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Zhang JX, Xu JH, Yuan B, Wang XD, Mao XH, Wang JL, Zhang XLL, Yuan Y. Detection of Burkholderia pseudomallei with CRISPR-Cas12a based on specific sequence tags. Front Public Health 2023; 11:1153352. [PMID: 37250090 PMCID: PMC10211466 DOI: 10.3389/fpubh.2023.1153352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/07/2023] [Indexed: 05/31/2023] Open
Abstract
Melioidosis is a bacterial infection caused by Burkholderia pseudomallei (B. pseudomallei), posing a significant threat to public health. Rapid and accurate detection of B. pseudomallei is crucial for preventing and controlling melioidosis. However, identifying B. pseudomallei is challenging due to its high similarity to other species in the same genus. To address this issue, this study proposed a dual-target method that can specifically identify B. pseudomallei in less than 40 min. We analyzed 1722 B. pseudomallei genomes to construct large-scale pan-genomes and selected specific sequence tags in their core genomes that effectively distinguish B. pseudomallei from its closely related species. Specifically, we selected two specific tags, LC1 and LC2, which we combined with the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated proteins (Cas12a) system and recombinase polymerase amplification (RPA) pre-amplification. Our analysis showed that the dual-target RPA-CRISPR/Cas12a assay has a sensitivity of approximately 0.2 copies/reaction and 10 fg genomic DNA for LC1, and 2 copies/reaction and 20 fg genomic DNA for LC2. Additionally, our method can accurately and rapidly detect B. pseudomallei in human blood and moist soil samples using the specific sequence tags mentioned above. In conclusion, the dual-target RPA-CRISPR/Cas12a method is a valuable tool for the rapid and accurate identification of B. pseudomallei in clinical and environmental samples, aiding in the prevention and control of melioidosis.
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Affiliation(s)
- Jia-Xin Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jian-Hao Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bing Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiao-Dong Wang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xu-hu Mao
- Department of Clinical Microbiology and Immunology, The Third Military Medical University, Chongqing, China
| | - Jing-Lin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiang-Li-Lan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuan Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Zheng J, Liu L, Li X, Xu Z, Gai Z, Zhang X, Lei H, Shen X. Rapid and Simple Detection of Burkholderia gladioli in Food Matrices Using RPA-CRISPR/Cas12a Method. Foods 2023; 12:foods12091760. [PMID: 37174300 PMCID: PMC10178126 DOI: 10.3390/foods12091760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/14/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Pathogenic variants of Burkholderia gladioli pose a serious threat to human health and food safety, but there is a lack of rapid and sensitive field detection methods for Burkholderia gladioli. In this study, the CRISPR/Cas12a system combined with recombinant enzyme polymerase amplification (RPA) was used to detect Burkholderia gladioli in food. The optimized RPA-CRISPR/Cas12a assay was able to specifically and stably detect Burkholderia gladioli at a constant 37 °C without the assistance of large equipment. The detection limit of the method was evaluated at two aspects, the genomic DNA (gDNA) level and bacterial quantity, of which there were 10-3 ng/μL and 101 CFU/mL, respectively. Three kinds of real food samples were tested. The detection limit for rice noodles, fresh white noodles, and glutinous rice flour samples was 101 CFU/mL, 102 CFU/mL, and 102 CFU/mL, respectively, without any enrichment steps. The whole detection process, including sample pretreatment and DNA extraction, did not exceed one hour. Compared with the qPCR method, the established RPA-CRISPR /Cas12a method was simpler and even more sensitive. Using this method, a visual detection of Burkholderia gladioli that is suitable for field detection can be achieved quickly and easily.
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Affiliation(s)
- Jiale Zheng
- Guangdong Provincial Key Laboratory of Food Quality and Safety, National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, China
| | - Li Liu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, China
| | - Xiangmei Li
- Guangdong Provincial Key Laboratory of Food Quality and Safety, National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, China
| | - Zhenlin Xu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, China
| | - Zuoqi Gai
- Guangzhou Editgene Co., Ltd., Guangzhou 510630, China
| | - Xu Zhang
- Guangzhou Editgene Co., Ltd., Guangzhou 510630, China
| | - Hongtao Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety, National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xing Shen
- Guangdong Provincial Key Laboratory of Food Quality and Safety, National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, China
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Abstract
Glanders is an infectious disease that causes serious damage to the equine production chain in countries where it occurs endemically and poses a risk to public health. This study aimed to conduct an integrative review of the advances in the knowledge of glanders in Brazil over the last three decades since its re-emergence. Documentary research was conducted for the period between the years 2000 and 2022. SCOPUS and PUBMED databases were used to search for scientific articles, dissertations, and thesis, in addition to the Brazilian Digital Library of Thesis and Dissertations (BDTD). A total of 41 documents were retrieved, including 12 dissertations, five theses, and 24 scientific articles. The Federal Rural University of Pernambuco (UFRPE) group provided a noteworthy amount of material on this topic (25 documents, four theses, three dissertations, and 18 scientific articles). During this period, ten dissertations, one thesis, and six scientific articles published by other groups in other states of the Federation were also identified. It was concluded that there was a significant number of scientific publications with relevant data on the clinical, epidemiological, pathological, microbiological, serological, and molecular characteristics of glanders disease in Brazil. Additionally, training of human resources regarding this disease led to an increase in the nucleation of research groups, especially in the northeast region of Brazil. Despite significant advances, new research groups and specific funding are still needed for the development of more accurate diagnostic methods, immunizing production, training of veterinarians to recognize the disease, and more robust programs to control and eradicate the disease in Brazil.
