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Rais Y, Fu Z, Drabovich AP. Mass spectrometry-based proteomics in basic and translational research of SARS-CoV-2 coronavirus and its emerging mutants. Clin Proteomics 2021; 18:19. [PMID: 34384361 PMCID: PMC8358260 DOI: 10.1186/s12014-021-09325-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 08/07/2021] [Indexed: 01/08/2023] Open
Abstract
Molecular diagnostics of the coronavirus disease of 2019 (COVID-19) now mainly relies on the measurements of viral RNA by RT-PCR, or detection of anti-viral antibodies by immunoassays. In this review, we discussed the perspectives of mass spectrometry-based proteomics as an analytical technique to identify and quantify proteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and to enable basic research and clinical studies on COVID-19. While RT-PCR and RNA sequencing are indisputably powerful techniques for the detection of SARS-CoV-2 and identification of the emerging mutations, proteomics may provide confirmatory diagnostic information and complimentary biological knowledge on protein abundance, post-translational modifications, protein-protein interactions, and the functional impact of the emerging mutations. Pending advances in sensitivity and throughput of mass spectrometry and liquid chromatography, shotgun and targeted proteomic assays may find their niche for the differential quantification of viral proteins in clinical and environmental samples. Targeted proteomic assays in combination with immunoaffinity enrichments also provide orthogonal tools to evaluate cross-reactivity of serology tests and facilitate development of tests with the nearly perfect diagnostic specificity, this enabling reliable testing of broader populations for the acquired immunity. The coronavirus pandemic of 2019-2021 is another reminder that the future global pandemics may be inevitable, but their impact could be mitigated with the novel tools and assays, such as mass spectrometry-based proteomics, to enable continuous monitoring of emerging viruses, and to facilitate rapid response to novel infectious diseases.
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Affiliation(s)
- Yasmine Rais
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Zhiqiang Fu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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Los J, Gaydos CA, Gibert CL, Gorse GJ, Lykken J, Nyquist AC, Price CS, Radonovich LJ, Rattigan S, Reich N, Rodriguez-Barradas M, Simberkoff M, Bessesen M, Brown A, Cummings DAT, Perl TM. Take-home kits to detect respiratory viruses among healthcare personnel: Lessons learned from a cluster randomized clinical trial. Am J Infect Control 2021; 49:893-899. [PMID: 33581146 PMCID: PMC7874979 DOI: 10.1016/j.ajic.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Health care personnel (HCP) working in outpatient settings routinely interact with patients with acute respiratory illnesses. Absenteeism following symptom development and lack of staff trained to obtain samples limit efforts to identify pathogens among infected HCP. METHODS The Respiratory Protection Effectiveness Clinical Trial assessed respiratory infection incidence among HCP between 2011 and 2015. Research assistants obtained anterior nasal and oropharyngeal swabs from HCP in the workplace following development of respiratory illness symptoms and randomly while asymptomatic. Participants received take-home kits to self-collect swabs when absent from work. Samples mailed to a central laboratory were tested for respiratory viruses by reverse transcription polymerase chain reaction. RESULTS Among 2,862 participants, 3,467 swabs were obtained from symptomatic participants. Among symptomatic HCP, respiratory virus was detected in 904 of 3,467 (26.1%) samples. Self-collected samples by symptomatic HCP at home had higher rates of viral detection (40.3%) compared to 24% obtained by trained research assistants in the workplace (P < .001). CONCLUSIONS In this randomized clinical trial, take-home kits were an easily implemented, effective method to self-collect samples by HCP. Other studies have previously shown relative equivalence of self-collected samples to those obtained by trained healthcare workers. Take-home kit self-collection could diminish workforce exposures and decrease the demand for personnel protective equipment worn to protect workers who collect respiratory samples.
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Affiliation(s)
- Jenna Los
- Johns Hopkins University School of Medicine, Baltimore, MD.
| | | | | | - Geoffrey J Gorse
- VA St. Louis Health Care System and Saint Louis University School of Medicine St. Louis, MO
| | | | - Ann-Christine Nyquist
- Children's Hospital Colorado, Aurora, CO; University of Colorado School of Medicine, Aurora, CO
| | - Connie S Price
- University of Colorado School of Medicine, Aurora, CO; Denver Health and Hospital, Denver, CO
| | - Lewis J Radonovich
- Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Atlanta, GA
| | | | | | | | | | - Mary Bessesen
- University of Colorado School of Medicine, Aurora, CO; VA-Eastern Colorado Healthcare System, Denver, CO
| | | | | | - Trish M Perl
- Johns Hopkins University School of Medicine, Baltimore, MD; University of Texas Southwestern Medical Center, Dallas, TX
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Schofield C, Colombo RE, Richard SA, Chen WJ, Fairchok MP, Maves RC, Arnold JC, Danaher PJ, Deiss RG, Lalani T, Rajnik M, Millar EV, Coles CL, Burgess TH. Comparable Disease Severity by Influenza Virus Subtype in the Acute Respiratory Infection Consortium Natural History Study. Mil Med 2021; 185:e1008-e1015. [PMID: 32588899 DOI: 10.1093/milmed/usaa120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/13/2019] [Accepted: 01/07/2020] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION Since the influenza A/H1N1 pandemic of 2009 to 2010, numerous studies have described the clinical course and outcome of the different subtypes of influenza (A/H1N1, A/H3N2, and B). A recent systematic literature review concluded that there were no appreciable differences in either clinical presentation or disease severity among these subtypes, but study parameters limit the applicability of these results to military populations. We sought to evaluate differences in disease severity among influenza subtypes in a cohort of healthy, primarily outpatient adult U.S. Department of Defense beneficiaries. MATERIALS AND METHODS From 2009 to 2014, we enrolled otherwise healthy adults age 18 to 65 years with influenza-like illness in an observational cohort study based in 5 U.S. military medical centers. Serial nasopharyngeal swabs were collected for determination of etiology and viral shedding by polymerase chain reaction. The presence and severity of symptoms was assessed by interview and patient diary. RESULTS Over a 5-year period, a total of 157 adults with laboratory-confirmed influenza and influenza subtype were enrolled. Of these, 69 (44%) were positive for influenza A(H1N1), 69 (44%) for influenza A(H3N2), and 19 (12%) for influenza B. About 61% were male, 64% were active duty military personnel, and 72% had received influenza vaccine in the past 8 months. Almost 10% were hospitalized with influenza. Seasonal influenza virus distribution among enrollees mirrored that of nationwide trends each year of study. Individuals with A/H1N1 had upper respiratory composite scores that were lower than those with A/H3N2. Multivariate models indicated that individuals with A(H1N1) and B had increased lower respiratory symptom scores when compared to influenza A(H3N2) (A[H1N1]: 1.51 [95% CI 0.47, 2.55]; B: 1.46 [95% CI 0.09, 2.83]), whereas no other differences in symptom severity scores among influenza A(H1N1), influenza A(H3N2), and influenza B infection were observed. Overall, influenza season (maximum in 2012-2013 season) and female sex of the participant were found to be associated with increased influenza symptom severity. CONCLUSIONS Our study of influenza in a cohort of otherwise healthy, outpatient adult Department of Defense beneficiaries over 5 influenza seasons revealed few differences between influenza A(H1N1), influenza A(H3N2), and influenza B infection with respect to self-reported disease severity or clinical outcomes. This study highlights the importance of routine, active, and laboratory-based surveillance to monitor ongoing trends and severity of influenza in various populations to inform prevention measures.
