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Li Y, Kim H, Ju Y, Park Y, Kang T, Yong D, Park HG. Ultrasensitive Isothermal Detection of SARS-CoV-2 Based on Self-Priming Hairpin-Utilized Amplification of the G-Rich Sequence. Anal Chem 2022; 94:17448-17455. [PMID: 36480911 PMCID: PMC9743493 DOI: 10.1021/acs.analchem.2c03442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
The outbreak of the novel coronavirus disease 2019 (COVID-19) pandemic induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of fatalities all over the world. Unquestionably, the effective and timely testing for infected individuals is the most imperative for the prevention of the ongoing pandemic. Herein, a new method was established for detecting SARS-CoV-2 based on the self-priming hairpin-utilized isothermal amplification of the G-rich sequence (SHIAG). In this strategy, the target RNA binding to the hairpin probe (HP) was uniquely devised to lead to the self-priming-mediated extension followed by the continuously repeated nicking and extension reactions, consequently generating abundant G-rich sequences from the intended reaction capable of producing fluorescence signals upon specifically interacting with thioflavin T (ThT). Based on the unique isothermal design concept, we successfully identified SARS-CoV-2 genomic RNA (gRNA) as low as 0.19 fM with excellent selectivity by applying only a single HP and further verified its practical diagnostic capability by reliably testing a total of 100 clinical specimens for COVID-19 with 100% clinical sensitivity and specificity. This study would provide notable insights into the design and evolution of new isothermal strategies for the sensitive and facile detection of SARS-CoV-2 under resource constraints.
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Affiliation(s)
- Yan Li
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
| | - Hansol Kim
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
| | - Yong Ju
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
| | - Yeonkyung Park
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea
Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu,
Daejeon34141, Republic of Korea
- School of Pharmacy, Sungkyunkwan
University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do16419,
Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and
Research Institute of Bacterial Resistance, Yonsei University College of
Medicine, Seoul03722, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
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Zhao F, Liu J, Xiao D, Liu L, Gong J, Xu J, Li H, Zhao S, Zhang J. Pathogenic Analysis of the Bronchoalveolar Lavage Fluid Samples With Pediatric Refractory Mycoplasma pneumoniae Pneumonia. Front Cell Infect Microbiol 2020; 10:553739. [PMID: 33194797 PMCID: PMC7655529 DOI: 10.3389/fcimb.2020.553739] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/23/2020] [Indexed: 01/04/2023] Open
Abstract
Background: We conducted a pathogenic analysis in the bronchoalveolar lavage fluid (BALF) samples from refractory Mycoplasma pneumoniae pneumonia (RMPP) children. Methods: A total of 150 BALF samples from 60 RMPP patients were analyzed to investigate pathogenic changes. The characteristics of M. pneumoniae were analyzed through culture, real-time PCR, genotyping, antimicrobial susceptibility testing and proteomics. The other pathogens were determined using culture, sequencing and nucleic acid detection. Results: In 60 RMPP cases, the bacterial co-infection rate was 5%, while that of virus was 33.3%. The poor prognosis rate was 61.7%. The DNA positive rate among the 150 samples was 98.7%, while the culture positive rate was 56.7% for M. pneumoniae. Significant differences were noticed in the positivity of M. pneumoniae culture obtained from samples with a disease course of at least 3 weeks compared with those within 3 weeks. The genotype 1 M. pneumoniae strains showed a macrolide resistant (MLr) rate of 100%, and that for genotype 2 was 90.1%. Proteomics showed that there were 57 proteins up-regulated in the MLs M. pneumoniae, half of which were membrane-associated protein with adhesion or toxicity. Conclusions: Pediatric RMPP usually presented with viral co-infection, but it caused limited effects on the progression and prognosis of RMPP. Persistent presence of viable M. pneumoniae is not necessary in the later stage of RMPP. The expression of virulence factor in the MLr M. pneumoniae was higher than that of the MLs M. pneumoniae, which was more common in the RMPP children.
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Affiliation(s)
- Fei Zhao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Jinrong Liu
- Department of Respiratory Medicine, Beijing Children's Hospital Affiliated to Capital Medical University, National Center for Children's Health, Beijing, China
| | - Di Xiao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Liyong Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Jie Gong
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Juan Xu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Huimin Li
- Department of Respiratory Medicine, Beijing Children's Hospital Affiliated to Capital Medical University, National Center for Children's Health, Beijing, China
| | - Shunying Zhao
- Department of Respiratory Medicine, Beijing Children's Hospital Affiliated to Capital Medical University, National Center for Children's Health, Beijing, China
| | - Jianzhong Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
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Obande GA, Banga Singh KK. Current and Future Perspectives on Isothermal Nucleic Acid Amplification Technologies for Diagnosing Infections. Infect Drug Resist 2020; 13:455-483. [PMID: 32104017 PMCID: PMC7024801 DOI: 10.2147/idr.s217571] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 11/16/2019] [Indexed: 12/13/2022] Open
Abstract
Nucleic acid amplification technology (NAAT) has assumed a critical position in disease diagnosis in recent times and contributed significantly to healthcare. Application of these methods has resulted in a more sensitive, accurate and rapid diagnosis of infectious diseases than older traditional methods like culture-based identification. NAAT such as the polymerase chain reaction (PCR) is widely applied but seldom available to resource-limited settings. Isothermal amplification (IA) methods provide a rapid, sensitive, specific, simpler and less expensive procedure for detecting nucleic acid from samples. However, not all of these IA techniques find regular applications in infectious diseases diagnosis. Disease diagnosis and treatment could be improved, and the rapidly increasing problem of antimicrobial resistance reduced, with improvement, adaptation, and application of isothermal amplification methods in clinical settings, especially in developing countries. This review centres on some isothermal techniques that have found documented applications in infectious diseases diagnosis, highlighting their principles, development, strengths, setbacks and imminent potentials for use at points of care.
