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Muacevic A, Adler JR, LNU P, Sharma K, Sharma A, Sharma N, Modi M. Comparison of Protein B Polymerase Chain Reaction (PCR) With IS6110 PCR for Diagnosis of Tuberculous Meningitis Patients. Cureus 2023; 15:e33783. [PMID: 36798623 PMCID: PMC9926138 DOI: 10.7759/cureus.33783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2023] [Indexed: 01/16/2023] Open
Abstract
Purpose Tuberculous meningitis (TBM) is a diagnostic challenge. With the conventional staining and culture techniques being too insensitive and time-consuming, and the commercial detection systems being costly, polymerase chain reaction (PCR) seems lucrative for routine laboratories. The purpose of this study was to evaluate the diagnostic potential of protein b antigen polymerase chain reaction (Pab PCR) for TBM, in comparison to IS6110. Another purpose was to compute a cut-off at which adenosine deaminase (ADA) could diagnose TBM. Material and methods This is a prospective case-control study to measure the diagnostic accuracy of PCR, BACTEC culture, Lowenstein-Jensen (LJ) culture, ADA, and acid-fast bacilli (AFB) smear tests in TBM. CSF from 50 TBM patients (10 confirmed, 40 clinically suspected) and 40 controls was subjected to Pab PCR and IS6110 PCR, and performance was compared against culture and composite reference standards. Results The overall sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of Pab PCR in diagnosing TBM were 82%, 100%, 100%, and 81.63%, respectively, and that of IS6110 PCR were 74%, 100%, 100%, and 75.47%, respectively. Both PCRs outperformed culture (p<0.001). Though performance of both PCRs was comparable (p=0.335) with excellent agreement (k=0.86), Pab PCR detected four additional cases, one culture-positive and three culture-negative clinically suspected. ADA of 6.5 IU/L was able to differentiate between TBM and non-TBM with 86% sensitivity and 63% specificity. Conclusions Molecular tools such as PCR have the potential to increase the clinician's ability to diagnose tuberculous meningitis. Pab PCR is a rapid and reliable method for diagnosing TBM in routine microbiology laboratories.
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Datta A, Gupta P, Bhattacharya B, Das A, Chatterjee S, Banerjee A. Evidence of sexual transfer of mycobacteria from male to female partners reporting to an IVF clinic. Trop Doct 2022; 52:331-334. [PMID: 35196202 DOI: 10.1177/00494755221074754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Female genital tuberculosis (GTB) contributes significantly to infertility in low- and middle-income countries. Dissemination of infection from pulmonary and extrapulmonary sites is the major reason for causation of GTB. Additionally, sexual transmission of GTB from male partners has been reported. We selected 81 couples desiring babies from an in vitro fertilization clinic. We used multiplex-PCR for mycobacterial detection in semen of males, in the endometrium of their female counterparts and in the products of conception (POC) from miscarriage. Data interpretation shows that these pregnancies failed owing to sexual transmission of mycobacteria. We noticed by multiplex PCR that mycobacterial infestation in the female can take place in either endometrium or POC from asymptomatic males harbouring mycobacteria in their semen. Therefore, we propose sexual transfer of mycobacteria to be a probable cause of miscarriage. Thus, we suggest multiplex PCR based screening of semen for all males of the couples attempting successful childbirth.
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Affiliation(s)
- Abira Datta
- Central Research Laboratory, PGIMSR and ESI hospital, Kankurgachhi, Kolkata, West Bengal, India.,Reproductive Medicine Unit, Calcutta Fertility Mission, Kolkata, West Bengal, India
| | - Prabuddha Gupta
- Amity Institute of Biotechnology Kolkata, 530170Amity University Kolkata, Major Arterial Road (South-East), Action Area II, Newtown, Kolkata, West Bengal, India
| | - Basudev Bhattacharya
- Reproductive Medicine Unit, Calcutta Fertility Mission, Kolkata, West Bengal, India
| | - Arabinda Das
- Department of Statistics, 271538Acharya Prafulla Chandra College, West Bengal, India
| | | | - Asesh Banerjee
- Amity Institute of Biotechnology Kolkata, 530170Amity University Kolkata, Major Arterial Road (South-East), Action Area II, Newtown, Kolkata, West Bengal, India
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Ahlawat S, Chaudhary R, Dangi M, Bala K, Singh M, Chhillar AK. Advances in tuberculous meningitis diagnosis. Expert Rev Mol Diagn 2020; 20:1229-1241. [PMID: 33259249 DOI: 10.1080/14737159.2020.1858805] [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: 10/22/2022]
Abstract
Introduction: Tuberculous meningitis (TBM) is the most devastating form of central nervous system tuberculosis (TB) and causes high mortality worldwide. Nonspecific clinical manifestations and limited sensitivity of existing laboratory methods make the diagnosis elusive due to the paucibacillary nature of the infection. Areas Covered: We reviewed current literature on the adequacy and limitations of globally existing laboratory methods for diagnosing TBM. Expert opinion: TBM is deadliest among all TB forms, as the outcome may lead to death in 50% of cases, and survivors undergo irreversible neurological disorders. Therefore, early diagnosis and prompt treatment are cornerstones of effective disease management. Conventional microscopy and culture are widely used modalities but remain inadequate in most TBM cases. Although expanded use of rapid molecular tests such as real-time PCR and Xpert Ultra, even in resource-limited settings, hold promising results for TB diagnosis but need optimization for early detection of TBM. Moreover, CSF IGRA is also used but unable to differentiate between active and latent TB. Overall no single test for diagnosing TBM has adequate accuracy so, there is an urgent need to devise a point-of-care test.
