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Jäger HY, Atz Zanotelli D, Maixner F, Nicklisch N, Alt KW, Meller H, Pap I, Szikossy I, Pálfi G, Zink AR. Hit or miss - A metagenomic evaluation of intra-bone variability of host pathogen load in tuberculosis-infected human remains. Tuberculosis (Edinb) 2023; 143S:102392. [PMID: 38012935 DOI: 10.1016/j.tube.2023.102392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 07/11/2023] [Accepted: 07/26/2023] [Indexed: 11/29/2023]
Abstract
Many sampling protocols have been established to successfully retrieve human DNA from archaeological remains, however the systematic detection of ancient pathogens remains challenging. Here, we present a first assessment of the intra-bone variability of metagenomic composition in human skeletal remains and its effect on the sampling success for Mycobacterium tuberculosis (MTB) and human endogenous DNA. For this purpose, four bone samples from published peer-reviewed studies with PCR-based evidence for ancient MTB DNA were selected. Two bone samples of a Neolithic individual from Halberstadt, Germany and two ribs of two 18th-century Hungarian church mummies were sampled at multiple locations for equal amounts, followed by DNA extraction and library construction. Shotgun sequencing data was generated for taxonomic profiling as well as quantitative and qualitative evaluation of MTB and human endogenous DNA. Despite low variance in microbial diversity within and across samples, intra-bone variability of up to 36.45- and 62.88-fold for authentic ancient MTB and human reads, respectively, was detected. This study demonstrates the variable sampling success for MTB and human endogenous DNA within single skeletal samples despite relatively consistent microbial composition and highlights how a multisampling approach can facilitate the detection of hotspots with highly concentrated pathogen and human endogenous DNA.
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Affiliation(s)
- Heidi Y Jäger
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
| | - Daniel Atz Zanotelli
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
| | - Nicole Nicklisch
- Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria; State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany.
| | - Kurt W Alt
- Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria; State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany.
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany.
| | - Ildikó Pap
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép Fasor 52, Hungary; Department of Anthropology, Hungarian Natural History Museum, 1083, Budapest, Ludovika Tér 2-6, Hungary; Department of Biological Anthropology, Eötvös Loránd University, Faculty of Science, 1117, Budapest, Pázmány Péter Sétány 1/c, Hungary.
| | - Ildikó Szikossy
- Department of Anthropology, Hungarian Natural History Museum, 1083, Budapest, Ludovika Tér 2-6, Hungary; Department of Biological Anthropology, Eötvös Loránd University, Faculty of Science, 1117, Budapest, Pázmány Péter Sétány 1/c, Hungary.
| | - György Pálfi
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép Fasor 52, Hungary.
| | - Albert R Zink
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
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Zeineldin MM, Lehman K, Camp P, Farrell D, Thacker TC. Diagnostic Evaluation of the IS1081-Targeted Real-Time PCR for Detection of Mycobacterium bovis DNA in Bovine Milk Samples. Pathogens 2023; 12:972. [PMID: 37623932 PMCID: PMC10458061 DOI: 10.3390/pathogens12080972] [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: 06/21/2023] [Revised: 07/10/2023] [Accepted: 07/21/2023] [Indexed: 08/26/2023] Open
Abstract
The ability of Mycobacterium bovis (M. bovis) to survive in bovine milk has emerged as a serious public health concern. The first objective of this study was to evaluate the diagnostic utility of IS1081-targeted real-time PCR for the detection of M. bovis DNA in different fractions of bovine milk. In a model study, bovine milk samples were spiked with serially diluted M. bovis BCG to investigate the detection limit of M. bovis DNA in whole milk and milk fractions (cream, pellet, and pellet + cream combined) using IS1081 real-time PCR. The assay was then used to detect M. bovis DNA in whole milk and milk fractions from naturally infected animals. The results showed that the IS1081 real-time PCR was more sensitive when detecting M. bovis DNA in the cream layer alone and cream + pellet combined compared to whole milk or the pellet alone. While PCR-based diagnostic assays for the detection of M. bovis in milk samples provide a quicker diagnostic tool for bovine tuberculosis, safe processing, and handling of M. bovis-infected milk samples remain a challenge and pose a human health risk. PrimeStore Molecular Transport Medium (MTM) has been shown to rapidly inactivate infected specimens while preserving nucleic acid for subsequent Molecular analysis. Therefore, the secondary objective of this study was to evaluate the ability of MTM to inactivate M. bovis BCG in spiked milk samples as well as its ability to preserve BCG DNA for the PCR assay. The results showed that MTM can successfully inactivate BCG alone or in spiked milk samples while preserving DNA for the PCR assay. The CT values of M. bovis BCG alone and spiked milk samples aliquoted in MTM and without MTM were similar at various dilutions. Taken together, our results indicate that using DNA extracted from the milk cream fraction alone or combined milk cream and pellet improved the recovery rate of M. bovis DNA in bovine milk samples. MTM has the potential to provide a safe and rapid sample processing tool for M. bovis inactivation in milk samples and preserve DNA for molecular diagnostics.
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Affiliation(s)
| | | | | | | | - Tyler C. Thacker
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA 50010, USA; (M.M.Z.)
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Pagaduan JV, Altawallbeh G. Advances in TB testing. Adv Clin Chem 2023; 115:33-62. [PMID: 37673521 PMCID: PMC10056534 DOI: 10.1016/bs.acc.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Globally, tuberculosis (TB) was the leading cause of death from a single infectious agent until the coronavirus (COVID-19) pandemic. In 2020, an estimated 10 million people fell ill with TB and a total of 1.5 million people died from the disease. About one-quarter of the global population, almost two billion people, is estimated to be latently infected with Mycobacterium tuberculosis (MTB). Although latent TB infection (LTBI) is asymptomatic and noncontagious, about 5-10% of LTBI patients have a lifetime risk of progression to active TB. The diagnosis and treatment of active cases are extremely vital for TB control programs. However, achieving the End TB goal of 2035 without the ability to identify and treat the pool of latently infected individuals will be a big challenge. To do so, improved technology to provide more accurate diagnostic tools and accessibility are crucial. Therefore, this chapter covers the current WHO-endorsed tests and advances in diagnostic and screening tests for active and latent TB.
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Affiliation(s)
- Jayson V Pagaduan
- Intermountain Central Laboratory Intermountain Medical Center, Murray, UT, United States
| | - Ghaith Altawallbeh
- Intermountain Central Laboratory Intermountain Medical Center, Murray, UT, United States.
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4
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Chang A, Mzava O, Djomnang LAK, Lenz JS, Burnham P, Kaplinsky P, Andama A, Connelly J, Bachman CM, Cattamanchi A, Steadman A, De Vlaminck I. Metagenomic DNA sequencing to quantify Mycobacterium tuberculosis DNA and diagnose tuberculosis. Sci Rep 2022; 12:16972. [PMID: 36216964 PMCID: PMC9551046 DOI: 10.1038/s41598-022-21244-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/26/2022] [Indexed: 12/29/2022] Open
Abstract
Tuberculosis (TB) remains a significant cause of mortality worldwide. Metagenomic next-generation sequencing has the potential to reveal biomarkers of active disease, identify coinfection, and improve detection for sputum-scarce or culture-negative cases. We conducted a large-scale comparative study of 428 plasma, urine, and oral swab samples from 334 individuals from TB endemic and non-endemic regions to evaluate the utility of a shotgun metagenomic DNA sequencing assay for tuberculosis diagnosis. We found that the composition of the control population had a strong impact on the measured performance of the diagnostic test: the use of a control population composed of individuals from a TB non-endemic region led to a test with nearly 100% specificity and sensitivity, whereas a control group composed of individuals from TB endemic regions exhibited a high background of nontuberculous mycobacterial DNA, limiting the diagnostic performance of the test. Using mathematical modeling and quantitative comparisons to matched qPCR data, we found that the burden of Mycobacterium tuberculosis DNA constitutes a very small fraction (0.04 or less) of the total abundance of DNA originating from mycobacteria in samples from TB endemic regions. Our findings suggest that the utility of a minimally invasive metagenomic sequencing assay for pulmonary tuberculosis diagnostics is limited by the low burden of M. tuberculosis and an overwhelming biological background of nontuberculous mycobacterial DNA.
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Affiliation(s)
- Adrienne Chang
- grid.5386.8000000041936877XNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY USA
| | - Omary Mzava
- grid.5386.8000000041936877XNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY USA
| | - Liz-Audrey Kounatse Djomnang
- grid.5386.8000000041936877XNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY USA
| | - Joan Sesing Lenz
- grid.5386.8000000041936877XNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY USA
| | - Philip Burnham
- grid.5386.8000000041936877XNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY USA
| | - Peter Kaplinsky
- grid.5386.8000000041936877XNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY USA
| | - Alfred Andama
- grid.11194.3c0000 0004 0620 0548Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | | | | | - Adithya Cattamanchi
- grid.266102.10000 0001 2297 6811Center for Tuberculosis and Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA USA
| | | | - Iwijn De Vlaminck
- grid.5386.8000000041936877XNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY USA
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Integration of cytopathology with molecular tests to improve the lab diagnosis for TBLN suspected patients. PLoS One 2022; 17:e0265499. [PMID: 35358212 PMCID: PMC8970391 DOI: 10.1371/journal.pone.0265499] [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: 11/05/2021] [Accepted: 03/02/2022] [Indexed: 11/25/2022] Open
Abstract
Background Tuberculosis lymphadenitis (TBLN) diagnosis is often challenging in most resource poor settings. Often cytopathologic diagnosis of TBLN suspected patients is inconclusive impeding timely clinical management of TBLN suspected patients, further exposing suspected patients either for unnecessary use of antibiotics or empirical treatment. This may lead to inappropriate treatment outcome or more suffering of suspected patients from the disease. In this study, an integrated diagnostic approach has been evaluated to elucidate its utility in the identification of TBLN suspected patients. Methods A cross-sectional study was conducted on 96 clinically diagnosed TBLN suspected patients, where fine needle aspirate (FNA) samples were collected at the time of diagnosis. FNA cytology, Ziehl-Neelsen (ZN), Auramine O (AO) staining, GeneXpert MTB/RIF and Real time PCR (RT-PCR) were performed on concentrated FNA samples. Considering culture as a gold standard, the sensitivity, specificity, positive and negative predictive values were calculated. Cohen’s Kappa value was used to measure interrater variability and level of agreement and a P-value of <0.05 was considered as statistically significant. Result Out of the 96 FNA sample, 12 (12.5%) were identified to have Mycobacterium tuberculosis (Mtb) using ZN staining, 27 (28.1%) using AO staining, 51 (53.2%) using FNAC, 43 (44.7%) using GeneXpert MTB/RIF, 51 (53.1%) using Real time PCR (RT-PCR) and 36 (37.5%) using Lowenstein-Jensen (LJ) culture. Compared to LJ culture, the sensitivities of GeneXpert MTB/RIF, RT-PCR, and FNAC were 91.7%, 97.2%, and 97.2%, respectively and the specificities were 83.3%, 73.3%, and 68.3%, respectively. GeneXpert MTB/RIF and RT-PCR when combined with FNAC detected 61 (63.5%) cases as having Mtb, and the sensitivity and specificity was 100% and 58.3%, respectively. Conclusion FNA cytology and RT-PCR detected more TBLN cases compared to other Mtb detection tools and the detection sensitivity even improved when FNA cytology was combined with GeneXpert MTB/RIF, performed on concentrated FNA sample, suggesting the combined tests as an alternative approach for improved diagnosis of TBLN.
