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Feng Y, He T, Zhang B, Yuan H, Zhou Y. Epidemiology and diagnosis technologies of human metapneumovirus in China: a mini review. Virol J 2024; 21:59. [PMID: 38454484 PMCID: PMC10921660 DOI: 10.1186/s12985-024-02327-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
Human metapneumovirus (HMPV) is a newly identified pathogen causing acute respiratory tract infections in young infants worldwide. Since the initial document of HMPV infection in China in 2003, Chinese scientists have made lots of efforts to prevent and control this disease, including developing diagnosis methods, vaccines and antiviral agents against HMPV, as well as conducting epidemiological investigations. However, effective vaccines or special antiviral agents against HMPV are currently not approved, thus developing early diagnosis methods and knowing its epidemiological characteristics will be beneficial for HMPV control. Here, we summarized current research focused on the epidemiological characteristics of HMPV in China and its available detection methods, which will be beneficial to increase the public awareness and disease control in the future.
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Affiliation(s)
- Yuan Feng
- Xiangtan Central Hospital, Xiangtan, 411100, Hunan, China
| | - Tao He
- Xiangtan Maternal and Child Health Hospital, Xiangtan, 411100, China
| | - Bo Zhang
- Xiangtan Central Hospital, Xiangtan, 411100, Hunan, China
| | - Haibin Yuan
- Xiangtan Central Hospital, Xiangtan, 411100, Hunan, China
| | - Yinfei Zhou
- Xiangtan Central Hospital, Xiangtan, 411100, Hunan, China.
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Comparative Evaluation of Allplex Respiratory Panels 1, 2, 3, and BioFire FilmArray Respiratory Panel for the Detection of Respiratory Infections. Diagnostics (Basel) 2021; 12:diagnostics12010009. [PMID: 35054176 PMCID: PMC8775103 DOI: 10.3390/diagnostics12010009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/17/2021] [Indexed: 12/02/2022] Open
Abstract
Multiplex nucleic acid amplification assays that simultaneously detect multiple respiratory pathogens in a single nasopharyngeal swab (NPS) specimen are widely used for rapid clinical diagnostics. We evaluated Allplex Respiratory Panel (RP) 1, 2, 3, and the BioFire FilmArray RP assay for detecting respiratory pathogens from NPS specimens. In all, 181 NPS specimens obtained from patients suspected of having respiratory infections during the non-influenza season (August–December 2019) were included. The Allplex RP 1, 2, and 3 detected 154 samples positive for respiratory viruses, whereas the BioFire FilmArray detected viruses in 98 samples. Co-infection with two or more viruses was detected in 41 and 17 NPS specimens by Allplex RP and the BioFire FilmArray RP, respectively. For adenoviruses, Allplex RP 1 detected 31 specimens, compared to 34 by the BioFire FilmArray. In all, 64 NPS specimens were positive for human enterovirus (HEV) and human rhinovirus (HRV) on the Allplex RP, in contrast to 39 HEV/HRV on the BioFire FilmArray. The parainfluenza virus (PIV-1–4) detection rate differed between the two systems. Most discrepant results were observed for NPS specimens with high cycle threshold values obtained by Allplex RP. This study showed concordant performance of the Allplex RP 1, 2, 3, and the BioFire FilmArray RP for the simultaneous detection of multiple respiratory viruses.
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Mustafa Hellou M, Górska A, Mazzaferri F, Cremonini E, Gentilotti E, De Nardo P, Poran I, Leeflang MM, Tacconelli E, Paul M. Nucleic acid amplification tests on respiratory samples for the diagnosis of coronavirus infections: a systematic review and meta-analysis. Clin Microbiol Infect 2021; 27:341-351. [PMID: 33188933 PMCID: PMC7657614 DOI: 10.1016/j.cmi.2020.11.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/10/2020] [Accepted: 11/04/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Management and control of coronavirus disease 2019 (COVID-19) relies on reliable diagnostic testing. OBJECTIVES To evaluate the diagnostic test accuracy (DTA) of nucleic acid amplification tests (NAATs) for the diagnosis of coronavirus infections. DATA SOURCES PubMed, Web of Science, the Cochrane Library, Embase, Open Grey and conference proceeding until May 2019. PubMed and medRxiv were updated for COVID-19 on 31st August 2020. STUDY ELIGIBILITY Studies were eligible if they reported on agreement rates between different NAATs using clinical samples. PARTICIPANTS Symptomatic patients with suspected upper or lower respiratory tract coronavirus infection. METHODS The new NAAT was defined as the index test and the existing NAAT as reference standard. Data were extracted independently in duplicate. Risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 tool. Confidence regions (CRs) surrounding summary sensitivity/specificity pooled by bivariate meta-analysis are reported. Heterogeneity was assessed using meta-regression. RESULTS Fifty-one studies were included, 22 of which included 10 181 persons before COVID-19 and 29 including 8742 persons diagnosed with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The overall summary sensitivity was 89.1% (95%CR 84.0-92.7%) and specificity 98.9% (95%CR 98.0-99.4%). Nearly all the studies evaluated different PCRs as both index and reference standards. Real-time RT PCR assays resulted in significantly higher sensitivity than other tests. Reference standards at high risk of bias possibly exaggerated specificity. The pooled sensitivity and specificity of studies evaluating SARS-COV-2 were 90.4% (95%CR 83.7-94.5%) and 98.1% (95%CR 95.9-99.2), respectively. SARS-COV-2 studies using samples from the lower respiratory tract, real-time RT-PCR, and tests targeting the N or S gene or more than one gene showed higher sensitivity, and assays based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP), especially when targeting only the RNA-dependent RNA polymerase (RdRp) gene, showed significantly lower sensitivity compared to other studies. CONCLUSIONS Pooling all studies to date shows that on average 10% of patients with coronavirus infections might be missed with PCR tests. Variables affecting sensitivity and specificity can be used for test selection and development.
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Affiliation(s)
| | - Anna Górska
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Fulvia Mazzaferri
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Eleonora Cremonini
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Elisa Gentilotti
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Pasquale De Nardo
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Itamar Poran
- Medicine E, Rabin Medical Centre, Beilinson Hospital, Petah-Tikva, Israel
| | - Mariska M Leeflang
- Epidemiology and Data Science, Amsterdam Public Health, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona, Italy; Infectious Diseases, Department of Internal Medicine I, Tu¨bingen University Hospital, Tu¨bingen, Germany
| | - Mical Paul
- Infectious Diseases Institute, Rambam Health Care Campus, Haifa, Israel; The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.
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Ezhilan M, Suresh I, Nesakumar N. SARS-CoV, MERS-CoV and SARS-CoV-2: A Diagnostic Challenge. MEASUREMENT : JOURNAL OF THE INTERNATIONAL MEASUREMENT CONFEDERATION 2021; 168:108335. [PMID: 33519010 PMCID: PMC7833337 DOI: 10.1016/j.measurement.2020.108335] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/20/2020] [Accepted: 08/01/2020] [Indexed: 05/15/2023]
Abstract
The highly pathogenic MERS-CoV, SARS-CoV and SARS-CoV-2 cause acute respiratory syndrome and are often fatal. These new viruses pose major problems to global health in general and primarily to infection control and public health services. Accurate and selective assessment of MERS-CoV, SARS-CoV and SARS-CoV-2 would assist in the effective diagnosis of infected individual, offer clinical guidance and aid in assessing clinical outcomes. In this mini-review, we review the literature on various aspects, including the history and diversity of SARS-CoV-2, SARS-CoV and MERS-CoV, their detection methods in effective clinical diagnosis, clinical assessment of COVID-19, safety guidelines recommended by World Health Organization and legal regulations. This review article also deals with existing challenges and difficulties in the clinical diagnosis of SARS-CoV-2. Developing alternative diagnostic platforms by spotting the shortcomings of the existing point-of-care diagnostic devices would be useful in preventing future outbreaks.
