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Diagnostic challenges of tuberculous lymphadenitis using polymerase chain reaction analysis: a case study. Case Rep Infect Dis 2015; 2015:723726. [PMID: 25685567 PMCID: PMC4320933 DOI: 10.1155/2015/723726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 01/03/2015] [Accepted: 01/07/2015] [Indexed: 11/30/2022] Open
Abstract
This report presents a case of tuberculous lymphadenitis that was difficult to diagnose using polymerase chain reaction analysis. An 80-year-old Japanese female was hospitalized due to swollen cervical lymph nodes. Her lymph node tests revealed paradoxical polymerase chain reaction results. Polymerase chain reaction analysis of two biopsy tissues using the Cobas TaqMan revealed a positive result for Mycobacterium avium and a negative result for Mycobacterium tuberculosis. However, polymerase chain reaction analysis of a cultured colony of acid-fast bacteria from biopsy tissue using the Cobas TaqMan and an alternative polymerase chain reaction analysis of biopsy tissue yielded discordant results. The patient was diagnosed as having tuberculous lymphadenitis. She was treated with antitubercular drugs and subsequently had a reduction in cervical lymph node swelling. Polymerase chain reaction analysis is not 100% accurate; hence, its use as a diagnostic tool for mycobacterial infection requires increased attention.
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2
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Garvey G, Shakarisaz D, Ruiz-Ruiz F, Hagström AEV, Raja B, Pascente C, Kar A, Kourentzi K, Rito-Palomares M, Ruchhoeft P, Willson RC. Microretroreflector-sedimentation immunoassays for pathogen detection. Anal Chem 2014; 86:9029-35. [PMID: 25133758 PMCID: PMC4165457 DOI: 10.1021/ac501491t] [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] [Indexed: 01/19/2023]
Abstract
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Point-of-care detection of pathogens
is medically valuable but
poses challenging trade-offs between instrument complexity and clinical
and analytical sensitivity. Here we introduce a diagnostic platform
utilizing lithographically fabricated micron-scale forms of cubic
retroreflectors, arguably one of the most optically detectable human
artifacts, as reporter labels for use in sensitive immunoassays. We
demonstrate the applicability of this novel optical label in a simple
assay format in which retroreflector cubes are first mixed with the
sample. The cubes are then allowed to settle onto an immuno-capture
surface, followed by inversion for gravity-driven removal of nonspecifically
bound cubes. Cubes bridged to the capture surface by the analyte are
detected using inexpensive, low-numerical aperture optics. For model
bacterial and viral pathogens, sensitivity in 10% human serum was
found to be 104 bacterial cells/mL and 104 virus
particles/mL, consistent with clinical utility.
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Affiliation(s)
- Gavin Garvey
- Department of Chemical and Biomolecular Engineering, †Materials Engineering Program, ‡Department of Electrical and Computer Engineering, ⊥Department of Biology and Biochemistry, University of Houston , 4800 Calhoun Road, Houston, Texas 77004, United States
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3
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Utility of PCR amplification and DNA microarray hybridization of 16S rDNA for rapid diagnosis of bacteremia associated with hematological diseases. Int J Infect Dis 2012; 17:e271-6. [PMID: 23228627 DOI: 10.1016/j.ijid.2012.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 10/05/2012] [Accepted: 10/25/2012] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVES The rapid diagnosis of bacteremia is crucial for patient management including the choice of antimicrobial therapy, especially in cases of hematological disease, because neutropenia occurs frequently during antineoplastic chemotherapy or disease progression. We describe a rapid detection and identification system that uses universal PCR primers to amplify a variable region of bacterial 16S ribosomal DNA (rDNA), followed by DNA microarray hybridization. METHODS Probes for 72 microorganisms including most causal clinical pathogens were spotted onto a microarray plate. The DNA microarray and conventional methods of identification were applied to 335 cultures from patients with hematological diseases. RESULTS Forty-one samples (12.2%) tested positive by conventional blood culture test in a few days, while 40 cases (11.9%) were identified by the new method within 24 h. The sensitivity and specificity of this new method were 93% and 99%, respectively, compared with conventional blood culture testing. CONCLUSIONS PCR combined with a DNA microarray is useful for the management of febrile patients with hematological diseases.