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Affiliation(s)
- Sonia Ahlawat
- Centre for Biotechnology, Maharshi Dayanand University (MDU) , Rohtak, India.,Amity Institute of Biotechnology, Amity University Haryana , Manesar, India
| | - Renu Chaudhary
- Council of Scientific & Industrial Research (CSIR)-institute of Genomics and Integrative Biology (IGIB) , New Delhi, India
| | - Mehak Dangi
- Department of Bioinformatics, Maharshi Dayanand University (MDU) , Rohtak, India
| | - Kiran Bala
- Department of Neurology, University of Health Sciences (UHS) , Rohtak, India
| | - Machiavelli Singh
- Amity Institute of Biotechnology, Amity University Haryana , Manesar, India
| | - Anil Kumar Chhillar
- Centre for Biotechnology, Maharshi Dayanand University (MDU) , Rohtak, India
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Berwal A, Chawla K, Vishwanath S, Shenoy VP. Role of multiplex polymerase chain reaction in diagnosing tubercular meningitis. J Lab Physicians 2020; 9:145-147. [PMID: 28367034 PMCID: PMC5320881 DOI: 10.4103/0974-2727.199633] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Tuberculous meningitis (TBM) is one of the most serious manifestations of extrapulmonary tuberculosis. Timely and accurate diagnosis provides a favorable prognosis in patients with TBM. The study evaluated the use of multiplex polymerase chain reaction (PCR) in the diagnosis of TBM. A study was conducted on 74 patients clinically suspected with TBM. The cerebrospinal fluid (CSF) specimens were processed for smear microscopy, middle brook 7H9 culture, and multiplex PCR using primers directed against IS6110 gene and 38 kD protein for detection of Mycobacterium tuberculosis. The results were analyzed to assess the role of multiplex PCR in the diagnosis of TBM. A total of 26 (35.1%) patients were diagnosed with TBM. Microscopy was negative in all while culture was positive in two cases only. Comparing with clinical diagnosis and CSF adenosine deaminase levels of ≥10 U/L, multiplex PCR showed sensitivity, specificity, positive predictive value, and negative predictive value of 71.4%, 89.6%, 83.3%, and 81.2%, respectively, in the diagnosis of TBM.
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Affiliation(s)
- Anupam Berwal
- Department of Microbiology, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Kiran Chawla
- Department of Microbiology, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Shashidhar Vishwanath
- Department of Microbiology, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Vishnu Prasad Shenoy
- Department of Microbiology, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
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Paine SK, Basu A, Choudhury RG, Bhattacharya B, Chatterjee S, Bhattacharya C. Multiplex PCR from Menstrual Blood: A Non-Invasive Cost-Effective Approach to Reduce Diagnostic Dilemma for Genital Tuberculosis. Mol Diagn Ther 2018; 22:391-396. [PMID: 29549658 DOI: 10.1007/s40291-018-0322-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
AIM Genital tuberculosis (GTB) is a potent contributor to irreversible damage to the reproductive system and infertility in females. As no gold standard diagnostic tool is yet available, clinical suspicion and relatively insensitive approaches such as histopathology, laparoscopy and hysterosalpingogram are currently critical determinants in the diagnosis of GTB. Although a polymerase chain reaction (PCR)-based assay using endometrial tissue seems promising, sampling does require an invasive procedure. OBJECTIVE We hypothesized that menstrual blood may provide an alternate non-invasive source of samples for PCR-based GTB diagnosis. METHODS We enrolled 195 women with primary infertility in whom GTB was suspected. We obtained ethics committee approval from our institution and written informed consent from subjects. Endometrial tissue and menstrual blood was collected from the subjects and culture, histopathology, and multiplex PCR with both sample type was performed for each subject. RESULTS The sensitivity and specificity of multiplex PCR was, respectively, 90.2 and 86.1% for menstrual blood, 95.8 and 84.3% for endometrial tissue, and 64.8 and 93.2% for histopathology staining. CONCLUSIONS A strong clinical suspicion aided with multiplex PCR using menstrual blood may significantly reduce the diagnostic dilemma for GTB diagnosis in a non-invasive, sensitive, rapid, and cost-effective manner.
