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Lin M, Li YR, Lan QW, Long LJ, Liu JQ, Chen YW, Cao XJ, Wu GY, Li YP, Guo XG. Evaluation of GeneXpert EV assay for the rapid diagnosis of enteroviral meningitis: a systematic review and meta-analysis. Ann Clin Microbiol Antimicrob 2022; 21:25. [PMID: 35681153 PMCID: PMC9185958 DOI: 10.1186/s12941-022-00517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 05/26/2022] [Indexed: 11/25/2022] Open
Abstract
Background GeneXpert enterovirus Assay is a PCR-based assay for Enterovirus meningitis diagnosis. However, there is currently no research about the performance of GeneXpert enterovirus assay in the diagnosis of enterovirus meningitis. Thus, a systematic review and meta-analysis is significant on the topic. Methods Embase, Cochrane Library, Web of Science, and PubMed were systematically reviewed with retrieval types. Some criteria were used to filter the studies. Only studies published in English, that made a comparison between GeneXpert enterovirus assay and RT-PCR, and could be formulated in a 2*2 table, were included. The quality of the included studies was evaluated by QUADAS-2. The effect of the GeneXpert enterovirus assay was assessed by the Sensitivity, Specificity, Positive Likelihood Ratio, Negative Likelihood Ratio, Diagnosis Odds Ratio, and summary receiver operating characteristic (SROC) curve. Publication bias and heterogeneity were evaluated by the Deeks' funnel test and Bivariate Box plot respectively. Results 7 studies were recruited in the analysis. The Pooled Sensitivity was 0.96 [95% CI (0.94–0.97)], Pooled Specificity was 0.99 [95% CI (0.98–0.99)], Positive Likelihood Ratio was 130.46 [95% CI (35.79–475.58)], Negative Likelihood Ratio was 0.04 [95% CI (0.02–0.10)], and Diagnostic Odds Ratio was 3648.23 (95% CI [963.99–13,806.72)]. In SROC Curve, Area Under Curve (AUC) was 0.9980, and Q*= 0.9849. In Deeks' funnel test, the P-value was 0.807 (P > 0.05), indicating no publication bias. The Bivariate Box plot indicated no evident heterogeneity. Conclusions The GeneXpert enterovirus assay demonstrated high diagnostic accuracy in diagnosing enterovirus meningitis. Supplementary Information The online version contains supplementary material available at 10.1186/s12941-022-00517-3.
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Affiliation(s)
- Min Lin
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Chinese and Western Medicine in Clinical Medicine, The Clinical School of Chinese and Western Medicine, Guangzhou Medical University, Guangzhou, 511436, China
| | - Yun-Ran Li
- Department of Chinese and Western Medicine in Clinical Medicine, The Clinical School of Chinese and Western Medicine, Guangzhou Medical University, Guangzhou, 511436, China
| | - Qi-Wen Lan
- Department of Medical Imageology, The Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Li-Jun Long
- Department of Medical Laboratory Technology, The KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 511436, China
| | - Jia-Qi Liu
- Department of Chinese and Western Medicine in Clinical Medicine, The Clinical School of Chinese and Western Medicine, Guangzhou Medical University, Guangzhou, 511436, China
| | - Ying-Wen Chen
- Department of Chinese and Western Medicine in Clinical Medicine, The Clinical School of Chinese and Western Medicine, Guangzhou Medical University, Guangzhou, 511436, China
| | - Xun-Jie Cao
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Ge-Yuan Wu
- Department of Chinese and Western Medicine in Clinical Medicine, The Clinical School of Chinese and Western Medicine, Guangzhou Medical University, Guangzhou, 511436, China
| | - Ya-Ping Li
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Xu-Guang Guo
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China. .,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China. .,Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China. .,Department of Laboratory Medicine, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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Dize L, Silver B, Gaydos C. Comparison of the Cepheid GeneXpert CT/NG assay to the Hologic Aptima Combo2 assay for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae in self-collected rectal swabs. Diagn Microbiol Infect Dis 2017; 90:83-84. [PMID: 29174733 DOI: 10.1016/j.diagmicrobio.2017.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/10/2017] [Accepted: 10/18/2017] [Indexed: 11/17/2022]
Abstract
Self-collected rectal-swabs were tested for CT and NG on GeneXpert CT/NG as compared to APTIMA Combo2. Of 448 rectal-swabs, 22 were positive for CT; 7 for NG on both assays; two were discordant. Sensitivity and specificity of GeneXpert was 95.5% and 99.7% for chlamydia, respectively; for gonorrhea both were 100%.
