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Robinson M, Einav S. Towards Predicting Progression to Severe Dengue. Trends Microbiol 2020; 28:478-486. [PMID: 31982232 DOI: 10.1016/j.tim.2019.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/04/2019] [Accepted: 12/09/2019] [Indexed: 12/30/2022]
Abstract
There is an urgent need for prognostic assays to predict progression to severe dengue infection, which is a major global threat. While the majority of symptomatic dengue patients experience an acute febrile illness, 5-20% progress to severe infection associated with significant morbidity and mortality. Early monitoring and administration of supportive care reduce mortality and clinically usable biomarkers to predict severe dengue are needed. Here, we review recent discoveries of gene sets, anti-dengue antibody properties, and inflammatory markers with potential utility as predictors of disease progression. Upon larger scale validation and development of affordable sample-to-answer technologies, some of these biomarkers may be utilized to develop the first prognostic assay for improving patient care and allocating healthcare resources more effectively in dengue endemic countries.
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Affiliation(s)
- Makeda Robinson
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirit Einav
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Abstract
The clinical microbiology laboratory relies on traditional diagnostic methods such as culturing, Gram stains, and biochemical testing. Receipt of a high-quality specimen with an appropriate test order is integral to accurate testing. Recent technological advancements have led to decreased time to results and improved diagnostic accuracy. Examples of advancements discussed in this chapter include automation of bacterial culture processing and incubation, as well as introduction of mass spectrometry for the proteomic identification of microorganisms. In addition, molecular testing is increasingly common in the clinical laboratory. Commercially available multiplex molecular assays simultaneously test for a broad array of syndromic-related pathogens, providing rapid and sensitive diagnostic results. Molecular advancements have also transformed point-of-care (POC) microbiology testing, and molecular POC assays may largely supplant traditional rapid antigen testing in the future. Integration of new technologies with traditional testing methods has led to improved quality and value in the clinical microbiology laboratory. After reviewing this chapter, the reader will be able to:List key considerations for specimen collection for microbiology testing. Discuss the advantages and limitations of automation in the clinical microbiology laboratory. Describe the evolution of microorganism identification methods. Discuss the benefits and limitations of molecular microbiology point-of-care testing. Summarize currently available multiplex molecular microbiology testing options.
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Beard K, Brendish N, Malachira A, Mills S, Chan C, Poole S, Clark T. Pragmatic multicentre randomised controlled trial evaluating the impact of a routine molecular point-of-care 'test-and-treat' strategy for influenza in adults hospitalised with acute respiratory illness (FluPOC): trial protocol. BMJ Open 2019; 9:e031674. [PMID: 31852699 PMCID: PMC6937093 DOI: 10.1136/bmjopen-2019-031674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Influenza infections often remain undiagnosed in patients admitted to hospital due to lack of routine testing. When tested for, the diagnosis and treatment of influenza are often delayed due to the slow turnaround times of centralised laboratory PCR testing. Newer molecular systems, have comparable accuracy to laboratory PCR testing, and can generate a result in under 1 hour, making them potentially deployable as point-of-care tests (POCTs). High-quality evidence for the impact of routine POCT for influenza on clinical outcomes is, however, currently lacking. This large pragmatic multicentre randomised controlled trial aims to address this evidence gap. METHODS AND ANALYSIS The FluPOC trial is a pragmatic, multicentre, randomised controlled trial evaluating adults admitted to a large teaching hospital and a district general hospital with an acute respiratory illness, during influenza season and defined by Public Health England. Up to 840 patients will be recruited over up to three influenza seasons, and randomised (1:1) to receive either POCT using the FilmArray respiratory panel, or routine clinical care. Clinical and infection control teams will be informed of the results in real time and where influenza is detected clinical teams will be encouraged to offer neuraminidase inhibitor (NAI) treatment in accordance with national guidelines. Those allocated to standard clinical care will have a swab taken for later analysis to allow assessment of missed diagnoses. The outcomes assessment will be by retrospective case note analysis. The outcome measures include the proportion of influenza-positive patients detected and appropriately treated with NAIs, isolation facility use, antibiotic use, length of hospital stay, complications and mortality. ETHICS AND DISSEMINATION Prior to commencing the study, approval was obtained from the South Central Hampshire A Ethics Committee (reference 17/SC/0368, granted 7 September 2017). Results generated from this protocol will be published in peer-reviewed scientific journals and presented at national and international conferences. TRIAL REGISTRATION NUMBER ISRCTN17197293.
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Affiliation(s)
- Kate Beard
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Nathan Brendish
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Ahalya Malachira
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Samuel Mills
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Cathleen Chan
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Stephen Poole
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Tristan Clark
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
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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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Young BA, Hanson KE, Gomez CA. Molecular Diagnostic Advances in Transplant Infectious Diseases. Curr Infect Dis Rep 2019; 21:52. [PMID: 31773290 DOI: 10.1007/s11908-019-0704-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW The infectious complications of transplantation can have devastating consequences for patients. Early and accurate diagnosis is essential to good outcomes. This review describes recent advances in pathogen-directed diagnostic testing and discusses the role of new methods for transplant infectious diseases. RECENT FINDINGS Several molecular assays have been introduced into clinical practice in recent years. When the results of rapid testing are linked to patient-specific interventions, improved outcomes can be realized. Syndromic testing along with metagenomic next-generation sequencing (mNGS) represents novel approaches to infection diagnosis. However, the optimal use of these tests for transplant patients along with an overall assessment of cost-effectiveness demands further study. Molecular diagnostics are revolutionizing transplant care. Clinicians need to be aware of the current diagnostic landscape and have a working knowledge of the nuances related to test performance, result interpretation, and cost.
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Affiliation(s)
- Brittany A Young
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,Associated Regional and University Pathologists Laboratories (ARUP), Salt Lake City, UT, USA
| | - Kimberly E Hanson
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,Associated Regional and University Pathologists Laboratories (ARUP), Salt Lake City, UT, USA.,Department of Medicine, Division of Infectious Diseases, University of Utah, Salt Lake City, UT, USA
| | - Carlos A Gomez
- Department of Medicine, Division of Infectious Diseases, University of Utah, Salt Lake City, UT, USA. .,University of Utah School of Medicine, 30 North 1900 East, Room 4B319, Salt Lake City, UT, 84132, USA.
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Blair RH, Dawson ED, Taylor AW, Johnson JE, Slinskey AH, O'Neil K, Smolak AW, Toth E, Liikanen K, Stoughton RS, Smith CB, Talbot S, Rowlen KL. Clinical validation of the FluChip-8G Influenza A+B Assay for influenza type and subtype identification. J Clin Virol 2019; 118:20-27. [PMID: 31382226 PMCID: PMC6717662 DOI: 10.1016/j.jcv.2019.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/17/2019] [Accepted: 07/25/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND The FluChip-8G Influenza A+B Assay is a multiplexed influenza RT-PCR and microarray-based assay with same day turnaround time, developed to subtype seasonal A viruses (H1N1pdm2009 and H3N2), distinguish B viruses as Yamagata or Victoria lineage, and is the only FDA cleared assay capable of positive identification of a wide variety of A subtypes as "non-seasonal" A viruses from human nasal specimens. OBJECTIVE To evaluate clinical performance of the FluChip-8G Influenza A+B Assay for detection of seasonal influenza viruses in nasal and nasopharyngeal swab specimens, and to evaluate performance for detection of non-seasonal influenza viruses using contrived samples. STUDY DESIGN For seasonal viruses, a multisite study of the FluChip-8G Influenza A+B Assay using prospectively and retrospectively collected nasal and nasopharyngeal swabs was performed using the FDA-cleared CDC Human Flu Dx Panel as the comparator assay. For non-seasonal viruses, testing was performed at a single site using contrived samples from 100 unique non-seasonal strains representing 41 subtypes. RESULTS Sensitivity (95% CI) and specificity (95% CI) for each target group, respectively, from results of 1689 clinical specimens were: seasonal H1N1pdm2009: 96.4% (87.9-99.0), 99.3% (98.8-99.6), seasonal H3N2: 91.8% (87.7-94.7), 99.7% (99.2-99.9), Influenza B Victoria: 100% (94.0-100.0), 99.9% (99.6-100.0), and Influenza B Yamagata: 95.6% (89.2-98.3), 99.9% (99.6-100.0). The sensitivity and specificity from contrived influenza A non-seasonal viruses was determined to be 99.0% (94.6-99.8) and 100% (96.7-100.0). CONCLUSION The FluChip-8G Influenza A+B Assay has robust sensitivity and specificity for detecting and identifying all target virus groups, including non-seasonal influenza A, with same day results.
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Affiliation(s)
- Rebecca H Blair
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
| | - Erica D Dawson
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA.
| | - Amber W Taylor
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
| | - James E Johnson
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
| | - Amelia H Slinskey
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
| | - Kelly O'Neil
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
| | - Andrew W Smolak
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
| | - Evan Toth
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
| | - Kyle Liikanen
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
| | | | - Catherine B Smith
- Influenza Division, the Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30333, USA
| | - Sarah Talbot
- Influenza Division, the Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30333, USA
| | - Kathy L Rowlen
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
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Locher K, Roscoe D, Jassem A, Wong T, Hoang LMN, Charles M, Bryce E, Grant J, Stefanovic A. FilmArray respiratory panel assay: An effective method for detecting viral and atypical bacterial pathogens in bronchoscopy specimens. Diagn Microbiol Infect Dis 2019; 95:114880. [PMID: 31607515 PMCID: PMC7132745 DOI: 10.1016/j.diagmicrobio.2019.114880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/05/2019] [Accepted: 07/30/2019] [Indexed: 12/17/2022]
Abstract
The BioFire FilmArray Respiratory Panel (FA RP) is a rapid multiplexed molecular assay approved for detection of viral and atypical bacterial pathogens in nasopharyngeal specimens. This study aimed to evaluate the performance of the BioFire FilmArray Respiratory Panel v1.7 on bronchoscopy specimens. We tested 133 bronchial specimens (87 archived and 46 prospectively collected) with the FA RP and compared the results to the Luminex NxTAG Respiratory Pathogen Panel (NxTAG RPP). After discordant analysis, 123 specimens gave concordant results using the FA RP and the NxTAG RPP for an overall agreement of 93.9% (kappa = 0.88 [95% CI 0.80–0.96]), a positive percent agreement of 93.7% (95% CI 83.7–97.7) and a negative percent agreement of 94.1% (95% CI 84.9–98.1). In conclusion, the BioFire FilmArray RP performed reliably to detect a broad range of respiratory pathogens in bronchoscopy specimens.
