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Schwellnus M, Adami PE, Bougault V, Budgett R, Clemm HH, Derman W, Erdener U, Fitch K, Hull JH, McIntosh C, Meyer T, Pedersen L, Pyne DB, Reier-Nilsen T, Schobersberger W, Schumacher YO, Sewry N, Soligard T, Valtonen M, Webborn N, Engebretsen L. International Olympic Committee (IOC) consensus statement on acute respiratory illness in athletes part 1: acute respiratory infections. Br J Sports Med 2022; 56:bjsports-2022-105759. [PMID: 35863871 DOI: 10.1136/bjsports-2022-105759] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2022] [Indexed: 11/04/2022]
Abstract
Acute illnesses affecting the respiratory tract are common and form a significant component of the work of Sport and Exercise Medicine (SEM) clinicians. Acute respiratory illness (ARill) can broadly be classified as non-infective ARill and acute respiratory infections (ARinf). The aim of this consensus is to provide the SEM clinician with an overview and practical clinical approach to ARinf in athletes. The International Olympic Committee (IOC) Medical and Scientific Commission appointed an international consensus group to review ARill (non-infective ARill and ARinf) in athletes. Six subgroups of the IOC Consensus group were initially established to review the following key areas of ARill in athletes: (1) epidemiology/risk factors for ARill, (2) ARinf, (3) non-infective ARill including ARill due to environmental exposure, (4) acute asthma and related conditions, (5) effects of ARill on exercise/sports performance, medical complications/return-to-sport and (6) acute nasal/vocal cord dysfunction presenting as ARill. Several systematic and narrative reviews were conducted by IOC consensus subgroups, and these then formed the basis of sections in the consensus documents. Drafting and internal review of sections were allocated to 'core' members of the consensus group, and an advanced draft of the consensus document was discussed during a meeting of the main consensus core group in Lausanne, Switzerland on 11 to 12 October 2021. Final edits were completed after the meeting. This consensus document (part 1) focusses on ARinf, which accounts for the majority of ARill in athletes. The first section of this consensus proposes a set of definitions and classifications of ARinf in athletes to standardise future data collection and reporting. The remainder of the consensus paper examines a wide range of clinical considerations related to ARinf in athletes: epidemiology, risk factors, pathology/pathophysiology, clinical presentation and diagnosis, management, prevention, medical considerations, risks of infection during exercise, effects of infection on exercise/sports performance and return-to-sport guidelines.
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Affiliation(s)
- Martin Schwellnus
- Sport, Exercise Medicine and Lifestyle Institute (SEMLI), Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- International Olympic Committee Research Centre, Pretoria, South Africa
| | - Paolo Emilio Adami
- Health and Science Department, World Athletics, Monaco, Monaco Principality
| | - Valerie Bougault
- Laboratoire Motricité Humaine Expertise Sport Santé, Université Côte d'Azur, Nice, France
| | - Richard Budgett
- Medical and Scientific Department, International Olympic Committee, Lausanne, Switzerland
| | - Hege Havstad Clemm
- Department of Pediatric and Adolescent Medicine, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Wayne Derman
- International Olympic Committee Research Centre, Pretoria, South Africa
- Institute of Sport and Exercise Medicine (ISEM), Department of Sport Science, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Uğur Erdener
- Medical and Scientific Department, International Olympic Committee, Lausanne, Switzerland
| | - Ken Fitch
- School of Human Science; Sports, Exercise and Health, University of Western Australia, Perth, Western Australia, Australia
| | - James H Hull
- Department of Respiratory Medicine, Royal Brompton Hospital, London, UK
- Institute of Sport, Exercise and Health (ISEH), University College London (UCL), London, UK
| | | | - Tim Meyer
- Institute of Sports and Preventive Medicine, Saarland University, Saarbrucken, Germany
| | - Lars Pedersen
- Department of Respiratory Medicine, Bispebjerg Hospital, Copenhagen, Denmark
| | - David B Pyne
- Research Institute for Sport and Exercise, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Tonje Reier-Nilsen
- The Norwegian Olympic Sports Centre, Oslo, Norway
- Trauma Research Center, Department of Sports Medicine, Norwegian School of Sport Sciences, Oslo, Norway
| | - Wolfgang Schobersberger
- Institute for Sports Medicine, Alpine Medicine & Health Tourism (ISAG), University Hospital - Tirol Kliniken Innsbruck and Private University UMIT Tirol, Hall, Austria
| | | | - Nicola Sewry
- Sport, Exercise Medicine and Lifestyle Institute (SEMLI), Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- International Olympic Committee Research Centre, Pretoria, South Africa
| | - Torbjørn Soligard
- Medical and Scientific Department, International Olympic Committee, Lausanne, Switzerland
| | | | - Nick Webborn
- Centre for Sport and Exercise Science and Medicine, University of Brighton, Brighton, UK
| | - Lars Engebretsen
- Medical and Scientific Department, International Olympic Committee, Lausanne, Switzerland
- Trauma Research Center, Department of Sports Medicine, Norwegian School of Sport Sciences, Oslo, Norway
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Zhang C, Sun L, Wang D, Li Y, Zhang L, Wang L, Peng J. Advances in antimicrobial resistance testing. Adv Clin Chem 2022; 111:1-68. [DOI: 10.1016/bs.acc.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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3
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Jeong S, Lee N, Park MJ, Jeon K, Song W. Currently Used Laboratory Methodologies for Assays Detecting PD-1, PD-L1, PD-L2 and Soluble PD-L1 in Patients with Metastatic Breast Cancer. Cancers (Basel) 2021; 13:cancers13205225. [PMID: 34680373 PMCID: PMC8534186 DOI: 10.3390/cancers13205225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/07/2021] [Accepted: 10/13/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Several methods targeting the programmed death protein-1 (PD-1) axis have been developed and evaluated for the detection of immune checkpoint levels that are strongly involved in immunotherapy for patients with metastatic breast cancer. Variations in different assays used in diverse studies have affected their result interpretation and clinical utility. When applying these assays to the laboratory, a comprehensive understanding of the characteristics of them should be recognized. We reviewed applied laboratory techniques for detecting PD-1, PD-ligand (L)1, PD-L2, and soluble PD-L1, which are important for selecting metastatic cancer patients for immunotherapy. Advances in methodologies according to the epoch are also investigated to gain insight into immunologic techniques and to facilitate appropriate laboratory settings for evaluating the PD-1 axis status, which are useful for estimating outcomes and planning patient-tailored immunotherapy strategies. Abstract Approximately 20% of breast cancer (BC) patients suffer from distant metastasis. The incidence and prevalence rates of metastatic BC have increased annually. Immune checkpoint inhibitors are an emerging area of treatment, especially for metastatic patients with poor outcomes. Several antibody drugs have been developed and approved for companion testing of the programmed death protine-1 (PD-1) axis. We reviewed currently used laboratory methodologies for assays determining PD-1 axis to provide a comprehensive understanding of principles, advantages, and drawbacks involved in their implementation. The most commonly used method is immunohistochemistry (92.9%) for PD-L1 expression using tissue samples (96.4%). The commonly used anti-PD-L1 antibody clone were commercially available 22C3 (30.8%), SP142 (19.2%), SP263 (15.4%), and E1L3N (11.5%). Enzyme-linked immunosorbent assay and electrochemiluminescent immunoassay that target soluble PD-ligand (L)1 were developed and popularized in 2019–2021, in contrast to 2016–2018. Easy accessibility and non-invasiveness due to the use of blood samples, quantitative outputs, and relatively rapid turnaround times make them more preferable. Regarding scoring methods, a combination of tumor and immune cells (45.5% in 2016–2018 to 57.1% in 2019–2021) rather than each cell alone became more popular. Information about antibody clones, platforms, scoring methods, and related companion drugs is recommended for reporting PD-L1 expression.
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Affiliation(s)
- Seri Jeong
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07440, Korea; (S.J.); (N.L.); (M.-J.P.)
| | - Nuri Lee
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07440, Korea; (S.J.); (N.L.); (M.-J.P.)
| | - Min-Jeong Park
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07440, Korea; (S.J.); (N.L.); (M.-J.P.)
| | - Kibum Jeon
- Department of Laboratory Medicine, Hangang Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07440, Korea;
| | - Wonkeun Song
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07440, Korea; (S.J.); (N.L.); (M.-J.P.)
- Correspondence: ; Tel.: +82-2-829-5259
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Design and Evaluation of Multiplex One-Step Reverse Transcription PCR-Dipstick Chromatography Method for the Analysis of Seven Respiratory Pathogens. Curr Microbiol 2021; 78:3656-3666. [PMID: 34338833 PMCID: PMC8326646 DOI: 10.1007/s00284-021-02621-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022]
Abstract
Influenza A, influenza B, severe acute respiratory syndrome coronavirus 2, adenovirus, respiratory syncytial virus, Mycoplasma pneumoniae, and Chlamydophila pneumoniae are common pathogens that can cause severe pneumonia and other symptoms, resulting in acute lower respiratory tract infections. The objective of this study was to design and evaluate a sensitive and specific multiplex one-step reverse transcription PCR (RT-PCR)–dipstick chromatography method for simultaneous rapid detection of these seven pathogens. Streptavidin-coated blue latex particles were used to read out a positive signal. Based on the DNA–DNA hybridization of oligonucleotide sequences (Tag) for forward primer with the complementary oligonucleotide sequence (cTag) on the dipstick and biotin–streptavidin interactions, PCR products were able to be illuminated visually on the dipstick. The specificity and the limit of detection (LOD) were also evaluated. Moreover, the clinical performance of this method was compared with Sanger sequencing for 896 samples. No cross reaction with other pathogens was found, confirming the high specificity of this method. The LOD was 10 copies/µL for each of the tested pathogens, and the whole procedure took less than 40 min. Using 896 samples, the sensitivity and specificity were shown to be no lower than 94.5%. The positive predictive value was higher than 82.1%, and the negative predictive value was higher than 99.5%. The kappa value between the PCR–dipstick chromatography method and Sanger sequencing ranged from 0.869 to 0.940. In summary, our one-step RT-PCR–dipstick chromatography method is a sensitive and specific tool for rapidly detecting multiplex respiratory pathogens.
