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Taylor GM, White-Iribhogbe K, Cole G, Ashby D, Stewart GR, Dawson-Hobbis H. Bioarchaeological investigation of individuals with suspected multibacillary leprosy from the mediaeval leprosarium of St Mary Magdalen, Winchester, Hampshire, UK. J Med Microbiol 2024; 73. [PMID: 38362924 DOI: 10.1099/jmm.0.001806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Abstract
Introduction. We have examined four burials from the St Mary Magdalen mediaeval leprosarium cemetery in Winchester, Hampshire, UK. One (Sk.8) was a male child, two (Sk.45 and Sk.52) were adolescent females and the fourth (Sk.512) was an adult male. The cemetery was in use between the 10th and 12th centuries. All showed skeletal lesions of leprosy. Additionally, one of the two females (Sk.45) had lesions suggestive of multi-cystic tuberculosis and the second (Sk.52) of leprogenic odontodysplasia (LO), a rare malformation of the roots of the permanent maxillary incisors.Gap statement. Relatively little is known of the manifestations of lepromatous leprosy (LL) in younger individuals from the archaeological record.Aims and Methodology. To address this, we have used ancient DNA testing and osteological examination of the individuals, supplemented with X-ray and microcomputed tomography (micro-CT) scan as necessary to assess the disease status.Results and Conclusions. The presence of Mycobacterium leprae DNA was confirmed in both females, and genotyping showed SNP type 3I-1 strains but with a clear genotypic variation. We could not confirm Mycobacterium tuberculosis complex DNA in the female individual SK.45. High levels of M. leprae DNA were found within the pulp cavities of four maxillary teeth from the male child (Sk.8) with LO, consistent with the theory that the replication of M. leprae in alveolar bone may interfere with root formation at key stages of development. We report our biomolecular findings in these individuals and review the evidence this site has contributed to our knowledge of mediaeval leprosy.
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Affiliation(s)
- G Michael Taylor
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, GU2 7XH, Surrey, UK
| | - Katie White-Iribhogbe
- Centre of African Studies, School of Oriental and African Studies (SOAS), University of London, Thornhaugh Street, Russell Square, London, WC1H 0XG, UK
| | - Garrard Cole
- UCL Institute of Archaeology, 31-34 Gordon Square, London, WC1H 0PY, UK
| | - David Ashby
- School of History, Archaeology and Philosophy, University of Winchester, Sparkford Road, Winchester, Hampshire, SO22 4NR, UK
| | - Graham R Stewart
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, GU2 7XH, Surrey, UK
| | - Heidi Dawson-Hobbis
- School of History, Archaeology and Philosophy, University of Winchester, Sparkford Road, Winchester, Hampshire, SO22 4NR, UK
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2
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Ellis HC, Moffatt MF, Churchward C, Cuthbertson L, Cookson WO, Loebinger MR. Molecular assessment of mycobacterial burden in the treatment of nontuberculous mycobacterial disease. ERJ Open Res 2023; 9:00435-2022. [PMID: 36949959 PMCID: PMC10026000 DOI: 10.1183/23120541.00435-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/16/2022] [Indexed: 11/12/2022] Open
Abstract
Introduction Nontuberculous pulmonary disease causes significant morbidity and mortality. Efforts to tackle infections are hampered by the lack of reliable biomarkers for diagnosis, assessment and prognostication. The aim of this study was to develop molecular assays capable of identifying and quantifying multiple nontuberculous mycobacterial (NTM) species and to examine their utility in following individual patients' clinical courses. Methods DNA was extracted from 410 sputum samples obtained longitudinally from a cohort of 38 patients who were commencing treatment for either Mycobacterium abscessus or Mycobacterium avium complex or who were patients with bronchiectasis who had never had positive cultures for mycobacteria. NTM quantification was performed with quantitative PCR assays developed in-house. Results The molecular assays had high in vitro sensitivity and specificity for the detection and accurate quantification of NTM species. The assays successfully identified NTM DNA from human sputum samples (in vivo sensitivity: 0.86-0.87%; specificity: 0.62-0.95%; area under the curve: 0.74-0.92). A notable association between NTM copy number and treatment (Friedman ANOVA (df)=22.8 (3), p≤0.01 for M. abscessus treatment group) was also demonstrated. Conclusion The quantitative PCR assays developed in this study provide affordable, real-time and rapid measurement of NTM burden, with significant implications for prompt management decisions.
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Affiliation(s)
- Huw C. Ellis
- Host Defence Unit, Royal Brompton Hospital, London, UK
- Imperial College London, London, UK
| | | | | | | | | | - Michael R. Loebinger
- Host Defence Unit, Royal Brompton Hospital, London, UK
- Imperial College London, London, UK
- Corresponding author: Michael Loebinger ()
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3
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Morais FCL, Bello GL, Costi C, Schmid KB, Soares TDS, Barcellos RB, Unis G, Dias CF, da Silva PEA, Rossetti ML. Detection of non-tuberculosus mycobacteria (NTMs) in lung samples using 16S rRNA. Mem Inst Oswaldo Cruz 2022; 117:e220031. [PMID: 35920498 PMCID: PMC9337835 DOI: 10.1590/0074-02760220031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Non-tuberculous mycobacteria (NTMs) cause diseases known as mycobacteriosis
and are an important cause of morbidity and mortality. The diagnosis of
pulmonary disease caused by NTM is hampered by its clinical similarity with
tuberculosis (TB) and by the lack of an accurate and rapid laboratory
diagnosis. OBJECTIVES Detect DNA from NTMs directly from lung samples using real-time polymerase
chain reaction (qPCR) for amplification of 16S rRNA. Additionally, DNA
sequencing (hsp65 and rpoB genes) was used
to identify the species of MNTs. METHODS A total of 68 sputum samples (54 with suspected NTMs and 14 with TB) from
patients treated at a referral hospital were used. FINDINGS Of these, 27/54 (50%) were qPCR positive for NTMs and 14/14 TB patients
(controls) were qPCR negative with an almost perfect concordance
(Kappa of 0.93) with the Mycobacterium
spp. culture. Sequencing confirmed the presence of NTM in all positive
samples. The most common species was Mycobacterium gordonae
(33%), followed by Mycobacterium abscessus (26%),
Mycobacterium fortuitum (22%), Mycobacterium
avium (15%) and Mycobacterium peregrinum
(4%). MAIN CONCLUSIONS The qPCR technique for detecting NTMs targeting 16S rRNA has the potential
to detect NTMs and rapidly differentiate from Mycobacterium
tuberculosis. However, it is necessary to identify the species
to help in the differential diagnosis between disease and contamination, and
to guide the choice of the therapeutic scheme.