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4
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Clinical Evaluation of COBAS TaqMan PCR for the Detection of Mycobacterium tuberculosis and M. avium Complex. Tuberc Res Treat 2012; 2012:170459. [PMID: 23029612 PMCID: PMC3458270 DOI: 10.1155/2012/170459] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 08/17/2012] [Accepted: 08/21/2012] [Indexed: 11/30/2022] Open
Abstract
A retrospective observational study was performed to determine the sensitivity and limitation of PCR test for the detection of Mycobacterium tuberculosis and M. avium complex. We obtained clinical specimens collected from the respiratory tract, cultured M. tuberculosis or M. avium complex, and performed PCR analysis. A total of 299 samples (M. tuberculosis, 177; M. avium, 35; M. intracellulare, 87) were analyzed by COBAS TaqMan PCR from April 2007 to March 2011. The PCR positivity rates were 50–55%, 70–100%, 88–98%, and 100% in smear-negative, smear 1+, 2+, and 3+ groups, respectively. The PCR positivity of tuberculosis in smear 1+ was 80.6%, which was statistically significantly (P < 0.001) lower than that of smear 2+ (97.3%). From January 2005 to March 2007, we collected an additional 138 samples (M. tuberculosis, 74; M. avium, 21; M. intracellulare, 43), which were analyzed by COBAS Amplicor PCR. The PCR positivity rates obtained using COBAS TaqMan PCR and COBAS Amplicor PCR were not significantly different. The sensitivity of PCR test for mycobacteria is not sufficient in case of smear 1+. Careful consideration must be given to the interpretation of negative PCR test results in smear 1+, because smear-positive tuberculosis is the criterion for isolation.
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5
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Affiliation(s)
- Paul Yager
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061;
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6
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Tuyama M, Boente RF, Rebelo MC, Igreja RP, Barroso DE. The utility of the polymerase chain reaction assay for aetiologic definition of unspecified bacterial meningitis cases. Mem Inst Oswaldo Cruz 2008; 103:138-42. [DOI: 10.1590/s0074-02762008000200003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Accepted: 03/20/2008] [Indexed: 11/22/2022] Open
Affiliation(s)
- Mari Tuyama
- Fiocruz, Brasil; Universidade Federal do Rio de Janeiro, Brasil
| | | | - Maria C Rebelo
- Instituto Estadual de Infectologia São Sebastião, Brasil
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7
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Yang S, Rothman RE. PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings. THE LANCET. INFECTIOUS DISEASES 2004; 4:337-48. [PMID: 15172342 PMCID: PMC7106425 DOI: 10.1016/s1473-3099(04)01044-8] [Citation(s) in RCA: 539] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Molecular diagnostics are revolutionising the clinical practice of infectious disease. Their effects will be significant in acute-care settings where timely and accurate diagnostic tools are critical for patient treatment decisions and outcomes. PCR is the most well-developed molecular technique up to now, and has a wide range of already fulfilled, and potential, clinical applications, including specific or broad-spectrum pathogen detection, evaluation of emerging novel infections, surveillance, early detection of biothreat agents, and antimicrobial resistance profiling. PCR-based methods may also be cost effective relative to traditional testing procedures. Further advancement of technology is needed to improve automation, optimise detection sensitivity and specificity, and expand the capacity to detect multiple targets simultaneously (multiplexing). This review provides an up-to-date look at the general principles, diagnostic value, and limitations of the most current PCR-based platforms as they evolve from bench to bedside.
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Affiliation(s)
- Samuel Yang
- The Johns Hopkins University, School of Medicine, Department of Emergency Medicine, Baltimore, MD, USA
| | - Richard E Rothman
- The Johns Hopkins University, School of Medicine, Department of Emergency Medicine, Baltimore, MD, USA
- Correspondence: Dr Richard E Rothman, Department of Emergency Medicine, Johns Hopkins School of Medicine, 1830 E Monument Street, Suite 6–100, Baltimore, MD 21205, USA
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8
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Mitterer G, Huber M, Leidinger E, Kirisits C, Lubitz W, Mueller MW, Schmidt WM. Microarray-based identification of bacteria in clinical samples by solid-phase PCR amplification of 23S ribosomal DNA sequences. J Clin Microbiol 2004; 42:1048-57. [PMID: 15004052 PMCID: PMC356827 DOI: 10.1128/jcm.42.3.1048-1057.2004] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rapid identification of the bacteria in clinical samples is important for patient management and antimicrobial therapy. We describe a DNA microarray-based PCR approach for the quick detection and identification of bacteria from cervical swab specimens from mares. This on-chip PCR method combines the amplification of a variable region of bacterial 23S ribosomal DNA and the simultaneous sequence-specific detection on a solid phase. The solid phase contains bacterial species-specific primers covalently bound to a glass support. During the solid-phase amplification reaction the polymerase elongates perfectly matched primers and incorporates biotin-labeled nucleotides. The reaction products are visualized by streptavidin-cyanine 5 staining, followed by fluorescence scanning. This procedure successfully identified from pure cultures 22 bacteria that are common causes of abortion and sterility in mares. Using the on-chip PCR method, we also tested 21 cervical swab specimens from mares for the presence of pathogenic bacteria and compared the results with those of conventional bacteriological culture methods. Our method correctly identified the bacteria in 12 cervical swab samples, 8 of which contained more than one bacterial species. Due to the higher sensitivity of the on-chip PCR, this method identified bacteria in five cervical swab samples which were not detected by the conventional identification procedure. Our results show that this method will have great potential to be incorporated into the routine microbiology laboratory.