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Hemida MG. The next-generation coronavirus diagnostic techniques with particular emphasis on the SARS-CoV-2. J Med Virol 2021; 93:4219-4241. [PMID: 33751621 PMCID: PMC8207115 DOI: 10.1002/jmv.26926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 12/15/2022]
Abstract
The potential zoonotic coronaviruses (SARS-CoV, MERS-CoV, and SARS-CoV-2) are of global health concerns. Early diagnosis is the milestone in their mitigation, control, and eradication. Many diagnostic techniques are showing great success and have many advantages, such as the rapid turnover of the results, high accuracy, and high specificity and sensitivity. However, some of these techniques have several pitfalls if samples were not collected, processed, and transported in the standard ways and if these techniques were not practiced with extreme caution and precision. This may lead to false-negative/positive results. This may affect the downstream management of the affected cases. These techniques require regular fine-tuning, upgrading, and optimization. The continuous evolution of new strains and viruses belong to the coronaviruses is hampering the success of many classical techniques. There are urgent needs for next generations of coronaviruses diagnostic assays that overcome these pitfalls. This new generation of diagnostic tests should be able to do simultaneous, multiplex, and high-throughput detection of various coronavirus in one reaction. Furthermore, the development of novel assays and techniques that enable the in situ detection of the virus on the environmental samples, especially air, water, and surfaces, should be given considerable attention in the future. These approaches will have a substantial positive impact on the mitigation and eradication of coronaviruses, including the current SARS-CoV-2 pandemic.
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Affiliation(s)
- Maged G. Hemida
- Department of Microbiology, College of Veterinary MedicineKing Faisal UniversityAl AhsaSaudi Arabia
- Department of Virology, Faculty of Veterinary MedicineKafrelsheikh UniversityKafr ElsheikhEgypt
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Lipkin WI, Mishra N, Briese T. Screening for Viral Infections. ENCYCLOPEDIA OF VIROLOGY 2021. [PMCID: PMC7836304 DOI: 10.1016/b978-0-12-814515-9.00052-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This article reviews methods for diagnosis of viral infections including histopathology, culture, nucleic acid tests, and serology. We discuss the principles that underlie individual assays as well as their strengths and limitations. Our intent is to provide insights into selecting strategies for viral diagnosis and discovery that can be pursued by accessing more detailed and granular protocols.
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7
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Bor G, Man E, Ugurlu O, Ceylan AE, Balaban S, Durmus C, Pinar Gumus Z, Evran S, Timur S. in vitro
Selection of Aptamer for Imidacloprid Recognition as Model Analyte and Construction of a Water Analysis Platform. ELECTROANAL 2020. [DOI: 10.1002/elan.202000075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Gulsah Bor
- Department of Biochemistry Faculty of Science Ege University 35100 Izmir Turkey
| | - Ezgi Man
- Department of Biochemistry Faculty of Science Ege University 35100 Izmir Turkey
| | - Ozge Ugurlu
- Department of Biochemistry Faculty of Science Ege University 35100 Izmir Turkey
| | - Ayse Elcin Ceylan
- Department of Biochemistry Faculty of Science Ege University 35100 Izmir Turkey
| | - Simge Balaban
- Department of Biochemistry Faculty of Science Ege University 35100 Izmir Turkey
| | - Ceren Durmus
- Department of Biochemistry Faculty of Science Ege University 35100 Izmir Turkey
| | - Z. Pinar Gumus
- Central Research Test and Analysis Laboratory Application and Research Center Ege University 35100 Izmir Turkey
| | - Serap Evran
- Department of Biochemistry Faculty of Science Ege University 35100 Izmir Turkey
| | - Suna Timur
- Department of Biochemistry Faculty of Science Ege University 35100 Izmir Turkey
- Central Research Test and Analysis Laboratory Application and Research Center Ege University 35100 Izmir Turkey
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Jeong S, Park MJ, Song W, Kim HS. Advances in laboratory assays for detecting human metapneumovirus. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:608. [PMID: 32566634 PMCID: PMC7290561 DOI: 10.21037/atm.2019.12.42] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Human metapneumovirus (HMPV) is one of the major causes of acute respiratory tract infection (ARI) and shows high morbidity and mortality, particularly in children and immunocompromised patients. Various methods for detecting HMPV have been developed and applied in clinical laboratories. When reviewing the literature, we found that polymerase chain reaction (PCR)-based assays have been most frequently and consistently used to detect HMPV. The most commonly used method was multiplex reverse transcriptase-PCR (RT-PCR; 57.4%), followed by real-time RT-PCR (38.3%). Multiplex RT-PCR became the more popular method in 2011-2019 (69.7%), in contrast to 2001-2009 (28.6%). The advent of multiplex PCR in detecting broader viral pathogens in one run and coinfected viruses influenced the change in user preference. Further, newly developed microarray technologies and ionization mass spectrometry were introduced in 2011-2019. Viral culture (including shell vial assays) and fluorescent immunoassays (with or without culture) were once the mainstays. However, the percentage of studies employing culture and fluorescent immunoassays decreased from 21.4% in 2001-2010 to 15.2% in 2011-2019. Meanwhile, the use of PCR-based methods of HMPV detection increased from 78.6% in 2001-2010 to 84.8% in 2011-2019. The increase in PCR-based methods might have occurred because PCR methods demonstrated better diagnostic performance, shorter hands-on and run times, less hazards to laboratory personnel, and more reliable results than traditional methods. When using these assays, it is important to acquire a comprehensive understanding of the principles, advantages, disadvantages, and precautions for data interpretation. In the future, the combination of nanotechnology and advanced genetic platforms such as next-generation sequencing will benefit patients with HMPV infection by facilitating efficient therapeutic intervention. Analytical and clinical validation are required before using new techniques in clinical laboratories.
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Affiliation(s)
- Seri Jeong
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Min-Jeong Park
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Hyon-Suk Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
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Epalza C, Hallin M, Busson L, Debulpaep S, De Backer P, Vandenberg O, Levy J. Role of Viral Molecular Panels in Diagnosing the Etiology of Fever in Infants Younger Than 3 Months. Clin Pediatr (Phila) 2020; 59:45-52. [PMID: 31709801 PMCID: PMC7206330 DOI: 10.1177/0009922819884582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
As infants with proven viral infection present lower risk of bacterial infection, we evaluated how molecular methods detecting viruses on respiratory secretions could contribute to etiological diagnostic of these febrile episodes. From November 2010 to May 2011, we enrolled all febrile infants <90 days presenting to emergency room. Standard workup included viral rapid antigenic test and viral culture on nasopharyngeal aspirate. Samples negative by rapid testing were tested by molecular methods. From 208 febrile episodes (198 infants) with standard techniques, rate of documented microbiological etiology was 13% at emergency department, 47% during hospitalization, and 64% with viral cultures. Molecular methods increased microbiologically documented etiology rate by 12%, to 76%. Contribution of molecular methods was the highest in infants without clinical source of infection, increasing documentation by 18%, from 50% to 68%. Making viral molecular results rapidly available could help identifying a higher proportion of infants at low risk of serious bacterial infection.
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Affiliation(s)
- Cristina Epalza
- Saint Pierre University Hospital, Bruxelles, Belgium,Université Libre de Bruxelles, Bruxelles, Belgium,Cristina Epalza, Pediatric Department, Saint Pierre University Hospital, Université Libre de Bruxelles, Bruxelles, Belgium.
| | - Marie Hallin
- Saint Pierre University Hospital, Bruxelles, Belgium,Université Libre de Bruxelles, Bruxelles, Belgium
| | - Laurent Busson
- Saint Pierre University Hospital, Bruxelles, Belgium,Université Libre de Bruxelles, Bruxelles, Belgium
| | - Sara Debulpaep
- Saint Pierre University Hospital, Bruxelles, Belgium,Université Libre de Bruxelles, Bruxelles, Belgium
| | - Paulette De Backer
- Saint Pierre University Hospital, Bruxelles, Belgium,Université Libre de Bruxelles, Bruxelles, Belgium
| | - Olivier Vandenberg
- Saint Pierre University Hospital, Bruxelles, Belgium,Université Libre de Bruxelles, Bruxelles, Belgium
| | - Jack Levy
- Saint Pierre University Hospital, Bruxelles, Belgium,Université Libre de Bruxelles, Bruxelles, Belgium
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Viral Etiology of Acute Respiratory Infections in Pediatric Patients in Lebanon. Mediterr J Hematol Infect Dis 2019; 11:e2019059. [PMID: 31700584 PMCID: PMC6827722 DOI: 10.4084/mjhid.2019.059] [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: 06/24/2019] [Accepted: 09/25/2019] [Indexed: 11/08/2022] Open
Abstract
Background Acute respiratory infections (ARI) are the leading cause of death worldwide, especially among children. The majority of these infections in children are of viral etiology. In this study, we evaluated the incidence of viral ARI among children in Lebanon. Patients and Methods Children presenting with symptoms of ARI were prospectively recruited between September 2009 to February 2012. Nasopharyngeal aspirates were obtained from patients and screened for 11 respiratory viruses using a multiplex Luminex-based PCR assay. Results Two hundred twenty-one patients were recruited with a median age of 1 year (IQR: 0 - 5). Out of 221 patients, 116 (52.5%) were positive for at least one virus, the majority (103/116; 88.8%) of which were in children under 6-year of age. Overall, 188 viruses were detected. Rhinovirus (RhV) was the most common virus detected in 81 (69.8%) patients followed by coxsackie virus and echovirus (CVEV) which were detected as one target in the panel in 45 (38.8%), and parainfluenza viruses (PIV types: 1, 2, 3, 4) in 24 (20.7%) patients. Coinfection with more than one virus was detected in 49 (42.9%) patients. RhV and CVEV were the most common viruses associated with co-infections and higher risk of rhinorrhea. Conclusions Viral pathogens account for at least half of the ARIs in Lebanon, with a high frequency of co-infections being detected.