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Affiliation(s)
- Madeshwari Ezhilan
- School of Electrical and Electronics Engineering, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), SASTRA Deemed University, Thanjavur 613401, Tamil Nadu, India
| | - Indhu Suresh
- School of Electrical and Electronics Engineering, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), SASTRA Deemed University, Thanjavur 613401, Tamil Nadu, India
| | - Noel Nesakumar
- School of Chemical and Biotechnology, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), SASTRA Deemed University, Thanjavur 613401, Tamil Nadu, India
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Rahimi A, Mirzazadeh A, Tavakolpour S. Genetics and genomics of SARS-CoV-2: A review of the literature with the special focus on genetic diversity and SARS-CoV-2 genome detection. Genomics 2021; 113:1221-1232. [PMID: 33007398 PMCID: PMC7525243 DOI: 10.1016/j.ygeno.2020.09.059] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
The outbreak of 2019-novel coronavirus disease (COVID-19), caused by SARS-CoV-2, started in late 2019; in a short time, it has spread rapidly all over the world. Although some possible antiviral and anti-inflammatory medications are available, thousands of people are dying daily. Well-understanding of the SARS-CoV-2 genome is not only essential for the development of new treatments/vaccines, but it also can be used for improving the sensitivity and specificity of current approaches for virus detection. Accordingly, we reviewed the most critical findings related to the genetics of the SARS-CoV-2, with a specific focus on genetic diversity and reported mutations, molecular-based diagnosis assays, using interfering RNA technology for the treatment of patients, and genetic-related vaccination strategies. Additionally, considering the unanswered questions or uncertainties in these regards, different topics were discussed.
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Affiliation(s)
- Azadeh Rahimi
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Azin Mirzazadeh
- Department of Medical Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran,Joint Bioinformatics Graduate Program, University of Arkansas Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Soheil Tavakolpour
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, United States.
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Zhao L, Li G, Wang J, Zhao M, Wang L, Feng Z, Ma X. Development and evaluation of a panel of multiplex one-tube nested real time PCR assay for simultaneous detection of 14 respiratory viruses in five reactions. J Med Virol 2020; 92:3073-3080. [PMID: 31981228 PMCID: PMC7228275 DOI: 10.1002/jmv.25686] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/20/2020] [Indexed: 11/10/2022]
Abstract
Multiplex real-time quantitative polymerase chain reaction (mRT-qPCR) assay is commonly used to detect respiratory viruses, however, the sensitivity is limited for most reports. A panel of locked nucleic acid based multiplex closed one-tube nested real-time PCR (mOTNRT-PCR) assay consisting of five separate internally controlled RT-qPCR assays was developed for detection of 14 respiratory viruses. The sensitivity and reproducibility of mOTNRT-PCR panel were evaluated using plasmid standards and the specificity was evaluated using clinical samples. The clinical performance of mOTNRT-PCR panel was further evaluated with 468 samples collected from patients with an acute respiratory infection and compared with individual real-time PCR (RT-qPCR) assay. The analytical sensitivities of mOTNRT-PCR panel ranged from 2 to 20 copies/reaction, and no cross-reaction with common respiratory viruses was observed. The coefficients of variation of intra-assay and inter-assay were between 0.35% and 8.29%. Totally 35 clinical samples detected by mOTNRT-PCR assay panel were missed by RT-qPCR and confirmed true positive by sequencing of nested PCR products. The mOTNRT-PCR assay panel provides a more sensitive and high-throughput method for the detection of 14 respiratory viruses.
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Affiliation(s)
- Li Zhao
- Department of Blood TransfusionChildren's Hospital of Hebei ProvinceShijiazhuangHebeiChina
| | - Gui‐xia Li
- Institute of Pediatric ResearchChildren's Hospital of Hebei ProvinceShijiazhuangHebeiChina
| | - Ji Wang
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Meng‐chuan Zhao
- Institute of Pediatric ResearchChildren's Hospital of Hebei ProvinceShijiazhuangHebeiChina
| | - Le Wang
- Institute of Pediatric ResearchChildren's Hospital of Hebei ProvinceShijiazhuangHebeiChina
| | - Zhi‐shan Feng
- Department of Laboratory MedicineHebei General HospitalShijiazhuangHebeiChina
| | - Xue‐jun Ma
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
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Zhang N, Wang L, Deng X, Liang R, Su M, He C, Hu L, Su Y, Ren J, Yu F, Du L, Jiang S. Recent advances in the detection of respiratory virus infection in humans. J Med Virol 2020; 92:408-417. [PMID: 31944312 DOI: 10.1002/jmv.v92.410.1002/jmv.25674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 01/12/2020] [Indexed: 05/24/2023]
Abstract
Respiratory tract viral infection caused by viruses or bacteria is one of the most common diseases in human worldwide, while those caused by emerging viruses, such as the novel coronavirus, 2019-nCoV that caused the pneumonia outbreak in Wuhan, China most recently, have posed great threats to global public health. Identification of the causative viral pathogens of respiratory tract viral infections is important to select an appropriate treatment, save people's lives, stop the epidemics, and avoid unnecessary use of antibiotics. Conventional diagnostic tests, such as the assays for rapid detection of antiviral antibodies or viral antigens, are widely used in many clinical laboratories. With the development of modern technologies, new diagnostic strategies, including multiplex nucleic acid amplification and microarray-based assays, are emerging. This review summarizes currently available and novel emerging diagnostic methods for the detection of common respiratory viruses, such as influenza virus, human respiratory syncytial virus, coronavirus, human adenovirus, and human rhinovirus. Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. It is anticipated that such data will assist researchers and clinicians to develop appropriate diagnostic strategies for timely and effective detection of respiratory virus infections.
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Affiliation(s)
- Naru Zhang
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, China
| | - Lili Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Xiaoqian Deng
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Ruiying Liang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Meng Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Chen He
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Lanfang Hu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Yudan Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Jing Ren
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Fei Yu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York
| | - Shibo Jiang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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Zhang N, Wang L, Deng X, Liang R, Su M, He C, Hu L, Su Y, Ren J, Yu F, Du L, Jiang S. Recent advances in the detection of respiratory virus infection in humans. J Med Virol 2020; 92:408-417. [PMID: 31944312 PMCID: PMC7166954 DOI: 10.1002/jmv.25674] [Citation(s) in RCA: 272] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 01/12/2020] [Indexed: 12/20/2022]
Abstract
Respiratory tract viral infection caused by viruses or bacteria is one of the most common diseases in human worldwide, while those caused by emerging viruses, such as the novel coronavirus, 2019‐nCoV that caused the pneumonia outbreak in Wuhan, China most recently, have posed great threats to global public health. Identification of the causative viral pathogens of respiratory tract viral infections is important to select an appropriate treatment, save people's lives, stop the epidemics, and avoid unnecessary use of antibiotics. Conventional diagnostic tests, such as the assays for rapid detection of antiviral antibodies or viral antigens, are widely used in many clinical laboratories. With the development of modern technologies, new diagnostic strategies, including multiplex nucleic acid amplification and microarray‐based assays, are emerging. This review summarizes currently available and novel emerging diagnostic methods for the detection of common respiratory viruses, such as influenza virus, human respiratory syncytial virus, coronavirus, human adenovirus, and human rhinovirus. Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. It is anticipated that such data will assist researchers and clinicians to develop appropriate diagnostic strategies for timely and effective detection of respiratory virus infections. Respiratory tract viral infection including 2019‐nCoV poses great threats worldwide. Currently available and novel emerging diagnostic methods are summarized for several common respiratory viruses, including influenza virus, human respiratory syncytial virus, coronavirus, human adenovirus and human rhinovirus. Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. This review is aimed to assist researchers and clinicians to develop timely and effective diagnostic strategies to detect respiratory virus infections.
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Affiliation(s)
- Naru Zhang
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, China
| | - Lili Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Xiaoqian Deng
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Ruiying Liang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Meng Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Chen He
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Lanfang Hu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Yudan Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Jing Ren
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Fei Yu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York
| | - Shibo Jiang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York.,Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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Development and validation of a multiplex-PCR based assay for the detection of 18 pathogens in the cerebrospinal fluid of hospitalized children with viral encephalitis. J Virol Methods 2019; 277:113804. [PMID: 31863863 DOI: 10.1016/j.jviromet.2019.113804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND The Applied Biosystems 3500 Genetic Analyzer (ABI3500) allows for automated capillary electrophoresis on multiple targets. So far, the application of this method for detecting cerebrospinal fluid pathogens has hardly been reported. METHODS To assess the performance of multiplex-PCR assay for 18 pathogens detection, 127 CSF samples from hospitalized children with suspected viral encephalitis were prospectively collected from April to November 2018. The Sanger sequencing was applied to verify this assay. RESULTS All of the 18 target pathogens can be identified by multiplex-PCR assay at 104 copies (or CFU/mL) of each virus, bacterium and fungus. In contrast, 10 control microorganisms failed to be amplified. Approximately 68.5 % of the cases tested had positive results, the enterovirus accounted for the majority of the positive cases (63.8 %). Agreement between multiplex-PCR and sequencing was 91.49 %. CONCLUSIONS Our findings suggest that the ABI3500-based multiplex-PCR detection kit could be a valuable diagnostic tool for pathogen detection in CSF of children with suspected viral encephalitis.