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Affiliation(s)
- Franciele Costa Leite Morais
- Universidade Luterana do Brasil, Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, RS, Brasil
| | - Graziele Lima Bello
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Programa Institutos Nacionais de Ciência e Tecnologia, Porto Alegre, RS, Brasil
| | - Cíntia Costi
- Secretaria da Saúde do Rio Grande do Sul, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil.,Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
| | - Karen Barros Schmid
- Secretaria da Saúde do Rio Grande do Sul, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil.,Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
| | - Tainá Dos Santos Soares
- Universidade Luterana do Brasil, Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, RS, Brasil.,Secretaria da Saúde do Rio Grande do Sul, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Regina Bones Barcellos
- Secretaria da Saúde do Rio Grande do Sul, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil.,Universidade Federal do Rio de Janeiro, Programa de Pós-Graduação em Clínica Médica, Rio de Janeiro, RJ, Brasil
| | - Gisela Unis
- Secretaria da Saúde do Rio Grande do Sul, Hospital Sanatório Partenon, Porto Alegre, RS, Brasil
| | - Claudia Fontoura Dias
- Secretaria da Saúde do Rio Grande do Sul, Hospital Sanatório Partenon, Porto Alegre, RS, Brasil
| | - Pedro Eduardo Almeida da Silva
- Universidade Federal do Rio Grande, Faculdade de Medicina, Centro de Pesquisas em Microbiologia Médica, Rio Grande, RS, Brasil
| | - Maria Lucia Rossetti
- Universidade Luterana do Brasil, Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, RS, Brasil.,Instituto Nacional de Ciência e Tecnologia em Tuberculose, Programa Institutos Nacionais de Ciência e Tecnologia, Porto Alegre, RS, Brasil.,Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
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4
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Peixoto ADS, Montenegro LML, Lima AS, Melo FL, Barbosa Júnior WL, Neves MMC, Ramos JP, Schindler HC, Medeiros ZM. Identification of nontuberculous mycobacteria species by multiplex real-time PCR with high-resolution melting. Rev Soc Bras Med Trop 2020; 53:e20200211. [PMID: 33174954 PMCID: PMC7670742 DOI: 10.1590/0037-8682-0211-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/02/2020] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION: Nontuberculous mycobacteria (NTM) species, as human pathogens,
are increasing in the world, as is the difficulty of accurately identifying
them. Differential diagnosis, especially between the M.
tuberculosis complex and NTM species, and the characterization
of NTM species is important. This study aimed to evaluate the performance of
a molecular system based on multiplex real-time PCR with high-resolution
melting (HRM) for the identification and differentiation of NTM species of
clinical importance of an endemic area for tuberculosis in northeastern
Brazil. METHODS: The technical protocol of the molecular system was based on multiplex
real-time PCR-HRM, and evaluated the sensitivity and specificity of the
detection of NTM species in mycobacterial clinical isolates from the studied
region. The gold standard method was specific gene sequencing. RESULTS: The sensitivity and specificity of multiplex real-time PCR-HRM modified for
differentiation between NTM and M. tuberculosis were 90%
and 100%, respectively. The PCR-HRM sensitivities for the characterization
of NTM species (M. kansasii, M. abscesses, M. avium, and M.
fortuitum) were 94.59%, 80%, 57.14%, and 54%, respectively.
CONCLUSIONS The multiplex real-time PCR-HRM modified assay has the potential to rapidly
and efficiently identify nontuberculous mycobacteria of clinical importance,
which is crucial for immediate implementation of the appropriate therapy and
thus avoiding complications and sequelae in patients.
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Affiliation(s)
- Aline Dos Santos Peixoto
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Imunologia, Recife, PE, Brasil.,Universidade de Pernambuco, Pós-Graduação em Ciências da Saúde, Recife, PE, Brasil
| | | | - Andrea Santos Lima
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Imunologia, Recife, PE, Brasil
| | - Fábio Lopes Melo
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Parasitologia, Recife, PE, Brasil
| | | | | | - Jesus Pais Ramos
- Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Laboratório Nacional de Referência para Tuberculose, Rio de Janeiro, RJ, Brasil
| | | | - Zulma Maria Medeiros
- Universidade de Pernambuco, Pós-Graduação em Ciências da Saúde, Recife, PE, Brasil.,Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Parasitologia, Recife, PE, Brasil
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5
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Cowman S, van Ingen J, Griffith DE, Loebinger MR. Non-tuberculous mycobacterial pulmonary disease. Eur Respir J 2019; 54:13993003.00250-2019. [PMID: 31221809 DOI: 10.1183/13993003.00250-2019] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/31/2019] [Indexed: 02/03/2023]
Abstract
Nontuberculous mycobacterial pulmonary disease (NTM-PD) is a challenging infection which is becoming increasingly prevalent, particularly in the elderly, for reasons which are unknown. While underlying lung disease is a well-established risk factor for NTM-PD, it may also occur in apparently healthy individuals. No single common genetic or immunological defect has been identified in this group, and it is likely that multiple pathways contribute towards host susceptibility to NTM-PD which further interact with environmental and microbiological factors leading to the development of disease.The diagnosis of NTM-PD relies on the integration of clinical, radiological and microbiological results. The clinical course of NTM-PD is heterogeneous, with some patients remaining stable without the need for treatment and others developing refractory disease associated with considerable mortality and morbidity. Treatment regimens are based on the identity of the isolated species, drug sensitivity testing (for some agents) and the severity of disease. Multiple antibiotics are typically required for prolonged periods of time and treatment is frequently poorly tolerated. Surgery may be beneficial in selected cases. In some circumstances cure may not be attainable and there is a pressing need for better regimens to treat refractory and drug-resistant NTM-PD.This review summarises current knowledge on the epidemiology, aetiology and diagnosis of NTM-PD and discusses the treatment of two of the most clinically significant species, the M. avium and M. abscessus complexes, with a focus on refractory disease and novel therapies.