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Affiliation(s)
- Godwin Attah Obande
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
- Department of Microbiology, Faculty of Science, Federal University Lafia, Lafia, Nasarawa State, Nigeria
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
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Dash S, Chaudhry R, Dhawan B, Dey AB, Kabra SK, Das BK. Clinical spectrum and diagnostic yields of Mycoplasma pneumoniae as a causative agent of community-acquired pneumonia. J Lab Physicians 2018; 10:44-49. [PMID: 29403204 PMCID: PMC5784292 DOI: 10.4103/jlp.jlp_62_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/22/2017] [Indexed: 12/02/2022] Open
Abstract
INTRODUCTION Infection with Mycoplasma pneumoniae (M. pneumonia) occurs worldwide which accounts for 15%-20% of cases of community-acquired pneumonia and indistinguishable clinically from other infectious causes of pneumonia. AIM The aim of this study was to evaluate the real-time polymerase chain reaction (PCR) and to correlate it with other diagnostic methods such as culture, serology (ELISA), and conventional PCR along with the clinical signs and symptoms produced by M. pneumonia. MATERIALS AND METHODS A total of 130 patients of all age groups presenting with clinical features of lower respiratory tract infections were enrolled over a period of 1 year and 2 months in a tertiary care hospital in Delhi. M. pneumoniae in throat swab samples was detected by real-time PCR, compared with culture, serology, conventional PCR, and clinical signs and symptoms. Univariate analyses were conducted to determine the association of M. pneumoniae infection among different categories of patients. RESULTS Out of a total of 130 patients, 18 patients (14%) were positive for M. pneumoniae by any test; culture was positive in nine patients (50%), serology (IgM) in eight patients (44.4%), PCR in five patients (27.7%), and real-time PCR was positive in six patients (33.3%). Clinical signs and symptoms were higher in incidence in M. pneumoniae-positive patients. Age-matched healthy controls (30) were included in the study, and all were negative for any diagnostic test performed (P = 0.026). CONCLUSION It was concluded that combination of M. pneumoniae-specific testing modalities is required for the diagnosis of this etiological agent rather than a single diagnostic method.
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Affiliation(s)
- Saroj Dash
- Department of Microbiology, AIIMS, New Delhi, India
| | | | - Benu Dhawan
- Department of Microbiology, AIIMS, New Delhi, India
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Hønsvall BK, Robertson LJ. From research lab to standard environmental analysis tool: Will NASBA make the leap? WATER RESEARCH 2017; 109:389-397. [PMID: 27960143 DOI: 10.1016/j.watres.2016.11.052] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/21/2016] [Accepted: 11/22/2016] [Indexed: 05/07/2023]
Abstract
Nucleic acid sequence-based amplification (NASBA) is a sensitive and efficient molecular tool for amplification of RNA and has been widely adopted in clinical diagnostics. Monitoring of water and other environmental samples demands sensitive techniques, as potential pathogens may be in low concentrations and require only a few infectious units to infect their host. NASBA has qualities that should be advantageous for analysis of environmental samples, such as short reaction times, high sensitivity, and not readily affected by inhibitory substances that are often abundant in environmental samples. NASBA is well suited for incorporation into lab-on-a-chip (LOC) devices, as part of analysis systems that can be taken into the field for on-site screening. In this review, we explore advantages and drawbacks of NASBA as a tool for environmental analyses, and try to answer the question of whether it will be a recognised technique in the same manner as in clinical diagnostics.
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Affiliation(s)
- Birgitte K Hønsvall
- University College of Southeast Norway, Raveien 205, 3184 Borre, Norway; Trilobite Microsystems AS, Raveien 205, 3184 Borre, Norway.
| | - Lucy J Robertson
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Adamstuen Campus, Oslo, Norway.
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Diaz MH, Winchell JM. The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae. Front Microbiol 2016; 7:232. [PMID: 27014191 PMCID: PMC4781879 DOI: 10.3389/fmicb.2016.00232] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 02/15/2016] [Indexed: 12/12/2022] Open
Abstract
Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen.
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Affiliation(s)
| | - Jonas M. Winchell
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, AtlantaGA, USA
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Optimization of influencing factors of nucleic acid adsorption onto silica-coated magnetic particles: Application to viral nucleic acid extraction from serum. J Chromatogr A 2014; 1325:31-9. [DOI: 10.1016/j.chroma.2013.11.059] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Revised: 11/22/2013] [Accepted: 11/30/2013] [Indexed: 11/18/2022]
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Detection of viruses directly from the fresh leaves of a Phalaenopsis orchid using a microfluidic system. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2013; 9:1274-82. [DOI: 10.1016/j.nano.2013.05.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 05/29/2013] [Accepted: 05/31/2013] [Indexed: 11/18/2022]
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Chang CM, Chang WH, Wang CH, Wang JH, Mai JD, Lee GB. Nucleic acid amplification using microfluidic systems. LAB ON A CHIP 2013; 13:1225-42. [PMID: 23407669 DOI: 10.1039/c3lc41097h] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In the post-human-genome-project era, the development of molecular diagnostic techniques has advanced the frontiers of biomedical research. Nucleic-acid-based technology (NAT) plays an especially important role in molecular diagnosis. However, most research and clinical protocols still rely on the manual analysis of individual samples by skilled technicians which is a time-consuming and labor-intensive process. Recently, with advances in microfluidic designs, integrated micro total-analysis-systems have emerged to overcome the limitations of traditional detection assays. These microfluidic systems have the capability to rapidly perform experiments in parallel and with a high-throughput which allows a NAT analysis to be completed in a few hours or even a few minutes. These features have a significant beneficial influence on many aspects of traditional biological or biochemical research and this new technology is promising for improving molecular diagnosis. Thus, in the foreseeable future, microfluidic systems developed for molecular diagnosis using NAT will become an important tool in clinical diagnosis. One of the critical issues for NAT is nucleic acid amplification. In this review article, recent advances in nucleic acid amplification techniques using microfluidic systems will be reviewed. Different approaches for fast amplification of nucleic acids for molecular diagnosis will be highlighted.
