach to identify such polypeptides with sera from melioidosis patients using a small insert genomic expression library created from clinically confirmed local virulent isolates of B. pseudomallei. After 2 rounds of immunoscreening, 6 sero-positive clones expressing immunogenic peptides were sequenced and their identities were: benzoate 1,2-dioxygenase beta subunit, a putative 200 kDa antigen p200, phosphotransferase enzyme family protein, short chain dehydrogenase and 2 hypothetical proteins. These immunogens were then transferred to an ELISA platform for further large scale screening. By combining shotgun expression library and ELISA assays, we identified 2 polypeptides BPSS1904 (benzoate 1,2-dioxygenase beta subunit) and BPSL3130 (hypothetical protein), which had sensitivities of 78.9% and 79.4% and specificities of 88.1% and 94.8%, respectively in ELISA test, thus suggesting that both are potential candidate antigens for the serodiagnosis of infections caused by B. pseudomallei.
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Affiliation(s)
- Suat Moi Puah
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
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33
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Price EP, Dale JL, Cook JM, Sarovich DS, Seymour ML, Ginther JL, Kaufman EL, Beckstrom-Sternberg SM, Mayo M, Kaestli M, Glass MB, Gee JE, Wuthiekanun V, Warner JM, Baker A, Foster JT, Tan P, Tuanyok A, Limmathurotsakul D, Peacock SJ, Currie BJ, Wagner DM, Keim P, Pearson T. Development and validation of Burkholderia pseudomallei-specific real-time PCR assays for clinical, environmental or forensic detection applications. PLoS One 2012; 7:e37723. [PMID: 22624061 PMCID: PMC3356290 DOI: 10.1371/journal.pone.0037723] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 04/23/2012] [Indexed: 11/18/2022] Open
Abstract
The bacterium Burkholderia pseudomallei causes melioidosis, a rare but serious illness that can be fatal if untreated or misdiagnosed. Species-specific PCR assays provide a technically simple method for differentiating B. pseudomallei from near-neighbor species. However, substantial genetic diversity and high levels of recombination within this species reduce the likelihood that molecular signatures will differentiate all B. pseudomallei from other Burkholderiaceae. Currently available molecular assays for B. pseudomallei detection lack rigorous validation across large in silico datasets and isolate collections to test for specificity, and none have been subjected to stringent quality control criteria (accuracy, precision, selectivity, limit of quantitation (LoQ), limit of detection (LoD), linearity, ruggedness and robustness) to determine their suitability for environmental, clinical or forensic investigations. In this study, we developed two novel B. pseudomallei specific assays, 122018 and 266152, using a dual-probe approach to differentiate B. pseudomallei from B. thailandensis, B. oklahomensis and B. thailandensis-like species; other species failed to amplify. Species specificity was validated across a large DNA panel (>2,300 samples) comprising Burkholderia spp. and non-Burkholderia bacterial and fungal species of clinical and environmental relevance. Comparison of assay specificity to two previously published B. pseudomallei-specific assays, BurkDiff and TTS1, demonstrated comparable performance of all assays, providing between 99.7 and 100% specificity against our isolate panel. Last, we subjected 122018 and 266152 to rigorous quality control analyses, thus providing quantitative limits of assay performance. Using B. pseudomallei as a model, our study provides a framework for comprehensive quantitative validation of molecular assays and provides additional, highly validated B. pseudomallei assays for the scientific research community.
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Affiliation(s)
- Erin P. Price
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Menzies School of Health Research, Casuarina, Northern Territory, Australia
| | - Julia L. Dale
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - James M. Cook
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Derek S. Sarovich
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Menzies School of Health Research, Casuarina, Northern Territory, Australia
| | - Meagan L. Seymour
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jennifer L. Ginther
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Emily L. Kaufman
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Stephen M. Beckstrom-Sternberg
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Mark Mayo
- Menzies School of Health Research, Casuarina, Northern Territory, Australia
| | - Mirjam Kaestli
- Menzies School of Health Research, Casuarina, Northern Territory, Australia
| | - Mindy B. Glass
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jay E. Gee
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jeffrey M. Warner
- Microbiology and Immunology, School of Veterinary and Biomedical Sciences, James Cook University, Townsville, Queensland, Australia
| | - Anthony Baker
- Microbiology and Immunology, School of Veterinary and Biomedical Sciences, James Cook University, Townsville, Queensland, Australia
| | - Jeffrey T. Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Patrick Tan
- Genome Institute of Singapore, Singapore, Singapore
| | - Apichai Tuanyok
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sharon J. Peacock
- 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
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Bart J. Currie
- Menzies School of Health Research, Casuarina, Northern Territory, Australia
| | - David M. Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Talima Pearson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail:
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