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Meumann EM, Limmathurotsakul D, Dunachie SJ, Wiersinga WJ, Currie BJ. Burkholderia pseudomallei and melioidosis. Nat Rev Microbiol 2024; 22:155-169. [PMID: 37794173 DOI: 10.1038/s41579-023-00972-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2023] [Indexed: 10/06/2023]
Abstract
Burkholderia pseudomallei, the causative agent of melioidosis, is found in soil and water of tropical and subtropical regions globally. Modelled estimates of the global burden predict that melioidosis remains vastly under-reported, and a call has been made for it to be recognized as a neglected tropical disease by the World Health Organization. Severe weather events and environmental disturbance are associated with increased case numbers, and it is anticipated that, in some regions, cases will increase in association with climate change. Genomic epidemiological investigations have confirmed B. pseudomallei endemicity in newly recognized regions, including the southern United States. Melioidosis follows environmental exposure to B. pseudomallei and is associated with comorbidities that affect the immune response, such as diabetes, and with socioeconomic disadvantage. Several vaccine candidates are ready for phase I clinical trials. In this Review, we explore the global burden, epidemiology and pathophysiology of B. pseudomallei as well as current diagnostics, treatment recommendations and preventive measures, highlighting research needs and priorities.
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Affiliation(s)
- Ella M Meumann
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Northern Territory, Australia.
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- NDM Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- NDM Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Willem J Wiersinga
- Division of Infectious Diseases, Center for Experimental Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Northern Territory, Australia
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2
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Feng Y, Chen M, Wei X, Zhu H, Zhang J, Zhang Y, Xue L, Huang L, Chen G, Chen M, Ding Y, Wu Q. Pseudotargeted Metabolomic Fingerprinting and Deep Learning for Identification and Visualization of Common Pathogens. Front Microbiol 2022; 13:830832. [PMID: 35359729 PMCID: PMC8960985 DOI: 10.3389/fmicb.2022.830832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass (MALDI-TOF) spectrometry fingerprinting has reduced turnaround times, costs, and labor as conventional procedures in various laboratories. However, some species strains with high genetic correlation have not been directly distinguished using conventional standard procedures. Metabolomes can identify these strains by amplifying the minor differences because they are directly related to the phenotype. The pseudotargeted metabolomics method has the advantages of both non-targeted and targeted metabolomics. It can provide a new semi-quantitative fingerprinting with high coverage. We combined this pseudotargeted metabolomic fingerprinting with deep learning technology for the identification and visualization of the pathogen. A variational autoencoder framework was performed to identify and classify pathogenic bacteria and achieve their visualization, with prediction accuracy exceeding 99%. Therefore, this technology will be a powerful tool for rapidly and accurately identifying pathogens.
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Affiliation(s)
- Ying Feng
- Guangzhou Institute of Chemistry, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agricultural and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agricultural and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xianhu Wei
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agricultural and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Honghui Zhu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agricultural and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agricultural and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Youxiong Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agricultural and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agricultural and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Lanyan Huang
- Guangzhou Institute of Chemistry, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agricultural and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guoyang Chen
- Guangzhou Institute of Chemistry, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agricultural and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Minling Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agricultural and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yu Ding
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agricultural and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
- *Correspondence: Yu Ding,
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agricultural and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Qingping Wu,
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3
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Watthanaworawit W, Roberts T, Hopkins J, Gassiep I, Norton R, Robinson MT, Silisouk J, Sar P, Sao S, Amornchai P, Limmathurotsakul D, Wuthiekanun V, Nosten F, Simpson AJH, Turner P, Ling CL. A multi-country study using MALDI-TOF mass spectrometry for rapid identification of Burkholderia pseudomallei. BMC Microbiol 2021; 21:213. [PMID: 34266382 PMCID: PMC8283998 DOI: 10.1186/s12866-021-02276-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 06/21/2021] [Indexed: 11/10/2022] Open
Abstract
Background Burkholderia pseudomallei is the bacterial causative agent of melioidosis, a difficult disease to diagnose clinically with high mortality if not appropriately treated. Definitive diagnosis requires isolation and identification of the organism. With the increased adoption of MALDI-TOF MS for the identification of bacteria, we established a method for rapid identification of B. pseudomallei using the Vitek MS, a system that does not currently have B. pseudomallei in its in-vitro diagnostic database. Results A routine direct spotting method was employed to create spectra and SuperSpectra. An initial B. pseudomallei SuperSpectrum was created at Shoklo Malaria Research Unit (SMRU) from 17 reference isolates (46 spectra). When tested, this initial SMRU SuperSpectrum was able to identify 98.2 % (54/55) of Asian isolates, but just 46.7 % (35/75) of Australian isolates. Using spectra (430) from different reference and clinical isolates, two additional SMRU SuperSpectra were created. Using the combination of all SMRU SuperSpectra with seven existing SuperSpectra from Townsville, Australia 119 (100 %) Asian isolates and 31 (100 %) Australian isolates were correctly identified. In addition, no misidentifications were obtained when using these 11 SuperSpectra when tested with 34 isolates of other bacteria including the closely related species Burkholderia thailandensis and Burkholderia cepacia. Conclusions This study has established a method for identification of B. pseudomallei using Vitek MS, and highlights the impact of geographical differences between strains for identification using this technique. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02276-1.