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Affiliation(s)
- Chen-Min Chang
- Institute of Oral Medicine, National Cheng Kung University, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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Simpkins A, Strickland SM, Oliver J, Murray DL, Steele JCH, Park YD, Sharma S. Complete resolution of advanced Mycoplasma pneumoniae encephalitis mimicking brain mass lesions: report of two pediatric cases and review of literature. Neuropathology 2011; 32:91-9. [PMID: 21615517 DOI: 10.1111/j.1440-1789.2011.01225.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mycoplasma pneumoniae is a well-known cause of atypical pneumonia. CNS involvement is a relatively frequent extrapulmonary manifestation, most commonly manifesting as encephalitis in the pediatric population. We present two unusual cases of M. pneumoniae encephalitis that presented with symptoms and imaging findings suggesting mass occupying lesions, and worsening altered mental status. Biopsy of the lesions was necessary in both cases to aid with diagnosis. Histopathologic features excluded neoplasm, and established the diagnosis of encephalitis, but did not point toward its etiology. The only finding that indicated M. pneumoniae as the most likely pathogen was serum IgM positivity in the absence of any other identifiable infectious source, and complete neurologic recovery following specific anti-mycoplasmal treatment. The patients were successfully treated with antibiotics and steroids, with the second case also requiring intravenous immunoglobulin and anti-epileptics. The clinical presentation and histopathologic findings suggested an immune-mediated pathogenesis, but acute disseminated encephalomyelitis was excluded due to extensive gray matter involvement. Disease resolution despite status epilepticus and herniation in case 2 is a novel finding of the study. Current principles of diagnosis and management of encephalitis as the presenting manifestation of mycoplasmal infection are discussed.
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Affiliation(s)
- Alexis Simpkins
- Department of Pathology, Medical College of Georgia, Augusta, Georgia 30912, USA
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11
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Volokhov DV, Graham LJ, Brorson KA, Chizhikov VE. Mycoplasma testing of cell substrates and biologics: Review of alternative non-microbiological techniques. Mol Cell Probes 2011; 25:69-77. [DOI: 10.1016/j.mcp.2011.01.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 12/22/2010] [Accepted: 01/04/2011] [Indexed: 11/25/2022]
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12
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Tang P, Chiu C. Metagenomics for the discovery of novel human viruses. Future Microbiol 2010; 5:177-89. [PMID: 20143943 DOI: 10.2217/fmb.09.120] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Modern laboratory techniques for the detection of novel human viruses are greatly needed as physicians and epidemiologists increasingly deal with infectious diseases caused by new or previously unrecognized pathogens. There are many clinical syndromes in which viruses are suspected to play a role, but for which traditional microbiology techniques routinely fail in uncovering the etiologic agent. In addition, new viruses continue to challenge the human population owing to the encroachment of human settlements into animal and livestock habitats, globalization, climate change, growing numbers of immunocompromised people and bioterrorism. Metagenomics-based tools, such as microarrays and high-throughput sequencing are ideal for responding to these challenges. Pan-viral microarrays, containing representative sequences from all known viruses, have been used to detect novel and distantly-related variants of known viruses. Sequencing-based methods have also been successfully employed to detect novel viruses and have the potential to detect the full spectrum of viruses, including those present in low numbers.
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Affiliation(s)
- Patrick Tang
- British Columbia Centre for Disease Control, Department of Pathology & Laboratory Medicine, University of British Columbia, 655 West 12th Avenue, Vancouver, BC, V5Z 4R4, Canada.
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Wittek M, Stürmer M, Doerr HW, Berger A. Molecular assays for monitoring HIV infection and antiretroviral therapy. Expert Rev Mol Diagn 2009; 7:237-46. [PMID: 17489731 DOI: 10.1586/14737159.7.3.237] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Infection with HIV results in lifelong persistence of the virus in the body of infected persons, independent of antiretroviral treatment. Therefore, efficient and meaningful therapy monitoring has been developed since its introduction in the 1980s. Whereas, primarily, the measurement of the CD4 cell count was the most important clinical marker of disease progression, nowadays the estimation of plasma viral load with molecular methods plays a major role as a marker of therapy success. To optimize therapy changes in patients failing on antiretroviral therapy regimen, HIV-1 genotyping has been introduced and is now widely accepted as an additional diagnostic tool. Due to this increase in diagnostic parameters, clinicians and virologists have to cope with many different methods. This review should give a brief overview of the current commercially available assays for detection and quantification of HIV, as well as for HIV-1 genotypic resistance testing. Quantitative reverse transcriptase PCR, real-time PCR, nucleic acid sequence-based amplification and the branched DNA system are described in detail, and the advantages and disadvantages are discussed. In addition, two commercially available HIV-1 genotyping assays are compared. However, a general recommendation to favor one system over the other cannot be given, because the final decision of which system to use should be decided on the individual requirements.
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Affiliation(s)
- Miriam Wittek
- Institute for Medical Virology, JW Goethe University Hospital, Frankfurt, Germany.
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Atkinson TP, Balish MF, Waites KB. Epidemiology, clinical manifestations, pathogenesis and laboratory detection of Mycoplasma pneumoniae infections. FEMS Microbiol Rev 2008; 32:956-73. [PMID: 18754792 DOI: 10.1111/j.1574-6976.2008.00129.x] [Citation(s) in RCA: 313] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Since its initial description in the 1940s and eventual elucidation as a highly evolved pathogenic bacterium, Mycoplasma pneumoniae has come to be recognized as a worldwide cause of primary atypical pneumonia. Beyond its ability to cause severe lower respiratory illness and milder upper respiratory symptoms it has become apparent that a wide array of extrapulmonary infectious and postinfectious events may accompany the infections in humans caused by this organism. Autoimmune disorders and chronic diseases such as asthma and arthritis are increasingly being associated with this mycoplasma, which frequently persists in individuals for prolonged periods. The reductive evolutionary process that has led to the minimal genome of M. pneumoniae suggests that it exists as a highly specialized parasitic bacterium capable of residing in an intracellular state within the respiratory tissues, occasionally emerging to produce symptoms. This review includes discussion of some of the newer aspects of our knowledge on this pathogen, characteristics of clinical infections, how it causes disease, the recent emergence of macrolide resistance, and the status of laboratory diagnostic methods.