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Oreskovic A, Waalkes A, Holmes EA, Rosenthal CA, Wilson DPK, Shapiro AE, Drain PK, Lutz BR, Salipante SJ. Characterizing the molecular composition and diagnostic potential of Mycobacterium tuberculosis urinary cell-free DNA using next-generation sequencing. Int J Infect Dis 2021; 112:330-337. [PMID: 34562627 PMCID: PMC8627387 DOI: 10.1016/j.ijid.2021.09.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Urine cell-free DNA (cfDNA) is an attractive target for diagnosing pulmonary Mycobacterium tuberculosis (MTB) infection, but has not been thoroughly characterized as a biomarker. METHODS This study was performed to investigate the size and composition of urine cfDNA from tuberculosis (TB) patients with minimal bias using next-generation sequencing (NGS). A combination of DNA extraction and single-stranded sequence library preparation methods demonstrated to recover short, highly degraded cfDNA fragments was employed. Urine cfDNA from 10 HIV-positive patients with pulmonary TB and two MTB-negative controls was examined. RESULTS MTB-derived cfDNA was identifiable by NGS from all MTB-positive patients and was absent from negative controls. MTB cfDNA was significantly shorter than human cfDNA, with median fragment lengths of ≤19-52 bp and 42-92 bp, respectively. MTB cfDNA abundance increased exponentially with decreased fragment length, having a peak fragment length of ≤19 bp in most samples. In addition, we identified a larger fraction of short human genomic cfDNA, ranging from 29 to 53 bp, than previously reported. Urine cfDNA fragments spanned the MTB genome with relative uniformity, but nucleic acids derived from multicopy elements were proportionately over-represented. CONCLUSIONS TB urine cfDNA is a potentially powerful biomarker but is highly fragmented, necessitating special procedures to maximize its recovery and detection.
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Affiliation(s)
- Amy Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Elizabeth A Holmes
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Christopher A Rosenthal
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Douglas P K Wilson
- Umkhuseli Innovation and Research Management, Pietermaritzburg, South Africa; Edendale Hospital, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Adrienne E Shapiro
- Department of Medicine, University of Washington, Seattle, Washington, USA; Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Paul K Drain
- Department of Medicine, University of Washington, Seattle, Washington, USA; Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, USA; Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA.
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7
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Xiang Y, Yan H, Zheng B, Faheem A, Guo A, Hu C, Hu Y. Light-Regulated Natural Fluorescence of the PCC 6803@ZIF-8 Composite as an Encoded Microsphere for the Detection of Multiple Biomarkers. ACS Sens 2021; 6:2574-2583. [PMID: 34156832 DOI: 10.1021/acssensors.1c00104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The use of color-encoded microspheres for a bead-based assay has attracted increasing attention for high-throughput multiplexed bioassays. A fluorescent PCC 6803@ZIF-8 composite was prepared as a bead-based assay platform by a self-assembled zeolitic imidazolate framework (ZIF-8) on the surface of inactivated PCC 6803 cells. The composite fluorescence owing to the presence of pigment proteins in PCC 6803 could be gradually bleached with the prolongation of the ultraviolet light irradiation time. The composites with different fluorescence intensities were therefore obtained as encoded microspheres for the multiplexed assay. ZIF-8 provides a stable, rigid shell and a large specific surface area for composites, which prevent the composites from breakage during use and storage, simplify the protein immobilization procedure, reduce non-specific adsorption, and enhance the detection sensitivity. The encoded composites were successfully used to detect multiple DNA insertion sequences of Mycobacterium tuberculosis. The presented strategy offers an innovative color-encoding method for high-throughput multiplexed bioassays without the need of using chemically synthesized fluorescent materials.
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Affiliation(s)
- Yuqiang Xiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Huaduo Yan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Bingjie Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Aroosha Faheem
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Aizhen Guo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Changmin Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yonggang Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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8
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Wang X, Wang G, Wang Y, Quan S, Qi H, Sun L, Shen C, Huang H, Jiao W, Shen A. Development and Preliminary Application of Multiplex Loop-Mediated Isothermal Amplification Coupled With Lateral Flow Biosensor for Detection of Mycobacterium tuberculosis Complex. Front Cell Infect Microbiol 2021; 11:666492. [PMID: 33987108 PMCID: PMC8110928 DOI: 10.3389/fcimb.2021.666492] [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: 02/10/2021] [Accepted: 04/07/2021] [Indexed: 12/27/2022] Open
Abstract
The aim of this study was to develop a simple and reliable method to detect Mycobacterium tuberculosis complex (MTBC) and verify its clinical application preliminarily. A loop-mediated isothermal amplification method coupled with lateral flow biosensor (LAMP-LFB) assay, was developed and evaluated for detection of MTBC. Two sets of primers, which targeted IS6110 and IS1081 sequences of MTBC, were designed for establishment of multiplex LAMP-LFB assay. The amplicons were labelled with biotin and fluorescein isothiocyanate (FITC) by adding FITC labelled primer and biotin-14-dATP and biotin-14-dCTP and could be visualized using LFB. The optimal reaction conditions of multiplex LAMP-LFB assay confirmed were 66°C for 50 min. The analytical sensitivity of multiplex LAMP-LFB is 10 fg of genomic templates using pure culture, and no cross-reactivity with other common bacteria and non-tuberculous mycobacteria strains was obtained. A total of 143 clinical samples collected from 100 TB patients (62 definite TB cases and 38 probable TB cases) and 43 non-TB patients were used for evaluating the feasibility of multiplex LAMP-LFB assay. The multiplex LAMP-LFB (82.0%, 82/100) showed higher sensitivity than culture (47.0%, 47/100, P < 0.001) and Xpert MTB/RIF (54.0%, 54/100, P < 0.001). Importantly, the multiplex LAMP-LFB assay detected additional 28 probable TB cases, which increased the percentage of definite TB cases from 62.0% (62/100) to 90.0% (90/100). The specificity of multiplex LAMP-LFB assay in patients without TB was 97.7% (42/43). Therefore, multiplex LAMP-LFB assay is a simple, reliable, and sensitive method for MTBC detection, especially in probable TB cases and resource limited settings.
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Affiliation(s)
- Xingyun Wang
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Guirong Wang
- National Tuberculosis Clinical Laboratory, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yacui Wang
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Shuting Quan
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Hui Qi
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Lin Sun
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Chen Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Hairong Huang
- National Tuberculosis Clinical Laboratory, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Weiwei Jiao
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Adong Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
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9
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Novel molecular transport medium used in combination with Xpert MTB/RIF ultra provides rapid detection of Mycobacterium bovis in African buffaloes. Sci Rep 2021; 11:7061. [PMID: 33782515 PMCID: PMC8007588 DOI: 10.1038/s41598-021-86682-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/16/2021] [Indexed: 11/17/2022] Open
Abstract
Mycobacterium bovis is the causative agent of bovine tuberculosis (bTB) in wildlife. Confirmation of M. bovis infection relies on mycobacterial culture, which is time-consuming. Collection and transportation of infectious material also pose a human health risk. PrimeStore Molecular Transport Medium (MTM) has been shown to effectively inactivate infectious organisms, making it a safe method for handling infectious samples. This study investigated an in-field sampling technique for rapid, safe detection of M. bovis in buffalo tissues. Potentially infected tissues from bTB test-positive buffaloes were swabbed at post-mortem examination and stored in PrimeStore MTM at ambient temperature until Xpert MTB/RIF Ultra testing was performed. Additionally, tissue samples were frozen and transported before homogenisation for culture and Ultra testing. Oral swabs were collected from M. bovis-unexposed buffaloes as a negative control cohort. Mycobacterium tuberculosis complex (MTBC) DNA was detected by Ultra in 13/16 tissue swabs and 9/16 matched tissue homogenates from culture-confirmed M. bovis-positive buffalo tissues. MTBC DNA was not detected in swabs from M. bovis-unexposed animals, showing the potentially high specificity of Ultra with PrimeStore swabs. PrimeStore MTM sample processing, in combination with the Ultra assay, has the potential to provide a safe, rapid post-mortem screening test for M. bovis in buffaloes.
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10
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Lin CR, Wang HY, Lin TW, Lu JJ, Hsieh JCH, Wu MH. Development of a two-step nucleic acid amplification test for accurate diagnosis of the Mycobacterium tuberculosis complex. Sci Rep 2021; 11:5750. [PMID: 33707640 PMCID: PMC7952592 DOI: 10.1038/s41598-021-85160-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/02/2021] [Indexed: 12/28/2022] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) remains one of the top 10 leading causes of death globally. The early diagnosis of MTBC can reduce mortality and mitigate disease transmission. However, current nucleic acid amplification diagnostic test methods are generally time-consuming and show suboptimal diagnostic performance, especially in extrapulmonary MTBC samples or acid-fast stain (AFS)-negative cases. Thus, development of an accurate assay for the diagnosis of MTBC is necessary, particularly under the above mentioned conditions. In this study, a single-tube nested real-time PCR assay (N-RTP) was developed and compared with a newly in-house-developed high-sensitivity real-time PCR assay (HS-RTP) using 134 clinical specimens (including 73 pulmonary and 61 extrapulmonary specimens). The amplification efficiency of HS-RTP and N-RTP was 99.8% and 100.7%, respectively. The sensitivity and specificity of HS-RTP and N-RTP for the diagnosis of MTBC in these specimens were 97.5% (77/79) versus 94.9% (75/79) and 80.0% (44/55) versus 89.1% (49/55), respectively. The sensitivity and specificity of HS-RTP and N-RTP for the diagnosis of MTBC in pulmonary specimens were 96.3% (52/54) versus 96.3% (52/54) and 73.7.0% (14/19) versus 89.5% (17/19), respectively; in extrapulmonary specimens, the sensitivity and specificity of HS-RTP and N-RTP were 100% (25/25) versus 92% (23/25) and 83.3% (30/36) versus 88.9% (32/36), respectively. Among the AFS-negative cases, the sensitivity and specificity of HS-RTP and N-RTP were 97.0% (32/33) versus 90.9% (30/33) and 88.0% (44/50) versus 92.0% (46/50), respectively. Overall, the sensitivity of HS-RTP was higher than that of N-RTP, and the performance was not compromised in extrapulmonary specimens and under AFS-negative conditions. In contrast, the specificity of the N-RTP assay was higher than that of the HS-RTP assay in all types of specimens. In conclusion, the HS-RTP assay would be useful for screening patients suspected of exhibiting an MTBC infection due to its higher sensitivity, while the N-RTP assay could be used for confirmation because of its higher specificity. Our results provide a two-step method (screen to confirm) that simultaneously achieves high sensitivity and specificity in the diagnosis of MTBC.