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Affiliation(s)
- Laura Dize
- International Sexually Transmitted Diseases Research Laboratory, Division of Infectious Diseases, Johns Hopkins University, Baltimore, MD, USA.
| | - Barbara Silver
- International Sexually Transmitted Diseases Research Laboratory, Division of Infectious Diseases, Johns Hopkins University, Baltimore, MD, USA
| | - Charlotte Gaydos
- International Sexually Transmitted Diseases Research Laboratory, Division of Infectious Diseases, Johns Hopkins University, Baltimore, MD, USA
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Abstract
Since the last Handbook of Clinical Neurology volume on this topic, viral diagnosis has made tremendous strides, moving from the margin to the mainstream of clinical care. For many years, conventional virus isolation was the mainstay of viral diagnosis since it was sensitive and “open-minded.” However, growth in conventional cell culture entails an inherent delay that limits its clinical impact. Although rapid culture and viral antigen methods detect fewer pathogens and are less sensitive than conventional culture, both require less expertise and have greatly reduced time to result. Polymerase chain reaction has ushered in a new era in virology, especially in the diagnosis of neurologic diseases. Molecular amplification methods are rapid, highly sensitive, can be automated, quantitative, and detect viruses not amenable to routine culture. User-friendly, walk-away tests with results in an hour, as well as multiplex tests that can detect 20 viruses in a single reaction, are now a reality. As the variety of test methods and commercial products proliferate, the challenges for clinicians and laboratories are selecting which tests to utilize in which clinical scenarios, and understanding how to interpret the results. The advantages and limitations of each method are discussed in this chapter, with special attention to neurologic disease.
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Slika S, Abbas F, Mahfouz R. Implementation of the Cepheid Xpert EV assay for rapid detection of enteroviral meningitis: experience of a tertiary care center and a technical review. Genet Test Mol Biomarkers 2013; 17:232-5. [PMID: 23297804 DOI: 10.1089/gtmb.2012.0291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIMS Rapid molecular detection of enterovirus in cerebrospinal fluid (CSF) has revolutionized the diagnosis and treatment modalities of patients with meningitis and largely affected cost of unnecessary antibiotic use and length of stay in hospitals. MATERIALS AND METHODS Between January 2010 and July 2012, we tested 220 CSF samples on the GeneXpert DX real-time polymerase chain reaction system (by Cepheid) using the Xpert EV kit assays. In addition, we reported 14 sample results cross-validated with an external referral laboratory as well as the results of external proficiency testing. RESULTS Out of all tested samples, 19% were positive for enterovirus. Furthermore, all referred and proficiency testing specimens were concordant with the peer-reviewed and tested samples. CONCLUSION Implementation of the Cepheid Xpert EV assay for rapid detection of enteroviral meningitis has been successful in our laboratory. This molecular diagnostic test is currently utilized by our staff physicians as a major tool in assessment and management of patients with meningitis.
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Affiliation(s)
- Silva Slika
- Department of Pathology & Laboratory Medicine, American University of Beirut Medical Center (AUBMC), Beirut, Lebanon
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de Crom SCM, Obihara CC, van Loon AM, Argilagos-Alvarez AA, Peeters MF, van Furth AM, Rossen JWA. Detection of enterovirus RNA in cerebrospinal fluid: comparison of two molecular assays. J Virol Methods 2011; 179:104-7. [PMID: 22024398 DOI: 10.1016/j.jviromet.2011.10.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 09/22/2011] [Accepted: 10/10/2011] [Indexed: 10/16/2022]
Abstract
Enterovirus (EV) and human parechovirus (HPeV) are a major cause of infection in childhood. A rapid diagnostic test may improve the management of patients with EV and HPeV infection. The aim of this study is to evaluate the performance of the GeneXpert enterovirus assay (GXEA) for detection of EV RNA compared to a user-developed reverse-transcriptase (RT) quantitative real-time PCR (qPCR) in routine clinical practice. Also a RT-qPCR assay for detection of HPeV RNA in different clinical samples was developed and evaluated. Cerebrospinal fluid (CSF) from 232 patients suspected for meningitis was collected and tested for EV and HPeV using RT-qPCR assays. In parallel an aliquot of the samples was tested using the GXEA and viral culture. EV RNA was detected in 22 (19.0%) and 28 (24.1%) of 116 samples using the GXEA and RT-qPCR assay, respectively. EV was isolated from 10 of 116 (8.6%) samples by viral culture. GXEA had a sensitivity, specificity, positive predictive value and negative predictive value of 82.1%, 100%, 100% and 96.2%, respectively. In this study, molecular assays were superior to viral culture for detecting EV RNA in CSF. GXEA showed a high specificity but a lower sensitivity for the detection of EV RNA compared to the RT-qPCR assay.
