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Lai MY, Abdul Hamid MH, Jelip J, Mudin RN, Lau YL. Evaluation of A Simple DNA Extraction Method and Its Combination with Loop-Mediated Isothermal Amplification Assays for Rapid Plasmodium knowlesi Diagnosis. Trop Med Infect Dis 2023; 8:389. [PMID: 37624327 PMCID: PMC10458645 DOI: 10.3390/tropicalmed8080389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/24/2023] [Accepted: 07/01/2023] [Indexed: 08/26/2023] Open
Abstract
The initial and vital stage in the diagnosis of malaria involves extracting DNA. The efficiency of malaria testing is restricted by the multiple steps involved in commercial DNA extraction kits. We attempted to improve an existing loop-mediated isothermal amplification (LAMP) for the detection of Plasmodium knowlesi by using a simple DNA extraction approach, making it a feasible option for mass screening. We utilized a simple nucleic acid extraction method directly from whole blood for the detection of P. knowlesi, taking only 5 min to complete. The extracted DNA was evaluated by two fluorescent-based LAMP and one colorimetric-based LAMP assay. The detection limit for both SYTO-LAMP and SYBR green-LAMP was 0.00001% and 0.0001% parasitemia, respectively. Meanwhile, neutral red-LAMP had a detection limit of 0.01% parasitemia. Combining this simple and inexpensive DNA extraction method, SYTO-LAMP could serve as an alternative molecular diagnosis for the detection of P. knowlesi and other human Plasmodium spp.
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Affiliation(s)
- Meng-Yee Lai
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | | | - Jenarun Jelip
- Vector Borne Disease Sector, Ministry of Health, Putrajaya 62000, Malaysia
| | - Rose Nani Mudin
- Vector Borne Disease Sector, Ministry of Health, Putrajaya 62000, Malaysia
| | - Yee-Ling Lau
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
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2
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Fukushima K, Matsumoto Y, Matsuki T, Saito H, Motooka D, Komukai S, Fukui E, Yamuchi J, Nitta T, Niitsu T, Abe Y, Nabeshima H, Nagahama Y, Nii T, Tsujino K, Miki K, Kitada S, Kumanogoh A, Akira S, Nakamura S, Kida H. MGIT-seq for the Identification of Nontuberculous Mycobacteria and Drug Resistance: a Prospective Study. J Clin Microbiol 2023; 61:e0162622. [PMID: 36946719 PMCID: PMC10117113 DOI: 10.1128/jcm.01626-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Because nontuberculous mycobacterial pulmonary disease is a considerable health burden, a simple and clinically applicable analytical protocol enabling the identification of subspecies and drug-resistant disease is required to determine the treatment strategy. We aimed to develop a simplified workflow consisting only of direct sequencing of mycobacterial growth indicator tube cultures (MGIT-seq). In total, 138 patients were prospectively enrolled between April 2021 and May 2022, and culture-positive MGIT broths were subjected to sequencing using MinION, a portable next-generation sequencer. Sequence analysis was conducted to identify species using core genome multilocus sequence typing and to predict macrolide and amikacin (AMK) resistance based on previously reported mutations in rrl, rrs, and erm(41). The results were compared to clinical tests for species identification and drug susceptibility. A total of 116 patients with positive MGIT cultures were included in the analysis. MGIT-seq yielded 99.1% accuracy in species-level identification and identified 98 isolates (84.5%) at the subspecies level. Macrolide and AMK resistance were detected in 19.4% and 1.9% of Mycobacterium avium complex (MAC) and Mycobacterium abscessus isolates. The predicted macrolide and AMK resistance was consistent with the results of conventional drug susceptibility tests, with specificities of 97.6% and 100.0%, respectively. Direct MGIT-seq has achieved comprehensive identification and drug resistance detection of nontuberculous mycobacteria, which could be applicable to determine the treatment strategy by a single test in clinical practice.
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Affiliation(s)
- Kiyoharu Fukushima
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
- Global Center for Medical Engineering and Informatics, Suita, Osaka, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Takanori Matsuki
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Haruko Saito
- Department of Clinical Laboratory, National Hospital Organization, Osaka Toneyama Medical Centre, Toyonaka, Osaka, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
| | - Sho Komukai
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
- Department of Biomedical Statistics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Eriko Fukui
- Department of General Thoracic surgery, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - June Yamuchi
- Department of Clinical Laboratory, National Hospital Organization, Osaka Toneyama Medical Centre, Toyonaka, Osaka, Japan
| | - Tadayoshi Nitta
- Department of Clinical Laboratory, National Hospital Organization, Osaka Toneyama Medical Centre, Toyonaka, Osaka, Japan
| | - Takayuki Niitsu
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yuko Abe
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Hiroshi Nabeshima
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Yasuharu Nagahama
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Takuro Nii
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Kazuyuki Tsujino
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Keisuke Miki
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | | | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Japan for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - Shizuo Akira
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Japan for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - Hiroshi Kida
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
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3
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Host Immune Response and Novel Diagnostic Approach to NTM Infections. Int J Mol Sci 2020; 21:ijms21124351. [PMID: 32570978 PMCID: PMC7352966 DOI: 10.3390/ijms21124351] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 02/07/2023] Open
Abstract
The incidence and prevalence of non-tuberculous mycobacteria (NTM) infections are steadily increasing worldwide, partially due to the increased incidence of immunocompromised conditions, such as the post-transplantation state. The importance of proper diagnosis and management of NTM infection has been recently recognized. Host immunological responses play integral roles in vulnerability to NTM infections, and may contribute to the onset of specific types of NTM infection. Furthermore, distinct NTM species are known to affect and attenuate these host immune responses in unique manners. Therefore, host immune responses must be understood with respect to each causative NTM species. Here, we review innate, cellular-mediated, and humoral immunity to NTM and provide perspectives on novel diagnostic approaches regarding each NTM species.
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Karimi H, Oudghiri A, En-Nanei L, Mzibri ME, Laglaoui A, Chaoui I, Abid M. Frequency of genomic mutations mediating resistance of Mycobacterium tuberculosis isolates to rifampicin in Northern Morocco. Rev Inst Med Trop Sao Paulo 2020; 62:e37. [PMID: 32520212 PMCID: PMC7274765 DOI: 10.1590/s1678-9946202062037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/22/2020] [Indexed: 11/22/2022] Open
Abstract
Drug resistant tuberculosis (DR-TB) is challenging particularly in developing countries. As such, a previous investigation gave the first insight into the mutational status of the Rifampicin Resistance Determining Region (RRDR) of rpoB gene among a restricted number of MTB patients’ residents in the Northern Morocco. The purpose of this study was to investigate rpoB mutation types and frequencies associated with resistance to Rifampicin in a larger panel of MTB patients and to evaluate the usefulness of these mutations to improve the diagnosis of resistance to Rifampicin. A panel of 301 consecutive sputum samples belonging to patients suscpected of having TB from Northern Morocco was collected at the Pasteur Institute of Tangier between 2014-2017. Samples were subjected to conventionel microbiological tests. Evaluation of rpoB muational status was assessed by PCR amplification and sequencing of the RRDR of the rpoB gene. DST results showed that 26.4% of strains were MDR. Sequencing results reported single point mutations in 36 of 65 RIFR isolates of which two had two mutations. Aminoacid substitutions in the codon Ser531Leu occurred at the highest frequency (34.46%). Overall, 10 aminoacid substitutions have been registered, and the H526S substitution was reported for the first time. The present study highlighted that resistance to RIF is a reliable marker of MDR-TB, the common mutations successfully detected in the rpoB 531, rpoB526 and rpoB516 codons provide a foundation for the implementation of molecular approaches such as Hain and GeneXpert as a routine tests to detect DR-TB. However, considerable work is still necessary to identify extensive mutations associated with DR-TB.
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Affiliation(s)
- Hind Karimi
- FST de Tanger, Equipe de Recherche Biotechnologie et Génie des Biomolécules, Tanger, Morocco.,Institut Pasteur du Maroc, Laboratoire de Biologie Moléculaire, Service de Recherche, Tanger, Morocco
| | - Amal Oudghiri
- FST de Tanger, Equipe de Recherche Biotechnologie et Génie des Biomolécules, Tanger, Morocco.,Centre National de l'Energie, des Sciences et Techniques Nucléaires, Unité de Recherches Médicales et Biologiques, Rabat, Morocco
| | - Latifa En-Nanei
- Institut Pasteur du Maroc, Laboratoire de Biologie Moléculaire, Service de Recherche, Tanger, Morocco
| | - Mohammed El Mzibri
- Centre National de l'Energie, des Sciences et Techniques Nucléaires, Unité de Recherches Médicales et Biologiques, Rabat, Morocco
| | - Amin Laglaoui
- FST de Tanger, Equipe de Recherche Biotechnologie et Génie des Biomolécules, Tanger, Morocco
| | - Imane Chaoui
- Centre National de l'Energie, des Sciences et Techniques Nucléaires, Unité de Recherches Médicales et Biologiques, Rabat, Morocco
| | - Mohammed Abid
- Institut Pasteur du Maroc, Laboratoire de Biologie Moléculaire, Service de Recherche, Tanger, Morocco
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5
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Abstract
Infectious diseases are one of the main causes of morbidity and mortality worldwide. With new pathogens continuously emerging, known infectious diseases reemerging, increasing microbial resistance to antimicrobial agents, global environmental change, ease of world travel, and an increasing immunosuppressed population, recognition of infectious diseases plays an ever-important role in surgical pathology. This becomes particularly significant in cases where infectious disease is not suspected clinically and the initial diagnostic workup fails to include samples for culture. As such, it is not uncommon that a lung biopsy becomes the only material available in the diagnostic process of an infectious disease. Once the infectious nature of the pathological process is established, careful search for the causative agent is advised. This can often be achieved by examination of the hematoxylin and eosin-stained sections alone as many organisms or their cytopathic effects are visible on routine staining. However, ancillary studies such as histochemical stains, immunohistochemistry, in situ hybridization, or molecular techniques may be needed to identify the organism in tissue sections or for further characterization, such as speciation.
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Affiliation(s)
- Annikka Weissferdt
- Associate Professor, Department of Pathology, Division of Pathology and Laboratory Medicinec, The University of Texas MD Anderson Cancer Center, Houston, TX USA
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6
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Fata A, Bojdy A, Maleki M, Hosseini Farash BR, Ghazvini K, Tajzadeh P, Vakili V, Moghaddas E, Mastroeni P, Rahmani S. Fish tank granuloma: An emerging skin disease in Iran mimicking Cutaneous Leishmaniasis. PLoS One 2019; 14:e0221367. [PMID: 31536497 PMCID: PMC6752854 DOI: 10.1371/journal.pone.0221367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/05/2019] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE Mycobacterium marinum causes a rare cutaneous disease known as fish tank granuloma (FTG). The disease manifestations resemble those associated with Cutaneous Leishmaniasis (CL). The aim of this study was to determine whether FTG was the cause of cutaneous lesions in patients who were referred to the Parasitology laboratory of Imam Reza Hospital in Mashhad to be investigated for CL. MATERIALS/METHODS One hundered patients, clinically diagnosed with CL between April 2014 and March 2015, were included in this study. Ziehl-Neelsen staining was performed to identify acid-fast Mycobacterium in addition to bacterial cultures using Löwenstein-Jensen medium. Skin lesion samples were also collected and kept on DNA banking cards for PCR testing. RESULTS Twenty-nine of the 100 individuals with skin lesions, and therefore suspected of suffering from CL, tested positive for Mycobacterium marinum by PCR. Of these, 21 (72.4%) were male and 8(27.6%) were female. In 97% of these cases the lesions were located on hands and fingers. These patients had a history of manipulating fish and had been in contact with aquarium water. A sporotrichoid appearance was observed in 58.6% of the patients with mycobacterial lesions; 67% of patients had multiple head appearance. CONCLUSION Patients suspected to have CL and who test negative for CL could be affected by FTG. Therefore, after obtaining an accurate case history, molecular diagnosis is recommended for cases that give a negative result by conventional methods.