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Affiliation(s)
- Rinaldo Aparecido Mota
- Departament of Veterinary Medicine, Universidade Federal Rural de Pernambuco, Rua Dom Manuel de Medeiros, sn, Recife, Dois Irmãos, Pernambuco, 52171-900, Brazil.
| | - José Wilton Pinheiro Junior
- Departament of Veterinary Medicine, Universidade Federal Rural de Pernambuco, Rua Dom Manuel de Medeiros, sn, Recife, Dois Irmãos, Pernambuco, 52171-900, Brazil
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Falcão MVD, Laroucau K, Vorimore F, Deshayes T, Santana VLA, Silva KPC, do Nascimento SA, de Castro RS, Araújo FR, Mota RA. Molecular characterization of Burkholderia mallei strains isolated from horses in Brazil (2014-2017). Infect Genet Evol 2022; 99:105250. [PMID: 35183750 DOI: 10.1016/j.meegid.2022.105250] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 11/24/2021] [Accepted: 02/14/2022] [Indexed: 05/01/2023]
Abstract
Glanders is an infectious zoonosis caused by Burkholderia (B.) mallei that mainly affects equids. The objective of this work was to provide additional knowledge on the diversity of the strains circulating in Brazil. Six Burkholderia mallei isolates obtained during necropsies of glanderous horses between 2014 and 2017 in two different states (Pernambuco and Alagoas) were analyzed by polymerase chain reaction-high-resolution melting (PCR-HRM). While four strains (9902 RSC, BM_campo 1, BM_campo 3 and UFAL2) clustered in the L3B2 branch, which already includes the Brazilian 16-2438_BM#8 strain, two strains (BM_campo 2.1 and BM_campo 2.2) clustered within the L3B3sB3 branch, which mostly includes older isolates, from Europe and the Middle East. Whole genome sequencing of two of these strains (UFAL2 and BM_campo 2.1), belonging to different branches, confirmed the HRM typing results and refined the links between the strains, including the description of the L3B3Sb3Gp1SbGp1 genotype, never reported so far for contemporary strains. These results suggest different glanders introduction events in Brazil, including a potential link with strains of European origin, related to colonization or trade.
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Affiliation(s)
- Marcus V D Falcão
- Federal Rural University of Pernambuco, Department of Veterinary Medicine, Recife, Pernambuco, Brazil
| | - Karine Laroucau
- Bacterial Zoonoses unit, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Maisons-Alfort, France
| | - Fabien Vorimore
- Bacterial Zoonoses unit, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Maisons-Alfort, France
| | - Thomas Deshayes
- Bacterial Zoonoses unit, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Maisons-Alfort, France
| | - Vania L A Santana
- Ministry of Agriculture, Livestock and Food Supply, Recife, Pernambuco, Brazil
| | - Karla P C Silva
- Federal University of Alagoas, Department of Veterinary Medicine, Maceió, Alagoas, Brazil
| | - Sergio A do Nascimento
- Federal Rural University of Pernambuco, Department of Veterinary Medicine, Recife, Pernambuco, Brazil
| | - Roberto S de Castro
- Federal Rural University of Pernambuco, Department of Veterinary Medicine, Recife, Pernambuco, Brazil
| | - Flabio R Araújo
- Embrapa Gado de Corte, Campo Grande, Mato Grosso do Sul, Brazil
| | - Rinaldo A Mota
- Federal Rural University of Pernambuco, Department of Veterinary Medicine, Recife, Pernambuco, Brazil.
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Moawad AA, Silge A, Bocklitz T, Fischer K, Rösch P, Roesler U, Elschner MC, Popp J, Neubauer H. A Machine Learning-Based Raman Spectroscopic Assay for the Identification of Burkholderia mallei and Related Species. Molecules 2019; 24:E4516. [PMID: 31835527 DOI: 10.3390/molecules24244516] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 11/25/2022] Open
Abstract
Burkholderia (B.) mallei, the causative agent of glanders, and B. pseudomallei, the causative agent of melioidosis in humans and animals, are genetically closely related. The high infectious potential of both organisms, their serological cross-reactivity, and similar clinical symptoms in human and animals make the differentiation from each other and other Burkholderia species challenging. The increased resistance against many antibiotics implies the need for fast and robust identification methods. The use of Raman microspectroscopy in microbial diagnostic has the potential for rapid and reliable identification. Single bacterial cells are directly probed and a broad range of phenotypic information is recorded, which is subsequently analyzed by machine learning methods. Burkholderia were handled under biosafety level 1 (BSL 1) conditions after heat inactivation. The clusters of the spectral phenotypes and the diagnostic relevance of the Burkholderia spp. were considered for an advanced hierarchical machine learning approach. The strain panel for training involved 12 B. mallei, 13 B. pseudomallei and 11 other Burkholderia spp. type strains. The combination of top- and sub-level classifier identified the mallei-complex with high sensitivities (>95%). The reliable identification of unknown B. mallei and B. pseudomallei strains highlighted the robustness of the machine learning-based Raman spectroscopic assay.
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Falcão MVD, Silveira PPM, Santana VLA, da Rocha LO, Chaves KP, Mota RA. First record of Burkholderia mallei Turkey 10 strain originating from glanderous horses from Brazil. Braz J Microbiol 2019; 50:1125-1127. [PMID: 31321739 DOI: 10.1007/s42770-019-00113-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 06/25/2019] [Indexed: 11/30/2022] Open
Abstract
Burkholderia (B.) mallei is the causative agent of glanders in Equidae. This study describes the first record of the Turkey 10 strain of B. mallei in glanderous horses in Northeastern of Brazil. This description should contribute to the future actions of diagnosis, control, and eradication of this disease in Brazil.