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Affiliation(s)
- Steven Cowman
- Host Defence Unit, Royal Brompton Hospital, London, UK.,Imperial College, London, UK
| | - Jakko van Ingen
- Dept of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - David E Griffith
- Dept of Medicine, The University of Texas Health Science Center at Tyler, Tyler, TX, United States
| | - Michael R Loebinger
- Host Defence Unit, Royal Brompton Hospital, London, UK .,Imperial College, London, UK
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6
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Cho MJ, Kim MJ, Kim K, Choi YW, Lee SJ, Whang YM, Chang IH. The immunotherapeutic effects of recombinant Bacillus Calmette-Guérin resistant to antimicrobial peptides on bladder cancer cells. Biochem Biophys Res Commun 2018; 509:167-174. [PMID: 30579607 DOI: 10.1016/j.bbrc.2018.12.097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 12/13/2018] [Indexed: 11/25/2022]
Abstract
PURPOSE Although Mycobacterium bovis Bacillus Calmette-Guérin (BCG) is the most widely used bladder cancer immunotherapy, innate immune responses involving antimicrobial peptides (AMPs) cause BCG failure and unwanted side effects. Here, we generated genetically modified BCG strains with improved immunotherapeutic effects by adding genes that confer evasion of AMPs. MATERIALS AND METHODS We constructed recombinant BCG (rBCG) strains expressing Streptococcal inhibitor of complement (Sic), which confers resistance to human α-defensin-1 and cathelicidin, and d-alanyl carrier protein ligase (dltA), which confers resistance to cationic AMPs. Sic and dltA were separately cloned into the pMV306 plasmid and introduced into BCG via electroporation. Then, the efficacy of the rBCGs was tested in a growth inhibition assay using two bladder cancer cell lines (5637, T24). RESULTS We confirmed the presence of cDNA segments corresponding to the Sic and dltA genes in total mRNA of the rBCG strains containing Sic (rBCG-Sic) and dltA (rBCG-dltA), and these rBCGs showed higher survival against AMPs. The growth inhibitory effects of rBCGs on bladder cancer cells were significantly enhanced compared to those of the parent BCG, and THP-1 migration also increased. After 8 h of infection, the levels of internalization were higher in rBCG-infected bladder cancer cells than in BCG-infected cells, and cells infected with rBCGs showed increased release of antitumor cytokines, such as IL-6/12, TNF-α, and INF-γ, resulting in inhibition of bacterial killing and immune modulation via antimicrobial peptides. CONCLUSIONS rBCG-Sic and rBCG-dltA can effectively evade BCG-stimulated AMPs, and may be significantly improved immunotherapeutic tools to treat bladder cancer.
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Affiliation(s)
- Min-Ji Cho
- Department of Urology, College of Medicine, Chung-Ang University, Seoul, Republic of Korea
| | - Myeong Joo Kim
- Department of Urology, College of Medicine, Chung-Ang University, Seoul, Republic of Korea
| | - Kijeong Kim
- College of Medicine, Chung-Ang University, Seoul, Republic of Korea
| | - Young Wook Choi
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Sang-Jin Lee
- Genitourinary Cancer Branch, Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Young Mi Whang
- Department of Urology, College of Medicine, Chung-Ang University, Seoul, Republic of Korea.
| | - In Ho Chang
- Department of Urology, College of Medicine, Chung-Ang University, Seoul, Republic of Korea.
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7
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Bentaleb EM, Abid M, El Messaoudi MD, Lakssir B, Ressami EM, Amzazi S, Sefrioui H, Ait Benhassou H. Development and evaluation of an in-house single step loop-mediated isothermal amplification (SS-LAMP) assay for the detection of Mycobacterium tuberculosis complex in sputum samples from Moroccan patients. BMC Infect Dis 2016; 16:517. [PMID: 27677540 PMCID: PMC5039794 DOI: 10.1186/s12879-016-1864-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 09/22/2016] [Indexed: 11/16/2022] Open
Abstract
Background Tuberculosis (TB) is a major global health problem and remains the leading cause of morbidity and mortality in developing countries. Routinely used TB diagnostic methods, in most endemic areas, are time-consuming, often less-sensitive, expensive and inaccessible to most patients. Therefore, there is an urgent need for the development of early, easy to use and effective diagnosis tools of TB, which can be effectively integrated into resource limited settings, to anticipate the early treatment and limit further spread of the disease. Over the last decade, Loop-mediated isothermal amplification (LAMP) assays have become a powerful tool for rapid diagnosis of infectious diseases because of the simplicity of device requirements. Indeed, LAMP is a simple, quick and cost effective Isothermal Nucleic Acid Amplification diagnostic test (INAAT) that has the potential to be used in TB endemic settings of resource-poor countries. Methods In the present study, we have developed a simple and rapid TB molecular diagnostic test using a Single-Step Loop-mediated isothermal DNA amplification (SS-LAMP) method for the detection of Mycobacterium tuberculosis complex (MTBC) strains, with a simplified sample preparation procedure, eliminating DNA extraction prior to LAMP amplification, DNA initial denaturation and enzymatic inactivation steps during the amplification process. To perform our in-house SS-LAMP assay, a set of six specific primers was specifically designed to recognize eight distinct regions on the MTBC species-specific repetitive insertion sequence 6110 (IS6110). The amplification of the targeted DNA was carried out under isothermal conditions at 65 °C within 1 h. Our protocol was firstly optimized using 60 of confirmed MTBC isolates and a recombinant pGEMeasy-IS6110 vector for sensitivity testing. Thereafter, the assay was evaluated on liquefied sputum specimens collected from 157 Moroccan patients suspected of having TB. Results Our SS-LAMP developed assay was able to detect MTBC DNA directly from liquefied sputum samples without any prior DNA extraction, denaturation nor the final enzymatic inactivation step. When compared to routinely used Löwenstein Jensen (LJ) Culture method, our SS-LAMP assay is rapid and showed specificity and sensitivity of 99.14 % and 82.93 % respectively which are within the international standards. In addition, the limit of detection of our assay was found to be as little as 10 copies of bacterial DNA. Conclusion To our knowledge, this is the first study using a single step LAMP (SS-LAMP) procedure as a rapid, easy to perform and cost effective testing for TB early detection. This innovative assay could be suitable for low-income countries with restricted health equipment facilities.
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Affiliation(s)
- El Mehdi Bentaleb
- Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Center, Avenue Mohamed El Jazouli - Madinat Al Irfane, 10100, Rabat, Morocco.,Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Mohammed Abid
- Laboratory of Mycobacteria Genetics, Pasteur Institute of Morocco, Tangier, Morocco
| | | | - Brahim Lakssir
- Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Center, Avenue Mohamed El Jazouli - Madinat Al Irfane, 10100, Rabat, Morocco
| | - El Mostafa Ressami
- Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Center, Avenue Mohamed El Jazouli - Madinat Al Irfane, 10100, Rabat, Morocco
| | - Saaïd Amzazi
- Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Hassan Sefrioui
- Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Center, Avenue Mohamed El Jazouli - Madinat Al Irfane, 10100, Rabat, Morocco
| | - Hassan Ait Benhassou
- Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Center, Avenue Mohamed El Jazouli - Madinat Al Irfane, 10100, Rabat, Morocco.