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Affiliation(s)
- Chien-Ru Lin
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan.,Ph.D. Program in Biomedical Engineering, Chang Gung University, Taoyuan City, Taiwan
| | - Ting-Wei Lin
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan
| | - Jang-Jih Lu
- School of Medicine, Chang Gung University, Taoyuan City, Taiwan.,Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan City, Taiwan
| | - Jason Chia-Hsun Hsieh
- Division of Haematology/Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan.,Division of Haematology/Oncology, Department of Internal Medicine, New Taipei Municipal Hospital, New Taipei City, Taiwan
| | - Min-Hsien Wu
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan, Taiwan. .,Division of Haematology/Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan. .,Department of Chemical Engineering, Ming Chi University of Technology, New Taipei City, Taiwan.
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11
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DNA Thermo-Protection Facilitates Whole-Genome Sequencing of Mycobacteria Direct from Clinical Samples. J Clin Microbiol 2020; 58:JCM.00670-20. [PMID: 32719032 PMCID: PMC7512152 DOI: 10.1128/jcm.00670-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 07/15/2020] [Indexed: 02/03/2023] Open
Abstract
Mycobacterium tuberculosis is the leading cause of death from bacterial infection. Improved rapid diagnosis and antimicrobial resistance determination, such as by whole-genome sequencing, are required. Our aim was to develop a simple, low-cost method of preparing DNA for sequencing direct from M. tuberculosis-positive clinical samples (without culture). Simultaneous sputum liquefaction, bacteria heat inactivation (99°C/30 min), and enrichment for mycobacteria DNA were achieved using an equal volume of thermo-protection buffer (4 M KCl, 0. Mycobacterium tuberculosis is the leading cause of death from bacterial infection. Improved rapid diagnosis and antimicrobial resistance determination, such as by whole-genome sequencing, are required. Our aim was to develop a simple, low-cost method of preparing DNA for sequencing direct from M. tuberculosis-positive clinical samples (without culture). Simultaneous sputum liquefaction, bacteria heat inactivation (99°C/30 min), and enrichment for mycobacteria DNA were achieved using an equal volume of thermo-protection buffer (4 M KCl, 0.05 M HEPES buffer, pH 7.5, 0.1% dithiothreitol [DTT]). The buffer emulated intracellular conditions found in hyperthermophiles, thus protecting DNA from rapid thermodegradation, which renders it a poor template for sequencing. Initial validation experiments employed mycobacteria DNA, either extracted or intracellular. Next, mock clinical samples (infection-negative human sputum spiked with 0 to 105Mycobacterium bovis BCG cells/ml) underwent liquefaction in thermo-protection buffer and heat inactivation. DNA was extracted and sequenced. Human DNA degraded faster than mycobacteria DNA, resulting in target enrichment. Four replicate experiments achieved M. tuberculosis detection at 101 BCG cells/ml, with 31 to 59 M. tuberculosis complex reads. Maximal genome coverage (>97% at 5× depth) occurred at 104 BCG cells/ml; >91% coverage (1× depth) occurred at 103 BCG cells/ml. Final validation employed M. tuberculosis-positive clinical samples (n = 20), revealing that initial sample volumes of ≥1 ml typically yielded higher mean depths of M. tuberculosis genome coverage, with an overall range of 0.55 to 81.02. A mean depth of 3 gave >96% 1-fold tuberculosis (TB) genome coverage (in 15/20 clinical samples). A mean depth of 15 achieved >99% 5-fold genome coverage (in 9/20 clinical samples). In summary, direct-from-sample sequencing of M. tuberculosis genomes was facilitated by a low-cost thermo-protection buffer.
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12
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Lyu L, Li Z, Pan L, Jia H, Sun Q, Liu Q, Zhang Z. Evaluation of digital PCR assay in detection of M.tuberculosis IS6110 and IS1081 in tuberculosis patients plasma. BMC Infect Dis 2020; 20:657. [PMID: 32894079 PMCID: PMC7487892 DOI: 10.1186/s12879-020-05375-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
Background Tuberculosis is still a significant diagnostic and therapeutic challenge with high proportion of smear- and culture- negative incidences worldwide. The conventional diagnostic tests are time-consuming and have a low sensitivity. Digital PCR is a novel technology which can detect target sequences with relatively low abundance and obtain the absolute copy numbers of the targets. Methods We assessed the accuracy of dPCR in TB diagnosis using more than 250 specimens, and for the first time, we selected M.tuberculosis-specific IS1081 in addition to widely used IS6110 as the amplification targets for dPCR. The quantification of target DNA was calculated using QuantaSoft Version 1.7.4.0917 (BioRad), and SPSS version 13.0 software (SPSS Inc., Chicago, IL, USA) was used for statistical analyses. Results IS6110-dPCR was more sensitive than IS1081, with the sensitivity and specificity accounting for 40.6 and 93.4% respectively. When we classified the TB patients by personal factors for high copy number of M.tuberculosis derived DNA in plasma: bilateral TB, extrapulmonary TB and disseminated TB, the sensitivity of both IS6110- and IS1081- dPCR was the highest in patients with disseminated TB (IS6110, 100%; IS1081, 68.8%), while their sensitivity was a bit higher in patients with extrapulmonary TB (IS6110, 50.0%; IS1081, 39.3%) than that in bilateral TB (IS6110, 43.3%; IS1081, 33.3%). Compared with traditional TB diagnostic tests, joint detection IS6110 & IS1081-dPCR was not as sensitive as smear microscope or mycobacterial culture, but it was higher than IS6110 qPCR (p < 0.05) and was able to detect 47.4% of smear-negative TB patients. Conclusion Our study suggested that plasma IS6110-dPCR is a rapid, moderate accurate and less-invasive method to detect M.tuberculosis DNA in plasma of TB patients and IS6110 & IS1081-dPCR has a potential to aid diagnosis of smear-negative TB.
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Affiliation(s)
- Lingna Lyu
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Machang Road, Tongzhou District, Beijing, 101149, China
| | - Zihui Li
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Machang Road, Tongzhou District, Beijing, 101149, China
| | - Liping Pan
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Machang Road, Tongzhou District, Beijing, 101149, China
| | - Hongyan Jia
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Machang Road, Tongzhou District, Beijing, 101149, China
| | - Qi Sun
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Machang Road, Tongzhou District, Beijing, 101149, China
| | - Qiuyue Liu
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Machang Road, Tongzhou District, Beijing, 101149, China
| | - Zongde Zhang
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Machang Road, Tongzhou District, Beijing, 101149, China.
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13
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Jiao WW, Wang Y, Wang GR, Wang YC, Xiao J, Sun L, Li JQ, Wen SA, Zhang TT, Ma Q, Huang HR, Shen AD. Development and Clinical Validation of Multiple Cross Displacement Amplification Combined With Nanoparticles-Based Biosensor for Detection of Mycobacterium tuberculosis: Preliminary Results. Front Microbiol 2019; 10:2135. [PMID: 31572340 PMCID: PMC6753184 DOI: 10.3389/fmicb.2019.02135] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/30/2019] [Indexed: 11/25/2022] Open
Abstract
Tuberculosis is still a major threat to global public health. Here, a novel diagnosis assay, termed as multiple cross displacement amplification combined with nanoparticle-based lateral flow biosensor (MCDA-LFB), was developed to simultaneously detect IS6110 and IS1081 of Mycobacterium tuberculosis (MTB) in DNA extracted from reference strain H37Rv and clinical samples. The amplification can be finished within 30 min at a fixed temperature (67°C), thus the whole procedure, including rapid template preparation (15 min), isothermal reaction (30 min) and result reporting (2 min), can be completed within 50 min. The limit of detection of multiplex MCDA assay was 10 fg per reaction. By using the multiplex MCDA protocol, cross-reaction with non-mycobacteria and non-tuberculous mycobacteria (NTM) strains was not observed. Among clinically diagnosed TB patients, the sensitivity of liquid culture, Xpert MTB/RIF and multiplex MCDA assay was 42.0% (50/119), 49.6% (59/119), and 88.2% (105/119), respectively. Among culture positive samples, the sensitivity of Xpert MTB/RIF and multiplex MCDA assay was 86.0% (43/50) and 98.0% (49/50), respectively. Among culture negative samples, the sensitivity of Xpert MTB/RIF and multiplex MCDA assay was 23.2% (16/69) and 81.2% (56/69), respectively. The specificity was 100% (60/60) for Xpert MTB/RIF and 98.3% (59/60) for multiplex MCDA. Therefore, the multiplex MCDA assay for MTB detection is rapid, sensitive and easy to use and may be a promising test for early diagnosis of TB.
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Affiliation(s)
- Wei-Wei Jiao
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yi Wang
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Gui-Rong Wang
- National Tuberculosis Clinical Laboratory, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Ya-Cui Wang
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Jing Xiao
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Lin Sun
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Jie-Qiong Li
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Shu-An Wen
- National Tuberculosis Clinical Laboratory, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Ting-Ting Zhang
- National Tuberculosis Clinical Laboratory, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Qi Ma
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Hai-Rong Huang
- National Tuberculosis Clinical Laboratory, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - A-Dong Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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14
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Wu X, Tan G, Gao R, Yao L, Bi D, Guo Y, Yu F, Fan L. Assessment of the Xpert MTB/RIF Ultra assay on rapid diagnosis of extrapulmonary tuberculosis. Int J Infect Dis 2019; 81:91-96. [PMID: 30738907 DOI: 10.1016/j.ijid.2019.01.050] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/27/2019] [Accepted: 01/31/2019] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE To evaluate the diagnostic performance of Xpert MTB/RIF Ultra for EPTB (Extrapulmonary Tuberculosis) patients on different types of extrapulmonary specimens from different anatomic sites. METHODS Patients with suspected EPTB were prospectively included, extrapulmonary specimens were collected and subjected to culture, Xpert and Xpert Ultra assays in accordance with relevant guidelines. RESULTS A total of 225 cases were included which contained 200 EPTB cases (43 culture-positive EPTB, 157 culture-negative EPTB which were diagnosed based on pathological results and a satisfied response to anti-TB treatment) and 25 non-EPTB cases. Sensitivities of Xpert Ultra and Xpert for culture-positive cases were 83.7% (95%CI, 68.7-92.7) and 67.4% (95% CI, 51.3-80.5) respectively. Specificities of Xpert Ultra and Xpert were 92.0% (95% CI, 72.5-98.6) and 96.0% (95% CI, 77.7-99.8) respectively. The sensitivities of Xpert Ultra, Xpert and culture for 200 EPTB cases were 52.5% (105/200, 95% CI, 45.4-59.6), 34.0% (68/200, 95% CI, 27.6-41.1) and 21.5% (43/200, 95% CI, 16.2-28.0) respectively. By comparison among different types of specimens, Xpert Ultra can detect 78.9% (56/71) of EPTB on fine-needle aspiration (FNA) tissues which was higher than that on pleural fluid (43.7% (45/103), p<0.05. CONCLUSIONS Xpert Ultra assay had a higher sensitivity than those of Xpert and culture on extrapulmonary specimens, which could be a promising approach for rapid EPTB diagnosis.