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Affiliation(s)
- Kerstin Locher
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada.
| | - Diane Roscoe
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Agatha Jassem
- British Columbia Center for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Titus Wong
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Linda M N Hoang
- British Columbia Center for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Marthe Charles
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Elizabeth Bryce
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Jennifer Grant
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Aleksandra Stefanovic
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
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Fulminant myocarditis due to the influenza B virus in adults: Report of two cases and literature review. BIOMEDICA 2019; 39:11-19. [PMID: 31529829 DOI: 10.7705/biomedica.v39i3.4645] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Indexed: 11/21/2022]
Abstract
La miocarditis es una enfermedad inflamatoria del miocardio. Las infecciones virales son la causa más común, aunque también puede deberse a reacciones de hipersensibilidad y de etiología autoinmunitaria, entre otras. El espectro clínico de la enfermedad es variado y comprende desde un curso asintomático, seguido de dolor torácico, arritmias y falla cardiaca aguda, hasta un cuadro fulminante. El término 'fulminante' se refiere al desarrollo de un shock cardiogénico con necesidad de soporte vasopresor e inotrópico o dispositivos de asistencia circulatoria, ya sea oxigenación por membrana extracorpórea o balón de contrapulsación intraaórtico. Cerca del 10 % de los casos de falla cardiaca por miocarditis corresponde a miocarditis fulminante. La miocarditis por influenza se considera una condición infrecuente; no obstante, su incidencia ha aumentado desde el 2009 a raíz de la pandemia de influenza por el virus AH1N1. Por su parte, la miocarditis por influenza de tipo B sigue siendo una condición infrecuente. Se describen aquí dos casos confirmados de miocarditis fulminante por el virus de la influenza B atendidos en un centro cardiovascular, que requirieron dispositivos de asistencia circulatoria mecánica.
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Shaman J, Morita H, Birger R, Boyle M, Comito D, Lane B, Ligon C, Smith H, Desalle R, Planet P. Asymptomatic Summertime Shedding of Respiratory Viruses. J Infect Dis 2019; 217:1074-1077. [PMID: 29300926 PMCID: PMC7107397 DOI: 10.1093/infdis/jix685] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/29/2017] [Indexed: 11/17/2022] Open
Abstract
To determine rates of both symptomatic and asymptomatic infection among ambulatory adults, we collected nasopharyngeal swab specimens, demographic characteristics, and survey information from 1477 adult visitors to a New York City tourist attraction during April–July 2016. Multiplex polymerase chain reaction analysis was used to identify specimens positive for common respiratory viruses. A total of 7.2% of samples tested positive for respiratory viruses; among positive samples, 71.0% contained rhinovirus, and 21.5% contained coronavirus. Influenza virus, respiratory syncytial virus, and parainfluenza virus were also detected. Depending on symptomatologic definition, 57.7%–93.3% of positive samples were asymptomatic. These findings indicate that significant levels of asymptomatic respiratory viral shedding exist during summer among the ambulatory adult population.
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Affiliation(s)
- Jeffrey Shaman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University.,Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, New York
| | - Haruka Morita
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University
| | - Ruthie Birger
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University
| | - Mary Boyle
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University
| | - Devon Comito
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University
| | - Benjamin Lane
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University
| | - Chanel Ligon
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University
| | - Hannah Smith
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University
| | - Rob Desalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, New York
| | - Paul Planet
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, New York.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania.,Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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Banerjee D, Kanwar N, Hassan F, Lankachandra K, Selvarangan R. Comparative analysis of Four sample-to-answer influenza A/B and RSV nucleic acid amplification assays using adult respiratory specimens. J Clin Virol 2019; 118:9-13. [PMID: 31302479 DOI: 10.1016/j.jcv.2019.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/14/2019] [Accepted: 07/03/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND The use of Sample-to-answer (STA) platforms for the detection of influenza A/B and respiratory syncytial virus (RSV) have greatly improved patient care. These diagnostic assays based on nucleic acid amplification are rapid, accurate and relatively easy to perform. OBJECTIVES We compared four such platforms for detecting FluA, FluB, and RSV from adult respiratory specimens: Hologic Panther Fusion® Flu A/B/RSV (Fusion), Cobas® Influenza A/B & RSV (Liat), Luminex Aries® Flu A/B & RSV (Aries), and Diasorin SimplexaTM Flu A/B & RSV (Simplexa). STUDY DESIGN Nasopharyngeal (NP) swabs (n = 224) from adults were tested on these platforms and results were compared to Center for Disease Control and Prevention recommended real-time RT-PCR assay for influenza A/B and RSV. Subtyping for FluA and FluB was performed for discrepant analysis where applicable. RESULTS Of the 82 FluA, 26 FluB, 15 RSV-positive specimens tested, the positive and negative percentage agreements (PPA and NPA respectively) for FluA detection were 100/100 (Fusion), 95.1/100 (Liat), 92.5/100 (Aries), and 84.1/99.3 (Simplexa); PPA and NPA for FluB detection were 92.3/99.5 (Fusion), 96/99.5 (Liat), 100/99.5 (Aries), and 80.8/100 (Simplexa); and for RSV detection were 100/100 (Fusion), 100/100 (Liat), 88.6/99.5 (Aries), and 73.3/100 (Simplexa). 82 confirmed FluA included 23 pH1N1 and 57 H3N2 strains with 2 strains remaining untyped. Of the 26 confirmed FluB, 25 were of the Yamagata lineage and 1 of unknown lineage. CONCLUSION Only 2 STA platforms demonstrated >95% PPA for the detection of all three targets while all the 4 platforms demonstrated >95% NPA for FluA, FluB and RSV.
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Affiliation(s)
- Dithi Banerjee
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA.
| | - Neena Kanwar
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Ferdaus Hassan
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Kamani Lankachandra
- Department of Pathology and Laboratory Medicine, Truman Medical Center, Kansas City, Missouri, USA
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
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Silveira FP, Saul M, Nowalk MP, Saul S, Sax TM, Eng H, Zimmerman RK, Balasubramani GK. Determination of Eligibility for Influenza Research: A Clinical Informatics Approach. Open Forum Infect Dis 2019; 6:ofz231. [PMID: 31205975 PMCID: PMC6557306 DOI: 10.1093/ofid/ofz231] [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: 01/18/2019] [Accepted: 05/31/2019] [Indexed: 11/14/2022] Open
Abstract
Background A clinical informatics algorithm (CIA) was developed to systematically identify potential enrollees for a test-negative, case-control study to determine influenza vaccine effectiveness, to improve enrollment over manual records review. Further testing may enhance the CIA for increased efficiency. Methods The CIA generated a daily screening list by querying all medical record databases for patients admitted in the last 3 days, using specified terms and diagnosis codes located in admission notes, emergency department notes, chief complaint upon registration, or presence of a respiratory viral panel charge or laboratory result (RVP). Classification and regression tree analysis (CART) and multivariable logistic regression were used to refine the algorithm. Results Using manual records review, 204 patients (<4/day) were approached and 144 were eligible in the 2014-2015 season compared with 3531 (12/day) patients who were approached and 1136 who were eligible in the 2016-2017 season using a CIA. CART analysis identified RVP as the most important indicator from the CIA list for determining eligibility, identifying 65%-69% of the samples and predicting 1587 eligible patients. RVP was confirmed as the most significant predictor in regression analysis, with an odds ratio (OR) of 4.9 (95% confidence interval [CI], 4.0-6.0). Other significant factors were indicators in admission notes (OR, 2.3 [95% CI, 1.9-2.8]) and emergency department notes (OR, 1.8 [95% CI, 1.4-2.3]). Conclusions This study supports the benefits of a CIA to facilitate recruitment of eligible participants in clinical research over manual records review. Logistic regression and CART identified potential eligibility screening criteria reductions to improve the CIA's efficiency.
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Affiliation(s)
- Fernanda P Silveira
- Department of Medicine, School of Medicine, University of Pittsburgh, Pennsylvania
| | - Melissa Saul
- Department of Medicine, School of Medicine, University of Pittsburgh, Pennsylvania
| | - Mary Patricia Nowalk
- Department of Family Medicine, School of Medicine, University of Pittsburgh, Pennsylvania
| | - Sean Saul
- Department of Family Medicine, School of Medicine, University of Pittsburgh, Pennsylvania
| | - Theresa M Sax
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pennsylvania
| | - Heather Eng
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pennsylvania
| | - Richard K Zimmerman
- Department of Family Medicine, School of Medicine, University of Pittsburgh, Pennsylvania
| | - Goundappa K Balasubramani
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pennsylvania
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Wagner K, Springer B, Pires V, Keller P. High-throughput screening of bacterial pathogens in clinical specimens using 16S rDNA qPCR and fragment analysis. Diagn Microbiol Infect Dis 2019; 93:287-292. [DOI: 10.1016/j.diagmicrobio.2018.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/09/2018] [Accepted: 11/12/2018] [Indexed: 11/29/2022]
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63
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Bernal LJ, Velandia-Romero M, Guevara C, Castellanos JE. Human Metapneumovirus: Laboratory Methods for Isolation, Propagation, and Plaque Titration. Intervirology 2019; 61:301-306. [PMID: 30917376 DOI: 10.1159/000497309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/24/2019] [Indexed: 11/19/2022] Open
Abstract
The human metapneumovirus (hMPV) is an important viral agent associated with severe infections of the upper and lower airways, especially in young children and immunosuppressed subjects. Nevertheless, in vitro studies of hMPV are very difficult due to the little knowledge we have on its laboratory manipulation. OBJECTIVE The aim of this study was to isolate and propagate hMPV from patients, and to establish a method to quantify the virus by plaque assay. METHOD As part of a Latin American respiratory virus surveillance study, 12 nasal secretion samples - hMPV-positive by direct fluorescence - were inoculated on LLC-MK2 cells to isolate the virus. The supernatants were re-inoculated and the cytopathic effect and syncytium formation were evaluated daily; the infection was confirmed by immunofluorescence and RT-PCR. A protocol to titrate the harvested virus was established inoculating serial dilutions on LLC-MK2 cells, and agarose was then added as an overlay. After different time periods, the monolayers were fixed and stained with Naphthol blue/black or crystal violet and finally the viral titer was obtained. RESULTS Eight out of 12 hMPV-positive respiratory samples were positive for the isolation and confirmed by RT-PCR and immunofluorescence, but the cytopathic effect and syncytium formation were observed only in 5 cultures. One out of 8 viral isolates was used for propagation and plaque assay standardization. We found that incubation for 7 days in the semisolid overlay yielded plaques with appropriate size and shape to be counted, although crystal violet staining showed slightly larger plaques than those seen with Naphthol blue/black staining. CONCLUSIONS The isolation and propagation from patient-derived hMPV and the standardization of a practical, reliable, and inexpensive method of detection and quantification of hMPV were carried out, without the additional use of antibodies that had not been reported previously. These results offer some important insights for future studies of cellular and molecular biology of hMPV.