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Affiliation(s)
- Wanitda Watthanaworawit
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.
| | - Tamalee Roberts
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Jill Hopkins
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ian Gassiep
- University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
| | - Robert Norton
- Pathology, Townsville Hospital, Townsville, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Matthew T Robinson
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Joy Silisouk
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Poda Sar
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Sena Sao
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Premjit Amornchai
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J H Simpson
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Clare L Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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4
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Cornish NE, Anderson NL, Arambula DG, Arduino MJ, Bryan A, Burton NC, Chen B, Dickson BA, Giri JG, Griffith NK, Pentella MA, Salerno RM, Sandhu P, Snyder JW, Tormey CA, Wagar EA, Weirich EG, Campbell S. Clinical Laboratory Biosafety Gaps: Lessons Learned from Past Outbreaks Reveal a Path to a Safer Future. Clin Microbiol Rev 2021; 34:e0012618. [PMID: 34105993 PMCID: PMC8262806 DOI: 10.1128/cmr.00126-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Patient care and public health require timely, reliable laboratory testing. However, clinical laboratory professionals rarely know whether patient specimens contain infectious agents, making ensuring biosafety while performing testing procedures challenging. The importance of biosafety in clinical laboratories was highlighted during the 2014 Ebola outbreak, where concerns about biosafety resulted in delayed diagnoses and contributed to patient deaths. This review is a collaboration between subject matter experts from large and small laboratories and the federal government to evaluate the capability of clinical laboratories to manage biosafety risks and safely test patient specimens. We discuss the complexity of clinical laboratories, including anatomic pathology, and describe how applying current biosafety guidance may be difficult as these guidelines, largely based on practices in research laboratories, do not always correspond to the unique clinical laboratory environments and their specialized equipment and processes. We retrospectively describe the biosafety gaps and opportunities for improvement in the areas of risk assessment and management; automated and manual laboratory disciplines; specimen collection, processing, and storage; test utilization; equipment and instrumentation safety; disinfection practices; personal protective equipment; waste management; laboratory personnel training and competency assessment; accreditation processes; and ethical guidance. Also addressed are the unique biosafety challenges successfully handled by a Texas community hospital clinical laboratory that performed testing for patients with Ebola without a formal biocontainment unit. The gaps in knowledge and practices identified in previous and ongoing outbreaks demonstrate the need for collaborative, comprehensive solutions to improve clinical laboratory biosafety and to better combat future emerging infectious disease outbreaks.