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Performance evaluation of the Panther Fusion® respiratory tract panel. J Clin Virol 2019; 123:104232. [PMID: 31869661 PMCID: PMC7172494 DOI: 10.1016/j.jcv.2019.104232] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/29/2019] [Accepted: 12/09/2019] [Indexed: 12/21/2022]
Abstract
Clinical specificity of Panther Fusion® is between 96 %–100 %, compared to LDT. Clinical sensitivity Panther Fusion® is between 71.9 %–100 %, compared to LDT. Overall linear regression showed good correlations between LDT and Panther Fusion® for all viruses, except RV and PIV-4. The Panther Fusion® provides a random-access system with continuous loading and shorter sample-to-answer times compared to LDT.
Background Respiratory tract infections are among the most common infections during winter season. Rapid diagnostics is required for clinical decision making regarding isolation of patients and appropriate therapy. Objectives The aim of this study was to evaluate the analytical and clinical performance characteristics of the Panther Fusion® respiratory panel using published laboratory-developed real-time PCR assays (LDT). Study design Analytical sensitivity of Panther Fusion® Flu A/B/RSV was assessed by testing dilutions of cell culture isolates. Clinical performance assessment included the complete Panther Fusion® respiratory panel (Flu-A/B/RSV, PIV 1-4 and AdV/hMPV/RV) and consisted of a retrospective and a prospective study-arm. The retrospective evaluation included 201, stored (−80 °C) samples collected between February 2006 and January 2017. Prospective evaluation was performed on 1045 unselected pretreated respiratory tract samples from patients presented to our hospital between November 2017 and May 2018. Results Analytical sensitivity was generally slightly lower for the Panther Fusion® assays. Clinical specificity and sensitivity was between 96 %–100 % and 71.9 %–100 %, respectively. Discrepant results were found in 146 samples of which 88 samples tested LDT positive / Panther Fusion® negative and 58 samples were LDT negative / Panther Fusion® positive. A total of ten discrepant samples with Ct-values <30 were sequenced to confirm the presence of 7 RV-C not-detected by LDT and 1 RV-A and 2 ADV-2 not detected by Panther Fusion®. Conclusions The Panther Fusion® provides a random-access system with continuous loading and much shorter sample-to-answer times compared to LDT, albeit with a slightly less clinical sensitivity compared to the LDT.
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Wen S, Lv F, Chen X, Zhu L, Li H, Lin L, Zhang H. Application of a nucleic acid-based multiplex kit to identify viral and atypical bacterial aetiology of lower respiratory tract infection in hospitalized children. J Med Microbiol 2019; 68:1211-1218. [PMID: 31225788 DOI: 10.1099/jmm.0.001006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Shunhang Wen
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Fangfang Lv
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Xiaofang Chen
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Lili Zhu
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Haiyan Li
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Li Lin
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Hailin Zhang
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
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Luo S, Xie Z, Huang J, Xie Z, Xie L, Zhang M, Li M, Wang S, Li D, Zeng T, Zhang Y, Fan Q, Deng X. Simultaneous Differentiation of the N1 to N9 Neuraminidase Subtypes of Avian Influenza Virus by a GeXP Analyzer-Based Multiplex Reverse Transcription PCR Assay. Front Microbiol 2019; 10:1271. [PMID: 31231349 PMCID: PMC6568037 DOI: 10.3389/fmicb.2019.01271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/22/2019] [Indexed: 11/13/2022] Open
Abstract
To date, nine neuraminidase (NA) subtypes of avian influenza virus (AIV) have been identified in poultry and wild birds. Rapid and effective methods for differentiating these nine NA subtypes are needed. We developed and validated a rapid, sensitive, and robust method utilizing a GeXP analyzer-based multiplex RT-PCR assay and capillary electrophoresis for the simultaneous differentiation of the N1 to N9 subtypes in a single-tube reaction. Ten pairs of primers-nine subtype-specific pairs and one pan-AIV pair-were screened and used to establish the GeXP multiplex RT-PCR assay. A single subtype was detected using the developed GeXP assay; the N1 to N9 AIV subtypes individually generated two target peaks: the NA subtype-specific peak and the general AIV peak. Different concentrations of multiplexed subtypes were tested with this GeXP assay and the peaks of the corresponding NA subtypes were generated, suggesting that this GeXP assay is useful for identifying NA subtypes in mixed samples. Moreover, no peaks were generated for other important avian viruses, indicating negative results and validating the lack of cross-reactions between AIV subtypes and other avian pathogens. RNA templates synthesized through in vitro transcription were used to analyze the sensitivity of the assay; the limit of detection was 100 copies per reaction mixture. The results obtained from clinical samples using this GeXP method were consistent with the results of the neuraminidase inhibition (NI) test, and the ability of the GeXP assay to identify mixed infections was superior to amplicon sequencing of isolated viruses. In conclusion, this GeXP assay is proposed as a specific, sensitive, rapid, high-throughput, and versatile diagnostic tool for nine NA subtypes of AIV.
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Affiliation(s)
- Sisi Luo
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Zhixun Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Jiaoling Huang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Zhiqin Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Liji Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Minxiu Zhang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Meng Li
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Sheng Wang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Dan Li
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Tingting Zeng
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Yanfang Zhang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Qing Fan
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
| | - Xianwen Deng
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
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13
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Feng ZS, Zhao L, Wang J, Qiu FZ, Zhao MC, Wang L, Duan SX, Zhang RQ, Chen C, Qi JJ, Fan T, Li GX, Ma XJ. A multiplex one-tube nested real time RT-PCR assay for simultaneous detection of respiratory syncytial virus, human rhinovirus and human metapneumovirus. Virol J 2018; 15:167. [PMID: 30376870 PMCID: PMC6208169 DOI: 10.1186/s12985-018-1061-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/19/2018] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV), human Rhinovirus (HRV) and human Metapneumo Virus (HMPV) are important viral pathogens causing acute respiratory tract infections in the hospitalized patients. Sensitive and accurate detection of RSV, HRV and HMPV is necessary for clinical diagnosis and treatment. RESULTS A locked nucleic acid (LNA)-based multiplex closed one-tube nested real-time RT-PCR (mOTNRT-PCR) assay was developed for simultaneous detection of RSV, HRV and HMPV. The sensitivity, specificity, reproducibility and clinical performance of mOTNRT-PCR were evaluated and compared with individual real time PCR (RT-qPCR) assay using clinical samples. The analytical sensitivity of mOTNRT-PCR assay was 5 copies/reaction for RSV, HRV and HMPV, respectively, and no cross-reaction with other common respiratory viruses was observed. The coefficients of variation (CV) of intra-assay and inter-assay were between 0.51 to 3.67%. Of 398 nasopharyngeal aspirates samples tested, 109 (27.39%), 150 (37.69%) and 44 (11.06%) were positive for RSV, HRV and HMPV, respectively, whereas 95 (23.87%), 137 (34.42%) and 38 (9.55%) were positive for RSV, HRV and HMPV, respectively, by individual RT-qPCR assay. Thirty three samples that were positive by mOTNRT-PCR but negative by RT-qPCR were confirmed as true positives by sequencing using reported traditional two-step nested PCR assay. CONCLUSION mOTNRT-PCR assay reveals extremely higher sensitivity than that of RT-qPCR assay for detecting RSV, HRV and HMPV in clinical settings.
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Affiliation(s)
- Zhi-Shan Feng
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China
| | - Li Zhao
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China.,Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Ji Wang
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Fang-Zhou Qiu
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China.,Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Meng-Chuan Zhao
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China
| | - Le Wang
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China
| | - Su-Xia Duan
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China
| | - Rui-Qing Zhang
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China.,Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Chen Chen
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Ju-Ju Qi
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China.,Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Tao Fan
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China.,Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Gui-Xia Li
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China.
| | - Xue-Jun Ma
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China.
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14
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Li X, Chen B, Zhang S, Li X, Chang J, Tang Y, Wu Y, Lu X. Rapid Detection of Respiratory Pathogens for Community-Acquired Pneumonia by Capillary Electrophoresis-Based Multiplex PCR. SLAS Technol 2018; 24:105-116. [PMID: 30048599 DOI: 10.1177/2472630318787452] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Community-acquired pneumonia (CAP) is a common infectious disease linked to high rates of morbidity and mortality. Fast and accurate identification of the pathogens responsible for CAP will aid in diagnosis. We established a capillary electrophoresis-based multiplex PCR (CEMP) panel to enable the detection of viral and bacterial pathogens associated with CAP. The assay simultaneously detects and identifies the 13 common unculturable CAP viral and bacterial pathogens within 4 h. We evaluated the performance of a commercially available panel with 314 samples collected from CAP patients. We compared the results to those obtained with the liquid chip-based Luminex xTAG Respiratory Viral Panel (RVP) Fast Kit (for viruses) and the agarose gel-based Seegene PneumoBacter ACE Detection Kit (for atypical bacteria). All positive samples were further verified by the Sanger sequencing method. The sensitivity, specificity, positive predictive value, and negative predictive value of CEMP were 97.31%, 100%, 100%, and 99.85%, respectively. CEMP provides a rapid and accurate method for the high-throughput detection of pathogens in patients with CAP.