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Affiliation(s)
- Marcus Vinícius D Falcão
- Department of Veterinary Medicine, Laboratory of Infectious Diseases of Domestic Animals, Federal Rural University of Pernambuco, Manoel de Medeiros street, w/n, Dois Irmãos, Recife, PE, CEP: 52171-900, Brazil.
| | - Pedro P M Silveira
- Federal Superintendence of Agriculture, Livestock and Supply in the State of Pernambuco, Ministry of Agriculture, Livestock and Supply, General San Martin Avenue, 1000, Bongi, Recife, PE, CEP: 50630-060, Brazil
| | - Vania L A Santana
- Federal Superintendence of Agriculture, Livestock and Supply in the State of Pernambuco, Ministry of Agriculture, Livestock and Supply, General San Martin Avenue, 1000, Bongi, Recife, PE, CEP: 50630-060, Brazil
| | - Larissa O da Rocha
- Academic Unit of Viçosa, Laboratory of Infectious Diseases of Domestic Animals, Federal University of Alagoas, Manoel Severino Barbosa, w/n, Bom Sucesso, Viçosa, AL, CEP: 57309-005, Brazil
| | - Karla P Chaves
- Academic Unit of Viçosa, Laboratory of Infectious Diseases of Domestic Animals, Federal University of Alagoas, Manoel Severino Barbosa, w/n, Bom Sucesso, Viçosa, AL, CEP: 57309-005, Brazil
| | - Rinaldo A Mota
- Department of Veterinary Medicine, Laboratory of Infectious Diseases of Domestic Animals, Federal Rural University of Pernambuco, Manoel de Medeiros street, w/n, Dois Irmãos, Recife, PE, CEP: 52171-900, Brazil
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7
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Elschner MC, Neubauer H, Sprague LD. The Resurrection of Glanders in a new Epidemiological Scenario: A Beneficiary of “Global Change”. Curr Clin Micro Rpt 2017. [DOI: 10.1007/s40588-017-0058-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Lau SKP, Lee KC, Lo GCS, Ding VSY, Chow WN, Ke TYH, Curreem SOT, To KKW, Ho DTY, Sridhar S, Wong SCY, Chan JFW, Hung IFN, Sze KH, Lam CW, Yuen KY, Woo PCY. Metabolomic Profiling of Plasma from Melioidosis Patients Using UHPLC-QTOF MS Reveals Novel Biomarkers for Diagnosis. Int J Mol Sci 2016; 17:307. [PMID: 26927094 PMCID: PMC4813170 DOI: 10.3390/ijms17030307] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/15/2016] [Accepted: 02/22/2016] [Indexed: 12/22/2022] Open
Abstract
To identify potential biomarkers for improving diagnosis of melioidosis, we compared plasma metabolome profiles of melioidosis patients compared to patients with other bacteremia and controls without active infection, using ultra-high-performance liquid chromatography-electrospray ionization-quadruple time-of-flight mass spectrometry. Principal component analysis (PCA) showed that the metabolomic profiles of melioidosis patients are distinguishable from bacteremia patients and controls. Using multivariate and univariate analysis, 12 significant metabolites from four lipid classes, acylcarnitine (n = 6), lysophosphatidylethanolamine (LysoPE) (n = 3), sphingomyelins (SM) (n = 2) and phosphatidylcholine (PC) (n = 1), with significantly higher levels in melioidosis patients than bacteremia patients and controls, were identified. Ten of the 12 metabolites showed area-under-receiver operating characteristic curve (AUC) >0.80 when compared both between melioidosis and bacteremia patients, and between melioidosis patients and controls. SM(d18:2/16:0) possessed the largest AUC when compared, both between melioidosis and bacteremia patients (AUC 0.998, sensitivity 100% and specificity 91.7%), and between melioidosis patients and controls (AUC 1.000, sensitivity 96.7% and specificity 100%). Our results indicate that metabolome profiling might serve as a promising approach for diagnosis of melioidosis using patient plasma, with SM(d18:2/16:0) representing a potential biomarker. Since the 12 metabolites were related to various pathways for energy and lipid metabolism, further studies may reveal their possible role in the pathogenesis and host response in melioidosis.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Kim-Chung Lee
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - George C S Lo
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Vanessa S Y Ding
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Wang-Ngai Chow
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Tony Y H Ke
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Shirly O T Curreem
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Kelvin K W To
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Deborah T Y Ho
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Siddharth Sridhar
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Sally C Y Wong
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Jasper F W Chan
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Ivan F N Hung
- Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Department of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Kong-Hung Sze
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Ching-Wan Lam
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China.
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Monecke S, Friedrichs A, Pöhlmann C, Hochauf K, Gunzer F, Wiesner D, Sickert W, Steinmetz I, Scholz H, Ehricht R, Schmoock G, Jacobs E. An imported case of melioidosis presenting as pyelonephritis/urosepsis. JMM Case Rep 2015. [DOI: 10.1099/jmmcr.0.000073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Stefan Monecke
- Alere Technologies GmbH, Löbstedter Strasse 103-105, D-07749 Jena, Germany
- Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Fetscherstrasse 74, D-01307 Dresden, Germany
| | - Anette Friedrichs
- Department of Internal Medicine I, University Hospital Schleswig-Holstein, Campus Kiel, Schittenhelmstrasse12, D-24105 Kiel, Germany
| | - Christoph Pöhlmann
- Department of Laboratory Medicine, Robert-Bosch-Hospital, Auerbachstraße 110, D-70376 Stuttgart, Germany
| | - Kristina Hochauf
- Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Fetscherstrasse 74, D-01307 Dresden, Germany
| | - Florian Gunzer
- Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Fetscherstrasse 74, D-01307 Dresden, Germany
| | - Diana Wiesner
- Deaconesses' Hospital Dessau, Gropiusallee 3, D-06846 Dessau-Roßlau, Germany
| | | | - Ivo Steinmetz
- Friedrich-Loeffler-Institute for Medical Microbiology, University of Greifswald, Lutherstrasse 6, D-17489 Greifswald, Germany
| | - Holger Scholz
- Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, D-80937 Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Ralf Ehricht
- Alere Technologies GmbH, Löbstedter Strasse 103-105, D-07749 Jena, Germany
| | - Gernot Schmoock
- Friedrich Loeffler Institute, Institute of Bacterial Infections and Zoonoses, Naumburger Strasse 96a, D-07743 Jena, Germany
| | - Enno Jacobs
- Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Fetscherstrasse 74, D-01307 Dresden, Germany
