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Costa P, Botelho A, Couto I, Viveiros M, Inácio J. Standing of nucleic acid testing strategies in veterinary diagnosis laboratories to uncover Mycobacterium tuberculosis complex members. Front Mol Biosci 2014; 1:16. [PMID: 25988157 PMCID: PMC4428369 DOI: 10.3389/fmolb.2014.00016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/25/2014] [Indexed: 12/03/2022] Open
Abstract
Nucleic acid testing (NAT) designate any molecular approach used for the detection, identification, and characterization of pathogenic microorganisms, enabling the rapid, specific, and sensitive diagnostic of infectious diseases, such as tuberculosis. These assays have been widely used since the 90s of the last century in human clinical laboratories and, subsequently, also in veterinary diagnostics. Most NAT strategies are based in the polymerase chain reaction (PCR) and its several enhancements and variations. From the conventional PCR, real-time PCR and its combinations, isothermal DNA amplification, to the nanotechnologies, here we review how the NAT assays have been applied to decipher if and which member of the Mycobacterium tuberculosis complex is present in a clinical sample. Recent advances in DNA sequencing also brought new challenges and have made possible to generate rapidly and at a low cost, large amounts of sequence data. This revolution with the high-throughput sequencing (HTS) technologies makes whole genome sequencing (WGS) and metagenomics the trendiest NAT strategies, today. The ranking of NAT techniques in the field of clinical diagnostics is rising, and we provide a SWOT (Strengths, Weaknesses, Opportunities, and Threats) analysis with our view of the use of molecular diagnostics for detecting tuberculosis in veterinary laboratories, notwithstanding the gold standard being still the classical culture of the agent. The complementary use of both classical and molecular diagnostics approaches is recommended to speed the diagnostic, enabling a fast decision by competent authorities and rapid tackling of the disease.
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Affiliation(s)
- Pedro Costa
- Instituto Nacional de Investigação Agrária e Veterinária IPLisboa, Portugal
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical da Universidade Nova de LisboaLisboa, Portugal
| | - Ana Botelho
- Instituto Nacional de Investigação Agrária e Veterinária IPLisboa, Portugal
| | - Isabel Couto
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical da Universidade Nova de LisboaLisboa, Portugal
- Centro de Recursos Microbiológicos (CREM), Universidade Nova de LisboaCaparica, Portugal
| | - Miguel Viveiros
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical da Universidade Nova de LisboaLisboa, Portugal
- Centro de Malária e Outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical da Universidade Nova de LisboaLisboa, Portugal
| | - João Inácio
- School of Pharmacy and Biomolecular Sciences, University of BrightonBrighton, UK
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Sharma K, Gupta N, Sharma A, Singh G, Gupta PK, Rajwanshi A, Varma SC, Sharma M. Multiplex polymerase chain reaction using insertion sequence 6110 (IS6110) and mycobacterial protein fraction from BCG of Rm 0.64 in electrophoresis target genes for diagnosis of tuberculous lymphadenitis. Indian J Med Microbiol 2013; 31:24-8. [DOI: 10.4103/0255-0857.108714] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Experimental model of tuberculosis in the domestic goat after endobronchial infection with Mycobacterium caprae. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2011; 18:1872-81. [PMID: 21880849 DOI: 10.1128/cvi.05323-11] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Caprine tuberculosis (TB) has increased in recent years, highlighting the need to address the problem the infection poses in goats. Moreover, goats may represent a cheaper alternative for testing of prototype vaccines in large ruminants and humans. With this aim, a Mycobacterium caprae infection model has been developed in goats. Eleven 6-month-old goats were infected by the endobronchial route with 1.5 × 10(3) CFU, and two other goats were kept as noninfected controls. The animals were monitored for clinical and immunological parameters throughout the experiment. After 14 weeks, the goats were euthanized, and detailed postmortem analysis of lung lesions was performed by multidetector computed tomography (MDCT) and direct observation. The respiratory lymph nodes were also evaluated and cultured for bacteriological analysis. All infected animals were positive in a single intradermal comparative cervical tuberculin (SICCT) test at 12 weeks postinfection (p.i.). Gamma interferon (IFN-γ) antigen-specific responses were detected from 4 weeks p.i. until the end of the experiment. The humoral response to MPB83 was especially strong at 14 weeks p.i. (13 days after SICCT boost). All infected animals presented severe TB lesions in the lungs and associated lymph nodes. M. caprae was recovered from pulmonary lymph nodes in all inoculated goats. MDCT allowed a precise quantitative measure of TB lesions. Lesions in goats induced by M. caprae appeared to be more severe than those induced in cattle by M. bovis over a similar period of time. The present work proposes a reliable new experimental animal model for a better understanding of caprine tuberculosis and future development of vaccine trials in this and other species.