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8
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Culture-Independent Detection of Nontuberculous Mycobacteria in Clinical Respiratory Samples. J Clin Microbiol 2016; 54:2395-8. [PMID: 27413194 DOI: 10.1128/jcm.01410-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 07/06/2016] [Indexed: 11/20/2022] Open
Abstract
Culture-based detection of nontuberculous Mycobacteria (NTM) in respiratory samples is time consuming and can be subject to overgrowth by nonmycobacterial bacteria. We describe a single-reaction TaqMan quantitative PCR assay for the direct detection of NTM species in clinical samples that is specific, sensitive, and robust.
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9
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Kim JU, Cha CH, Park SH. Direct identification of mycobacteria from liquid media using a triplex real-time PCR coupled with pyrosequencing method. J Microbiol Methods 2015; 119:83-6. [PMID: 26471200 DOI: 10.1016/j.mimet.2015.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/10/2015] [Accepted: 10/10/2015] [Indexed: 11/25/2022]
Abstract
Culture in enriched broth, as well as on a solid medium, is recommended for primary isolation of mycobacteria. With the introduction of liquid mycobacterial culture methods, a substantial workload regarding the identification of culture-recovered mycobacterial species, particularly Mycobacterium tuberculosis complex (MTC), has been imposed on our laboratory. We thus developed a triplex, real-time PCR coupled with pyrosequencing assay that can directly identify mycobacterial species from liquid media, which can reduce the workload. In this assay, real-time PCR simultaneously detects MTC and Mycobacterium xenopi, and amplifies the region of 16S rRNA gene containing hypervariable region A for pyrosequencing analysis; subsequent, pyrosequencing identifies many other nontuberculous mycobacteria. The assay was evaluated using 333 DNA samples directly prepared from liquid media, including 24 reference strains and 309 clinical isolates. Three hundred and twenty-eight (98.5%) of the 333 samples were correctly identified. The remaining five were determined as indeterminate. In conclusion, this coupled assay would be an alternative method for rapid identification of mycobacteria directly from liquid media in a clinical laboratory with a high workload in regions where tuberculosis is endemic.
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Affiliation(s)
- Jeong-Uk Kim
- Department of Laboratory Medicine, Gangneung Asan Hospital, University of Ulsan College of Medicine, Gangneung, Republic of Korea.
| | - Choong-Hwan Cha
- Department of Laboratory Medicine, Gangneung Asan Hospital, University of Ulsan College of Medicine, Gangneung, Republic of Korea
| | - Seon-Hee Park
- Department of Laboratory Medicine, Gangneung Asan Hospital, University of Ulsan College of Medicine, Gangneung, Republic of Korea
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10
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Kim K, Hong SH, Kim BJ, Kim BR, Lee SY, Kim GN, Shim TS, Kook YH, Kim BJ. Separation of Mycobacterium abscessus into subspecies or genotype level by direct application of peptide nucleic acid multi-probe- real-time PCR method into sputa samples. BMC Infect Dis 2015; 15:325. [PMID: 26259717 PMCID: PMC4531893 DOI: 10.1186/s12879-015-1076-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/31/2015] [Indexed: 11/30/2022] Open
Abstract
Background Recently, we introduced a novel peptide nucleic acid (PNA) multi-probe real time PCR method targeting the hsp65 gene (hsp65 PNA RT-PCR) to distinguish Mycobacterium abscessus groups. Methods Here, we evaluated the usefulness of the hsp65 PNA RT-PCR for the direct identification of the M. abscessus group at the subspecies and genotype levels from sputa samples. The method was applied to total sputa DNA from 60 different patients who were identified as having mycobacterial infections via rpoB PCR restriction analysis of the same cultures. Results The hsp65 PNA RT-PCR method had higher sensitivity than the multi-probe real-time PCR assay targeting hsp65 (HMPRT-PCR) for the detection of M. abscessus from sputum [96.7 % (29/30 samples) vs. 70 % (21/30 samples); 100 % specificity]. Conclusions These results suggest that the PNA-based method is feasible for the detection of M. abscessus members not only from cultures but also directly from sputa. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-1076-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kijeong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 156-756, Republic of Korea.
| | - Seok-Hyun Hong
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Byoung-Jun Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Bo-Ram Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - So-Young Lee
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Ga-Na Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Tae Sun Shim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Yoon-Hoh Kook
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Bum-Joon Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
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O'Connor JA, O'Reilly B, Corcoran GD, O'Mahony J, Lucey B. Mycobacterium diagnostics: from the primitive to the promising. Br J Biomed Sci 2015; 72:32-41. [PMID: 25906489 DOI: 10.1080/09674845.2015.11666793] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The field of clinical microbiology has been revolutionised by genomic and proteomic methods, which have facilitated more rapid diagnosis and characterisation of infection in many cases. In contrast, mycobacteriological evolution has tended to retain the traditional methods of smear microscopy for detection of acid-fast bacilli to indicate mycobacteria, along with culture, and in synergy with more modern molecular methods. Thus, efforts have been focused on reducing the time to diagnosis of infection, while increasing the amount of diagnostic information available, including more definitive speciation, and more rapid susceptibility test results. Although smear microscopy remains a mainstay for the laboratory-based diagnosis of mycobacterial infection, molecular testing has vastly reduced the time needed for identification of Mycobacterium tuberculosis in particular, when compared with traditional culture-based techniques. Molecular methods may also yield antimicrobial susceptibility results through testing for the most common resistance-inducing mutations to some of the antimicrobial agents of choice. However, the diversity of resistance mutations already characterised suggests that these currently-available molecular detection systems should be accompanied by culture-based susceptibility testing. This review compares the efficacy of microscopic, phenotypic, proteomic and genotypic methods available for mycobacterial diagnosis. The diversity of methods currently in use reflects the complexity of this area of diagnostic microbiology.
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Lin L, Yin X, Wang Q. Rapid differentiation of mycobacteria by simplex real-time PCR with melting temperature calling analysis. J Appl Microbiol 2015; 119:853-8. [PMID: 26119243 DOI: 10.1111/jam.12884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 05/27/2015] [Accepted: 06/05/2015] [Indexed: 12/01/2022]
Abstract
AIMS This study aimed to develop a rapid, simple and cost-effective method for the differentiation of Mycobacterium species. METHODS AND RESULTS A total of 80 clinical mycobacterial isolates belonging to 12 different species and 16 reference strains of 16 different species were differentiated by the simplex real-time PCR coupled with melting temperature calling analysis. By comparing their melting profiles with those of the reference strains, all clinical mycobacterial isolates were differentiated as Mycobacterium tuberculosis complex or nontuberculous mycobacteria, and the latter were further divided into five groups. In comparison with 16S-23S internal transcribed spacer sequencing method as the gold standard method, both sensitivity and specificity of the assay were 100% when it was used for the differentiation between Myco. tuberculosis complex and nontuberculous mycobacteria. CONCLUSIONS The simplex real-time PCR coupled with melting temperature calling analysis could be an alternative method for the differentiation between Myco. tuberculosis complex and nontuberculous mycobacteria. SIGNIFICANCE AND IMPACT OF THE STUDY Rapid differentiation of mycobacteria could shorten the diagnostic time of mycobacterial diseases. It is also helpful for achieving optimal therapy and appropriate patient management.