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11
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Lau SKP, Lam CW, Curreem SOT, Lee KC, Chow WN, Lau CCY, Sridhar S, Wong SCY, Martelli P, Hui SW, Yuen KY, Woo PCY. Metabolomic profiling of Burkholderia pseudomallei using UHPLC-ESI-Q-TOF-MS reveals specific biomarkers including 4-methyl-5-thiazoleethanol and unique thiamine degradation pathway. Cell Biosci 2015; 5:26. [PMID: 26097677 PMCID: PMC4475313 DOI: 10.1186/s13578-015-0018-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 05/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Burkholderia pseudomallei is an emerging pathogen that causes melioidosis, a serious and potentially fatal disease which requires prolonged antibiotics to prevent relapse. However, diagnosis of melioidosis can be difficult, especially in culture-negative cases. While metabolomics represents an uprising tool for studying infectious diseases, there were no reports on its applications to B. pseudomallei. To search for potential specific biomarkers, we compared the metabolomics profiles of culture supernatants of B. pseudomallei (15 strains), B. thailandensis (3 strains), B. cepacia complex (14 strains), P. aeruginosa (4 strains) and E. coli (3 strains), using ultra-high performance liquid chromatography-electrospray ionization-quadruple time-of-flight mass spectrometry (UHPLC-ESI-Q-TOF-MS). Multi- and univariate analyses were used to identify specific metabolites in B. pseudomallei. RESULTS Principal component and partial-least squares discrimination analysis readily distinguished the metabolomes between B. pseudomallei and other bacterial species. Using multi-variate and univariate analysis, eight metabolites with significantly higher levels in B. pseudomallei were identified. Three of the eight metabolites were identified by MS/MS, while five metabolites were unidentified against database matching, suggesting that they may be potentially novel compounds. One metabolite, m/z 144.048, was identified as 4-methyl-5-thiazoleethanol, a degradation product of thiamine (vitamin B1), with molecular formula C6H9NOS by database searches and confirmed by MS/MS using commercially available authentic chemical standard. Two metabolites, m/z 512.282 and m/z 542.2921, were identified as tetrapeptides, Ile-His-Lys-Asp with molecular formula C22H37N7O7 and Pro-Arg-Arg-Asn with molecular formula C21H39N11O6, respectively. To investigate the high levels of 4-methyl-5-thiazoleethanol in B. pseudomallei, we compared the thiamine degradation pathways encoded in genomes of B. pseudomallei and B. thailandensis. While both B. pseudomallei and B. thailandensis possess thiaminase I which catalyzes degradation of thiamine to 4-methyl-5-thiazoleethanol, thiM, which encodes hydroxyethylthiazole kinase responsible for degradation of 4-methyl-5-thiazoleethanol, is present and expressed in B. thailandensis as detected by PCR/RT-PCR, but absent or not expressed in all B. pseudomallei strains. This suggests that the high 4-methyl-5-thiazoleethanol level in B. pseudomallei is likely due to the absence of hydroxyethylthiazole kinase and hence reduced downstream degradation. CONCLUSION Eight novel biomarkers, including 4-methyl-5-thiazoleethanol and two tetrapeptides, were identified in the culture supernatant of B. pseudomallei.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Room 423, University Pathology Building, Queen Mary Hospital, Pok Fu Lam, Hong Kong ; Research Centre of Infection and Immunology, The University of Hong Kong, Pok Fu Lam, Hong Kong ; Carol Yu Centre for Infection, The University of Hong Kong, Pok Fu Lam, Hong Kong ; Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ching-Wan Lam
- Department of Pathology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Shirly O T Curreem
- Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Kim-Chung Lee
- Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Wang-Ngai Chow
- Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Candy C Y Lau
- Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Siddharth Sridhar
- Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Sally C Y Wong
- Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | | | - Suk-Wai Hui
- Ocean Park Corporation, Aqua City, Hong Kong
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Room 423, University Pathology Building, Queen Mary Hospital, Pok Fu Lam, Hong Kong ; Research Centre of Infection and Immunology, The University of Hong Kong, Pok Fu Lam, Hong Kong ; Carol Yu Centre for Infection, The University of Hong Kong, Pok Fu Lam, Hong Kong ; Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Room 423, University Pathology Building, Queen Mary Hospital, Pok Fu Lam, Hong Kong ; Research Centre of Infection and Immunology, The University of Hong Kong, Pok Fu Lam, Hong Kong ; Carol Yu Centre for Infection, The University of Hong Kong, Pok Fu Lam, Hong Kong ; Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
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Schmoock G, Elschner M, Sprague LD. Clear distinction between Burkholderia mallei and Burkholderia pseudomallei using fluorescent motB primers. Acta Vet Scand 2015; 57:13. [PMID: 25887130 PMCID: PMC4364355 DOI: 10.1186/s13028-015-0104-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/24/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A frame-shift mutation in the flagellum motor gene motB coding for the chemotaxis MotB protein of Burkholderia mallei has been utilized to design a conventional duplex PCR assay with fluorescent labelled primers. FINDINGS Species specificity was tested with a panel of 13 Burkholderia type strains. A total of 41 B. mallei field strains, 36 B. pseudomallei field strains, and 1 B. thailandensis field strain from different geographic regions were tested and correctly identified. Testing of 55 non-Burkholderia bacterial species revealed 100% specificity of the assay. The minimum detection limit was 1 pg DNA or 160 GE for B. mallei and 130 GE for B. pseudomallei, respectively. CONCLUSIONS This assay enables the clear distinction between B. mallei and B. pseudomallei/B. thailandensis.
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Affiliation(s)
- Gernot Schmoock
- Friedrich-Loeffler-Institut, Bundesforschungsinstitut für Tiergesundheit, Naumburger Str. 96a, DE-07743, Jena, Germany.
| | - Mandy Elschner
- Friedrich-Loeffler-Institut, Bundesforschungsinstitut für Tiergesundheit, Naumburger Str. 96a, DE-07743, Jena, Germany.
- National and OIE Reference Laboratory for Glanders, Friedrich-Loeffler-Institut, Bundesforschungsinstitut für Tiergesundheit, Naumburger Str. 96a, DE-07743, Jena, Germany.
| | - Lisa D Sprague
- Friedrich-Loeffler-Institut, Bundesforschungsinstitut für Tiergesundheit, Naumburger Str. 96a, DE-07743, Jena, Germany.