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Affiliation(s)
- Suman K Paine
- ICMR-Regional Medical Research Centre, NE Region, Assam, 786001, India.
| | - Analabha Basu
- National Institute of Biomedical Genomics, Kalyani, India
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Hu LX, Yang ZH, Zhang D, Zhao DM, Zhu JH. Sensitive and rapid detection of Pectobacterium atrosepticum by targeting the gyrB gene using a real-time loop-mediated isothermal amplification assay. Lett Appl Microbiol 2017; 63:289-96. [PMID: 27450435 DOI: 10.1111/lam.12618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 11/29/2022]
Abstract
UNLABELLED This study reports the development of a real-time, loop-mediated isothermal amplification (RealAmp) assay for the detection of Pectobacterium atrosepticum (P. atrosepticum). A phylogenetic tree was constructed based on the gyrB gene of P. atrosepticum and related species. Pectobacterium atrosepticum from different sources can be clustered in the same branch with 100% support rate. The RealAmp primers targeting the gyrB gene of P. atrosepticum worked most efficiently at 61·0°C. Compared with 55 related bacterial strains, the eight P. atrosepticum strains displayed positive reaction in the RealAmp assay. The melting temperature (Tm) of P. atrosepticum amplified products was about 85·0°C. The detection limit of the RealAmp assay for the detection of P. atrosepticum in pure culture was approx. 3 CFU reaction(-1) . The detection limit of the RealAmp assay for the detection of P. atrosepticum in artificially contaminated samples was 22 CFU reaction(-1) . The detection rate of the RealAmp assay for the detection of potato tubers was 28·5-32·0% higher than that of the conventional PCR. In summary, a specific, sensitive and rapid RealAmp assay based on the gyrB gene of P. atrosepticum, which can be easily performed and real-time monitored, was established. SIGNIFICANCE AND IMPACT OF THE STUDY Potato blackleg caused by Pectobacterium atrosepticum (P. atrosepticum) which is mainly transmitted through the seed potato leads to the decline in potato production. To reduce yield loss, rapid detection of P. atrosepticum in seed potato remains essential. Based on the gyrB gene of P. atrosepticum, species-specific primers were designed. A real-time, loop-mediated isothermal amplification (RealAmp) assay was established for the detection of P. atrosepticum. The RealAmp assay is a specific, rapid and sensitive method for P. atrosepticum detection. Therefore, it provides an effective diagnosis of potato blackleg in both the growing and stored potato.
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Affiliation(s)
- L X Hu
- College of Plant Protection, Agricultural University of Hebei, Baoding, China
| | - Z H Yang
- College of Plant Protection, Agricultural University of Hebei, Baoding, China
| | - D Zhang
- College of Plant Protection, Agricultural University of Hebei, Baoding, China
| | - D M Zhao
- College of Plant Protection, Agricultural University of Hebei, Baoding, China
| | - J H Zhu
- College of Plant Protection, Agricultural University of Hebei, Baoding, China.
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Akhtar F, Javed MT, Khan MN, Akhtar P, Hussain SM, Aslam MS, Kausar R, Qamar M, Cagiola M. The use of PCR technique in the identification of Mycobacterium species responsible for bovine tuberculosis in cattle and buffaloes in Pakistan. Trop Anim Health Prod 2015; 47:1169-75. [PMID: 25953024 DOI: 10.1007/s11250-015-0844-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 04/28/2015] [Indexed: 12/01/2022]
Abstract
Bovine tuberculosis is one of the important diseases of dairy and wild animals. The disease is prevalent all over the world, though developed countries have tremendously reduced the prevalence through eradication campaigns. The prevalence of disease in Pakistan on the basis of tuberculin testing or culture isolation of the organism has been reported previously. It is, however, important to use the latest diagnostic tools, i.e. PCR to confirm the type of Mycobacterium infecting the animals in Pakistan. Therefore, the present study was carried out to assess the utility of direct PCR on milk samples and nasal swabs to confirm the type of Mycobacterium infecting the animals. This study was carried out on 215 cattle and buffaloes of more than 2 years of age present at two livestock farms. The tuberculin results showed 22.5% prevalence at one farm and 25.9% at the other with an overall prevalence of 24.7%. The 92.5% of milk samples and/or nasal swabs showed positive PCR for Mycobacterium genus, 86.8% for Mycobacterium tuberculosis complex and 77.4% for Mycobacterium bovis. The M. bovis by PCR was detected in 13.2% of milk samples, 24.5% of nasal swabs and 39.6% of both milk samples + nasal swabs. The results suggested that there are 60% higher chance for a nasal swab to yield a positive PCR for M. bovis than the milk sample. It can be concluded from the present study that tuberculin testing is a useful method in studying the prevalence of disease as the PCR for Mycobacterium genus was positive in 92.5%, M. tuberculosis complex in 86.8% and Mycobacterium bovis in 77.4% cases.