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Affiliation(s)
- L Lin
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - X Yin
- Clinical Laboratory, The Fifth Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong Province, China
| | - Q Wang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
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Kim JU, Cha CH, An HK. Direct identification of mycobacteria from clinical specimens by multiplex real-time PCR. J Appl Microbiol 2015; 118:1498-506. [PMID: 25715744 DOI: 10.1111/jam.12780] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/03/2015] [Accepted: 02/18/2015] [Indexed: 11/26/2022]
Abstract
AIMS To directly identify clinically relevant mycobacteria from clinical specimens, we have developed a multiplex real-time PCR assay with hydrolysis probes that can identify 20 mycobacterial species. METHODS AND RESULTS The assay was initially evaluated using 248 strains, including both reference strains and clinical isolates. Then, the assay was implemented according to a scheme in our laboratory. The scheme based on the clinical differences between the Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM) consisted of three stepwise PCRs. MTC and NTM were differentially detected in the step 1 PCR, and the NTM species were identified in the step 2 and step 3 PCRs. During a 2·5-year period, 1877 isolates of MTC (1142 directly recovered from clinical specimens) and 596 isolates of NTM (143 directly recovered from clinical specimens) were detected, and the species of 590 (99·0%) of the 596 NTM isolates were identified. CONCLUSIONS Our experience shows that this is a new paradigm for rapidly and accurately identifying clinically relevant mycobacteria, in which a multiplex real-time PCR assay is directly applied to clinical specimens in a stepwise fashion. SIGNIFICANCE AND IMPACT OF THE STUDY This study is the first report of a multiplex real-time PCR assay for identifying clinically important mycobacterial species directly from clinical specimens and its application in a clinical microbiology laboratory.
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Affiliation(s)
- J-U Kim
- Department of Laboratory Medicine, Gangneung Asan Hospital, University of Ulsan College of Medicine, Gangneung, Korea
| | - C H Cha
- Department of Laboratory Medicine, Gangneung Asan Hospital, University of Ulsan College of Medicine, Gangneung, Korea
| | - H K An
- Department of Laboratory Medicine, Gangneung Asan Hospital, University of Ulsan College of Medicine, Gangneung, Korea
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Kwon JK, Chi BH, Choi SY, Kim SJ, Lee TJ, Kim K, Chang IH. Murine β-defensin-2 may regulate the effect of bacillus Calmette-Guérin (BCG) in normal mouse bladder. Urol Oncol 2015; 33:111.e9-16. [PMID: 25573055 DOI: 10.1016/j.urolonc.2014.10.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 10/23/2014] [Accepted: 10/23/2014] [Indexed: 11/19/2022]
Abstract
PURPOSE We investigated whether bacillus Calmette-Guérin (BCG)-induced secretion of murine β-defensin-2 (mBD2) and determined whether mBD2 regulated BCG effects in the normal mouse bladder. MATERIALS AND METHODS A total of 140 C57BL/6 female mice were divided into 28 groups, and the experiment was performed over 3 steps. In the first step (20 groups), mice bladders were stimulated with different doses of BCG (multiplicity of infection [MOI] 0, 1, 10, 30, and 100) and histological analysis was conducted in bladder specimens isolated at different times (0, 4, 8, and 24h after instillation) to determine optimal dose and time point of BCG internalization and urine mBD2 and cytokine concentration. In the second step (4 groups), BCG internalization and urine cytokine levels were measured after pretreatment of different recombinant mBD2 (rmBD2) (0, 1, 2.5, and 5 ng/ml) at optimal dose and time point. In the third step (4 groups), BCG internalization and urine cytokine levels were compared between pretreatment conditions (control, rmBD2, anti-mBD2 Ab, and rmBD2+anti-mBD2 Ab). Urine was collected for estimating mBD2 levels and a multiplex analysis for 9 cytokines. Real-time polymerase chain reaction assay was used for estimating the relative BCG cell number in mice bladder tissue. RESULTS Bladder edema was induced by BCG (MOI 30 and 100), which progressed to an inflammatory infiltrate composed primarily of neutrophils and increased mBD2 secretion at 4 hours after instillation. Relative BCG cell number and urinary cytokine levels (interferon-γ and interleukins [IL]-2, -4, -6, and -10) response pattern was characterized by a peak at 4 hours after instillation followed by rapid decline. The levels of interferon-γ, and IL-1β, -2, -4, -6, and -10 and relative BCG cell numbers decreased in a dose-dependent manner according to pretreatment with rmBD2 protein, and the responses were potentiated in the anti-mBD2 pretreatment group at 4 hours after BCG (MOI 30) instillation. CONCLUSION The present results suggest that the mouse urothelium produces mBD2 in response to intravesicular BCG as a defense mechanism against BCG, and blocking mBD2 by an anti-mBD2 antibody increased the effectiveness of BCG.
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Affiliation(s)
- Jong Kyou Kwon
- Department of Urology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Byung Hoon Chi
- Department of Urology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Se Young Choi
- Department of Urology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Soon-Ja Kim
- Department of Urology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Tae-Jin Lee
- Department of Pathology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Kijeong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - In Ho Chang
- Department of Urology, Chung-Ang University Hospital, Seoul, Republic of Korea.
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Evaluation of performance of the Real-Q NTM-ID kit for rapid identification of eight nontuberculous mycobacterial species. J Clin Microbiol 2014; 52:4053-5. [PMID: 25165078 DOI: 10.1128/jcm.01957-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We evaluated a multiplex real-time PCR and melting curve analysis assay (Real-Q NTM-ID kit; Biosewoom, Seoul, South Korea) for the identification of eight common nontuberculous mycobacterial species, using 30 type strains and 230 consecutive clinical isolates. The concordance rate of this assay with multigene sequence-based typing was 97.0% (223/230 isolates).