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Affiliation(s)
- Lilia J Bernal
- Facultad de Odontología, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | | | - Jaime E Castellanos
- Facultad de Odontología, Universidad Nacional de Colombia, Bogotá, Colombia, .,Grupo de Virología, Universidad El Bosque, Bogotá, Colombia,
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Galanti M, Birger R, Ud-Dean M, Filip I, Morita H, Comito D, Anthony S, Freyer GA, Ibrahim S, Lane B, Ligon C, Rabadan R, Shittu A, Tagne E, Shaman J. Longitudinal active sampling for respiratory viral infections across age groups. Influenza Other Respir Viruses 2019; 13:226-232. [PMID: 30770641 PMCID: PMC6468062 DOI: 10.1111/irv.12629] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 12/03/2022] Open
Abstract
Background Respiratory viral infections are a major cause of morbidity and mortality worldwide. However, their characterization is incomplete because prevalence estimates are based on syndromic surveillance data. Here, we address this shortcoming through the analysis of infection rates among individuals tested regularly for respiratory viral infections, irrespective of their symptoms. Methods We carried out longitudinal sampling and analysis among 214 individuals enrolled at multiple New York City locations from fall 2016 to spring 2018. We combined personal information with weekly nasal swab collection to investigate the prevalence of 18 respiratory viruses among different age groups and to assess risk factors associated with infection susceptibility. Results 17.5% of samples were positive for respiratory viruses. Some viruses circulated predominantly during winter, whereas others were found year round. Rhinovirus and coronavirus were most frequently detected. Children registered the highest positivity rates, and adults with daily contacts with children experienced significantly more infections than their counterparts without children. Conclusion Respiratory viral infections are widespread among the general population with the majority of individuals presenting multiple infections per year. The observations identify children as the principal source of respiratory infections. These findings motivate further active surveillance and analysis of differences in pathogenicity among respiratory viruses.
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Affiliation(s)
- Marta Galanti
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Ruthie Birger
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Minhaz Ud-Dean
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Ioan Filip
- Department of Systems Biology, Columbia University, New York, New York
| | - Haruka Morita
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Devon Comito
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Simon Anthony
- Department of Epidemiology, Columbia University, New York, New York
| | - Greg A Freyer
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Sadiat Ibrahim
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Benjamin Lane
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Chanel Ligon
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Raul Rabadan
- Department of Systems Biology, Columbia University, New York, New York
| | - Atinuke Shittu
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Eudosie Tagne
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Jeffrey Shaman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
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65
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Affiliation(s)
- Marilynn Ransom Fairfax
- Department of Pathology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Clinical Microbiology Laboratories, DMC University Laboratories, 4201 St. Antoine Street, Detroit, MI 48201, USA.
| | - Martin H Bluth
- Department of Pathology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Pathology Laboratories, Michigan Surgical Hospital, 21230 Dequindre Road, Warren, MI 48091, USA
| | - Hossein Salimnia
- Department of Pathology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Clinical Microbiology Laboratories, DMC University Laboratories, 4201 St. Antoine Street, Detroit, MI 48201, USA
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Abstract
Enterovirus D68 (EV-D68) is a pathogen that causes outbreaks of respiratory illness across the world, mostly in children, and can be especially severe in those with asthma. Clusters of acute flaccid myelitis, a poliomyelitis-like neuromuscular weakness syndrome, often occur concurrent with EV-D68 respiratory outbreaks. Seroepidemiologic studies have found that the serum of nearly everyone older than 2 to 5 years contains anti-EV-D68 neutralizing antibodies, which suggests that EV-D68 is a ubiquitous pathogen of childhood. However, knowledge of the viral epitopes against which the humoral immune response is directed is only inferred from previous studies of related viruses. Although neutralizing antibodies protect newborn mice from lethal EV-D68 inoculation via nonphysiologic routes, cotton rats have a mixed phenotype of both benefit and possible exacerbation when inoculated intranasally. The human antibody response to EV-D68 needs to be studied further to clarify the role of antibodies in protection versus pathogenesis, which might differ among respiratory and neurologic disease phenotypes.
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Affiliation(s)
- Matthew R Vogt
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - James E Crowe
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee.,Departments of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee
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67
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Schmitz JE, Tang YW. The GenMark ePlex ®: another weapon in the syndromic arsenal for infection diagnosis. Future Microbiol 2018; 13:1697-1708. [PMID: 30547684 DOI: 10.2217/fmb-2018-0258] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
As one of the most recent additions to the syndromic testing landscape, the ePlex® platform by GenMark Diagnostics is a system that combines the manufacturer's signature electrochemical detection technology with updated microfluidics, providing a new option for multiplex testing that is both rapid and requires minimal hands-on steps. In this review, we detail the ePlex platform and its current/future syndromic panels, with a particular focus on the respiratory pathogen panel - the platform's first assay to undergo clinical trials and receive regulatory approval in the USA. By keeping informed of these ever-expanding laboratory options, clinicians and microbiologists can stay positioned at the forefront of infectious disease diagnosis.
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Affiliation(s)
- Jonathan E Schmitz
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center & School of Medicine, Nashville, TN 37232, USA
| | - Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA.,Department of Pathology & Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065 USA
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68
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Hijano DR, Maron G, Hayden RT. Respiratory Viral Infections in Patients With Cancer or Undergoing Hematopoietic Cell Transplant. Front Microbiol 2018; 9:3097. [PMID: 30619176 PMCID: PMC6299032 DOI: 10.3389/fmicb.2018.03097] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/29/2018] [Indexed: 12/25/2022] Open
Abstract
Survival rates for pediatric cancer have steadily improved over time but it remains a significant cause of morbidity and mortality among children. Infections are a major complication of cancer and its treatment. Community acquired respiratory viral infections (CRV) in these patients increase morbidity, mortality and can lead to delay in chemotherapy. These are the result of infections with a heterogeneous group of viruses including RNA viruses, such as respiratory syncytial virus (RSV), influenza virus (IV), parainfluenza virus (PIV), metapneumovirus (HMPV), rhinovirus (RhV), and coronavirus (CoV). These infections maintain a similar seasonal pattern to those of immunocompetent patients. Clinical manifestations vary significantly depending on the type of virus and the type and degree of immunosuppression, ranging from asymptomatic or mild disease to rapidly progressive fatal pneumonia Infections in this population are characterized by a high rate of progression from upper to lower respiratory tract infection and prolonged viral shedding. Use of corticosteroids and immunosuppressive therapy are risk factors for severe disease. The clinical course is often difficult to predict, and clinical signs are unreliable. Accurate prognostic viral and immune markers, which have become part of the standard of care for systemic viral infections, are currently lacking; and management of CRV infections remains controversial. Defining effective prophylactic and therapeutic strategies is challenging, especially considering, the spectrum of immunocompromised patients, the variety of respiratory viruses, and the presence of other opportunistic infections and medical problems. Prevention remains one of the most important strategies against these viruses. Early diagnosis, supportive care and antivirals at an early stage, when available and indicated, have proven beneficial. However, with the exception of neuraminidase inhibitors for influenza infection, there are no accepted treatments. In high-risk patients, pre-emptive treatment with antivirals for upper respiratory tract infection (URTI) to decrease progression to LRTI is a common strategy. In the future, viral load and immune markers may prove beneficial in predicting severe disease, supporting decision making and monitor treatment in this population.
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Affiliation(s)
- Diego R. Hijano
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, United States
| | - Gabriela Maron
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, United States
| | - Randall T. Hayden
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, United States
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69
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Belongia EA, King JP, Kieke BA, Pluta J, Al-Hilli A, Meece JK, Shinde V. Clinical Features, Severity, and Incidence of RSV Illness During 12 Consecutive Seasons in a Community Cohort of Adults ≥60 Years Old. Open Forum Infect Dis 2018; 5:ofy316. [PMID: 30619907 PMCID: PMC6306566 DOI: 10.1093/ofid/ofy316] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/23/2018] [Indexed: 01/15/2023] Open
Abstract
Background The epidemiology and burden of respiratory syncytial virus (RSV) illness are not well defined in older adults. Methods Adults ≥60 years old seeking outpatient care for acute respiratory illness were recruited from 2004–2005 through 2015–2016 during the winter seasons. RSV was identified from respiratory swabs by multiplex polymerase chain reaction. Clinical characteristics and outcomes were ascertained by interview and medical record abstraction. The incidence of medically attended RSV was estimated for each seasonal cohort. Results RSV was identified in 243 (11%) of 2257 enrollments (241 of 1832 individuals), including 121 RSV type A and 122 RSV type B. The RSV clinical outcome was serious in 47 (19%), moderate in 155 (64%), and mild in 41 (17%). Serious outcomes included hospital admission (n = 29), emergency department visit (n = 13), and pneumonia (n = 23) and were associated with lower respiratory tract symptoms during the enrollment visit. Moderate outcomes included receipt of a new antibiotic prescription (n = 144; 59%), bronchodilator/nebulizer (n = 45; 19%), or systemic corticosteroids (n = 28; 12%). The relative risk of a serious outcome was significantly increased in persons aged ≥75 years (vs 60–64 years) and in those with chronic obstructive pulmonary disease or congestive heart failure. The average seasonal incidence was 139 cases/10 000, and it was significantly higher in persons with cardiopulmonary disease compared with others (rate ratio, 1.89; 95% confidence interval, 1.44–2.48). Conclusions RSV causes substantial outpatient illness with lower respiratory tract involvement. Serious outcomes are common in older patients and those with cardiopulmonary disease.
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Affiliation(s)
| | | | - Burney A Kieke
- Marshfield Clinic Research Institute, Marshfield, Wisconsin
| | - Joanna Pluta
- Marshfield Clinic Health System, Marshfield, Wisconsin
| | - Ali Al-Hilli
- Marshfield Clinic Health System, Marshfield, Wisconsin
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70
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Madigan VM, Sinickas VG, Giltrap D, Kyriakou P, Ryan K, Chan HT, Clifford V. Health service impact of testing for respiratory pathogens using cartridge-based multiplex array versus molecular batch testing. Pathology 2018; 50:758-763. [PMID: 30389216 PMCID: PMC7111697 DOI: 10.1016/j.pathol.2018.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/18/2018] [Accepted: 08/23/2018] [Indexed: 12/26/2022]
Abstract
There is increasing demand for access to rapid microbiological testing, with a view to improving clinical outcomes. The possibility of rapid testing has been facilitated by development of cartridge-based random access molecular technologies that are now widely available. Whether the expense of cartridge-based assays is justified in terms of clinical or laboratory cost savings is controversial. This prospective study evaluated the impact of the Biofire FilmArray Respiratory Panel (‘FilmArray’), a cartridge-based random access molecular test, compared with standard batched molecular testing using an ‘in-house’ respiratory polymerase chain reaction (PCR) on laboratory and health service outcomes for adult patients at a tertiary-level adult hospital in Melbourne, Australia. Laboratory result turnaround time was significantly reduced with the FilmArray (median 4.4 h) compared to a standard validated in-house respiratory PCR assay (median 21.6 h, p < 0.0001) and there was a significant increase in diagnostic yield with the Filmarray (71/124, 57.3%) compared to in-house PCR (79/200; 39.5%; p = 0.002). Despite improved result turnaround time and increased diagnostic yield from testing, there was no corresponding reduction in hospital length of stay or use of isolation beds. Although cartridge-based molecular testing reduced turnaround time to result for respiratory pathogen testing, it did not impact on health service outcomes such as hospital length of stay. Further work is warranted to determine whether cartridge-based tests at the point of care can improve clinical and health service impacts.