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Affiliation(s)
- Nancy E. Cornish
- Centers for Disease Control and Prevention, Center for Surveillance, Epidemiology and Laboratory Services (CSELS), Atlanta, Georgia, USA
| | - Nancy L. Anderson
- Centers for Disease Control and Prevention, Center for Surveillance, Epidemiology and Laboratory Services (CSELS), Atlanta, Georgia, USA
| | - Diego G. Arambula
- Centers for Disease Control and Prevention, Center for Surveillance, Epidemiology and Laboratory Services (CSELS), Atlanta, Georgia, USA
| | - Matthew J. Arduino
- Centers for Disease Control and Prevention, National Center for Emerging & Zoonotic Infectious Diseases (NCEZID), Atlanta, Georgia, USA
| | - Andrew Bryan
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Nancy C. Burton
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health (NIOSH), Cincinnati, Ohio, USA
| | - Bin Chen
- Centers for Disease Control and Prevention, Center for Surveillance, Epidemiology and Laboratory Services (CSELS), Atlanta, Georgia, USA
| | - Beverly A. Dickson
- Department of Clinical Pathology, Texas Health Presbyterian Hospital Dallas, Dallas, Texas, USA
| | - Judith G. Giri
- Centers for Disease Control and Prevention, Center for Global Health (CGH), Atlanta, Georgia, USA
| | | | | | - Reynolds M. Salerno
- Centers for Disease Control and Prevention, Center for Surveillance, Epidemiology and Laboratory Services (CSELS), Atlanta, Georgia, USA
| | - Paramjit Sandhu
- Centers for Disease Control and Prevention, Center for Surveillance, Epidemiology and Laboratory Services (CSELS), Atlanta, Georgia, USA
| | - James W. Snyder
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Christopher A. Tormey
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Pathology & Laboratory Medicine Service, Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
| | - Elizabeth A. Wagar
- Department of Laboratory Medicine, University of Texas, M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Elizabeth G. Weirich
- Centers for Disease Control and Prevention, Center for Surveillance, Epidemiology and Laboratory Services (CSELS), Atlanta, Georgia, USA
| | - Sheldon Campbell
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Pathology & Laboratory Medicine Service, Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
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Stavrou C, Veraitch O, Morris-Jones S, Walker SL. Leg ulceration due to cutaneous melioidosis in a returning traveller. BMJ Case Rep 2021; 14:14/6/e241490. [PMID: 34127500 PMCID: PMC8204165 DOI: 10.1136/bcr-2020-241490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
A 26-year-old man, returned to the UK having travelled extensively in Asia. He was referred with a 3-month history of distal leg ulceration following an insect bite while in Thailand. Despite multiple courses of oral antibiotics, he developed two adjacent ulcers. A wound swab isolated an organism identified as Burkholderia thailandensis. The histology of the skin biopsy was non-specific. A diagnosis of cutaneous melioidosis was made, based on clinical and microbiological grounds. The ulcers re-epithelialised on completion of intravenous ceftazidime followed by 3 months of high dose co-trimoxazole and wound care. Many clinical microbiology laboratories have limited diagnostics for security-related organisms, with the result that B. pseudomallei, the causative bacterium of melioidosis, may be misidentified. This case highlights the importance of maintaining high levels of clinical suspicion and close microbiological liaison in individuals returning from South-East Asia and northern Australia with such symptoms.
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Affiliation(s)
- Christiana Stavrou
- Department of Dermatology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Ophelia Veraitch
- Department of Dermatology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Stephen Morris-Jones
- Clinical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Stephen L Walker
- Hospital for Tropical Diseases and Department of Dermatology, University College London Hospitals NHS Foundation Trust, London, UK.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Department of Clinical Research, London, UK
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Sabna S, Kamboj DV, Rajoria S, Kumar RB, Babele P, Goel AK, Tuteja U, Gupta MK, Alam SI. Protein biomarker elucidation for the verification of biological agents in the taxonomic group of Gammaproteobacteria using tandem mass spectrometry. World J Microbiol Biotechnol 2021; 37:74. [PMID: 33779874 DOI: 10.1007/s11274-021-03039-w] [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: 11/24/2020] [Accepted: 03/16/2021] [Indexed: 12/01/2022]
Abstract
Some pathogenic microbes can be used for nefarious applications and instigate population-based fear. In a bio-threat scenario, rapid and accurate methods to detect biological agents in a wide range of complex environmental and clinical matrices, is of paramount importance for the implementation of mitigation protocols and medical countermeasures. This study describes targeted and shot-gun tandem MS based approaches for the verification of biological agents from the environmental samples. The marker proteins and peptides were elucidated by an exhaustive literature mining, in silico analysis of prioritized proteins, and MS/MS analysis of abundant proteins from selected bacterial species. For the shot-gun methodology, tandem MS analysis of abundant peptides was carried from spiked samples. The validation experiments employing a combination of shot-gun tandem MS analysis and a targeted search reported here is a proof of concept to show the applicability of the methodology for the unambiguous verification of biological agents at sub-species level, even with limited fractionation of crude protein extracts from environmental samples.