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Lau SK, Chan SY, Curreem SO, Hui SW, Lau CC, Lee P, Ho CC, Martelli P, Woo PC. Burkholderia pseudomallei in soil samples from an oceanarium in Hong Kong detected using a sensitive PCR assay. Emerg Microbes Infect 2014; 3:e69. [PMID: 26038496 DOI: 10.1038/emi.2014.69] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 08/05/2014] [Accepted: 08/11/2014] [Indexed: 12/18/2022]
Abstract
Melioidosis, caused by Burkholderia pseudomallei, is an emerging infectious disease with an expanding geographical distribution. Although assessment of the environmental load of B. pseudomallei is important for risk assessment in humans or animals in endemic areas, traditional methods of bacterial culture for isolation have low sensitivities and are labor-intensive. Using a specific polymerase chain reaction (PCR) assay targeting a Tat domain protein in comparison with a bacterial culture method, we examined the prevalence of B. pseudomallei in soil samples from an oceanarium in Hong Kong where captive marine mammals and birds have contracted melioidosis. Among 1420 soil samples collected from various sites in the oceanarium over a 15-month period, B. pseudomallei was detected in nine (0.6%) soil samples using bacterial culture, whereas it was detected in 96 (6.8%) soil samples using the specific PCR assay confirmed by sequencing. The PCR-positive samples were detected during various months, with higher detection rates observed during summer months. Positive PCR detection was significantly correlated with ambient temperature (P<0.0001) and relative humidity (P=0.011) but not with daily rainfall (P=0.241) or a recent typhoon (P=0.787). PCR-positive samples were obtained from all sampling locations, with the highest detection rate in the valley. Our results suggest that B. pseudomallei is prevalent and endemic in the oceanarium. The present PCR assay is more sensitive than the bacterial culture method, and it may be used to help better assess the transmission of melioidosis and to design infection control measures for captive animals in this unique and understudied environment.
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Schmoock G, Ehricht R, Sprague LD. DNA microarray-based detection of Coxiella burnetii, the causative agent of Q fever. Acta Vet Scand 2014; 56:27. [PMID: 24886299 PMCID: PMC4025541 DOI: 10.1186/1751-0147-56-27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 05/05/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND An easy-to-handle microarray assay based on the cost-effective ArrayTube™ platform has been designed for the rapid and unequivocal identification of Coxiella burnetii, the causative agent of Q fever. The gene targets include the chromosomally coded markers icd, omp/com1, and IS1111 as well as the plasmid coded markers cbbE and cbhE. RESULTS A representative panel comprising 50 German C. burnetii isolates and 10 clinical samples was examined to validate the test. All tested isolates harboured plasmid QpH1 and were correctly identified, corresponding to 100% sensitivity. The assay's limit of detection was 100 genome equivalents (GE) for icd, omp/com1, cbbE and cbhE and 10 GE for IS1111. Assay specificity was 100% as determined by analysing a panel of 37 non-Coxiella strains. CONCLUSIONS The present array is a rational assembly of established and evaluated targets for the rapid and unequivocal detection of C. burnetii. This array could be applied to the screening of vaginal swabs from small ruminants; screening of environmental samples e.g. on farms or screening of human samples.
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Eu LC, Ong KC, Hiu J, Vadivelu J, Nathan S, Wong KT. In situ hybridization to detect and identify Burkholderia pseudomallei in human melioidosis. Mod Pathol 2014; 27:657-64. [PMID: 24186135 DOI: 10.1038/modpathol.2013.184] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 08/28/2013] [Accepted: 08/29/2013] [Indexed: 11/10/2022]
Abstract
Burkholderia pseudomallei causes a potentially fatal infection called melioidosis. We have developed a nonfluorescent, colorimetric in situ hybridization assay using a specific probe to target 16s rRNA of B. pseudomallei in formalin-fixed, paraffin-embedded infected tissues for diagnostic purposes and to study infectious disease pathology. A 63-base pair DNA probe was synthesized and labeled with digoxigenin by PCR. Probe specificity was confirmed by BLAST analysis and by testing on appropriate microbial controls. The in situ hybridization assay was specifically and consistently positive for B. pseudomallei, showing strongly and crisply stained, single bacillus and bacilli clusters in mainly inflamed tissues in seven human acute melioidosis cases and experimentally infected mouse tissues. Intravascular and extravascular bacilli were detected in both intracellular and extracellular locations in various human organs, including lung, spleen, kidney, liver, bone marrow, and aortic mycotic aneurysm, particularly in the inflamed areas. Intravascular, intracellular bacteria in melioidosis have not been previously reported. Although the identity of infected intravascular leukocytes has to be confirmed, extravascular, intracellular bacilli appear to be found mainly within macrophages and neutrophils. Rarely, large intravascular, extracellular bacillary clusters/emboli could be detected in both human and mouse tissues. B. cepacia and non-Burkholderia pathogens (16 microbial species) all tested negative. Nonpathogenic B. thailandensis showed some cross-hybridization but signals were less intense. This in situ hybridization assay could be usefully adapted for B. pseudomallei identification in other clinical specimens such as pus and sputum.
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Affiliation(s)
- Lin Chuan Eu
- Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kien Chai Ong
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jessie Hiu
- Forensic Department, Queen Elizabeth Hospital, Sabah, Malaysia
| | - Jamunarani Vadivelu
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sheila Nathan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Kum Thong Wong
- Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Tomlinson J, Harrison C, Boonham N, Goodchild SA, Weller SA. Influence of the length of target DNA overhang proximal to the array surface on discrimination of single-base mismatches on a 25-mer oligonucleotide array. BMC Res Notes 2014; 7:251. [PMID: 24742004 PMCID: PMC3997201 DOI: 10.1186/1756-0500-7-251] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 04/09/2014] [Indexed: 01/16/2023] Open
Abstract
Background The performance of probes on an oligonucleotide microarray can be characterised in terms of hybridisation signal strength and the ability to discriminate sequence mismatches between the probe and the hybridising target strand, such as those resulting from SNPs. Various properties of the probe affect mismatch discrimination, such as probe length and the position of mismatched bases, and the effects of these factors have been well characterised in a variety of array formats. Results A low-density microarray was developed to systematically investigate the effect of a probe’s position within hybridised target PCR products on the tolerance and discrimination of single-nucleotide mismatches between the probe and target. In line with previous reports, hybridisation signals were attenuated by different degrees depending on the identity of the mismatch, the position of the mismatch within the probe, and the length of the PCR product. However, the same mismatch caused different degrees of attenuation depending on the position of the probe within the hybridising product, such that improved mismatch discrimination was observed for PCR products where a greater proportion of the total length was proximal to the array surface. Conclusions These results suggest that the degree of mismatch discrimination can be influenced by the choice of PCR primers, providing a means by which array performance could be fine-tuned in addition to manipulation of the properties of the probes themselves.