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Affiliation(s)
- Victoria M Madigan
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia.
| | - Vincent G Sinickas
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Dawn Giltrap
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Peter Kyriakou
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Katherine Ryan
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Hiu-Tat Chan
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Vanessa Clifford
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia; The University of Melbourne, Melbourne, Vic, Australia; Murdoch Children's Research Institute, Parkville, Vic, Australia
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71
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Das S, Dunbar S, Tang YW. Laboratory Diagnosis of Respiratory Tract Infections in Children - the State of the Art. Front Microbiol 2018; 9:2478. [PMID: 30405553 PMCID: PMC6200861 DOI: 10.3389/fmicb.2018.02478] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
Abstract
In the pediatric population, respiratory infections are the most common cause of physician visits. Although many respiratory illnesses are self-limiting viral infections that resolve with time and supportive care, it can be critical to identify the causative pathogen at an early stage of the disease in order to implement effective antimicrobial therapy and infection control. Over the last few years, diagnostics for respiratory infections have evolved substantially, with the development of novel assays and the availability of updated tests for newer strains of pathogens. Newer laboratory methods are rapid, highly sensitive and specific, and are gradually replacing the conventional gold standards, although the clinical utility of these assays is still under evaluation. This article reviews the current laboratory methods available for testing for respiratory pathogens and discusses the advantages and disadvantages of each approach.
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Affiliation(s)
- Shubhagata Das
- Global Scientific Affairs, Luminex Corporation, Austin, TX, United States
| | - Sherry Dunbar
- Global Scientific Affairs, Luminex Corporation, Austin, TX, United States
| | - Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, Weill Medical College of Cornell University, New York, NY, United States.,Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, Weill Medical College of Cornell University, New York, NY, United States
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72
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García-León ML, Noyola DE, Wong-Chew RM. Comparison of two multiplex PCR techniques for the study of respiratory viruses in Mexican children with pneumonia. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2018. [PMCID: PMC7148932 DOI: 10.1016/j.eimce.2018.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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73
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García-León ML, Noyola DE, Wong-Chew RM. Comparison of two multiplex PCR techniques for the study of respiratory viruses in Mexican children with pneumonia. Enferm Infecc Microbiol Clin 2018; 36:458-459. [PMID: 29510861 PMCID: PMC7130272 DOI: 10.1016/j.eimc.2018.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/09/2018] [Accepted: 01/11/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Miguel L García-León
- División de investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico
| | - Daniel E Noyola
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Rosa M Wong-Chew
- División de investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico.
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74
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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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75
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Hassibi A, Manickam A, Singh R, Bolouki S, Sinha R, Jirage KB, McDermott MW, Hassibi B, Vikalo H, Mazarei G, Pei L, Bousse L, Miller M, Heshami M, Savage MP, Taylor MT, Gamini N, Wood N, Mantina P, Grogan P, Kuimelis P, Savalia P, Conradson S, Li Y, Meyer RB, Ku E, Ebert J, Pinsky BA, Dolganov G, Van T, Johnson KA, Naraghi-Arani P, Kuimelis RG, Schoolnik G. Multiplexed identification, quantification and genotyping of infectious agents using a semiconductor biochip. Nat Biotechnol 2018; 36:738-745. [PMID: 30010676 DOI: 10.1038/nbt.4179] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/23/2018] [Indexed: 02/04/2023]
Abstract
The emergence of pathogens resistant to existing antimicrobial drugs is a growing worldwide health crisis that threatens a return to the pre-antibiotic era. To decrease the overuse of antibiotics, molecular diagnostics systems are needed that can rapidly identify pathogens in a clinical sample and determine the presence of mutations that confer drug resistance at the point of care. We developed a fully integrated, miniaturized semiconductor biochip and closed-tube detection chemistry that performs multiplex nucleic acid amplification and sequence analysis. The approach had a high dynamic range of quantification of microbial load and was able to perform comprehensive mutation analysis on up to 1,000 sequences or strands simultaneously in <2 h. We detected and quantified multiple DNA and RNA respiratory viruses in clinical samples with complete concordance to a commercially available test. We also identified 54 drug-resistance-associated mutations that were present in six genes of Mycobacterium tuberculosis, all of which were confirmed by next-generation sequencing.
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Affiliation(s)
| | | | | | | | - Ruma Sinha
- InSilixa, Inc., Sunnyvale, California, USA
| | | | | | - Babak Hassibi
- Electrical Engineering Department, California Institute of Technology, Pasadena, California, USA
| | - Haris Vikalo
- Electrical and Computer Engineering Department, University of Texas at Austin, Austin, Texas, USA
| | | | - Lei Pei
- InSilixa, Inc., Sunnyvale, California, USA
| | - Luc Bousse
- InSilixa, Inc., Sunnyvale, California, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Yuan Li
- InSilixa, Inc., Sunnyvale, California, USA
| | | | - Edmond Ku
- InSilixa, Inc., Sunnyvale, California, USA
| | | | - Benjamin A Pinsky
- Department of Medicine, Stanford University, Stanford, California, USA
| | | | - Tran Van
- InSilixa, Inc., Sunnyvale, California, USA
| | | | | | | | - Gary Schoolnik
- InSilixa, Inc., Sunnyvale, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA
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76
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Meyers L, Ginocchio CC, Faucett AN, Nolte FS, Gesteland PH, Leber A, Janowiak D, Donovan V, Dien Bard J, Spitzer S, Stellrecht KA, Salimnia H, Selvarangan R, Juretschko S, Daly JA, Wallentine JC, Lindsey K, Moore F, Reed SL, Aguero-Rosenfeld M, Fey PD, Storch GA, Melnick SJ, Robinson CC, Meredith JF, Cook CV, Nelson RK, Jones JD, Scarpino SV, Althouse BM, Ririe KM, Malin BA, Poritz MA. Automated Real-Time Collection of Pathogen-Specific Diagnostic Data: Syndromic Infectious Disease Epidemiology. JMIR Public Health Surveill 2018; 4:e59. [PMID: 29980501 PMCID: PMC6054708 DOI: 10.2196/publichealth.9876] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/29/2018] [Accepted: 04/12/2018] [Indexed: 12/22/2022] Open
Abstract
Background Health care and public health professionals rely on accurate, real-time monitoring of infectious diseases for outbreak preparedness and response. Early detection of outbreaks is improved by systems that are comprehensive and specific with respect to the pathogen but are rapid in reporting the data. It has proven difficult to implement these requirements on a large scale while maintaining patient privacy. Objective The aim of this study was to demonstrate the automated export, aggregation, and analysis of infectious disease diagnostic test results from clinical laboratories across the United States in a manner that protects patient confidentiality. We hypothesized that such a system could aid in monitoring the seasonal occurrence of respiratory pathogens and may have advantages with regard to scope and ease of reporting compared with existing surveillance systems. Methods We describe a system, BioFire Syndromic Trends, for rapid disease reporting that is syndrome-based but pathogen-specific. Deidentified patient test results from the BioFire FilmArray multiplex molecular diagnostic system are sent directly to a cloud database. Summaries of these data are displayed in near real time on the Syndromic Trends public website. We studied this dataset for the prevalence, seasonality, and coinfections of the 20 respiratory pathogens detected in over 362,000 patient samples acquired as a standard-of-care testing over the last 4 years from 20 clinical laboratories in the United States. Results The majority of pathogens show influenza-like seasonality, rhinovirus has fall and spring peaks, and adenovirus and the bacterial pathogens show constant detection over the year. The dataset can also be considered in an ecological framework; the viruses and bacteria detected by this test are parasites of a host (the human patient). Interestingly, the rate of pathogen codetections, on average 7.94% (28,741/362,101), matches predictions based on the relative abundance of organisms present. Conclusions Syndromic Trends preserves patient privacy by removing or obfuscating patient identifiers while still collecting much useful information about the bacterial and viral pathogens that they harbor. Test results are uploaded to the database within a few hours of completion compared with delays of up to 10 days for other diagnostic-based reporting systems. This work shows that the barriers to establishing epidemiology systems are no longer scientific and technical but rather administrative, involving questions of patient privacy and data ownership. We have demonstrated here that these barriers can be overcome. This first look at the resulting data stream suggests that Syndromic Trends will be able to provide high-resolution analysis of circulating respiratory pathogens and may aid in the detection of new outbreaks.