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Affiliation(s)
- Xiaocui Wu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Guangkun Tan
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Rongliang Gao
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Lan Yao
- Clinic and Research Center of Tuberculosis, Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Dexi Bi
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Yinjuan Guo
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Fangyou Yu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Lin Fan
- Clinic and Research Center of Tuberculosis, Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
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15
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Evaluation of the Xpert MTB/RIF Ultra Assay for Direct Detection of Mycobacterium tuberculosis Complex in Smear-Negative Extrapulmonary Samples. J Clin Microbiol 2018; 56:JCM.00659-18. [PMID: 29950333 DOI: 10.1128/jcm.00659-18] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/20/2018] [Indexed: 02/07/2023] Open
Abstract
The rapid detection of Mycobacterium tuberculosis complex (MTUBC) in clinical samples is essential for successful treatment. New techniques such as real-time PCR have been developed in order to facilitate rapid diagnosis, but their sensitivity is low in extrapulmonary specimens, due to the low bacillary load in such samples. A next-generation assay has recently been developed to try to overcome this limitation. The aim of this study was to analyze the effectiveness of the Xpert MTB/RIF Ultra (GX-Ultra) for the detection of MTUBC DNA in 108 smear-negative extrapulmonary specimens that were MTUBC culture positive. In addition, 40 extrapulmonary culture-negative samples and 20 samples with nontuberculous mycobacteria were tested to evaluate the specificity of the assay. All samples were collected between May 1999 and May 2017. The GX-Ultra detected DNA of MTUBC in 82 extrapulmonary specimens that were MTUBC culture positive (75.9% sensitivity; 95% confidence interval [CI], 66.6 to 83.4%). The assay was negative for all clinical specimens that were MTUBC culture negative and the samples with nontuberculous mycobacteria (100% specificity). Furthermore, two (1.8%) samples presented mutations related to rifampin resistance. The highest sensitivity was obtained in samples of lymph nodes (94.1%) and nonsterile fluids (93.7%), followed by tissue specimens (86.6%), stool material (80%), abscess aspirates (64.7%), and sterile fluids (60.5%). Pleural fluids, one of the least optimal samples for detecting DNA of MTUBC, were GX-Ultra positive in 10/21 (47.6%) of cases. In summary, GX-Ultra showed excellent specificity and high sensitivity in paubacillary specimens, making it a useful tool for rapid diagnosis of extrapulmonary tuberculosis.
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The New Xpert MTB/RIF Ultra: Improving Detection of Mycobacterium tuberculosis and Resistance to Rifampin in an Assay Suitable for Point-of-Care Testing. mBio 2017; 8:mBio.00812-17. [PMID: 28851844 PMCID: PMC5574709 DOI: 10.1128/mbio.00812-17] [Citation(s) in RCA: 378] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The Xpert MTB/RIF assay (Xpert) is a rapid test for tuberculosis (TB) and rifampin resistance (RIF-R) suitable for point-of-care testing. However, it has decreased sensitivity in smear-negative sputum, and false identification of RIF-R occasionally occurs. We developed the Xpert MTB/RIF Ultra assay (Ultra) to improve performance. Ultra and Xpert limits of detection (LOD), dynamic ranges, and RIF-R rpoB mutation detection were tested on Mycobacterium tuberculosis DNA or sputum samples spiked with known numbers of M. tuberculosis H37Rv or Mycobacterium bovis BCG CFU. Frozen and prospectively collected clinical samples from patients suspected of having TB, with and without culture-confirmed TB, were also tested. For M. tuberculosis H37Rv, the LOD was 15.6 CFU/ml of sputum for Ultra versus 112.6 CFU/ml of sputum for Xpert, and for M. bovis BCG, it was 143.4 CFU/ml of sputum for Ultra versus 344 CFU/ml of sputum for Xpert. Ultra resulted in no false-positive RIF-R specimens, while Xpert resulted in two false-positive RIF-R specimens. All RIF-R-associated M. tuberculosis rpoB mutations tested were identified by Ultra. Testing on clinical sputum samples, Ultra versus Xpert, resulted in an overall sensitivity of 87.5% (95% confidence interval [CI], 82.1, 91.7) versus 81.0% (95% CI, 74.9, 86.2) and a sensitivity on sputum smear-negative samples of 78.9% (95% CI, 70.0, 86.1) versus 66.1% (95% CI, 56.4, 74.9). Both tests had a specificity of 98.7% (95% CI, 93.0, 100), and both had comparable accuracies for detection of RIF-R in these samples. Ultra should significantly improve TB detection, especially in patients with paucibacillary disease, and may provide more-reliable RIF-R detection. The Xpert MTB/RIF assay (Xpert), the first point-of-care assay for tuberculosis (TB), was endorsed by the World Health Organization in December 2010. Since then, 23 million Xpert tests have been procured in 130 countries. Although Xpert showed high overall sensitivity and specificity with pulmonary samples, its sensitivity has been lower with smear-negative pulmonary samples and extrapulmonary samples. In addition, the prediction of rifampin resistance (RIF-R) in paucibacillary samples and for a few rpoB mutations has resulted in both false-positive and false-negative results. The present study is the first demonstration of the design features and operational characteristics of an improved Xpert Ultra assay. This study also shows that the Ultra format overcomes many of the known shortcomings of Xpert. The new assay should significantly improve TB detection, especially in patients with paucibacillary disease, and provide more-reliable detection of RIF-R.
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17
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Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria. Clin Microbiol Rev 2016; 29:239-90. [PMID: 26912567 DOI: 10.1128/cmr.00055-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.
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Forst J, Brown TA. Inability of 'Whole Genome Amplification' to Improve Success Rates for the Biomolecular Detection of Tuberculosis in Archaeological Samples. PLoS One 2016; 11:e0163031. [PMID: 27654468 PMCID: PMC5031403 DOI: 10.1371/journal.pone.0163031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 09/01/2016] [Indexed: 11/30/2022] Open
Abstract
We assessed the ability of whole genome amplification (WGA) to improve the efficiency of downstream polymerase chain reactions (PCRs) directed at ancient DNA (aDNA) of members of the Mycobacterium tuberculosis complex (MTBC). Using extracts from a variety of bones and a tooth from human skeletons with or without lesions indicative of tuberculosis, from multiple time periods, we obtained inconsistent results. We conclude that WGA does not provide any advantage in studies of MTBC aDNA. The sporadic nature of our results are probably due to the fact that WGA is itself a PCR-based procedure which, although designed to deal with fragmented DNA, might be inefficient with the low concentration of templates in an aDNA extract. As such, WGA is subject to similar, if not the same, restrictions as PCR when applied to aDNA.
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Affiliation(s)
- Jannine Forst
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester, United Kingdom
| | - Terence A. Brown
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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Witas HW, Donoghue HD, Kubiak D, Lewandowska M, Gładykowska-Rzeczycka JJ. Molecular studies on ancient M. tuberculosis and M. leprae: methods of pathogen and host DNA analysis. Eur J Clin Microbiol Infect Dis 2015. [PMID: 26210385 PMCID: PMC4545183 DOI: 10.1007/s10096-015-2427-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Humans have evolved alongside infectious diseases for millennia. Despite the efforts to reduce their incidence, infectious diseases still pose a tremendous threat to the world population. Fast development of molecular techniques and increasing risk of new epidemics have resulted in several studies that look to the past in order to investigate the origin and evolution of infectious diseases. Tuberculosis and leprosy have become frequent targets of such studies, owing to the persistence of their molecular biomarkers in ancient material and the characteristic skeletal lesions each disease may cause. This review examines the molecular methods used to screen for the presence of M. tuberculosis and M. leprae ancient DNA (aDNA) and their differentiation in ancient human remains. Examples of recent studies, mainly from Europe, that employ the newest techniques of molecular analysis are also described. Moreover, we present a specific approach based on assessing the likely immunological profile of historic populations, in order to further elucidate the influence of M. tuberculosis and M. leprae on historical human populations.
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Affiliation(s)
- H W Witas
- Department of Molecular Biology, Medical University of Łódź, Łódź, Poland,
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Kouzaki Y, Maeda T, Sasaki H, Tamura S, Hamamoto T, Yuki A, Sato A, Miyahira Y, Kawana A. A Simple and Rapid Identification Method for Mycobacterium bovis BCG with Loop-Mediated Isothermal Amplification. PLoS One 2015. [PMID: 26208001 PMCID: PMC4514781 DOI: 10.1371/journal.pone.0133759] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacillus Calmette-Guérin (BCG) is widely used as a live attenuated vaccine against Mycobacterium tuberculosis and is an agent for standard prophylaxis against the recurrence of bladder cancer. Unfortunately, it can cause severe infectious diseases, especially in immunocompromised patients, and the ability to immediately distinguish BCG from other M. tuberculosis complexes is therefore important. In this study, we developed a simple and easy-to-perform identification procedure using loop-mediated amplification (LAMP) to detect deletions within the region of difference, which is deleted specifically in all M. bovis BCG strains. Reactions were performed at 64°C for 30 min and successful targeted gene amplifications were detected by real-time turbidity using a turbidimeter and visual inspection of color change. The assay had an equivalent detection limit of 1.0 pg of genomic DNA using a turbidimeter whereas it was 10 pg with visual inspection, and it showed specificity against 49 strains of 44 pathogens, including M. tuberculosis complex. The expected LAMP products were confirmed through identical melting curves in real-time LAMP procedures. We employed the Procedure for Ultra Rapid Extraction (PURE) kit to isolate mycobacterial DNA and found that the highest sensitivity limit with a minimum total cell count of mycobacterium (including DNA purification with PURE) was up to 1 × 103 cells/reaction, based on color changes under natural light with FDA reagents. The detection limit of this procedure when applied to artificial serum, urine, cerebrospinal fluid, and bronchoalveolar lavage fluid samples was also about 1 × 103 cells/reaction. Therefore, this substitute method using conventional culture or clinical specimens followed by LAMP combined with PURE could be a powerful tool to enable the rapid identification of M. bovis BCG as point-of-care testing. It is suitable for practical use not only in resource-limited situations, but also in any clinical situation involving immunocompromised patients because of its convenience, rapidity, and cost effectiveness.