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Albuquerque YMMD, Lima ALMDA, Lins AK, Magalhães M, Magalhães V. Quantitative real-time PCR (q-PCR) for sputum smear diagnosis of pulmonary tuberculosis among people with HIV/AIDS. Rev Inst Med Trop Sao Paulo 2014; 56:139-42. [PMID: 24626416 PMCID: PMC4085841 DOI: 10.1590/s0036-46652014000200009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 08/01/2013] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVE To assess quantitative real-time polymerase chain reaction (q-PCR) for the sputum smear diagnosis of pulmonary tuberculosis (PTB) in patients living with HIV/AIDS with a clinical suspicion of PTB. METHOD This is a prospective study to assess the accuracy of a diagnostic test, conducted on 140 sputum specimens from 140 patients living with HIV/AIDS with a clinical suspicion of PTB, attended at two referral hospitals for people living with HIV/AIDS in the city of Recife, Pernambuco, Brazil. A Löwenstein-Jensen medium culture and 7H9 broth were used as gold standard. RESULTS Of the 140 sputum samples, 47 (33.6%) were positive with the gold standard. q-PCR was positive in 42 (30%) of the 140 patients. Only one (0.71%) did not correspond to the culture. The sensitivity, specificity and accuracy of the q-PCR were 87.2%, 98.9% and 95% respectively. In 39 (93%) of the 42 q-PCR positive cases, the CT (threshold cycle) was equal to or less than 37. CONCLUSION q-PCR performed on sputum smears from patients living with HIV/AIDS demonstrated satisfactory sensitivity, specificity and accuracy, and may therefore be recommended as a method for diagnosing PTB.
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Affiliation(s)
- Yvana Maria Maia de Albuquerque
- Tropical Medicine Post-graduation, Universidade Federal de Pernambuco, RecifePE, Brazil, Tropical Medicine Post-graduation, Universidade Federal de Pernambuco, Recife-PE, Brazil
| | | | - Ana Kelly Lins
- Laboratório Marcelo Magalhães, RecifePE, Brazil, Laboratório Marcelo Magalhães, Recife-PE, Brazil
| | - Marcelo Magalhães
- Laboratório Marcelo Magalhães, RecifePE, Brazil, Laboratório Marcelo Magalhães, Recife-PE, Brazil
| | - Vera Magalhães
- Tropical Medicine Post-graduation, Universidade Federal de Pernambuco, RecifePE, Brazil, Tropical Medicine Post-graduation, Universidade Federal de Pernambuco, Recife-PE, Brazil
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Shekhawat SD, Jain RK, Gaherwar HM, Purohit HJ, Taori GM, Daginawala HF, Kashyap RS. Heat shock proteins: possible biomarkers in pulmonary and extrapulmonary tuberculosis. Hum Immunol 2013; 75:151-8. [PMID: 24269695 DOI: 10.1016/j.humimm.2013.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 10/08/2013] [Accepted: 11/11/2013] [Indexed: 11/17/2022]
Abstract
Tuberculosis (TB) and Tuberculous meningitis (TBM) caused by Mycobacterium tuberculosis (MTB) continue to be a major cause of morbidity and mortality. Therefore there is a need to explore potential biomarkers and heat shock proteins [Hsp(s)] could be one such candidate. We found that host (Hsp 25, Hsp 60, Hsp 70 and Hsp 90) and MTB Hsp(s) (Hsp 16, Hsp 65 and Hsp 71) to be an important feature of the immune response in human clinical samples of pulmonary and extrapulmonary TB patients and in MTB infected monocytes. Notably, the host (Hsp 25, Hsp 70 and Hsp 90) and MTB (Hsp 16, Hsp 65 and Hsp 71) Hsp(s) increases significantly in the clinical samples as well as in cell line model after TB infection. Collectively, results revealed that alteration in immune response leads to a change in the both host and MTB Hsp profile, highlighting them as possible biomarkers for the disease.
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Affiliation(s)
- Seema D Shekhawat
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur 440 010, India
| | - Ruchika K Jain
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur 440 010, India
| | - Hari M Gaherwar
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur 440 010, India
| | - Hemant J Purohit
- Environmental Genomics Unit, National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440 020, India
| | - Girdhar M Taori
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur 440 010, India
| | - Hatim F Daginawala
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur 440 010, India
| | - Rajpal S Kashyap
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur 440 010, India.
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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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Abstract
In recent years, quantitative real-time PCR tests have been extensively developed in clinical microbiology laboratories for routine diagnosis of infectious diseases, particularly bacterial diseases. This molecular tool is well-suited for the rapid detection of bacteria directly in clinical specimens, allowing early, sensitive and specific laboratory confirmation of related diseases. It is particularly suitable for the diagnosis of infections caused by fastidious growth species, and the number of these pathogens has increased recently. This method also allows a rapid assessment of the presence of antibiotic resistance genes or gene mutations. Although this genetic approach is not always predictive of phenotypic resistances, in specific situations it may help to optimize the therapeutic management of patients. Finally, an approach combining the detection of pathogens, their mechanisms of antibiotic resistance, their virulence factors and bacterial load in clinical samples could lead to profound changes in the care of these infected patients.
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Affiliation(s)
- Max Maurin
- Laboratoire de Bactériologie, Département des Agents Infectieux, Institut de Biologie et Pathologie, CHU de Grenoble, Université Joseph Fourier Grenoble 1, France.
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Yin X, Zheng L, Wu L, Cao N, Zheng F, Hu Y, Lin M, Zhang P, Wang Q. Comparative evaluation of two rapid methods for differentiating mycobacteria. Tuberculosis (Edinb) 2013; 93:227-31. [PMID: 23414675 DOI: 10.1016/j.tube.2013.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 01/08/2013] [Accepted: 01/10/2013] [Indexed: 10/27/2022]
Abstract
The real-time PCR with duplex primer sets and the MPB64-based immunochromatographic assay are newly developed methods for rapid differentiation of mycobacteria. The aim of this study is to evaluate the two methods for differentiation between Mycobacterium tuberculosis complex and nontuberculous mycobacteria. A total of 95 clinical mycobacterial isolates belonging to 22 different species and 16 reference strains of 16 different species were differentiated by duplex real-time PCR method and MPB64-based immunochromatographic assay method. The two methods were evaluated by comparison with conventional biochemical technique as the gold standard method. The duplex real-time PCR method correctly differentiated all reference strains as well as the MPB64-based immunochromatographic assay method. For clinical isolates, the accuracy of the duplex real-time PCR method (100%) was slightly higher than the MPB64-based immunochromatographic assay method (97.9%), but there was no statistical significance between the two methods (P > 0.05), and there was an excellent agreement between them (Kappa = 0.957). The duplex real-time PCR method possesses greater potential for differentiation of mycobacteria in the clinical laboratory than the MPB64-based immunochromatographic assay method. However, the MPB64-based immunochromatographic assay method is more convenient than the duplex real-time PCR method when the number of sample is small.