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Affiliation(s)
- Sasikumar Sabna
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Dev Vrat Kamboj
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Sakshi Rajoria
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Ravi Bhushan Kumar
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Prabhakar Babele
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Ajay Kumar Goel
- Bioprocess Technology Division, Defence Research & Development Establishment, Gwalior, India
| | - Urmil Tuteja
- Microbiology Division, Defence Research & Development Establishment, Gwalior, India
| | | | - Syed Imteyaz Alam
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India.
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7
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Pentella MA. Update on Biosafety and Emerging Infections for the Clinical Microbiology Laboratory. Clin Lab Med 2020; 40:473-482. [PMID: 33121616 DOI: 10.1016/j.cll.2020.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Biosafety risks are prevalent in all areas of the clinical laboratories. Clinical laboratorians have become accustomed to accepting these risks. When an emerging pathogen appears, the concerns become elevated. Since the appearance of Ebola virus in the United States in 2014, biosafety practices have made progress. A recent Association of Public Health Laboratories survey shows that clinical laboratories are unprepared for current and emerging biosafety challenges. This article focuses on the biosafety program that clinical laboratory leaders should build to meet the needs of clinical laboratories; biosafety challenges of automated laboratory systems, facilities, personnel, and practices; and the relationship with occupational health.
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Affiliation(s)
- Michael A Pentella
- College of Public Health, University of Iowa, Iowa City, IA, USA; State Hygienic Laboratory, University of Iowa, Coralville, IA, USA.
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8
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Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based identification of security-sensitive bacteria: Considerations for Canadian Bruker users. ACTA ACUST UNITED AC 2020; 46:333-338. [PMID: 33315990 DOI: 10.14745/ccdr.v46i10a04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Background The use of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) systems for bacterial identification has rapidly become a front line tool for diagnostic laboratories, superseding classical microbiological methods that previously triggered the identification of higher risk pathogens. Unknown Risk Group 3 isolates have been misidentified as less pathogenic species due to spectral library availability, content and quality. Consequently, exposure to higher risk pathogens has been reported within Canadian laboratory staff following the implementation of MALDI-TOF MS. This overview aims to communicate the potential risk to laboratory staff of inaccurate identification of security-sensitive biological agents (SSBA) bacteria and to provide suggestions to mitigate. Methods Cultures were manipulated in a Biosafety Level 3 laboratory, prepared for MALDI-TOF MS analysis via full chemical extraction and analysed on a Bruker Microflex LT instrument. Data were analyzed with Biotyper software; comparing raw spectra against MS profiles in three libraries: Bruker Taxonomy; Bruker Security-Restricted; and National Microbiology Laboratory (NML) SSBA libraries. Four years of Bruker MALDI-TOF MS data acquired in-house were reviewed. Results In general, the Bruker MS spectral libraries were less successful in identifying the SSBA bacteria. More successful was the NML library. For example, using a high score cut-off (greater than 2.0), the Bruker SR library was unable to identify 52.8% of our Risk Group 3 agents and near neighbours to the species-level with confidence, whereas the custom NML library was unable to identify only 20.3% of the samples. Conclusion The last four years of data demonstrated both the importance of library selection and the limitations of the various spectral libraries. Enhanced standard operating procedures are advised to reduce laboratory exposure to SSBAs when using MALDI-TOF MS as a front line identification tool.
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Chua KH, Tan EW, Chai HC, Puthucheary SD, Lee PC, Puah SM. Rapid identification of melioidosis agent by an insulated isothermal PCR on a field-deployable device. PeerJ 2020; 8:e9238. [PMID: 32518734 PMCID: PMC7261116 DOI: 10.7717/peerj.9238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/05/2020] [Indexed: 12/17/2022] Open
Abstract
Background Burkholderia pseudomallei causes melioidosis, a serious illness that can be fatal if untreated or misdiagnosed. Culture from clinical specimens remains the gold standard but has low diagnostic sensitivity. Method In this study, we developed a rapid, sensitive and specific insulated isothermal Polymerase Chain Reaction (iiPCR) targeting bimA gene (Burkholderia Intracellular Motility A; BPSS1492) for the identification of B. pseudomallei. A pair of novel primers: BimA(F) and BimA(R) together with a probe were designed and 121 clinical B. pseudomallei strains obtained from numerous clinical sources and 10 ATCC non-targeted strains were tested with iiPCR and qPCR in parallel. Results All 121 B. pseudomallei isolates were positive for qPCR while 118 isolates were positive for iiPCR, demonstrating satisfactory agreement (97.71%; 95% CI [93.45–99.53%]; k = 0.87). Sensitivity of the bimA iiPCR/POCKIT assay was 97.52% with the lower detection limit of 14 ng/µL of B. pseudomallei DNA. The developed iiPCR assay did not cross-react with 10 types of non-targeted strains, indicating good specificity. Conclusion This bimA iiPCR/POCKIT assay will undoubtedly complement other methodologies used in the clinical laboratory for the rapid identification of this pathogen.