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Affiliation(s)
- Xue Li
- 1 Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,2 College of Medicine, Capital Medical University, Beijing, China
| | - Bo Chen
- 3 Ningbo HEALTH Gene Technologies Co., Ltd., Ningbo, China
| | - Shaoya Zhang
- 1 Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xiuyuan Li
- 1 Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,2 College of Medicine, Capital Medical University, Beijing, China
| | - Junxia Chang
- 4 Department of Laboratory Medicine, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Yanyan Tang
- 1 Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,2 College of Medicine, Capital Medical University, Beijing, China
| | - Yong Wu
- 3 Ningbo HEALTH Gene Technologies Co., Ltd., Ningbo, China
| | - Xinxin Lu
- 1 Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, China.,2 College of Medicine, Capital Medical University, Beijing, China
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15
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Simultaneous detection of eight avian influenza A virus subtypes by multiplex reverse transcription-PCR using a GeXP analyser. Sci Rep 2018; 8:6183. [PMID: 29670227 PMCID: PMC5906657 DOI: 10.1038/s41598-018-24620-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 04/03/2018] [Indexed: 01/16/2023] Open
Abstract
Recent studies have demonstrated that at least eight subtypes of avian influenza virus (AIV) can infect humans, including H1, H2, H3, H5, H6, H7, H9 and H10. A GeXP analyser-based multiplex reverse transcription (RT)-PCR (GeXP-multiplex RT-PCR) assay was developed in our recent studies to simultaneously detect these eight AIV subtypes using the haemagglutinin (HA) gene. The assay consists of chimeric primer-based PCR amplification with fluorescent labelling and capillary electrophoresis separation. RNA was extracted from chick embryo allantoic fluid or liquid cultures of viral isolates. In addition, RNA synthesised via in vitro transcription was used to determine the specificity and sensitivity of the assay. After selecting the primer pairs, their concentrations and GeXP-multiplex RT-PCR conditions were optimised. The established GeXP-multiplex RT-PCR assay can detect as few as 100 copies of premixed RNA templates. In the present study, 120 clinical specimens collected from domestic poultry at live bird markets and from wild birds were used to evaluate the performance of the assay. The GeXP-multiplex RT-PCR assay specificity was the same as that of conventional RT-PCR. Thus, the GeXP-multiplex RT-PCR assay is a rapid and relatively high-throughput method for detecting and identifying eight AIV subtypes that may infect humans.
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16
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Development of a GeXP-multiplex PCR assay for the simultaneous detection and differentiation of six cattle viruses. PLoS One 2017; 12:e0171287. [PMID: 28166243 PMCID: PMC5293189 DOI: 10.1371/journal.pone.0171287] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 01/19/2017] [Indexed: 01/22/2023] Open
Abstract
Foot-and-mouth disease virus (FMDV), Bluetongue virus (BTV), Vesicular stomatitis Virus (VSV), Bovine viral diarrheal (BVDV), Bovine rotavirus (BRV), and Bovine herpesvirus 1 (IBRV) are common cattle infectious viruses that cause a great economic loss every year in many parts of the world. A rapid and high-throughput GenomeLab Gene Expression Profiler (GeXP) analyzer-based multiplex PCR assay was developed for the simultaneous detection and differentiation of these six cattle viruses. Six pairs of chimeric primers consisting of both the gene-specific primer and a universal primer were designed and used for amplification. Then capillary electrophoresis was used to separate the fluorescent labeled PCR products according to the amplicons size. The specificity of GeXP-multiplex PCR assay was examined with samples of the single template and mixed template of six viruses. The sensitivity was evaluated using the GeXP-multiplex PCR assay on serial 10-fold dilutions of ssRNAs obtained via in vitro transcription. To further evaluate the reliability, 305 clinical samples were tested by the GeXP-multiplex PCR assay. The results showed that the corresponding virus specific fragments of genes were amplified. The detection limit of the GeXP-multiplex PCR assay was 100 copies/μL in a mixed sample of ssRNAs containing target genes of six different cattle viruses, whereas the detection limit for the Gexp-mono PCR assay for a single target gene was 10 copies/μL. In detection of viruses in 305 clinical samples, the results of GeXP were consistent with simplex real-time PCR. Analysis of positive samples by sequencing demonstrated that the GeXP-multiplex PCR assay had no false positive samples of nonspecific amplification. In conclusion, this GeXP-multiplex PCR assay is a high throughput, specific, sensitive, rapid and simple method for the detection and differentiation of six cattle viruses. It is an effective tool that can be applied for the rapid differential diagnosis of clinical samples and for epidemiological investigation.
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17
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Wang L, Zhao M, Shi Z, Feng Z, Guo W, Yang S, Liu L, Li G. A GeXP-Based Assay for Simultaneous Detection of Multiple Viruses in Hospitalized Children with Community Acquired Pneumonia. PLoS One 2016; 11:e0162411. [PMID: 27627439 PMCID: PMC5023126 DOI: 10.1371/journal.pone.0162411] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/22/2016] [Indexed: 12/01/2022] Open
Abstract
The GeXP-based assay has recently been developed for simultaneous detection of multiple pathogens. So far, the application of the GeXP assay to test larger clinical samples has hardly been reported. Community-acquired pneumonia (CAP) is the leading cause of death in children worldwide and a substantial proportion of childhood CAP is caused by viruses. Rapid and accurate diagnosis of virus infection is important for the clinical management of CAP. In this study, we explored the GeXP assay for simultaneous detection of 20 types/subtypes of viruses in hospitalized children with CAP. A total of 1699 nasopharyngeal swabs were prospectively collected and viral nucleic acid was extracted and assayed. Using viral genomic DNA or RNA as template, we showed that at the concentration of 104 copies of DNA or RNA of each virus/μl, all 20 target viruses were simultaneously identified by the GeXP assay. Fifteen control microorganisms, in contrast, failed to be amplified by the assay. About 65% of cases tested in this study had viral infection, with patients aged <3 years having a 70% positive rate, significantly higher than that in patients aged > 3 years (40%). The most frequently detected virus was RSV followed by PIV3, HRV, ADV and HBoV. Seasonal distribution analysis revealed that RSV was the most predominant in autumn and winter, while in spring and summer PIV3 and RSV were the most frequently identified with similar positive percentages. One hundred twenty randomly-chosen samples tested by the GeXP assay were re-evaluated by mono-RT-PCR, the results showed 97.5% diagnosis agreement between these 2 methods. Our findings suggest that the GeXP assay could be a valuable diagnostic tool for virus infection in pediatric patients with CAP.