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Affiliation(s)
- Xiaomao Yin
- Laboratory Medical Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province 510515, PR China
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Comparison of a DNA Based PCR Approach with Conventional Methods for the Detection of Mycobacterium tuberculosis in Morocco. Mediterr J Hematol Infect Dis 2012; 4:e2012049. [PMID: 22973493 PMCID: PMC3435128 DOI: 10.4084/mjhid.2012.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 07/09/2012] [Indexed: 01/22/2023] Open
Abstract
Background Worldwide, tuberculosis (TB) is a major public health problem and the rapid diagnosis and appropriate chemotherapy become the first priority and a serious challenge to improve TB treatment. In the objective of early TB diagnosis and rapid detection of Mycobacterium tuberculosis (MTB) in the clinical specimens, the utility of the Polymerase Chain Reaction (PCR) using the Insertion Sequence 6110 “IS6110" as target was compared to conventional methods. Methods Out of 305 patients with different clinical manifestations: suspected, new, drug relapse, drug failure and chronic cases were enrolled in this study and tested by mycobacteriological and PCR techniques for the investigation about the tubercle bacilli. Results The results of the in house “IS6110" PCR showed a good sensitivity (92.4%) and high specificity (98.0%), the positive and negative predictive values were 96.4 % and 95.3 % respectively. Conclusion This study showed clearly that the PCR testing using the “IS6110" in the routine analysis is a potential tool for the rapid TB diagnosis, especially for critical cases and would be of great interest to help the clinician in the misdiagnosed critical cases by the traditional radiology.
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Choi YJ, Kim HJ, Shin HB, Nam HS, Lee SH, Park JS, Park KS, Baek KA. Evaluation of peptide nucleic acid probe-based real-time PCR for detection of Mycobacterium tuberculosis complex and nontuberculous mycobacteria in respiratory specimens. Ann Lab Med 2012; 32:257-63. [PMID: 22779066 PMCID: PMC3384806 DOI: 10.3343/alm.2012.32.4.257] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 02/17/2012] [Accepted: 05/15/2012] [Indexed: 02/03/2023] Open
Abstract
Background A peptide nucleic acid (PNA) probe-based real-time PCR (PNAqPCR™ TB/NTM detection kit; PANAGENE, Korea) assay has been recently developed for the simultaneous detection of Mycobacterium tuberculosis complex (MTBC) and nontuberculous mycobacteria (NTM) in clinical specimens. The study was aimed at evaluation of the performance of PNA probe-based real-time PCR in respiratory specimens. Methods To evaluate potential cross-reactivity, the extracted DNA specimens from Mycobacterium species and non-mycobacterial species were tested using PNA probe-based real-time PCR assay. A total of 531 respiratory specimens (482 sputum specimens and 49 bronchoalveolar washing fluid specimens) were collected from 230 patients in July and August, 2011. All specimens were analyzed for the detection of mycobacteria by direct smear examination, mycobacterial culture, and PNA probe-based real-time PCR assay. Results In cross-reactivity tests, no false-positive or false-negative results were evident. When the culture method was used as the gold standard test for comparison, PNA probe-based real-time PCR assay for detection of MTBC had a sensitivity and specificity of 96.7% (58/60) and 99.6% (469/471), respectively. Assuming the combination of culture and clinical diagnosis as the standard, the sensitivity and specificity of the new real-time PCR assay for detection of MTBC were 90.6% (58/64) and 99.6% (465/467), respectively. The new real-time PCR for the detection of NTM had a sensitivity and specificity of 69.0% (29/42) and 100% (489/489), respectively. Conclusions The new real-time PCR assay may be useful for the detection of MTBC in respiratory specimens and for discrimination of NTM from MTBC.
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Affiliation(s)
- Young Jin Choi
- Department of Laboratory Medicine, Soonchunhyang University College of Medicine, Cheonan, Korea.
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Kim BJ, Yi SY, Shim TS, Do SY, Yu HK, Park YG, Kook YH, Kim BJ. Discovery of a novel hsp65 genotype within Mycobacterium massiliense associated with the rough colony morphology. PLoS One 2012; 7:e38420. [PMID: 22693637 PMCID: PMC3367924 DOI: 10.1371/journal.pone.0038420] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 05/09/2012] [Indexed: 11/19/2022] Open
Abstract
So far, genetic diversity among strains within Mycobacterium massiliense has rarely been studied. To investigate the genetic diversity among M. massiliense, we conducted phylogenetic analysis based on hsp65 (603-bp) and rpoB (711-bp) sequences from 65 M. massiliense Korean isolates. We found that hsp65 sequence analysis could clearly differentiate them into two distinct genotypes, Type I and Type II, which were isolated from 35 (53.8%) and 30 patients (46.2%), respectively. The rpoB sequence analysis revealed a total of four genotypes (R-I to R-IV) within M. massiliense strains, three of which (R-I, R-II and R-III) correlated with hsp65 Type I, and other (R-IV), which correlated with Type II. Interestingly, genotyping by the hsp65 method agreed well with colony morphology. Despite some exceptions, Type I and II correlated with smooth and rough colonies, respectively. Also, both types were completely different from one another in terms of MALDI-TOF mass spectrometry profiles of whole lipid. In addition, we developed PCR-restriction analysis (PRA) based on the Hinf I digestion of 644-bp hsp65 PCR amplicons, which enables the two genotypes within M. massiliense to be easily and reliably separated. In conclusion, two distinct hsp65 genotypes exist within M. massiliense strains, which differ from one another in terms of both morphology and lipid profile. Furthermore, our data indicates that Type II is a novel M. massiliense genotype being herein presented for the first time. The disparity in clinical traits between these two hsp65 genotypes needs to be exploited in the future study.
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Affiliation(s)
- Byoung-Jun Kim
- Department of Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Su-Yeon Yi
- Department of Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Tae-Sun Shim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, Republic of Korea
| | - Seung Yeon Do
- Department of Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hee-Kyung Yu
- Korean Institute of Tuberculosis, Korean National Tuberculosis Association, Chungcheongbuk-Do, Republic of Korea
| | - Young-Gil Park
- Korean Institute of Tuberculosis, Korean National Tuberculosis Association, Chungcheongbuk-Do, Republic of Korea
| | - Yoon-Hoh Kook
- Department of Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
- * E-mail:
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25
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Palomino JC. Current developments and future perspectives for TB diagnostics. Future Microbiol 2012; 7:59-71. [PMID: 22191447 DOI: 10.2217/fmb.11.133] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
TB persists as a global epidemic with high morbidity and mortality, especially in low-income countries. It is the only infectious disease ever declared as a global emergency by the WHO. The HIV pandemic and the emergence of drug resistance represent two additional obstacles to better control of the disease. Important progress has been made in the last decade in TB diagnostics. Major needs still exist, such as the availability of a real point-of-care test, a better diagnosis of TB in immune-compromised populations and in children, and the possibility to predict progression to disease in latently infected people. This review will summarize the current developments in TB diagnostics and the perspectives for future developments in the field.