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Affiliation(s)
- Christina Schofield
- Infectious Disease Service, Madigan Army Medical Center, 9040 Jackson Ave, Fort Lewis, Washington, Washington DC 98431
| | - Rhonda E Colombo
- Infectious Disease Service, Madigan Army Medical Center, 9040 Jackson Ave, Fort Lewis, Washington, Washington DC 98431.,Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 2088.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 2088
| | - Stephanie A Richard
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 2088.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 2088
| | - Wei-Ju Chen
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 2088.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 2088
| | - Mary P Fairchok
- Infectious Disease Service, Madigan Army Medical Center, 9040 Jackson Ave, Fort Lewis, Washington, Washington DC 98431.,Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 2088.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 2088
| | - Ryan C Maves
- Division of Infectious Disease, Naval Medical Center San Diego, 34800 Bob Wilson Dr, San Diego, CA 92134
| | - John C Arnold
- Division of Infectious Disease, Naval Medical Center San Diego, 34800 Bob Wilson Dr, San Diego, CA 92134
| | - Patrick J Danaher
- Infectious Disease Service, San Antonio Military Medical Center, 3551 Roger Brooke Dr, San Antonio, TX 78234
| | - Robert G Deiss
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 2088.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 2088.,Division of Infectious Disease, Naval Medical Center San Diego, 34800 Bob Wilson Dr, San Diego, CA 92134
| | - Tahaniyat Lalani
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 2088.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 2088.,Infectious Disease Division, Naval Medical Center Portsmouth, 620 John Paul Jones Cir, Portsmouth, VA 23708
| | - Michael Rajnik
- Division of Infectious Disease, Walter Reed National Military Medical Center, 4494 Palm Rd N, Bethesda, MD 20889
| | - Eugene V Millar
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 2088.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 2088
| | - Christian L Coles
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 2088.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 2088
| | - Timothy H Burgess
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 2088
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Ezhilan M, Suresh I, Nesakumar N. SARS-CoV, MERS-CoV and SARS-CoV-2: A Diagnostic Challenge. MEASUREMENT : JOURNAL OF THE INTERNATIONAL MEASUREMENT CONFEDERATION 2021; 168:108335. [PMID: 33519010 PMCID: PMC7833337 DOI: 10.1016/j.measurement.2020.108335] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/20/2020] [Accepted: 08/01/2020] [Indexed: 05/15/2023]
Abstract
The highly pathogenic MERS-CoV, SARS-CoV and SARS-CoV-2 cause acute respiratory syndrome and are often fatal. These new viruses pose major problems to global health in general and primarily to infection control and public health services. Accurate and selective assessment of MERS-CoV, SARS-CoV and SARS-CoV-2 would assist in the effective diagnosis of infected individual, offer clinical guidance and aid in assessing clinical outcomes. In this mini-review, we review the literature on various aspects, including the history and diversity of SARS-CoV-2, SARS-CoV and MERS-CoV, their detection methods in effective clinical diagnosis, clinical assessment of COVID-19, safety guidelines recommended by World Health Organization and legal regulations. This review article also deals with existing challenges and difficulties in the clinical diagnosis of SARS-CoV-2. Developing alternative diagnostic platforms by spotting the shortcomings of the existing point-of-care diagnostic devices would be useful in preventing future outbreaks.
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Affiliation(s)
- Madeshwari Ezhilan
- School of Electrical and Electronics Engineering, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), SASTRA Deemed University, Thanjavur 613401, Tamil Nadu, India
| | - Indhu Suresh
- School of Electrical and Electronics Engineering, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), SASTRA Deemed University, Thanjavur 613401, Tamil Nadu, India
| | - Noel Nesakumar
- School of Chemical and Biotechnology, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), SASTRA Deemed University, Thanjavur 613401, Tamil Nadu, India
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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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Bramhachari PV. Advanced Immunotechnological Methods for Detection and Diagnosis of Viral Infections: Current Applications and Future Challenges. DYNAMICS OF IMMUNE ACTIVATION IN VIRAL DISEASES 2020. [PMCID: PMC7121190 DOI: 10.1007/978-981-15-1045-8_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Diagnosis and identification of viruses is an important component of diagnostic virology laboratory. Although various modes of diagnostic methods are now available at disposal, a vast majority of the diseases across the globe remain undiagnosed. This is largely due to the overlapping undifferentiated set of symptoms across myriad set of RNA and DNA viral diseases. As such, it becomes critical to take into consideration several factors for viral diagnosis ranging from the type and quality of specimen collected, time of specimen collection, mode of transport, accuracy, specificity, sensitivity, and the type of diagnostic method used. This chapter broadly emphasizes various methods on diagnostic virology ranging from the classical methods of diagnosis to the most recently developed molecular methods of detection of virus.
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von Lilienfeld-Toal M, Berger A, Christopeit M, Hentrich M, Heussel CP, Kalkreuth J, Klein M, Kochanek M, Penack O, Hauf E, Rieger C, Silling G, Vehreschild M, Weber T, Wolf HH, Lehners N, Schalk E, Mayer K. Community acquired respiratory virus infections in cancer patients-Guideline on diagnosis and management by the Infectious Diseases Working Party of the German Society for haematology and Medical Oncology. Eur J Cancer 2016; 67:200-212. [PMID: 27681877 PMCID: PMC7125955 DOI: 10.1016/j.ejca.2016.08.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 08/17/2016] [Accepted: 08/17/2016] [Indexed: 01/11/2023]
Abstract
BACKGROUND Community acquired viruses (CRVs) may cause severe disease in cancer patients. Thus, efforts should be made to diagnose CRV rapidly and manage CRV infections accordingly. METHODS A panel of 18 clinicians from the Infectious Diseases Working Party of the German Society for Haematology and Medical Oncology have convened to assess the available literature and provide recommendations on the management of CRV infections including influenza, respiratory syncytial virus, parainfluenza virus, human metapneumovirus and adenovirus. RESULTS CRV infections in cancer patients may lead to pneumonia in approximately 30% of the cases, with an associated mortality of around 25%. For diagnosis of a CRV infection, combined nasal/throat swabs or washes/aspirates give the best results and nucleic acid amplification based-techniques (NAT) should be used to detect the pathogen. Hand hygiene, contact isolation and face masks have been shown to be of benefit as general infection management. Causal treatment can be given for influenza, using a neuraminidase inhibitor, and respiratory syncytial virus, using ribavirin in addition to intravenous immunoglobulins. Ribavirin has also been used to treat parainfluenza virus and human metapneumovirus, but data are inconclusive in this setting. Cidofovir is used to treat adenovirus pneumonitis. CONCLUSIONS CRV infections may pose a vital threat to patients with underlying malignancy. This guideline provides information on diagnosis and treatment to improve the outcome.