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MESH Headings
- Abortion, Veterinary/microbiology
- Animals
- Bacteria/genetics
- Bacteria/isolation & purification
- Base Sequence
- DNA Primers
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/genetics
- DNA, Ribosomal/isolation & purification
- Female
- Horses
- Oligonucleotide Array Sequence Analysis
- Polymerase Chain Reaction/methods
- Pregnancy
- Pregnancy Complications, Infectious/microbiology
- Pregnancy Complications, Infectious/veterinary
- RNA, Bacterial/genetics
- RNA, Bacterial/isolation & purification
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/isolation & purification
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Affiliation(s)
- Georg Mitterer
- Institute of Microbiology & Genetics, University of Vienna, 1030 Vienna, Austria
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9
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Reno WL, Mcdaniel DO, Turner WW, Williams MD. Polymerase Chain Reaction for the Detection of Bacteremia. Am Surg 2001. [DOI: 10.1177/000313480106700603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Analysis of blood by polymerase chain reaction (PCR) is a more rapid and sensitive method to detect bacteremia than blood culture. The PCR was performed on blood obtained from patients during blood culture draws and on blood from normal volunteers. Eighty-seven patients provided 125 blood samples for blood culture comparison with PCR. Specific PCR primers for Staphylococcus aureus and Escherichia coli that targeted conserved regions common to Gram-positive and Gram-negative bacteria were used. Selective stringency conditions identified other Gram-positive and Gram-negative bacteria. The blood culture agreed with the PCR in 93 of the 125 patient specimens (74%). In 29 of these specimens the PCR was positive yet the blood culture was negative. When clinical information was included with positive blood culture to define sepsis in these patients and their specimens were added to the positive blood cultures the statistical accuracy of PCR was 93 per cent. Only three of the 78 specimens with negative PCR had positive blood cultures. The PCR was negative in all but one of the 50 volunteers. PCR is more sensitive than blood culture, and it can quickly rule out bacteremia.
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Affiliation(s)
- William L. Reno
- Departments of Surgery, University of Mississippi Medical Center, Jackson, Mississippi
- G.V. (Sonny) Montgomery Veterans Affairs Medical Center, Jackson, Mississippi
| | - D. Olga Mcdaniel
- Departments of Surgery, University of Mississippi Medical Center, Jackson, Mississippi
- Departments of Neurology, University of Mississippi Medical Center, Jackson, Mississippi
| | - William W. Turner
- Departments of Surgery, University of Mississippi Medical Center, Jackson, Mississippi
- G.V. (Sonny) Montgomery Veterans Affairs Medical Center, Jackson, Mississippi
| | - Mark D. Williams
- Departments of Surgery, University of Mississippi Medical Center, Jackson, Mississippi
- G.V. (Sonny) Montgomery Veterans Affairs Medical Center, Jackson, Mississippi
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10
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Anthony RM, Brown TJ, French GL. Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array. J Clin Microbiol 2000; 38:781-8. [PMID: 10655385 PMCID: PMC86203 DOI: 10.1128/jcm.38.2.781-788.2000] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/1999] [Accepted: 10/29/1999] [Indexed: 11/20/2022] Open
Abstract
The rapid identification of bacteria in blood cultures and other clinical specimens is important for patient management and antimicrobial therapy. We describe a rapid (<4 h) detection and identification system that uses universal PCR primers to amplify a variable region of bacterial 23S ribosomal DNA, followed by reverse hybridization of the products to a panel of oligonucleotides. This procedure was successful in discriminating a range of bacteria in pure cultures. When this procedure was applied directly to 158 unselected positive blood culture broths on the day when growth was detected, 125 (79.7%) were correctly identified, including 4 with mixed cultures. Nine (7.2%) yielded bacteria for which no oligonucleotide targets were present in the oligonucleotide panel, and 16 culture-positive broths (10.3%) produced no PCR product. In seven of the remaining eight broths, streptococci were identified but not subsequently grown, and one isolate of Staphylococcus aureus was misidentified as a coagulase-negative staphylococcus. The accuracy, range, and discriminatory power of the assay can be continually extended by adding further oligonucleotides to the panel without significantly increasing complexity or cost.