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Thacker TC, Harris B, Palmer MV, Waters WR. Improved specificity for detection of Mycobacterium bovis in fresh tissues using IS6110 real-time PCR. BMC Vet Res 2011; 7:50. [PMID: 21867516 PMCID: PMC3170578 DOI: 10.1186/1746-6148-7-50] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 08/25/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Culture of M. bovis from diagnostic specimens is the gold standard for bovine tuberculosis diagnostics in the USA. Detection of M. bovis by PCR in tissue homogenates may provide a simple rapid method to complement bacterial culture. A significant impediment to PCR based assays on tissue homogenates is specificity since mycobacteria other than M. bovis may be associated with the tissues. RESULTS Previously published IS6110 based PCR diagnostic assays, along with one developed in house, were tested against environmental mycobacteria commonly isolated from diagnostic tissues submitted to the National Veterinary Services Laboratory. A real-time PCR assay was developed (IS6110_T) that had increased specificity over other IS6110 based assays. Of the 13 non-tuberculous mycobacteria tested with IS6110_T only M. wolinskyi was positive. Thirty M. bovis infected tissue homogenates and 18 control tissues were used to evaluate the potential for the assay as a diagnostic test. In this small sample, IS6110_T detected 20/30 samples from M. bovis infected animals and 0/18 control tissues. CONCLUSIONS The IS6110_T assay provides a PCR based assay system that is compatible with current diagnostic protocols for the detection of M. bovis in the USA and compliments current testing strategies.
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Affiliation(s)
- Tyler C Thacker
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa, USA.
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Pinto H, Bica CG, Palaci M, Dietze R, Basso LA, Santos DS. Using polymerase chain reaction with primers based on the plcB-plcC intergenic region to detect Mycobacterium tuberculosis in clinical samples. J Bras Pneumol 2008; 33:437-42. [PMID: 17982536 DOI: 10.1590/s1806-37132007000400013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Accepted: 11/28/2006] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE To develop a system for the molecular diagnosis of tuberculosis by polymerase chain reaction (PCR), constructing primers based on the difference in gene organization of the intergenic region of phospholipase C (plcB-plcC region), which differentiates Mycobacterium tuberculosis from other mycobacteria. METHODS A PCR product of the expected size (432 bp) was obtained from M. tuberculosis and M. africanum only. A total of 33 mycobacterial isolates and 273 clinical samples from patients suspected of having tuberculosis were examined. These were used in the comparative study of the PCR technique versus culture. RESULTS For PCR versus culture, the data showed 93.8% accuracy (p < 0.0001), 93.1% sensitivity (CI: 88.7-96.0), and 96.4% specificity (CI: 96.1-99.4). The Kappa value (0.82) shows that there was a near-perfect concordance between the two tests. CONCLUSION The use of the plcB-plcC region in PCR amplification was found to be an important and reliable tool for the specific diagnosis of tuberculosis in the samples analyzed.
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Yeboah-Manu D, Yates MD, Wilson SM. Application of a simple multiplex PCR to aid in routine work of the mycobacterium reference laboratory. J Clin Microbiol 2001; 39:4166-8. [PMID: 11682550 PMCID: PMC88507 DOI: 10.1128/jcm.39.11.4166-4168.2001] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A PCR specific for spacer regions 33 and 34 of the direct repeat region of the Mycobacterium tuberculosis complex was developed to complement the biochemical differentiation of M. tuberculosis, Mycobacterium bovis, M. bovis BCG, and Mycobacterium africanum subtypes I and II. In addition, this approach was incorporated into a multiplex PCR that included primers specific for IS6110 and the 65-kDa antigen gene in order to differentiate members of the M. tuberculosis complex from atypical mycobacteria.