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Affiliation(s)
- Le Wang
- Institute of Pediatric Research, Children’s Hospital of Hebei Province, Shijiazhuang 050031, China
| | - Mengchuan Zhao
- Graduate School of Hebei Medical University, Shijiazhuang 050000, China
| | - Zhongren Shi
- Institute of Pediatric Research, Children’s Hospital of Hebei Province, Shijiazhuang 050031, China
| | - Zhishan Feng
- Institute of Pediatric Research, Children’s Hospital of Hebei Province, Shijiazhuang 050031, China
| | - Weiwei Guo
- Institute of Pediatric Research, Children’s Hospital of Hebei Province, Shijiazhuang 050031, China
| | - Shuo Yang
- Institute of Pediatric Research, Children’s Hospital of Hebei Province, Shijiazhuang 050031, China
| | - Lanping Liu
- Institute of Pediatric Research, Children’s Hospital of Hebei Province, Shijiazhuang 050031, China
- * E-mail: (LL); (GL)
| | - Guixia Li
- Institute of Pediatric Research, Children’s Hospital of Hebei Province, Shijiazhuang 050031, China
- Department of Laboratory Medicine, Children’s Hospital of Hebei Province, Shijiazhuang 050031, China
- * E-mail: (LL); (GL)
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18
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Simultaneous detection of 13 viruses involved in meningoencephalitis using a newly developed multiplex PCR Mag-array system. Int J Infect Dis 2016; 49:80-6. [DOI: 10.1016/j.ijid.2016.05.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/27/2016] [Accepted: 05/19/2016] [Indexed: 02/07/2023] Open
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19
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Reverse transcription genome exponential amplification reaction assay for rapid and universal detection of human rhinoviruses. Arch Virol 2016; 161:1891-8. [PMID: 27132014 DOI: 10.1007/s00705-016-2858-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/04/2016] [Indexed: 10/21/2022]
Abstract
Human rhinoviruses (HRVs) have long been recognized as the cause of more than one-half of acute viral upper respiratory illnesses, and they are associated with more-serious diseases in children, such as asthma, acute otitis media and pneumonia. A rapid and universal test for of HRV infection is in high demand. In this study, a reverse transcription genome exponential amplification reaction (RT-GEAR) assay targeting the HRV 5' untranslated region (UTR) was developed for pan-HRV detection. The reaction was performed in a single tube in one step at 65 °C for 60 min using a real-time fluorometer (Genie(®)II; Optigene). The RT-GEAR assay showed no cross-reactivity with common human enteroviruses, including HEV71, CVA16, CVA6, CVA10, CVA24, CVB5, Echo30, and PV1-3 or with other common respiratory viruses including FluA H3, FluB, PIV1-4, ADV3, RSVA, RSVB and HMPV. With in vitro-transcribed RNA containing the amplified regions of HRV-A60, HRV-B06 and HRV-C07 as templates, the sensitivity of the RT-GEAR assay was 5, 50 and 5 copies/reaction, respectively. Experiments to evaluate the clinical performance of the RT-GEAR assay were also carried out with a panel of 143 previously verified samples, and the results were compared with those obtained using a published semi-nested PCR assay followed by sequencing. The tested panel comprised 91 HRV-negative samples and 52 HRV-positive samples (18 HRV-A-positive samples, 3 HRV-B-positive samples and 31 HRV-C-positive samples). The sensitivity and specificity of the pan-HRVs RT-GEAR assay was 98.08 % and 100 %, respectively. The kappa correlation between the two methods was 0.985. The RT-GEAR assay based on a portable Genie(®)II fluorometer is a sensitive, specific and rapid assay for the universal detection of HRV infection.
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20
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Using Nucleic Acid Amplification Techniques in a Syndrome-Oriented Approach: Detection of Respiratory Agents. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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21
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Guan H, Wang J, Wang C, Yang M, Liu L, Yang G, Ma X. Etiology of Multiple Non-EV71 and Non-CVA16 Enteroviruses Associated with Hand, Foot and Mouth Disease in Jinan, China, 2009-June 2013. PLoS One 2015; 10:e0142733. [PMID: 26562154 PMCID: PMC4642993 DOI: 10.1371/journal.pone.0142733] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/26/2015] [Indexed: 11/18/2022] Open
Abstract
Hand, foot, and mouth disease (HFMD) is an infectious disease caused by human enterovirus 71 (EV71), coxsackievirus A16 (CVA16) and other enteroviruses. It is of interest that other enteroviruses associated with HFMD in Jinan have been rarely reported. The aim of the present study is to detect and characterize the circulating serotypes of non-EV71 and non-CVA16 enteroviruses associated with HFMD in Jinan city, Shandong province, China. A total of 400 specimens were collected from clinically diagnosed HFMD cases in Jinan from January 2009 to June 2013. All specimens were infected with non-EV71 and non-CVA16 enteroviruses previously confirmed by RT-PCR or real-time PCR according to the protocols at that time. The GeXP-based multiplex RT-PCR assay (GeXP assay) was performed to investigate the pathogen spectrum of 15 enteroviruses (coxsackieviruses A4, A5, A6, A9, A10, A16; coxsackieviruses B1, B3, B5; Echoviruses 6, 7, 11, 13, 19 and EV71) infections associated with HMFD. For GeXP assay negative samples, reverse transcription nested PCR (nested RT-PCR) based on the 5’ -untranslated region (5’- UTR) sequence and phylogenetic analysis were conducted to further explore the etiology of multiple enteroviruses. The results showed that a total of twenty serotypes of enteroviruses (including EV71 and CVA16) were identified by GeXP assay and nested RT-PCR. The most circulating twelve serotypes of enteroviruses with HFMD in Jinan from 2009 to June 2013 were EV71, CVA16, CVA10, CVA6, CVA12, CVA2, Echo3, CVA4, CVA9, CVB1, CVB3 and Echo6. CVA10 and CVA6 were the most prevalent pathogens other than EV71 and CVA16 in Jinan and their most prevalent seasons were spring and summer, and a slight increase was observed in autumn and early winter. It should be noted that mixed-infections were identified by GeXP assay and the phylogenetic tree clearly discriminated the multiple pathogens associated with HFMD. Our results thus demonstrate that there was a clear lack of a reliable testing method for EV71 and CVA16 and multiple non-EV71 and non-CVA16 enteroviruses associated with HFMD were present in Jinan. The GeXP assay combined with nested RT-PCR based on 5’-UTR region could meet the need for the national surveillance of multiple enteroviruses or the investigation of epidemic outbreaks triggered by enteroviruses in the future.
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Affiliation(s)
- Hengyun Guan
- Viral Disease Inspection Laboratory, Jinan Municipal Center for Disease Control and Prevention, Jinan, China
| | - Ji Wang
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chunrong Wang
- Viral Disease Inspection Laboratory, Jinan Municipal Center for Disease Control and Prevention, Jinan, China
| | - Mengjie Yang
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lanzheng Liu
- Viral Disease Inspection Laboratory, Jinan Municipal Center for Disease Control and Prevention, Jinan, China
- * E-mail: (LZL); (XJM)
| | - Guoliang Yang
- Viral Disease Inspection Laboratory, Jinan Municipal Center for Disease Control and Prevention, Jinan, China
| | - Xuejun Ma
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- * E-mail: (LZL); (XJM)
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22
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Zhang YF, Xie ZX, Xie LJ, Deng XW, Xie ZQ, Luo SS, Huang L, Huang JL, Zeng TT. GeXP analyzer-based multiplex reverse-transcription PCR assay for the simultaneous detection and differentiation of eleven duck viruses. BMC Microbiol 2015; 15:247. [PMID: 26518004 PMCID: PMC4628294 DOI: 10.1186/s12866-015-0590-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 10/23/2015] [Indexed: 01/21/2023] Open
Abstract
Background Duck viral pathogens primarily include the avian influenza virus (AIV) subtypes H5, H7, and H9; duck hepatitis virus (DHV); duck tembusu virus (DTMUV); egg drop syndrome virus (EDSV); duck enteritis virus (DEV); Newcastle disease virus (NDV); duck circovirus (DuCV); muscovy duck reovirus (MDRV); and muscovy duck parvovirus (MDPV). These pathogens cause great economic losses to China’s duck breeding industry. Result A rapid, specific, sensitive and high-throughput GeXP-based multiplex PCR assay consisting of chimeric primer-based PCR amplification with fluorescent labeling and capillary electrophoresis separation was developed and optimized to simultaneously detect these eleven viral pathogens. Single and mixed pathogen cDNA/DNA templates were used to evaluate the specificity of the GeXP-multiplex assay. Corresponding specific DNA products were amplified from each pathogen. Other pathogens, including duck Escherichia coli, duck Salmonella, duck Staphylococcus aureus, Pasteurella multocida, infectious bronchitis virus, and Mycoplasma gallisepticum, did not result in amplification products. The detection limit of GeXP was 103copies when all twelve pre-mixed plasmids containing the target genes of eleven types of duck viruses were present. To further evaluate the reliability of GeXP, 150 clinical field samples were evaluated. Comparison with the results of conventional PCR methods for the field samples, the GeXP-multiplex PCR method was more sensitive and accurate. Conclusion This GeXP-based multiplex PCR method can be utilized for the rapid differential diagnosis of clinical samples as an effective tool to prevent and control duck viruses with similar clinical symptoms.