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Affiliation(s)
| | - Christine C Ginocchio
- BioFire Diagnostics, Salt Lake City, UT, United States.,bioMérieux USA, Durham, NC, United States.,Hofstra Northwell School of Medicine, Hempstead, NY, United States
| | | | - Frederick S Nolte
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Per H Gesteland
- Departments of Pediatrics and Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Amy Leber
- Laboratory of Microbiology and Immunoserology, Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, United States
| | - Diane Janowiak
- Department of Lab Operations, South Bend Medical Foundation, South Bend, IN, United States
| | - Virginia Donovan
- Department of Pathology, New York University Winthrop Hospital, Mineola, NY, United States
| | - Jennifer Dien Bard
- Clinical Microbiology and Virology Laboratory, Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA, United States.,Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Silvia Spitzer
- Molecular Genetics Laboratory, Stony Brook University Medical Center, Stony Brook, NY, United States
| | - Kathleen A Stellrecht
- Department of Pathology and Laboratory Medicine, Albany Medical Center, Albany, NY, United States
| | - Hossein Salimnia
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Rangaraj Selvarangan
- Clinical Microbiology, Virology and Molecular Infectious Diseases Laboratory, Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, United States
| | - Stefan Juretschko
- Department of Pathology and Laboratory Medicine, Division of Infectious Disease Diagnostics, Northwell Health, Lake Success, NY, United States
| | - Judy A Daly
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Jeremy C Wallentine
- Department of Pathology, Intermountain Medical Center, Murray, UT, United States
| | - Kristy Lindsey
- Laboratory of Microbiology, University of Massachusetts Medical School-Baystate, Springfield, MA, United States
| | - Franklin Moore
- Laboratory of Microbiology, University of Massachusetts Medical School-Baystate, Springfield, MA, United States
| | - Sharon L Reed
- Department of Pathology and Medicine, Divisions of Clinical Pathology and Infectious Diseases, UC San Diego, San Diego, CA, United States
| | - Maria Aguero-Rosenfeld
- Department of Clinical Laboratories, New York University Langone Health, New York, NY, United States
| | - Paul D Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Gregory A Storch
- Department of Pediatrics, Washington University, St. Louis, MO, United States
| | - Steve J Melnick
- Department of Pathology and Clinical Laboratories, Nicklaus Children's Hospital, Miami, FL, United States
| | - Christine C Robinson
- Department of Pathology and Laboratory Medicine, Microbiology/Virology Laboratory Section, Children's Hospital Colorado, Aurora, CO, United States
| | - Jennifer F Meredith
- Department of Laboratory Services, Microbiology Section, Greenville Health System, Greenville, SC, United States
| | | | | | - Jay D Jones
- BioFire Diagnostics, Salt Lake City, UT, United States
| | | | - Benjamin M Althouse
- University of Washington, Seattle, WA, United States.,New Mexico State University, Las Cruces, NM, United States
| | | | - Bradley A Malin
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN, United States
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Chan M, Koo SH, Jiang B, Lim PQ, Tan TY. Comparison of the Biofire FilmArray Respiratory Panel, Seegene AnyplexII RV16, and Argene for the detection of respiratory viruses. J Clin Virol 2018; 106:13-17. [PMID: 30007137 PMCID: PMC7185839 DOI: 10.1016/j.jcv.2018.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 05/18/2018] [Accepted: 07/05/2018] [Indexed: 01/24/2023]
Abstract
BACKGROUND Respiratory infections are common reasons for hospital admission, and are associated with enormous economic burden due to significant morbidity and mortality. The wide spectrum of microbial agents underlying the pathology renders the diagnosis of respiratory infections challenging. Molecular diagnostics offer an advantage to the current serological and culture-based methods in terms of sensitivity, coverage, hands-on time, and time to results. OBJECTIVES This study aimed to compare the clinical performance of three commercial kits for respiratory viral detection. STUDY DESIGN The performance of FilmArray Respiratory Panel, AnyplexII RV16, and Argene was compared using clinical respiratory samples (n = 224, comprising 189 nasopharyngeal swabs in Universal Transport Medium (UTM) and 35 endotracheal aspirates), based on common overlapping targets across the platforms. Influenza A "equivocal" and "no-subtype" samples by FilmArray were further compared to a laboratory-developed Influenza A/B test. RESULTS AND CONCLUSIONS The overall performance of all three platforms appeared to be comparable with regards to sensitivities (95.8-97.9%) and specificities (96.1-98.0%), detection of coinfections, and distinguishment of influenza from non-influenza cases. "Equivocal" and "no-subtype" samples by FilmArray mostly represented weak Influenza A by laboratory-developed test. Lower respiratory tract samples had comparable final-run success-rates and discordant-rates as compared to UTM. Coronavirus HKU1, which was not targeted by AnyplexII RV16, were detected as OC43. The expected test volume would be the main determinant for the selection of platform. Among the platforms, the FilmArray is the most automated but is of the lowest-throughput and has the highest reagent cost.
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Affiliation(s)
- Maurice Chan
- Department of Laboratory Medicine, Changi General Hospital, Singapore
| | - Seok Hwee Koo
- Clinical Trials & Research Unit, Changi General Hospital, Singapore
| | - Boran Jiang
- Department of Laboratory Medicine, Changi General Hospital, Singapore
| | - Pei Qi Lim
- Clinical Trials & Research Unit, Changi General Hospital, Singapore
| | - Thean Yen Tan
- Department of Laboratory Medicine, Changi General Hospital, Singapore.
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78
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Dou Y, Li Y, Ma C, Zhu H, Du J, Liu H, Liu Q, Chen R, Tan Y. Rapid diagnosis of human adenovirus B, C and E in the respiratory tract using multiplex quantitative polymerase chain reaction. Mol Med Rep 2018; 18:2889-2897. [PMID: 30015894 PMCID: PMC6102718 DOI: 10.3892/mmr.2018.9253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/28/2018] [Indexed: 01/10/2023] Open
Abstract
Human adenovirus (HAdV) is increasingly recognized as a major cause of human respiratory tract viral infections. Its outbreaks and epidemics in various populations resulted in considerable morbidity and mortality. Therefore, a rapid and specific assay for HAdV in clinical samples is of crucial importance to diagnosing HAdV infections. The present study aimed to develop and evaluate a multiplex quantitative polymerase chain reaction (qPCR) assay for the rapid detection and accurate quantification of HAdV B, C and E. The lower limit of detection for this assay was two genomic copies per reaction, and quantitative linearity ranged from 2 to 2×106 copies per reaction of the input viral DNA. Furthermore, 3,160 throat swab samples that tested HAdV negative by the immunofluorescence assay were collected and retested using the multiplex qPCR assay. The results showed that 2,906 samples were HAdV negative and the other 254 samples were HAdV positive. The HAdV species identified included B (184 samples), C (51 samples), and E (39 samples). Among the three HAdV species, HAdV B and E were detected from 8 samples, and HAdV C and E were detected from other 12 samples. The overall results demonstrated that the sensitivity and specificity of the proposed assay were 100% (254/254) and 99.6% (2894/2906), respectively. From the perspective of routine clinical diagnosis, this assay represented a rapid (≤1.5 h) and economic strategy, and had the potential to be used for the rapid and accurate diagnosis of human respiratory infections caused by HAdV B, C and E.
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Affiliation(s)
- Yuhong Dou
- Department of Clinical Laboratory, Shenzhen Shajing Hospital Affiliated of Guangzhou Medical University, Shenzhen, Guangdong 518104, P.R. China
| | - Yuxia Li
- Department of Clinical Laboratory, Shenzhen Shajing Hospital Affiliated of Guangzhou Medical University, Shenzhen, Guangdong 518104, P.R. China
| | - Caifeng Ma
- Department of Clinical Laboratory, Shenzhen Shajing Hospital Affiliated of Guangzhou Medical University, Shenzhen, Guangdong 518104, P.R. China
| | - Huijun Zhu
- Department of Clinical Laboratory, Shenzhen Shajing Hospital Affiliated of Guangzhou Medical University, Shenzhen, Guangdong 518104, P.R. China
| | - Jikun Du
- Department of Clinical Laboratory, Shenzhen Shajing Hospital Affiliated of Guangzhou Medical University, Shenzhen, Guangdong 518104, P.R. China
| | - Helu Liu
- Department of Clinical Laboratory, Shenzhen Shajing Hospital Affiliated of Guangzhou Medical University, Shenzhen, Guangdong 518104, P.R. China
| | - Qiong Liu
- Department of Clinical Laboratory, Shenzhen Shajing Hospital Affiliated of Guangzhou Medical University, Shenzhen, Guangdong 518104, P.R. China
| | - Rui Chen
- Department of Clinical Laboratory, The Second People's Hospital of Futian District, Shenzhen, Guangdong 518049, P.R. China
| | - Ying Tan
- Department of Biology, South University of Science and Technology, Shenzhen, Guangdong 518055, P.R. China
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79
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A Hogan C, Caya C, Papenburg J. Rapid and simple molecular tests for the detection of respiratory syncytial virus: a review. Expert Rev Mol Diagn 2018; 18:617-629. [PMID: 29890085 DOI: 10.1080/14737159.2018.1487293] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION Respiratory syncytial virus (RSV) is a leading cause of acute respiratory infections. The clinical manifestations of RSV are indistinguishable from other etiologies of acute respiratory infection. Therefore, accurate and timely laboratory testing is needed to impact clinical management. There are now multiple rapid, low-complexity, commercially available assays for RSV. These tests present significant performance advantages compared to older antigen detection tests. Accurate and rapid diagnosis of RSV has the potential for enabling timely cessation of unnecessary antibiotics and implementation of good infection control practices. Furthermore, a recently approved RSV diagnostic assay can reduce the test turnaround time to 13 min or less. Areas covered: The authors aim to review the importance of rapid and accurate testing for RSV and will describe the available molecular RSV diagnostic assays approved for use at the point-of-care. Expert commentary: Further independent evaluations are needed to confirm that the accuracy of the low-complexity assays is indeed similar to reverse transcriptase polymerase chain reaction across the age spectrum, and in immunosuppressed hosts. In the future, the challenge will be to achieve a balance between increasingly sophisticated multiplex diagnostic platforms and tests that are sufficiently simple to be used at the point-of-care.
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Affiliation(s)
- Catherine A Hogan
- a Division of Infectious Diseases, Department of Microbiology , McGill University Health Centre , Montréal , Canada.,b Department of Pathology , Stanford University School of Medicine , Stanford , CA , USA.,c Clinical Microbiology Laboratory , Stanford University Medical Center , Palo Alto , CA , USA
| | - Chelsea Caya
- d Infectious Diseases and Immunity in Global Health Program , Research Institute of the McGill University Health Centre , CA , USA
| | - Jesse Papenburg
- e Division of Pediatric Infectious Diseases, Departments of Microbiology and Pediatrics , McGill University Health Centre , CA , USA
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80
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Xu L, Jiang X, Zhu Y, Duan Y, Huang T, Huang Z, Liu C, Xu B, Xie Z. A Multiplex Asymmetric Reverse Transcription-PCR Assay Combined With an Electrochemical DNA Sensor for Simultaneously Detecting and Subtyping Influenza A Viruses. Front Microbiol 2018; 9:1405. [PMID: 30013525 PMCID: PMC6036258 DOI: 10.3389/fmicb.2018.01405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/07/2018] [Indexed: 12/21/2022] Open
Abstract
The reliable and rapid detection of viral pathogens that cause respiratory infections provide physicians several advantages in treating patients and managing outbreaks. The Luminex respiratory virus panel (RVP) assay has been shown to be comparable to or superior to culture/direct fluorescent-antibody assays (DFAs) and nucleic acid tests that are used to diagnose respiratory viral infections. We developed a multiplex asymmetric reverse transcription (RT)-PCR assay that can simultaneously differentiate all influenza A virus epidemic subtypes. The amplified products were hybridized with an electrochemical DNA sensor, and the results were automatically acquired. The limits of detection (LoDs) of both the Luminex RVP assay and the multiplex RT-PCR-electrochemical DNA sensor were 101 TCID50 for H1N1 virus and 102 TCID50 for H3N2 virus. The specificity assessment of the multiplex RT-PCR-electrochemical DNA sensor showed no cross-reactivity among different influenza A subtypes or with other non-influenza respiratory viruses. In total, 3098 respiratory tract specimens collected from padiatric patients diagnosed with pneumonia were tested. More than half (43, 53.75%) of the specimens positive for influenza A viruses could not be further subtyped using the Luminex RVP assay. Among the remaining 15 specimens that were not subtyped, not degraded, and in sufficient amounts for the multiplex RT-PCR-electrochemical DNA sensor test, all (100%) were H3N2 positive. Therefore, the sensitivity of the Luminex RVP assay for influenza A virus was 46.25%, whereas the sensitivity of the multiplex RT-PCR-electrochemical DNA sensor for the clinical H1N1 and H3N2 specimens was 100%. The sensitivities of the multiplex RT-PCR-electrochemical DNA sensor for the avian H5N1, H5N6, H9N2, and H10N8 viruses were 100%, whereas that for H7N9 virus was 85.19%. We conclude that the multiplex RT-PCR-electrochemical DNA sensor is a reliable method for the rapid and accurate detection of highly variable influenza A viruses in respiratory infections with greater detection sensitivity than that of the Luminex xTAG assay. The high mutation rate of influenza A viruses, particularly H3N2 during the 2014 to 2016 epidemic seasons, has a strong impact on diagnosis. A study involving more positive specimens from all influenza A virus epidemic subtypes is required to fully assess the performance of the assay.