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Affiliation(s)
- D Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
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Van Soolingen D. Molecular epidemiology of tuberculosis and other mycobacterial infections: main methodologies and achievements. J Intern Med 2001; 249:1-26. [PMID: 11168781 DOI: 10.1046/j.1365-2796.2001.00772.x] [Citation(s) in RCA: 203] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In the last decade, DNA fingerprint techniques have become available to study the interperson transmission of tuberculosis and other mycobacterial infections. These methods have facilitated epidemiological studies at a population level. In addition, the species identification of rarely encountered mycobacteria has improved significantly. This article describes the state of the art of the main molecular typing methods for Mycobacterium tuberculosis complex and non-M. tuberculosis complex (atypical) mycobacteria. Important new insights that have been gained through molecular techniques into epidemiological aspects and diagnosis of mycobacterial diseases are highlighted.
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MESH Headings
- Animals
- Contact Tracing
- DNA Fingerprinting
- DNA, Bacterial/genetics
- Genetics, Microbial/trends
- Genotype
- Humans
- Molecular Epidemiology/methods
- Mycobacterium/classification
- Mycobacterium/genetics
- Mycobacterium/isolation & purification
- Mycobacterium Infections, Nontuberculous/epidemiology
- Mycobacterium Infections, Nontuberculous/genetics
- Mycobacterium Infections, Nontuberculous/transmission
- Mycobacterium tuberculosis/genetics
- Nontuberculous Mycobacteria/genetics
- Polymorphism, Restriction Fragment Length
- RNA, Bacterial/genetics
- Reproducibility of Results
- Sequence Analysis, DNA
- Sequence Analysis, RNA
- Transformation, Bacterial
- Tuberculosis/epidemiology
- Tuberculosis/genetics
- Tuberculosis/transmission
- Tuberculosis, Multidrug-Resistant/epidemiology
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Affiliation(s)
- D Van Soolingen
- Mycobacteria Reference Department, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.
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Herrera EA, Pérez O, Segovia M. Differentiation between Mycobacterium tuberculosis and Mycobacterium bovis by a multiplex-polymerase chain reaction. THE JOURNAL OF APPLIED BACTERIOLOGY 1996; 80:596-604. [PMID: 8698660 DOI: 10.1111/j.1365-2672.1996.tb03263.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A multiplex-polymerase chain reaction (PCR) assay, based on one-step amplification and detection of three different mycobacterial genomic fragments, was designed for differentiation between Mycobacterium bovis and Mycobacterium tuberculosis. The oligonucleotide primers were chosen from the groEL gene, present in the genus Mycobacterium sp., from the IS6110 insertion sequence, present in Myco. tuberculosis complex and from the mtp40 gene, identified as a specific-species Myco. tuberculosis genomic fragment. This amplification method allowed the detection of two fragments of 576 and 317 base pairs in Myco. bovis and three fragments of 576, 396 and 317 base pairs in Myco. tuberculosis strains, including atypical strains of Myco. tuberculosis where the copy number of the IS6110 element is low. The multiplex-PCR assay described may be a very useful tool for the rapid and specific differentiation of these related mycobacteria and easy to use in medical and veterinary microbiology laboratories.