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Affiliation(s)
- Yan-Fang Zhang
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
| | - Zhi-Xun Xie
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
| | - Li-Ji Xie
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
| | - Xian-Wen Deng
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
| | - Zhi-Qin Xie
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
| | - Si-Si Luo
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
| | - Li Huang
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
| | - Jiao-Ling Huang
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
| | - Ting-Ting Zeng
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
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Wang Y, Ostlund EN, Jun Y, Nie FP, Li YG, Johnson DJ, Lin R, Li ZG. Combining reverse-transcription multiplex PCR and microfluidic electrophoresis to simultaneously detect seven mosquito-transmitted zoonotic encephalomyelitis viruses. Vet J 2015; 212:27-35. [PMID: 27256022 DOI: 10.1016/j.tvjl.2015.10.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/10/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
Abstract
Several mosquito-transmitted viruses are causative agents for zoonotic encephalomyelitis. Rapid identification of these viruses in mosquito populations is an effective method for surveying these diseases. To detect multiple mosquito-transmitted viral agents, including West Nile virus, Saint Louis encephalitis virus, Venezuelan equine encephalomyelitis virus, Western equine encephalomyelitis virus, Eastern equine encephalomyelitis virus, Highlands J virus and Japanese encephalitis virus, an assay using multiplex reverse-transcription PCR combined with microfluidic electrophoresis was developed and evaluated. Tailed nested primers were used in the assay to amplify specific viral genomic segments, and products with specific length were further analyzed by using a microfluidic electrophoresis chip. The assay exhibited good specificity and analytical sensitivity (10(2) copies/µL). This technology can be helpful in the quarantine and surveillance of exotic encephalomyelitis viruses which are transmitted by mosquitoes.
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Affiliation(s)
- Yu Wang
- School of Life Sciences, Chongqing University, Chongqing 400030, China; Technical Center of Chongqing Entry Inspection and Quarantine Bureau, Engineering Research Center for Import and Export Food Safety, Chongqing 400020, China
| | - Eileen N Ostlund
- Diagnostic Virology Laboratory, National Veterinary Services Laboratories, STAS/VS/APHIS/USDA, Ames, IA 50010, USA
| | - Yang Jun
- Technical Center of Chongqing Entry Inspection and Quarantine Bureau, Engineering Research Center for Import and Export Food Safety, Chongqing 400020, China
| | - Fu-Ping Nie
- Technical Center of Chongqing Entry Inspection and Quarantine Bureau, Engineering Research Center for Import and Export Food Safety, Chongqing 400020, China
| | - Ying-Guo Li
- School of Life Sciences, Chongqing University, Chongqing 400030, China; Technical Center of Chongqing Entry Inspection and Quarantine Bureau, Engineering Research Center for Import and Export Food Safety, Chongqing 400020, China
| | - Donna J Johnson
- Diagnostic Virology Laboratory, National Veterinary Services Laboratories, STAS/VS/APHIS/USDA, Ames, IA 50010, USA
| | - Rui Lin
- School of Life Sciences, Chongqing University, Chongqing 400030, China
| | - Zheng-Guo Li
- School of Life Sciences, Chongqing University, Chongqing 400030, China.
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Zhou L, Zhao F, Hu B, Fang Y, Miao Y, Huang Y, Ji D, Zhang J, Xu L, Zhang Y, Bao Z, Zhao H. A Creative Helicobacter pylori Diagnosis Scheme Based on Multiple Genetic Analysis System: Qualification and Quantitation. Helicobacter 2015; 20:343-52. [PMID: 25640660 DOI: 10.1111/hel.12206] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Currently, several diagnostic assays for Helicobacter pylori (H. pylori) are available, but each has some limitations. Further, a high-flux quantitative assay is required to assist clinical diagnosis and monitor the effectiveness of therapy and novel vaccine candidates. METHODS Three hundred and eighty-seven adult patients [nonulcer dyspepsia (NUD) 295, peptic ulcer disease (PUD) 77, gastric cancer (GC) 15] were enrolled for gastrointestinal endoscopies. Three biopsy samples from gastric antrum were collected for the following tests: culture, rapid urease test (RUT), histopathology, conventional polymerase chain reaction (PCR), and Multiple Genetic Analysis System (MGAS). The diagnostic capability of H. pylori for all methods was evaluated through the receiver operating characteristic (ROC) curves. RESULTS Based on the gold standard, the sensitivity and specificity of MGAS were 92.9 and 92.4%, and positive predict value (PPV) and negative predict value (NPV) were 96.0 and 87.1%, respectively. All the above parameters of MGAS were higher than that of culture (except its specificity), RUT and histopathology, and nearly closed to that of conventional PCR. The area under curve (AUC) was 0.7575 (Culture), 0.8870 (RUT), 0.9000 (Histopathology), 0.9496 (Conventional PCR), and 0.9277 (MGAS). No significant statistical difference was observed for the H. pylori DNA load in different disease groups (p = .067). In contrast, a statistically significant difference in the H. pylori DNA copy number was observed based on age (p = .043) and gender (p = .021). CONCLUSIONS The data showed that MGAS performed well in detecting H. pylori infection. Furthermore, the quantitative analysis showed that the load of H. pylori was significantly different within both age and gender groups. These results suggested that MGAS could be a potential alternative method for clinical detection and monitoring of the effectiveness of H. pylori therapy.
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Affiliation(s)
- Lifang Zhou
- Department of Laboratory Medicine, Laboratory of Molecular Biology, Huadong Hospital affiliated to, Fudan University, Shanghai, China
| | - Fuju Zhao
- Department of Laboratory Medicine, Laboratory of Molecular Biology, Huadong Hospital affiliated to, Fudan University, Shanghai, China
| | - Binjie Hu
- Department of Laboratory Medicine, Laboratory of Molecular Biology, Huadong Hospital affiliated to, Fudan University, Shanghai, China
| | - Yi Fang
- Department of Laboratory Medicine, Laboratory of Molecular Biology, Huadong Hospital affiliated to, Fudan University, Shanghai, China
| | - Yingxin Miao
- Department of Laboratory Medicine, Laboratory of Molecular Biology, Huadong Hospital affiliated to, Fudan University, Shanghai, China
| | - Yiqin Huang
- Department of Gastroenterology, Gerontology Institute of Shanghai affiliated to, Huadong Hospital, Fudan University, Shanghai, China
| | - Da'nian Ji
- Department of Endoscopy, Huadong Hospital, Fudan University, Shanghai, China
| | - Jinghao Zhang
- Department of Laboratory Medicine, Laboratory of Molecular Biology, Huadong Hospital affiliated to, Fudan University, Shanghai, China
| | - Lingli Xu
- Shanghai AB Sciex Analytical Instrument Trading Co., Ltd, Shanghai, China
| | - Yanmei Zhang
- Shanghai Shine Clinical Laboratories, Inc., The Research base of MDT, DCMST, Ministry of Health, Shanghai, China
| | - Zhijun Bao
- Department of Gastroenterology, Gerontology Institute of Shanghai affiliated to, Huadong Hospital, Fudan University, Shanghai, China
| | - Hu Zhao
- Department of Laboratory Medicine, Laboratory of Molecular Biology, Huadong Hospital affiliated to, Fudan University, Shanghai, China
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Simultaneous detection of eight swine reproductive and respiratory pathogens using a novel GeXP analyser-based multiplex PCR assay. J Virol Methods 2015; 224:9-15. [PMID: 26259690 DOI: 10.1016/j.jviromet.2015.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 07/21/2015] [Accepted: 08/05/2015] [Indexed: 11/21/2022]
Abstract
A new high-throughput GenomeLab Gene Expression Profiler (GeXP) analyser-based multiplex PCR assay was developed for the detection of eight reproductive and respiratory pathogens in swine. The reproductive and respiratory pathogens include North American porcine reproductive and respiratory syndrome virus (PRRSV-NA), classical swine fever virus (CSFV), porcine circovirus 2 (PCV-2), swine influenza virus (SIV) (including H1 and H3 subtypes), porcine parvovirus (PPV), pseudorabies virus (PRV) and Japanese encephalitis virus (JEV). Nine pairs of specific chimeric primers were designed and used to initiate PCRs, and one pair of universal primers was used for subsequent PCR cycles. The specificity of the GeXP assay was examined using positive controls for each virus. The sensitivity was evaluated using serial ten-fold dilutions of in vitro-transcribed RNA from all of the RNA viruses and plasmids from DNA viruses. The GeXP assay was further evaluated using 114 clinical specimens and was compared with real-time PCR/single RT-PCR methods. The specificity of the GeXP assay for each pathogen was examined using single cDNA/DNA template. Specific amplification peaks of the reproductive and respiratory pathogens were observed on the GeXP analyser. The minimum copies per reaction detected for each virus by the GeXP assay were as follows: 1000 copies/μl for PRV; 100 copies/μl for CSFV, JEV, PCV-2 and PPV; and 10 copies/μl for SIV-H1, SIV-H3 and PRRSV-NA. Analysis of 114 clinical samples using the GeXP assay demonstrated that the GeXP assay had comparable detection to real-time PCR/single RT-PCR. This study demonstrated that the GeXP assay is a new method with high sensitivity and specificity for the identification of these swine reproductive and respiratory pathogens. The GeXP assay may be adopted for molecular epidemiological surveys of these reproductive and respiratory pathogens in swine populations.