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Affiliation(s)
- Jenny Tomlinson
- The Food and Environment Research Agency, Sand Hutton, YO41 1LZ York, UK.
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Tonelli A, Sacchini F, Krasteva I, Zilli K, Scacchia M, Beaurepaire C, Nantel A, Pini A. One test microbial diagnostic microarray for identification of Mycoplasma mycoides subsp. mycoides and other Mycoplasma species. Mol Biotechnol 2013; 52:285-99. [PMID: 22271459 DOI: 10.1007/s12033-012-9497-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The present study describes the use of microarray technology for rapid identification and differentiation of Mycoplasma mycoides subsp. mycoides from other mycoplasmas that may be pathogenic to ruminants, including those of the Mycoplasma mycoides cluster, genetically and antigenically strictly correlated with Mycoplasma mycoides subsp. mycoides. A microarray containing genetic sequences of 55 different bacterial species from Acholeplasma, Mycoplasma, Spiroplasma and Ureaplasma genera was constructed. Sequences to genes of interest were collected in FASTA format from NCBI. The collected sequences were processed with OligoPicker software. Oligonucleotides were then checked for their selectivity with BLAST searches in GenBank. The microarray was tested with ATCC/NCTC strains of Mycoplasma spp. of veterinary importance in ruminants including Mycoplasma belonging to the mycoides cluster as well as Mycoplasma mycoides subsp. mycoides and Mycoplasma mycoides subsp. capri field strains. The results showed that but one ATCC/NCTC reference strains hybridized with their species-specific sequences showed a profile/signature different and distinct from each other. The heat-map of the hybridization results for the nine genes interrogated for Mycoplasma mycoides subsp. mycoides demonstrated that the reference strain Mycoplasma mycoides subsp mycoides PG1 was positive for all of the gene sequences spotted on the microarray. CBPP field, vaccine and reference strains were all typed to be M. mycoides subsp. mycoides, and seven of the nine strains gave positive hybridization results for all of the nine genes. Two Italian strains were negative for some of the genes. Comparison with non-Mycoplasma mycoides subsp. mycoides reference strains showed some positive signals or considerable homology to Mycoplasma mycoides subsp. mycoides genes. As expected, some correlations were observed between the strictly genetically and antigenically correlated Mycoplasma mycoides subsp. mycoides and Mycoplasma mycoides subsp. capri strains. Specifically, we observed that some Italian Mycoplasma mycoides subsp. mycoides strains were positive for two out of the three Mycoplasma mycoides subsp. capri genes, differently from what has been observed for other European or African Mycoplasma mycoides subsp. mycoides strains. This study highlighted the use of microarray technology as a simple and effective method for a single-step identification and differentiation of Mycoplasma mycoides subsp. mycoides from other mycoplasmas that may be pathogenic to ruminants, including those of the Mycoplasma mycoides cluster, genetically and antigenically strictly correlated with Mycoplasma mycoides subsp. mycoides. The opportunity to discriminate several mycoplasmas in a single analysis enhances diagnostic rapidity and may represent a useful tool to screen occasionally mycoplasmas affecting animal farming in territories where diagnostic laboratory support is limited. The heat-map of the hybridization results of the comparative genomic hybridizations DNA-designed chip clearly indicates that the microarray performs well for the identification of the tested Mycoplasma mycoides subsp. mycoides reference and field strains, discriminating them from other mycoplasmas.
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Affiliation(s)
- A Tonelli
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", (Istituto G. Caporale), Teramo, Italy.
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Janse I, Hamidjaja RA, Hendriks ACA, van Rotterdam BJ. Multiplex qPCR for reliable detection and differentiation of Burkholderia mallei and Burkholderia pseudomallei. BMC Infect Dis 2013; 13:86. [PMID: 23409683 PMCID: PMC3579680 DOI: 10.1186/1471-2334-13-86] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 02/08/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Burkholderia mallei and B. pseudomallei are two closely related species of highly virulent bacteria that can be difficult to detect. Pathogenic Burkholderia are endemic in many regions worldwide and cases of infection, sometimes brought by travelers from unsuspected regions, also occur elsewhere. Rapid, sensitive methods for identification of B. mallei and B. pseudomallei are urgently needed in the interests of patient treatment and epidemiological surveillance. METHODS Signature sequences for sensitive, specific detection of pathogenic Burkholderia based on published genomes were identified and a qPCR assay was designed and validated. RESULTS A single-reaction quadruplex qPCR assay for the detection of pathogenic Burkholderia, which includes a marker for internal control of DNA extraction and amplification, was developed. The assay permits differentiation of B. mallei and B. pseudomallei strains, and probit analysis showed a very low detection limit. Use of a multicopy signature sequence permits detection of less than 1 genome equivalent per reaction. CONCLUSIONS The new assay permits rapid detection of pathogenic Burkholderia and combines enhanced sensitivity, species differentiation, and inclusion of an internal control for both DNA extraction and PCR amplification.
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Affiliation(s)
- Ingmar Janse
- Laboratory for Zoonoses and Environmental Microbiology, National Institute for Public Health and the Environment (RIVM), Anthonie van Leeuwenhoeklaan 9, Bilthoven, MA, 3721, The Netherlands.