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Affiliation(s)
- E A Herrera
- Departamento de Genética y Microbiología, Hospital General Universitario de Murcia, Spain
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Down JA, O'Connell MA, Dey MS, Walters AH, Howard DR, Little MC, Keating WE, Zwadyk P, Haaland PD, McLaurin DA, Cole G. Detection of Mycobacterium tuberculosis in respiratory specimens by strand displacement amplification of DNA. J Clin Microbiol 1996; 34:860-5. [PMID: 8815097 PMCID: PMC228906 DOI: 10.1128/jcm.34.4.860-865.1996] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A total of 294 clinical respiratory specimens, including 75 with culture-positive results, were tested for the presence of Mycobacterium tuberculosis by strand displacement amplification (SDA) of DNA. A region of the IS6110 insertion element and an internal control sequence were amplified and then detected by a chemiluminescence assay. Receiver operator-characteristic curves were used to evaluate three methods for declaring specimens positive for M. tuberculosis. By the preferred method, SDA chemiluminescence results were converted to theoretical numbers of M. tuberculosis organisms. A positive threshold (PT) value, above which 95% of the SDA results were judged to be M. tuberculosis positive (sensitivity = 95%), was found to be 2.4 M. tuberculosis organisms per SDA reaction. The analogous PT value for 95% sensitivity on smear-positive specimens was 3.6 M. tuberculosis organisms per reaction. The PT of 2.4 M. tuberculosis organisms per reaction detected 100% of culture-positive, smear-positive specimens (sensitivity = 100%), while 95% sensitivity was achieved with a PT of 15.5 M. tuberculosis organisms per reaction. Specificities, which were calculated with respect to culture- and smear-negative specimens, ranged from 96% at a PT of 15.5 M. tuberculosis organisms to 84% at a PT of 2.4 M. tuberculosis organisms per reaction. The M. tuberculosis-negative specimens were also segregated according to whether the patients received antituberculosis chemotherapy. SDA specificity ranged from 90% (PT = 2.4 M. tuberculosis organisms) to 98% (PT = 15.5 M. tuberculosis organisms) for the M. tuberculosis-negative specimens from patients who had not received chemotherapy. SDA specificity in the M. tuberculosis-negative specimens from patients who received chemotherapy was lower (85 to 94%). This study represents the first large-scale demonstration of M. tuberculosis detection in clinical sputum specimens by isothermal DNA amplification with SDA.
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Affiliation(s)
- J A Down
- Becton Dickinson Research Center, Research Triangle Park, North Carolina 27709-2016, USA.
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Aranaz A, Liébana E, Pickering X, Novoa C, Mateos A, Domínguez L. Use of polymerase chain reaction in the diagnosis of tuberculosis in cats and dogs. Vet Rec 1996; 138:276-80. [PMID: 8711884 DOI: 10.1136/vr.138.12.276] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Samples from four dogs and four cats suspected of having tuberculosis were processed for histopathology, bacterial culture and polymerase chain reaction (PCR). A simple, rapid method for the extraction of DNA from tissue samples was used in two PCR assays designed to confirm the diagnosis of tuberculosis. The PCR assays detected all the culture-positive samples from these animals and no false positive results were obtained. The PCR technique was successful for the direct detection of organisms from the Mycobacterium tuberculosis complex and reduced the time needed for a diagnosis to two days.
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Affiliation(s)
- A Aranaz
- Departamento de Patología Animal I (Sanidad Animal), Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
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11
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Tötsch M, Böcker W, Brömmelkamp E, Fille M, Kreczy A, Ofner D, Schmid KW, Dockhorn-Dworniczak B. Diagnostic value of different PCR assays for the detection of mycobacterial DNA in granulomatous lymphadenopathy. J Pathol 1996; 178:221-6. [PMID: 8683393 DOI: 10.1002/(sici)1096-9896(199602)178:2<221::aid-path441>3.0.co;2-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Diagnosis of mycobacterial infection is made by assessment of characteristic histological features, staining of acid-fast bacilli, or agar culture. Recent advances in molecular biology have provided alternative approaches for the detection of mycobacteria, but only limited data are available dealing with the comparative evaluation of these methods. In order to determine the diagnostic applicability of polymerase chain reaction (PCR)-based assays, 20 formalin-fixed and paraffin-embedded lymph nodes with bacille Calmette-Guérin (BCG) lymphadenitis were investigated which in Löwenstein Jensen agar culture were either positive or negative (ten cases each); ten lymph nodes with non-specific lymphadenitis served as negative controls. Ziehl-Neelsen staining as well as three different PCR assays (including nested PCR), amplifying a specific sequence of the Mycobacterium tuberculosis complex or sequences of the 65 kD antigen gene, were performed. Positive culture was only obtained from lymph nodes which had been surgically removed within 20 weeks after vaccination (P < 0.001). In contrast to microscopic examination, which yielded no more information than agar culture, PCR detection of mycobacterial DNA was unrelated to culture findings. Combined use of different assays, as well as DNA extraction from at least three paraffin sections from each specimen, resulted in the detection of mycobacterial DNA in all lymph nodes with amplifiable DNA (18 out of 20 cases). Controls remained consistently negative. Thus, the combined use of different PCR assays is proposed as a rapid and sensitive technique for the detection of mycobacterial DNA in formalin-fixed and paraffin-embedded tissue.