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MESH Headings
- Adenovirus Infections, Human/diagnosis
- Adenovirus Infections, Human/epidemiology
- Adenovirus Infections, Human/therapy
- Antiviral Agents/therapeutic use
- Cidofovir
- Community-Acquired Infections/diagnosis
- Community-Acquired Infections/epidemiology
- Community-Acquired Infections/therapy
- Cytosine/analogs & derivatives
- Cytosine/therapeutic use
- Germany
- Hand Hygiene
- Humans
- Immunoglobulins, Intravenous/therapeutic use
- Immunologic Factors/therapeutic use
- Influenza, Human/diagnosis
- Influenza, Human/epidemiology
- Influenza, Human/therapy
- Lung/diagnostic imaging
- Masks
- Medical Oncology
- Metapneumovirus
- Neoplasms/epidemiology
- Neuraminidase/antagonists & inhibitors
- Nucleic Acid Amplification Techniques
- Organophosphonates/therapeutic use
- Oseltamivir/therapeutic use
- Paramyxoviridae Infections/diagnosis
- Paramyxoviridae Infections/epidemiology
- Paramyxoviridae Infections/therapy
- Patient Isolation
- Pneumonia, Viral/diagnosis
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/therapy
- Respiratory Syncytial Virus Infections/diagnosis
- Respiratory Syncytial Virus Infections/epidemiology
- Respiratory Syncytial Virus Infections/therapy
- Respiratory Tract Infections/diagnosis
- Respiratory Tract Infections/epidemiology
- Respiratory Tract Infections/therapy
- Ribavirin/therapeutic use
- Tomography, X-Ray Computed
- Virus Diseases/diagnosis
- Virus Diseases/epidemiology
- Virus Diseases/therapy
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Affiliation(s)
- Marie von Lilienfeld-Toal
- Department of Haematology and Medical Oncology, Jena University Hospital, Jena, Germany; Centre for Sepsis Control and Care (CSCC), University Hospital Jena, Germany; Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institut, Jena, Germany.
| | - Annemarie Berger
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Germany
| | - Maximilian Christopeit
- Department of Stem Cell Transplantation, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Marcus Hentrich
- Department of Haematology and Oncology, Red Cross Hospital, Munich, Germany
| | - Claus Peter Heussel
- Department of Diagnostic and Interventional Radiology, University Hospital, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany; Department of Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik at University of Heidelberg, Heidelberg, Germany
| | - Jana Kalkreuth
- Department of Haematology and Medical Oncology, Jena University Hospital, Jena, Germany
| | - Michael Klein
- Department I of Internal Medicine, Prosper-Hospital, Recklinghausen, Germany
| | - Matthias Kochanek
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Olaf Penack
- Department of Hematology, Oncology and Tumorimmunology, Charité Campus Virchow, Berlin, Germany
| | - Elke Hauf
- Department III of Internal Medicine, The University Hospital Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Christina Rieger
- Lehrpraxis der Ludwig-Maximilians-Universität München, Germering, Germany
| | - Gerda Silling
- Department of Haematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Maria Vehreschild
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany; German Centre for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Thomas Weber
- Department of Hematology and Oncology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Hans-Heinrich Wolf
- Department of Hematology and Oncology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Nicola Lehners
- Department of Haematology and Oncology, University Hospital of Heidelberg, Heidelberg, Germany
| | - Enrico Schalk
- Department of Haematology and Oncology, Medical Centre, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Karin Mayer
- Department of Haematology and Oncology, University Hospital Bonn, Bonn, Germany
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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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Molecular and Mass Spectrometry Detection and Identification of Causative Agents of Bloodstream Infections. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Shih HI, Wang HC, Su IJ, Hsu HC, Wang JR, Sun HFS, Chou CH, Ko WC, Hsieh MI, Wu CJ. Viral Respiratory Tract Infections in Adult Patients Attending Outpatient and Emergency Departments, Taiwan, 2012-2013: A PCR/Electrospray Ionization Mass Spectrometry Study. Medicine (Baltimore) 2015; 94:e1545. [PMID: 26402811 PMCID: PMC4635751 DOI: 10.1097/md.0000000000001545] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Viral etiologies of respiratory tract infections (RTIs) have been less studied in adult than in pediatric populations. Furthermore, the ability of PCR/electrospray ionization mass spectrometry (PCR/ESI-MS) to detect enteroviruses and rhinoviruses in respiratory samples has not been well evaluated. We sought to use PCR/ESI-MS to comprehensively investigate the viral epidemiology of adult RTIs, including testing for rhinoviruses and enteroviruses. Nasopharyngeal or throat swabs from 267 adults with acute RTIs (212 upper RTIs and 55 lower RTIs) who visited a local clinic or the outpatient or emergency departments of a medical center in Taiwan between October 2012 and June 2013 were tested for respiratory viruses by both virus isolation and PCR/ESI-MS. Throat swabs from 15 patients with bacterial infections and 27 individuals without active infections were included as control samples. Respiratory viruses were found in 23.6%, 47.2%, and 47.9% of the 267 cases by virus isolation, PCR/ESI-MS, and both methods, respectively. When both methods were used, the influenza A virus (24.3%) and rhinoviruses (9.4%) were the most frequently identified viruses, whereas human coronaviruses, human metapneumovirus (hMPV), enteroviruses, adenoviruses, respiratory syncytial virus, and parainfluenza viruses were identified in small proportions of cases (<5% of cases for each type of virus). Coinfection was observed in 4.1% of cases. In the control group, only 1 (2.4%) sample tested positive for a respiratory virus by PCR/ESI-MS. Patients who were undergoing steroid treatment, had an active malignancy, or suffered from chronic obstructive pulmonary disease (COPD) were at risk for rhinovirus, hMPV, or parainfluenza infections, respectively. Overall, immunocompromised patients, patients with COPD, and patients receiving dialysis were at risk for noninfluenza respiratory virus infection. Rhinoviruses (12.7%), influenza A virus (10.9%), and parainfluenza viruses (7.3%) were the most common viruses involved in the 55 cases of lower RTIs. The factors of parainfluenza infection, old age, and immunosuppression were independently associated with lower RTIs. In conclusion, PCR/ESI-MS improved the diagnostic yield for viral RTIs. Non-influenza respiratory virus infections were associated with patients with comorbidities and with lower RTIs. Additional studies that delineate the clinical need for including non-influenza respiratory viruses in the diagnostic work-up in these populations are warranted.