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Affiliation(s)
- Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - E Wei Tan
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Hwa Chia Chai
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - S D Puthucheary
- Faculty of Medicine, University of Malaya, University of Malaya, Kuala Lumpur, Malaysia
| | - Ping Chin Lee
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
| | - Suat Moi Puah
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Abstract
The causative agent of melioidosis, Burkholderia pseudomallei, a tier 1 select agent, is endemic in Southeast Asia and northern Australia, with increased incidence associated with high levels of rainfall. Increasing reports of this condition have occurred worldwide, with estimates of up to 165,000 cases and 89,000 deaths per year. The ecological niche of the organism has yet to be clearly defined, although the organism is associated with soil and water. The culture of appropriate clinical material remains the mainstay of laboratory diagnosis. Identification is best done by phenotypic methods, although mass spectrometric methods have been described. Serology has a limited diagnostic role. Direct molecular and antigen detection methods have limited availability and sensitivity. Clinical presentations of melioidosis range from acute bacteremic pneumonia to disseminated visceral abscesses and localized infections. Transmission is by direct inoculation, inhalation, or ingestion. Risk factors for melioidosis include male sex, diabetes mellitus, alcohol abuse, and immunosuppression. The organism is well adapted to intracellular survival, with numerous virulence mechanisms. Immunity likely requires innate and adaptive responses. The principles of management of this condition are drainage and debridement of infected material and appropriate antimicrobial therapy. Global mortality rates vary between 9% and 70%. Research into vaccine development is ongoing.
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Affiliation(s)
- I Gassiep
- Pathology Queensland, Townsville Hospital, Townsville, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - M Armstrong
- Pathology Queensland, Townsville Hospital, Townsville, Queensland, Australia
| | - R Norton
- Pathology Queensland, Townsville Hospital, Townsville, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
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11
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Elucidation of protein biomarkers for verification of selected biological warfare agents using tandem mass spectrometry. Sci Rep 2020; 10:2205. [PMID: 32042063 PMCID: PMC7010682 DOI: 10.1038/s41598-020-59156-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 01/22/2020] [Indexed: 11/10/2022] Open
Abstract
Some pathogens and toxins have the potential to be used as weapons of mass destruction and instigate population-based fear. Efforts to mitigate biothreat require development of efficient countermeasures which in turn relies on fast and accurate methods to detect the biological agents in a range of complex matrices including environmental and clinical samples. We report here an mass spectrometry (MS) based methodology, employing both targeted and shot-gun approaches for the verification of biological agents from the environmental samples. Our shot-gun methodology relied on tandem MS analysis of abundant peptides from the spiked samples, whereas, the targeted method was based on an extensive elucidation of marker proteins and unique peptides resulting in the generation of an inclusion list of masses reflecting relevant peptides for the unambiguous identification of nine bacterial species [listed as priority agents of bioterrorism by Centre for Disease Control and Prevention (CDC)] belonging to phylogenetically diverse genera. The marker peptides were elucidated by extensive literature mining, in silico analysis, and tandem MS (MS/MS) analysis of abundant proteins of the cultivated bacterial species in our laboratory. A combination of shot-gun MS/MS analysis and the targeted search using a panel of unique peptides is likely to provide unambiguous verification of biological agents at sub-species level, even with limited fractionation of crude protein extracts from environmental samples. The comprehensive list of peptides reflected in the inclusion list, makes a valuable resource for the multiplex analysis of select biothreat agents and further development of targeted MS/MS assays.