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Affiliation(s)
- Farah Akhtar
- Department of Pathology, Faculty of Veterinary Science, University of Agriculture, Faisalabad, Pakistan
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8
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Correlates of treatment outcomes and drug resistance among pulmonary tuberculosis patients attending tertiary care hospitals of Kolkata, India. PLoS One 2014; 9:e109563. [PMID: 25289974 PMCID: PMC4188738 DOI: 10.1371/journal.pone.0109563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 09/02/2014] [Indexed: 12/03/2022] Open
Abstract
Background Worldwide highest number of new pulmonary tuberculosis (PTB) cases, was reported from India in 2012. Adverse treatment outcomes and emergence of drug resistance further complicated the prevailing scenario owing to increased duration, cost and toxicity associated with the treatment of drug-resistant cases. Hence to reinforce India’s fight against TB, identification of the correlates of adverse treatment outcomes and drug resistance, seemed critical. Methods To estimate the associations between diagnostic findings, patient types (based on treatment outcomes), drug resistance and socio-demographic characteristics of PTB patients, a cross-sectional study was conducted in two tertiary-care hospitals in Kolkata between April 2010 and March 2013. Altogether, 350 consenting Mycobacterium tuberculosis sputum-culture positive PTB patients were interviewed about their socio-demographic background, evaluated regarding their X-ray findings (minimal/moderately advanced/far advanced/cavities), sputum-smear positivity, and treatment history/outcomes (new/defaulter/relapse/treatment-failure cases). Multiple-allele-specific polymerase chain reaction (MAS-PCR) was conducted to diagnose drug resistance. Results Among all participants, 31.43% were newly diagnosed, while 44%, 15.43% and 9.14% patients fell into the categories of relapsed, defaulters and treatment-failures, respectively. 12.29% were multi-drug-resistant (MDR: resistant to at least isoniazid and rifampicin), 57.71% had non-MDR two-drug resistance and 12% had single-drug resistance. Subjects with higher BMI had lower odds of being a relapse/defaulter/treatment failure case while females were more likely to be defaulters and older age-groups had more relapse. Elderly, females, unmarried, those with low BMI and higher grade of sputum-smear positivity were more likely to have advanced X-ray features. Higher grade of sputum-smear positivity and advanced chest X-ray findings were associated with relapse/treatment-failures. Elderly, unmarried, relapse/defaulter/treatment-failure cases had higher odds and those with higher BMI and moderately/far advanced X-ray findings had lower odds of having MDR/non-MDR two-drug resistant PTB. Conclusion Targeted intervention and appropriate counseling are needed urgently to prevent adverse treatment outcomes and development of drug resistance among PTB patients in Kolkata.
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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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Tak T, Dhawan S, Reynolds C, Shukla SK. Current diagnosis and treatment of infective endocarditis. Expert Rev Anti Infect Ther 2014; 1:639-54. [PMID: 15482161 DOI: 10.1586/14787210.1.4.639] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The incidence of infective endocarditis continues to rise with a yearly incidence of around 15,000 to 20,000 new cases in the USA. As a result, rapid diagnosis, effective treatment and prompt recognition of complications are essential to desirable clinical outcomes. Recent guidelines such as the Duke criteria have incorporated echocardiography for diagnosis of infective endocarditis, making this diagnostic test mandatory for patients with suspected infective endocarditis. The diversity of pathogens that can cause infective endocarditis, some of which cannot be cultured easily, makes diagnosis even more difficult. Coagulase-negative staphylococci and viridans streptococci groups continue to be the major causative microorganisms of infective endocarditis. In the case of culture-negative endocarditis or infective endocarditis caused by fastidious microorganisms, the polymerase chain reaction and probe-based diagnostic methods are available to clinical reference laboratories.
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Affiliation(s)
- Tahir Tak
- Department of Internal Medicine, Marshfield Clinic, 1000 North Oak Avenue, Marshfield, WI 54449, USA.
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Rapid detection of Mycobacterium tuberculosis in clinical samples by multiplex polymerase chain reaction (mPCR). World J Microbiol Biotechnol 2013; 29:2389-95. [PMID: 23807412 DOI: 10.1007/s11274-013-1407-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 06/17/2013] [Indexed: 10/26/2022]
Abstract
Although the multi-copy and specific element IS6110 provides a good target for the detection of Mycobacterium tuberculosis complex by PCR techniques, the emergence of IS6110-negative strains suggested that false negative may occur if IS6110 alone is used as the target for detection. In this report, a multiplex polymerase chain reaction (mPCR) system was developed using primers derived from the insertion sequence IS6110 and an IS-like elements designated as B9 (GenBank accession no. U78639.1) to overcome the problem of detecting negative or low copy IS6110 containing strains of M. tuberculosis. The mPCR was evaluated using 346 clinical samples which included 283 sputum, 19 bronchial wash, 18 pleural fluid, 9 urine, 7 CSF, 6 pus, and 4 gastric lavage samples. Our results showed that the sensitivity (93.1 %) and specificity (89.6 %) of the mPCR system exceeds that of the conventional method of microscopy and culture. The mPCR assay provides an efficient strategy to detect and identify M. tuberculosis from clinical samples and enables prompt diagnosis when rapid identification of infecting mycobacteria is necessary.
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Calvo L, Gregorio I, García A, Fernández MT, Goñi P, Clavel A, Peleato ML, Fillat MF. A new pentaplex-nested PCR to detect five pathogenic bacteria in free living amoebae. WATER RESEARCH 2013; 47:493-502. [PMID: 23168310 DOI: 10.1016/j.watres.2012.09.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 09/19/2012] [Accepted: 09/21/2012] [Indexed: 06/01/2023]
Abstract
Changes in water use and anthropogenic activity have major impacts on the quality of natural aquatic ecosystems, water distribution and wastewater plants. One of the main problems is the presence of some pathogenic microorganisms that are resistant to disinfection procedures when they are hosted by free living amoeba and that in many cases are hardly detectable by culture-based procedures. In this work we report a sensitive, low-cost procedure consisting of a pentaplex-nested PCR that allows simultaneous detection of Legionella pneumophila, Mycobacterium spp., Pseudomonas spp., Vibrio cholerae and the microcystin-producing cyanobacteria Microcystis aeruginosa. The method has been used to detect the presence of these pathogenic bacteria in water and inside free living amoeba. Its validation in 72 samples obtained from different water sources from Aragon (Spain) evidences that Mycobacterium and Pseudomonas spp are prevailing as amoeba-resistant bacteria.