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Affiliation(s)
- Yuji Kouzaki
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Takuya Maeda
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, Saitama, Japan
- * E-mail:
| | - Hiroaki Sasaki
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Shinsuke Tamura
- Department of Pediatrics, National Defense Medical College, Saitama, Japan
| | - Takaaki Hamamoto
- Department of Laboratory Medicine, National Defense Medical College Hospital, Saitama, Japan
| | - Atsushi Yuki
- Department of Laboratory Medicine, National Defense Medical College Hospital, Saitama, Japan
| | - Akinori Sato
- Department of Urology, National Defense Medical College, Saitama, Japan
| | - Yasushi Miyahira
- Department of Global Infectious Diseases and Tropical Medicine, National Defense Medical College, Saitama, Japan
| | - Akihiko Kawana
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, Saitama, Japan
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Bacteriological diagnosis and molecular strain typing of Mycobacterium bovis and Mycobacterium caprae. Res Vet Sci 2014; 97 Suppl:S30-43. [DOI: 10.1016/j.rvsc.2014.04.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 04/08/2014] [Accepted: 04/24/2014] [Indexed: 11/24/2022]
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Rapid detection of Mycobacterium tuberculosis by recombinase polymerase amplification. PLoS One 2014; 9:e103091. [PMID: 25118698 PMCID: PMC4138011 DOI: 10.1371/journal.pone.0103091] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/25/2014] [Indexed: 11/21/2022] Open
Abstract
Improved access to effective tests for diagnosing tuberculosis (TB) has been designated a public health priority by the World Health Organisation. In high burden TB countries nucleic acid based TB tests have been restricted to centralised laboratories and specialised research settings. Requirements such as a constant electrical supply, air conditioning and skilled, computer literate operators prevent implementation of such tests in many settings. Isothermal DNA amplification technologies permit the use of simpler, less energy intensive detection platforms more suited to low resource settings that allow the accurate diagnosis of a disease within a short timeframe. Recombinase Polymerase Amplification (RPA) is a rapid, low temperature isothermal DNA amplification reaction. We report here RPA-based detection of Mycobacterium tuberculosis complex (MTC) DNA in <20 minutes at 39°C. Assays for two MTC specific targets were investigated, IS6110 and IS1081. When testing purified MTC genomic DNA, limits of detection of 6.25 fg (IS6110) and 20 fg (IS1081)were consistently achieved. When testing a convenience sample of pulmonary specimens from suspected TB patients, RPA demonstrated superior accuracy to indirect fluorescence microscopy. Compared to culture, sensitivities for the IS1081 RPA and microscopy were 91.4% (95%CI: 85, 97.9) and 86.1% (95%CI: 78.1, 94.1) respectively (n = 71). Specificities were 100% and 88.6% (95% CI: 80.8, 96.1) respectively. For the IS6110 RPA and microscopy sensitivities of 87.5% (95%CI: 81.7, 93.2) and 70.8% (95%CI: 62.9, 78.7) were obtained (n = 90). Specificities were 95.4 (95% CI: 92.3,98.1) and 88% (95% CI: 83.6, 92.4) respectively. The superior specificity of RPA for detecting tuberculosis was due to the reduced ability of fluorescence microscopy to distinguish Mtb complex from other acid fast bacteria. The rapid nature of the RPA assay and its low energy requirement compared to other amplification technologies suggest RPA-based TB assays could be of use for integration into a point-of-care test for use in resource constrained settings.
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Müller R, Roberts CA, Brown TA. Biomolecular identification of ancientMycobacterium tuberculosiscomplex DNA in human remains from Britain and continental Europe. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 153:178-89. [DOI: 10.1002/ajpa.22417] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 10/21/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Romy Müller
- Manchester Institute of Biotechnology; Faculty of Life Sciences, University of Manchester; Manchester M1 7DN UK
| | | | - Terence A. Brown
- Manchester Institute of Biotechnology; Faculty of Life Sciences, University of Manchester; Manchester M1 7DN UK
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Clustered tuberculosis in a low-burden country: nationwide genotyping through 15 years. J Clin Microbiol 2012; 50:2660-7. [PMID: 22675129 DOI: 10.1128/jcm.06358-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular genotyping of Mycobacterium tuberculosis has proved to be a powerful tool in tuberculosis surveillance, epidemiology, and control. Based on results obtained through 15 years of nationwide IS6110 restriction fragment length polymorphism (RFLP) genotyping of M. tuberculosis cases in Denmark, a country on the way toward tuberculosis elimination, we discuss M. tuberculosis transmission dynamics and point to areas for control interventions. Cases with 100% identical genotypes (RFLP patterns) were defined as clustered, and a cluster was defined as cases with an identical genotype. Of 4,601 included cases, corresponding to 76% of reported and 97% of culture-verified tuberculosis cases in the country, 56% were clustered, of which 69% were Danes. Generally, Danes were more often in large clusters (≥ 50 persons), older (mean age, 45 years), and male (male/female ratio, 2.5). Also, Danes had a higher cluster frequency within a 2-year observation window (60.8%), and higher clustering rate of new patterns over time, compared to immigrants. A dominant genotype, cluster 2, constituted 44% of all clustered and 35% of all genotyped cases. This cluster was primarily found among Danish males, 30 to 59 years of age, often socially marginalized, and with records of alcohol abuse. In Danes, cluster 2 alone was responsible for the high cluster frequency level. Immigrants had a higher incidence of clustered tuberculosis at a younger age (0 to 39 years). To achieve tuberculosis elimination in Denmark, high-risk transmission environments, like the cluster 2 environment in Danes, and specific transmission chains in immigrants in the capital area, e.g., homeless/socially marginalized Somalis/Greenlanders, often with alcohol abuse, must be targeted, including groups with a high risk of reactivation.
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Kamper-Jørgensen Z, Andersen AB, Kok-Jensen A, Kamper-Jørgensen M, Bygbjerg IC, Andersen PH, Thomsen VO, Lillebaek T. Migrant tuberculosis: the extent of transmission in a low burden country. BMC Infect Dis 2012; 12:60. [PMID: 22423983 PMCID: PMC3342118 DOI: 10.1186/1471-2334-12-60] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 03/18/2012] [Indexed: 11/17/2022] Open
Abstract
Background Human migration caused by political unrest, wars and poverty is a major topic in international health. Infectious diseases like tuberculosis follow their host, with potential impact on both the migrants and the population in the recipient countries. In this study, we evaluate Mycobacterium tuberculosis transmission between the national population and migrants in Denmark. Methods Register study based on IS6110-RFLP results from nationwide genotyping of tuberculosis cases during 1992 through 2004. Cases with 100% identical genotypes were defined as clustered and part of a transmission chain. Origin of clusters involving both Danes and migrants was defined as Danish/migrant/uncertain. Subsequently, the proportion of cases likely infected by the "opposite" ethnic group was estimated. Results 4,631 cases were included, representing 99% of culture confirmed cases during 1992 through 2004. Migrants contributed 61.6% of cases. Up to 7.9% (95% CI 7.0-8.9) of migrants were infected by Danes. The corresponding figure was 5.8% (95% CI 4.8-7.0) for Danes. Thus, transmission from Danes to migrants occurred up to 2.5 (95% CI 1.8-3.5) times more frequent than vice versa (OR = 1). A dominant strain, Cluster-2, was almost exclusively found in Danes, particular younger-middle-aged males. Conclusions Transmission between Danes and migrants is limited, and risk of being infected by the "opposite" ethnic group is highest for migrants. TB-control efforts should focus on continues micro-epidemics, e.g. with Cluster-2 in Danes, prevention of reactivation TB in high-risk migrants, and outbreaks in socially marginalized migrants, such as Somalis and Greenlanders. Fears that TB in migrants poses a threat for resident Danes seem exaggerated and unjustified. We believe this to be true for other low incidence countries as well.
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Affiliation(s)
- Zaza Kamper-Jørgensen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark.
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Characteristics of non-clustered tuberculosis in a low burden country. Tuberculosis (Edinb) 2012; 92:226-31. [PMID: 22406154 DOI: 10.1016/j.tube.2012.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 01/24/2012] [Accepted: 02/06/2012] [Indexed: 11/23/2022]
Abstract
Molecular genotyping studies often focus on clustered tuberculosis and recent transmission. Less attention has been paid to non-clustered tuberculosis. However, non-clustered cases also contribute significantly to the tuberculosis burden, especially in low-incidence countries. The objective of this study is to characterize non-clustered tuberculosis cases in Denmark and point out potential implications for tuberculosis control. The study is based on nationwide IS6110-RFLP genotyping of tuberculosis cases from 1992 through 2004, corresponding to 98% of culture verified cases. Of 3988 cases, 45% were non-clustered. Both Danes and immigrants had a peak incidence of non-clustered tuberculosis at older ages, 80-89 years (4.3 cases/10(5) population/year) and 60-69 years (28.8 cases/10(5) population/year), respectively. In addition, immigrants had a peak at 20-29 years (43.2 cases/10(5) inhabitants/year). In Danes, the incidence of non-clustered tuberculosis decreased during the study period and was predominantly found in elderly persons, presumably reactivating infection acquired during 1910-40, when tuberculosis incidence was high. In immigrants, the incidence was high at all ages, presumably reflecting reactivation of imported infections. In the future, the number of non-clustered tuberculosis cases will decrease, as older Danes die, and as time since primary infection increases for immigrants residing in Denmark. TB control should include focus on non-clustered cases.
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Obaid S, Weil AG, Rahme R, Gendron C, Shedid D. Mycobacterium bovis spondylodiscitis after intravesical Bacillus Calmette-Guérin therapy. Surg Neurol Int 2011; 2:162. [PMID: 22140647 PMCID: PMC3228380 DOI: 10.4103/2152-7806.89879] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 09/23/2011] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Intravesical instillations of live-attenuated Bacillus Calmette-Guérin (BCG) are a well-known and effective method for prevention and treatment of bladder carcinoma and carcinoma in situ. Although considered a safe procedure with rare side effects, local and systemic complications may occur. While long bone ostemolyelitis has been well described, very few reports of BCG spondylodiscitis exist in the literature. CASE DESCRIPTION A 67-year-old man developed low back pain, anorexia, and weight loss 11 months after a 6-week course of intravesical BCG instillations for the treatment of bladder carcinoma in situ. Imaging studies revealed L1-L2 spondylodiscitis with epidural and bilateral psoas abscesses. Tissue cultures obtained by percutaneous computed tomography-guided aspiration were positive for Mycobacterium bovis. Despite triple antituberculous therapy (isoniazid, rifampin, and ethambutol), clinical and radiological progression occurred. Therefore, L1 and L2 corpectomies with extensive debridement were performed, followed by 360° anterior-posterior instrumented fusion. After 20 months of follow-up, the patient remains asymptomatic and recurrence-free. CONCLUSION Mycobacterium bovis spondylodiscitis is a rare complication of intravesical BCG therapy. Although medical therapy with antituberculous agents is the first-line treatment, surgical decompression, debridement, and stabilization may be necessary in refractory cases.
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Affiliation(s)
- Sami Obaid
- Division of Neurosurgery, Hôpital Notre-Dame du CHUM, University of Montreal, Montreal, QC, Canada
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Schürch AC, van Soolingen D. DNA fingerprinting of Mycobacterium tuberculosis: from phage typing to whole-genome sequencing. INFECTION GENETICS AND EVOLUTION 2011; 12:602-9. [PMID: 22067515 DOI: 10.1016/j.meegid.2011.08.032] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 07/12/2011] [Accepted: 08/19/2011] [Indexed: 11/26/2022]
Abstract
Current typing methods for Mycobacterium tuberculosis complex evolved from simple phenotypic approaches like phage typing and drug susceptibility profiling to DNA-based strain typing methods, such as IS6110-restriction fragment length polymorphisms (RFLP) and variable number of tandem repeats (VNTR) typing. Examples of the usefulness of molecular typing are source case finding and epidemiological linkage of tuberculosis (TB) cases, international transmission of MDR/XDR-TB, the discrimination between endogenous reactivation and exogenous re-infection as a cause of relapses after curative treatment of tuberculosis, the evidence of multiple M. tuberculosis infections, and the disclosure of laboratory cross-contaminations. Simultaneously, phylogenetic analyses were developed based on single nucleotide polymorphisms (SNPs), genomic deletions usually referred to as regions of difference (RDs) and spoligotyping which served both strain typing and phylogenetic analysis. National and international initiatives that rely on the application of these typing methods have brought significant insight into the molecular epidemiology of tuberculosis. However, current DNA fingerprinting methods have important limitations. They can often not distinguish between genetically closely related strains and the turn-over of these markers is variable. Moreover, the suitability of most DNA typing methods for phylogenetic reconstruction is limited as they show a high propensity of convergent evolution or misinfer genetic distances. In order to fully explore the possibilities of genotyping in the molecular epidemiology of tuberculosis and to study the phylogeny of the causative bacteria reliably, the application of whole-genome sequencing (WGS) analysis for all M. tuberculosis isolates is the optimal, although currently still a costly solution. In the last years WGS for typing of pathogens has been explored and yielded important additional information on strain diversity in comparison to the classical DNA typing methods. With the ongoing cost reduction of DNA sequencing it is possible that WGS will become the sole diagnostic tool in the secondary laboratory diagnosis of tuberculosis for identification, drug susceptibility testing and genetic characterization.