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Affiliation(s)
- Abdolmajid Fata
- Cutaneous leishmaniasis Research Center, Mashhad University of Medical Sciences, Mashhad, Khorasan-e-Razavi, Iran
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Khorasan-e-Razavi, Iran
| | - Amin Bojdy
- Department of Infectious Diseases, Imam Reza Hospital, Mashhad University of Medical Sciences, Mashhad, Khorasan-e-Razavi, Iran
| | - Masoud Maleki
- Department of Dermatology, Imam Reza Hospital, Mashhad University of Medical Sciences, Mashhad, Khorasan-e-Razavi, Iran
| | - Bibi Razieh Hosseini Farash
- Cutaneous leishmaniasis Research Center, Mashhad University of Medical Sciences, Mashhad, Khorasan-e-Razavi, Iran
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Khorasan-e-Razavi, Iran
| | - Kiarash Ghazvini
- Department of Microbiology, Quem Hospital, Mashhad University of Medical Sciences, Mashhad, Khorasan-e-Razavi, Iran
| | - Parastoo Tajzadeh
- Department of Medical Lab Sciences, Faculty of nursing, Kashmar, Mashhad University of Medical Sciences, Mashhad, Khorasan-e-Razavi, Iran
| | - Vida Vakili
- Department of Social Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Khorasan-e-Razavi, Iran
| | - Elham Moghaddas
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Khorasan-e-Razavi, Iran
| | - Pietro Mastroeni
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Shadi Rahmani
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Khorasan-e-Razavi, Iran
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7
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Chuensirikulchai K, Laopajon W, Phunpae P, Apiratmateekul N, Surinkaew S, Tayapiwatana C, Pata S, Kasinrerk W. Sandwich antibody-based biosensor system for identification of Mycobacterium tuberculosis complex and nontuberculous mycobacteria. J Immunoassay Immunochem 2019; 40:590-604. [PMID: 31462139 DOI: 10.1080/15321819.2019.1659814] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Mycobacterial infection, leading to pulmonary disease, remains a world health problem. Clinical symptoms of pulmonary disease caused by Mycobacterium tuberculosis complex (MTBC) and nontuberculous mycobacteria (NTM) are very similar. A rapid method for the differentiation of MTBC and NTM infection is essential for appropriate therapy. In this study, we aim to establish an antibody-based biosensor system for the identification of MTBC and NTM infection. Monoclonal antibodies (mAbs) specific for Ag85B proteins of mycobacteria were generated and characterized. The generated anti-Ag85B mAb clones AM85B-5 and AM85B-8 reacted to Ag85B of Mycobacterium spp.; in contrast, clone AM85B-9 specifically reacted to Ag85B of MTBC. By employing the produced mAbs, single and sandwich antibody-based biosensors using bio-layer interferometry were established for determination of Ag85B proteins. The sandwich antibody-based biosensor system was demonstrated to be suitable for detection of Ag85B protein and identification of MTBC and NTM. Using anti-Ag85B mAbs AM85B-8 and AM85B-9 as immobilized antibodies on sensor chips and using mAb AM85B-5 as secondary antibody, the established sandwich antibody-based biosensor could discriminate MTBC and NTM. The developed biosensor system can be used for culture confirmation of mycobacteria and speciation to MTBC and NTM.
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Affiliation(s)
- Kantinan Chuensirikulchai
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Witida Laopajon
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Biomedical Technology Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at the Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Ponrut Phunpae
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Napaporn Apiratmateekul
- Department of Medical Technology, Faculty of Allied Health Sciences, Naresuan University, Pitsanulok, Thailand
| | - Sirirat Surinkaew
- Biomedical Technology Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at the Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Biomedical Technology Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at the Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Supansa Pata
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Biomedical Technology Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at the Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Watchara Kasinrerk
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Biomedical Technology Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at the Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
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8
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Shirato K. Detecting amplicons of loop-mediated isothermal amplification. Microbiol Immunol 2019; 63:407-412. [PMID: 31342547 PMCID: PMC7168367 DOI: 10.1111/1348-0421.12734] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 11/30/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) assays are used to detect diverse pathogens. Initially, LAMP amplicons were detected using electrophoresis; later, real-time monitoring based on turbidity was developed to overcome the problem of contamination with environmental DNA. Recently, real-time monitoring of fluorescence signals using a quenching primer and probe has improved the reliability of amplification signals. Here, methods of detecting LAMP amplicons are reviewed.
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Affiliation(s)
- Kazuya Shirato
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Disease, Musashimurayama, Tokyo, Japan
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9
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Respiratory infections due to nontuberculous mycobacterias. Med Clin (Barc) 2018; 150:191-197. [PMID: 28923675 DOI: 10.1016/j.medcli.2017.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 07/17/2017] [Indexed: 12/30/2022]
Abstract
The most common infections caused by nontuberculous mycobacteria (NTM) are lung infections. The microorganisms causing these infections most frequently are Mycobacterium avium complex, Mycobacterium kansasii and Mycobacterium abscessus complex. Their incidence has increased in the last three decades. After identifying an NTM in the respiratory tract, clinical and radiological aspects must be considered to determine if isolations are clinically relevant. Predisposing conditions that could contribute to infection must also be investigated. Pulmonary disease due to NTM is presented in three clinical forms: a) pneumonitis due to hypersensitivity; b) fibrocavitary form; and c) nodular-bronchiectasic. The diagnosis of respiratory disease due to NTM does not make it obligatory to immediately initiate treatment. Before initiating the latter, other factors must be considered, such as age, comorbidities, life expectancy, due to the prolonged nature of treatments, with potential side effects and, in many cases, only a slight response to the treatment.
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10
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A single tube system for the detection of Mycobacterium tuberculosis DNA using gold nanoparticles based FRET assay. J Microbiol Methods 2017; 139:165-167. [DOI: 10.1016/j.mimet.2017.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/30/2017] [Accepted: 06/01/2017] [Indexed: 11/24/2022]
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11
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González-García A, Fortún J, Elorza Navas E, Martín-Dávila P, Tato M, Gómez-Mampaso E, Moreno S. The changing epidemiology of tuberculosis in a Spanish tertiary hospital (1995-2013). Medicine (Baltimore) 2017; 96:e7219. [PMID: 28658113 PMCID: PMC5500035 DOI: 10.1097/md.0000000000007219] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Important epidemiological changes and improvement of new diagnostic approaches, mainly molecular tools, might have impacted the management and outcome of tuberculosis (TB) in the last years in industrialized countries. In order to describe the epidemiological trends, and changes in clinical, diagnostic, and therapeutic aspects in patients with TB, an observational study was performed in a tertiary hospital in Western Europe (Madrid, Spain).All adult patients (>16 years) with a diagnosis of TB in the period 1995 to 2013 were included in the study.TB was diagnosed in 1284 patients, including 304 (24%) foreign-born and 298 (23.2%) human immunodeficiency virus (HIV)-infected patients. The proportion of foreign-born patients increased significantly, from 7.4% (1995) to 40.3% (2013), P < .001, while the proportion of patients with HIV infection decreased (from 41% to 15%, P < .001). Extrapulmonary locations of TB increased (from 23.9% to 37.1%, P < .001), although the miliary forms were less frequent (from 16% to 5.6%, P < .001). Pulmonary involvement remained constant during the period of study (from 50% to 46%, P = .18). The yield of microbiological diagnostic methods in different clinical specimens has remained very similar. Only molecular techniques have improved the diagnosis in respiratory, urinary, and peritoneal samples. The global cure rate was 64.8% and mortality rate was 9.1% (6.5% directly attributable to TB). Mortality has decreased significantly during the years of study (from 11% to 2%, P < .001).There has been a significant decline in the number of patients with TB. Changes in HIV coinfection and immigration have conditioned other epidemiological and clinical aspects of the disease, including the clinical presentation, treatment response, and mortality. Only the use of molecular tests has provided an improvement in the diagnosis of pulmonary and extrapulmonary TB.
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Affiliation(s)
| | | | | | | | - Marta Tato
- Department of Microbiology, University Hospital Ramón y Cajal, University of Alcalá, IRYCIS, Madrid, Spain
| | - Enrique Gómez-Mampaso
- Department of Microbiology, University Hospital Ramón y Cajal, University of Alcalá, IRYCIS, Madrid, Spain
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12
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Detection of embB Gene Mutations in EMB-Resistant Mycobacterium tuberculosis Isolates From Isfahan Province by PCR-SSCP and Direct Sequencing. Jundishapur J Microbiol 2016. [DOI: 10.5812/jjm.39594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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13
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Rajaram S, Gupta P, Gupta B, Kaur IR, Goel N. Laparoscopy in the diagnosis of tuberculosis in chronic pelvic pain. Int J Mycobacteriol 2016; 5:318-323. [DOI: 10.1016/j.ijmyco.2016.06.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 10/21/2022] Open
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14
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Guenaoui K, Harir N, Ouardi A, Zeggai S, Sellam F, Bekri F, Cherif Touil S. Use of GeneXpert Mycobacterium tuberculosis/rifampicin for rapid detection of rifampicin resistant Mycobacterium tuberculosis strains of clinically suspected multi-drug resistance tuberculosis cases. ANNALS OF TRANSLATIONAL MEDICINE 2016; 4:168. [PMID: 27275481 DOI: 10.21037/atm.2016.05.09] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Multi-drug resistance (MDR) TB is defined as tuberculosis (TB) disease caused by a strain of Mycobacterium tuberculosis (MTB) that was resistant to at least isoniazid and rifampicin (RIF). Emerging Multidrug-Resistant TB is one of the major concerns of health policy and rapid detection of M. tuberculosis and detection of RIF resistance in infected patients are essential for disease management. The aim of this study was to evaluate patterns of RIF resistance in cases of sputum positive pulmonary TB by using GeneXpert MTB/RIF and comparing between phenotypic and genotypic testing of RIF resistance in MTB strains of clinically suspected MDR-TB isolated cases in western Algeria. METHODS In this study 50 sputum positive cases of pulmonary TB who were potential MDR suspect were included. Their sputum samples were collected and subjected to sputum smear microscopy, culture and conventional MTB/RIF test followed by GeneXpert MTB/RIF assay. RESULTS Of total 50 cases included in this study, MTB was detected in all patients (100%) by GeneXpert MTB/RIF. However, RIF's resistance was detected in only 21 cases (42%) by GeneXpert MTB/RIF. All RIF resistant strains detected by GeneXpert MTB/RIF were phenotypically confirmed as MDR strains. 42.85% of cases were retreatment failure cases, retreatment cases smear positive at 4 months were 23.82%. While 19.05% of cases were retreatment cases smear positive at diagnosis, and 14.28% patient had history of contact with MDR-TB. Sensitivity, specificity, positive predictive value and negative predictive value of Xpert MTB/RIF to detect RIF resistance in comparison to conventional phenotypic drug susceptibility technique were found equal to the rates of 100%, 100%, 100% and 100%, respectively. CONCLUSIONS GeneXpert MTB/RIF assay is efficient and reliable technique for the rapid diagnostic of TB. It's simplicity, high sensitivity and specificity for RIF resistance detection make this technique a very attractive tool for diagnostic of MTB and RIF resistance in MDR cases.