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Affiliation(s)
- L Calvo
- Department of Biochemistry and Molecular and Cell Biology, Faculty of Sciences, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
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Krothapalli S, May MK, Hestekin CN. Capillary electrophoresis-single strand conformation polymorphism for the detection of multiple mutations leading to tuberculosis drug resistance. J Microbiol Methods 2012; 91:147-54. [PMID: 22884688 PMCID: PMC3699206 DOI: 10.1016/j.mimet.2012.07.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Revised: 07/19/2012] [Accepted: 07/20/2012] [Indexed: 11/23/2022]
Abstract
Drug resistant tuberculosis (TB) is a major health problem in both developed and developing countries. Mutations in the Mycobacterium (M.) tuberculosis bacterial genome, such as those to the rpoB gene and mabA-inhA promoter region, have been linked to TB drug resistance in against rifampicin and isoniazid, respectively. The rapid, accurate, and inexpensive identification of these and other mutations leading to TB drug resistance is an essential tool for improving human health. Capillary electrophoresis (CE) single strand conformation polymorphism (SSCP) can be a highly sensitive technique for the detection of genetic mutation that has not been previously explored for drug resistance mutations in M. tuberculosis. This work explores the potential of CE-SSCP through the optimization of variables such as polymer separation matrix concentration, capillary wall coating, electric field strength, and temperature on resolution of mutation detection. The successful detection of an rpoB gene mutation and two mabA-inhA promoter region mutations while simultaneously differentiating a TB-causing mycobacteria from a non-TB bacteria was accomplished using the optimum conditions of 4.5% (w/v) PDMA in a PDMA coated capillary at 20°C using a separation voltage of 278 V/cm. This multiplexed analysis that can be completed in a few hours demonstrates the potential of CE-SSCP to be an inexpensive and rapid analysis method.
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Affiliation(s)
- Sowmya Krothapalli
- University of Arkansas, Department of Biomedical Engineering, Fayetteville, AR 4188 Bell Engineering Center, Fayetteville, AR-72701
| | - Michael K. May
- University of Arkansas, Department of Biomedical Engineering, Fayetteville, AR 4188 Bell Engineering Center, Fayetteville, AR-72701
| | - Christa N. Hestekin
- University of Arkansas, Department of Biomedical Engineering, Fayetteville, AR 4188 Bell Engineering Center, Fayetteville, AR-72701
- University of Arkansas, Department of Chemical Engineering, Fayetteville, AR 3202 Bell Engineering Center, Fayetteville, AR-72701
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Chowdhury IH, Sen A, Bahar B, Hazra A, Chakraborty U, Choudhuri S, Goswami A, Pal NK, Bhattacharya B. A molecular approach to identification and profiling of first-line-drug-resistant mycobacteria from sputum of pulmonary tuberculosis patients. J Clin Microbiol 2012; 50:2082-4. [PMID: 22461679 PMCID: PMC3372138 DOI: 10.1128/jcm.06093-11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 03/15/2012] [Indexed: 11/20/2022] Open
Abstract
Conventional and molecular techniques were applied to detect and characterize drug resistance of mycobacteria in the sputum samples of clinically confirmed tuberculosis. The sensitivities of mycobacterium detection by ZN staining, culture, multiplex PCR, and restriction fragment length polymorphism (RFLP) were 27.7%, 19.9%, 92.9%, and 95.7%, respectively, but all were 100% specific. The conventional and multiple-allele-specific PCR (MAS-PCR) methods enabled establishment of the drug resistance in 19.3% and 86.9% cases, respectively. We demonstrated that molecular techniques have potential in the accurate diagnosis of tuberculosis.