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Bousquet A, Gueudet T, Biot F, Bigaillon C, Gominet M, Mérens A. Accidental exposure to Burkholderia pseudomallei: awareness is also needed for urine specimens. Clin Microbiol Infect 2019; 26:265-266. [PMID: 31639469 DOI: 10.1016/j.cmi.2019.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 11/25/2022]
Affiliation(s)
- A Bousquet
- Department of Laboratory, Bégin Military Teaching Hospital, Saint-Mandé, France.
| | - T Gueudet
- Department of Microbiology, Schuh Laboratory, Strasbourg, France
| | - F Biot
- French Armed Forces Biomedical Research Institute, Brétigny-sur-Orge, France
| | - C Bigaillon
- Department of Laboratory, Bégin Military Teaching Hospital, Saint-Mandé, France
| | - M Gominet
- Department of Infectious Diseases, Bégin Military Teaching Hospital, Saint Mandé, France
| | - A Mérens
- French Armed Forces Biomedical Research Institute, Brétigny-sur-Orge, France
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Identification of Burkholderia pseudomallei by Use of the Vitek Mass Spectrometer. J Clin Microbiol 2019; 57:JCM.00081-19. [PMID: 30842230 DOI: 10.1128/jcm.00081-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 02/27/2019] [Indexed: 02/07/2023] Open
Abstract
Burkholderia pseudomallei is the causative agent of melioidosis. This condition most often presents as pneumonia and bacteremia, with mortality rates of 9% to 70%. Therefore, early identification of this organism may aid in directing appropriate management. This study aimed to use the Vitek matrix-assisted laser desorption ionization-time of flight mass spectrometer to create a spectrum for the rapid identification of B. pseudomallei Spectra from 85 isolate cultures were acquired using the Vitek mass spectrometer research mode. A SuperSpectrum was created using peak matching and subsequently activated for analysis of organism identification. All 85 isolates were correctly identified as B. pseudomallei A total of 899 spectra were analyzed and demonstrated a specificity of 99.8%. Eighty-one clinical isolates were used, of which 10 were neuromelioidosis, and no discernible spectrum difference was appreciated. Spectrum acquisition from a single spot was only successful in 374/899 (41%) of isolates. This increased to 100% when 3 spots of the same extract were analyzed. The Vitek mass spectrometer can be used for the rapid identification of B. pseudomallei with a high level of specificity.
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The Brief Case: Misidentification of Brucella melitensis as Ochrobactrum anthropi by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). J Clin Microbiol 2018; 56:56/6/e00914-17. [PMID: 29802238 DOI: 10.1128/jcm.00914-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Misidentification of Risk Group 3/Security Sensitive Biological Agents by MALDI-TOF MS in Canada: November 2015-October 2017. ACTA ACUST UNITED AC 2018; 44:110-115. [PMID: 31007621 DOI: 10.14745/ccdr.v44i05a04] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Background Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) is a technology increasingly used in diagnostic identification of microorganisms. However, anecdotal evidence suggests that this technology is associated with misidentification of Risk Group 3 (RG3)/Security Sensitive Biological Agents (SSBA) resulting in exposure risks to laboratory personnel. Objective To investigate and characterize incidents related to the use of MALDI-TOF MS in Canada between November 6, 2015, and October 10, 2017. Methods Cases were identified from laboratory incident reports in the national Laboratory Incident Notification Canada (LINC) surveillance system. Eligible cases referred directly to MALDI-TOF MS or one of three RG3/SSBA organisms, Brucella species, Francisella tularensis and Burkholderia pseudomallei. A questionnaire was developed to identify potential risk factors leading to the exposure. Reporters from organizations with selected incidents were interviewed using the questionnaire. Data were entered into an Excel spreadsheet and standard descriptive statistical analysis performed to assess common characteristics and identify possible risk factors. Results There were eight eligible incidents and a total of 39 laboratory workers were exposed to RG3/SSBA organisms. In five (out of eight) of the incidents, the reporters indicated that their device was equipped with both clinical and research reference libraries. For six incidents where reporters knew the type of library used, only the clinical library was employed at the time of the incident even though both libraries were available in five of these incidents. In all eight cases, the exposure occurred during the sample preparation stage with analyses performed on an open bench and directly from the specimen. And in all eight cases, patient specimens were received without information regarding potential risk. Conclusion This first national study characterizing the nature and extent of laboratory incidents involving RG3/SSBA that are related to the use of MALDI-TOF MS identifies risk factors and provides baseline data that can inform mitigation strategies.