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Affiliation(s)
- Kheira Guenaoui
- 1 Laboratoty of molecular microbiology, proteomics and Health, Department of Biology, Djillali Liabes University of Sidi bel Abbes, Sidi Bel Abbès, Algeria ; 2 Department of Pneumophtisiology (point B), CHU Oran, Oran, Algeria ; 3 Department of Biological Hematology, Tenon Hospital, Paris, France
| | - Noria Harir
- 1 Laboratoty of molecular microbiology, proteomics and Health, Department of Biology, Djillali Liabes University of Sidi bel Abbes, Sidi Bel Abbès, Algeria ; 2 Department of Pneumophtisiology (point B), CHU Oran, Oran, Algeria ; 3 Department of Biological Hematology, Tenon Hospital, Paris, France
| | - Aissa Ouardi
- 1 Laboratoty of molecular microbiology, proteomics and Health, Department of Biology, Djillali Liabes University of Sidi bel Abbes, Sidi Bel Abbès, Algeria ; 2 Department of Pneumophtisiology (point B), CHU Oran, Oran, Algeria ; 3 Department of Biological Hematology, Tenon Hospital, Paris, France
| | - Soumia Zeggai
- 1 Laboratoty of molecular microbiology, proteomics and Health, Department of Biology, Djillali Liabes University of Sidi bel Abbes, Sidi Bel Abbès, Algeria ; 2 Department of Pneumophtisiology (point B), CHU Oran, Oran, Algeria ; 3 Department of Biological Hematology, Tenon Hospital, Paris, France
| | - Feriel Sellam
- 1 Laboratoty of molecular microbiology, proteomics and Health, Department of Biology, Djillali Liabes University of Sidi bel Abbes, Sidi Bel Abbès, Algeria ; 2 Department of Pneumophtisiology (point B), CHU Oran, Oran, Algeria ; 3 Department of Biological Hematology, Tenon Hospital, Paris, France
| | - Farid Bekri
- 1 Laboratoty of molecular microbiology, proteomics and Health, Department of Biology, Djillali Liabes University of Sidi bel Abbes, Sidi Bel Abbès, Algeria ; 2 Department of Pneumophtisiology (point B), CHU Oran, Oran, Algeria ; 3 Department of Biological Hematology, Tenon Hospital, Paris, France
| | - Sakina Cherif Touil
- 1 Laboratoty of molecular microbiology, proteomics and Health, Department of Biology, Djillali Liabes University of Sidi bel Abbes, Sidi Bel Abbès, Algeria ; 2 Department of Pneumophtisiology (point B), CHU Oran, Oran, Algeria ; 3 Department of Biological Hematology, Tenon Hospital, Paris, France
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15
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Omar SV, Peters RPH, Ismail NA, Jonkman K, Dreyer AW, Said HM, Gwala T, Ismail N, Fourie PB. Field evaluation of a novel preservation medium to transport sputum specimens for molecular detection of Mycobacterium tuberculosis in a rural African setting. Trop Med Int Health 2016; 21:776-82. [PMID: 27098085 DOI: 10.1111/tmi.12701] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES To assess the performance of an innovative method of transporting sputum to centralised facilities for molecular detection of Mycobacterium tuberculosis: using a swab to inoculate sputum in a transport medium, PrimeStore(®) Molecular Transport Medium (PS-MTM). METHODS Two sputum specimens were obtained from suspected patients with tuberculosis (TB) at rural healthcare facilities in South Africa. A swab was taken from each specimen and placed into PS-MTM, prior to it being processed by either liquid culture or Xpert MTB/RIF assay (Xpert). RESULTS A total of 141 patients (including 47 with laboratory-confirmed TB) were included in this analysis. M. tuberculosis was detected at 29% by culture and 29% by Xpert, whereas 31% tested positive by IS6110 real-time PCR of PS-MTM from the culture and 36% from the Xpert-paired specimen. Concordance between the method under evaluation with culture was 82% (McNemar, P = 0.55) and 84% (McNemar, P = 0.05) for Xpert. Stratified by culture result, the detection rate by IS6110 real-time PCR of PS-MTM was similar to Xpert for patients with positive culture (P = 0.32), but significantly higher if culture was negative (P = 0.008). CONCLUSIONS These results suggest that swab collection of sputum into PS-MTM for transport is a promising method for diagnosis of TB in rural healthcare settings, thereby potentially improving the options available for molecular diagnosis of TB in countries incapable of applying decentralised high-tech molecular testing.
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Affiliation(s)
- Shaheed V Omar
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.,Centre for Tuberculosis, National TB Reference Laboratory, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Remco P H Peters
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.,Anova Health Institute, Johannesburg, South Africa
| | - Nazir A Ismail
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.,Centre for Tuberculosis, National TB Reference Laboratory, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | | | - Andries W Dreyer
- Centre for Tuberculosis, National TB Reference Laboratory, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Halima M Said
- Centre for Tuberculosis, National TB Reference Laboratory, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Thabisile Gwala
- Centre for Tuberculosis, National TB Reference Laboratory, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Nabila Ismail
- Centre for Tuberculosis, National TB Reference Laboratory, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - P Bernard Fourie
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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16
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Nasr Esfahani B, Zarkesh Esfahani FS, Bahador N, Moghim S, Radaei T, Rezaei Yazdi H, Ghasemian Safaei H, Fazeli H. Analysis of DNA gyrA Gene Mutation in Clinical and Environmental Ciprofloxacin-Resistant Isolates of Non-Tuberculous Mycobacteria Using Molecular Methods. Jundishapur J Microbiol 2016; 9:e30018. [PMID: 27217921 PMCID: PMC4870840 DOI: 10.5812/jjm.30018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 10/20/2015] [Accepted: 12/22/2015] [Indexed: 12/20/2022] Open
Abstract
Background During the past several years, nontuberculous mycobacteria (NTM) have been reported as some of the most important agents of infection in immunocompromised patients. Objectives The aim of this study was to evaluate the ciprofloxacin susceptibility of clinical and environmental NTM species isolated from Isfahan province, Iran, using the agar dilution method, and to perform an analysis of gyrA gene-related ciprofloxacin resistance. Materials and Methods A total of 41 clinical and environmental isolates of NTM were identified by conventional and multiplex PCR techniques. The isolates were separated out of water, blood, abscess, and bronchial samples. The susceptibility of the isolates to 1 µg/mL, 2 µg/mL and 4 µg/mL of ciprofloxacin concentrations was determined by the agar dilution method according to CLSI guidelines. A 120-bp area of the gyrA gene was amplified, and PCR-SSCP templates were defined using polyacrylamide gel electrophoresis. The 120-bp of gyrA amplicons with different PCR-SSCP patterns were sequenced. Results The frequency of the identified isolates was as follows: Mycobacterium fortuitum, 27 cases; M. gordonae, 10 cases; M. smegmatis, one case; M. conceptionense, one case; and M. abscessus, two cases. All isolates except for M. abscessus were sensitive to all three concentrations of ciprofloxacin. The PCR-SSCP pattern of the gyrA gene of resistant M. abscessus isolates showed four different bands. The gyrA sequencing of resistant M. abscessus isolates showed 12 alterations in nucleotides compared to the M. abscessus ATCC 19977 resistant strain; however, the amino acid sequences were similar. Conclusions This study demonstrated the specificity and sensitivity of the PCR-SSCP method for finding mutations in the gyrA gene. Due to the sensitivity of most isolates to ciprofloxacin, this antibiotic should be considered an appropriate drug for the treatment of related diseases.
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Affiliation(s)
- Bahram Nasr Esfahani
- Department of Microbiology, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Fatemeh Sadat Zarkesh Esfahani
- Department of Microbiology, Science and Research Branch, Islamic Azad University, Fars, IR Iran
- Corresponding author: Fatemeh Sadat Zarkesh Esfahani, Department of Microbiology, Science and Research Branch, Islamic Azad University, Fars, IR Iran. Tel: +98-9133007218, Fax: +98-3133932376, E-mail:
| | - Nima Bahador
- Department of Microbiology, Science and Research Branch, Islamic Azad University, Fars, IR Iran
| | - Sharareh Moghim
- Department of Microbiology, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Tooba Radaei
- Department of Microbiology, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Hadi Rezaei Yazdi
- Department of Microbiology, Jahrom University of Medical Sciences, Jahrom, IR Iran
| | | | - Hossein Fazeli
- Department of Microbiology, Isfahan University of Medical Sciences, Isfahan, IR Iran
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17
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Sharma JB. Current Diagnosis and Management of Female Genital Tuberculosis. J Obstet Gynaecol India 2015; 65:362-71. [PMID: 26663993 PMCID: PMC4666212 DOI: 10.1007/s13224-015-0780-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 08/25/2015] [Indexed: 01/09/2023] Open
Abstract
Female genital tuberculosis (FGTB) is an important cause of significant morbidity, short- and long-term sequelae especially infertility whose incidence varies from 3 to 16 % cases in India. Mycobacterium tuberculosis is the etiological agent for tuberculosis. The fallopian tubes are involved in 90-100 % cases, endometrium is involved in 50-80 % cases, ovaries are involved in 20-30 % cases, and cervix is involved in 5-15 % cases of genital TB. Tuberculosis of vagina and vulva is rare (1-2 %). The diagnosis is made by detection of acid-fast bacilli on microscopy or culture on endometrial biopsy or on histopathological detection of epithelioid granuloma on biopsy. Polymerase chain reaction may be false positive and alone is not sufficient to make the diagnosis. Laparoscopy and hysteroscopy can diagnose genital tuberculosis by various findings. Treatment is by giving daily therapy of rifampicin (R), isoniazid (H), pyrazinamide (Z) and ethambutol (E) for 2 months followed by daily 4 month therapy of rifampicin (R) and isoniazid (H). Alternatively 2 months intensive phase of RHZE can be daily followed by alternate day combination phase (RH) of 4 months. Three weekly dosing throughout therapy (RHZE thrice weekly for 2 months followed by RH thrice weekly for 4 months) can be given as directly observed treatment short-course. Surgery is rarely required only as drainage of abscesses. There is a role of in vitro fertilization and embryo transfer in women whose fallopian tubes are damaged but endometrium is healthy. Surrogacy or adoption is needed for women whose endometrium is also damaged.