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Affiliation(s)
- S C M de Crom
- Department of Pediatrics, St. Elisabeth Hospital, Post-office Box 90151, 5000 LC, Tilburg, The Netherlands
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Emmadi R, Boonyaratanakornkit JB, Selvarangan R, Shyamala V, Zimmer BL, Williams L, Bryant B, Schutzbank T, Schoonmaker MM, Amos Wilson JA, Hall L, Pancholi P, Bernard K. Molecular methods and platforms for infectious diseases testing a review of FDA-approved and cleared assays. J Mol Diagn 2011; 13:583-604. [PMID: 21871973 DOI: 10.1016/j.jmoldx.2011.05.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 05/09/2011] [Accepted: 05/27/2011] [Indexed: 01/03/2023] Open
Abstract
The superior sensitivity and specificity associated with the use of molecular assays has greatly improved the field of infectious disease diagnostics by providing clinicians with results that are both accurate and rapidly obtained. Herein, we review molecularly based infectious disease diagnostic tests that are Food and Drug Administration approved or cleared and commercially available in the United States as of December 31, 2010. We describe specific assays and their performance, as stated in the Food and Drug Administration's Summary of Safety and Effectiveness Data or the Office of In Vitro Diagnostic Device Evaluation and Safety's decision summaries, product inserts, or peer-reviewed literature. We summarize indications for testing, limitations, and challenges related to implementation in a clinical laboratory setting for a wide variety of common pathogens. The information presented in this review will be particularly useful for laboratories that plan to implement or expand their molecular offerings in the near term.
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Affiliation(s)
- Rajyasree Emmadi
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, USA.
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Ninove L, Nougairede A, Gazin C, Zandotti C, Drancourt M, de Lamballerie X, Charrel RN. Comparative detection of enterovirus RNA in cerebrospinal fluid: GeneXpert system vs. real-time RT-PCR assay. Clin Microbiol Infect 2011; 17:1890-4. [PMID: 21848972 DOI: 10.1111/j.1469-0691.2011.03487.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enteroviruses (EVs) constitute the most common cause of aseptic meningitis in both children and adults. Molecular techniques have now been recognized as the reference standard for the diagnosis of EV infections, and the rapidity of the molecular diagnosis of EV meningitis has been shown to be a determining factor in the management of patients. The rapid documentation of EV RNA in cerebrospinal fluid (CSF) is key to adapting patient management and the therapeutic regimen. To shorten the time needed for virological documentation, we implemented EV RNA detection in two point-of-care (POC) laboratories. Here, we present the results of the POC detection of EV RNA with the Xpert EV kit on the GeneXpert integrated system, and a comparison with the real-time RT-PCR (rtRT-PCR) assay routinely used in the core virology laboratory. From January to September 2009, a total of 310 CSF samples were tested. The rtRT-PCR gave 81 positive, 225 negative and four 'indeterminate' results. POC results were concordant in 81.6% (253/310). Most of the discrepancies consisted of 'indeterminate' results at the POC level (16%). Calculated performances (excluding the indeterminate results) of the Xpert EV kit on the GeneXpert system in POC settings were 100%, 98.9%, 97.6% and 100% for Sensibility, Specificity, positive predictive value and negative predictive value, respectively. Taken together, these results indicate that the implementation of POC detection of EV RNA can provide robust results in <4 h, and may have a significant impact on patient management, therapeutic attitude, and hospitalization costs.
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Affiliation(s)
- L Ninove
- Laboratory of Clinical Microbiology, AP-HM Timone, Université de la Méditerranée, Marseille, France.