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Affiliation(s)
- Lili Xu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Xiwen Jiang
- DAAN Gene Co., Ltd., Sun Yat-sen University, Guangzhou, China
- The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, China
| | - Yun Zhu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Yali Duan
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Taosheng Huang
- DAAN Gene Co., Ltd., Sun Yat-sen University, Guangzhou, China
- The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, China
| | - Zhiwen Huang
- DAAN Gene Co., Ltd., Sun Yat-sen University, Guangzhou, China
- The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, China
| | - Chunyan Liu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Baoping Xu
- National Clinical Research Center for Respiratory Diseases, Department of Respiratory, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
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81
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Diaz-Decaro JD, Green NM, Godwin HA. Critical evaluation of FDA-approved respiratory multiplex assays for public health surveillance. Expert Rev Mol Diagn 2018; 18:631-643. [PMID: 29886764 PMCID: PMC7103694 DOI: 10.1080/14737159.2018.1487294] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Introduction: Clinical management and identification of respiratory diseases has become more rapid and increasingly specific due to widespread use of PCR(polymerase chain reaction) multiplex technologies. Although significantly improving clinical diagnosis, multiplexed PCR assays could have a greater impact on local and global disease surveillance. The authors wish to propose methods of evaluating respiratory multiplex assays to maximize diagnostic yields specifically for surveillance efforts. Areas covered: The authors review multiplexed assays and critically assess what barriers have limited these assays for disease surveillance and how these barriers might be addressed. The manuscript focuses specifically on the case study of using multiplexed assays for surveillance of respiratory pathogens. The authors also provide a method of validation of specific surveillance measures. Expert commentary: Current commercially available respiratory multiplex PCR assays are widely used for clinical diagnosis; however, specific barriers have limited their use for surveillance. Key barriers include differences in testing phase requirements and diagnostic performance evaluation. In this work the authors clarify phase testing requirements and introduce unique diagnostic performance measures that simplify the use of these assays on a per target basis for disease surveillance.
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Affiliation(s)
- John D Diaz-Decaro
- a Los Angeles County Public Health Laboratories , Research & Training Unit , Downey , CA , USA.,b UCLA Fielding School of Public Health , Environmental Health Sciences , Los Angeles , CA , USA
| | - Nicole M Green
- a Los Angeles County Public Health Laboratories , Research & Training Unit , Downey , CA , USA
| | - Hilary A Godwin
- b UCLA Fielding School of Public Health , Environmental Health Sciences , Los Angeles , CA , USA
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82
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Walter JM, Wunderink RG. Testing for Respiratory Viruses in Adults With Severe Lower Respiratory Infection. Chest 2018; 154:1213-1222. [PMID: 29908153 PMCID: PMC6224704 DOI: 10.1016/j.chest.2018.06.003] [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: 03/08/2018] [Revised: 05/29/2018] [Accepted: 06/04/2018] [Indexed: 12/31/2022] Open
Abstract
Viral pathogens are a common cause of severe lower respiratory tract infection in adults. Our ability to rapidly and accurately identify viral infections has dramatically improved as slow culture-based techniques have been largely replaced by multiplex high-throughput systems. Given these advances, reevaluation of the role of respiratory viral testing in adults presenting with lower respiratory tract infection is important. This article reviews the potential benefits of testing, provides an overview of the most commonly used diagnostic techniques, and considers whether current evidence supports routine testing.
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Affiliation(s)
- James M Walter
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
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83
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Hassibi A, Ebert J, Bolouki S, Anemogiannis A, Mazarei G, Li Y, Johnson KA, Van T, Mantina P, Gharooni T, Jirage K, Pei L, Sinha R, Manickam A, Zia A, Naraghi-Arani P, Schoolnik G, Kuimelis RG. An array-based melt curve analysis method for the identification and classification of closely related pathogen strains. Biol Methods Protoc 2018; 3:bpy005. [PMID: 32161799 PMCID: PMC6994036 DOI: 10.1093/biomethods/bpy005] [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: 01/17/2018] [Revised: 04/23/2018] [Accepted: 05/08/2018] [Indexed: 11/13/2022] Open
Abstract
PCR-based techniques are widely used to identify disease causing bacterial and viral pathogens, especially in point-of-care or near-patient clinical settings that require rapid results and sample-to-answer workflows. However, such techniques often fail to differentiate between closely related species that have highly variable genomes. Here, a homogenous (closed-tube) pathogen identification and classification method is described that combines PCR amplification, array-based amplicon sequence verification, and real-time detection using an inverse fluorescence fluorescence-resonance energy transfer technique. The amplification is designed to satisfy the inclusivity criteria and create ssDNA amplicons, bearing a nonradiating quencher moiety at the 5'-terminus, for all the related species. The array includes fluorescent-labeled probes which preferentially capture the variants of the amplicons and classify them through solid-phase thermal denaturing (melt curve) analysis. Systematic primer and probe design algorithms and empirical validation methods are presented and successfully applied to the challenging example of identification of, and differentiation between, closely related human rhinovirus and human enterovirus strains.
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Affiliation(s)
- Arjang Hassibi
- InSilixa, Inc., 1000 Hamlin Court, Sunnyvale, CA 94089, USA
| | - Jessica Ebert
- InSilixa, Inc., 1000 Hamlin Court, Sunnyvale, CA 94089, USA
| | - Sara Bolouki
- InSilixa, Inc., 1000 Hamlin Court, Sunnyvale, CA 94089, USA
| | | | | | - Yuan Li
- InSilixa, Inc., 1000 Hamlin Court, Sunnyvale, CA 94089, USA
| | | | - Tran Van
- InSilixa, Inc., 1000 Hamlin Court, Sunnyvale, CA 94089, USA
| | | | | | - Kshama Jirage
- InSilixa, Inc., 1000 Hamlin Court, Sunnyvale, CA 94089, USA
| | - Lei Pei
- InSilixa, Inc., 1000 Hamlin Court, Sunnyvale, CA 94089, USA
| | - Ruma Sinha
- InSilixa, Inc., 1000 Hamlin Court, Sunnyvale, CA 94089, USA
| | - Arun Manickam
- InSilixa, Inc., 1000 Hamlin Court, Sunnyvale, CA 94089, USA
| | - Amin Zia
- InSilixa, Inc., 1000 Hamlin Court, Sunnyvale, CA 94089, USA
| | | | - Gary Schoolnik
- InSilixa, Inc., 1000 Hamlin Court, Sunnyvale, CA 94089, USA
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84
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Kaku N, Hashiguchi K, Iwanaga Y, Akamatsu N, Matsuda J, Kosai K, Uno N, Morinaga Y, Kitazaki T, Hasegawa H, Miyazaki T, Fukuda M, Izumikawa K, Mukae H, Yanagihara K. Evaluation of FilmArray respiratory panel multiplex polymerase chain reaction assay for detection of pathogens in adult outpatients with acute respiratory tract infection. J Infect Chemother 2018; 24:734-738. [PMID: 29895452 PMCID: PMC7128419 DOI: 10.1016/j.jiac.2018.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 05/01/2018] [Accepted: 05/16/2018] [Indexed: 12/27/2022]
Abstract
Although viruses are the major pathogen that causes upper respiratory tract infection (URTI) and acute bronchitis, antibiotics have been prescribed. This was a prospective observational study in influenza epidemics that enrolled adult outpatients who visited a hospital with respiratory tract infection symptoms. In this study, we evaluated the usefulness of FilmArray respiratory panel (RP). Fifty patients were enrolled. FilmArray RP detected the pathogens in 28 patients. The common pathogens were influenza virus (n = 14), respiratory syncytial virus (n = 6), and human rhinovirus (n = 6). Of the 14 patients with influenza virus, 6 were negative for the antigen test. The physicians diagnosed and treated the patients without the result of FilmArray in this study. Of the patients with positive FilmArray RP, 9 were treated with antibiotics; however, bacteria were detected in only 3 patients. By implementing FilmArray RP, URTI and acute bronchitis would be precisely diagnosed, and inappropriate use of antibiotics can be reduced.
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Affiliation(s)
- Norihito Kaku
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.
| | - Kohji Hashiguchi
- Department of Respiratory Medicine, Japanese Red Cross Nagasaki Genbaku Hospital, Nagasaki, Japan
| | - Yuki Iwanaga
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Norihiko Akamatsu
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Junichi Matsuda
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kosuke Kosai
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Naoki Uno
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yoshitomo Morinaga
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takeshi Kitazaki
- Department of Respiratory Medicine, Japanese Red Cross Nagasaki Genbaku Hospital, Nagasaki, Japan
| | - Hiroo Hasegawa
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Taiga Miyazaki
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Masaaki Fukuda
- Department of Respiratory Medicine, Japanese Red Cross Nagasaki Genbaku Hospital, Nagasaki, Japan
| | - Koichi Izumikawa
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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85
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Kodama F, Nace DA, Jump RLP. Respiratory Syncytial Virus and Other Noninfluenza Respiratory Viruses in Older Adults. Infect Dis Clin North Am 2018; 31:767-790. [PMID: 29079159 PMCID: PMC5846091 DOI: 10.1016/j.idc.2017.07.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Fumihiro Kodama
- Department of Infectious Diseases, Sapporo City General Hospital, 13 Chome 1-1, Kita 11 Jonishi, Chuo-ku, Sapporo, Hokkaido 060-8604, Japan
| | - David A Nace
- Division of Geriatric Medicine, Department of Medicine, University of Pittsburgh, 3471 Fifth Avenue, Kaufmann Building Suite 500, Pittsburgh, PA 15213, USA
| | - Robin L P Jump
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH 44195-5029, USA; Geriatric Research, Education, and Clinical Center (GRECC), Specialty Care Center of Innovation, Louis Stokes Cleveland Veterans Affairs Medical Center, 111C(W), 10701 East Boulevard, Cleveland, OH 44106, USA.