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Affiliation(s)
- R M Anthony
- Department of Microbiology, King's College St. Thomas' Campus, St. Thomas' Hospital, London SE1 7EH, United Kingdom
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Bergeron MG, Ouellette M. Preventing antibiotic resistance through rapid genotypic identification of bacteria and of their antibiotic resistance genes in the clinical microbiology laboratory. J Clin Microbiol 1998; 36:2169-72. [PMID: 9665984 PMCID: PMC104995 DOI: 10.1128/jcm.36.8.2169-2172.1998] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
- M G Bergeron
- Centre de Recherche en Infectiologie de l'Université Laval, Faculty of Medicine, Québec, Canada.
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12
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Steffan P, Vazquez JA, Boikov D, Xu C, Sobel JD, Akins RA. Identification of Candida species by randomly amplified polymorphic DNA fingerprinting of colony lysates. J Clin Microbiol 1997; 35:2031-9. [PMID: 9230376 PMCID: PMC229897 DOI: 10.1128/jcm.35.8.2031-2039.1997] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We have characterized a method that produces simple yet diagnostic fingerprints that are unique to isolates of Candida species. DNA from individual colonies can be amplified from crude single-colony lysates. Randomly amplified polymorphic DNA (RAPD) fingerprints generated from a single primer correctly identified the species of most (>98%) of the isolates identified with CHROMagar Candida plates as non-Candida albicans Candida species. RAPD fingerprints were much more informative than the plates, since they distinguished between all tested species and required less time. Most (91%) of these identifications agreed with those assigned by API 20C tests. In almost every incident of species identity mismatch, electrophoretic karyotyping showed that the RAPD fingerprint was correct. This underscores the improved objectivity and reliability of this method over those of conventional diagnostic tools. The identities of approximately 30% of C. albicans isolates identified in clinical laboratories by positive germ tube tests are not verified by either testing on CHROMagar Candida plates or RAPD fingerprinting. Data suggest that clinical isolates conventionally identified as C. albicans in clinical settings are heterogeneous, consisting of both misidentified and atypical yeasts. RAPD fingerprints obtained from primary culture plate colonies allows for rapid, highly accurate determinations of Candida species, hence permitting earlier selection of appropriate antifungal agents in the clinical setting.
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Affiliation(s)
- P Steffan
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, USA
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13
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Zambon JJ. Principles of evaluation of the diagnostic value of subgingival bacteria. ANNALS OF PERIODONTOLOGY 1997; 2:138-48. [PMID: 9151550 DOI: 10.1902/annals.1997.2.1.138] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This paper describes steps in the process of evaluating subgingival bacteria assays for the diagnosis of periodontal disease. The first step examines the infectious etiology of periodontal disease in pointing to specific oral bacteria as periodontal pathogens. Second is characterization of the laboratory test to detect and quantitate these pathogens as to sensitivity, specificity, and positive and negative predictive value. Third is the role of the laboratory test in the diagnosis of the different forms of periodontal disease which is related to the current clinical rather than microbiological definition of these diseases. The fourth and most important step is an analysis of the significance of subgingival bacterial tests in clinical decision-making.
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Affiliation(s)
- J J Zambon
- Department of Periodontology, School of Dental Medicine, State University of New York at Buffalo, USA
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14
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Bergeron MG, Quellette M. Diagnosing bacterial infectious diseases in one hour: an essential upcoming revolution. Infection 1995; 23:69-72. [PMID: 7622265 DOI: 10.1007/bf01833867] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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15
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Affiliation(s)
- J J Zambon
- Department of Periodontology, School of Dental Medicine, State University of New York at Buffalo, USA
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16
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Abstract
The application of molecular biology to microbiology has led to a surge of new information about most infectious microorganisms, the pathogenesis of the infections they cause, and the specific microbial antigens involved in the immune response to these infections. The simultaneous application of the same techniques to diagnosis and epidemiology has also shown great promise, but these developments have not yet had a major effect on the routine practice of medicine. For some purposes, direct probe tests perform as well as other available methods. However, for most infections, these methods have not been proven sufficiently sensitive. The latest generation of highly sensitive diagnostics based on the polymerase chain reaction will overcome this technical obstacle and may revolutionize the management of many infections. Difficulties inherent in performing these tests will require special procedures and training in clinical laboratories to ensure that they are performed reliably. Nucleic acid-based methods for epidemiologic typing of microorganisms and for identification of noncultivatable pathogens are particularly useful for analysis of poorly cultivatable, dangerous, or otherwise untypeable microorganisms.
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Affiliation(s)
- N C Engleberg
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor
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