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Karger A, Stock R, Ziller M, Elschner MC, Bettin B, Melzer F, Maier T, Kostrzewa M, Scholz HC, Neubauer H, Tomaso H. Rapid identification of Burkholderia mallei and Burkholderia pseudomallei by intact cell Matrix-assisted Laser Desorption/Ionisation mass spectrometric typing. BMC Microbiol 2012; 12:229. [PMID: 23046611 PMCID: PMC3534143 DOI: 10.1186/1471-2180-12-229] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 09/25/2012] [Indexed: 11/17/2022] Open
Abstract
Background Burkholderia (B.) pseudomallei and B. mallei are genetically closely related species. B. pseudomallei causes melioidosis in humans and animals, whereas B. mallei is the causative agent of glanders in equines and rarely also in humans. Both agents have been classified by the CDC as priority category B biological agents. Rapid identification is crucial, because both agents are intrinsically resistant to many antibiotics. Matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-TOF MS) has the potential of rapid and reliable identification of pathogens, but is limited by the availability of a database containing validated reference spectra. The aim of this study was to evaluate the use of MALDI-TOF MS for the rapid and reliable identification and differentiation of B. pseudomallei and B. mallei and to build up a reliable reference database for both organisms. Results A collection of ten B. pseudomallei and seventeen B. mallei strains was used to generate a library of reference spectra. Samples of both species could be identified by MALDI-TOF MS, if a dedicated subset of the reference spectra library was used. In comparison with samples representing B. mallei, higher genetic diversity among B. pseudomallei was reflected in the higher average Eucledian distances between the mass spectra and a broader range of identification score values obtained with commercial software for the identification of microorganisms. The type strain of B. pseudomallei (ATCC 23343) was isolated decades ago and is outstanding in the spectrum-based dendrograms probably due to massive methylations as indicated by two intensive series of mass increments of 14 Da specifically and reproducibly found in the spectra of this strain. Conclusions Handling of pathogens under BSL 3 conditions is dangerous and cumbersome but can be minimized by inactivation of bacteria with ethanol, subsequent protein extraction under BSL 1 conditions and MALDI-TOF MS analysis being faster than nucleic amplification methods. Our spectra demonstrated a higher homogeneity in B. mallei than in B. pseudomallei isolates. As expected for closely related species, the identification process with MALDI Biotyper software (Bruker Daltonik GmbH, Bremen, Germany) requires the careful selection of spectra from reference strains. When a dedicated reference set is used and spectra of high quality are acquired, it is possible to distinguish both species unambiguously. The need for a careful curation of reference spectra databases is stressed.
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Affiliation(s)
- Axel Karger
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Biology, Südufer 10, Greifswald-Insel Riems D-17493, Germany
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Frickmann H, Chantratita N, Gauthier YP, Neubauer H, Hagen RM. DISCRIMINATION OF Burkholderia mallei/pseudomallei FROM Burkholderia thailandensis BY SEQUENCE COMPARISON OF A FRAGMENT OF THE RIBOSOMAL PROTEIN S21 (RPSU) GENE. Eur J Microbiol Immunol (Bp) 2012; 2:148-156. [PMID: 23227305 DOI: 10.1556/eujmi.2.2012.2.8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Discrimination of Burkholderia (B.) pseudomallei and B. mallei from environmental B. thailandensis is challenging. We describe a discrimination method based on sequence comparison of the ribosomal protein S21 (rpsU) gene.The rpsU gene was sequenced in ten B. pseudomallei, six B. mallei, one B. thailandensis reference strains, six isolates of B. pseudomallei, and 37 of B. thailandensis. Further rpsU sequences of six B. pseudomallei, three B. mallei, and one B. thailandensis were identified via NCBI GenBank. Three to four variable base-positions were identified within a 120-base-pair fragment, allowing discrimination of the B. pseudomallei/mallei-cluster from B. thailandensis, whose sequences clustered identically. All B. mallei and three B. pseudomallei sequences were identical, while 17/22 B. pseudomallei strains differed in one nucleotide (78A>C). Sequences of the rpsU fragment of 'out-stander' reference strains of B. cepacia, B. gladioli, B. plantarii, and B. vietnamensis clustered differently.Sequence comparison of the described rpsU gene fragment can be used as a supplementary diagnostic procedure for the discrimination of B. mallei/pseudomallei from B. thailandensis as well as from other species of the genus Burkholderia, keeping in mind that it does not allow for a differentiation between B. mallei and B. pseudomallei.
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Affiliation(s)
- H Frickmann
- Department of Tropical Medicine at the Bernhard Nocht Institute, German Armed Forces Hospital Hamburg, Germany ; Institute for Medical Microbiology, Virology and Hygiene, University of Rostock Hospital, Rostock, Germany
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Kaestli M, Richardson LJ, Colman RE, Tuanyok A, Price EP, Bowers JR, Mayo M, Kelley E, Seymour ML, Sarovich DS, Pearson T, Engelthaler DM, Wagner DM, Keim PS, Schupp JM, Currie BJ. Comparison of TaqMan PCR assays for detection of the melioidosis agent Burkholderia pseudomallei in clinical specimens. J Clin Microbiol 2012; 50:2059-62. [PMID: 22442327 DOI: 10.1128/JCM.06737-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Melioidosis is an emerging infectious disease caused by the soil bacterium Burkholderia pseudomallei. In diagnostic and forensic settings, molecular detection assays need not only high sensitivity with low limits of detection but also high specificity. In a direct comparison of published and newly developed TaqMan PCR assays, we found the TTS1-orf2 assay to be superior in detecting B. pseudomallei directly from clinical specimens. The YLF/BTFC multiplex assay (targeting the Yersinia-like fimbrial/Burkholderia thailandensis-like flagellum and chemotaxis region) also showed high diagnostic sensitivity and provides additional information on possible geographic origin.