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Jung BK, Kim JK. Laboratory Investigation of Human Rhinovirus Infection in Cheonan, Korea. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2019. [DOI: 10.15324/kjcls.2019.51.3.329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Bo Kyeung Jung
- Department of Laboratory Medicine, Dankook University Hospital, Cheonan, Korea
| | - Jae Kyung Kim
- Department of Biomedical Laboratory Science, Dankook University College of Health Sciences, Cheonan, Korea
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12
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Seo MY, Chung KA. Density and Distribution of the Mosquito Population Inhabiting Jeju Region, 2018. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2019. [DOI: 10.15324/kjcls.2019.51.3.336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Min Young Seo
- Department of Clinical Laboratory Science, Gwangju Health Science University, Gwangju, Korea
| | - Kyoung A Chung
- Department of Clinical Laboratory Science, Gwangju Health Science University, Gwangju, Korea
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Landry ML, Foxman EF. Antiviral Response in the Nasopharynx Identifies Patients With Respiratory Virus Infection. J Infect Dis 2019; 217:897-905. [PMID: 29281100 PMCID: PMC5853594 DOI: 10.1093/infdis/jix648] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/12/2017] [Indexed: 12/19/2022] Open
Abstract
Background Despite the high burden of respiratory infection and the importance of early and accurate diagnosis, there is no simple diagnostic test to rule in viral infection as a cause of respiratory symptoms. Methods We performed RNA sequencing on human nasal epithelial cells following stimulation of the intracellular viral recognition receptor RIG-I. Next, we evaluated whether measuring identified host mRNAs and proteins from patient nasopharyngeal swabs could predict the presence of a respiratory virus in the sample. Results Our first study showed that a signature of 3 mRNAs, CXCL10, IFIT2, and OASL, predicted respiratory virus detection with an accuracy of 97% (95% confidence interval [CI], 0.9–1.0), and identified proteins correlating with virus detection. In a second study, elevated CXCL11 or CXCL10 protein levels identified samples containing respiratory viruses, including viruses not on the initial test panel. Overall area under the curve (AUC) values were: CXCL11 AUC = 0.901 (95% CI, 0.86–0.94); CXCL10 AUC = 0.85 (95% CI, 0.80–0.91). Conclusions Host antiviral mRNAs and single host proteins detectable using nasopharyngeal swabs accurately predict the presence of viral infection. This approach holds promise for developing rapid, cost-effective tests to improve management of patients with respiratory illnesses.
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Affiliation(s)
- Marie L Landry
- Department of Laboratory Medicine Yale University School of Medicine, New Haven, Connecticut.,Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Ellen F Foxman
- Department of Laboratory Medicine Yale University School of Medicine, New Haven, Connecticut
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Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections. Clin Microbiol Rev 2018; 32:32/1/e00042-18. [PMID: 30541871 DOI: 10.1128/cmr.00042-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.
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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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16
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Hassan F, Crawford J, Bonner AB, Ledeboer NA, Selvarangan R. Multicenter evaluation of the Alere™ i influenza A&B assay using respiratory specimens collected in viral transport media. Diagn Microbiol Infect Dis 2018; 92:294-298. [PMID: 30077505 DOI: 10.1016/j.diagmicrobio.2018.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/22/2018] [Accepted: 07/02/2018] [Indexed: 12/30/2022]
Abstract
Rapid and accurate detection of influenza virus is critical for proper patient management. The Alere™ i Influenza A&B assay is an isothermal nucleic acid amplification test capable of detecting influenza A and B viruses directly from respiratory specimens. In this multicenter clinical trial conducted in the US, we evaluated the clinical performance of the Alere™ i Influenza A&B assay against that of the Prodesse ProFlu+ assay. A total of 1243 fresh, leftover nasal or nasopharyngeal swabs eluted in viral transport medium were tested by both assays. Sensitivity and specificity of the Alere™ i Influenza A&B assay were 97.8% (95% CI 94.6-99.2) and 96.6% (95% CI 95.2-97.5) for influenza A and 92.9% (95% CI 85.5-96.9) and 98.3% (95% CI 97.4-98.0) for influenza B. The Alere™ i Influenza A&B assay is an ideal molecular assay for influenza virus detection due to its high sensitivity and specificity with minimal hands-on and turn-around-time.
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Affiliation(s)
- Ferdaus Hassan
- Dept of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO
| | - Jordan Crawford
- Dept of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO
| | | | | | - Rangaraj Selvarangan
- Dept of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO.
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17
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Goriacko P, Saiman L, Zachariah P. Antibiotic Use in Hospitalized Children With Respiratory Viruses Detected by Multiplex Polymerase Chain Reaction. Pediatr Infect Dis J 2018; 37:443-446. [PMID: 28877158 DOI: 10.1097/inf.0000000000001775] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Multiplex polymerase chain reaction-based methods are increasingly used to detect respiratory pathogens in children. While rapid identification of viruses has been shown to reduce antibiotic use, the impact of detecting specific viruses on antibiotic utilization has not been ascertained. This study compared antibiotic utilization among hospitalized children who tested positive for different respiratory viruses at admission. METHODS A single-center study of hospitalized children under 21 years of age who tested positive at admission for at least 1 respiratory virus by multiplex polymerase chain reaction from October 1, 2012 to October 1, 2015 was performed. Multivariable logistic regression was used to determine the association of testing positive for specific viruses with the use of antibiotics for ≥ 2 days, adjusted for demographic and clinical characteristics. RESULTS The study included 1416 patients with a median age of 2.1 years (interquartile range: 0.6-6.2 years). Patients positive for influenza (odds ratio: 2.0, 95% confidence interval: 1.1-3.4) and human metapneumovirus (odds ratio: 2.0, 95% confidence interval: 1.1-3.7) were more likely to receive ≥ 2 days of treatment compared with patients positive for respiratory syncytial virus (RSV). Other variables affecting prolonged use of antibiotics included respiratory support, primary nonrespiratory diagnosis, complex comorbid conditions and admission to the intensive care unit. CONCLUSIONS Providers are more likely to use antibiotics in non-RSV-infected patients compared with RSV. These trends likely represent concern about bacterial superinfection and may reflect lack of familiarity with these pathogens.
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Affiliation(s)
- Pavel Goriacko
- From the Department of Pharmacy, Montefiore Medical Center, Bronx
| | - Lisa Saiman
- Department of Pediatrics, Columbia University Medical Center, New York.,Department of Infection Prevention and Control, New York-Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Philip Zachariah
- Department of Pediatrics, Columbia University Medical Center, New York.,Department of Infection Prevention and Control, New York-Presbyterian Morgan Stanley Children's Hospital, New York, NY
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18
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Multicenter Clinical Evaluation of the Alere i Respiratory Syncytial Virus Isothermal Nucleic Acid Amplification Assay. J Clin Microbiol 2018; 56:JCM.01777-17. [PMID: 29263208 DOI: 10.1128/jcm.01777-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 12/12/2017] [Indexed: 02/07/2023] Open
Abstract
The Alere i respiratory syncytial virus (RSV) assay is an isothermal nucleic acid amplification test capable of detecting RSV directly from respiratory specimens, with results being available in ≤13 min after test initiation. The objective of this study was to evaluate the performance characteristics of the Alere i RSV assay in a point-of-care setting by using direct nasopharyngeal (NP) swab specimens (direct NP) and nasopharyngeal swab specimens eluted and transported in viral transport medium (VTM NP). The study was a prospective, multicenter, clinical trial conducted at 9 sites across the United States to evaluate the clinical performance of the Alere i RSV assay with respiratory specimens obtained from both children (age, <18 years) and older adults (age, >60 years). The performance of the Alere i RSV assay was compared with that of the reference method, the Prodesse ProFlu+ real-time reverse transcriptase PCR (RT-PCR) assay. All specimens with discrepant test results were tested further by a second FDA-cleared PCR assay (the Verigene respiratory virus plus nucleic acid test; Luminex Inc., TX). A total of 554 subjects with signs and symptoms of respiratory infections were enrolled, and respiratory samples were collected in this study. In comparison with the ProFlu+ real-time RT-PCR, the overall sensitivity and specificity of Alere i RSV assay for the detection of RSV were 98.6% (95% confidence interval [CI], 94.4 to 99.7%) and 98.0% (95% CI, 95.8 to 99.1%), respectively, for direct NP and 98.6% (95% CI, 94.4 to 99.7%) and 97.8% (95% CI, 95.5 to 98.9%), respectively, for VTM NP. The Alere i RSV is a highly sensitive and specific molecular assay ideal for rapid RSV detection in patients in the point-of-care setting due to its minimal hands-on time and rapid result availability.