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Loens K, Beck T, Ursi D, Overdijk M, Sillekens P, Goossens H, Ieven M. Evaluation of different nucleic acid amplification techniques for the detection of M. pneumoniae, C. pneumoniae and Legionella spp. in respiratory specimens from patients with community-acquired pneumonia. J Microbiol Methods 2008; 73:257-62. [DOI: 10.1016/j.mimet.2008.02.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Revised: 01/21/2008] [Accepted: 02/15/2008] [Indexed: 11/30/2022]
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Yoo JH, Choi SM, Choi JH, Kwon EY, Park C, Shin WS. Construction of internal control for the quantitative assay of Aspergillus fumigatus using real-time nucleic acid sequence-based amplification. Diagn Microbiol Infect Dis 2008; 60:121-4. [DOI: 10.1016/j.diagmicrobio.2007.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Revised: 08/06/2007] [Accepted: 08/07/2007] [Indexed: 11/25/2022]
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Development of real-time multiplex nucleic acid sequence-based amplification for detection of Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Legionella spp. in respiratory specimens. J Clin Microbiol 2007; 46:185-91. [PMID: 18032625 DOI: 10.1128/jcm.00447-07] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Real-time multiplex isothermal nucleic acid sequence-based amplification (NASBA) was developed to detect Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Legionella spp. in respiratory specimens using the NucliSens Basic Kit (bioMérieux, Boxtel, The Netherlands). Oligonucleotide primers were derived from the M. pneumoniae, C. pneumoniae, and Legionella pneumophila 16S rRNA. For real-time detection, molecular beacons were used. Specificity was established on a panel of bacterial strains. The analytical sensitivity of the assay was determined by testing dilutions of wild-type in vitro-generated RNA in water and dilutions of reference strains in lysis buffer or added to pools of respiratory specimens. Subsequently, a limited number of M. pneumoniae-, C. pneumoniae-, and L. pneumophila-positive and -negative clinical specimens were analyzed. Specific detection of the 16S rRNA of the three organisms was achieved. The analytical sensitivity of the multiplex NASBA on spiked respiratory specimens was slightly diminished compared to the results obtained with the single-target (mono) real-time assays. We conclude that the proposed real-time multiplex NASBA assay, although less sensitive than the real-time mono NASBA assay, is a promising tool for the detection of M. pneumoniae, C. pneumoniae, and Legionella spp. in respiratory specimens, regarding handling, speed, and number of samples that can be analyzed in a single run.
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GRACIAS KIEVS, MCKILLIP JOHNL. NUCLEIC ACID SEQUENCE-BASED AMPLIFICATION (NASBA) IN MOLECULAR BACTERIOLOGY: A PROCEDURAL GUIDE. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1745-4581.2007.00099.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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de Andrade TS, Cury AE, de Castro LGM, Hirata MH, Hirata RDC. Rapid identification of Fonsecaea by duplex polymerase chain reaction in isolates from patients with chromoblastomycosis. Diagn Microbiol Infect Dis 2007; 57:267-72. [PMID: 17338941 DOI: 10.1016/j.diagmicrobio.2006.08.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 08/06/2006] [Accepted: 08/29/2006] [Indexed: 11/26/2022]
Abstract
Fonsecaea pedrosoi is the most common etiologic agent of chromoblastomycosis. F. pedrosoi and other dematiaceous fungi are usually identified by morphologic studies. We have developed a duplex polymerase chain reaction (PCR) targeting the ribosomal DNA for rapid and more specific identification of the genus Fonsecaea. DNA samples from 103 isolates of Fonsecaea species and other dematiaceous fungi were amplified by PCR using universal and specific primers targeting ITS1-5.8S-ITS2 region of the ribosomal DNA. Universal primers were used for detection of non-Fonsecaea DNA. Fonsecaea-specific PCR product was found in 70 (68.0%) isolates including 4 strains that did not develop conidiogenesis. Thirty non-Fonsecaea and 3 Fonsecaea compacta isolates were negative by duplex PCR. These results were confirmed by DNA sequencing analysis indicating the high specificity of the duplex PCR assay. In conclusion, the duplex PCR is a rapid and specific assay for identification of Fonsecaea isolates mainly for the strains that are difficult to identify by morphologic methods.
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Affiliation(s)
- Tânia Sueli de Andrade
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brasil.
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Loens K, Bergs K, Ursi D, Goossens H, Ieven M. Evaluation of NucliSens easyMAG for automated nucleic acid extraction from various clinical specimens. J Clin Microbiol 2006; 45:421-5. [PMID: 17166966 PMCID: PMC1829055 DOI: 10.1128/jcm.00894-06] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The objectives of this study were to evaluate the performance of the NucliSens easyMAG platform for nucleic acid extraction from different clinical specimens compared to NucliSens miniMAG platform and manual QIAGEN extraction. The NucliSens easyMAG and the NucliSens miniMAG showed equal performance on 215 throat swabs since real-time nucleic acid sequence-based amplification scored the same samples positive for Mycoplasma pneumoniae (n=9) and Chlamydia pneumoniae (n=5) RNAs, although internal control RNA was slightly better detected with the NucliSens easyMAG (99.3% versus 96.8%). NucliSens easyMAG extracted nucleic acids more efficiently (higher recovery and/or fewer inhibitors) compared to QIAGEN extraction by showing, on average, lower Ct values in real-time LightCycler PCR, although 4 individual specimen out of 45 were found positive only with QIAGEN. For nine M. pneumoniae-positive throat swabs, the mean difference in Ct values between NucliSens easyMAG extraction and QIAGEN extraction was -2.26 (range, -5.77 to +0.60); for the detection of five C. pneumoniae-positive throat swabs, the average difference in Ct values between the two methods was -3.38 (range, -6.62 to -2.02); and for the detection of cytomegalovirus in 24 blood samples, the mean difference in Ct values between the two methods was -0.95 (range, -5.51 to +1.68). The NucliSens easyMAG is considerably easier to perform, efficiently extracts nucleic acids from throat swabs and whole blood, is automated, and has high throughput.
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Affiliation(s)
- K Loens
- Department of Medical Microbiology, University of Antwerp, Universiteitsplein 1 S009a, B-2610 Wilrijk, Belgium.