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Schmoock G, Ehricht R, Melzer F, Elschner M, Tomaso H, Neubauer H, Al Dahouk S. Development of a diagnostic multiplex polymerase chain reaction microarray assay to detect and differentiate Brucella spp. Diagn Microbiol Infect Dis 2011; 71:341-53. [PMID: 21982564 DOI: 10.1016/j.diagmicrobio.2011.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 08/17/2011] [Accepted: 08/17/2011] [Indexed: 01/01/2023]
Abstract
Brucellosis is a worldwide zoonosis leading to tremendous economic losses and severe human illness. Fast and reliable laboratory tests are needed to detect disease in both humans and animals and to monitor the production of safe food products and feed. For rapid identification of the genus Brucella and differentiation of its species, a multiplex polymerase chain reaction microarray assay based on 11 signature sequences and redundant oligonucleotide probes was developed. The gene targets included genus-specific sequences in bcsp31, perA, cgs, and omp2b, as well as chromosomal regions displaying species-specific hybridization patterns. Brucella reference strains and a representative panel of 102 field isolates were unambiguously identified by their hybridization patterns. The differentiation of species, however, was limited in members of the groups B. suis bv 3/4/B. canis and B. neotomae/B. microti. In summary, the newly developed Brucella ArrayTube® assay is an easy-to-handle molecular test for high-throughput and parallel analysis.
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Affiliation(s)
- Gernot Schmoock
- Friedrich Loeffler Institute, Institute of Bacterial Infections and Zoonoses, Jena, Germany
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Christerson L, Ruettger A, Gravningen K, Ehricht R, Sachse K, Herrmann B. High-resolution genotyping of Chlamydia trachomatis by use of a novel multilocus typing DNA microarray. J Clin Microbiol 2011; 49:2838-43. [PMID: 21697318 DOI: 10.1128/JCM.00883-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Typing of Chlamydia trachomatis is important to understanding its epidemiology. Currently used methods such as DNA sequencing of the ompA gene and multilocus sequence typing (MLST) either offer limited epidemiological resolution or are laborious and expensive, or both. DNA microarray technology using the ArrayStrip format is an affordable alternative for genotyping. In this study, we developed a new multilocus typing (MLT) DNA microarray, based on the target regions of a high-resolution MLST system as well as software for easy analysis. Validation of the array was done by typing 80 previously MLST-typed clinical specimens from unselected adolescents in school. The MLT array showed 100% specificity and provided 2.4-times-higher resolution than ompA sequencing, separating the commonly predominating ompA E/Bour genotype into 7 MLT array genotypes. The MLT array reproduced epidemiological findings revealed by the MLST system and showed sufficient sensitivity to work with clinical specimens. Compared to MLST analysis, the expenses needed for testing a sample with the MLT array are considerably lower. Moreover, testing can be completed within 1 working day rather than 3 or 4 days, with data analysis not requiring highly specialized personnel. The present MLT array represents a powerful alternative in C. trachomatis genotyping.
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Hagen RM, Frickmann H, Elschner M, Melzer F, Neubauer H, Gauthier YP, Racz P, Poppert S. Rapid identification of Burkholderia pseudomallei and Burkholderia mallei by fluorescence in situ hybridization (FISH) from culture and paraffin-embedded tissue samples. Int J Med Microbiol 2011; 301:585-90. [PMID: 21658996 DOI: 10.1016/j.ijmm.2011.04.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 04/12/2011] [Accepted: 04/20/2011] [Indexed: 11/18/2022] Open
Abstract
We evaluated newly developed probes for rapid identification of Burkholderia (B.) pseudomallei and B. mallei and differentiation from B. thailandensis by fluorescence in situ hybridization (FISH). FISH correctly identified 100% of the tested B. pseudomallei (11), B. mallei (11), and B. thailandensis (1) strains, excluded 100% of all tested negative controls (61), and allowed demonstration of B. pseudomallei infection in a paraffin-embedded spleen tissue sample of an experimentally infected mouse.
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Affiliation(s)
- Ralf M Hagen
- Department for Tropical Medicine at the Bernhard Nocht Institute, Bundeswehr Hospital Hamburg, Bernhard-Nocht-Strasse, Germany.
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Ho CC, Lau CC, Martelli P, Chan SY, Tse CW, Wu AK, Yuen KY, Lau SK, Woo PC. Novel pan-genomic analysis approach in target selection for multiplex PCR identification and detection of Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia cepacia complex species: a proof-of-concept study. J Clin Microbiol 2011; 49:814-21. [PMID: 21177905 DOI: 10.1128/JCM.01702-10] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Burkholderia pseudomallei, Burkholderia thailandensis, and the Burkholderia cepacia complex differ greatly in pathogenicity and epidemiology. Yet, they are occasionally misidentified by biochemical profiling, and even 16S rRNA gene sequencing may not offer adequate discrimination between certain species groups. Using the 23 B. pseudomallei, four B. thailandensis, and 16 B. cepacia complex genome sequences available, we identified gene targets specific to each of them (a Tat domain protein, a 70-kDa protein, and a 12-kDa protein for B. pseudomallei, B. thailandensis, and the B. cepacia complex, respectively), with an in-house developed algorithm. Using these targets, we designed a robust multiplex PCR assay useful for their identification and detection from soil and simulated sputum samples. For all 43 B. pseudomallei, seven B. thailandensis, and 20 B. cepacia complex (B. multivorans, n = 6; B. cenocepacia, n = 3; B. cepacia, n = 4; B. arboris, n = 2; B. contaminans, B. anthina, and B. pyrrocinia, n = 1 each; other unnamed members, n = 2) isolates, the assay produced specific products of predicted size without false positives or negatives. Of the 60 soil samples screened, 19 (31.6%) and 29 (48.3%) were positive for B. pseudomallei and the B. cepacia complex, respectively, and in four (6.7%) soil samples, the organisms were codetected. DNA sequencing confirmed that all PCR products originated from their targeted loci. This novel pan-genomic analysis approach in target selection is simple, computationally efficient, and potentially applicable to any species that harbors species-specific genes. A multiplex PCR assay for rapid and accurate identification and detection of B. pseudomallei, B. thailandensis, and the B. cepacia complex was developed and verified.
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