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19
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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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20
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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: 120] [Impact Index Per Article: 17.1] [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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21
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Xu L, Zhu Y, Ren L, Xu B, Liu C, Xie Z, Shen K. Characterization of the nasopharyngeal viral microbiome from children with community-acquired pneumonia but negative for Luminex xTAG respiratory viral panel assay detection. J Med Virol 2017; 89:2098-2107. [PMID: 28671295 PMCID: PMC7166964 DOI: 10.1002/jmv.24895] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/17/2017] [Indexed: 12/24/2022]
Abstract
In the present study, 50 nasopharyngeal swabs from children with community‐acquired pneumonia (CAP) but negative for 18 common respiratory viruses, as measured by the Luminex xTAG Respiratory Viral Panel Assay, were subjected to multiplex metagenomic analyses using a next‐generation sequencing platform. Taxonomic analysis showed that all sequence reads could be assigned to a specific species. An average of 95.13% were assigned to the Bacteria kingdom, whereas, only 0.72% were potentially virus derived. This snapshot of the respiratory tract virome revealed most viral reads to be respiratory tract related, classified into four known virus families: Paramyxoviridae, Herpesviridae, Anelloviridae, and Polyomaviridae. Importantly, we detected a novel human parainfluenza virus 3 (HPIV 3) strain with a 32‐bp insertion in the haemagglutinin‐neuraminidase (HN) gene that produced a negative result in the Luminex assay, highlighting the strength of virome metagenomic analysis to identify not only novel viruses but also viruses likely to be missed by ordinary clinical tests. Thus, virome metagenomic analysis could become a viable clinical diagnostic method.
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Affiliation(s)
- Lili Xu
- MOE Key Laboratory of Major Diseases in Children, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Yun Zhu
- MOE Key Laboratory of Major Diseases in Children, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Lili Ren
- Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Baoping Xu
- MOE Key Laboratory of Major Diseases in Children, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection diseases, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Chunyan Liu
- MOE Key Laboratory of Major Diseases in Children, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Zhengde Xie
- MOE Key Laboratory of Major Diseases in Children, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Kunling Shen
- MOE Key Laboratory of Major Diseases in Children, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection diseases, Beijing Children's Hospital, Capital Medical University, Beijing, China
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22
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Yan Y, Luo JY, Chen Y, Wang HH, Zhu GY, He PY, Guo JL, Lei YL, Chen ZW. A multiplex liquid-chip assay based on Luminex xMAP technology for simultaneous detection of six common respiratory viruses. Oncotarget 2017; 8:96913-96923. [PMID: 29228581 PMCID: PMC5722533 DOI: 10.18632/oncotarget.18533] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 06/02/2017] [Indexed: 12/27/2022] Open
Abstract
We utilized one-step multiplex reverse transcription-PCR (RT-PCR) and Luminex xMAP technology to develop a respiratory multiplex liquid-chip assay (rMLA) for simultaneous detection of 6 common respiratory viruses, including influenza virus type A (FluA) and type B (FluB), para-influenza virus type 3 (PIV-3), respiratory syncytial virus (RSV), human metapneumovirus (MPV) and a threatening virus to China, Middle East Respiratory Syndrome coronavirus (MERS-CoV). Performance of rMLA was evaluated by comparing with real-time RT-PCR. Detection data from clinical specimens showed that the rMLA had diagnostic sensitivities of 97.10% for FluA, 94.59% for FluB, 98.68% for PIV-3, 94.87% for RSV and 95.92% for MPV (No Data for MERS-CoV due to the lack of positive specimens). Data of analytical sensitivities showed that the detection limits of the rMLA assay were 5–25 viral RNA copies per μl for FluA, FluB, PIV-3 and MERS-CoV, approximate to the real-time RT-PCR assay; while the values were 8 and 22copies/μl for MPV and RSV, lower than the real-time RT-PCR(78 and 114 copies/μl respectively). The results indicated that the rMLA is a sensitive, specific detection tool and comparable to real-time RT-PCR, especially suitable for high-throughput detection of respiratory specimens.
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Affiliation(s)
- Yong Yan
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Jian-Yong Luo
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Yin Chen
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Heng-Hui Wang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Guo-Ying Zhu
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Pei-Yan He
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Jin-Lei Guo
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Yong-Liang Lei
- Lishui Municipal Center for Disease Control and Prevention, Lishui 323000, China
| | - Zhong-Wen Chen
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
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23
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Shi X, Liu X, Wang Q, Das A, Ma G, Xu L, Sun Q, Peddireddi L, Jia W, Liu Y, Anderson G, Bai J, Shi J. A multiplex real-time PCR panel assay for simultaneous detection and differentiation of 12 common swine viruses. J Virol Methods 2016; 236:258-265. [PMID: 27506582 PMCID: PMC7119729 DOI: 10.1016/j.jviromet.2016.08.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 11/17/2022]
Abstract
A multiplex real-time PCR panel assay was developed for the detection of 12 major swine pathogens including VSV-IN, VSV-NJ, SVDV, CSFV, ASFV, FMDV, PCV2, PPV, PRV, PRRSV-NA, PRRSV-EU;. The panel assay was 100% specific against common swine pathogens;. Limits of detection of the assay were ranged 1–16 copies per reaction;. Detection sensitivity was not reduced by multiplexing three targets into one PCR reaction.
Mixed infection with different pathogens is common in swine production systems especially under intensive production conditions. Quick and accurate detection and differentiation of different pathogens are necessary for epidemiological surveillance, disease management and import and export controls. In this study, we developed and validated a panel of multiplex real-time PCR/RT-PCR assays composed of four subpanels, each detects three common swine pathogens. The panel detects 12 viruses or viral serotypes, namely, VSV-IN, VSV-NJ, SVDV, CSFV, ASFV, FMDV, PCV2, PPV, PRV, PRRSV-NA, PRRSV-EU and SIV. Correlation coefficients (R2) and PCR amplification efficiencies of all singular and triplex real-time PCR reactions are within the acceptable range. Comparison between singular and triplex real-time PCR assays of each subpanel indicates that there is no significant interference on assay sensitivities caused by multiplexing. Specificity tests on 226 target clinical samples or 4 viral strains and 91 non-target clinical samples revealed that the real-time PCR panel is 100% specific, and there is no cross amplification observed. The limit of detection of each triplex real-time PCR is less than 10 copies per reaction for DNA, and less than 16 copies per reaction for RNA viruses. The newly developed multiplex real-time PCR panel also detected different combinations of co-infections as confirmed by other means of detections.
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Affiliation(s)
- Xiju Shi
- Beijing Entry-Exit Inspection & Quarantine Bureau, Beijing, China; Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Xuming Liu
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Qin Wang
- China Institute of Veterinary Drug Control, Beijing, China
| | - Amaresh Das
- Foreign Animal Diseases Diagnostic Laboratory, NVSL, APHIS, USDA, Greenport, NY, United States
| | - Guiping Ma
- Beijing Entry-Exit Inspection & Quarantine Bureau, Beijing, China
| | - Lu Xu
- China Institute of Veterinary Drug Control, Beijing, China
| | - Qing Sun
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Lalitha Peddireddi
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Wei Jia
- Foreign Animal Diseases Diagnostic Laboratory, NVSL, APHIS, USDA, Greenport, NY, United States
| | - Yanhua Liu
- Beijing Entry-Exit Inspection & Quarantine Bureau, Beijing, China
| | - Gary Anderson
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States.
| | - Jishu Shi
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States.
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24
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Subramony A, Zachariah P, Krones A, Whittier S, Saiman L. Impact of Multiplex Polymerase Chain Reaction Testing for Respiratory Pathogens on Healthcare Resource Utilization for Pediatric Inpatients. J Pediatr 2016; 173:196-201.e2. [PMID: 27039227 PMCID: PMC5452417 DOI: 10.1016/j.jpeds.2016.02.050] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/15/2016] [Accepted: 02/18/2016] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To assess whether multiplex polymerase chain reaction (mPCR) vs non-mPCR testing impacts the use of antibiotics, chest radiographs, and isolation precautions. STUDY DESIGN We retrospectively compared use of antibiotics, chest radiographs, and isolation precautions for patients <18 years old (excluding neonates) hospitalized at a tertiary referral center tested for respiratory pathogens in the emergency department or during the first 2 hospital days, during 2 periods: June 2010-June 2012 (non-mPCR group) vs October 2012-May 2014 (mPCR group). RESULTS Subjects (n = 2430) in the mPCR group were older, had more complex chronic conditions, and were admitted to the pediatric intensive care unit more often compared with the non-mPCR (n = 2349) group. Subjects in the mPCR group had more positive tests (42.4% vs 14.4%, P < .01), received fewer days of antibiotics (4 vs 5 median antibiotic days, P < .01), fewer chest radiographs performed, (59% vs 78%, P < .01), and were placed in isolation longer (20 vs 0 median isolation-hours, P < .01) compared with the non-mPCR group. In multivariable regression, patients tested with mPCR were less likely to receive antibiotics for ≥2 days (OR 0.5, 95% CI 0.5-0.6), chest radiographs at admission (OR 0.4, 95% CI 0.3-0.4), and more likely to be in isolation for ≥2 days (OR 2.4, 95% CI 2.1-2.8) compared with the non-mPCR group. CONCLUSIONS Use of mPCR testing for respiratory viruses among hospitalized patients was significantly associated with decreased healthcare resource utilization, including decreased use of antibiotics and chest radiographs, and increased use of isolation precautions.
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Affiliation(s)
- Anupama Subramony
- Department of Pediatrics, Cohen Children's Medical Center, Hofstra-Northwell School of Medicine, New Hyde Park, NY.
| | - Philip Zachariah
- Department of Pediatrics, Columbia University Medical Center, New York, NY,NewYork-Presbyterian Hospital, New York, NY
| | - Ariella Krones
- Department of Medicine, Virginia Commonwealth University Medical Center, Richmond, VA
| | - Susan Whittier
- Department of Pediatrics, Columbia University Medical Center, New York, NY,NewYork-Presbyterian Hospital, New York, NY
| | - Lisa Saiman
- Department of Pediatrics, Columbia University Medical Center, New York, NY,NewYork-Presbyterian Hospital, New York, NY
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25
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Clinical Evaluation of the Luminex NxTAG Respiratory Pathogen Panel. J Clin Microbiol 2016; 54:1912-1914. [PMID: 27122378 DOI: 10.1128/jcm.00482-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/22/2016] [Indexed: 11/20/2022] Open
Abstract
An evaluation of the Luminex NxTAG Respiratory Pathogen Panel was performed on 404 clinical respiratory specimens. Clinical sensitivities and specificities of the assay compared to those of the reference methods were 80.0% to 100.0% and 98.9% to 100.0%, respectively. Correct genotyping information was provided for 95.5% of influenza virus A specimens. The closed-tube format of the assay simplified the workflow and minimized carryover contamination.