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Affiliation(s)
| | | | - Bojlul Bahar
- Cell and Molecular Biology Laboratory, School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
| | | | - Urmita Chakraborty
- Department of Microbiology, Institute of Postgraduate Medical Education and Research (IPGME&R), Kolkata, India
| | | | - Avranil Goswami
- Department of Microbiology, Institute of Postgraduate Medical Education and Research (IPGME&R), Kolkata, India
| | - Nishith Kumar Pal
- Department of Microbiology, Institute of Postgraduate Medical Education and Research (IPGME&R), Kolkata, India
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Lee CS, Lee J. Evaluation of new gyrB-based real-time PCR system for the detection of B. fragilis as an indicator of human-specific fecal contamination. J Microbiol Methods 2010; 82:311-8. [PMID: 20643165 DOI: 10.1016/j.mimet.2010.07.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 07/05/2010] [Accepted: 07/05/2010] [Indexed: 11/18/2022]
Abstract
A rapid and specific gyrB-based real-time PCR system has been developed for detecting Bacteroides fragilis as a human-specific marker of fecal contamination. Its specificity and sensitivity was evaluated by comparison with other 16S rRNA gene-based primers using closely related Bacteroides and Prevotella. Many studies have used 16S rRNA gene-based method targeting Bacteroides because this genus is relatively abundant in human feces and is useful for microbial source tracking. However, 16S rRNA gene-based primers are evolutionarily too conserved among taxa to discriminate between human-specific species of Bacteroides and other closely related genera, such as Prevotella. Recently, one of the housekeeping genes, gyrB, has been used as an alternative target in multilocus sequence analysis (MLSA) to provide greater phylogenetic resolution. In this study, a new B. fragilis-specific primer set (Bf904F/Bf958R) was designed by alignments of 322 gyrB genes and was compared with the performance of the 16S rRNA gene-based primers in the presence of B. fragilis, Bacteroides ovatus and Prevotella melaninogenica. Amplicons were sequenced and a phylogenetic tree was constructed to confirm the specificity of the primers to B. fragilis. The gyrB-based primers successfully discriminated B. fragilis from B. ovatus and P. melaninogenica. Real-time PCR results showed that the gyrB primer set had a comparable sensitivity in the detection of B. fragilis when compared with the 16S rRNA primer set. The host-specificity of our gyrB-based primer set was validated with human, pig, cow, and dog fecal samples. The gyrB primer system had superior human-specificity. The gyrB-based system can rapidly detect human-specific fecal source and can be used for improved source tracking of human contamination.
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Affiliation(s)
- Chang Soo Lee
- College of Public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, Ohio 43210, USA
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Poroca DDR, Lima AS, Lima JFDA, Cruz HLAD, Montenegro RDA, Melo FLD, Schindler HC, Montenegro LML. [Differentiation of micobacteria by multiplex PCR]. Rev Soc Bras Med Trop 2010; 42:716-22. [PMID: 20209361 DOI: 10.1590/s0037-86822009000600020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 11/09/2009] [Indexed: 11/22/2022] Open
Abstract
This study aimed to optimize a method based on the polymerase chain reaction - multiplex PCR - for differentiation of mycobacteria species of interest for public health. The multiplex PCR was based on simultaneous amplification of the hsp65 gene, which is present in all species of the Mycobacterium genus, the dnaJ gene, which is present only in Mycobacterium tuberculosis and Mycobacterium avium and the IS6110 insertion sequence, which is present in the Mycobacterium tuberculosis complex, generating amplicons of 165 bp, 365 bp and 541 bp, respectively. The detection limit was 1 fg for the hsp65 target, 100 pg for dnaJ and 0.1 fg for IS6110. The multiplex PCR detected down to 100 pg of DNA of Mycobacterium tuberculosis. The system was shown to be specific and sensitive for detection of Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium avium and Mycobacterium smegmatis. The results obtained using reference strains of mycobacteria showed that multiplex PCR may be a fast, sensitive and specific tool for differentiation of mycobacteria.
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Affiliation(s)
- Diogo da Rocha Poroca
- Laboratório de Imunoepidemiologia, Departamento de Imunologia, Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, PE
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17
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Zenteno-Cuevas R, Zenteno JC, Cuellar A, Cuevas B, Sampieri CL, Riviera JE, Parissi A. Mutations in rpoB and katG genes in Mycobacterium isolates from the Southeast of Mexico. Mem Inst Oswaldo Cruz 2009; 104:468-72. [PMID: 19547874 DOI: 10.1590/s0074-02762009000300012] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 01/28/2009] [Indexed: 11/21/2022] Open
Abstract
The most frequent mutations associated with rifampin and isoniazid resistance in Mycobacterium are the substitutions at codons 531 and 315 in the rpoB and katG genes, respectively. Hence, the aim of this study was to characterize these mutations in Mycobacterium isolates from patients suspected to be infected with drug-resistant (DR) pulmonary tuberculosis (TB) in Veracruz, Mexico. Drug susceptibility testing of 25 clinical isolates revealed that five were susceptible while 20 (80%) were DR (15% of the annual prevalence for Veracruz). Of the DR isolates, 15 (75%) were resistant to rifampin, 17 (85%) to isoniazid and 15 (75%) were resistant to both drugs (MDR). Sequencing analysis performed in the isolates showed that 14 (93%) had mutations in the rpoB gene; seven of these (47%) exhibited a mutation at 531 (S-->L). Ten (58%) of the 20 resistant isolates showed mutations in katG; nine (52%) of these 10 exhibited a mutation at 315 (S-->T). In conclusion, the DR profile of the isolates suggests a significant number of different DR-TB strains with a low frequency of mutation at codons 531 and 315 in rpoB and katG, respectively. This result leads us to consider different regions of the same genes, as well as other genes for further analysis, which is important if a genetic-based diagnosis of DR-TB is to be developed for this region.
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Affiliation(s)
- R Zenteno-Cuevas
- Laboratorio de Ecología y Salud, Instituto de Salud Pública, Universidad Veracruzana, Veracruz, México.