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26
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A pressure-driven column-based technique for the efficient extraction of DNA from respiratory samples. Clin Chim Acta 2015; 445:122-6. [DOI: 10.1016/j.cca.2015.03.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/01/2015] [Accepted: 03/13/2015] [Indexed: 11/22/2022]
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Chen H, Zhu Z, Lu JJ, Liu S. Charging YOYO-1 on capillary wall for online DNA intercalation and integrating this approach with multiplex PCR and bare narrow capillary-hydrodynamic chromatography for online DNA analysis. Anal Chem 2015; 87:1518-22. [PMID: 25555111 PMCID: PMC4318619 DOI: 10.1021/ac504257b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Multiplex polymerase chain reaction
(PCR) has been widely utilized
for high-throughput pathogen identification. Often, a dye is used
to intercalate the amplified DNA fragments, and identifications of
the pathogens are carried out by DNA melting curve analysis or gel
electrophoresis. Integrating DNA amplification and identification
is a logic path toward maximizing the benefit of multiplex PCR. Although
PCR and gel electrophoresis have been integrated, replenishing the
gels after each run is tedious and time-consuming. In this technical
note, we develop an approach to address this issue. We perform multiplex
PCR inside a capillary, transfer the amplified fragments to a bare
narrow capillary, and measure their lengths online using bare narrow
capillary–hydrodynamic chromatography (BaNC-HDC), a new technique
recently developed in our laboratory for free-solution DNA separation.
To intercalate the DNA with YOYO-1 (a fluorescent dye) for BaNC-HDC,
we flush the capillary column with a YOYO-1 solution; positively charged
YOYO-1 is adsorbed (or charged) onto the negatively charged capillary
wall. As DNA molecules are driven down the column for separation,
they react with the YOYO-1 stored on the capillary wall and are online-intercalated
with the dye. With a single YOYO-1 charging, the column can be used
for more than 40 runs, although the fluorescence signal intensities
of the DNA peaks decrease gradually. Although the dye-DNA intercalation
occurs during the separation, it does not affect the retention times,
separation efficiencies, or resolutions.
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Affiliation(s)
- Huang Chen
- Department of Chemistry and Biochemistry, University of Oklahoma , 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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28
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Zumla A, Al-Tawfiq JA, Enne VI, Kidd M, Drosten C, Breuer J, Muller MA, Hui D, Maeurer M, Bates M, Mwaba P, Al-Hakeem R, Gray G, Gautret P, Al-Rabeeah AA, Memish ZA, Gant V. Rapid point of care diagnostic tests for viral and bacterial respiratory tract infections--needs, advances, and future prospects. THE LANCET. INFECTIOUS DISEASES 2014; 14:1123-1135. [PMID: 25189349 PMCID: PMC7106435 DOI: 10.1016/s1473-3099(14)70827-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Respiratory tract infections rank second as causes of adult and paediatric morbidity and mortality worldwide. Respiratory tract infections are caused by many different bacteria (including mycobacteria) and viruses, and rapid detection of pathogens in individual cases is crucial in achieving the best clinical management, public health surveillance, and control outcomes. Further challenges in improving management outcomes for respiratory tract infections exist: rapid identification of drug resistant pathogens; more widespread surveillance of infections, locally and internationally; and global responses to infections with pandemic potential. Developments in genome amplification have led to the discovery of several new respiratory pathogens, and sensitive PCR methods for the diagnostic work-up of these are available. Advances in technology have allowed for development of single and multiplexed PCR techniques that provide rapid detection of respiratory viruses in clinical specimens. Microarray-based multiplexing and nucleic-acid-based deep-sequencing methods allow simultaneous detection of pathogen nucleic acid and multiple antibiotic resistance, providing further hope in revolutionising rapid point of care respiratory tract infection diagnostics.
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Affiliation(s)
- Alimuddin Zumla
- Division of Infection and Immunity, University College London, London, UK; NIHR Biomedical Research Center, University College London Hospitals, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK; Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia; UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia.
| | | | - Virve I Enne
- Division of Infection and Immunity, University College London, London, UK
| | - Mike Kidd
- Division of Infection and Immunity, University College London, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Judy Breuer
- Division of Infection and Immunity, University College London, London, UK; NIHR Biomedical Research Center, University College London Hospitals, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Marcel A Muller
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - David Hui
- Division of Respiratory Medicine and Stanley Ho Center for emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong
| | - Markus Maeurer
- Therapeutic Immunology, Departments of Laboratory Medicine and Microbiology, Tumour and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Matthew Bates
- Division of Infection and Immunity, University College London, London, UK; UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Peter Mwaba
- UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Rafaat Al-Hakeem
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia
| | - Gregory Gray
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Philippe Gautret
- Assistance Publique Hôpitaux de Marseille, CHU Nord, Pôle Infectieux, Institut Hospitalo-Universitaire Méditerranée Infection & Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), Marseille, France
| | - Abdullah A Al-Rabeeah
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia
| | - Ziad A Memish
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia; Al-Faisal University, Riyadh, Saudi Arabia
| | - Vanya Gant
- Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
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29
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A two-tube multiplex reverse transcription PCR assay for simultaneous detection of viral and bacterial pathogens of infectious diarrhea. BIOMED RESEARCH INTERNATIONAL 2014; 2014:648520. [PMID: 24711998 PMCID: PMC3966319 DOI: 10.1155/2014/648520] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 01/26/2014] [Accepted: 02/02/2014] [Indexed: 12/20/2022]
Abstract
Diarrhea caused by viral and bacterial infections is a major health problem in developing countries. The purpose of this study is to develop a two-tube multiplex PCR assay using automatic electrophoresis for simultaneous detection of 13 diarrhea-causative viruses or bacteria, with an intended application in provincial Centers for Diseases Control and Prevention, China. The assay was designed to detect rotavirus A, norovirus genogroups GI and GII, human astrovirus, enteric adenoviruses, and human bocavirus (tube 1), and Salmonella, Vibrio parahaemolyticus, diarrheagenic Escherichia coli, Campylobacter jejuni, Shigella, Yersinia, and Vibrio cholera (tube 2). The analytical specificity was examined with positive controls for each pathogen. The analytical sensitivity was evaluated by performing the assay on serial tenfold dilutions of in vitro transcribed RNA, recombinant plasmids, or bacterial culture. A total of 122 stool samples were tested by this two-tube assay and the results were compared with those obtained from reference methods. The two-tube assay achieved a sensitivity of 20–200 copies for a single virus and 102-103 CFU/mL for bacteria. The clinical performance demonstrated that the two-tube assay had comparable sensitivity and specificity to those of reference methods. In conclusion, the two-tube assay is a rapid, cost-effective, sensitive, specific, and high throughput method for the simultaneous detection of enteric bacteria and virus.
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30
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Tong J, Buch S, Yao H, Wu C, Tong HI, Wang Y, Lu Y. Monocytes-derived macrophages mediated stable expression of human brain-derived neurotrophic factor, a novel therapeutic strategy for neuroAIDS. PLoS One 2014; 9:e82030. [PMID: 24505242 PMCID: PMC3914783 DOI: 10.1371/journal.pone.0082030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 10/19/2013] [Indexed: 12/30/2022] Open
Abstract
HIV-1 associated dementia remains a significant public health burden. Clinical and experimental research has shown that reduced levels of brain-derived neurotrophic factor (BDNF) may be a risk factor for neurological complications associated with HIV-1 infection. We are actively testing genetically modified macrophages for their possible use as the cell-based gene delivery vehicle for the central nervous system (CNS). It can be an advantage to use the natural homing/migratory properties of monocyte-derived macrophages to deliver potentially neuroprotective BDNF into the CNS, as a non-invasive manner. Lentiviral-mediated gene transfer of human (h)BDNF plasmid was constructed and characterized. Defective lentiviral stocks were generated by transient transfection of 293T cells with lentiviral transfer plasmid together with packaging and envelope plasmids. High titer lentiviral vector stocks were harvested and used to transduce human neuronal cell lines, primary cultures of human peripheral mononocyte-derived macrophages (hMDM) and murine myeloid monocyte-derived macrophages (mMDM). These transduced cells were tested for hBDNF expression, stability, and neuroprotective activity. The GenomeLab GeXP Genetic Analysis System was used to evaluate transduced cells for any adverse effects by assessing gene profiles of 24 reference genes. High titer vectors were prepared for efficient transduction of neuronal cell lines, hMDM, and mMDM. Stable secretion of high levels of hBDNF was detected in supernatants of transduced cells using western blot and ELISA. The conditioned media containing hBDNF were shown to be protective to neuronal and monocytic cell lines from TNF-α and HIV-1 Tat mediated cytotoxicity. Lentiviral vector-mediated gene transduction of hMDM and mMDM resulted in high-level, stable expression of the neuroprotective factorBDNF in vitro. These findings form the basis for future research on the potential use of BDNF as a novel therapy for neuroAIDS.