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26
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Wansaula Z, Olsen SJ, Casal MG, Golenko C, Erhart LM, Kammerer P, Whitfield N, McCotter OZ. Surveillance for severe acute respiratory infections in Southern Arizona, 2010-2014. Influenza Other Respir Viruses 2016; 10:161-9. [PMID: 26590069 PMCID: PMC4814863 DOI: 10.1111/irv.12360] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2015] [Indexed: 11/28/2022] Open
Abstract
Background The Binational Border Infectious Disease Surveillance program began surveillance for severe acute respiratory infections (SARI) on the US–Mexico border in 2009. Here, we describe patients in Southern Arizona. Methods Patients admitted to five acute care hospitals that met the SARI case definition (temperature ≥37·8°C or reported fever or chills with history of cough, sore throat, or shortness of breath in a hospitalized person) were enrolled. Staff completed a standard form and collected a nasopharyngeal swab which was tested for selected respiratory viruses by reverse transcription polymerase chain reaction. Results From October 2010–September 2014, we enrolled 332 SARI patients. Fifty‐two percent were male and 48% were white non‐Hispanic. The median age was 63 years (47% ≥65 years and 5·2% <5 years). During hospitalization, 51 of 230 (22%) patients required intubation, 120 of 297 (40%) were admitted to intensive care unit, and 28 of 278 (10%) died. Influenza vaccination was 56%. Of 309 cases tested, 49 (16%) were positive for influenza viruses, 25 (8·1%) for human metapneumovirus, 20 (6·5%) for parainfluenza viruses, 16 (5·2%) for coronavirus, 11 (3·6%) for respiratory syncytial virus, 10 (3·2%) for rhinovirus, 4 (1·3%) for rhinovirus/enterovirus, 3 (1·0%) for enteroviruses, and 3 (1·0%) for adenovirus. Among the 49 influenza‐positive specimens, 76% were influenza A (19 H3N2, 17 H1N1pdm09, and 1 not subtyped), and 24% were influenza B. Conclusion Influenza viruses were a frequent cause of SARI in hospitalized patients in Southern Arizona. Monitoring respiratory illness in border populations will help better understand the etiologies. Improving influenza vaccination coverage may help prevent some SARI cases.
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Affiliation(s)
- Zimy Wansaula
- Arizona Department of Health Services, Office of Border Health, Tucson, AZ, USA
| | - Sonja J Olsen
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mariana G Casal
- Arizona Department of Health Services, Office of Border Health, Tucson, AZ, USA
| | - Catherine Golenko
- Arizona Department of Health Services, Office of Infectious Disease Services, Phoenix, AZ, USA
| | - Laura M Erhart
- Arizona Department of Health Services, Office of Infectious Disease Services, Phoenix, AZ, USA
| | | | - Natalie Whitfield
- Clinical and Molecular Microbiology, University of Arizona, Tucson, AZ, USA
| | - Orion Z McCotter
- Arizona Department of Health Services, Office of Border Health, Tucson, AZ, USA.,Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
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27
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Using Nucleic Acid Amplification Techniques in a Syndrome-Oriented Approach: Detection of Respiratory Agents. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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28
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Leonard DG. Respiratory Infections. MOLECULAR PATHOLOGY IN CLINICAL PRACTICE 2016. [PMCID: PMC7123443 DOI: 10.1007/978-3-319-19674-9_52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The majority of respiratory tract infections (RTIs) are community acquired and are the single most common cause of physician office visits and among the most common causes of hospitalizations. The morbidity and mortality associated with RTIs are significant and the financial and social burden high due to lost time at work and school. The scope of clinical symptoms can significantly overlap among the respiratory pathogens, and the severity of disease can vary depending on patient age, underlying disease, and immune status, thereby leading to inaccurate presumptions about disease etiology. The rapid and accurate diagnosis of the causative agent of RTIs improves patient care, reduces morbidity and mortality, promotes effective hospital bed utilization and antibiotic stewardship, and reduces length of stay. This chapter focuses on the clinical utility, advantages, and disadvantages of viral and bacterial tests cleared by the Food and Drug Administration (FDA), and new promising technologies for the detection of bacterial agents of pneumonia currently in development or in US FDA clinical trials are briefly reviewed.
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Affiliation(s)
- Debra G.B. Leonard
- Pathology and Laboratory Medicine, University of Vermont College of Medicine and University of Vermont Medical Center, Burlington, Vermont USA
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29
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García‐Arroyo L, Prim N, Martí N, Roig MC, Navarro F, Rabella N. Benefits and drawbacks of molecular techniques for diagnosis of viral respiratory infections. Experience with two multiplex PCR assays. J Med Virol 2016; 88:45-50. [PMID: 26100363 PMCID: PMC7166422 DOI: 10.1002/jmv.24298] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2015] [Indexed: 11/08/2022]
Abstract
Molecular techniques have represented a major step forward in the diagnosis of viral respiratory infections. They are considered highly sensitive and specific compared to conventional techniques. In this study two nucleic acid amplification tests (NAATs) were compared to conventional methods (immunofluorescence and viral culture). The aim of this work was to discuss the clinical interpretation of the results obtained by NAATs on the basis of the two-decade experience of our group and the literature. Eighty nasopharyngeal aspirates were collected from children under six years attended for acute respiratory illness at the pediatric emergency room of a third level Hospital. Both NAATs tested (Seeplex(®) and Clart(®)) showed an overall higher performance regarding sensitivity (76% and 90%, respectively). Compared to Seeplex(®), the Clart(®) system tripled the number of multiple detections (8 by Seeplex(®) vs. 25 by Clart(®)). In some specimens both NAATs detected different viruses. Given these discrepancies and the fact that detection of viral nucleic acids is not necessarily related to the current clinical syndrome, the interpretation of molecular results may not always be so straightforward. The pros and cons of NAATs should always be taken into account when giving a result.
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Affiliation(s)
| | - Núria Prim
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
| | - Neus Martí
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
| | - Maria Carme Roig
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Núria Rabella
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de BarcelonaBarcelonaSpain
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30
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Sanchez JL, Cooper MJ, Myers CA, Cummings JF, Vest KG, Russell KL, Sanchez JL, Hiser MJ, Gaydos CA. Respiratory Infections in the U.S. Military: Recent Experience and Control. Clin Microbiol Rev 2015; 28:743-800. [PMID: 26085551 PMCID: PMC4475643 DOI: 10.1128/cmr.00039-14] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
This comprehensive review outlines the impact of military-relevant respiratory infections, with special attention to recruit training environments, influenza pandemics in 1918 to 1919 and 2009 to 2010, and peacetime operations and conflicts in the past 25 years. Outbreaks and epidemiologic investigations of viral and bacterial infections among high-risk groups are presented, including (i) experience by recruits at training centers, (ii) impact on advanced trainees in special settings, (iii) morbidity sustained by shipboard personnel at sea, and (iv) experience of deployed personnel. Utilizing a pathogen-by-pathogen approach, we examine (i) epidemiology, (ii) impact in terms of morbidity and operational readiness, (iii) clinical presentation and outbreak potential, (iv) diagnostic modalities, (v) treatment approaches, and (vi) vaccine and other control measures. We also outline military-specific initiatives in (i) surveillance, (ii) vaccine development and policy, (iii) novel influenza and coronavirus diagnostic test development and surveillance methods, (iv) influenza virus transmission and severity prediction modeling efforts, and (v) evaluation and implementation of nonvaccine, nonpharmacologic interventions.
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Affiliation(s)
- Jose L Sanchez
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA
| | - Michael J Cooper
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA
| | | | - James F Cummings
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA
| | - Kelly G Vest
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA
| | - Kevin L Russell
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA
| | - Joyce L Sanchez
- Mayo Clinic, Division of General Internal Medicine, Rochester, Minnesota, USA
| | - Michelle J Hiser
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA Oak Ridge Institute for Science and Education, Postgraduate Research Participation Program, U.S. Army Public Health Command, Aberdeen Proving Ground, Aberdeen, Maryland, USA
| | - Charlotte A Gaydos
- International STD, Respiratory, and Biothreat Research Laboratory, Division of Infectious Diseases, Johns Hopkins University, Baltimore, Maryland, USA
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31
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Wei L, Chan KH, Ip DKM, Fang VJ, Fung ROP, Leung GM, Peiris MJS, Cowling BJ. Burden, seasonal pattern and symptomatology of acute respiratory illnesses with different viral aetiologies in children presenting at outpatient clinics in Hong Kong. Clin Microbiol Infect 2015; 21:861-6. [PMID: 26033670 PMCID: PMC7129816 DOI: 10.1016/j.cmi.2015.05.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/19/2015] [Accepted: 05/21/2015] [Indexed: 11/18/2022]
Abstract
Respiratory viruses cause acute respiratory diseases with a broad and overlapping spectrum of symptoms. We examined the clinical symptoms and explored the patterns of various respiratory viral infections in children in Hong Kong. Among 2090 specimens collected from outpatient care (2007–2010), 1343 (64.3%) were positive for any virus by the xTAG assay, and 81 (3.9%) were positive for co-infection. The most frequently detected viruses among children aged 6–15 years were enterovirus/rhinovirus and influenza virus A, whereas most non-influenza viruses were more frequently detected in younger children. Higher body temperature was more common for illnesses associated with influenza viruses than for those associated with non-influenza viruses, but other symptoms were largely similar across all infections. The seasonality pattern varied among different viruses, with influenza virus A being the predominant virus detected in winter, and enterovirus/rhinovirus being more commonly detected than influenza virus A in the other three seasons, except for 2009.