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Affiliation(s)
- M Tötsch
- Department of Pathology, University of Münster, Germany
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Sinclair K, Challans JA, Kazwala RR, Hewinson RG, Sharp JM. A multiplex polymerase chain reaction for distinguishing Mycobacterium tuberculosis from Mycobacterium tuberculosis complex. Mol Cell Probes 1995; 9:291-5. [PMID: 8569767 DOI: 10.1016/s0890-8508(95)91524-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A multiplex polymerase chain reaction has been developed which is able to distinguish Mycobacterium tuberculosis from other members of the M. tuberculosis complex. The assay is based on the simultaneous amplification of two different targets: a 396bp region from the mtp40 species-specific gene sequence of M. tuberculosis and a 245bp fragment from the M. tuberculosis complex insertion sequence IS986. Results have been obtained for 54 mycobacterial strains including five non-M. tuberculosis complex isolates. All 49 strains of the M. tuberculosis complex were positive for IS986 but only the 27 M. tuberculosis isolates were positive for both IS986 and mtp40.
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Affiliation(s)
- K Sinclair
- Moredun Research Institute, Edinburgh, Scotland, UK
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13
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Liébana E, Aranaz A, Mateos A, Vilafranca M, Gomez-Mampaso E, Tercero JC, Alemany J, Suarez G, Domingo M, Dominguez L. Simple and rapid detection of Mycobacterium tuberculosis complex organisms in bovine tissue samples by PCR. J Clin Microbiol 1995; 33:33-6. [PMID: 7699061 PMCID: PMC227874 DOI: 10.1128/jcm.33.1.33-36.1995] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Mycobacterium bovis is a slowly growing microorganism, and confirmation of the diagnosis by conventional culture is a lengthy process. A simple, rapid method for the extraction of DNA from bovine tissue samples was developed and used in a PCR designed for the diagnosis of tuberculosis. Tissues from 81 cattle from tuberculosis-infected herds (group 1) and 19 cattle from tuberculosis-free herds (group 2) were tested in this PCR, and the results were compared with those of conventional culture. The PCR assay detected 71.4% of the culture-positive animals from group 1. Tissue from all animals in group 2 were negative in the PCR assay and by culture. The described method could be used as a rapid screening technique which would be complementary to culture of tissue specimens for the routine diagnosis of bovine tuberculosis. The PCR technique is much faster than culture and reduces the time for diagnosis from several months to 2 days. It also provides for the detection of M. bovis when rapidly growing Mycobacterium spp. are present in the sample and may be able to detect the presence of M. bovis in samples even when organisms have become nonviable.
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Affiliation(s)
- E Liébana
- Departamento de Patología Animal I (Sanidad Animal), Facultad de Veterinaria, Universidad Complutense de Madrid, Spain
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14
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Bricker BJ, Halling SM. Differentiation of Brucella abortus bv. 1, 2, and 4, Brucella melitensis, Brucella ovis, and Brucella suis bv. 1 by PCR. J Clin Microbiol 1994; 32:2660-6. [PMID: 7852552 PMCID: PMC264138 DOI: 10.1128/jcm.32.11.2660-2666.1994] [Citation(s) in RCA: 326] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Several PCR assays which identify the genus Brucella but do not discriminate among species have been reported. We describe a PCR assay that comprises five oligonucleotide primers which can identify selected biovars of four species of Brucella. Individual biovars within a species are not differentiated. The assay can identify three biovars (1, 2, and 4) of B. abortus, all three biovars of B. melitensis, biovar 1 of B. suis, and all B. ovis biovars. These biovars include all of the Brucella species typically isolated from cattle in the United States, a goal of the present research. The assay exploits the polymorphism arising from species-specific localization of the genetic element IS711 in the Brucella chromosome. Identity is determined by the size(s) of the product(s) amplified from primers hybridizing at various distances from the element. The performance of the assay with U.S. field isolates was highly effective. When 107 field isolates were screened by the described method, there was 100% agreement with the identifications made by conventional methods. Six closely related bacteria (Agrobacterium radiobacter, Agrobacterium rhizogenes, Ochrobactrum anthropi, Rhizobium leguminosarum, Rhizobium meliloti, and Rhodospirillum rubrum) and two control bacteria (Bordetella bronchiseptica and Escherichia coli) tested negative by the assay.