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Affiliation(s)
- Jing Tong
- MOE Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Institute of TCM & Natural Products, School of Pharmaceutical Sciences, Wuhan University, Wuhan, People's Republic of China
- Department of Public Health Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Shilpa Buch
- University of Nebraska Medical Center, Pharmacology and Experimental Neuroscience, Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Honghong Yao
- University of Nebraska Medical Center, Pharmacology and Experimental Neuroscience, Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Chengxiang Wu
- Department of Public Health Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Hsin-I Tong
- Department of Public Health Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Youwei Wang
- MOE Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Institute of TCM & Natural Products, School of Pharmaceutical Sciences, Wuhan University, Wuhan, People's Republic of China
- * E-mail: (YW); (YL)
| | - Yuanan Lu
- Department of Public Health Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- * E-mail: (YW); (YL)
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31
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Shi X, Zhang C, Shi M, Yang M, Zhang Y, Wang J, Shen H, Zhao G, Ma X. Development of a single multiplex amplification refractory mutation system PCR for the detection of rifampin-resistant Mycobacterium tuberculosis. Gene 2013; 530:95-9. [DOI: 10.1016/j.gene.2013.07.060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 07/10/2013] [Accepted: 07/15/2013] [Indexed: 11/29/2022]
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Detection of respiratory viruses using a multiplex real-time PCR assay in Germany, 2009/10. Arch Virol 2013; 159:669-76. [PMID: 24126621 PMCID: PMC7086993 DOI: 10.1007/s00705-013-1876-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 10/02/2013] [Indexed: 10/26/2022]
Abstract
The aim of this study was to determine the prevalence of respiratory viruses and to prospectively evaluate the performance of the fast-track diagnostics (FTD) respiratory pathogens multiplex PCR assay shortly after the 2009/10 influenza pandemic. Highly sensitive monoplex real-time PCR assays served as references. Discrepant results were further analyzed by the xTAG RVP Fast assay. A total of 369 respiratory samples from children and adults were collected prospectively in Germany from December 2009 until June 2010. The sensitivity and specificity of the FTD assay after resolution of discrepant results was 92.2 % and 99.5 %, respectively. Lowest specificity of the FTD assay was observed for human bocavirus. Multiple detections were recorded in 33/369 (8.9 %) of the samples by monoplex PCR and in 43/369 (11.7 %) using the FTD assay. The most prevalent viruses were respiratory syncytial virus and human metapneumovirus. Only pandemic influenza virus A/H1N1 (2009), and not seasonal influenza virus, was detected. Viruses other than influenza virus accounted for the majority of acute respiratory infections. The FTD assay can be easily implemented in general diagnostic laboratories and facilitate the optimization of patient-management schemes.
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33
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Shen H, Shi W, Wang J, Wang M, Li J, Zhang C, Nie K, Yang M, Zhang Y, Li A, Tan W, Ma X. Development of a new resequencing pathogen microarray based assay for detection of broad-spectrum respiratory tract viruses in patients with community-acquired pneumonia. PLoS One 2013; 8:e75704. [PMID: 24086618 PMCID: PMC3785410 DOI: 10.1371/journal.pone.0075704] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 08/20/2013] [Indexed: 11/24/2022] Open
Abstract
A Resequencing Pathogen Microarray (RPM) is a single, highly multiplexed assay for detecting and differentiating similarly related pathogens by using closely overlapping probe sets to determine a target organism’s nucleotide sequence. In this study, a new RPM (RPM-IVDC1) that consisted of 224-bp detector tiles corresponding to 9 influenza A subtypes, 11 rhinoviruses, 28 enteroviruses and 38 other respiratory viruses was developed and optimized to provide individual and simultaneous detection sensitivities ranging from 15 to 750 genomic copies for 16 common respiratory pathogens. A total of 110 consecutive patients with community-acquired pneumonia (CAP) admitted to 5 district general hospitals in Beijing during a 1-year period were assessed using the new assay. Among the children (under age 5) and adult patients (above age 18), respiratory syncytial virus (RSV) and rhinovirus (RV) were the most common etiological agents, respectively, which is consistent with reference assays. Atypical pathogens that may cause CAP-like illness, including rubella virus, measles virus, influenza type C virus, human herpesvirus (HHV) were also detected. The results show the capability of RPM-IVDC1 for the accurate detection and identification of multiple virus types, which may be of significant use in epidemic surveillance and outbreak investigations of atypical pathogens.
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Affiliation(s)
- Hongwei Shen
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Futian District Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Weixian Shi
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Control and Prevention, Beijing, China
| | - Ji Wang
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Miao Wang
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jin Li
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chen Zhang
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kai Nie
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mengjie Yang
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Zhang
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Aihua Li
- Institute for Immunization and Prevention, Beijing Center for Disease Control and Prevention, Beijing, China
| | - Wenjie Tan
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- * E-mail: (XJM); (WJT)
| | - Xuejun Ma
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- * E-mail: (XJM); (WJT)
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A two-tube multiplex reverse transcription PCR assay for simultaneous detection of sixteen human respiratory virus types/subtypes. BIOMED RESEARCH INTERNATIONAL 2013; 2013:327620. [PMID: 23984344 PMCID: PMC3747601 DOI: 10.1155/2013/327620] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 06/25/2013] [Indexed: 11/17/2022]
Abstract
There is a need for the development of a rapid and sensitive diagnosis of respiratory viral pathogens. With an intended application in provincial Centers for Diseases Control and Prevention, in this study, we present a two-tube multiplex RT-PCR assay (two-tube assay) using automatic electrophoresis to simultaneously detect sixteen common respiratory viruses. The specificity and the sensitivity of the assay were tested. The assay could detect 20-200 copies per reaction when each viral type was assayed individually, 2000 copies with 9 premixed viral targets in the multiplexed assay in tube 1, and 200 copies with 8 premixed templates in tube 2. A total of 247 specimens were used to evaluate the two-tube assay, and the results were compared with those obtained from the Luminex xTAG RVP Fast assay. The discordant results were confirmed by sequencing or by the Seeplex RV15 ACE detection kit. There were no false positives, but six false negatives occurred with the two-tube assay. In conclusion, the two-tube assay is demonstrated to have great potential for routine surveillance of respiratory virus infection in China.
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Hu X, Xu B, Yang Y, Liu D, Yang M, Wang J, Shen H, Zhou X, Ma X. A high throughput multiplex PCR assay for simultaneous detection of seven aminoglycoside-resistance genes in Enterobacteriaceae. BMC Microbiol 2013; 13:58. [PMID: 23497180 PMCID: PMC3637108 DOI: 10.1186/1471-2180-13-58] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Accepted: 03/11/2013] [Indexed: 11/24/2022] Open
Abstract
Background The aminoglycoside-resistance genes encoding aminoglycoside modifying enzymes and 16S rRNA methyltransferases are main factors contributing to increasing resistance to aminoglycosides. Characterization and distribution of antimicrobial resistance gene profiles provide important information on the potential difficulty of treatment of bacteria. Several molecular methods have been developed to investigate the prevalence of aminoglycoside-resistance genes. These existing methods are time-consuming, labor-intensive, expensive or limited sensitivity in the epidemiological investigation. Therefore, it is necessary to develop a rapid, less-costly and high throughput and sensitive method to investigate the distribution of antimicrobial resistance gene in clinical isolates. Results In this study, we developed a GeXP analyzer-based multiplex PCR assay to simultaneously detect seven aminoglycoside-resistance genes, including aac(3)-II, aac(6′)-Ib, aac(6′)-II, ant(3″)-I,aph(3′)-VI,armA and rmtB, and to analyze the distribution of these genes in clinical Enterobacteriaceae isolates. Under optimized conditions, this assay achieved a limit-of-detection as low as 10 copies of each of the seven genes. The presented method was applied to analyze the distribution of aminoglycoside-resistance genes in 56 clinical Enterobacteriaceae isolates, and the results were compared with that of the conventional single PCR assay. Kappa values of the two methods for detecting each of the seven resistance genes were 0.831, 0.846, 0.810, 0.909, 0.887, 0.810 and 0.825, respectively. Conclusion This GeXP assay is demonstrated to be a rapid, cost-effective and high throughput method with high sensitivity and specificity for simultaneously detecting seven common aminoglycoside-resistance genes.
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Affiliation(s)
- Xiumei Hu
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
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