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Affiliation(s)
- L Wei
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - K-H Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - D K M Ip
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
| | - V J Fang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - R O P Fung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - G M Leung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - M J S Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region; Centre of Influenza Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - B J Cowling
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
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32
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Lin Y, Fu Y, Xu M, Su L, Cao L, Xu J, Cheng X. Evaluation of a PCR/ESI-MS platform to identify respiratory viruses from nasopharyngeal aspirates. J Med Virol 2015; 87:1867-71. [PMID: 25959799 PMCID: PMC7166901 DOI: 10.1002/jmv.24262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2015] [Indexed: 11/24/2022]
Abstract
Acute respiratory tract infection is a major cause of morbidity and mortality worldwide, particularly in infants and young children. High‐throughput, accurate, broad‐range tools for etiologic diagnosis are critical for effective epidemic control. In this study, the diagnostic capacities of an Ibis platform based on the PCR/ESI‐MS assay were evaluated using clinical samples. Nasopharyngeal aspirates (NPAs) were collected from 120 children (<5 years old) who were hospitalized with lower respiratory tract infections between November 2010 and October 2011. The respiratory virus detection assay was performed using the PCR/ESI‐MS assay and the DFA. The discordant PCR/ESI‐MS and DFA results were resolved with RT‐PCR plus sequencing. The overall agreement for PCR/ESI‐MS and DFA was 98.3% (118/120). Compared with the results from DFA, the sensitivity and specificity of the PCR/ESI‐MS assay were 100% and 97.5%, respectively. The PCR/ESI‐MS assay also detected more multiple virus infections and revealed more detailed subtype information than DFA. Among the 12 original specimens with discordant results between PCR/ESI‐MS and DFA, 11 had confirmed PCR/ESI‐MS results. Thus, the PCR/ESI‐MS assay is a high‐throughput, sensitive, specific and promising method to detect and subtype conventional viruses in respiratory tract infections and allows rapid identification of mixed pathogens. J. Med. Virol. 87:1867–1871, 2015. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Yong Lin
- Department of Laboratory Medicine, Huashan Hospital of Fudan University, Shanghai, China.,Department of Center Laboratory, Jingan District Center Hospital of Shanghai, Shanghai, China
| | - Yongfeng Fu
- Department of Medical Microbiology and Parasitology, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Menghua Xu
- Department of Clinical Laboratory Center, Children's Hospital of Fudan University, Shanghai, China
| | - Liyun Su
- Department of Clinical Laboratory Center, Children's Hospital of Fudan University, Shanghai, China
| | - Lingfeng Cao
- Department of Clinical Laboratory Center, Children's Hospital of Fudan University, Shanghai, China
| | - Jin Xu
- Department of Clinical Laboratory Center, Children's Hospital of Fudan University, Shanghai, China
| | - Xunjia Cheng
- Department of Medical Microbiology and Parasitology, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
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33
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Sung H, Kang JO, Lee NY, Lee CK, Kim HS, Lee KM, Kim EC. Comparison of Nasopharyngeal Aspirates and Nasopharyngeal Flocked Swabs for Respiratory Virus Detection. ANNALS OF CLINICAL MICROBIOLOGY 2015. [DOI: 10.5145/acm.2015.18.4.119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Heungsup Sung
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jung Oak Kang
- Department of Laboratory Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Chang Kyu Lee
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Han-Sung Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Kyu Man Lee
- Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Eui Chong Kim
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
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34
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Huff MD, Weisman D, Adams J, Li S, Green J, Malone LL, Clemmons S. The frequency of tetracycline resistance genes co-detected with respiratory pathogens: a database mining study uncovering descriptive trends throughout the United States. BMC Infect Dis 2014; 14:460. [PMID: 25152108 PMCID: PMC4156627 DOI: 10.1186/1471-2334-14-460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 08/18/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Center for Disease Control and Prevention (CDC) indicates that one of the largest problems threatening healthcare includes antibiotic resistance. Tetracycline, an effective antibiotic that has been in use for many years, is becoming less successful in treating certain pathogens. To better understand the temporal patterns in the growth of antibiotic resistance, patient diagnostic test records can be analyzed. METHODS Data mining methods including frequent item set mining and association rules via the Apriori algorithm were used to analyze results from 80,241 Target Enriched Multiplex-PCR (TEM-PCR) reference laboratory tests. From the data mining results, five common respiratory pathogens and their co-detection rates with tetracycline resistance genes (TRG) were further analyzed and organized according to year, patient age, and geography. RESULTS From 2010, all five pathogens were associated with at least a 24% rise in co-detection rate for TRGs. Patients from 0-2 years old exhibited the lowest rate of TRG co-detection, while patients between 13-50 years old displayed the highest frequency of TRG co-detection. The Northeastern region of the United States recorded the highest rate of patients co-detected with a TRG and a respiratory pathogen. Along the East-west gradient, the relative frequency of co-detection between TRGs and respiratory pathogens decreased dramatically. CONCLUSIONS Significant trends were uncovered regarding the co-detection frequencies of TRGs and respiratory pathogens over time. It is valuable for the field of public health to monitor trends regarding the spread of resistant infectious disease, especially since tetracycline continues to be utilized a treatment for various microbial infections. Analyzing large datasets containing TEM-PCR results for co-detections provides valuable insights into trends of antibiotic resistance gene expression so that the effectiveness of first-line treatments can be continuously monitored.
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Affiliation(s)
- Matthew D Huff
- />Diatherix Laboratories Inc., 601 Genome Way, Suite 2100, Huntsville, Al 35806 USA
| | - David Weisman
- />Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125-3393 USA
| | - John Adams
- />Knoxville Infectious Disease Consultants, P.C., 2210 Sutherland Ave., Suite 110, Knoxville, TN 37919 USA
| | - Song Li
- />Hudson Alpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | - Jessica Green
- />Diatherix Laboratories Inc., 601 Genome Way, Suite 2100, Huntsville, Al 35806 USA
| | - Leslie L Malone
- />Diatherix Laboratories Inc., 601 Genome Way, Suite 2100, Huntsville, Al 35806 USA
| | - Scott Clemmons
- />Diatherix Laboratories Inc., 601 Genome Way, Suite 2100, Huntsville, Al 35806 USA
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35
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Salez N, Nougairede A, Ninove L, Zandotti C, de Lamballerie X, Charrel RN. Xpert Flu for point-of-care diagnosis of human influenza in industrialized countries. Expert Rev Mol Diagn 2014; 14:411-8. [PMID: 24707995 DOI: 10.1586/14737159.2014.901152] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Respiratory infections, particularly those caused by influenza viruses, represent the third-most important cause of death in the world due to infectious diseases. Nevertheless, despite the enormous publicity attracted by epidemics due to these viruses, laboratory diagnosis, documentation and recording of respiratory diseases is still unsatisfactory. Available diagnostic tests capable of providing results rapidly are either limited and insufficiently sensitive or highly sensitive and specific but insufficiently rapid. Considerable investment and research efforts have been made towards the development of new diagnostics for influenza A and B viruses and the Xpert(®) Flu assay (Cepheid(®), CA, USA) has emerged as one of the most promising. In this article, we review current knowledge of the Xpert Flu test, discuss its potential value as a point-of-care test and outline the potential leads for future development.
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Affiliation(s)
- Nicolas Salez
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", and IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France
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36
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Abstract
Gastroenteritis persists as a worldwide problem, responsible for approximately 2 million deaths annually. Traditional diagnostic methods used in the clinical microbiology laboratory include a myriad of tests, such as culture, microscopy, and immunodiagnostics, which can be labor intensive and suffer from long turnaround times and, in some cases, poor sensitivity. [corrected]. This article reviews recent advances in genomic and proteomic technologies that have been applied to the detection and identification of gastrointestinal pathogens. These methods simplify and speed up the detection of pathogenic microorganisms, and their implementation in the clinical microbiology laboratory has potential to revolutionize the diagnosis of gastroenteritis.
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37
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Kaslow RA, Stanberry LR, Le Duc JW. Diagnosis, Discovery and Dissection of Viral Diseases. VIRAL INFECTIONS OF HUMANS 2014. [PMCID: PMC7122662 DOI: 10.1007/978-1-4899-7448-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Richard A. Kaslow
- Department of Epidemiology, University of Alabama, Birmingham School of Public Health, Birmingham, Alabama USA
| | - Lawrence R. Stanberry
- Departmant of Pediatrics, Columbia University College of Physicians and Surgeons, New York, New York USA
| | - James W. Le Duc
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas USA
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38
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Vempilly J, Abejie B, Diep V, Gushiken M, Rawat M, Tyner TR. The synergetic effect of ambient PM2.5 exposure and rhinovirus infection in airway dysfunction in asthma: a pilot observational study from the Central Valley of California. Exp Lung Res 2013; 39:434-40. [PMID: 24245976 DOI: 10.3109/01902148.2013.840693] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Elevated levels of particulate matter PM2.5 and rhinovirus infection have been known to exacerbate asthma. However, the combined effect of rhinovirus infection and high PM2.5 has not been investigated. PURPOSE To investigate the effect of PM2.5 and concomitant rhinovirus infection on airway function in asthma in an area with high PM2.5 concentration. METHODS Asthmatics and their matched controls were monitored for lung function, exhaled nitric oxide (eNO) and respiratory symptoms on days with varying levels of PM2.5. As the study was a repeated measure design, repeated clinical findings, and laboratory data were used in the mixed model analysis. RESULTS Wheezing and dyspnea in asthmatics were worsened with increasing ambient PM2.5. Increasing PM2.5 decreased FEV1% predicted (-0.51, -0.79 to -0.23) and FEF25-75% predicted (-0.66, -1.07 to -0.24) in subjects with asthma (all P < .01). Rhino viral infection reduced FEF25-75% predicted in subjects with asthma (-11.7, -20 to -2.9). The reductions in FEV25-75 and FEV1 per 10 μg/m(3) increase in ambient PM2.5 were 6% and 5% respectively. A significant interaction was observed between presence of rhinovirus infection and elevated PM2.5 in asthmatics causing a 4-fold decrease in FEF25-75 (P = .01) and a 2-fold decrease in FEV1% predicted values (P = .01) compared with asthmatics with no rhino viral infection. CONCLUSIONS Increasing ambient PM2.5 and low temperature independently worsened airway function in asthma. The interaction between rhinovirus and PM2.5 significantly impairs airway function in asthma. A larger sample size study is suggested to investigate these observations.