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Tracz DM, Tober AD, Antonation KS, Corbett CR. MALDI-TOF mass spectrometry and high-consequence bacteria: safety and stability of biothreat bacterial sample testing in clinical diagnostic laboratories. J Med Microbiol 2018; 67:341-346. [PMID: 29458687 DOI: 10.1099/jmm.0.000695] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We considered the application of MALDI-TOF mass spectrometry for BSL-3 bacterial diagnostics, with a focus on the biosafety of live-culture direct-colony testing and the stability of stored extracts. Biosafety level 2 (BSL-2) bacterial species were used as surrogates for BSL-3 high-consequence pathogens in all live-culture MALDI-TOF experiments. Viable BSL-2 bacteria were isolated from MALDI-TOF mass spectrometry target plates after 'direct-colony' and 'on-plate' extraction testing, suggesting that the matrix chemicals alone cannot be considered sufficient to inactivate bacterial culture and spores in all samples. Sampling of the instrument interior after direct-colony analysis did not recover viable organisms, suggesting that any potential risks to the laboratory technician are associated with preparation of the MALDI-TOF target plate before or after testing. Secondly, a long-term stability study (3 years) of stored MALDI-TOF extracts showed that match scores can decrease below the threshold for reliable species identification (<1.7), which has implications for proficiency test panel item storage and distribution.
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Affiliation(s)
- Dobryan M Tracz
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Ashley D Tober
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Kym S Antonation
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Cindi R Corbett
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
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Suttisunhakul V, Pumpuang A, Ekchariyawat P, Wuthiekanun V, Elrod MG, Turner P, Currie BJ, Phetsouvanh R, Dance DAB, Limmathurotsakul D, Peacock SJ, Chantratita N. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of Burkholderia pseudomallei from Asia and Australia and differentiation between Burkholderia species. PLoS One 2017; 12:e0175294. [PMID: 28384252 PMCID: PMC5383291 DOI: 10.1371/journal.pone.0175294] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 03/23/2017] [Indexed: 11/21/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is increasingly used for rapid bacterial identification. Studies of Burkholderia pseudomallei identification have involved small isolate numbers drawn from a restricted geographic region. There is a need to expand the reference database and evaluate B. pseudomallei from a wider geographic distribution that more fully captures the extensive genetic diversity of this species. Here, we describe the evaluation of over 650 isolates. Main spectral profiles (MSP) for 26 isolates of B. pseudomallei (N = 5) and other Burkholderia species (N = 21) were added to the Biotyper database. MALDI-TOF MS was then performed on 581 B. pseudomallei, 19 B. mallei, 6 B. thailandensis and 23 isolates representing a range of other bacterial species. B. pseudomallei originated from northeast and east Thailand (N = 524), Laos (N = 12), Cambodia (N = 14), Hong Kong (N = 4) and Australia (N = 27). All 581 B. pseudomallei were correctly identified, with 100% sensitivity and specificity. Accurate identification required a minimum inoculum of 5 x 107 CFU/ml, and identification could be performed on spiked blood cultures after 24 hours of incubation. Comparison between a dendrogram constructed from MALDI-TOF MS main spectrum profiles and a phylogenetic tree based on recA gene sequencing demonstrated that MALDI-TOF MS distinguished between B. pseudomallei and B. mallei, while the recA tree did not. MALDI-TOF MS is an accurate method for the identification of B. pseudomallei, and discriminates between this and other related Burkholderia species.
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Affiliation(s)
- Vichaya Suttisunhakul
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Apinya Pumpuang
- Department of Clinical Pathology, Faculty of Medicine, Navamindradhiraj University, Bangkok, Thailand
| | - Peeraya Ekchariyawat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Mindy G. Elrod
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Zoonotic and Emerging Infectious Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Paul Turner
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Bart J. Currie
- Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Northern Territory, Australia; Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Rattanaphone Phetsouvanh
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - David A. B. Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sharon J. Peacock
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - 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
- * E-mail:
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18
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Reply to "Burkholderia pseudomallei: Challenges for the Clinical Microbiology Laboratory-a Response from the Front Line". J Clin Microbiol 2017; 55:983-984. [PMID: 28232504 DOI: 10.1128/jcm.02438-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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19
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Tracz DM, Tyler AD, Cunningham I, Antonation KS, Corbett CR. Custom database development and biomarker discovery methods for MALDI-TOF mass spectrometry-based identification of high-consequence bacterial pathogens. J Microbiol Methods 2017; 134:54-57. [PMID: 28108323 DOI: 10.1016/j.mimet.2017.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/16/2017] [Accepted: 01/16/2017] [Indexed: 11/18/2022]
Abstract
A high-quality custom database of MALDI-TOF mass spectral profiles was developed with the goal of improving clinical diagnostic identification of high-consequence bacterial pathogens. A biomarker discovery method is presented for identifying and evaluating MALDI-TOF MS spectra to potentially differentiate biothreat bacteria from less-pathogenic near-neighbour species.