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Affiliation(s)
- Juan Carlos Palomino
- Mycobacteriology Unit, Institute of Tropical Medicine, Nationalestraat 155, 2000, Antwerp, Belgium.
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26
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Perng CL, Chen HY, Chiueh TS, Wang WY, Huang CT, Sun JR. Identification of non-tuberculous mycobacteria by real-time PCR coupled with a high-resolution melting system. J Med Microbiol 2012; 61:944-951. [PMID: 22493281 DOI: 10.1099/jmm.0.042424-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are increasingly important opportunistic pathogens responsible for a variety of clinical diseases. The aim of this study was to evaluate a novel technique, real-time PCR coupled with high-resolution melting analysis (real-time PCR-HRMA), for NTM identification. Two pairs of unique primers targeted to the 16S rRNA gene and the 16S-23S internal transcribed spacer region were selected for further evaluation. A total of 149 mycobacterial clinical isolates were subjected to analysis using the real-time PCR-HRMA system. Overall, 134 NTM identified by the 16S rRNA full-gene sequencing method were categorized into four major groups: Mycobacterium avium complex, Mycobacterium chelonae group, Mycobacterium gordonae and Mycobacterium fortuitum group. Of the 134 prevalent mycobacterial isolates, 101 mycobacteria (75.4 %) could be identified correctly by the real-time PCR-HRMA system. The individual sensitivities for the M. avium complex, M. chelonae group, M. gordonae and M. fortuitum groups were 90.9, 89.1, 100 and 36.8 %, respectively. The specificity of identifying these groups varied from 96.4 to 100 %. When identification failed, mostly it was attributable to various species in the M. fortuitum group. The real-time PCR-HRMA system is therefore a rapid and sensitive method for identifying prevalent NTM in a clinical laboratory.
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Affiliation(s)
- Cherng-Lih Perng
- Graduate Institute of Pathology, National Defense Medical Center, Taipei, Taiwan, ROC.,Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan, ROC
| | - Hsing-Yu Chen
- Department of Clinical Pathology, Taipei City Hospital Renai Branch, Taipei, Taiwan, ROC
| | - Tzong-Shi Chiueh
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan, ROC.,Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan, ROC
| | - Wei-Yao Wang
- Division of Infectious Disease, Fong-Yuan Hospital, Taichung, Taiwan, ROC.,Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chun-Ting Huang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan, ROC
| | - Jun-Ren Sun
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan, ROC.,Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan, ROC
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27
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Multiplex real-time PCR assay and melting curve analysis for identifying Mycobacterium tuberculosis complex and nontuberculous mycobacteria. J Clin Microbiol 2011; 50:483-7. [PMID: 22162553 DOI: 10.1128/jcm.06155-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multiplex real-time PCR assay and melting curve analysis for identifying 23 mycobacterial species was developed and evaluated using 77 reference strains and 369 clinical isolates. Concordant results were obtained for all 189 (100%) isolates of the Mycobacterium tuberculosis complex and 169 (93.9%) isolates of nontuberculous mycobacteria. Our results showed that this multiplex real-time PCR assay is an effective tool for the mycobacterial identification from cultures.
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28
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Sankar S, Ramamurthy M, Nandagopal B, Sridharan G. An appraisal of PCR-based technology in the detection of Mycobacterium tuberculosis. Mol Diagn Ther 2011; 15:1-11. [PMID: 21250760 DOI: 10.1007/bf03257188] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Tuberculosis is an under-recognized yet catastrophic health problem, particularly in developing countries. The HIV pandemic has served to increase the number of susceptible individuals, and multidrug-resistance and poor socioeconomic conditions also augment the prevalence and the consequences of the disease. To control the disease and its spread, it is vital that tuberculosis diagnostics are accurate and rapid. Whereas microscopy and culture have several limitations (low sensitivity is a problem for the former, while the latter has a delayed turnaround time), PCR-based techniques targeting regions of the Mycobacterium tuberculosis genome such as IS6110 have proved to be useful. The purpose of this review is to assess the use of PCR-RFLP, nested PCR and real-time PCR protocols and the choice of target regions for the detection of M. tuberculosis. Real-time PCR for the detection of M. tuberculosis target genes in clinical specimens has contributed to improving diagnosis and epidemiologic surveillance in the past decade. However, targeting one genome sequence such as IS6110 may not by itself be sufficiently sensitive to reach 100% diagnosis, especially in the case of pulmonary tuberculosis. Additional testing for target genome sequences such as hsp65 seems encouraging. An interesting approach would be a multiplex real-time PCR targeting both IS6110 and hsp65 to achieve comprehensive and specific molecular diagnosis. This technology needs development and adequate field testing before it becomes the acceptable gold standard for diagnosis.
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Affiliation(s)
- Sathish Sankar
- Division of Biomedical Research, Sri Narayani Hospital and Research Centre, Thirumalaikodi, Sripuram, Vellore, Tamil Nadu, India.
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29
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First report of disseminated Mycobacterium skin infections in two liver transplant recipients and rapid diagnosis by hsp65 gene sequencing. J Clin Microbiol 2011; 49:3733-8. [PMID: 21880973 DOI: 10.1128/jcm.05088-11] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We present here the first report of disseminated skin Mycobacterium infections in two liver transplant recipients, in which hsp65 gene sequencing was used for rapid species identification. Both patients had hepatitis B virus-related cirrhosis and diabetes mellitus and presented with progressive generalized, nodular skin lesions. In one patient, a 50-year-old woman who had frequent contact with marine fish, an acid-fast bacillus was isolated from skin biopsy tissue after 2 months of culture. While awaiting phenotypic identification results, hsp65 gene sequencing showed that it was most closely related to that of Mycobacterium marinum with 100% nucleotide identity. The patient was treated with oral rifampin, ethambutol, and moxifloxacin. In the other patient, a 59-year-old woman, direct PCR for Mycobacterium using hsp65 gene from skin biopsy tissue was positive, with the sequence most closely related to that of M. haemophilum with 100% nucleotide identity. Based on PCR results, the patient was treated with clarithromycin, ethambutol, moxifloxacin, and amikacin. A strain of M. haemophilum was only isolated after 3 months. Skin lesions of both patients resolved after 1 year of antimycobacterial therapy. Nontuberculous Mycobacterium infections should be considered in liver transplant recipients presenting with chronic, nodular skin lesions. This report highlights the crucial role of hsp65 gene PCR and sequencing on both cultured isolates and direct clinical specimens for rapid diagnosis of slow-growing Mycobacterium infection.
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