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Affiliation(s)
- Hsin-I Shih
- From the Departments of Emergency Medicine (H-IS, H-CH); Public Health (H-IS); Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University (C-HC, W-CK, C-JW); National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes (H-CW, I-JS, J-RW, M-IH, C-JW); Department of Medical Laboratory Science and Biotechnology (J-RW); and Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan (HSS)
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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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Hardick J, Dugas A, Goheen J, Rothman R, Gaydos C. Prospective comparison of RT-PCR/ESI-MS to Prodesse ProFlu Plus and Cepheid GenXpert for the detection of Influenza A and B viruses. J Virol Methods 2015; 214:43-5. [PMID: 25681525 PMCID: PMC4560249 DOI: 10.1016/j.jviromet.2015.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 01/30/2015] [Accepted: 01/31/2015] [Indexed: 11/16/2022]
Abstract
RT-PCR/ESI-MS was compared to two gold standards, Prodesse ProFlu Plus and Cepheid ExpertFlu.
RT-PCR/ESI-MS has previously demonstrated the capability to detect and identify respiratory viral pathogens in nasopharyngeal swabs. This study expands on previous research by performing a prospective evaluation of RT-PCR/ESI-MS to detect and identify Influenza A and B viruses compared to Prodesse ProFlu Plus and combined ProFlu Plus and Cepheid Xpert Flu. ProFlu Plus was also used as a gold standard for comparison for respiratory syncytial virus detection. Using ProFlu Plus as a gold standard, RT-PCR/ESI-MS had sensitivity and specificity of 82.1% (23/28) and 100% (258/258), respectively, for Influenza A, 100% (16/16) and 99.6% (269/270), respectively for Influenza B, and 88.6% (39/44) and 99.6% (241/242) for any Influenza virus. Using matching results from ProFlu Plus and Xpert Flu as a gold standard, RT-PCR/ESI-MS had 85.2% (23/27) and 100% (259/259) sensitivity and specificity respectively for Influenza A, 100% (14/14) and 99.6% (270/272), respectively for Influenza B virus. Overall, RT-PCR/ESI-MS was not as sensitive as the combined gold standard of ProFlu Plus and Xpert Flu, although it has the capability of detecting other respiratory viruses.
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Affiliation(s)
- Justin Hardick
- Johns Hopkins University School of Medicine, Division of Infectious Diseases, United States.
| | - Andrea Dugas
- Johns Hopkins University School of Medicine, Department of Emergency Medicine, United States
| | - Joshua Goheen
- Johns Hopkins University School of Medicine, Division of Infectious Diseases, United States
| | - Richard Rothman
- Johns Hopkins University School of Medicine, Department of Emergency Medicine, United States
| | - Charlotte Gaydos
- Johns Hopkins University School of Medicine, Division of Infectious Diseases, United States
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Role of Analytics in Viral Safety. VACCINE ANALYSIS: STRATEGIES, PRINCIPLES, AND CONTROL 2015. [PMCID: PMC7122056 DOI: 10.1007/978-3-662-45024-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
In summary, this chapter reviews the principles of how the current and routine tests detect adventitious agents, and reviews how novel and emerging methods differ in their detection principles. These facets may permit novel methods to emerge to supplement, refine, or replace the routine methods. We have suggested a framework for risk assessment to assure biosafety in vaccines and suggested quantitative modeling to help crystallize thinking about the place of testing, either routine or novel, in this assurance. We assert that testing for adventitious agents should not be the sole basis on which product biosafety is assured. Appropriate sourcing and quality control of raw and starting materials, adherence to principles of Good Manufacturing Practices, including environmental and personnel monitoring and process validation, and finally, testing as verification are the package needed for maximal assurance of biosafety. Thus, a pathway forward to a new paradigm for adventitious agent testing exists in which detection of a broader array of potential adventitious agents might be included in the testing, with adequate sensitivity to provide the needed assurance of verification that there has been no catastrophic breach, in the context of the overall process, design, and adherence to cGMP. Furthermore, it is our hope that we may be able to implement the 3 Rs policy to reduce, replace, and/or refine the use of animals in product safety testing, at the same time that we provide greater assurance of the biosafety of vaccines.
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Improving the diagnosis of bloodstream infections: PCR coupled with mass spectrometry. BIOMED RESEARCH INTERNATIONAL 2014; 2014:501214. [PMID: 24818144 PMCID: PMC4000954 DOI: 10.1155/2014/501214] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 02/27/2014] [Indexed: 12/22/2022]
Abstract
The reference method for the diagnosis of bloodstream infections is blood culture followed by biochemical identification and antibiotic susceptibility testing of the isolated pathogen. This process requires 48 to 72 hours. The rapid administration of the most appropriate antimicrobial treatment is crucial for the survival of septic patients; therefore, a rapid method that enables diagnosis directly from analysis of a blood sample without culture is needed. A recently developed platform that couples broad-range PCR amplification of pathogen DNA with electrospray ionization mass spectrometry (PCR/ESI-MS) has the ability to identify virtually any microorganism from direct clinical specimens. To date, two clinical evaluations of the PCR/ESI-MS technology for the diagnosis of bloodstream infections from whole blood have been published. Here we discuss them and describe recent improvements that result in an enhanced sensitivity. Other commercially available assays for the molecular diagnosis of bloodstream infections from whole blood are also reviewed. The use of highly sensitive molecular diagnostic methods in combination with conventional procedures could substantially improve the management of septic patients.
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Hardick J, Sadiq S, Perelstein E, Peterson S, Rothman R, Gaydos CA. A case-control study evaluating RT-PCR/ESI-MS technology compared to direct fluorescent antibody and xTAG RVP PCR. Diagn Microbiol Infect Dis 2014; 79:187-9. [PMID: 24657170 PMCID: PMC4557781 DOI: 10.1016/j.diagmicrobio.2014.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 02/03/2014] [Accepted: 02/11/2014] [Indexed: 11/02/2022]
Abstract
Waste nasopharyngeal swabs (N = 244) were evaluated by the reverse-transcriptase polymerase chain reaction/electrospray ionization mass spectrometry PLEX-ID Broad Respiratory Virus Surveillance Kit version 2.5 compared to direct fluorescent antibody and xTAG Respiratory Virus Panel for percent agreement, sensitivity, and specificity. Sensitivity and specificity were 91% (111/122) and 95.1% (116/122), respectively. Sensitivity by virus, except parainfluenza, was 92.9-100%, and specificity was 99-100%.