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Wang XS, Zhang Z, Wang HC, Cai JL, Xu QW, Li MQ, Chen YC, Qian XP, Lu TJ, Yu LZ, Zhang Y, Xin DQ, Na YQ, Chen WF. Rapid identification of UCA1 as a very sensitive and specific unique marker for human bladder carcinoma. Clin Cancer Res 2006; 12:4851-8. [PMID: 16914571 DOI: 10.1158/1078-0432.ccr-06-0134] [Citation(s) in RCA: 359] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
PURPOSE The most common genitourinary malignancy in China is bladder transitional cell carcinoma (TCC). Early diagnosis of new and recurrent bladder cancers, followed by timely treatment, will help decrease mortality. There are currently no satisfactory markers for bladder cancer available in clinics. Better diagnostic methods are highly demanded. EXPERIMENTAL DESIGN In this research, we have used comprehensive expressed sequence tag analysis, serial analysis of gene expression, and microarray analysis and quickly discovered a candidate marker, urothelial carcinoma associated 1 (UCA1). The UCA1 gene was characterized and its performance as a urine marker was analyzed by reverse transcription-PCR with urine sediments. A total of 212 individuals were included in this study, 94 having bladder cancers, 33 ureter/pelvic cancers, and 85 normal and other urinary tract disease controls. RESULTS UCA1 was identified as a novel noncoding RNA gene dramatically up-regulated in TCC and it is the most TCC-specific gene yet identified. The full-length cDNA was 1,439 bp, and sequence analysis showed that it belonged to the human endogenous retrovirus H family. Clinical tests showed that UCA1 assay was highly specific (91.8%, 78 of 85) and very sensitive (80.9%, 76 of 94) in the diagnosis of bladder cancer and was especially valuable for superficial G2-G3 patients (sensitivity 91.1%, 41 of 45). It showed excellent differential diagnostic performance in various urinary tract diseases without TCC. CONCLUSIONS UCA1 is a very sensitive and specific unique marker for bladder cancer. It could have important implications in postoperative noninvasive follow-up. This research also highlights a shortcut to new cancer diagnostic assays through integration of in silico isolation methods with translational clinical tests based on RNA detection protocols.
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Affiliation(s)
- Xiao-Song Wang
- Department of Urology, First Hospital of Peking University, Institute of Urology, Peking University, Beijing, China
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Loens K, Beck T, Goossens H, Ursi D, Overdijk M, Sillekens P, Ieven M. Development of conventional and real-time nucleic acid sequence-based amplification assays for detection of Chlamydophila pneumoniae in respiratory specimens. J Clin Microbiol 2006; 44:1241-4. [PMID: 16597845 PMCID: PMC1448673 DOI: 10.1128/jcm.44.4.1241-1244.2006] [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] [Indexed: 11/20/2022] Open
Abstract
Isothermal nucleic acid sequence-based amplification (NASBA) was applied to the detection of Chlamydophila pneumoniae 16S rRNA by using the NucliSens basic kit (bioMérieux, Boxtel, The Netherlands). The assay was originally developed as a conventional NASBA assay with electrochemiluminescence detection and was subsequently adapted to a real-time NASBA format by using a molecular beacon. C. pneumoniae RNA prepared from a plasmid construct was used to assess the analytical sensitivity of the assay. The sensitivity of the NASBA assay was 10 molecules of in vitro wild-type C. pneumoniae RNA and 0.1 inclusion-forming unit (IFU) of C. pneumoniae. In spiked respiratory specimens, the sensitivity of the C. pneumoniae NASBA assay varied between 0.1 and 1 IFU/100 mul sample, depending on the type of specimen. Finally, conventional and real-time NASBA were applied to respiratory specimens previously tested by PCR. A 100% concordance between the test results was obtained.
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Affiliation(s)
- K Loens
- Department of Medical Microbiology, University of Antwerp, Universiteitsplein 1 S3, B-2610 Wilrijk, Belgium.
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Loens K, Ieven M, Pattyn S, Sillekens P, Goossens H. Sensitivity of detection of rhinoviruses in spiked clinical samples by nucleic acid sequence-based amplification in the presence of an internal control. J Microbiol Methods 2006; 66:73-8. [PMID: 16318891 DOI: 10.1016/j.mimet.2005.10.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Revised: 10/04/2005] [Accepted: 10/20/2005] [Indexed: 11/19/2022]
Abstract
The objectives of the study were to determine the sensitivity of Nucleic Acid Sequence-Based Amplification (NASBA) for the detection of rhinovirus (RV) serotype 15 in water and in spiked respiratory specimens in the presence of a newly developed internal control (IC). The sensitivity of NASBA on RNA was 10 molecules per reaction. The sensitivity of RV NASBA on RV-15 in water and in respiratory specimens was equal to that in tissue culture. Addition of 10(4) molecules of rhinovirus internal control (RV IC) did not affect the sensitivity. Viral RNA should be extracted from clinical specimens as rapidly as possible after collection, since loss of detectable RNA occurs after 2 h. NASBA allows a sensitive detection of RV RNA in spiked respiratory specimens in the presence of an internal control.
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Affiliation(s)
- Katherine Loens
- Microbiology/Centre for Molecular Diagnostics, University Hospital Antwerp, Wilrijkstraat 10, B-2650 Edegem, Belgium.
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Development of conventional and real-time NASBA for the detection of Legionella species in respiratory specimens. J Microbiol Methods 2006; 67:408-15. [PMID: 16730822 DOI: 10.1016/j.mimet.2006.04.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 03/30/2006] [Accepted: 04/14/2006] [Indexed: 11/18/2022]
Abstract
Isothermal nucleic acid sequence-based amplification (NASBA) was applied to detect Legionella 16S rRNA. The assay was originally developed as a Legionella pneumophila conventional NASBA assay with electrochemiluminescence (ECL) detection and was subsequently adapted to a L. pneumophila real-time NASBA format and a Legionella spp. real-time NASBA using molecular beacons. L. pneumophila RNA prepared from a plasmid construct was used to assess the analytical sensitivity of the assay. The sensitivity of the NASBA assay was 10 molecules of in vitro wild type L. pneumophila RNA and 0.1-1 colony-forming units (CFU) of L. pneumophila. In spiked respiratory specimens, the sensitivity of the NASBA assays was 1-10000 CFU of L. pneumophila serotype 1 depending on the background. After dilution of the nucleic acid extract prior to amplification, 1-10 CFU of L. pneumophila serotype 1 could be detected with both detection methods. Finally, 27 respiratory specimens, well characterized by culture and PCR, collected during a L. pneumophila outbreak, were tested by conventional and real-time NASBAs. All 11 PCR positive samples were positive by conventional NASBA, 9/11 and 10/11 were positive by L. pneumophila real-time NASBA and Legionella spp. real-time NASBA, respectively.