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Affiliation(s)
- Jai B. Sharma
- Department of Obstetrics and Gynaecology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029 India
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18
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Hadifar S, Moghim S, Fazeli H, GhasemianSafaei H, Havaei SA, Farid F, Esfahani BN. Molecular typing of Iranian mycobacteria isolates by polymerase chain reaction-restriction fragment length polymorphism analysis of 360-bp rpoB gene. Adv Biomed Res 2015; 4:152. [PMID: 26380237 PMCID: PMC4550954 DOI: 10.4103/2277-9175.161579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 02/15/2015] [Indexed: 11/30/2022] Open
Abstract
Background: Diagnosis and typing of Mycobacterium genus provides basic tools for investigating the epidemiology and pathogenesis of this group of bacteria. Polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) is an accurate method providing diagnosis and typing of species of mycobacteria. The present study is conducted by the purpose of determining restriction fragment profiles of common types of mycobacteria by PRA method of rpoB gene in this geographical region. Materials and Methods: Totally 60 clinical and environmental isolates from February to October, 2013 were collected and subcultured and identified by phenotypic methods. A 360 bp fragment of the rpoB gene amplified by PCR and products were digested by MspI and HaeIII enzymes. Results: In the present study, of all mycobacteria isolates identified by PRA method, 13 isolates (21.66%) were Mycobacterium tuberculosis, 34 isolates (56.66%) were rapidly growing Nontuberculosis Mycobacteria (NTM) that including 26 clinical isolates (43.33%) and 8 environmental isolates (13.33%), 11 isolates (18.33%) were clinical slowly growing NTM. among the clinical NTM isolates, Mycobacterium fortuitum Type I with the frequency of 57.77% was the most prevalent type isolates. Furthermore, an unrecorded of the PRA pattern of Mycobacterium conceptionense (HeaIII: 120/90/80, MspI: 120/105/80) was found. This study demonstrated that the PRA method was high discriminatory power for identification and typing of mycobacteria species and was able to identify 96.6% of all isolates. Conclusion: Based on the result of this study, rpoB gene could be a potentially useful tool for identification and investigation of molecular epidemiology of mycobacterial species.
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Affiliation(s)
- Shima Hadifar
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Sharareh Moghim
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Hossein Fazeli
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Hajieh GhasemianSafaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Seyed Asghar Havaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Fariba Farid
- Department of Health, Isfahan Provincial Health Office, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Bahram Nasr Esfahani
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
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19
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Agrawal V, Kaul A, Prasad N, Sharma K, Agarwal V. Etiological diagnosis of granulomatous tubulointerstitial nephritis in the tropics. Clin Kidney J 2015; 8:524-30. [PMID: 26413276 PMCID: PMC4581389 DOI: 10.1093/ckj/sfv071] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/17/2015] [Indexed: 12/24/2022] Open
Abstract
Background Granulomatous tubulointerstitial nephritis (GIN) is common due to infections, drugs or sarcoidosis. However, the cause is often difficult to establish and the studies are limited. We studied the etiology of GIN and compared the clinical and histological features and outcome in different etiologies at a tertiary care center in North India. Methods Renaö biopsies from GIN cases diagnosed from January 2004 to April 2014 were retrieved. Stain for acid fast bacilli was performed in all biopsies. Etiological diagnosis was based on clinical features, extra-renal manifestations, radiology, history of drug intake and demonstration of infective agent. Tissue PCR for tubercular DNA was performed in seven biopsies. Results Seventeen GIN patients [mean age 35 ± 15 years; males 11] were identified. Tuberculosis was the commonest etiology followed by idiopathic, sarcoidosis and fungal. Both tuberculosis and sarcoidosis patients presented with subnephrotic proteinuria and raised serum creatinine. Acid fast bacilli were demonstrated in 1/9 and necrosis was demonstrated in 3/9 granulomas in tuberculosis. Tissue PCR for tubercular DNA was positive in six TB patients and negative in one sarcoidosis patient. Patients responded well to appropriate therapy. Conclusion Etiological diagnosis of GIN is essential for timely and appropriate therapy. Tuberculosis is the commonest etiology (53%) in the tropics. Necrosis in granuloma, demonstration of acid fast bacilli, blood interferon gamma release assay and urine culture is not sensitive for the diagnosis of tuberculosis in GIN. Our findings suggest that tissue PCR for tuberculosis performed in an appropriate clinical setting is useful in the diagnostic evaluation of GIN.
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Affiliation(s)
- Vinita Agrawal
- Department of Pathology , Sanjay Gandhi Post Graduate Institute of Medical Sciences , Lucknow, Uttar Pradesh , India
| | - Anupama Kaul
- Department of Nephrology , Sanjay Gandhi Postgraduate Institute of Medical Sciences , Lucknow, Uttar Pradesh , India
| | - Narayan Prasad
- Department of Nephrology , Sanjay Gandhi Postgraduate Institute of Medical Sciences , Lucknow, Uttar Pradesh , India
| | - Kusum Sharma
- Department of Medical Microbiology , Post Graduate Institute of Medical Education and Research , Chandigarh , India
| | - Vikas Agarwal
- Department of Clinical Immunology , Sanjay Gandhi Postgraduate Institute of Medical Sciences , Lucknow, Uttar Pradesh , India
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20
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Neonakis IK, Spandidos DA, Gitti Z. Mycobacterium heraklionense sp. nov.: A case series. Exp Ther Med 2015; 10:1401-1403. [PMID: 26622497 PMCID: PMC4578118 DOI: 10.3892/etm.2015.2683] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/14/2015] [Indexed: 11/07/2022] Open
Abstract
Mycobacterium heraklionense sp. nov. (M. heraklionense) is a novel non-tuberculous mycobacterium belonging to the Mycobacterium terrae complex that has recently been described. It has a world-wide distribution. Recently, a case of tenosynovitis in an immunocompetent individual caused by M. heraklionense was reported, indicating that it has the ability to cause diseases. In the present study, in order to provide a more detailed profile of this mycobacterium and to obtain a more complete overall picture of its clinical significance, we report all available data regarding the initial 12 cases of its isolation. Of the 12 patients, 5 (42%) eventually died within a period of 3 months following the isolation of the mycobacterium. However, any connection between the presence of M. heraklionense and these deaths could not be documented. These 5 patients were all males with a mean age of 74.6 years suffering from serious underlying diseases, which most probably were the cause of death. Additional data from possible new cases of M. heraklionense isolation are anticipated.
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Affiliation(s)
- Ioannis K Neonakis
- Department of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, University Hospital of Heraklion, Heraklion, Crete, Greece
| | - Demetrios A Spandidos
- Department of Laboratory Medicine, School of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Zoe Gitti
- Department of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, University Hospital of Heraklion, Heraklion, Crete, Greece
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21
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Miller S, Karaoz U, Brodie E, Dunbar S. Solid and Suspension Microarrays for Microbial Diagnostics. METHODS IN MICROBIOLOGY 2015; 42:395-431. [PMID: 38620236 PMCID: PMC7172482 DOI: 10.1016/bs.mim.2015.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Advancements in molecular technologies have provided new platforms that are being increasingly adopted for use in the clinical microbiology laboratory. Among these, microarray methods are particularly well suited for diagnostics as they allow multiplexing, or the ability to test for multiple targets simultaneously from the same specimen. Microarray technologies commonly used for the detection and identification of microbial targets include solid-state microarrays, electronic microarrays and bead suspension microarrays. Microarray methods have been applied to microbial detection, genotyping and antimicrobial resistance gene detection. Microarrays can offer a panel approach to diagnose specific patient presentations, such as respiratory or gastrointestinal infections, and can discriminate isolates by genotype for tracking epidemiology and outbreak investigations. And, as more information has become available on specific genes and pathways involved in antimicrobial resistance, we are beginning to be able to predict susceptibility patterns based on sequence detection for particular organisms. With further advances in automated microarray processing methods and genotype-phenotype prediction algorithms, these tests will become even more useful as an adjunct or replacement for conventional antimicrobial susceptibility testing, allowing for more rapid selection of targeted therapy for infectious diseases.
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Affiliation(s)
- Steve Miller
- Clinical Microbiology Laboratory, University of California, San Francisco, California, USA
| | - Ulas Karaoz
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Eoin Brodie
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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22
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Colman RE, Schupp JM, Hicks ND, Smith DE, Buchhagen JL, Valafar F, Crudu V, Romancenco E, Noroc E, Jackson L, Catanzaro DG, Rodwell TC, Catanzaro A, Keim P, Engelthaler DM. Detection of Low-Level Mixed-Population Drug Resistance in Mycobacterium tuberculosis Using High Fidelity Amplicon Sequencing. PLoS One 2015; 10:e0126626. [PMID: 25970423 PMCID: PMC4430321 DOI: 10.1371/journal.pone.0126626] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 04/03/2015] [Indexed: 12/20/2022] Open
Abstract
Undetected and untreated, low-levels of drug resistant (DR) subpopulations in clinical Mycobacterium tuberculosis (Mtb) infections may lead to development of DR-tuberculosis, potentially resulting in treatment failure. Current phenotypic DR susceptibility testing has a theoretical potential for 1% sensitivity, is not quantitative, and requires several weeks to complete. The use of "single molecule-overlapping reads" (SMOR) analysis with next generation DNA sequencing for determination of ultra-rare target alleles in complex mixtures provides increased sensitivity over standard DNA sequencing. Ligation free amplicon sequencing with SMOR analysis enables the detection of resistant allele subpopulations at ≥0.1% of the total Mtb population in near real-time analysis. We describe the method using standardized mixtures of DNA from resistant and susceptible Mtb isolates and the assay's performance for detecting ultra-rare DR subpopulations in DNA extracted directly from clinical sputum samples. SMOR analysis enables rapid near real-time detection and tracking of previously undetectable DR sub-populations in clinical samples allowing for the evaluation of the clinical relevance of low-level DR subpopulations. This will provide insights into interventions aimed at suppressing minor DR subpopulations before they become clinically significant.