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Affiliation(s)
- B J Bricker
- National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Ames, Iowa 50010
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15
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Zwadyk P, Down JA, Myers N, Dey MS. Rendering of mycobacteria safe for molecular diagnostic studies and development of a lysis method for strand displacement amplification and PCR. J Clin Microbiol 1994; 32:2140-6. [PMID: 7814537 PMCID: PMC263956 DOI: 10.1128/jcm.32.9.2140-2146.1994] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Two criteria must be met before mycobacterial specimens can be tested by DNA amplification methods: (i) the sample must be rendered noninfectious, and (ii) the organisms must be lysed to free the DNA. Previous publications reporting DNA amplification of mycobacteria have concentrated on lysis and amplification procedures and have not addressed the issue of sample safety. We have shown that heating of samples below 100 degrees C may not consistently kill mycobacteria; however, heating at 100 degrees C in a boiling-water bath or a forced-air oven for a minimum of 5 min kills mycobacteria, including Mycobacterium thermoresistibile. Furthermore, heating at 100 degrees C for 30 min consistently lyses mycobacteria to produce short fragments of DNA that are suitable for amplification by PCR and strand displacement amplification. This procedure works with clinical samples digested by the n-acetyl cysteine-NaOH method as well as with suspensions of organisms in phosphate buffer. This paper also demonstrates the feasibility of using strand displacement amplification with clinical specimens.
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Affiliation(s)
- P Zwadyk
- Veterans Affairs Medical Center, Durham, North Carolina 27705
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Noordhoek GT, Kolk AH, Bjune G, Catty D, Dale JW, Fine PE, Godfrey-Faussett P, Cho SN, Shinnick T, Svenson SB. Sensitivity and specificity of PCR for detection of Mycobacterium tuberculosis: a blind comparison study among seven laboratories. J Clin Microbiol 1994; 32:277-84. [PMID: 8150935 PMCID: PMC263025 DOI: 10.1128/jcm.32.2.277-284.1994] [Citation(s) in RCA: 306] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
PCR is, in principle, a simple and rapid test for use in the detection of Mycobacterium tuberculosis. However, virtually no data are available on the reliability and reproducibility of the method. In order to assess the validity of PCR for the detection of mycobacteria in clinical samples, seven laboratories participated in a blinded study of 200 sputum, saliva, and water samples containing either known numbers of Mycobacterium bovis BCG cells or no added organisms. Each laboratory used its own protocol for pretreatment, DNA extraction, and detection of the amplification product. Insertion sequence IS6110 was the target for DNA amplification. Several participating laboratories reported high levels of false-positive PCR results, with rates ranging from 3 to 20% and with one extreme value of 77%. The levels of sensitivity also ranged widely among the different participants. A positive PCR result was reported for 2 to 90% of the samples with 10(3) mycobacteria. Although most participants did include control tests to check the sensitivity and specificity of the PCR, the sequence of operations from sample pretreatment to purification of DNA from bacteria was not always monitored adequately. During these procedures cross-contaminating DNA was introduced and/or bacterial DNA was lost. The results of the study show that the implementation of an effective system for monitoring sensitivity and specificity is required before the PCR can be used reliably in the diagnosis of tuberculosis.