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Affiliation(s)
- Justin Hardick
- Johns Hopkins University School of Medicine, Division of Infectious Diseases, Baltimore, MD, USA.
| | - Sufyan Sadiq
- Johns Hopkins University, Department of Emergency Medicine, Baltimore, MD, USA
| | | | - Stephen Peterson
- Johns Hopkins University, Department of Emergency Medicine, Baltimore, MD, USA
| | - Richard Rothman
- Johns Hopkins University School of Medicine, Division of Infectious Diseases, Baltimore, MD, USA; Johns Hopkins University, Department of Emergency Medicine, Baltimore, MD, USA
| | - Charlotte A Gaydos
- Johns Hopkins University School of Medicine, Division of Infectious Diseases, Baltimore, MD, USA; Johns Hopkins University, Department of Emergency Medicine, Baltimore, MD, USA
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Chen J, Fu Y, Ju L, Miao X, Shen Y, He L, Wang W, Jin J, Shao L, Sampath R, Ecker DJ, Zhang Y, Li M, Cheng X, Zhang W. Detection and identification of viral pathogens in patients with hand, foot, and mouth disease by multilocus PCR, reverse-transcription PCR and electrospray ionization mass spectrometry. J Clin Virol 2014; 59:115-9. [DOI: 10.1016/j.jcv.2013.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/11/2013] [Accepted: 11/18/2013] [Indexed: 11/25/2022]
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Metzgar D, Lovari R, Ray K, Baynes D, Drapp D, Frinder M, Vijesurier R, Stemler M, Ofsaiof R, Carolan H, Welk J, Toleno D, Ranken R, Hall TA, Massire C, Sampath R, Blyn LB, Goveia J, Schneider G. Analytical characterization of an assay designed to detect and identify diverse agents of disseminated viral infection. J Clin Virol 2013; 59:177-83. [PMID: 24440177 DOI: 10.1016/j.jcv.2013.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 12/14/2013] [Accepted: 12/18/2013] [Indexed: 11/30/2022]
Abstract
BACKGROUND Diverse viruses often reactivate in or infect cancer patients, patients with immunocompromising infections or genetic conditions, and transplant recipients undergoing immunosuppressive therapy. These infections can disseminate, leading to death, transplant rejection, and other severe outcomes. OBJECTIVES To develop and characterize an assay capable of inclusive and accurate identification of diverse potentially disseminating viruses directly from plasma specimens. STUDY DESIGN We developed a PCR/electrospray ionization mass spectrometry (PCR/ESI-MS) assay designed to simultaneously detect and identify adenovirus, enterovirus, polyomaviruses JC and BK, parvovirus B19, HSV-1, HSV-2, VZV, EBV, CMV, and herpesviruses 6-8 in plasma specimens. The assay performance was characterized analytically, and the results from clinical plasma samples were compared to the results obtained from single-analyte real time PCR tests currently used in clinical practice. RESULTS The assay demonstrated sensitivity and specificity to diverse strains of the targeted viral families and robustness to interfering substances and potentially cross reacting organisms. The assay yielded 94% sensitivity when testing clinical plasma samples previously identified as positive using standard-of-care real-time PCR tests for a single target virus (available samples included positive samples for 11 viruses targeted by the assay). CONCLUSIONS The assay functioned as designed, providing simultaneous broad-spectrum detection and identification of diverse agents of disseminated viral infection. Among 156 clinical samples tested, 37 detections were made in addition to the detections matching the initial clinical positive results.
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Affiliation(s)
- David Metzgar
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States.
| | - Robert Lovari
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Keith Ray
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Darcie Baynes
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Darren Drapp
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Mark Frinder
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Roy Vijesurier
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Michelle Stemler
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Reuben Ofsaiof
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Heather Carolan
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Joseph Welk
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Donna Toleno
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Raymond Ranken
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Thomas A Hall
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Christian Massire
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Rangarajan Sampath
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Lawrence B Blyn
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Jon Goveia
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - George Schneider
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
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Reverse transcription-PCR-electrospray ionization mass spectrometry for rapid detection of biothreat and common respiratory pathogens. J Clin Microbiol 2013; 51:3300-7. [PMID: 23903543 DOI: 10.1128/jcm.01443-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Electrospray ionization mass spectrometry (ESI-MS) analysis of reverse transcription (RT)-PCR amplicons from human respiratory samples allows for broad pathogen identification approximately 8 h after collection. We investigated the performance characteristics of a high-throughput RT-PCR-coupled ESI-MS assay for distinguishing biothreat (BT) agents from common bacterial, fungal, and viral respiratory pathogens in bronchoalveolar lavage (BAL) fluid specimens from subjects with suspected respiratory infections. In a retrospective case series, 202 BAL fluid specimens were collected at the Johns Hopkins Hospital between August 2010 and February 2011 from patients with suspected acute respiratory infections. Samples were processed using standard bacterial, viral, and fungal testing in the clinical microbiology laboratory as part of routine care and then were blindly spiked with either water or nucleic acids from BT organisms (Bacillus anthracis, Yersinia pestis, Francisella tularensis, Brucella spp., Burkholderia spp., and Rickettsia prowazekii) and tested by RT-PCR-ESI-MS. The sensitivities and specificities of RT-PCR-ESI-MS versus standard clinical methods were as follows: for mock BT DNA, 98.5% sensitivity (95% confidence interval [CI], 94.2 to 99.7%) and 100% specificity (95% CI, 93.1 to 100.0%); for bacterial pathogens, 81.8% sensitivity (95% CI, 74.3 to 87.6%) and 73.6% specificity (95% CI, 64.2 to 81.4%); for viral pathogens, 93.3% sensitivity (95% CI, 66.0 to 99.7%) and 97.3% specificity (95% CI, 89.7 to 99.5%); for fungal pathogens, 42.6% sensitivity (95% CI, 29.5 to 56.7%) and 97.8% specificity (95% CI, 91.8 to 99.6%). Our data suggest that RT-PCR-ESI-MS is a useful adjunct to standard culture protocols for rapid detection of both BT and common respiratory pathogens; further study is required for assay validation, especially for fungal detection, and potential implementation.
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Abstract
Community-acquired pneumonia (CAP) accounts for major morbidity and mortality in the United States. With improved broad-spectrum antibiotics, the implementation of diagnostic studies has declined and most patients do not have an etiologic pathogen of CAP identified. To enhance the appropriate use of antiviral agents and prevent overuse of antibiotics, the successful management of CAP requires rapid and accurate diagnosis of the etiologic agent of CAP. This article provides an overview of the new rapid molecular tests for the diagnosis of influenza, other respiratory viruses, and bacteria compared with nonmolecular tests and how their use for directed therapy can enhance and improve the management of CAP.