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Affiliation(s)
- Anita C Schürch
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb/LIS, pb 22), P.O. Box 1, 3720 BA Bilthoven, The Netherlands.
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Yang B, Wang X, Li H, Li G, Cao Z, Cheng X. Comparison of loop-mediated isothermal amplification and real-time PCR for the diagnosis of tuberculous pleurisy. Lett Appl Microbiol 2011; 53:525-31. [DOI: 10.1111/j.1472-765x.2011.03141.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Reddington K, O'Grady J, Dorai-Raj S, Niemann S, van Soolingen D, Barry T. A novel multiplex real-time PCR for the identification of mycobacteria associated with zoonotic tuberculosis. PLoS One 2011; 6:e23481. [PMID: 21858140 PMCID: PMC3153498 DOI: 10.1371/journal.pone.0023481] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 07/18/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is the leading cause of death worldwide from a single infectious agent. An ability to detect the Mycobacterium tuberculosis complex (MTC) in clinical material while simultaneously differentiating its members is considered important. This allows for the gathering of epidemiological information pertaining to the prevalence, transmission and geographical distribution of the MTC, including those MTC members associated with zoonotic TB infection in humans. Also differentiating between members of the MTC provides the clinician with inherent MTC specific drug susceptibility profiles to guide appropriate chemotherapy. METHODOLOGY/PRINCIPAL FINDINGS The aim of this study was to develop a multiplex real-time PCR assay using novel molecular targets to identify and differentiate between the phylogenetically closely related M. bovis, M. bovis BCG and M. caprae. The lpqT gene was explored for the collective identification of M. bovis, M. bovis BCG and M. caprae, the lepA gene was targeted for the specific identification of M. caprae and a Region of Difference 1 (RD1) assay was incorporated in the test to differentiate M. bovis BCG. The multiplex real-time PCR assay was evaluated on 133 bacterial strains and was determined to be 100% specific for the members of the MTC targeted. CONCLUSIONS/SIGNIFICANCE The multiplex real-time PCR assay developed in this study is the first assay described for the identification and simultaneous differentiation of M. bovis, M. bovis BCG and M. caprae in one internally controlled reaction. Future validation of this multiplex assay should demonstrate its potential in the rapid and accurate diagnosis of TB caused by these three mycobacteria. Furthermore, the developed assay may be used in conjunction with a recently described multiplex real-time PCR assay for identification of the MTC and simultaneous differentiation of M. tuberculosis, M. canettii resulting in an ability to differentiate five of the eight members of the MTC.
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Affiliation(s)
- Kate Reddington
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Molecular Diagnostics Research Group, National Centre for Biomedical Engineering Science (NCBES), National University of Ireland, Galway, Ireland
| | - Justin O'Grady
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Molecular Diagnostics Research Group, National Centre for Biomedical Engineering Science (NCBES), National University of Ireland, Galway, Ireland
| | - Siobhan Dorai-Raj
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Molecular Diagnostics Research Group, National Centre for Biomedical Engineering Science (NCBES), National University of Ireland, Galway, Ireland
| | - Stefan Niemann
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Dick van Soolingen
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Thomas Barry
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Molecular Diagnostics Research Group, National Centre for Biomedical Engineering Science (NCBES), National University of Ireland, Galway, Ireland
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A case of Pott's disease with epidural abscess and probable cerebral tuberculoma following Bacillus Calmette-Guérin therapy for superficial bladder cancer. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2011; 21:e75-8. [PMID: 21358881 DOI: 10.1155/2010/572410] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Intravesical Bacillus Calmette-Guérin (BCG) immunotherapy is an accepted treatment for transitional cell carcinoma of the bladder. Carcinoma in situ of the bladder progresses to invasive muscular disease in approximately 54% of untreated patients, mandating early initiation of therapy once the diagnosis is confirmed. Should BCG treatment fail, an additional course of BCG combined with interferon-alpha, both administered intravesically, is a promising second-line immunotherapy. In greater than 95% of patients, BCG is tolerated without significant morbidity or mortality. However, both early (within three months of the original treatment) and late presentations of systemic infection resulting from intravesical BCG treatment have been described. The present study describes the course of a 75-year-old man with a late presentation of BCG vertebral osteomyelitis, discitis, epidural abscess, bilateral psoas abscesses and probable cerebral tuberculoma, following treatment regimens of intravesical BCG followed by intravesical BCG plus interferon-alpha 2b.
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Reddington K, O'Grady J, Dorai-Raj S, Maher M, van Soolingen D, Barry T. Novel multiplex real-time PCR diagnostic assay for identification and differentiation of Mycobacterium tuberculosis, Mycobacterium canettii, and Mycobacterium tuberculosis complex strains. J Clin Microbiol 2011; 49:651-7. [PMID: 21123525 PMCID: PMC3043491 DOI: 10.1128/jcm.01426-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 11/19/2010] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis (TB) in humans is caused by members of the Mycobacterium tuberculosis complex (MTC). Rapid detection of the MTC is necessary for the timely initiation of antibiotic treatment, while differentiation between members of the complex may be important to guide the appropriate antibiotic treatment and provide epidemiological information. In this study, a multiplex real-time PCR diagnostics assay using novel molecular targets was designed to identify the MTC while simultaneously differentiating between M. tuberculosis and M. canettii. The lepA gene was targeted for the detection of members of the MTC, the wbbl1 gene was used for the differentiation of M. tuberculosis and M. canettii from the remainder of the complex, and a unique region of the M. canettii genome, a possible novel region of difference (RD), was targeted for the specific identification of M. canettii. The multiplex real-time PCR assay was tested using 125 bacterial strains (64 MTC isolates, 44 nontuberculosis mycobacteria [NTM], and 17 other bacteria). The assay was determined to be 100% specific for the mycobacteria tested. Limits of detection of 2.2, 2.17, and 0.73 cell equivalents were determined for M. tuberculosis/M. canettii, the MTC, and M. canettii, respectively, using probit regression analysis. Further validation of this diagnostics assay, using clinical samples, should demonstrate its potential for the rapid, accurate, and sensitive diagnosis of TB caused by M. tuberculosis, M. canettii, and the other members of the MTC.
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Affiliation(s)
- Kate Reddington
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Molecular Diagnostics Research Group, NCBES, National University of Ireland, Galway, Ireland
| | - Justin O'Grady
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Molecular Diagnostics Research Group, NCBES, National University of Ireland, Galway, Ireland
| | - Siobhan Dorai-Raj
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Molecular Diagnostics Research Group, NCBES, National University of Ireland, Galway, Ireland
| | - Majella Maher
- Molecular Diagnostics Research Group, NCBES, National University of Ireland, Galway, Ireland
| | - Dick van Soolingen
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Thomas Barry
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Molecular Diagnostics Research Group, NCBES, National University of Ireland, Galway, Ireland
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Palma-Nicolás JP, Bocanegra-García V. [Innovative strategies to diagnose and monitor tuberculosis patients]. Arch Bronconeumol 2007; 43:225-32. [PMID: 17397587 DOI: 10.1016/s1579-2129(07)60055-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Mycobacterium tuberculosis is the single most deadly microorganism worldwide. A third of the world population is thought to have latent tuberculosis and approximately 2 million people die of the disease each year. Short and closely supervised treatment regimens are needed, but it is also essential to develop new strategies to ensure prompt diagnosis of the disease. In particular, cheap methods are needed to tackle tuberculosis from a population perspective. The present article reviews the advances in immunology and molecular strategies for epidemiological diagnosis and monitoring of tuberculosis patients.
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van Klingeren B, Dessens-Kroon M, van der Laan T, Kremer K, van Soolingen D. Drug susceptibility testing of Mycobacterium tuberculosis complex by use of a high-throughput, reproducible, absolute concentration method. J Clin Microbiol 2007; 45:2662-8. [PMID: 17537932 PMCID: PMC1951260 DOI: 10.1128/jcm.00244-07] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Accurate drug susceptibility testing (DST) for Mycobacterium tuberculosis is highly important for both therapy guidance and surveillance of drug resistance. Although liquid medium DST methods are used increasingly and seem most efficient and fast, the high costs hamper widespread implementation. In addition, an inability to check the colony morphology of the growing bacteria is a disadvantage of these methods. Moreover, these methods discriminate only between susceptibility and resistance and do not determine the MIC. In this paper, we describe a low-cost, reproducible, high-throughput, proportional absolute concentration DST method. The method uses a concentration series of antituberculosis drugs, including pyrazinamide in 7H10 medium, distributed semiautomatically in 25-well plates. The performance of this 25-well DST method was evaluated by the World Health Organization and the International Union against Tuberculosis and Lung Disease in 10 rounds of proficiency testing regarding sensitivity, specificity, efficiency, reproducibility, and predictive value for resistance and susceptibility. The performance of the method for these characteristics was 100% for isoniazid and from 96 to 100% for rifampin, 91 to 100% for streptomycin, and 85 to 100% for ethambutol. The method was 100% reproducible for all four drugs. The levels of drug resistance and the MIC distributions for the first-line antituberculosis drugs were determined for all 7,956 M. tuberculosis strains isolated in The Netherlands from 1998 to 2005 and amounted to 7.5% for isoniazid, 1.4% for rifampin, 8.5% for streptomycin, and 1.0% for ethambutol. Pyrazinamide testing was successful for 7,026 (88.3%) of the isolates and showed a resistance level of 0.8%.