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Affiliation(s)
- Dobryan M Tracz
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Andrea D Tyler
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Ian Cunningham
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Kym S Antonation
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Cindi R Corbett
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada; University of Manitoba, Department of Medical Microbiology and Infectious Diseases, Winnipeg, Manitoba R3E 0J9, Canada.
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Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) for the identification of highly pathogenic bacteria. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.04.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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21
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Burkholderia pseudomallei: Challenges for the Clinical Microbiology Laboratory. J Clin Microbiol 2016; 54:2866-2873. [PMID: 27654336 DOI: 10.1128/jcm.01636-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Melioidosis is a potentially fatal infection caused by the bacterium Burkholderia pseudomallei Clinical diagnosis of melioidosis can be challenging since there is no pathognomonic clinical syndrome, and the organism is often misidentified by methods used routinely in clinical laboratories. Although the disease is more prevalent in Thailand and northern Australia, sporadic cases may be encountered in areas where it is not endemic, including the United States. Since the organism is considered a tier 1 select agent according to the Centers for Disease Control and Prevention and the U.S. Department of Agriculture Animal and Plant Health Inspection Service, clinical laboratories must be proficient at rapidly recognizing isolates suspicious for B. pseudomallei, be able to safely perform necessary rule-out tests, and to refer suspect isolates to Laboratory Response Network reference laboratories. In this minireview, we report a case of melioidosis encountered at our institution and discuss the laboratory challenges encountered when dealing with clinical isolates suspicious for B. pseudomallei or clinical specimens from suspected melioidosis cases.
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Restricted Identification of Clinical Pathogens Categorized as Biothreats by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2016; 54:816. [PMID: 26763958 DOI: 10.1128/jcm.03250-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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Lau SKP, Sridhar S, Ho CC, Chow WN, Lee KC, Lam CW, Yuen KY, Woo PCY. Laboratory diagnosis of melioidosis: past, present and future. Exp Biol Med (Maywood) 2015; 240:742-51. [PMID: 25908634 DOI: 10.1177/1535370215583801] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Melioidosis is an emerging, potentially fatal disease caused by Burkholderia pseudomallei, which requires prolonged antibiotic treatment to prevent disease relapse. However, difficulties in laboratory diagnosis of melioidosis may delay treatment and affect disease outcomes. Isolation of B. pseudomallei from clinical specimens has been improved with the use of selective media. However, even with positive cultures, identification of B. pseudomallei can be difficult in clinical microbiology laboratories, especially in non-endemic areas where clinical suspicion is low. Commercial identification systems may fail to distinguish between B. pseudomallei and closely related species such as Burkholderia thailandensis. Genotypic identification of suspected isolates can be achieved by sequencing of gene targets such as groEL which offer higher discriminative power than 16S rRNA. Specific PCR-based identification of B. pseudomallei has also been developed using B. pseudomallei-specific gene targets such as Type III secretion system and Tat-domain protein. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a revolutionary technique for pathogen identification, has been shown to be potentially useful for rapid identification of B. pseudomallei, although existing databases require optimization by adding reference spectra for B. pseudomallei. Despite these advances in bacterial identification, diagnostic problems encountered in culture-negative cases remain largely unresolved. Although various serological tests have been developed, they are generally unstandardized "in house" assays and have low sensitivities and specificities. Although specific PCR assays have been applied to direct clinical and environmental specimens, the sensitivities for diagnosis remain to be evaluated. Metabolomics is an uprising tool for studying infectious diseases and may offer a novel approach for exploring potential diagnostic biomarkers. The metabolomics profiles of B. pseudomallei culture supernatants can be potentially distinguished from those of related bacterial species including B. thailandensis . Further studies using bacterial cultures and direct patient samples are required to evaluate the potential of metabolomics for improving diagnosis of melioidosis.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Siddharth Sridhar
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Chi-Chun Ho
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Wang-Ngai Chow
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kim-Chung Lee
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Ching-Wan Lam
- Department of Pathology, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China
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Bourassa L, Butler-Wu SM. MALDI-TOF Mass Spectrometry for Microorganism Identification. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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