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Affiliation(s)
- G T Noordhoek
- Public Health Laboratory, Leeuwarden, The Netherlands
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Nolte FS, Metchock B, McGowan JE, Edwards A, Okwumabua O, Thurmond C, Mitchell PS, Plikaytis B, Shinnick T. Direct detection of Mycobacterium tuberculosis in sputum by polymerase chain reaction and DNA hybridization. J Clin Microbiol 1993; 31:1777-82. [PMID: 8349753 PMCID: PMC265631 DOI: 10.1128/jcm.31.7.1777-1782.1993] [Citation(s) in RCA: 135] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A polymerase chain reaction (PCR) assay for the rapid diagnosis of pulmonary tuberculosis was developed by using oligonucleotide primers to amplify a fragment of IS6110, an insertion sequence repeated multiple times in the chromosome of Mycobacterium tuberculosis. Sediment obtained from sputa processed by the N-acetyl-L-cysteine-NaOH method was suspended in a simple lysis buffer and was heated at 100 degrees C for 30 min prior to amplification. A dUTP-uracil N-glycosylase PCR protocol was used to prevent false-positive test results because of the carryover of products from previous amplification reactions. The 317-bp amplicon was detected by direct gel analysis and Southern blotting and then hybridization with a biotin-labeled internal probe. Hybrid molecules were detected by using a commercially available avidin-alkaline phosphatase-chemiluminescent substrate system (Tropix, Inc., Bedford, Mass.). The analytical sensitivity of the assay was 10 fg of purified mycobacterial DNA. The limits of detection by culture (Middlebrook 7H11 agar and Lowenstein-Jensen medium) and by PCR were equivalent in terminal dilution experiments for organism suspensions and positive sputa. An internal control was used to detect the presence of amplification inhibitors in each negative reaction mixture. DNA was purified from inhibitory specimens by phenol-chloroform extraction and ethanol precipitation. PCR results were compared with results of microscopy and conventional culture for the detection of M. tuberculosis in 313 sputum specimens. There were 124 specimens that were positive for M. tuberculosis by conventional methods and 113 (91%) that were positive by PCR. PCR detected 105 of 110 (95%) of the smear-positive and 8 of 14 (57%) of the smear-negative specimens. There were no false-positive results by PCR (specificity, 100%). This PCR assay innovations that make application of this new technology feasible in clinical microbiology laboratories.
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Affiliation(s)
- F S Nolte
- Emory University Hospital, Atlanta, Georgia 30322
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Fishman JR, Walton DT, Flynn NM, Benson DR, deVere White RW. Tuberculous spondylitis as a complication of intravesical bacillus Calmette-Guerin therapy. J Urol 1993; 149:584-7. [PMID: 8437271 DOI: 10.1016/s0022-5347(17)36155-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We report a case of tuberculous spondylitis following intravesical bacillus Calmette-Guerin (BCG) instillation. A 90-year-old male physician living in South Africa received an uncomplicated 6-week course of intravesical BCG (Japanese 172 strain) for high grade superficial bladder carcinoma. He experienced a sudden onset of debilitating lower back pain 16 months following this treatment. A lytic lesion involving the anterior T11 and T12 vertebral bodies was diagnosed and subsequently biopsied. An acid-fast organism was isolated after 3 weeks of incubation and was confirmed through deoxyribonucleic acid probe hybridization as a mycobacterium. High performance liquid chromatography analysis speciated the organism as Mycobacterium bovis BCG, proving that it was acquired through the intravesical therapy.
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Affiliation(s)
- J R Fishman
- Department of Urology, University of California, School of Medicine, Davis, Sacramento
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MacPherson JM, Gajadhar AA. Differentiation of seven Eimeria species by random amplified polymorphic DNA. Vet Parasitol 1993; 45:257-66. [PMID: 8447068 DOI: 10.1016/0304-4017(93)90080-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Eimeria species were differentiated by the polymerase chain reaction using random amplified polymorphic DNA. Seven arbitrary primers ranging in length from ten to 20 nucleotides were used with DNA of seven species of eimerian oocysts to generate unique DNA fingerprints. DNA fragments ranging from 200 to 2200 base pairs (bp) were synthesized in the different reactions. Species-specific DNA fragment mobility patterns were observed in most cases. In several assays, multiple DNA fragments were synthesized and, in the majority of assays conducted, the Eimeria species could be easily differentiated. Only six of the 49 assays performed failed to generate DNA fragments.
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Affiliation(s)
- J M MacPherson
- Health of Animals Laboratory, Agriculture Canada, Saskatoon, Sask
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Ng V, Weir L, York MK, Hadley WK. Bordetella pertussis versus non-L. pneumophila Legionella spp.: a continuing diagnostic challenge. J Clin Microbiol 1992; 30:3300-1. [PMID: 1452724 PMCID: PMC270658 DOI: 10.1128/jcm.30.12.3300-3301.1992] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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22
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van Embden JD, van Soolingen D, Small PM, Hermans PW. Genetic markers for the epidemiology of tuberculosis. Res Microbiol 1992; 143:385-91. [PMID: 1360692 DOI: 10.1016/0923-2508(92)90051-o] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- J D van Embden
- Unit of Molecular Microbiology, National Institute of Public Health and Environmental Protection, Bilthoven, The Netherlands
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