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Affiliation(s)
- Bert van Klingeren
- Mycobacteria Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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Palma-Nicolás JP, Bocanegra-García V. Estrategias innovadoras para el diagnóstico y seguimiento de los pacientes tuberculosos. Arch Bronconeumol 2007. [DOI: 10.1157/13100542] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Brisse S, Supply P, Brosch R, Vincent V, Gutierrez MC. "A re-evaluation of M. prototuberculosis": continuing the debate. PLoS Pathog 2006; 2:e95. [PMID: 17009866 PMCID: PMC1579240 DOI: 10.1371/journal.ppat.0020095] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Park YK, Kang HY, Lim JG, Ha JS, Cho JO, Lee KC, Choi HS, Choi YH, Sheen SS, Bai GH. Analysis of DNA fingerprints of Mycobacterium Tuberculosis Isolates from Patients Registered at Health Center in Gyeonggi Province in 2004. Tuberc Respir Dis (Seoul) 2006. [DOI: 10.4046/trd.2006.60.3.290] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
| | | | | | - Jong Sik Ha
- Korean Institute of Tuberculosis, Seoul, Korea
| | - Jung Ok Cho
- Hygiene Policy Department, Gyeonggi Provincial Government, Gyeonggi Province, Korea
| | - Ka Chel Lee
- Hygiene Policy Department, Gyeonggi Provincial Government, Gyeonggi Province, Korea
| | - Hang Soon Choi
- Hygiene Policy Department, Gyeonggi Provincial Government, Gyeonggi Province, Korea
| | - Young Hwa Choi
- Ajou University School of Medicine, Gyeonggi Province, Korea
| | - Seung Soo Sheen
- Ajou University School of Medicine, Gyeonggi Province, Korea
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Kremer K, Arnold C, Cataldi A, Gutiérrez MC, Haas WH, Panaiotov S, Skuce RA, Supply P, van der Zanden AGM, van Soolingen D. Discriminatory power and reproducibility of novel DNA typing methods for Mycobacterium tuberculosis complex strains. J Clin Microbiol 2005; 43:5628-38. [PMID: 16272496 PMCID: PMC1287774 DOI: 10.1128/jcm.43.11.5628-5638.2005] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Revised: 04/18/2005] [Accepted: 06/23/2005] [Indexed: 11/20/2022] Open
Abstract
In recent years various novel DNA typing methods have been developed which are faster and easier to perform than the current internationally standardized IS6110 restriction fragment length polymorphism typing method. However, there has been no overview of the utility of these novel typing methods, and it is largely unknown how they compare to previously published methods. In this study, the discriminative power and reproducibility of nine recently described PCR-based typing methods for Mycobacterium tuberculosis were investigated using the strain collection of the interlaboratory study of Kremer et al. This strain collection contains 90 M. tuberculosis complex and 10 non-M. tuberculosis complex mycobacterial strains, as well as 31 duplicated DNA samples to assess reproducibility. The highest reproducibility was found with variable numbers of tandem repeat typing using mycobacterial interspersed repetitive units (MIRU VNTR) and fast ligation-mediated PCR (FLiP), followed by second-generation spoligotyping, ligation-mediated PCR (LM-PCR), VNTR typing using five repeat loci identified at the Queens University of Belfast (QUB VNTR), and the Amadio speciation PCR. Poor reproducibility was associated with fluorescent amplified fragment length polymorphism typing, which was performed in three different laboratories. The methods were ordered from highest discrimination to lowest by the Hunter-Gaston discriminative index as follows: QUB VNTR typing, MIRU VNTR typing, FLiP, LM-PCR, and spoligotyping. We conclude that both VNTR typing methods and FLiP typing are rapid, highly reliable, and discriminative epidemiological typing methods for M. tuberculosis and that VNTR typing is the epidemiological typing method of choice for the near future.
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Affiliation(s)
- Kristin Kremer
- Mycobacteria Reference Unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, P.O. Box 1, 3720 BA Bilthoven, The Netherlands.
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40
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Kanduma E, McHugh TD, Gillespie SH. Molecular methods for Mycobacterium tuberculosis strain typing: a users guide. J Appl Microbiol 2003; 94:781-91. [PMID: 12694442 DOI: 10.1046/j.1365-2672.2003.01918.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
There are now a wide range of techniques available to type Mycobacterium tuberculosis, the problem is to choose the correct technique. For large scale epidemiological studies the portability and standardization of IS6110 restriction fragment length polymorphism (RFLP) means that this remains the gold standard technique. In the next few years the internationally standard mycobacterial interspersed repetitive unit (MIRU) may come to challenge this primacy. Low copy number stains remain a problem and these can be typed by either polymorphic Guanine cytosine-rich repetitive sequence (PGRS) or MIRU-variable numbers of tandem repeat (VNTR). To confirm whether strains are part of a true cluster PGRS remains the method of choice. For local outbreaks and investigations of laboratory cross contamination where speed is of greatest importance suspect strains should be initially investigated using a PCR-based method. The superior reproducibility and discrimination of MIRU-VNTR means that these methods should be favoured. If matches are found, then further confirmation of identity can be achieved using IS6110 RFLP or PGRS if the strains prove to have a low IS6110 copy number.
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Affiliation(s)
- E Kanduma
- Clinical Laboratory, Kilimanjaro Christian Medical College, PO Box 3010, Moshi, Tanzania
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41
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van der Zanden AGM, Kremer K, Schouls LM, Caimi K, Cataldi A, Hulleman A, Nagelkerke NJD, van Soolingen D. Improvement of differentiation and interpretability of spoligotyping for Mycobacterium tuberculosis complex isolates by introduction of new spacer oligonucleotides. J Clin Microbiol 2002; 40:4628-39. [PMID: 12454164 PMCID: PMC154657 DOI: 10.1128/jcm.40.12.4628-4639.2002] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The direct repeat (DR) region in Mycobacterium tuberculosis complex strains is composed of multiple well-conserved 36-bp DRs interspersed with nonrepetitive DNA spacer sequences of similar size. Clinical isolates show extensive polymorphism in this DR region, and this has led to the development of a 43-spacer reversed line blot methodology: spoligotyping. Although this method has contributed significantly to the molecular epidemiology of tuberculosis in the last decade, the discriminatory power and the readability of this method were not found to be optimal. In order to improve the discriminatory power, the usefulness of 43 redesigned oligonucleotides and the usefulness of 51 new spacer oligonucleotides were evaluated. For 314 M. tuberculosis complex strains isolated in the central part of The Netherlands over a 5-year period, 264 different IS6110 RFLP types could be distinguished, and 160 different spoligotype patterns were identified by traditional spoligotyping. After the introduction of 51 new spacer oligonucleotides, 14 additional spoligotypes were recognized. This enabled us to split 11 clusters of isolates identified by the traditional spoligotyping. Furthermore, on the basis of the new spacer oligonucleotides a dichotomy was found among the Beijing genotype isolates. Among 76 Mycobacterium bovis strains, 20 patterns were found by traditional spoligotyping and 30 patterns were found by novel probe spoligotyping, respectively. Nine M. bovis subsp. caprae isolates yielded six patterns by traditional spoligotyping and eight patterns by novel probe spoligotyping. A part of the redesigned oligonucleotides slightly improved the reading of spoligotype patterns. The reproducibility of spoligotyping, based on internal control probes, invariably yielded a high score; only 4 (1%) of the 314 patient isolates gave discrepant results. Analysis of a set of 31 duplicate M. tuberculosis complex strains demonstrated a 10% error rate for the identification of blinded duplicate samples. In a redundancy analysis, 40 essential spacer oligonucleotides of the 94-spacer sequences were selected, yielding the same number of spoligotype patterns. We propose to leave the traditional commercialized first-generation membrane for spoligotyping unchanged for current applications and to introduce a second-generation spoligotyping membrane whenever extended discrimination is required, e.g., for low-copy-number IS6110 strains or for phylogenetic studies of Beijing genotype strains.
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Affiliation(s)
- A G M van der Zanden
- Medical Microbiology and Infectious Diseases, Gelre Hospitals, Location Lukas, Apeldoorn, The Netherlands.
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42
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Cabrera M, Canova S, Rosenzvit M, Guarnera E. Identification of Echinococcus granulosus eggs. Diagn Microbiol Infect Dis 2002; 44:29-34. [PMID: 12376028 DOI: 10.1016/s0732-8893(02)00414-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The eggs from Echinococcus granulosus contaminate the environment spreading out the disease among the herbivorous. The differential diagnosis of the embriophores recovered from the soil is very difficult by morphologic and immunologic methods. In this paper we evaluate the EgO/DNA-IM1 for identification of E. granulosus oncosphere DNA and differentiation of eggs from other Taeniid. The positive result of the PCR technique shows an amplification fragment of the expected size (285 bp) corresponding to the partial sequence of the mitochondrial gene of the cytochrome oxidase CO1 from E. granulosus (391 bp). The fragment is not present in the DNA from Echinococcus multilocularis, Taenia hydatigena, Taenia saginata, Diphyll-obothrium latum, and Hymenolepis nana. It could be useful to rule out Taenia taeniformis, Taenia solium, Taenia pisiformis, and Taenia crassiceps, which sequences do not belong to the primer. We concluded that the PCR amplification employing the EgO/DNA-IM1 primer set showed high sensitivity and specificity for the identification of Echinococcus granulosus eggs.
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Affiliation(s)
- Marta Cabrera
- Departamento de Parasitologi;a. Instituto Nacional de Enfermedades Infecciosas "Dr Carlos G Malbrán," Av Vélez Sársfield 563 (1281), Buenos Aires, Argentina
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43
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Abu-Nader R, Terrell CL. Mycobacterium bovis vertebral osteomyelitis as a complication of intravesical BCG use. Mayo Clin Proc 2002; 77:393-7. [PMID: 11936937 DOI: 10.4065/77.4.393] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We report a culture-proven case of Mycobacterium bovis vertebral osteomyelitis in a 76-year-old man who had undergone intravesical BCG therapy for bladder cancer 7 years previously. He presented with debilitating back pain and had radiographic evidence of T6-7 disk space destruction with involvement of adjacent vertebrae. Tissue culture from the disk space confirmed the diagnosis of vertebral osteomyelitis due to hematogenous spread of M. bovis. Treatment with antituberculous medications was begun soon after tissue diagnosis was made, and the patient fared well with medical therapy alone. Although uncommon, this infectious complication of BCG therapy should always be considered in the appropriate clinical setting. Timely diagnosis is important, because chemotherapy, when initiated early in the disease, can preclude the necessity for surgical intervention.
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Affiliation(s)
- Rima Abu-Nader
- Division of Infectious Diseases, University of Iowa Hospitals and Clinics, Iowa City, USA
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44
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Viana-Niero C, Gutierrez C, Sola C, Filliol I, Boulahbal F, Vincent V, Rastogi N. Genetic diversity of Mycobacterium africanum clinical isolates based on IS6110-restriction fragment length polymorphism analysis, spoligotyping, and variable number of tandem DNA repeats. J Clin Microbiol 2001; 39:57-65. [PMID: 11136749 PMCID: PMC87680 DOI: 10.1128/jcm.39.1.57-65.2001] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A collection of 105 clinical isolates originally identified as Mycobacterium africanum were characterized using both phenotypic and genotyping methods. The phenotypic methods included routine determination of cultural properties and biochemical tests used to discriminate among the members of the M. tuberculosis complex, whereas genotypic characterization was based on IS6110-restriction fragment length polymorphism (IS6110-RFLP) analysis, IS1081-RFLP analysis, direct repeat-based spacer oligonucleotide typing (spoligotyping), variable number of tandem DNA repeats (VNTR), and the polymorphism of the oxyR, pncA, and mtp40 loci. The results obtained showed that a majority of M. africanum isolates were characterized by a specific spoligotyping pattern that was intermediate between those of M. tuberculosis and M. bovis, which do not hybridize with spacers 33 to 36 and spacers 39 to 43, respectively. A tentative M. africanum-specific spoligotyping signature appeared to be absence of spacers 8, 9, and 39. Based on spoligotyping, as well as the polymorphism of oxyR and pncA, a total of 24 isolates were excluded from the final study (19 were identified as M. tuberculosis, 2 were identified as M. canetti, and 3 were identified as M. bovis). The remaining 81 M. africanum isolates were efficiently subtyped in three distinct subtypes (A1 to A3) by IS6110-RFLP analysis and spoligotyping. The A1 and A2 subgroups were relatively more homogeneous upon spoligotyping than A3. Further analysis of the three subtypes by VNTR corroborated the highly homogeneous nature of the A2 subtype but showed significant variations for subtypes A1 and A3. A phylogenetic tree based on a selection of isolates representing the three subtypes using VNTR and spoligotyping alone or in combination confirmed the subtypes described as well as the heterogeneity of subtype A3.