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Pitcher D, Chalker VJ, Sheppard C, George RC, Harrison TG. Real-time detection of Mycoplasma pneumoniae in respiratory samples with an internal processing control. J Med Microbiol 2006; 55:149-155. [PMID: 16434706 DOI: 10.1099/jmm.0.46281-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Real-time PCR was employed to detect a region of the P1 cytadhesin gene of Mycoplasma pneumoniae in clinical samples. An internal processing control was included that could be co-amplified simultaneously in the same reaction tube. The assay could reproducibly detect 1 x 10(3) M. pneumoniae organisms ml(-1) in clinical samples. There was no amplification of DNA or signal production from 15 other species of human mycoplasmas and 19 other bacterial species. Using a panel of 175 respiratory samples taken from patients with pneumonia of proven aetiology, the sensitivity was found to be 60 % and the specificity of the assay 96.7 % when compared with serology. This assay is suitable for same-day diagnosis of M. pneumoniae infection and batch processing of respiratory samples for clinical screening.
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Affiliation(s)
- David Pitcher
- Respiratory and Systemic Infection Laboratory, Health Protection Agency Centre for Infections, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Victoria J Chalker
- Respiratory and Systemic Infection Laboratory, Health Protection Agency Centre for Infections, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Carmen Sheppard
- Respiratory and Systemic Infection Laboratory, Health Protection Agency Centre for Infections, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Robert C George
- Respiratory and Systemic Infection Laboratory, Health Protection Agency Centre for Infections, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Timothy G Harrison
- Respiratory and Systemic Infection Laboratory, Health Protection Agency Centre for Infections, 61 Colindale Avenue, London NW9 5EQ, UK
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26
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Loens K, Beck T, Ursi D, Pattyn S, Goossens H, Ieven M. Two quality control exercises involving nucleic acid amplification methods for detection of Mycoplasma pneumoniae and Chlamydophila pneumoniae and carried out 2 years apart (in 2002 and 2004). J Clin Microbiol 2006; 44:899-908. [PMID: 16517874 PMCID: PMC1393091 DOI: 10.1128/jcm.44.3.899-908.2006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 09/15/2005] [Accepted: 01/09/2006] [Indexed: 11/20/2022] Open
Abstract
The quality performance of laboratories for the detection of Mycoplasma pneumoniae and Chlamydophila pneumoniae by two quality control (QC) exercises with a 2-year interval was investigated. For the 2002 QC exercise, specimens were spiked with M. pneumoniae at concentrations of 5,000, 500, 50, and 0 color-changing units (CCU)/100 microl. The limit of detectability was 50 CCU/100 microl. Therefore, this concentration was omitted from the 2004 panel and was excluded from the analysis. In 2002, 2 out of 12 participants obtained 100% correct results, 2 out of 12 produced false-positive results, and 10 out of 12 had between 0 out of 9 and 8 out of 9 correct positive results. In 2004, correct results were obtained in 15 out of 18 tests, and no false-positive results were reported. In 2002, specimens were spiked with C. pneumoniae at concentrations of 490, 49, 4.9, and 0 inclusion-forming units/100 microl (IFU/100 microl). In the 2004 panel, samples spiked with a lower dilution of 0.49 IFU/100 microl were added to the panel. For the C. pneumoniae QC, correct results were produced in 12 out of 16 and 13 out of 18 tests in 2002 and in 2004, respectively. Both multiplex PCR and nucleic acid sequence-based amplification (NASBA) formats scored a smaller number of samples positive than the monoplex reactions.
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Affiliation(s)
- K Loens
- Laboratory of Medical Microbiology, Department of Medicine, Universitaire Instelling Antwerpen, Wilrijk, Belgium.
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Saito R, Misawa Y, Moriya K, Koike K, Ubukata K, Okamura N. Development and evaluation of a loop-mediated isothermal amplification assay for rapid detection of Mycoplasma pneumoniae. J Med Microbiol 2005; 54:1037-1041. [PMID: 16192434 DOI: 10.1099/jmm.0.46071-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A loop-mediated isothermal amplification (LAMP) assay for the rapid detection ofMycoplasma pneumoniaewas developed and evaluated. The assay specifically amplified onlyM. pneumoniaesequences, and no cross-reactivity was observed for otherMycoplasmaspecies or respiratory bacterial species. The detection limit for this assay was found to be 2 × 102copies, corresponding to 2–20 colour changing units ofM. pneumoniaein 1 h, as observed in a real-time turbidimeter and electrophoretic analysis. The accuracy of the LAMP reaction was confirmed by restriction endonuclease analysis as well as direct sequencing of the amplified product. The assay was applied to 95 nasopharyngeal swab samples collected from patients or from healthy individuals, and compared to a real-time PCR assay in-house. A concordance of 100 % was observed between the two assays. The LAMP assay is easy to perform, shows a rapid reaction and is inexpensive. It may therefore be applied in the routine diagnosis ofM. pneumoniaeinfection in the clinical laboratory.