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Affiliation(s)
- Charlotte A Gaydos
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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20
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Li L, Chen QY, Li YY, Wang YF, Yang ZF, Zhong NS. Comparison among nasopharyngeal swab, nasal wash, and oropharyngeal swab for respiratory virus detection in adults with acute pharyngitis. BMC Infect Dis 2013; 13:281. [PMID: 23786598 DOI: 10.1186/1471-2334-13-281] [citation(s)] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Accepted: 06/17/2013] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND Acute pharyngitis is frequently seen in primary care. Acute viral pharyngitis may be easily misdiagnosed as acute bacterial pharyngitis. Laboratory-confirmed diagnosis of respiratory viruses is recommended. The purpose of this study was to compare the sensitivities among oropharyngeal swab (OPS), nasopharyngeal swab (NPS), and nasal wash (NW) in adults with acute pharyngitis. METHODS OPS, NPS, and NW were obtained from each participant with acute pharyngitis. The specimens were tested for 15 respiratory viruses by TaqMan real-time polymerase chain reaction. A sample was considered to be a true positive if any of the specimens was positive. The sensitivities among samples were compared by chi-square test or Fisher's exact test, as appropriate. RESULTS One hundred three triple samples collected consecutively by OPS, NPS, and NW were obtained. In 73 patients, one or more viruses were detected by any of the three methods. Among all viruses, the sensitivity of NPS was significantly higher than that of NW (74% vs. 49%, respectively; p < 0.01) and OPS (74% vs. 49%, respectively; p < 0.01). CONCLUSIONS Flocked NPS collection may be the most effective alternative to NW and OPS for detection of respiratory viruses in adults with acute pharyngitis using TaqMan real-time polymerase chain reaction.
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Affiliation(s)
- Li Li
- Guangzhou Institute of Respiratory Disease, State Key Laboratory of Respiratory Diseases (Guangzhou Medical University), The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Road, Guangzhou 510120, China
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21
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Li L, Chen QY, Li YY, Wang YF, Yang ZF, Zhong NS. Comparison among nasopharyngeal swab, nasal wash, and oropharyngeal swab for respiratory virus detection in adults with acute pharyngitis. BMC Infect Dis 2013; 13:281. [PMID: 23786598 PMCID: PMC3698019 DOI: 10.1186/1471-2334-13-281] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Accepted: 06/17/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acute pharyngitis is frequently seen in primary care. Acute viral pharyngitis may be easily misdiagnosed as acute bacterial pharyngitis. Laboratory-confirmed diagnosis of respiratory viruses is recommended. The purpose of this study was to compare the sensitivities among oropharyngeal swab (OPS), nasopharyngeal swab (NPS), and nasal wash (NW) in adults with acute pharyngitis. METHODS OPS, NPS, and NW were obtained from each participant with acute pharyngitis. The specimens were tested for 15 respiratory viruses by TaqMan real-time polymerase chain reaction. A sample was considered to be a true positive if any of the specimens was positive. The sensitivities among samples were compared by chi-square test or Fisher's exact test, as appropriate. RESULTS One hundred three triple samples collected consecutively by OPS, NPS, and NW were obtained. In 73 patients, one or more viruses were detected by any of the three methods. Among all viruses, the sensitivity of NPS was significantly higher than that of NW (74% vs. 49%, respectively; p < 0.01) and OPS (74% vs. 49%, respectively; p < 0.01). CONCLUSIONS Flocked NPS collection may be the most effective alternative to NW and OPS for detection of respiratory viruses in adults with acute pharyngitis using TaqMan real-time polymerase chain reaction.
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Affiliation(s)
- Li Li
- Guangzhou Institute of Respiratory Disease, State Key Laboratory of Respiratory Diseases (Guangzhou Medical University), The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Road, Guangzhou 510120, China
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A Murillo L, Hardick J, Jeng K, Gaydos CA. Evaluation of the Pan Influenza detection kit utilizing the PLEX-ID and influenza samples from the 2011 respiratory season. J Virol Methods 2013; 193:173-6. [PMID: 23764420 DOI: 10.1016/j.jviromet.2013.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 05/21/2013] [Accepted: 06/03/2013] [Indexed: 10/26/2022]
Abstract
A comparison study was performed between the PLEX-ID and the CDC RT-PCR method for the detection and identification of Influenza A viruses using nasopharyngeal samples (N=75) collected between January and May 2011. Overall agreement was 89.3% (67/75 kappa=0.57 95% CI 0.3-0.89). Positive percent agreement was 92.3% (60/65); negative percent agreement was 70% (7/10). H1N1 pdm09 identified: 42.6% (32/75) and 54.7% (41/75) by PLEX-ID and CDC RT-PCR, respectively. H3N2 identified: 29.3% (22/75) and 32% (24/75) of samples by PLEX-ID and CDC RT-PCR, respectively. Negatives identified: 16% (12/75) and 13.3% (10/75), by PLEX-ID and CDC RT-PCR respectively. For influenza viruses identified as H1N1 pdm09, Influenza A virus A/NEW YORK/15/2009(H1N1 pdm09) was the most prevalent genotype at 50% (16/32), followed by A/CALIFORNIA/05/2009(H1N1 pdm09) at 18.2% (6/32). Updated assay plates containing additional primers designed for H1N1 pdm09 HA and NA genes were utilized for this evaluation. Among H1N1 pdm09 samples, the HA gene was conserved in 96.9% (31/32) of samples. The NA gene was conserved in 96.9% (31/32).
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Affiliation(s)
- Luis A Murillo
- The Johns Hopkins University School of Medicine, Division of Infectious Diseases, 855 North Wolfe Street, Rangos Building, Room 530, Baltimore, MD 21205, United States.