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Affiliation(s)
- C Viana-Niero
- Centre National de Référence des Mycobactéries, Institut Pasteur, 75724-Paris Cedex 15, France
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45
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Van Soolingen D. Molecular epidemiology of tuberculosis and other mycobacterial infections: main methodologies and achievements. J Intern Med 2001; 249:1-26. [PMID: 11168781 DOI: 10.1046/j.1365-2796.2001.00772.x] [Citation(s) in RCA: 203] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In the last decade, DNA fingerprint techniques have become available to study the interperson transmission of tuberculosis and other mycobacterial infections. These methods have facilitated epidemiological studies at a population level. In addition, the species identification of rarely encountered mycobacteria has improved significantly. This article describes the state of the art of the main molecular typing methods for Mycobacterium tuberculosis complex and non-M. tuberculosis complex (atypical) mycobacteria. Important new insights that have been gained through molecular techniques into epidemiological aspects and diagnosis of mycobacterial diseases are highlighted.
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MESH Headings
- Animals
- Contact Tracing
- DNA Fingerprinting
- DNA, Bacterial/genetics
- Genetics, Microbial/trends
- Genotype
- Humans
- Molecular Epidemiology/methods
- Mycobacterium/classification
- Mycobacterium/genetics
- Mycobacterium/isolation & purification
- Mycobacterium Infections, Nontuberculous/epidemiology
- Mycobacterium Infections, Nontuberculous/genetics
- Mycobacterium Infections, Nontuberculous/transmission
- Mycobacterium tuberculosis/genetics
- Nontuberculous Mycobacteria/genetics
- Polymorphism, Restriction Fragment Length
- RNA, Bacterial/genetics
- Reproducibility of Results
- Sequence Analysis, DNA
- Sequence Analysis, RNA
- Transformation, Bacterial
- Tuberculosis/epidemiology
- Tuberculosis/genetics
- Tuberculosis/transmission
- Tuberculosis, Multidrug-Resistant/epidemiology
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Affiliation(s)
- D Van Soolingen
- Mycobacteria Reference Department, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.
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46
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Rua EC, Blacarce N, Drut R. Early bacille de Calmette-Guérin vaccination and Crohn's disease: possible relationship? Pediatr Dev Pathol 2000; 3:501-3. [PMID: 10890937 DOI: 10.1007/s100240010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- E C Rua
- Gastroenterology Unit, Hospital de Niños "Superiora Sor María Ludovica", 1900 La Plata, Argentina
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47
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Park YK, Bai GH, Kim SJ. Restriction fragment length polymorphism analysis of Mycobacterium tuberculosis isolated from countries in the western pacific region. J Clin Microbiol 2000; 38:191-7. [PMID: 10618086 PMCID: PMC88694 DOI: 10.1128/jcm.38.1.191-197.2000] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A total of 422 Mycobacterium tuberculosis isolates from eight countries were subjected to IS6110 and IS1081 DNA fingerprinting by means of restriction fragment analysis to characterize M. tuberculosis strains from each country. Chinese, Mongolian, Hong Kong, Filipino, and Korean isolates had comparatively more copies of IS6110 (proportion with eight or more copies; 95% +/- 5%), while Thai, Malaysian, and Vietnamese isolates had fewer copies (proportion with eight or more copies, 60% +/- 4%). We found a number of novel IS1081 types in this study. One IS1081 type was present in 56% of Filipino isolates, had a specific 6.6-kb PvuII fragment in its IS6110 DNA fingerprint, and was termed the "Filipino family." The IS1081 types of Thai isolates had interposing characteristics between the characteristics of northeastern Asian and southeastern Asian IS1081 types. A 1.3-kb single-copy IS6110 fragment was found only in Vietnamese M. tuberculosis isolates. Although M. tuberculosis isolates from each country had comparatively similar characteristics depending on the classification factor, each country's isolates showed characteristic DNA fingerprints and differed slightly from the isolates from the other countries in either the mode number of IS6110 copies or the distribution of IS1081 types.
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Affiliation(s)
- Y K Park
- Korean Institute of Tuberculosis, Korean National Tuberculosis Association, Seoul, Korea
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48
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Cousins DV, Whittington R, Marsh I, Masters A, Evans RJ, Kluver P. Mycobacteria distenct from Mycobacterium avium subsp. paratuberculosis isolated from the faeces of ruminants possess IS900-like sequences detectable IS900 polymerase chain reaction: implications for diagnosis. Mol Cell Probes 1999; 13:431-42. [PMID: 10657148 DOI: 10.1006/mcpr.1999.0275] [Citation(s) in RCA: 169] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PCR targeting the 5' end of IS 900 has been considered specific for identification of Mycobacterium avium subsp. paratuberculosis and is frequently applied to confirm the presence of this organism in the diagnosis of Johne's disease. IS 900 PCR has also been applied to studies of the aetiology of Crohn's disease. Mycobacterium spp. isolated from the faeces of 3 clinically normal animals in 2 Australian states appeared not to be M. paratuberculosis but were positive by IS 900 PCR. The isolates were characterized using mycobactin dependency, biochemical tests, IS 900 and 16 S rRNA sequencing and restriction fragment length polymorphism (RFLP) using IS 900 as probe. DNA sequencing confirmed that the isolates had between 71% and 79% homology with M. paratuberculosis in the region of IS 900 amplified, were most closely related to Mycobacterium scrofulaceum, and confirmed the usefulness of restriction enzyme analysis of amplified product to identify the false positive results. RFLP analysis with Bst Ell detected three to five copies of the IS 900 -like element in the isolates. These were located in molecular weight fragments that were clearly different to IS 900 in previously characterized strains of M. paratuberculosis. It is likely that these isolates are environmental mycobacteria. Southern blotting with an internal probe is unlikely to provide differentiation of M. paratuberculosis from these organisms. We recommend the adoption of restriction endonuclease analysis of IS 900 PCR product as a routine precaution to prevent the reporting of false positive IS 900 PCR results.
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Affiliation(s)
- D V Cousins
- Animal Health Laboratories, Agriculture Western Australia, Locked Bag No. 4, Bentley Delivery Service, Bentley, WA Australia.
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49
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Källenius G, Koivula T, Ghebremichael S, Hoffner SE, Norberg R, Svensson E, Dias F, Marklund BI, Svenson SB. Evolution and clonal traits of Mycobacterium tuberculosis complex in Guinea-Bissau. J Clin Microbiol 1999; 37:3872-8. [PMID: 10565899 PMCID: PMC85833 DOI: 10.1128/jcm.37.12.3872-3878.1999] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two hundred twenty-nine consecutive isolates of Mycobacterium tuberculosis complex from patients with pulmonary tuberculosis in Guinea-Bissau, which is located in West Africa, were analyzed for clonal origin by biochemical typing and DNA fingerprinting. By using four biochemical tests (resistance to thiophene-2-carboxylic acid hydrazide, niacin production, nitrate reductase test, and pyrazinamidase test), the isolates could be assigned to five different biovars. The characteristics of four strains conformed fully with the biochemical criteria for M. bovis, while those of 85 isolates agreed with the biochemical criteria for M. tuberculosis. The remaining 140 isolates could be allocated into one of three biovars (biovars 2 to 4) representing a spectrum between the classical bovine (biovar 1) and human (biovar 5) tubercle bacilli. By using two genotyping methods, restriction fragment length polymorphism analysis with IS6110 (IS6110 RFLP analysis) and spoligotyping, the isolates could be separated into three groups (groups A to C) of the M. tuberculosis complex. Group A (n = 95), which contained the majority of classical human M. tuberculosis isolates, had large numbers of copies of IS6110 elements (mean number of copies, 9) and a distinctive spoligotyping pattern that lacked spacers 33 to 36. Isolates of the major group, group B (n = 119), had fewer IS6110 copies (mean copy number, 5) and a spoligotyping pattern that lacked spacers 7 to 9 and 39 and mainly comprised isolates of biovars 1 to 4. Group C isolates (n = 15) had one to three IS6110 copies, had a spoligotyping pattern that lacked spacers 29 to 34, and represented biovar 3 to 5 isolates. Four isolates whose biochemical characteristics conformed with those of M. bovis clustered with the group B isolates and had spoligotype patterns that differed from those previously reported for M. bovis, in that they possessed spacers 40 to 43. Interestingly, isolates of group B and, to a certain extent, also isolates of group C showed a high degree of variability in biochemical traits, despite genotypic identity in terms of IS6110 RFLP and spoligotype patterns. We hypothesize that isolates of groups B and C have their evolutionary origin in West Africa, while group A isolates are of European descent.
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Affiliation(s)
- G Källenius
- Department of Bacteriology, Swedish Institute for Infectious Disease Control, S-17182 Solna, Sweden.
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50
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Serraino A, Marchetti G, Sanguinetti V, Rossi MC, Zanoni RG, Catozzi L, Bandera A, Dini W, Mignone W, Franzetti F, Gori A. Monitoring of transmission of tuberculosis between wild boars and cattle: genotypical analysis of strains by molecular epidemiology techniques. J Clin Microbiol 1999; 37:2766-71. [PMID: 10449449 PMCID: PMC85373 DOI: 10.1128/jcm.37.9.2766-2771.1999] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An epidemiological survey for the monitoring of bovine tuberculosis transmission was carried out in western Liguria, a region in northern Italy. Fifteen Mycobacterium bovis strains were isolated from 63 wild boar samples (62 from mandibular lymph nodes and 1 from a liver specimen). Sixteen mediastinal lymph nodes of 16 head of cattle were collected, and 15 Mycobacterium bovis strains were subsequently cultured. All M. bovis strains isolated from cattle and wild boars were genotyped by spoligotyping and by restriction fragment length polymorphism (RFLP) analysis with the IS6110 and IS1081 probes. All M. bovis strains showed the typical spoligotype characterized by the absence of the 39 to 43 spacers in comparison with the number in M. tuberculosis. A total of nine different clusters were identified by spoligotyping. The largest cluster included 9 strains isolated from wild boars and 11 strains isolated from cattle, thus confirming the possibility of transmission between the two animal species. Fingerprinting by RFLP analysis with the IS6110 probe showed an identical single-band pattern for 29 of 30 strains analyzed, and only 1 strain presented a five-band pattern. The use of IS1081 as a second probe was useful for differentiation of M. bovis from M. bovis BCG but not for differentiation among M. bovis strains, which presented the same undifferentiated genomic profile. In relation to the epidemiological investigation, we hypothesized that the feeding in pastures contaminated by cattle discharges could represent the most probable route of transmission of M. bovis between the two animal species. In conclusion, our results confirmed the higher discriminatory power of spoligotyping in relation to that of RFLP analysis for the differentiation of M. bovis genomic profiles. Our data showed the presence of a common M. bovis genotype in both cattle and wild boars, confirming the possible interspecies transmission of M. bovis.
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Affiliation(s)
- A Serraino
- Department of Veterinary Public Health and Animal Pathology, University of Bologna, Bologna, Italy
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