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MESH Headings
- Antitubercular Agents/pharmacology
- Antitubercular Agents/therapeutic use
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- Drug Resistance, Multiple, Bacterial/genetics
- Gene Frequency
- Genetic Loci
- High-Throughput Nucleotide Sequencing
- Humans
- Microbial Sensitivity Tests
- Molecular Diagnostic Techniques
- Mycobacterium tuberculosis/genetics
- Polymorphism, Single Nucleotide
- Sequence Analysis, DNA
- Sputum/microbiology
- Tuberculosis, Multidrug-Resistant/diagnosis
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/microbiology
- Tuberculosis, Pulmonary/diagnosis
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/microbiology
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Affiliation(s)
- Rebecca E. Colman
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - James M. Schupp
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - Nathan D. Hicks
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - David E. Smith
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - Jordan L. Buchhagen
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - Faramarz Valafar
- San Diego State University, San Diego, CA, United States of America
| | - Valeriu Crudu
- Phthisiopneumology Institute (PPI), Chisinau, Republic of Moldova
| | - Elena Romancenco
- University of California San Diego, San Diego, CA, United States of America
| | - Ecaterina Noroc
- Phthisiopneumology Institute (PPI), Chisinau, Republic of Moldova
| | - Lynn Jackson
- University of California San Diego, San Diego, CA, United States of America
| | - Donald G. Catanzaro
- University of Arkansas College of Education and Health Professions, Fayetteville, AR, United States of America
| | - Timothy C. Rodwell
- University of California San Diego, San Diego, CA, United States of America
| | - Antonino Catanzaro
- University of California San Diego, San Diego, CA, United States of America
| | - Paul Keim
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
- Center for Microbial Genetics & Genomics, Northern Arizona University, Flagstaff, AZ, United States of America
| | - David M. Engelthaler
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
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Seifert M, Catanzaro D, Catanzaro A, Rodwell TC. Genetic mutations associated with isoniazid resistance in Mycobacterium tuberculosis: a systematic review. PLoS One 2015; 10:e0119628. [PMID: 25799046 PMCID: PMC4370653 DOI: 10.1371/journal.pone.0119628] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 01/14/2015] [Indexed: 01/12/2023] Open
Abstract
Background Tuberculosis (TB) incidence and mortality are declining worldwide; however, poor detection of drug-resistant disease threatens to reverse current progress toward global TB control. Multiple, rapid molecular diagnostic tests have recently been developed to detect genetic mutations in Mycobacterium tuberculosis (Mtb) genes known to confer first-line drug resistance. Their utility, though, depends on the frequency and distribution of the resistance associated mutations in the pathogen population. Mutations associated with rifampicin resistance, one of the two first-line drugs, are well understood and appear to occur in a single gene region in >95% of phenotypically resistant isolates. Mutations associated with isoniazid, the other first-line drug, are more complex and occur in multiple Mtb genes. Objectives/Methodology A systematic review of all published studies from January 2000 through August 2013 was conducted to quantify the frequency of the most common mutations associated with isoniazid resistance, to describe the frequency at which these mutations co-occur, and to identify the regional differences in the distribution of these mutations. Mutation data from 118 publications were extracted and analyzed for 11,411 Mtb isolates from 49 countries. Principal Findings/Conclusions Globally, 64% of all observed phenotypic isoniazid resistance was associated with the katG315 mutation. The second most frequently observed mutation, inhA-15, was reported among 19% of phenotypically resistant isolates. These two mutations, katG315 and inhA-15, combined with ten of the most commonly occurring mutations in the inhA promoter and the ahpC-oxyR intergenic region explain 84% of global phenotypic isoniazid resistance. Regional variation in the frequency of individual mutations may limit the sensitivity of molecular diagnostic tests. Well-designed systematic surveys and whole genome sequencing are needed to identify mutation frequencies in geographic regions where rapid molecular tests are currently being deployed, providing a context for interpretation of test results and the opportunity for improving the next generation of diagnostics.
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Affiliation(s)
- Marva Seifert
- University of California San Diego, School of Medicine, La Jolla, California, United States of America
| | - Donald Catanzaro
- University of California San Diego, School of Medicine, La Jolla, California, United States of America
| | - Antonino Catanzaro
- University of California San Diego, School of Medicine, La Jolla, California, United States of America
| | - Timothy C. Rodwell
- University of California San Diego, School of Medicine, La Jolla, California, United States of America
- * E-mail:
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Rabiee-Faradonbeh M, Darban-Sarokhalil D, Feizabadi MM, Alvandi A, Momtaz H, Soleimani N, Gholipour A. Cloning of the Recombinant Cytochrome P450 Cyp141 Protein of Mycobacterium tuberculosis as a Diagnostic Target and Vaccine Candidate. IRANIAN RED CRESCENT MEDICAL JOURNAL 2014; 16:e18001. [PMID: 25763215 PMCID: PMC4329965 DOI: 10.5812/ircmj.18001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 04/08/2014] [Accepted: 04/23/2014] [Indexed: 11/18/2022]
Abstract
Background: Tuberculosis has been announced as a global emergency by World Health Organization and the second infectious agent of mortality worldwide. The general policy in the development of new vaccines is to develop some vaccines with higher efficiency not only for infants but also for adults compared with the Bacillus Calmette-Guerin vaccine. Recently, cytochrome P450 cyp141 has been introduced as a new target for detecting Mycobacterium tuberculosis from clinical samples. Objectives: The aim of this study was to clone this gene in order to pave the way for more evaluation. Materials and Methods: M. tuberculosis H37Rv DNA was extracted by a standard phenol-chlorophorm protocol. After designing the specific primers, P450 cyp141 gene was replicated by PCR. The purified PCR products were then subcloned into the pTZ57R/T plasmid vector. After extraction, enzyme digestion, and recombinant pTZ57R/T-cyp141 plasmid vector sequencing, the aforementioned products were cloned into a pET-26b plasmid vector. Then, the recombinant pET26b-cyp141 plasmid molecules were transformed to Escherichia coli strain BL21 (DE3) using the transformation method. Next, the recombinant pET26b-cyp141 plasmids were purified and evaluated by the enzyme digestion analysis. Results: The cloning of P450 cyp141 gene was confirmed by the enzyme digestion and sequencing of the recombinant pTZ57R/T-cyp141 and pET26b-cyp141 plasmid vectors. Conclusions: The results of this study demonstrated that the P450 cyp141 gene was successfully cloned into a pET26b plasmid vector as an expression vector. In this paper, for the first time in Iran, this gene was cloned for more purposes, including the expression and purification of the recombinant cytochrome P450 cyp141 protein.
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Affiliation(s)
- Mohammad Rabiee-Faradonbeh
- Department of Microbiology and Immunology, Faculty of Medicine, Cellular and Molecular Research Center, Shahrekord University of Medical Sciences, Shahrekord, IR Iran
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, Shahrekord,IR Iran
| | - Davood Darban-Sarokhalil
- Department of Microbiology and Immunology, Faculty of Medicine, Alborz University of Medical Sciences, Karaj, IR Iran
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Amirhooshang Alvandi
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, IR Iran
| | - Hasan Momtaz
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, Shahrekord,IR Iran
| | - Neda Soleimani
- Department of Pathology, Al-Zahra Hospital, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Abolfazl Gholipour
- Department of Microbiology and Immunology, Faculty of Medicine, Cellular and Molecular Research Center, Shahrekord University of Medical Sciences, Shahrekord, IR Iran
- Corresponding Author: Abolfazl Gholipour, Department of Microbiology and Immunology, Cellular and Molecular Research Center, Faculty of Medicine, Shahrekord University of Medical Sciences, Rahmatiyeh, Shahrekord, IR Iran. Tel: +98-3813346732, E-mail:
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Gerogianni I, Gravas S, Gourgoulianis K, Neonakis I, Petinaki E. Disseminated Bacillus Calmette-Guerin infections after intravesical therapy. Indian J Med Microbiol 2014; 32:438-9. [PMID: 25297033 DOI: 10.4103/0255-0857.142254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Intravesical instillation of Bacillus Calmette-Guerin (BCG) is the treatment of choice for superficial bladder carcinoma. Disseminated BCG infection presenting as granulomatous hepatitis or pneumonitis is a very rare complication of this treatment. Here we report a case series of seven patients previously treated with BCG presenting with pneumonitis. In two of the cases, identification of Mycobacterium bovis was achieved with molecular methods.
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Affiliation(s)
| | | | | | | | - E Petinaki
- Department of Microbiology, University Hospital of Larissa, Greece
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Comparison of cyp141 and IS6110 for detection of Mycobacterium tuberculosis from clinical specimens by PCR. J Infect Public Health 2014; 8:32-6. [PMID: 25304426 DOI: 10.1016/j.jiph.2014.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 04/23/2014] [Accepted: 08/24/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Tuberculosis is a major public health problem throughout the world. TB's worldwide patterns of prevalence coupled with the increase in incidence of HIV infection threaten the health and lives of humans worldwide. Rapid detection of TB and the rapidly initiation of the administration of medication are important strategies for stopping the transmission of this disease transmission and its resistance to anti-TB drugs. Molecular methods are advantageous relative to conventional techniques due to their greater speed and sensitivity in the detection of TB. METHODS In this study, we targeted the cyp141 gene for the detection of Mycobacterium tuberculosis from clinical specimens (n=123) by PCR and compared the sensitivity and specificity of this new target with those of IS6110 gene. RESULTS Targeting of the cyp141 gene is more sensitive (97.1% for cultured isolates and 85.7% for direct specimens) than the targeting of the commonly used IS6110 gene (95.1% for cultured isolates and 42.9% for direct specimens), and the specificities of these two target genes were equal (100%). CONCLUSIONS The cyp141 gene can be used as a new target for the direct detection of Mycobacterium tuberculosis that seems to be superior to IS6110.
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Song SH, Han M, Choi YS, Dan KS, Yang MG, Song J, Park SS, Lee JH. Proteomic profiling of serum from patients with tuberculosis. Ann Lab Med 2014; 34:345-53. [PMID: 25187886 PMCID: PMC4151002 DOI: 10.3343/alm.2014.34.5.345] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 12/31/2013] [Accepted: 05/29/2014] [Indexed: 11/19/2022] Open
Abstract
Background Effective treatment and monitoring of tuberculosis (TB) requires biomarkers that can be easily evaluated in blood samples. The aim of this study was to analyze the serum proteome of patients with TB and to identify protein biomarkers for TB. Methods Serum samples from 26 TB patients and 31 controls were analyzed by using nano-flow ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry in data-independent mode, and protein and peptide amounts were calculated by using a label-free quantitative approach. The generated data were analyzed by using principal component analysis and partial least squares discriminant analysis, a multivariate statistical method. Results Of more than 500 proteins identified, alpha-1-antitrypsin was the most discriminative, which was 4.4 times higher in TB patients than in controls. Peptides from alpha-1-antitrypsin and antithrombin III increased in TB patients and showed a high variable importance in the projection scores and coefficient in partial least square discriminant analysis. Conclusions Sera from patients with TB had higher alpha-1-antitrypsin levels than sera from control participants. Alpha-1-antitrypsin levels may aid in the diagnosis of TB.