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Jordana-Lluch E, Carolan HE, Giménez M, Sampath R, Ecker DJ, Quesada MD, Mòdol JM, Arméstar F, Blyn LB, Cummins LL, Ausina V, Martró E. Rapid diagnosis of bloodstream infections with PCR followed by mass spectrometry. PLoS One 2013; 8:e62108. [PMID: 23626775 PMCID: PMC3633912 DOI: 10.1371/journal.pone.0062108] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 03/19/2013] [Indexed: 01/30/2023] Open
Abstract
Achieving a rapid microbiological diagnosis is crucial for decreasing morbidity and mortality of patients with a bloodstream infection, as it leads to the administration of an appropriate empiric antimicrobial therapy. Molecular methods may offer a rapid alternative to conventional microbiological diagnosis involving blood culture. In this study, the performance of a new technology that uses broad-spectrum PCR coupled with mass spectrometry (PCR/ESI-MS) was evaluated for the detection of microorganisms directly from whole blood. A total of 247 whole blood samples and paired blood cultures were prospectively obtained from 175 patients with a suspicion of sepsis. Both sample types were analyzed using the PCR/ESI-MS technology, and the results were compared with those obtained by conventional identification methods. The overall agreement between conventional methods and PCR/ESI-MS performed in blood culture aliquots was 94.2% with 96.8% sensitivity and 98.5% specificity for the molecular method. When comparing conventional methods with PCR/ESI-MS performed in whole blood specimens, the overall agreement was 77.1% with 50% sensitivity and 93.8% specificity for the molecular method. Interestingly, the PCR/ESI-MS technology led to the additional identification of 13 pathogens that were not found by conventional methods. Using the PCR/ESI-MS technology the microbiological diagnosis of bloodstream infections could be anticipated in about half of the patients in our setting, including a small but significant proportion of patients newly diagnosed. Thus, this promising technology could be very useful for the rapid diagnosis of sepsis in combination with traditional methods.
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Affiliation(s)
- Elena Jordana-Lluch
- Microbiology Department, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Heather E. Carolan
- Ibis Biosciences, an Abbott company, Carlsbad, California, United States of America
| | - Montserrat Giménez
- Microbiology Department, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Rangarajan Sampath
- Ibis Biosciences, an Abbott company, Carlsbad, California, United States of America
| | - David J. Ecker
- Ibis Biosciences, an Abbott company, Carlsbad, California, United States of America
| | - M. Dolores Quesada
- Microbiology Department, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Josep M. Mòdol
- Emergency Room, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Fernando Arméstar
- Intensive Care Unit, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Lawrence B. Blyn
- Ibis Biosciences, an Abbott company, Carlsbad, California, United States of America
| | - Lendell L. Cummins
- Ibis Biosciences, an Abbott company, Carlsbad, California, United States of America
| | - Vicente Ausina
- Microbiology Department, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Bunyola, Spain
- * E-mail:
| | - Elisa Martró
- Microbiology Department, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
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Microbiota Evaluation of Patients With a Boston Type I Keratoprosthesis Treated With Topical 0.5% Moxifloxacin and 5% Povidone–Iodine. Cornea 2013; 32:407-11. [DOI: 10.1097/ico.0b013e31824a8b9b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Chen KF, Hsieh YH, Gaydos CA, Valsamakis A, Rothman RE. Derivation of a clinical prediction rule to predict hospitalization for influenza in EDs. Am J Emerg Med 2013; 31:529-34. [DOI: 10.1016/j.ajem.2012.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/10/2012] [Accepted: 10/16/2012] [Indexed: 12/01/2022] Open
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Abstract
PURPOSE OF REVIEW Shortly after the advent of severe acute respiratory syndrome and the avian influenza, the emergence of the influenza A(H1N1)2009 pandemic caused significant vibrations to the public health authorities and stressed the health systems worldwide. We sought to investigate whether this experience has altered our knowledge and our current and future practice on the management of severe acute respiratory infections (SARI) and community-acquired pneumonia. RECENT FINDINGS A changing epidemiology was demonstrated, with obesity and pregnancy beyond established risk groups for influenza A, other clinical syndromes beyond primary viral pneumonia, possible coinfections by other viral beyond bacterial pathogens and a disappointing performance of all available severity assessment tools. On the treatment topic, accumulating evidence suggesting worse outcomes argues against the use of corticosteroids, but some noninvasive ventilating modalities require further assessment. SUMMARY The recent influenza A(H1N1)2009 pandemic has highlighted our weaknesses relating to the diagnosis and assessment of severity of SARI, compromising early treatment and ultimate outcomes; further research based on this experience will help to improve prognosis and boost our future preparedness. An important message is the necessity of international collaboration for the rapid dissemination of locally acquired knowledge.
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Lavigne JP, Espinal P, Dunyach-Remy C, Messad N, Pantel A, Sotto A. Mass spectrometry: a revolution in clinical microbiology? Clin Chem Lab Med 2013; 51:257-70. [DOI: 10.1515/cclm-2012-0291] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 08/28/2012] [Indexed: 11/15/2022]
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Jordana-Lluch E, Martró Català E, Ausina Ruiz V. [Mass spectrometry in the clinical microbiology laboratory]. Enferm Infecc Microbiol Clin 2012; 30:635-44. [PMID: 22381225 PMCID: PMC7103318 DOI: 10.1016/j.eimc.2012.01.012] [Citation(s) in RCA: 9] [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: 09/27/2011] [Revised: 12/23/2011] [Accepted: 01/04/2012] [Indexed: 11/30/2022]
Abstract
Infectious diseases are still a cause of high mortality and morbidity rates. Current microbiological diagnostic methods are based on culture and phenotypic identification of isolated microorganisms, which can be obtained in about 24-48 h. Given that the microbiological identification is of major importance for patient management, new diagnostic methods are needed in order to detect and identify microorganisms in a timely and accurate manner. Over the last few years, several molecular techniques based on the amplification of microbial nucleic acids have been developed with the aim of reducing the time needed for the identification of the microorganisms involved in different infectious processes. On the other hand, mass spectrometry has emerged as a rapid and consistent alternative to conventional methods for microorganism identification. This review describes the most widely used mass spectrometry technologies -matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and electrospray ionization time-of-flight (ESI-TOF)-, both for protein and nucleic acid analysis, as well as the commercial platforms available. Related publications of most interest in clinical microbiology are also reviewed.