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Affiliation(s)
- Ryoichi Saito
- Department of Infection Control and Prevention, University of Tokyo Hospital, Bunkyo-ku, Tokyo 113-8655, Japan 2Department of Microbiology and Immunology, Graduate School of Allied Health Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan 3Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, Minato-ku, Tokyo 108-8641, Japan
| | - Yoshiki Misawa
- Department of Infection Control and Prevention, University of Tokyo Hospital, Bunkyo-ku, Tokyo 113-8655, Japan 2Department of Microbiology and Immunology, Graduate School of Allied Health Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan 3Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, Minato-ku, Tokyo 108-8641, Japan
| | - Kyoji Moriya
- Department of Infection Control and Prevention, University of Tokyo Hospital, Bunkyo-ku, Tokyo 113-8655, Japan 2Department of Microbiology and Immunology, Graduate School of Allied Health Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan 3Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, Minato-ku, Tokyo 108-8641, Japan
| | - Kazuhiko Koike
- Department of Infection Control and Prevention, University of Tokyo Hospital, Bunkyo-ku, Tokyo 113-8655, Japan 2Department of Microbiology and Immunology, Graduate School of Allied Health Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan 3Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, Minato-ku, Tokyo 108-8641, Japan
| | - Kimiko Ubukata
- Department of Infection Control and Prevention, University of Tokyo Hospital, Bunkyo-ku, Tokyo 113-8655, Japan 2Department of Microbiology and Immunology, Graduate School of Allied Health Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan 3Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, Minato-ku, Tokyo 108-8641, Japan
| | - Noboru Okamura
- Department of Infection Control and Prevention, University of Tokyo Hospital, Bunkyo-ku, Tokyo 113-8655, Japan 2Department of Microbiology and Immunology, Graduate School of Allied Health Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan 3Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, Minato-ku, Tokyo 108-8641, Japan
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28
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Ginevra C, Barranger C, Ros A, Mory O, Stephan JL, Freymuth F, Joannès M, Pozzetto B, Grattard F. Development and evaluation of Chlamylege, a new commercial test allowing simultaneous detection and identification of Legionella, Chlamydophila pneumoniae, and Mycoplasma pneumoniae in clinical respiratory specimens by multiplex PCR. J Clin Microbiol 2005; 43:3247-54. [PMID: 16000443 PMCID: PMC1169163 DOI: 10.1128/jcm.43.7.3247-3254.2005] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study describes the development and evaluation of a new commercial test, Chlamylege (Argene Inc.), which allows the simultaneous detection in respiratory samples of Chlamydophila pneumoniae, Mycoplasma pneumoniae, and most Legionella species, as well as PCR inhibitors, by using a multiplex PCR and microplate hybridization. The sensitivities of Chlamylege were 1 x 10(-3) IFU, 5 x 10(-2) color-changing units, and 1 CFU per reaction tube for C. pneumoniae, M. pneumoniae, and Legionella pneumophila, respectively. A cohort of 154 clinical samples from patients with documented respiratory infections was analyzed by the kit, including 2 samples from patients with C. pneumoniae infection, 9 samples from patients with M. pneumoniae infection, 19 samples from patients with Legionella species infection, and 114 samples that tested negative for the three pathogens. All the positive specimens were correctly detected and identified by the Chlamylege kit, and no false-positive result was observed with the negative samples. The kit was then evaluated in a pediatric prospective study that included 220 endotracheal aspirates, and the results were compared with those obtained by three single in-house PCR assays. Four specimens were found to be positive for C. pneumoniae and six were found to be positive for M. pneumoniae by using both strategies. The Chlamylege kit detected two additional samples positive for M. pneumoniae and one additional sample positive for a Legionella species other than L. pneumophila; these three samples were shown to be true positive by other techniques. These overall results demonstrate that the Chlamylege assay is sensitive, specific, and convenient for the rapid detection and identification of atypical pathogens in clinical samples from patients with respiratory infections.
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Affiliation(s)
- C Ginevra
- Laboratoire de Bactériologie-Virologie, GIMAP, Faculté de Médecine Jacques Lisfranc, Saint-Etienne, France
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29
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Beersma MFC, Dirven K, van Dam AP, Templeton KE, Claas ECJ, Goossens H. Evaluation of 12 commercial tests and the complement fixation test for Mycoplasma pneumoniae-specific immunoglobulin G (IgG) and IgM antibodies, with PCR used as the "gold standard". J Clin Microbiol 2005; 43:2277-85. [PMID: 15872256 PMCID: PMC1153783 DOI: 10.1128/jcm.43.5.2277-2285.2005] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Serology and nucleic acid amplification are the main diagnostic tools for the diagnosis of Mycoplasma pneumoniae infection. Since no reference standard is generally accepted, serologic assays for M. pneumoniae have not been evaluated on a broad scale. In this study, 12 commercially available serologic assays (for immunoglobulin G [IgG] and IgM) and the complement fixation test (CFT) were evaluated by using M. pneumoniae DNA detection by real-time PCR as the "gold standard." The assays tested were Platelia EIA (Bio-Rad), SeroMP EIA (Savyon), Serion classic EIA (Virion/Serion), Biotest EIA (Biotest), Ridascreen EIA (r-Biopharm), AniLabsystems EIA (Labsystems), Novum EIA (Novum Diagnostica), Diagnosys EIA (MP products), Genzyme/Virotech EIA, ImmunoWell EIA (Genbio), ImmunoCard EIA (Meridian), and SerodiaMycoII microparticle agglutination (Fujirebio). Serum samples (n = 46) from 27 PCR-positive patients with a known first day of disease and sera (n = 33) from PCR-negative controls were obtained from prospective studies of acute lower respiratory tract infections. Additionally, control sera (n = 63) from patients with acute viral or bacterial respiratory infections other than those caused by M. pneumoniae were tested. The results showed low specificities for both the Novum and the ImmunoCard IgM assays. The IgM assays with the best performances in terms of sensitivity and specificity were AniLabsystems (77% and 92%, respectively), SeroMP (71% and 88%, respectively), and CFT (65% and 97%, respectively). Good receiver operating characteristic areas under the curve were found for CFT (0.94), the Platelia assay (0.87), and the AniLabsystems assay (0.85). We conclude that there are few commercial serologic assays for the detection of M. pneumoniae infections with appropriate performances in terms of sensitivity and specificity and that PCR has become increasingly important for the diagnosis of M. pneumoniae infections in defined groups of patients.