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Evaluation of a rapid and completely automated real-time reverse transcriptase PCR assay for diagnosis of enteroviral meningitis. J Clin Microbiol 2010; 49:528-33. [PMID: 21159942 DOI: 10.1128/jcm.01570-10] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nucleic acid amplification tests (NAATs) for enterovirus RNA in cerebrospinal fluid (CSF) have emerged as the new gold standard for diagnosis of enteroviral meningitis, and their use can improve the management and decrease the costs for caring for children with enteroviral meningitis. The Xpert EV assay (Cepheid, Sunnyvale, CA) is a rapid, fully automated real-time PCR test for the detection of enterovirus RNA that was approved by the U.S. Food and Drug Administration for in vitro diagnostic use in March 2007. In this multicenter trial we established the clinical performance characteristics of the Xpert EV assay in patients presenting with meningitis symptoms relative to clinical truth. Clinical truth for enteroviral meningitis was defined as clinical evidence of meningitis, the absence of another detectable pathogen in CSF, and detection of enterovirus in CSF either by two reference NAATs or by viral culture. A total of 199 prospectively and 235 retrospectively collected specimens were eligible for inclusion in this study. The overall prevalence of enteroviral meningitis was 26.04%. The Xpert EV assay had a sensitivity of 94.69% (90% confidence interval [CI] = 89.79 to 97.66%), specificity of 100% (90% CI = 99.07 to 100%), positive predictive value of 100%, negative predictive value of 98.17, and an accuracy of 98.62% relative to clinical truth. The Xpert EV assay demonstrated a high degree of accuracy for diagnosis of enteroviral meningitis. The simplicity and on-demand capability of the Xpert EV assay should prove to be a valuable adjunct to the evaluation of suspected meningitis cases.
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POC tests: From antigen detection to molecular methods. Future trends. J Clin Virol 2010; 49:304-5. [DOI: 10.1016/j.jcv.2010.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Accepted: 08/19/2010] [Indexed: 11/21/2022]
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Pillet S, Billaud G, Omar S, Lina B, Pozzetto B, Schuffenecker I. Multicenter evaluation of the ENTEROVIRUS R-gene real-time RT-PCR assay for the detection of enteroviruses in clinical specimens. J Clin Virol 2009; 47:54-9. [PMID: 19879186 DOI: 10.1016/j.jcv.2009.09.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 09/25/2009] [Indexed: 11/18/2022]
Abstract
BACKGROUND The rapid molecular diagnosis of enteroviral meningitis has been shown important for an adequate management of the patients. OBJECTIVES A new CE-marked real-time RT-PCR assay (ENTEROVIRUS R-gene, Argene) was evaluated in two university hospital virology laboratories. STUDY DESIGN Reactivity, analytical sensitivity and specificity were evaluated using 54 prototype and 173 clinical human enterovirus (HEV) strains, a 12-sample HEV proficiency panel, and 30 non-HEV microorganisms. The clinical performance of the ENTEROVIRUS R-gene assay was evaluated by testing 197 cerebrospinal fluid (CSF) and 103 respiratory specimens, comparatively to the routinely used diagnostic techniques. RESULTS Sixty-four out of the 65 HEV serotypes tested were detected. The analytical sensitivity ranged between 10(-2.64) and 10(2.39)TCID(50)/50 microl. Cross-reactivity was observed with four human rhinoviruses. On 59 CSF specimens analyzed prospectively, the results of the ENTEROVIRUS R-gene assay showed a 94.8% concordance with those of the Smart enterovirus (EV) assay (Cepheid). On 138 CSF specimens tested retrospectively, the results of the ENTEROVIRUS R-gene assay showed a 97.1% concordance with those of either the GeneXpert EV assay (Cepheid) or the in-house RT-PCR HEV assays used at the time of specimen collection. On 103 respiratory specimens, the concordance between the results of the ENTEROVIRUS R-gene assay and those of the routine RT-PCRs or viral culture was 90.2% and 96.1% before and after retest, respectively. CONCLUSIONS The new test was found able to detect a large panel of enterovirus serotypes; it was sensitive when used on clinical specimens; and, easy and rapid to perform on a routine basis.
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Affiliation(s)
- Sylvie Pillet
- Laboratoire de Bactériologie-Virologie, GIMAP EA 3064 and University Hospital of Saint-Etienne, 42023 Saint-Etienne Cedex 2, France
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