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18
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Deshpande PS, Kashyap RS, Ramteke SS, Nagdev KJ, Purohit HJ, Taori GM, Daginawala HF. Evaluation of the IS6110 PCR assay for the rapid diagnosis of tuberculous meningitis. Cerebrospinal Fluid Res 2007; 4:10. [PMID: 17976247 PMCID: PMC2206054 DOI: 10.1186/1743-8454-4-10] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2007] [Accepted: 11/02/2007] [Indexed: 12/03/2022] Open
Abstract
Background Tuberculous meningitis (TBM) is one of the common clinical manifestations of extra-pulmonary tuberculosis. It is difficult to diagnose due to a lack of rapid, sensitive, and specific tests. Newer methods, which are easy and reliable, are required to diagnose TBM at an early stage. Thus our aim was to evaluate the polymerase chain reaction (PCR) technique, using primers directed against the IS6110 gene, for the detection of Mycobacterium tuberculosis in the CSF, for the diagnosis of TBM patients. Methods An in-house IS6110 PCR method using a specific pair of primers designed to amplify the insertion sequence, IS6110, in the M. tuberculosis genome was used to analyze CSF. A total of 80 CSF samples from different groups of patients were studied (confirmed TBM n = 35, clinically suspected TBM n = 16, non-TBM infectious meningitis n = 12, non infectious neurological diseases n = 17). Results PCR gave a sensitivity of 91.4% and specificity of 75.9% for the diagnosis of TBM in patients with TBM confirmed by culture. In 16 clinically diagnosed, but unconfirmed, TBM cases PCR was positive in 10 (62.5%) cases. There were seven (24.1%) PCR-positive cases among the 29 patients with non-TBM and non-infectious neurological disease. Conclusion We conclude that the performance of an in-house IS6110 PCR assay is valuable in the rapid diagnosis of tuberculous meningitis.
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Affiliation(s)
- Poonam S Deshpande
- Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur, India, 440010.
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Ghosh A, Saha S, Bhattacharya B, Chattopadhay S. Primary tuberculosis of thyroid gland: a rare case report. Am J Otolaryngol 2007; 28:267-70. [PMID: 17606045 DOI: 10.1016/j.amjoto.2006.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Accepted: 09/12/2006] [Indexed: 11/20/2022]
Abstract
Tuberculosis of the thyroid gland is a rare entity, and primary tuberculosis of thyroid is even uncommon. At one time, it was believed that thyroid gland is relatively immune to tuberculosis. There are about 200 cases of thyroid tuberculosis that had been reported in world literature. These include 156 cases reviewed by Goldfarb et al (Am J Med 1965;38:825) and 1 each by Crompton et al (Tubercle 1969;50:61-64), Johnson et al (Br J Surg 1973;60:668-669), Emry (J Laryngol Otol 1980;94:553-558), and Kukreja and Sharma ML (Ind J Surg 1982;44:190-192), and a histologic diagnosis by Das et al (Acta Cytol 1992;36:517-522) and Mondal and Patra (J Laryngol Otol 1995;109:36-38). Almost all cases had primary foci elsewhere in the body. Isolated tuberculosis of the thyroid gland is extremely rare, with few reported cases; when it does occur, it may prove difficult to diagnose (J Laryngol Otol 1980;94:553-558). Among the different manifestations of tuberculous thyroiditis, abscess of the thyroid appears to be the rarest and the most dangerous (Tubercle 1969;50:61-64). Sachs et al (Am J Med 1988;85:573-575) reported 4 cases of tuberculous thyroiditis that were diagnosed preoperatively, the rest of the cases were diagnosed either from surgical specimen or from autopsy. A case of primary tuberculosis of thyroid gland presenting as abscess and diagnosed preoperatively is reported here.
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Rafi W, Venkataswamy MM, Ravi V, Chandramuki A. Rapid diagnosis of tuberculous meningitis: a comparative evaluation of in-house PCR assays involving three mycobacterial DNA sequences, IS6110, MPB-64 and 65 kDa antigen. J Neurol Sci 2006; 252:163-8. [PMID: 17182062 DOI: 10.1016/j.jns.2006.11.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 10/30/2006] [Accepted: 11/06/2006] [Indexed: 11/18/2022]
Abstract
A PCR was standardized for amplifying three different mycobacterial--IS6110, MPB-64, 65 kDa DNA sequences. A comparative evaluation of the three PCR assays was carried out for the rapid diagnosis of tuberculous meningitis (TBM) using cerebrospinal fluid (CSF) specimens. While the IS6110 PCR was a single-step amplification reaction, the MPB-64 and 65 kDa antigen PCR assays were nested reactions. A total of 176 cerebrospinal fluid (CSF) samples from 176 patients were subjected to amplification of the three different mycobacterial sequences. Amongst them, 45 samples were obtained from confirmed cases of TBM (culture positive) and 56 samples were obtained from clinically suspected cases of TBM which were culture-negative. The remaining 75 CSF samples were categorized under the non-infectious and infectious illness of the central nervous system (CNS). Against a gold standard of culture, a sensitivity of 98% (NPV=99%) and a specificity of 100% (PPV=100%) was observed with the IS6110 PCR. Among the nested PCRs, a sensitivity of 91% (NPV=94%) and a specificity of 91% (PPV=85%) was observed with the MPB-64 assay, while the 65 kDa protocol had an associated sensitivity of 51% (NPV=76%) and a specificity of 92% (PPV=79%). These findings suggest that among the nested PCR assays, the MPB-64 PCR assay was associated with an enhanced degree of sensitivity and was comparable in terms of specificity. Our study also demonstrates that the IS6110 assay, while being a single-step PCR had the advantage of being a rapid test for the diagnosis of TBM, with increased sensitivity and enhanced specificity as compared to the nested PCR protocols.