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86
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Ko DH, Kim HS, Hyun J, Kim HS, Kim JS, Park KU, Song W. Comparison of the Luminex xTAG Respiratory Viral Panel Fast v2 Assay With Anyplex II RV16 Detection Kit and AdvanSure RV Real-Time RT-PCR Assay for the Detection of Respiratory Viruses. Ann Lab Med 2018. [PMID: 28643489 PMCID: PMC5500739 DOI: 10.3343/alm.2017.37.5.408] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background The accurate and rapid identification of the causative viruses is important for the timely diagnosis and management of respiratory infections. Multiplex molecular diagnostic techniques have been widely adopted to detect respiratory viruses. We compared the results of a newly upgraded, multiplex, molecular bead-based respiratory viral panel (RVP) assay with the results of Anyplex II RV16 detection kit and AdvanSure RV real-time RT-PCR assay. Methods We tested 254 respiratory specimens and cultured viral strains using the Luminex xTAG RVP Fast v2 assay (Luminex Molecular Diagnostics, Canada) and Anyplex II RV16 detection kit and compared the results. Specimens showing discordant results between the two assays were tested with a AdvanSure RV real-time RT-PCR assay. Results Of the 254 respiratory specimens, there was total agreement in the results between the xTAG RVP Fast v2 assay and the other real-time PCR assay in 94.1–100% of the specimens. The agreement levels were relatively low (94.1–97.6%) for specimens of adenovirus, coronavirus NL63, and parainfluenza type 3. In comparison to the other assay, the xTAG RVP Fast v2 assay detected a higher number of parainfluenza type 3 (4 cases) and metapneumovirus (9 cases). Conclusions The xTAG RVP Fast v2 assay showed comparable capabilities compared with the other assays; it will be useful for identifying respiratory viral infections in patients with respiratory symptoms. Clinicians should be aware of the characteristics of the assays they use, since different assays show different detectability for each virus.
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Affiliation(s)
- Dae Hyun Ko
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea.
| | - Jungwon Hyun
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Han Sung Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Jae Seok Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
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Rowan NR, Wang EW, Kanaan A, Sahu N, Williams JV, Phillips CD, Lee SE. Respiratory viral detection in the paranasal sinuses of patients with cystic fibrosis. Am J Rhinol Allergy 2018; 31:105-108. [PMID: 28452706 DOI: 10.2500/ajra.2017.31.4422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Pulmonary colonization with antibiotic-resistant organisms in patients with cystic fibrosis (CF) is often preceded by upper-airway infections. Although there is a well-described relationship between pulmonary respiratory viral infections and overall disease progression of CF, the pathogenicity of respiratory viral infections in the paranasal sinuses of patients with CF remains unknown. With recent advances in respiratory virus detection techniques, this study sought to detect the presence of respiratory viruses in the paranasal sinuses of patients with CF in comparison with healthy controls and to correlate the viral presence with clinical measures of sinonasal disease. METHODS This prospective individual cohort study compared 24 patients with CF with 14 healthy controls. Basic demographics, clinical measures of disease and respiratory viral screens (commercial multiplex) obtained directly from the paranasal sinuses were compared between the two groups. RESULTS Respiratory viruses were detected in 33% of patients with CF (8/24) compared with 0% of the healthy controls (0/14) (p = 0.017). Respiratory viruses were only detected during the winter months, and the most commonly identified were influenza A and human rhinovirus strains. There was no statistical difference in the 22-Item Sino-Nasal Outcome Test (SNOT-22) scores (p = 0.93) or modified Lund-Kennedy scores (p = 0.74) between patients with CF with a positive viral test and those without a positive result. CONCLUSIONS Respiratory viral detection is more commonly detected in the paranasal sinuses of patients with CF compared with healthy controls. Although respiratory viral presence did not correlate with a worse clinical severity of sinonasal disease, these findings may provide insight into the pathophysiology of CF and open new avenues for potential targeted therapy.
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Affiliation(s)
- Nicholas R Rowan
- Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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88
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Bruning AHL, Leeflang MMG, Vos JMBW, Spijker R, de Jong MD, Wolthers KC, Pajkrt D. Rapid Tests for Influenza, Respiratory Syncytial Virus, and Other Respiratory Viruses: A Systematic Review and Meta-analysis. Clin Infect Dis 2018; 65:1026-1032. [PMID: 28520858 PMCID: PMC7108103 DOI: 10.1093/cid/cix461] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/13/2017] [Indexed: 01/18/2023] Open
Abstract
Rapid diagnosis of respiratory virus infections contributes to patient care. This systematic review evaluates the diagnostic accuracy of rapid tests for the detection of respiratory viruses. We searched Medline and EMBASE for studies evaluating these tests against polymerase chain reaction as the reference standard. Of 179 studies included, 134 evaluated rapid tests for influenza viruses, 32 for respiratory syncytial virus (RSV), and 13 for other respiratory viruses. We used the bivariate random effects model for quantitative meta-analysis of the results. Most tests detected only influenza viruses or RSV. Summary sensitivity and specificity estimates of tests for influenza were 61.1% and 98.9%. For RSV, summary sensitivity was 75.3%, and specificity, 98.7%. We assessed the quality of studies using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) checklist. Because of incomplete reporting, the risk of bias was often unclear. Despite their intended use at the point of care, 26.3% of tests were evaluated in a laboratory setting. Although newly developed tests seem more sensitive, high-quality evaluations of these tests are lacking.
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Affiliation(s)
| | | | - Johanna M B W Vos
- Department of Pediatric Infectious Diseases, Emma Children's Hospital
| | | | - Menno D de Jong
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, The Netherlands
| | - Katja C Wolthers
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, The Netherlands
| | - Dasja Pajkrt
- Department of Pediatric Infectious Diseases, Emma Children's Hospital
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89
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Barnes SR, Wansaula Z, Herrick K, Oren E, Ernst K, Olsen SJ, Casal MG. Mortality estimates among adult patients with severe acute respiratory infections from two sentinel hospitals in southern Arizona, United States, 2010-2014. BMC Infect Dis 2018; 18:78. [PMID: 29433471 PMCID: PMC5809880 DOI: 10.1186/s12879-018-2984-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 01/31/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND From October 2010 through February 2016, Arizona conducted surveillance for severe acute respiratory infections (SARI) among adults hospitalized in the Arizona-Mexico border region. There are few accurate mortality estimates in SARI patients, particularly in adults ≥ 65 years old. The purpose of this study was to generate mortality estimates among SARI patients that include deaths occurring shortly after hospital discharge and identify risk factors for mortality. METHODS Patients admitted to two sentinel hospitals between 2010 and 2014 who met the SARI case definition were enrolled. Demographic data were used to link SARI patients to Arizona death certificates. Mortality within 30 days after the date of admission was calculated and risk factors were identified using logistic regression models. RESULTS Among 258 SARI patients, 47% were females, 51% were white, non-Hispanic and 39% were Hispanic. The median age was 63 years (range, 19 to 97 years) and 80% had one or more pre-existing health condition; 9% died in hospital. Mortality increased to 12% (30/258, 30% increase) when electronic vital records and a 30-day post-hospitalization time frame were used. Being age ≥ 65 years (OR = 4.0; 95% CI: 1.6-9.9) and having an intensive care unit admission (OR = 7.4; 95% CI: 3.0-17.9) were independently associated with mortality. CONCLUSION The use of electronic vital records increased SARI-associated mortality estimates by 30%. These findings may help guide prevention and treatment measures, particularly in high-risk persons in this highly fluid border population.
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Affiliation(s)
- Steve R. Barnes
- Arizona Department of Health Services, Border Infectious Disease Surveillance Program, 400 West Congress, Suite 116, Tucson, AZ 85701 USA
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N Martin Ave, Tucson, AZ 85724 USA
| | - Zimy Wansaula
- Arizona Department of Health Services, Border Infectious Disease Surveillance Program, 400 West Congress, Suite 116, Tucson, AZ 85701 USA
| | - Kristen Herrick
- Arizona Department of Health Services, Office of Infectious Disease Services, 150 N 18th Ave Phoenix, Phoenix, AZ 85007 USA
| | - Eyal Oren
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N Martin Ave, Tucson, AZ 85724 USA
| | - Kacey Ernst
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N Martin Ave, Tucson, AZ 85724 USA
| | - Sonja J. Olsen
- Influenza Division, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30329-4027 USA
| | - Mariana G. Casal
- Arizona Department of Health Services, Border Infectious Disease Surveillance Program, 400 West Congress, Suite 116, Tucson, AZ 85701 USA
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90
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Abstract
Human metapneumovirus (HMPV) is a leading cause of acute respiratory infection, particularly in children, immunocompromised patients, and the elderly. HMPV, which is closely related to avian metapneumovirus subtype C, has circulated for at least 65 years, and nearly every child will be infected with HMPV by the age of 5. However, immunity is incomplete, and re-infections occur throughout adult life. Symptoms are similar to those of other respiratory viral infections, ranging from mild (cough, rhinorrhea, and fever) to more severe (bronchiolitis and pneumonia). The preferred method for diagnosis is reverse transcription-polymerase chain reaction as HMPV is difficult to culture. Although there have been many advances made in the past 16 years since its discovery, there are still no US Food and Drug Administration-approved antivirals or vaccines available to treat HMPV. Both small animal and non-human primate models have been established for the study of HMPV. This review will focus on the epidemiology, transmission, and clinical manifestations in humans as well as the animal models of HMPV pathogenesis and host immune response.