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Affiliation(s)
- Sang Hoon Song
- Clinical Proteomics Laboratory, Seoul National University Hospital, Seoul, Korea. ; Biomedical Research Institute and Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Minje Han
- Clinical Proteomics Laboratory, Seoul National University Hospital, Seoul, Korea. ; Biomedical Research Institute and Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Yang Seon Choi
- Clinical Proteomics Laboratory, Seoul National University Hospital, Seoul, Korea
| | - Ki Soon Dan
- Clinical Proteomics Laboratory, Seoul National University Hospital, Seoul, Korea
| | - Man Gil Yang
- Clinical Proteomics Laboratory, Seoul National University Hospital, Seoul, Korea
| | - Junghan Song
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Sung Sup Park
- Clinical Proteomics Laboratory, Seoul National University Hospital, Seoul, Korea. ; Biomedical Research Institute and Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jae Ho Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
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Wildner LM, Bazzo ML, Liedke SC, Nogueira CL, Segat G, Senna SG, Schlindwein AD, Oliveira JGD, Rovaris DB, Bonjardim CA, Kroon EG, Ferreira PCP. Mycobacteria mobility shift assay: a method for the rapid identification of Mycobacterium tuberculosis and nontuberculous mycobacteria. Mem Inst Oswaldo Cruz 2014; 109:356-61. [PMID: 24821059 PMCID: PMC4131790 DOI: 10.1590/0074-0276130458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 03/11/2014] [Indexed: 12/04/2022] Open
Abstract
The identification of mycobacteria is essential because tuberculosis (TB) and
mycobacteriosis are clinically indistinguishable and require different therapeutic
regimens. The traditional phenotypic method is time consuming and may last up to 60
days. Indeed, rapid, affordable, specific and easy-to-perform identification methods
are needed. We have previously described a polymerase chain reaction-based method
called a mycobacteria mobility shift assay (MMSA) that was designed for
Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria
(NTM) species identification. The aim of this study was to assess the MMSA for the
identification of MTC and NTM clinical isolates and to compare its performance with
that of the PRA-hsp65 method. A total of 204 clinical isolates (102
NTM and 102 MTC) were identified by the MMSA and PRA-hsp65. For
isolates for which these methods gave discordant results, definitive species
identification was obtained by sequencing fragments of the 16S rRNA and
hsp65 genes. Both methods correctly identified all MTC isolates. Among
the NTM isolates, the MMSA alone assigned 94 (92.2%) to a complex or species, whereas
the PRA-hsp65 method assigned 100% to a species. A 91.5% agreement
was observed for the 94 NTM isolates identified by both methods. The MMSA provided
correct identification for 96.8% of the NTM isolates compared with 94.7% for
PRA-hsp65. The MMSA is a suitable auxiliary method for routine
use for the rapid identification of mycobacteria.
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Affiliation(s)
- Letícia Muraro Wildner
- Laboratório de Biologia Molecular e Micobactérias, Universidade Federal de Santa Catarina, Florianópolis, SC, Brasil
| | - Maria Luiza Bazzo
- Laboratório de Biologia Molecular e Micobactérias, Universidade Federal de Santa Catarina, Florianópolis, SC, Brasil
| | - Susie Coutinho Liedke
- Laboratório de Biologia Molecular e Micobactérias, Universidade Federal de Santa Catarina, Florianópolis, SC, Brasil
| | - Christiane Lourenço Nogueira
- Laboratório de Biologia Molecular e Micobactérias, Universidade Federal de Santa Catarina, Florianópolis, SC, Brasil
| | - Gabriela Segat
- Laboratório de Biologia Molecular e Micobactérias, Universidade Federal de Santa Catarina, Florianópolis, SC, Brasil
| | - Simone Gonçalves Senna
- Laboratório de Biologia Molecular e Micobactérias, Universidade Federal de Santa Catarina, Florianópolis, SC, Brasil
| | | | | | - Darcita B Rovaris
- Laboratório Central, Estado de Santa Catarina, Florianópolis, SC, Brasil
| | - Claudio A Bonjardim
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Erna G Kroon
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Paulo C P Ferreira
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
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Lima AS, Duarte RS, Montenegro LML, Schindler HC. Rapid detection and differentiation of mycobacterial species using a multiplex PCR system. Rev Soc Bras Med Trop 2014; 46:447-52. [PMID: 23982098 DOI: 10.1590/0037-8682-0097-2013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/22/2013] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION The early diagnosis of mycobacterial infections is a critical step for initiating treatment and curing the patient. Molecular analytical methods have led to considerable improvements in the speed and accuracy of mycobacteria detection. METHODS The purpose of this study was to evaluate a multiplex polymerase chain reaction system using mycobacterial strains as an auxiliary tool in the differential diagnosis of tuberculosis and diseases caused by nontuberculous mycobacteria (NTM) RESULTS: Forty mycobacterial strains isolated from pulmonary and extrapulmonary origin specimens from 37 patients diagnosed with tuberculosis were processed. Using phenotypic and biochemical characteristics of the 40 mycobacteria isolated in LJ medium, 57.5% (n=23) were characterized as the Mycobacterium tuberculosis complex (MTBC) and 20% (n=8) as nontuberculous mycobacteria (NTM), with 22.5% (n=9) of the results being inconclusive. When the results of the phenotypic and biochemical tests in 30 strains of mycobacteria were compared with the results of the multiplex PCR, there was 100% concordance in the identification of the MTBC and NTM species, respectively. A total of 32.5% (n=13) of the samples in multiplex PCR exhibited a molecular pattern consistent with NTM, thus disagreeing with the final diagnosis from the attending physician. CONCLUSIONS Multiplex PCR can be used as a differential method for determining TB infections caused by NTM a valuable tool in reducing the time necessary to make clinical diagnoses and begin treatment. It is also useful for identifying species that were previously not identifiable using conventional biochemical and phenotypic techniques.
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Affiliation(s)
- Andrea Santos Lima
- Departamento de Imunologia, Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Recife,
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Assessment of the BD MGIT TBc identification test for the detection of Mycobacterium tuberculosis complex in a network of mycobacteriology laboratories. BIOMED RESEARCH INTERNATIONAL 2014; 2014:398108. [PMID: 24587985 PMCID: PMC3920968 DOI: 10.1155/2014/398108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 11/18/2013] [Indexed: 11/23/2022]
Abstract
We evaluate the performance of the TBcID assay in a panel of 100 acid-fast bacilli cultures. Sixty-four isolates were TBcID positive for Mycobacterium tuberculosis complex (MTBC), whereas 36 gave negative results. These included 28 nontuberculous mycobacteria, one nonmycobacterial isolate, one M. tuberculosis, and six M. bovis BCG strains. This corresponds to a sensitivity of 90.14%, specificity of 100%, and positive and negative predictive values of 100% and 80.55%, respectively. The test is rapid, easy to perform and interpret, and does not require sample preparation or instrumentation. However, a negative result does not exclude the presence of a strain belonging to MTBC, especially when mutations in mpb64 gene are present or some M. bovis BCG strains are isolated. The TBcID showed potential to assist in the identification of MTBC when the implementation and usage of molecular methods are often not possible, principally in resource-limited countries.
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Zakham F, Chaoui I, Echchaoui AH, Chetioui F, Elmessaoudi MD, Ennaji MM, Abid M, Mzibri ME. Direct sequencing for rapid detection of multidrug resistant Mycobacterium tuberculosis strains in Morocco. Infect Drug Resist 2013; 6:207-13. [PMID: 24399879 PMCID: PMC3875366 DOI: 10.2147/idr.s47724] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is a major public health problem with high mortality and morbidity rates, especially in low-income countries. Disturbingly, the emergence of multidrug resistant (MDR) and extensively drug resistant (XDR) TB cases has worsened the situation, raising concerns of a future epidemic of virtually untreatable TB. Indeed, the rapid diagnosis of MDR TB is a critical issue for TB management. This study is an attempt to establish a rapid diagnosis of MDR TB by sequencing the target fragments of the rpoB gene which linked to resistance against rifampicin and the katG gene and inhA promoter region, which are associated with resistance to isoniazid. METHODS For this purpose, 133 sputum samples of TB patients from Morocco were enrolled in this study. One hundred samples were collected from new cases, and the remaining 33 were from previously treated patients (drug relapse or failure, chronic cases) and did not respond to anti-TB drugs after a sufficient duration of treatment. All samples were subjected to rpoB, katG and pinhA mutation analysis by polymerase chain reaction and DNA sequencing. RESULTS Molecular analysis showed that seven strains were isoniazid-monoresistant and 17 were rifampicin-monoresistant. MDR TB strains were identified in nine cases (6.8%). Among them, eight were traditionally diagnosed as critical cases, comprising four chronic and four drug-relapse cases. The last strain was isolated from a new case. The most recorded mutation in the rpoB gene was the substitution TCG > TTG at codon 531 (Ser531 Leu), accounting for 46.15%. Significantly, the only mutation found in the katG gene was at codon 315 (AGC to ACC) with a Ser315Thr amino acid change. Only one sample harbored mutation in the inhA promoter region and was a point mutation at the -15p position (C > T). CONCLUSION The polymerase chain reaction sequencing approach is an accurate and rapid method for detection of drug-resistant TB in clinical specimens, and could be of great interest in the management of TB in critical cases to adjust the treatment regimen and limit the emergence of MDR and XDR strains.
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Affiliation(s)
- Fathiah Zakham
- Unité de Biologie et Recherché Médicale, Centre National de l'Energie, des Sciences et des Techniques Nucléaires (CNESTEN), Rabat, Morocco ; Laboratoire de Microbiologie, Hygiène et Virologie, Faculté des Sciences et Techniques, Mohammedia, Morocco
| | - Imane Chaoui
- Unité de Biologie et Recherché Médicale, Centre National de l'Energie, des Sciences et des Techniques Nucléaires (CNESTEN), Rabat, Morocco
| | | | - Fouad Chetioui
- Laboratoire de Tuberculose Institut Pasteur, Casablanca, Morocco
| | | | - My Mustapha Ennaji
- Laboratoire de Microbiologie, Hygiène et Virologie, Faculté des Sciences et Techniques, Mohammedia, Morocco
| | - Mohammed Abid
- Laboratoire de Génétique Mycobacterienne, Institut Pasteur, Tangier, Morocco
| | - Mohammed El Mzibri
- Unité de Biologie et Recherché Médicale, Centre National de l'Energie, des Sciences et des Techniques Nucléaires (CNESTEN), Rabat, Morocco
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Evaluation of hsp65 nested PCR-restriction analysis (PRA) for diagnosing tuberculosis in a high burden country. BIOMED RESEARCH INTERNATIONAL 2013; 2013:391549. [PMID: 24260739 PMCID: PMC3821893 DOI: 10.1155/2013/391549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 09/08/2013] [Indexed: 11/17/2022]
Abstract
Current study evaluated the hsp65 Nested PCR Restriction Fragment Length Polymorphism Analysis (hsp65 Nested PCR-PRA) to detect and
identify Mycobacterium tuberculosis complex directly in clinical samples for a rapid and specific diagnosis of tuberculosis (TB). hsp65 Nested PCR-PRA was
applied directly to 218 clinical samples obtained from 127 patients suspected of TB or another mycobacterial infection from July 2009 to July 2010. The hsp65 Nested
PCR-PRA showed 100% sensitivity and 95.0 and 93.1% specificity in comparison with culture and microscopy (acid fast bacillus smear), respectively. hsp65 Nested
PCR-PRA was shown to be a fast and reliable assay for diagnosing TB, which may contribute towards a fast diagnosis that could help the selection of appropriate chemotherapeutic and early
epidemiological management of the cases which are of paramount importance in a high TB burden country.