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Affiliation(s)
- Joseph Vempilly
- 1Department of Medicine, Pulmonary & Critical Care Division, UCSF Fresno, California, USA
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39
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Abstract
Influenza viruses cause recurring epidemic outbreaks every year associated with high morbidity and mortality. Despite extensive research and surveillance efforts to control influenza outbreaks, the primary mitigation treatment for influenza is the development of yearly vaccine mixes targeted for the most prevalent virus strains. Consequently, the focus of many detection technologies has evolved toward accurate identification of subtype and understanding the evolution and molecular determinants of novel and pathogenic forms of influenza. The recent availability of potential antiviral treatments are only effective if rapid and accurate diagnostic tests for influenza epidemic management are available; thus, early detection of influenza infection is still important for prevention, containment, patient management, and infection control. This review discusses the current and emerging technologies for detection and strain identification of influenza virus and their specific gene targets, as well as their implications in patient management.
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Affiliation(s)
- Anthony P Malanoski
- Center for Bio/Molecular Science and Engineering, U. S. Naval Research Laboratory, 4555 Overlook Avenue, S. W., Code 6900, Washington, DC, 20375, USA
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40
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Pillet S, Lardeux M, Dina J, Grattard F, Verhoeven P, Le Goff J, Vabret A, Pozzetto B. Comparative evaluation of six commercialized multiplex PCR kits for the diagnosis of respiratory infections. PLoS One 2013; 8:e72174. [PMID: 24058410 PMCID: PMC3751960 DOI: 10.1371/journal.pone.0072174] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 07/12/2013] [Indexed: 11/26/2022] Open
Abstract
The molecular diagnosis of respiratory infection can be performed using different commercial multiplex-based PCR kits whose performances have been previously compared individually to those of conventional techniques. This study compared the practicability and the diagnostic performances of six CE-marked kits available in 2011 on the French market, including 2 detecting viruses and atypical bacteria (from Pathofinder and Seegene companies) and 4 detecting only viruses (from Abbott, Genomica, Qiagen and Seegene companies). The respective sensitivity, specificity, accuracy and agreement of each multiplex technique were calculated by comparison to commercial duplex PCR tests (Argene/bioMérieux) used as gold standard. Eighty-eight respiratory specimens with no pathogen (n = 11), single infections (n = 33) or co-infections (n = 44) were selected to cover 9 viruses or groups of viruses and 3 atypical bacteria. All samples were extracted using the NUCLISENS® easyMAG™ instrument (bioMérieux). The overall sensitivity ranged from 56.25% to 91.67% for viruses and was below 50% with both tests for bacteria. The overall specificity was excellent (>94% for all pathogens). For each tested kit, the overall agreement with the reference test was strong for viruses (kappa test >0.60) and moderate for bacteria. After the extraction step, the hands-on time varied from 50 min to 2h30 and the complete results were available in 2h30 to 9 h. The spectrum of tested agents and the technology used to reveal the PCR products as well as the laboratory organization are determinant for the selection of a kit.
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Affiliation(s)
- Sylvie Pillet
- Laboratory of Bacteriology and Virology, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Marina Lardeux
- Laboratory of Bacteriology and Virology, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Julia Dina
- Laboratory of Virology, University Hospital of Caen, Caen, France
| | - Florence Grattard
- Laboratory of Bacteriology and Virology, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Paul Verhoeven
- Laboratory of Bacteriology and Virology, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Jérôme Le Goff
- Université Paris Diderot, Sorbonne Paris Cité, Microbiology Department, Saint-Louis Hospital, APHP, Paris, France
| | - Astrid Vabret
- Laboratory of Virology, University Hospital of Caen, Caen, France
| | - Bruno Pozzetto
- Laboratory of Bacteriology and Virology, University Hospital of Saint-Etienne, Saint-Etienne, France
- * E-mail:
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A two-tube multiplex reverse transcription PCR assay for simultaneous detection of sixteen human respiratory virus types/subtypes. BIOMED RESEARCH INTERNATIONAL 2013; 2013:327620. [PMID: 23984344 PMCID: PMC3747601 DOI: 10.1155/2013/327620] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 06/25/2013] [Indexed: 11/17/2022]
Abstract
There is a need for the development of a rapid and sensitive diagnosis of respiratory viral pathogens. With an intended application in provincial Centers for Diseases Control and Prevention, in this study, we present a two-tube multiplex RT-PCR assay (two-tube assay) using automatic electrophoresis to simultaneously detect sixteen common respiratory viruses. The specificity and the sensitivity of the assay were tested. The assay could detect 20-200 copies per reaction when each viral type was assayed individually, 2000 copies with 9 premixed viral targets in the multiplexed assay in tube 1, and 200 copies with 8 premixed templates in tube 2. A total of 247 specimens were used to evaluate the two-tube assay, and the results were compared with those obtained from the Luminex xTAG RVP Fast assay. The discordant results were confirmed by sequencing or by the Seeplex RV15 ACE detection kit. There were no false positives, but six false negatives occurred with the two-tube assay. In conclusion, the two-tube assay is demonstrated to have great potential for routine surveillance of respiratory virus infection in China.
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Cho CH, Chulten B, Lee CK, Nam MH, Yoon SY, Lim CS, Cho Y, Kim YK. Evaluation of a novel real-time RT-PCR using TOCE technology compared with culture and Seeplex RV15 for simultaneous detection of respiratory viruses. J Clin Virol 2013; 57:338-42. [PMID: 23743345 PMCID: PMC7108272 DOI: 10.1016/j.jcv.2013.04.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 04/09/2013] [Accepted: 04/20/2013] [Indexed: 12/22/2022]
Abstract
Background Various kinds of commercial molecular systems have been developed for fast and more accurate detection of respiratory viruses. Anyplex™ II RV16 [RV16] was designed for simultaneous detection of 16 respiratory viruses using multiplex PCR coupled with TOCE™ technology. Objectives To compare the performance of RV16 with those of culture and Seeplex® RV15 ACE [RV15] by determining their sensitivity and specificity. Study design Seven hundred and thirty respiratory samples were tested by modified shell vial culture method, RV16, and RV15. For molecular tests, automated nucleic acid extraction and liquid handling system using MICROLAB Nimbus IVD (Hamilton, USA) was adopted to maximize the workflow and accuracy. Performance of each assay was determined against a composite reference standard. Results Two hundred and one samples (28%) out of 730 samples were positive by culture, while additional 281 (39%) were positive by RV16 or RV15. Sensitivities of RV16, RV15, and culture for virus tested were as follows: 100/93/63% for influenza A, 90/80/69% for influenza B, 98/94/63% for RSV, 98/52/23% for adenovirus, and 100/75/46% for PIV. For viruses not covered by culture, sensitivities of RV16 and RV15 were as follows: 99/81% for rhinovirus, 92/100% for coronavirus OC43, 100/56% for coronavirus 229E/NL63, 92/88% for metapneumovirus, 100/62% for bocavirus, and 91/91% for enterovirus. Overall, the specificities of culture, RV16, and RV15 (Seegene) were 100/99.9/99.9%. Conclusions RV16 assay was superior to culture method and RV15 and will be a promising tool for patient management and public health epidemiology.
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Affiliation(s)
- Chi Hyun Cho
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Republic of Korea
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Abstract
BACKGROUND Respiratory viral panels (RVPs) able to detect multiple pathogens are increasingly used in the management of pediatric inpatients. Despite this, few studies have examined whether the results of these tests are associated with clinically significant changes in medical management. METHODS In this retrospective cohort study, we identified pediatric inpatients between August 2009 and December 2010 for whom an RVP was ordered within 24 hours of admission to a large, tertiary-care children's hospital. We used linear regression to determine whether RVP was associated with length of stay (LOS), duration of antibiotics and the number of diagnostic microbiology tests ordered, adjusting for potential confounders. RESULTS We found that the association between results of the RVP and LOS was dependent on a patient's admission service, specifically admission to the hematology/oncology service. We also found that patients with a positive RVP had a shorter duration of intravenous antibiotic administration (P = 0.03; 42% reduction in the geometric mean), but that this was influenced by the primary admission service. We also found that positive results of the RVP were associated with decreased LOS and shorter duration of antibiotics in patients with some common respiratory diagnoses. CONCLUSIONS This study lacked sufficient evidence to claim an association between a positive RVP and LOS in pediatric patients, adjusting for their underlying diagnosis. However, we found that a positive RVP was associated with a shorter duration of intravenous antibiotic administration in certain groups of patients and those with some common respiratory diagnoses. These findings help clarify the utility of rapid viral testing in the management of hospitalized pediatric patients.