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Affiliation(s)
- Matthias F C Beersma
- Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
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Loens K, Ursi D, Goossens H, Ieven M. Molecular diagnosis of Mycoplasma pneumoniae respiratory tract infections. J Clin Microbiol 2004; 41:4915-23. [PMID: 14605118 PMCID: PMC262541 DOI: 10.1128/jcm.41.11.4915-4923.2003] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- K Loens
- Medical Microbiology, Universitaire Instelling Antwerpen, B2610 Wilrijk, Belgium.
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31
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Templeton KE, Scheltinga SA, Graffelman AW, Van Schie JM, Crielaard JW, Sillekens P, Van Den Broek PJ, Goossens H, Beersma MFC, Claas ECJ. Comparison and evaluation of real-time PCR, real-time nucleic acid sequence-based amplification, conventional PCR, and serology for diagnosis of Mycoplasma pneumoniae. J Clin Microbiol 2003; 41:4366-71. [PMID: 12958270 PMCID: PMC193789 DOI: 10.1128/jcm.41.9.4366-4371.2003] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Mycoplasma pneumoniae is a common cause of community-acquired pneumonia and lower-respiratory-tract infections. Diagnosis has traditionally been obtained by serological diagnosis, but increasingly, molecular techniques have been applied. However, the number of studies actually comparing these assays is limited. The development of a novel duplex real-time PCR assay for detection of M. pneumoniae in the presence of an internal control real-time PCR is described. In addition, real-time nucleic acid sequence-based amplification (NASBA) on an iCycler apparatus is evaluated. These assays were compared to serology and a conventional PCR assay for 106 clinical samples from patients with lower-respiratory-tract infection. Of the 106 samples, 12 (11.3%) were positive by all the molecular methods whereas serology with acute sample and convalescent samples detected 6 (5.6%) and 9 (8.5%), respectively. Clinical symptoms of the patients with Mycoplasma-positive results were compared to those of the other patients with lower-respiratory-tract infections, and it was found that the results for mean lower age numbers as well as the presence of chills, increased erythrocyte sedimentation rate, and raised C-reactive protein levels showed significant differences. Molecular methods are superior for diagnosis of M. pneumoniae, providing more timely diagnosis. In addition, using real-time methods involves less hands-on time and affords the ability to monitor the reaction in the same tube.
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Affiliation(s)
- Kate E Templeton
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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Loens K, Ieven M, Ursi D, Beck T, Overdijk M, Sillekens P, Goossens H. Detection of Mycoplasma pneumoniae by real-time nucleic acid sequence-based amplification. J Clin Microbiol 2003; 41:4448-50. [PMID: 12958290 PMCID: PMC193797 DOI: 10.1128/jcm.41.9.4448-4450.2003] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Real-time isothermal nucleic acid sequence-based amplification (RT-NASBA) was applied to the detection of Mycoplasma pneumoniae. In vitro-generated M. pneumoniae RNA was used to assess the sensitivity of the assay. The 95% hit rate was 148 molecules of M. pneumoniae RNA in the amplification and 10(4) molecules of in vitro-generated RNA after nucleic acid extraction. The sensitivity of the RT-NASBA and the conventional NASBA assays corresponded to 5 color-changing units (CCU) of M. pneumoniae. In spiked throat swabs, nasopharyngeal aspirates, bronchoalveolar lavages, and sputum, the sensitivity of both NASBA assays corresponded to 5 to 50 CCU of M. pneumoniae. A total of 17 clinical specimens positive for M. pneumoniae by PCR were also positive by conventional NASBA, but one specimen was negative by RT-NASBA. These results indicate that the sensitivity of detection of M. pneumoniae by RT-NASBA in respiratory samples might be slightly reduced compared to that by conventional NASBA. However, the real-time assay is superior in speed and ease of handling.
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Affiliation(s)
- K Loens
- Department of Medical Microbiology, University of Antwerp UIA, Antwerp, Belgium.
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Loens K, Ieven M, Ursi D, Foolen H, Sillekens P, Goossens H. Application of NucliSens Basic Kit for the detection of Mycoplasma pneumoniae in respiratory specimens. J Microbiol Methods 2003; 54:127-30. [PMID: 12732431 DOI: 10.1016/s0167-7012(03)00011-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A commercially available nucleic acid sequence-based amplification (NASBA) NucliSens Basic Kit (NBK) assay for the detection of Mycoplasma pneumoniae 16S rRNA in respiratory specimens was developed and compared to standard NASBA and PCR assays previously developed in our laboratory. The specificity and sensitivity of the NBK assay was comparable to the specificity and sensitivity of the corresponding standard NASBA assay. The NBK offers standardized reagents for the development of a NASBA assay for the detection of M. pneumoniae in respiratory specimens and is easily adaptable to other amplification targets.
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Affiliation(s)
- K Loens
- Department of Medical Microbiology, University of Antwerp, Universiteitsplein 1 S3, B-2610 Wilrijk, Belgium.
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Loens K, Ieven M, Ursi D, De Laat C, Sillekens P, Oudshoorn P, Goossens H. Improved detection of rhinoviruses by nucleic acid sequence-based amplification after nucleotide sequence determination of the 5' noncoding regions of additional rhinovirus strains. J Clin Microbiol 2003; 41:1971-6. [PMID: 12734236 PMCID: PMC154662 DOI: 10.1128/jcm.41.5.1971-1976.2003] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The isothermal nucleic acid sequence-based amplification (NASBA) system was applied for the detection of rhinoviruses using primers targeted at the 5' noncoding region (5' NCR) of the viral genome. The nucleotide sequence of the 5' NCRs of 34 rhinovirus isolates was determined to map the most conserved regions and design more appropriate primers and probes. The assay amplified RNA extracted from 30 rhinovirus reference strains and 88 rhinovirus isolates, it did not amplify RNA from 49 enterovirus isolates and other respiratory viruses. The assay allows one to discriminate between group A and B rhinoviruses. Sensitivities for the detection of group B and group A rhinoviruses was 20 and 200 50% tissue culture infective doses, respectively.
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Affiliation(s)
- K Loens
- Department of Microbiology, University of Antwerp UIA, Antwerp, Belgium.
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