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Affiliation(s)
- Nazly Shafagati
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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91
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Pernica J, Harman S, Kam A, Bailey J, Carciumaru R, Khan S, Fulford M, Thabane L, Slinger R, Main C, Smieja M, Loeb M. Short-course antimicrobial therapy for paediatric respiratory infections (SAFER): study protocol for a randomized controlled trial. Trials 2018; 19:83. [PMID: 29391051 PMCID: PMC5796490 DOI: 10.1186/s13063-018-2457-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 01/04/2018] [Indexed: 12/17/2022] Open
Abstract
Background Community-acquired pneumonia (CAP) is commonly diagnosed in children. The Infectious Disease Society of America guidelines recommend 10 days of high-dose amoxicillin for the treatment of non-severe CAP but 5-day “short course” therapy may be just as effective. Randomized trials in adults have already demonstrated non-inferiority of 5-day short-course treatment for adults hospitalized with severe CAP and for adults with mild CAP treated as outpatients. Minimizing exposure to antimicrobials is desirable to avoid harms including diarrhoea, rashes, severe allergic reactions, increased circulating antimicrobial resistance, and microbiome disruption. Methods The objective of this multicentre, randomized, non-inferiority, controlled trial is to investigate whether 5 days of high-dose amoxicillin is associated with lower rates of clinical cure 14–21 days later as compared to 10 days of high-dose amoxicillin, the reference standard. Recruitment and enrolment will occur in the emergency departments of McMaster Children’s Hospital and the Children’s Hospital of Eastern Ontario. All children in the study will receive 5 days of amoxicillin after which point they will receive either 5 days of a different formulation of amoxicillin or a placebo. Assuming a clinical failure rate of 5% in the reference arm, a non-inferiority margin of 7.5%, one-sided alpha set at 0.025 and power of 0.80, 270 participants will be required. Participants from a previous feasibility study (n = 60) will be rolled over into the current study. We will be performing multiplex respiratory virus molecular testing, quantification of nasopharyngeal pneumococcal genomic loads, salivary inflammatory marker testing, and faecal microbiome profiling on participants. Discussion This is a pragmatic study seeking to provide high-quality evidence for front-line physicians evaluating children presenting with mild CAP in North American emergency departments in the post-13-valent pneumococcal, conjugate vaccine era. High-quality evidence supporting the non-inferiority of short-course therapy for non-severe paediatric CAP should be generated prior to making changes to established guidelines. Trial registration ClinicalTrials.gov, NCT02380352. Registered on 2 March 2015. Electronic supplementary material The online version of this article (10.1186/s13063-018-2457-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jeffrey Pernica
- Division of Infectious Disease, Department of Pediatrics, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.
| | - Stuart Harman
- Division of Emergency Medicine, Department of Pediatrics, University of Ottawa, 401 Smyth Road, Ottawa, ON, K1H 8L1, Canada
| | - April Kam
- Division of Emergency Medicine, Department of Pediatrics, McMaster University, Hamilton, ON, Canada
| | - Jacob Bailey
- Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | | | - Sarah Khan
- Division of Infectious Disease, Department of Pediatrics, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Martha Fulford
- Division of Infectious Disease, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Lehana Thabane
- Department of Health Research Methods, Evidence, and Impact, Hamilton, ON, Canada
| | - Robert Slinger
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Cheryl Main
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Marek Smieja
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Mark Loeb
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
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92
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Aliabadi N, Messacar K, Pastula DM, Robinson CC, Leshem E, Sejvar JJ, Nix WA, Oberste MS, Feikin DR, Dominguez SR. Enterovirus D68 Infection in Children with Acute Flaccid Myelitis, Colorado, USA, 2014. Emerg Infect Dis 2018; 22:1387-94. [PMID: 27434186 PMCID: PMC4982171 DOI: 10.3201/eid2208.151949] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Odds of this viral infection in the nasopharynx were 10 times greater for children with this condition than for controls. During August 8, 2014–October 14, 2014, a total of 11 children with acute flaccid myelitis and distinctive neuroimaging changes were identified near Denver, Colorado, USA. A respiratory prodrome was experienced by 10, and nasopharyngeal specimens were positive for enterovirus D68 (EV-D68) for 4. To determine whether an association exists between EV-D68 infection and acute flaccid myelitis, we conducted a retrospective case–control study comparing these patients with 2 groups of outpatient control children (1 group tested for acute respiratory illness and 1 for Bordetella pertussis infection). Adjusted analyses indicated that, for children with acute flaccid myelitis, the odds of having EV-D68 infection were 10.3 times greater than for those tested for acute respiratory infection and 4.5 times greater than for those tested for B. pertussis infection. No statistical association was seen between acute flaccid myelitis and non–EV-D68 enterovirus or rhinovirus infection. These findings support an association between EV-D68 infection and acute flaccid myelitis.
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93
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Abstract
PURPOSE OF REVIEW We aim to review the epidemiology of respiratory viral infections and the strengths and limitations of multiplex respiratory pathogen panels that are currently available along with their respective features and differences. RECENT FINDINGS We give particular emphasis to the pathogens included on each test and evaluate their performance in the hospital setting. SUMMARY We conclude with a discussion on the evidence for the clinical utility of respiratory pathogen multiplex panels in hospitalized patients, including the potential for coinfection with viral and bacterial pathogens.
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94
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New Technologies for the Diagnosis of Infection. DIAGNOSTIC PATHOLOGY OF INFECTIOUS DISEASE 2018. [PMCID: PMC7152403 DOI: 10.1016/b978-0-323-44585-6.00006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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95
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96
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Nolte FS. Molecular Microbiology. PRINCIPLES AND APPLICATIONS OF MOLECULAR DIAGNOSTICS 2018. [PMCID: PMC7150357 DOI: 10.1016/b978-0-12-816061-9.00005-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background Nucleic acid (NA) amplification techniques are now commonly used to diagnose and manage patients with infectious diseases. The growth in the number of Food and Drug Administration–approved test kits and analyte-specific reagents has facilitated the use of this technology in clinical laboratories. Technological advances in NA amplification techniques, automation, NA sequencing, and multiplex analysis have reinvigorated the field and created new opportunities for growth. Simple, sample-in, answer-out molecular test systems are now widely available that can be deployed in a variety of laboratory and clinical settings. Molecular microbiology remains the leading area in molecular pathology in terms of both the numbers of tests performed and clinical relevance. NA-based tests have reduced the dependency of the clinical microbiology laboratory on more traditional antigen detection and culture methods and created new opportunities for the laboratory to impact patient care. Content This chapter reviews NA testing as it applies to specific pathogens or infectious disease syndromes, with a focus on those diseases for which NA testing is now considered the standard of care and highlights the unique challenges and opportunities that these tests present for clinical laboratories.
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97
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Affiliation(s)
- Mark D Gonzalez
- Department of Pathology, Children's Healthcare of Atlanta, 1405 Clifton Road, Northeast, Atlanta, GA 30322, USA
| | - Erin McElvania
- Department of Pathology, NorthShore University Health System, 2650 Ridge Avenue, Evanston, IL 60201, USA.
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98
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Huang HS, Tsai CL, Chang J, Hsu TC, Lin S, Lee CC. Multiplex PCR system for the rapid diagnosis of respiratory virus infection: systematic review and meta-analysis. Clin Microbiol Infect 2017; 24:1055-1063. [PMID: 29208560 PMCID: PMC7128951 DOI: 10.1016/j.cmi.2017.11.018] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 11/16/2017] [Accepted: 11/22/2017] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To provide a summary of evidence for the diagnostic accuracies of three multiplex PCR systems (mPCRs)-BioFire FilmArray RP (FilmArray), Nanosphere Verigene RV+ test (Verigene RV+) and Hologic Gen-Probe Prodesse assays-on the detection of viral respiratory infections. METHODS A comprehensive search up to 1 July 2017 was conducted on Medline and Embase for studies that utilized FilmArray, Verigene RV+ and Prodesse for diagnosis of viral respiratory infections. A summary of diagnostic accuracies for the following five viruses were calculated: influenza A virus (FluA), influenza B virus, respiratory syncytial virus, human metapneumovirus and adenovirus. Hierarchical summary receiver operating curves were used for estimating the viral detection performance per assay. RESULTS Twenty studies of 5510 patient samples were eligible for analysis. Multiplex PCRs demonstrated high diagnostic accuracy, with area under the receiver operating characteristic curve (AUROC) equal to or more than 0.98 for all the above viruses except for adenovirus (AUROC 0.89). FilmArray, Verigene RV+ and ProFlu+ (the only Prodesse assay with enough data) demonstrated a summary sensitivity for FluA of 0.911 (95% confidence interval, 0.848-0.949), 0.949 (95% confidence interval, 0.882-0.979) and 0.954 (95% confidence interval, 0.871-0.985), respectively. The three mPCRs were comparable in terms of detection of FluA. CONCLUSIONS Point estimates calculated from eligible studies showed that the three mPCRs (FilmArray, Verigene RV+ and ProFlu+) are highly accurate and may provide important diagnostic information for early identification of respiratory virus infections. In patients with low pretest probability for FluA, these three mPCRs can predict a low possibility of infection and may justify withholding empirical antiviral treatments.
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Affiliation(s)
- H-S Huang
- Department of Medicine, College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Health Economics and Outcome Research Group, National Taiwan University Hospital, Taipei, Taiwan
| | - C-L Tsai
- Department of Medicine, College of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - J Chang
- Department of Gastroenterology, Nutrition, and Hepatology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - T-C Hsu
- Health Economics and Outcome Research Group, National Taiwan University Hospital, Taipei, Taiwan; Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - S Lin
- Health Economics and Outcome Research Group, National Taiwan University Hospital, Taipei, Taiwan; Industrial Engineering and Operations Research Department at the University of California, Berkeley, California, USA
| | - C-C Lee
- Health Economics and Outcome Research Group, National Taiwan University Hospital, Taipei, Taiwan; Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan.
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99
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Rennert H, Ramrattan G, Chen Z, McIntire P, Michaeel A, Khazanova A, Jenkins SG, Sipley J. Evaluation of a human adenovirus viral load assay using the Altona RealStar® PCR test. Diagn Microbiol Infect Dis 2017; 90:257-263. [PMID: 29433999 DOI: 10.1016/j.diagmicrobio.2017.11.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 10/29/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022]
Abstract
This study evaluated the performance of the Altona Diagnostics RealStar® Adenovirus Research Use Only (RUO) real-time PCR reagents for HAdV quantitation in plasma samples from immunodeficient patients. The assay was linear from 2.30-9.17 log10 copies/mL (coefficient of determination; R2=0.998) with limits of detection and quantification of 2.19 log10 and 2.30 log10 copies/mL (>95% positivity rate), respectively. Assay precision was highly reproducible with coefficients of variance ranging from 0% to 4.7%. A comparison of 66 matched samples showed good agreement (R2=0.845) between the Altona and the reference laboratory assay, with an average negative bias (-0.24 log10 copies/mL). Genotyping analysis demonstrated that HAdV species B and C accounted for 77% of the positive samples. A significant (≥0.9 log10) difference in quantitation between both tests was found for three HAdV types (HAdV types A12, B14 and F41). In conclusion, the Altona RealStar® test is a reliable and sensitive assay for HAdV DNA quantitation.
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Affiliation(s)
- Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY.
| | - Girish Ramrattan
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital, New York, NY
| | - Zhengming Chen
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, New York, NY
| | - Patrick McIntire
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital, New York, NY
| | - Alber Michaeel
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Anna Khazanova
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital, New York, NY
| | - Stephen G Jenkins
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - John Sipley
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital, New York, NY
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100
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Abstract
The recent development of commercial panel-based molecular diagnostics for the rapid detection of pathogens in positive blood culture bottles, respiratory specimens, stool, and cerebrospinal fluid has resulted in a paradigm shift in clinical microbiology and clinical practice. This review focuses on U.S. Food and Drug Administration (FDA)-approved/cleared multiplex molecular panels with more than five targets designed to assist in the diagnosis of bloodstream, respiratory tract, gastrointestinal, or central nervous system infections. While these panel-based assays have the clear advantages of a rapid turnaround time and the detection of a large number of microorganisms and promise to improve health care, they present certain challenges, including cost and the definition of ideal test utilization strategies (i.e., optimal ordering) and test interpretation.
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