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Affiliation(s)
- Wasiulla Rafi
- Department of Neuromicrobiology, National Institute of Mental Health and Neurosciences, Bangalore, 560 029, India
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Itoh Y, Kawamura Y, Kasai H, Shah MM, Nhung PH, Yamada M, Sun X, Koyana T, Hayashi M, Ohkusu K, Ezaki T. dnaJ and gyrB gene sequence relationship among species and strains of genus Streptococcus. Syst Appl Microbiol 2006; 29:368-74. [PMID: 16487673 DOI: 10.1016/j.syapm.2005.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Indexed: 10/25/2022]
Abstract
The dnaJ and gyrB nucleotide sequences were determined for members of the genus Streptococcus. The average similarity between the species tested was 76.4% (69.7-100%) for dnaJ and 75.9 (70.1-98.7%) for gyrB. These data indicated that the dnaJ and gyrB genes are more divergent and more discriminatory than the 16S rDNA gene. Furthermore, the variation in the dnaJ nucleotide sequences among the mitis group was greater than that of the gyrB nucleotide sequences, especially between Streptococcus pneumoniae and Streptococcus mitis. Subsequently, the high discrimination power of dnaJ within the mitis group was confirmed. Thus, we conclude that the dnaJ and gyrB genes are efficient alternative targets for the classification of the genus Streptococcus, and that dnaJ is suitable for phylogenetic analysis of closely related Streptococcus strains.
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Affiliation(s)
- Yoko Itoh
- Department of Microbiology, Regeneration and Advanced Medical Science, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
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Kurabachew M, Enger Ø, Sandaa RA, Skuce R, Bjorvatn B. A multiplex polymerase chain reaction assay for genus-, group- and species-specific detection of mycobacteria. Diagn Microbiol Infect Dis 2004; 49:99-104. [PMID: 15183858 DOI: 10.1016/j.diagmicrobio.2004.03.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2003] [Accepted: 03/11/2004] [Indexed: 11/18/2022]
Abstract
We developed and evaluated a single-step, multiplex polymerase chain reaction (PCR) assay for distinguishing (1) between the Mycobacterium tuberculosis complex (MTBC) and mycobacteria other than tuberculosis (MOTT) and (2) between M. tuberculosis and M. bovis species. The assay targeted the 16S and the 23S rDNA to distinguish between MTBC and MOTT species, and the oxyR gene to distinguish between M. tuberculosis and M. bovis strains. Clinical samples and reference strains (N = 156) comprised 93 strains of M. tuberculosis, 44 of M. bovis, 1 M. africanum strain, and 18 strains representing 9 different species of MOTTs. MOTTs generated only a single PCR product of about 2.5 kilobase; however, all of the MTBC strains produced a 118 base pair (bp) fragment and an additional 270 bp fragment was obtained for M. tuberculosis and M. africanum when the primer pair oxyRTB-2.1/oxyRMT-1 was used. When oxyRTB-2.1/oxyRMB-1 primers were used, the 270 bp fragment was obtained for only M. bovis. The assay needed as little as 1 pg of purified genomic DNA to make a positive identification.
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Liu H, Li Y, Huang X, Kawamura Y, Ezaki T. Use of the dnaJ gene for the detection and identification of all Legionella pneumophila serogroups and description of the primers used to detect 16S rDNA gene sequences of major members of the genus Legionella. Microbiol Immunol 2004; 47:859-69. [PMID: 14638997 DOI: 10.1111/j.1348-0421.2003.tb03452.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We sequenced about 930 bp of the dnaJ gene from 15 Legionella pneumophila serogroups and some other members of the genus Legionella. As L. pneumophila 16S rDNA sequences could not discriminate between all subspecies and serogroups, we assessed the use of dnaJ gene sequences to differentiate between Legionella subspecies as well as between L. pneumophila serogroups. A phylogenetic analysis revealed that dnaJ gene sequences were more variable between the L. pneumophila serogroups than mip gene and 16S rDNA sequences. By studying 61 strains from 41 species of the genus Legionella, as well as other genera, we established a PCR method that could amplify 285 bp of dnaJ gene from all L. pneumophila serogroups. This primer set was more sensitive than mip gene primers and was able to detect 0.25 ng of purified DNA. We also describe the 16S rDNA primers that were used to detect most Legionella genus members.
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Affiliation(s)
- Hongsheng Liu
- Microbiology-Bioinformatics, Regeneration and Advanced Medical Science, Gifu University Graduate School of Medicine, Japan
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