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Kikuchi T, Kobashi Y, Hirano T, Tode N, Santoso A, Tamada T, Fujimura S, Mitsuhashi Y, Honda Y, Nukiwa T, Kaku M, Watanabe A, Ichinose M. Mycobacterium avium genotype is associated with the therapeutic response to lung infection. Clin Microbiol Infect 2013; 20:256-62. [PMID: 23829301 PMCID: PMC4231998 DOI: 10.1111/1469-0691.12285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/10/2013] [Accepted: 05/27/2013] [Indexed: 01/12/2023]
Abstract
Factors that can interfere with the successful treatment of Mycobacterium avium lung infection have been inadequately studied. To identify a potent predictor of therapeutic responses of M. avium lung infection, we analyzed variable number tandem repeats (VNTR) at 16 minisatellite loci of M. avium clinical isolates. Associations between the VNTR profiling data and a therapeutic response were evaluated in 59 subjects with M. avium lung infection. M. avium lung infection of 30 subjects in whom clarithromycin-containing regimens produced microbiological and radiographic improvement was defined as responsive disease, while that of the remaining 29 subjects was defined as refractory disease. In phylogenetic analysis using the genotypic distance aggregated from 16-dimensional VNTR data, 59 M. avium isolates were divided into three clusters, which showed a nearly significant association with therapeutic responses (p 0.06). We then subjected the raw 16-dimensional VNTR data directly to principal component analysis, and identified the genetic features that were significantly associated with the therapeutic response (p <0.05). By further analysis of logistic regression with a stepwise variable-selection, we constructed the highest likelihood multivariate model, adjusted for age, to predict a therapeutic response, using VNTR data from only four minisatellite loci. In conclusion, we identified four mycobacterial minisatellite loci that together were associated with the therapeutic response of M. avium lung infections.
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Affiliation(s)
- T Kikuchi
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Respiratory Medicine, Tohoku University Hospital, Sendai, Japan
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Han JI, Kang HM, Jang HJ, Noh S, Kang JH, Chang DW, Na KJ. What is your diagnosis? Lymph node aspirates from a dog with stillbirth. Vet Clin Pathol 2013; 42:391-2. [PMID: 23773033 DOI: 10.1111/vcp.12053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jae-Ik Han
- Laboratory of Veterinary Laboratory Medicine, College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea
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Weiss CH, Glassroth J. Pulmonary disease caused by nontuberculous mycobacteria. Expert Rev Respir Med 2013; 6:597-612; quiz 613. [PMID: 23234447 DOI: 10.1586/ers.12.58] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The propensity of various nontuberculous mycobacteria to cause lung disease varies widely and is conditioned by host factors; infection is believed to occur from environmental sources. Nontuberculous mycobacteria pulmonary disease (PNTM) is increasing worldwide and Mycobacterium avium complex is the most common cause. PNTM usually occurs in one of three prototypical forms: hypersensitivity pneumonitis, cavitary tuberculosis-like disease or nodular bronchiectasis. PNTM has been linked in some patients to genetic variants of the cystic fibrosis transmembrane conductance regulator gene and a distinct patient phenotype. Interactions between PNTM and other comorbidities are also increasingly appreciated. Guidelines for diagnosis, emphasizing chest imaging and microbiology, have been published; speciation using molecular techniques is critical for accuracy and for treatment decisions. Clinical trials are lacking to inform treatment for many species and experience with M. avium complex and several others species serves as a guide instead. Use of multiple drugs for a period of at least 12 months following sputum conversion is the norm for most species. In vitro drug susceptibility results for many drugs may not correlate with clinical outcomes and such testing should be done on a selective basis.
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Affiliation(s)
- Curtis H Weiss
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Hussain MM, Samir TM, Azzazy HM. Unmodified gold nanoparticles for direct and rapid detection of Mycobacterium tuberculosis complex. Clin Biochem 2013; 46:633-7. [DOI: 10.1016/j.clinbiochem.2012.12.020] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 12/20/2012] [Accepted: 12/24/2012] [Indexed: 11/25/2022]
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Polymerase Chain Reaction-Based Molecular Diagnosis of Cutaneous Infections in Dermatopathology. ACTA ACUST UNITED AC 2012; 31:241-6. [DOI: 10.1016/j.sder.2012.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 06/13/2012] [Indexed: 11/21/2022]
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Darban-Sarokhalil D, Imani Fooladi AA, Maleknejad P, Bameri Z, Aflaki M, Nomanpour B, Yaslianifard S, Modarresi MH, Feizabadi MM. Comparison of smear microscopy, culture, and real-time PCR for quantitative detection of Mycobacterium tuberculosis in clinical respiratory specimens. ACTA ACUST UNITED AC 2012; 45:250-5. [PMID: 23113553 DOI: 10.3109/00365548.2012.727465] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND As a rapid diagnostic technique, the real-time polymerase chain reaction (PCR) can detect Mycobacterium tuberculosis with a high sensitivity and specificity. However, further studies are needed to confirm it as a standard method. In this study, we evaluated the cyp141 gene for the detection and quantification of M. tuberculosis in respiratory specimens and compared the results with direct microscopy and culture. METHODS Sputum samples (n = 247) were collected from patients of the different provinces of Iran. DNA was extracted from clinical specimens and H37Rv strain. After measuring the standard strain DNA concentration by NanoDrop and using the Avogadro number, the DNA was diluted 6 times in order to obtain 1 × 10(6) to 10 template copies. A Taqman probe was designed for detection of the target in a real-time PCR using the specific primers. RESULTS Of 247 samples, 135 (55%) were culture-negative. Of 112 (45%) culture-positive samples, 88 were positive by both smear and culture and 24 were smear-negative but culture-positive. The real-time PCR enumerated 1.5E + 02 to 4.3E+ 03, 8.5E + 03 to 5.5E + 04, 7.2E + 04 to 1.1E + 06, and 1.2E + 06 to 8.1E + 07 M. tuberculosis cells in the specimens with smear-negative, 1-plus, 2-plus, and 3-plus codes, respectively. The overall sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the real-time PCR were 90.2% (101/112), 97.8% (132/135), 97.1%, and 92.3%, respectively. CONCLUSIONS The overall sensitivity and specificity, the results in comparison with those of the Xpert MTB/RIF kit, and the good correlation with molecular and phenotypic methods, show that cyp141 could be a good target for the quantification of M. tuberculosis in sputum and possibly other clinical specimens.
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Affiliation(s)
- Davood Darban-Sarokhalil
- Department of Pathobiology, School of Medicine, Alborz university of Medical Sciences, Karaj, Iran
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da Silva RM, Machado T, Bazzo ML. Diagnosis of the pulmonary tuberculosis by polymerase chain reaction: a comparative study between HIV-positive and -negative individuals. Braz J Microbiol 2012; 43:261-5. [PMID: 24031827 PMCID: PMC3768986 DOI: 10.1590/s1517-838220120001000030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2010] [Revised: 01/16/2012] [Indexed: 11/24/2022] Open
Abstract
This study was performed to assess the efficiency of polymerase chain reaction (PCR) directly from sputum for the diagnosis of pulmonary tuberculosis by comparison between HIV-positive and HIV-negative individuals. Sputum samples were collected from hospitalized patients admitted with a clinical diagnosis of pulmonary tuberculosis, and subjected to smear microscopy, culture on LJ medium and detection of M. tuberculosis by PCR. Sensitivity, specificity, and predictive values (positive and negative) were calculated using smear and/or culture at day 42 as the gold standard, by comparing the yield in HIV-positive and HIV-negative individuals. Regardless of serostatus, the technique’s yield had 62% sensitivity, 70% specificity, 79% positive predictive value, 50% negative predictive value, and 65% accuracy. HIV-negative had 64% sensitivity, 74% specificity, 75% positive predictive value, 63% negative predictive value, and 68% accuracy. HIV-positive had 59% sensitivity, 33% specificity, 87% positive predictive value, 10% negative predictive value, and 56% accuracy. The PCR showed a higher yield in HIV-negative individuals compared to HIV-positive individuals.
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Affiliation(s)
- Rosemeri Maurici da Silva
- Programa de Mestrado em Ciências da Saúde, Universidade do Sul de Santa Catarina , Tubarão, SC , Brasil
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40
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Chia JH, Wu TL, Su LH, Kuo AJ, Lai HC. Direct identification of mycobacteria from smear-positive sputum samples using an improved multiplex polymerase chain reaction assay. Diagn Microbiol Infect Dis 2012; 72:340-9. [PMID: 22280996 DOI: 10.1016/j.diagmicrobio.2011.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 11/22/2011] [Accepted: 12/10/2011] [Indexed: 11/26/2022]
Abstract
The rapid identification of mycobacteria from smear-positive sputum samples is very important. To identify the Mycobacterium tuberculosis complex (MTBC) and frequently isolated nontuberculous mycobacteria strains directly from smear-positive sputum samples, an improved multiplex polymerase chain reaction (PCR) assay was developed. Nine pairs of primers targeting the 16S-23S rDNA internal transcribed spacer-1, hsp65, and the early secretory antigen (ESAT-6) gene sequences were developed, and their efficacy was evaluated in comparison to traditional culturing and 16S rRNA gene sequencing methods. A total of 200 smear- and culture-positive sputum specimens collected between November 2005 and May 2006 were used for the analysis. The results of the assay showed an accurate identification rate for acid-fast bacilli (AFB) 3+, AFB 2+, and AFB rare/1+ samples of 98%, 95%, and 53%, respectively. The improved multiplex PCR method saves time and has advantages for identifying mycobacteria from AFB 2+ and 3+ sputum samples. The method is suitable for use in countries with a high MTBC prevalence rate.
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Affiliation(s)
- Ju-Hsin Chia
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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41
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Performance assessment of the CapitalBio mycobacterium identification array system for identification of mycobacteria. J Clin Microbiol 2011; 50:76-80. [PMID: 22090408 DOI: 10.1128/jcm.00320-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The CapitalBio Mycobacterium identification microarray system is a rapid system for the detection of Mycobacterium tuberculosis. The performance of this system was assessed with 24 reference strains, 486 Mycobacterium tuberculosis clinical isolates, and 40 clinical samples and then compared to the "gold standard" of DNA sequencing. The CapitalBio Mycobacterium identification microarray system showed highly concordant identification results of 100% and 98.4% for Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM), respectively. The sensitivity and specificity of the CapitalBio Mycobacterium identification array for identification of Mycobacterium tuberculosis isolates were 99.6% and 100%, respectively, for direct detection and identification of clinical samples, and the overall sensitivity was 52.5%. It was 100% for sputum, 16.7% for pleural fluid, and 10% for bronchoalveolar lavage fluid, respectively. The total assay was completed in 6 h, including DNA extraction, PCR, and hybridization. The results of this study confirm the utility of this system for the rapid identification of mycobacteria and suggest that the CapitalBio Mycobacterium identification array is a molecular diagnostic technique with high sensitivity and specificity that has the capacity to quickly identify most mycobacteria.
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42
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Darban-Sarokhalil D, Fooladi A, Bameri Z, Nasiri M, Feizabadi M. Cytochrome CYP141: a new target for direct detection of Mycobacterium tuberculosis from clinical specimens. Acta Microbiol Immunol Hung 2011; 58:211-7. [PMID: 21983322 DOI: 10.1556/amicr.58.2011.3.4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Cytochrome P450 CYP141 is an intermediary metabolic and respiratory protein that interferes with oxidation reduction in Mycobacterium tuberculosis. This conserved protein has also been debated as a hypothetical target for therapeutics. We used the sequences of CYP141 gene to develop a PCR for rapid detection of Mycobacterium tuberculosis from respiratory specimens. The sensitivity of this PCR for culture positive-smear positive and culture positive-smear negative samples were 92% and 62.5%, respectively. The overall sensitivity and specificity of this PCR was 85.7% and 97.8%. As compared with other studies, it appears that the CYP141 gene is a good target for direct detection of M. tuberculosis from respiratory specimens.