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Carreño-Durán LR, Larios-Serrato V, Jaimes-Díaz H, Pérez-Cervantes H, Zepeda-López H, Sánchez-Vallejo CJ, Olguín-Ruiz GE, Maldonado-Rodríguez R, Méndez-Tenorio A. Design of a set of probes with high potential for influenza virus epidemiological surveillance. Bioinformation 2013; 9:414-20. [PMID: 23750091 PMCID: PMC3670124 DOI: 10.6026/97320630009414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 04/10/2013] [Indexed: 11/23/2022] Open
Abstract
An Influenza Probe Set (IPS) consisting in 1,249 9-mer probes for genomic fingerprinting of closely and distantly related Influenza Virus strains was designed and tested in silico. The IPS was derived from alignments of Influenza genomes. The RNA segments of 5,133 influenza strains having diverse degree of relatedness were concatenated and aligned. After alignment, 9-mer sites having high Shannon entropy were searched. Additional criteria such as: G+C content between 35 to 65%, absence of dimer or trimer consecutive repeats, a minimum of 2 differences between 9mers and selecting only sequences with Tm values between 34.5 and 36.5oC were applied for selecting probes with high sequential entropy. Virtual Hybridization was used to predict Genomic Fingerprints to assess the capability of the IPS to discriminate between influenza and related strains. Distance scores between pairs of Influenza Genomic Fingerprints were calculated, and used for estimating Taxonomic Trees. Visual examination of both Genomic Fingerprints and Taxonomic Trees suggest that the IPS is able to discriminate between distant and closely related Influenza strains. It is proposed that the IPS can be used to investigate, by virtual or experimental hybridization, any new, and potentially virulent, strain.
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Affiliation(s)
- Luis R Carreño-Durán
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, Escuela Nacional de Ciencias Biológicas,
Instituto Politécnico Nacional, México City, Méxic
| | - V Larios-Serrato
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, Escuela Nacional de Ciencias Biológicas,
Instituto Politécnico Nacional, México City, Méxic
| | - Hueman Jaimes-Díaz
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, Escuela Nacional de Ciencias Biológicas,
Instituto Politécnico Nacional, México City, Méxic
| | - Hilda Pérez-Cervantes
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, Escuela Nacional de Ciencias Biológicas,
Instituto Politécnico Nacional, México City, Méxic
| | - Héctor Zepeda-López
- Laboratory of Conservation Medicine, Escuela Superior de Medicina, Instituto
Politécnico Nacional, México City, México
| | - Carlos Javier Sánchez-Vallejo
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, Escuela Nacional de Ciencias Biológicas,
Instituto Politécnico Nacional, México City, Méxic
| | - Gabriela Edith Olguín-Ruiz
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, Escuela Nacional de Ciencias Biológicas,
Instituto Politécnico Nacional, México City, Méxic
| | - Rogelio Maldonado-Rodríguez
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, Escuela Nacional de Ciencias Biológicas,
Instituto Politécnico Nacional, México City, Méxic
| | - Alfonso Méndez-Tenorio
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, Escuela Nacional de Ciencias Biológicas,
Instituto Politécnico Nacional, México City, Méxic
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Lipkin WI, Firth C. Viral surveillance and discovery. Curr Opin Virol 2013; 3:199-204. [PMID: 23602435 DOI: 10.1016/j.coviro.2013.03.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 03/20/2013] [Indexed: 01/27/2023]
Abstract
The field of virus discovery has burgeoned with the advent of high throughput sequencing platforms and bioinformatics programs that enable rapid identification and molecular characterization of known and novel agents, investments in global microbial surveillance that include wildlife and domestic animals as well as humans, and recognition that viruses may be implicated in chronic as well as acute diseases. Here we review methods for viral surveillance and discovery, strategies and pitfalls in linking discoveries to disease, and identify opportunities for improvements in sequencing instrumentation and analysis, the use of social media and medical informatics that will further advance clinical medicine and public health.
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Affiliation(s)
- Walter Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health of Columbia University, 722 West 168th Street, New York, NY 10025, USA.
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Respiratory virus multiplex RT-PCR assay sensitivities and influence factors in hospitalized children with lower respiratory tract infections. Virol Sin 2013; 28:97-102. [PMID: 23575731 PMCID: PMC7090616 DOI: 10.1007/s12250-013-3312-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Accepted: 03/18/2013] [Indexed: 01/18/2023] Open
Abstract
Multiplex RT-PCR assays have been widely used tools for detection and differentiation of a panel of respiratory viral pathogens. In this study, we evaluated the Qiagen ResPlex II V2.0 kit and explored factors influencing its sensitivity. Nasopharyngeal swab (NPS) specimens were prospectively collected from pediatric inpatients with lower respiratory tract infections at the time of admission in the Shenzhen Children’s Hospital from May 2009 to April 2010. Total nucleic acids were extracted using the EZ1 system (Qiagen, Germany) and 17 respiratory viruses and genotypes including influenza A virus (FluA), FluB, parainfluenza virus 1 (PIV1), PIV2, PIV3, PIV4, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), rhinoviruses (RhV), enteroviruses (EnV), human bocaviruses (hBoV), adenoviruses (AdV), four coronaviruses (229E, OC43, NL63 and HKU1), and FluA 2009 pandemic H1N1(H1N1-p) were detected and identified by the ResPlex II kit. In parallel, 16 real-time TaqMan quantitative RT-PCR assays were used to quantitatively detect each virus except for RhV. Influenza and parainfluenza viral cultures were also performed. Among the total 438 NPS specimens collected during the study period, one or more viral pathogens were detected in 274 (62.6%) and 201(45.9%) specimens by monoplex TaqMan RT-PCR and multiplex ResPlex, respectively. When results from monoplex PCR or cell culture were used as the reference standard, the multiplex PCR possessed specificities of 92.9–100.0%. The sensitivity of multiplex PCR for PIV3, hMPV, PIV1 and BoV were 73.1%, 70%, 66.7% and 55.6%, respectively, while low sensitivities (11.1%–40.0%) were observed for FluA, EnV, OC43, RSV and H1N1. Among the seven viruses/genotypes detected with higher frequencies, multiplex PCR sensitivities were correlated significantly with viral loads determined by the TaqMan RT-PCR in FluA, H1N1-p and RSV (p=0.011−0.000). The Qiagen ResPlex II multiplex RT-PCR kit possesses excellent specificity for simultaneous detection of 17 viral pathogens in NPS specimens in pediatric inpatients at the time of admission. The sensitivity of multiplex RT-PCR was influenced by viral loads, specimen process methods, primer and probe design and amplification condition.
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Jaton-Ogay K, Bille J. Microbiological diagnosis of community-acquired respiratory tract infections by nucleic acid detection. ACTA ACUST UNITED AC 2013; 2:947-61. [PMID: 23495868 DOI: 10.1517/17530059.2.8.947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Microbiological diagnostic procedures have changed significantly over the last decade. Initially the implementation of the polymerase chain reaction (PCR) resulted in improved detection tests for microbes that were difficult or even impossible to detect by conventional methods such as culture and serology, especially in community-acquired respiratory tract infections (CA-RTI). A further improvement was the development of real-time PCR, which allows end point detection and quantification, and many diagnostic laboratories have now implemented this powerful method. OBJECTIVE At present, new performant and convenient molecular tests have emerged targeting in parallel many viruses and bacteria responsible for lower and/or upper respiratory tract infections. The range of test formats and microbial agents detected is evolving very quickly and the added value of these new tests needs to be studied in terms of better use of antibiotics, better patient management, duration of hospitalization and overall costs. CONCLUSIONS Molecular tools for a better microbial documentation of CA-RTI are now available. Controlled studies are now required to address the relevance issue of these new methods, such as, for example, the role of some newly detected respiratory viruses or of the microbial DNA load in a particular patient at a particular time. The future challenge for molecular diagnosis will be to become easy to handle, highly efficient and cost-effective, delivering rapid results with a direct impact on clinical management.
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Affiliation(s)
- Katia Jaton-Ogay
- Institute of Microbiology, University Hospital Center of Lausanne and University of Lausanne, 1011 Lausanne, Switzerland +41 21 314 40 76 ; +41 21 314 40 60 ;
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Tang YW. Laboratory diagnosis of CNS infections by molecular amplification techniques. ACTA ACUST UNITED AC 2013; 1:489-509. [PMID: 23496356 DOI: 10.1517/17530059.1.4.489] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The initial presentation of symptoms and clinical manifestations of CNS infectious diseases often makes a specific diagnosis difficult and uncertain, and the emergence of polymerase chain reaction-led molecular techniques have been used in improving organism-specific diagnosis. These techniques have not only provided rapid, non-invasive detection of microorganisms causing CNS infections, but also demonstrated several neurologic disorders linked to infectious pathogens. Molecular methods performed on cerebrospinal fluid are recognized as the new 'gold standard' for some of these infections caused by microorganisms that are difficult to detect and identify. Although molecular techniques are predicted to be widely used in diagnosing and monitoring CNS infections, the limitations as well as strengths of these techniques must be clearly understood by both clinicians and laboratory personnel.
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Affiliation(s)
- Yi-Wei Tang
- Vanderbilt University Medical Center, 4605 TVC, Nashville, TN 37232-5310, USA +1 615 322 2035 ; +1 615 343 8420 ;
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Chen H, Chen X, Hu Y, Yan H. Reproducibility, fidelity, and discriminant validity of linear RNA amplification for microarray-based identification of major human enteric viruses. Appl Microbiol Biotechnol 2013; 97:4129-39. [DOI: 10.1007/s00253-013-4769-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 02/07/2013] [Accepted: 02/09/2013] [Indexed: 02/06/2023]
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Infectious Diseases, Vibrational Spectroscopic Approaches to Rapid Diagnostics. Infect Dis (Lond) 2013. [DOI: 10.1007/978-1-4614-5719-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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