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Affiliation(s)
- Davood Darban-Sarokhalil
- 1 Tehran University of Medical Sciences Department of Microbiology, School of Medicine Tehran Iran
| | - Abbas Fooladi
- 2 Baqiyatallah University of Medical Sciences Applied Microbiology Research Center Tehran Iran
| | - Zakaria Bameri
- 3 Zahedan University of Medical Sciences Research Center for Infectious Diseases and Tropical Medicine, Boo-Ali Hospital Zahedan Iran
| | - Mohammad Nasiri
- 1 Tehran University of Medical Sciences Department of Microbiology, School of Medicine Tehran Iran
| | - Mohammad Feizabadi
- 1 Tehran University of Medical Sciences Department of Microbiology, School of Medicine Tehran Iran
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43
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Alcaide F, Coll P. Advances in rapid diagnosis of tuberculosis disease and anti-tuberculous drug resistance. Enferm Infecc Microbiol Clin 2011; 29 Suppl 1:34-40. [PMID: 21420565 DOI: 10.1016/s0213-005x(11)70016-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Rapid diagnosis of tuberculosis (TB) and multidrug-resistant (resistance to at least rifampin and isoniazid) Mycobacterium tuberculosis (MDR-TB) is one of the cornerstones for global TB control as it allows early epidemiological and therapeutic interventions. The slow growth of the tubercle bacillus is the greatest obstacle to rapid diagnosis of the disease. However, considerable progress has recently been made in developing novel diagnostic tools, especially molecular methods (commercial and 'in-house'), for direct detection in clinical specimens. These methods, based on nucleic acid amplification (NAA) of different targets, aim to identify the M. tuberculosis complex and detect the specific chromosome mutations that are most frequently associated with phenotypic resistance to multiple drugs. In general, commercial methods are recommended since they have a better level of standardization, reproducibility and automation. Although some aspects such as cost-efficiency and the appropriate setting for the implementation of these techniques are not yet well established, organizations such as the WHO are strongly supporting the implementation and universal use of these new molecular methods. This chapter summarizes current knowledge and the available molecular methods for rapid diagnosis of TB and anti-tuberculous drug resistance in clinical microbiology laboratories.
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Affiliation(s)
- Fernando Alcaide
- Servicio de Microbiología, IDIBELL-Hospital Universitario de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain.
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Abstract
Drug-resistant tuberculosis (DRTB) is an emerging infectious disease threat to sub-Saharan Africa (SSA), particularly in the regions hit hardest by the HIV epidemic. Numerous challenges face clinicians and public health officials tasked with combating DRTB in SSA. These include difficulties providing effective diagnosis, treatment, and prevention of this illness. Furthermore, combating DRTB requires addressing various legal and ethical complexities. A sustained commitment to investigating as well as implementing new diagnostic, therapeutic, and preventative interventions is essential to defeating this threat.
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Dhama K, Mahendran M, Tiwari R, Dayal Singh S, Kumar D, Singh S, Sawant PM. Tuberculosis in Birds: Insights into the Mycobacterium avium Infections. Vet Med Int 2011; 2011:712369. [PMID: 21776352 PMCID: PMC3135220 DOI: 10.4061/2011/712369] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 03/25/2011] [Accepted: 05/05/2011] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis, a List B disease of World Organization for Animal Health, caused by M. avium or M. genavense predominantly affects poultry and pet or captive birds. Clinical manifestations in birds include emaciation, depression and diarrhea along with marked atrophy of breast muscle. Unlike tuberculosis in animals and man, lesions in lungs are rare. Tubercular nodules can be seen in liver, spleen, intestine and bone marrow. Granulomatous lesion without calcification is a prominent feature. The disease is a rarity in organized poultry sector due to improved farm practices, but occurs in zoo aviaries. Molecular techniques like polymerase chain reaction combined with restriction fragment length polymorphism and gene probes aid in rapid identification and characterization of mycobacteria subspecies, and overcome disadvantages of conventional methods which are slow, labour intensive and may at times fail to produce precise results. M. avium subsp. avium with genotype IS901+ and IS1245+ causes infections in animals and human beings too. The bacterium causes sensitivity in cattle to the tuberculin test. The paper discusses in brief the M. avium infection in birds, its importance in a zoonotic perspective, and outlines conventional and novel strategies for its diagnosis, prevention and eradication in domestic/pet birds and humans alike.
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Affiliation(s)
- Kuldeep Dhama
- Avian Diseases Section, Division of Pathology, Indian Veterinary Research Institute (IVRI), Izatnagar 243 122, India
| | - Mahesh Mahendran
- Avian Disease Diagnostic Laboratory, Animal Husbandry Department, Government of Kerala, Thiruvalla, Kerala 689 105, India
| | - Ruchi Tiwari
- Division of Bacteriology and Mycology, Indian Veterinary Research Institute (IVRI), Izatnagar 243 122, India
| | - Shambhu Dayal Singh
- Avian Diseases Section, Division of Pathology, Indian Veterinary Research Institute (IVRI), Izatnagar 243 122, India
| | - Deepak Kumar
- Division of Animal Biotechnology, Indian Veterinary Research Institute (IVRI), Izatnagar 243 122, India
| | - Shoorvir Singh
- Central Institute for Research on Goats, Makhdoom, Mathura 281 122, India
| | - Pradeep Mahadev Sawant
- Immunology Section, Division of Animal Biotechnology, Indian Veterinary Research Institute (IVRI), Izatnagar 243 122, India
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George G, Mony P, Kenneth J. Comparison of the efficacies of loop-mediated isothermal amplification, fluorescence smear microscopy and culture for the diagnosis of tuberculosis. PLoS One 2011; 6:e21007. [PMID: 21695047 PMCID: PMC3117872 DOI: 10.1371/journal.pone.0021007] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2011] [Accepted: 05/16/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Despite the advent of novel diagnostic techniques, smear microscopy remains as the most practical test available in resource-limited settings for tuberculosis (TB) diagnosis. Due to the low sensitivity of microscopy and the long time required for culture, feasible and accessible rapid diagnostic methods are urgently needed. Loop-mediated Isothermal Amplification (LAMP) is a promising nucleic-acid amplification assay, which could be accessible, cost-effective and more suited for use with unpurified samples. METHODOLOGY/PRINCIPAL FINDINGS In the current study, the objective was to assess the efficacy of a LAMP assay for tuberculosis compared with fluorescence smear microscopy as well as Löwenstein-Jensen (LJ) and Mycobacteria Growth Indicator Tube (MGIT) cultures for the diagnosis of pulmonary tuberculosis using sputum samples. Smear microscopy and culture were performed for decontaminated and concentrated sputum from TB suspects and the LAMP was also performed on these specimens. The LAMP and smear microscopy were compared, in series and in parallel, to culture. LAMP and smear microscopy showed sensitivities of 79.5% and 82.1% respectively and specificities of 93.8% and 96.9% respectively, compared to culture. LAMP and smear in series had sensitivity and specificity of 79.5% and 100.0% respectively. LAMP and smear in parallel had sensitivity and specificity of 82.1% and 90.6% respectively. CONCLUSIONS/SIGNIFICANCE The overall efficacies of LAMP and fluorescence smear microscopy in the current study were high and broadly similar. LAMP and smear in series had high specificity (100.0%) and can be used as a rule-in test combination. However, the performance of LAMP in smear negative samples was found to be insufficient.
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Affiliation(s)
- Geojith George
- Division of Infectious Disease, St. John's Research Institute, Bangalore, India
| | - Prem Mony
- Division of Epidemiology and Biostatistics, St. John's Research Institute, Bangalore, India
| | - John Kenneth
- Division of Infectious Disease, St. John's Research Institute, Bangalore, India
- * E-mail:
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Neonakis IK, Spandidos DA, Petinaki E. Female genital tuberculosis: A review. ACTA ACUST UNITED AC 2011; 43:564-72. [DOI: 10.3109/00365548.2011.568523] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Evaluation of TBc identification immunochromatographic assay for rapid identification of Mycobacterium tuberculosis complex in samples from broth cultures. J Clin Microbiol 2011; 49:1939-42. [PMID: 21411594 DOI: 10.1128/jcm.01906-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis (TB) is a disease of major public health concern worldwide, especially in developing countries. In addition, the human immunodeficiency virus (HIV) epidemic has increased the incidence of infection with nontuberculous mycobacteria (NTM). Rapid, accurate, and simple methods for differentiation of Mycobacterium tuberculosis complex (MTBC) isolates from NTM is greatly needed for successful control of the TB epidemic. This study was done to evaluate the clinical performance of the BD MGIT TBc identification test (TBc ID) for rapid identification of MTBC in samples from broth cultures. A total of 229 Ziehl-Neelsen (ZN) stain-positive MGIT cultures were tested using the TBc ID test, and the results were compared with those of the AccuProbe MTBC identification test (GenProbe, San Diego, CA). The agreement between the TBc ID test and the AccuProbe assay was 96% (kappa = 0.92; confidence interval [CI] = 0.869 to 0.971). The sensitivity, specificity, and negative and positive predictive values of the TBc ID test compared to the AccuProbe assay were 100%, 92.4%, 100%, and 92.2%, respectively. After additional molecular testing, the agreement between the two methods increased to 97.8% (kappa = 0.96; CI = 0.917 to 0.994), and the specificity and positive predictive value increased to 95.6% and 95.7%, respectively. The TBc ID test is a simple, sensitive, and specific test for identification of MTBC in samples from acid-fast bacillus (AFB) smear-positive cultures. The TBc ID test could be a good alternative to the AccuProbe test in TB diagnostic laboratories.
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Use of loop-mediated isothermal amplification of DNA for the rapid detection of Mycobacterium tuberculosis in clinical specimens. Eur J Clin Microbiol Infect Dis 2011; 30:937-42. [DOI: 10.1007/s10096-011-1195-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 01/28/2011] [Indexed: 10/18/2022]
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50
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Abstract
Nontuberculous mycobacteria (NTM) are generally hardy, ubiquitous environmental bacteria that vary in geographic distribution and pulmonary pathogenicity. Relatively few of the more than 115 species of NTM have been associated with lung disease. Diagnosis of disease due to NTM relies on a combination of clinical, imaging, and microbiologic data. Because NTM may present as acid-fast bacilli in respiratory secretions of patients with clinical and radiologic features that mimic tuberculosis, laboratory discrimination of NTM from Mycobacterium tuberculosis is a priority. This discrimination is now often rapidly achievable using molecular techniques, although some tests have limited sensitivity. NTM species have different antibiotic response patterns, and success with medical treatment alone varies. Macrolides are an essential component of therapy for many species but must be combined with other drugs.
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Affiliation(s)
- Babafemi Taiwo
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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