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Affiliation(s)
- Elena Jordana-Lluch
- Servicio de Microbiología, Fundación Instituto de Investigación en Ciencias de la Salud Germans Trias y Pujol, Hospital Universitario Germans Trias y Pujol, Universidad Autónoma de Barcelona, Badalona, Barcelona, España
| | - Elisa Martró Català
- Servicio de Microbiología, Fundación Instituto de Investigación en Ciencias de la Salud Germans Trias y Pujol, Hospital Universitario Germans Trias y Pujol, Universidad Autónoma de Barcelona, Badalona, Barcelona, España
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, España
| | - Vicente Ausina Ruiz
- Servicio de Microbiología, Fundación Instituto de Investigación en Ciencias de la Salud Germans Trias y Pujol, Hospital Universitario Germans Trias y Pujol, Universidad Autónoma de Barcelona, Badalona, Barcelona, España
- CIBER Enfermedades Respiratorias (CIBERES), Bunyola, Mallorca, España
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Detection, identification, and distribution of fungi in bronchoalveolar lavage specimens by use of multilocus PCR coupled with electrospray ionization/mass spectrometry. J Clin Microbiol 2012; 51:136-41. [PMID: 23100337 DOI: 10.1128/jcm.01907-12] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
As pulmonary fungal infections continue to increase due to an increasing number of immunocompromised patients, rapid detection and accurate identification of these fungal pathogens are critical. A broad fungal assay was developed by incorporating broad-range multilocus PCR amplification and electrospray ionization/mass spectrometry (PCR/ESI-MS) to detect and identify fungal organisms directly from clinical specimens. The aims of this study were to evaluate the performance of PCR/ESI-MS for detection, identification, and determination of the distribution of fungal organisms in bronchoalveolar lavage (BAL) fluid specimens. The BAL fluid specimens submitted for fungal culture at Vanderbilt University Medical Center between May 2005 and October 2011 were included. Cultures and identification were done using standard procedures. In addition, DNA was extracted from BAL fluid specimens, and fungal DNA amplification/identification were performed by PCR/ESI-MS. The results were compared with those of the standard cultures. A total of 691 nonduplicated BAL fluid specimens with sufficient leftover volume for molecular testing were evaluated using PCR/ESI-MS. Among them, 134 specimens (19.4%) were positive for fungi by both culture and PCR/ESI-MS testing. Of the dual-positive specimens, 125 (93.3%) were positive for Candida and Aspergillus species, with concordances between culture and PCR/ESI-MS results being 84 (67.2%) at the species level and 109 (87.2%) at the genus level. In addition, 243 (35.2%) and 30 (4.3%) specimens were positive only by PCR/ESI-MS or by culture, respectively (odds ratio [OR] = 11.95, 95% confidence interval [CI] = 7.90 to 18.17, P = 0.0000). Codetection of fungal organisms was noted in 23 (3.3%) specimens by PCR/ESI-MS, which was significantly higher than the 4 (0.6%) in which they were noted by culture (OR = 5.91, 95% CI = 1.93 to 20.27, P = 0.0002). Among 53 specimens in which cultures failed because of bacterial overgrowth, at least one fungus was identified in 26 specimens (47.3%) by PCR/ESI-MS. PCR/ESI-MS provides an advanced tool for rapid and sensitive detection, identification, and determination of the distribution of fungal organisms directly from BAL fluid specimens. Moreover, it detected fungal organisms in specimens in which cultures failed because of bacterial overgrowth. The clinical relevance of the significantly higher detection rate of fungal organisms by PCR/ESI-MS merits further investigation.
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Clinical accuracy of a PLEX-ID flu device for simultaneous detection and identification of influenza viruses A and B. J Clin Microbiol 2012; 51:40-5. [PMID: 23077123 DOI: 10.1128/jcm.01978-12] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Respiratory tract infections caused by influenza A and B viruses often present nonspecifically, and a rapid, high-throughput laboratory technique that can identify influenza viruses is clinically and epidemiologically desirable. The PLEX-ID Flu assay (Abbott Molecular Inc., Des Plaines, IL) incorporates multilocus PCR and electrospray ionization-mass spectrometry to detect and differentiate influenza A 2009 H1N1 (H1N1-p), seasonal H1N1 (H1N1-s), influenza A H3N2, and influenza B viruses in nasopharyngeal swab (NPS) specimens. The clinical performance characteristics of the PLEX-ID Flu assay in symptomatic patients were determined in this multicenter trial. A total of 2,617 prospectively and retrospectively collected NPS specimens from patients with influenza-like illness between February 2008 and 28 May 2010 were eligible for inclusion in the study. Each specimen was tested in parallel by the PLEX-ID Flu assay and by the Prodesse ProFLU+ assay (Prodesse Inc., Madison, WI), to detect influenza A and B viruses. Specimens testing positive for influenza A virus by ProFLU+ were subtyped as H1N1-p, H1N1-s, or H3N2 by using the ProFAST+ assay (Gen-Probe Prodesse Inc.). The reproducibility of the PLEX-ID Flu assay ranged from 98.3 to 100.0%, as determined by testing a nine-specimen panel at three clinical sites on each of 5 days. Positive percent agreements (PPAs) and negative percent agreements (NPAs) of the PLEX-ID Flu assay were 94.5% and 99.0% for influenza A virus and 96.0% and 99.9% for influenza B virus, respectively. For the influenza A virus subtyping characterization, the PLEX-ID Flu assay had PPAs and NPAs of 98.3% and 97.5% for H1N1-p, 88.6% and 100.0% for H1N1-s, and 98.0% and 99.9% for H3N2, respectively. The overall agreements between the PLEX-ID and Prodesse ProFLU+/ProFAST+ assays were 97.1 to 100.0%. Bidirectional Sanger sequencing analysis revealed that 87.5% of 96 discrepant results between the PLEX-ID Flu and ProFLU+/ProFAST+ assays were found upon influenza A virus detection and H1N1-p subtyping. The PLEX-ID Flu assay demonstrated a high level of accuracy for the simultaneous detection and identification of influenza A and B viruses in patient specimens, providing a new laboratory tool for the rapid diagnosis and management of influenza A and B virus infections.
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Diagnostic performance of two highly multiplexed respiratory virus assays in a pediatric cohort. J Clin Virol 2012; 55:168-72. [PMID: 22832060 PMCID: PMC3586269 DOI: 10.1016/j.jcv.2012.06.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/26/2012] [Accepted: 06/28/2012] [Indexed: 11/20/2022]
Abstract
Background Rapid detection of respiratory viruses is important for management and infection control in hospitalized patients. Multiplex nucleic acid tests (NATs) have begun to replace conventional methods as gold standards for respiratory virus detection. Objective To compare the performance of two large multiplex NATS, ResPlex II (RPII) and Respiratory Virus Surveillance kit with electrospray ionization mass spectrometry (RVS/MS) using nasopharyngeal aspirates (NPAs) from hospitalized children who had been tested previously with conventional methods. Study design Stored residual NPAs (N = 306) were tested concomitantly by RPII and RVS/MS. Alternate NATs were used to adjudicate discordant results. Results More viruses were detected with multiplex NATs (RPII, 110; RVS/MS, 109) than conventional assays (86); diagnostic gain was primarily for fastidious viruses (coronaviruses and enteroviruses [EVs]/human rhinoviruses [HRVs]). Total positive and negative agreement between the multiplex NATs for all viruses detected was quite high (86% positive agreement, 99% negative agreement). Most individual viruses were detected with fairly equivalent accuracy by the multiplex NATs, except for adenoviruses (RPII sensitivity 40%) and human metapneumovirus (RVS/MS sensitivity 42%). RPII had the advantage of detecting EVs and HRVs, however, it demonstrated considerable EV/HRV cross-reactivity (29 HRV-positive specimens by real-time PCR were positive for EV by RPII and 21 specimens positive for HRV only by RT-PCR were dual positive for EV/HRV by RPII). RPII also had reduced sensitivity for HRV detection (in 36 specimens, HRV was detected by RT-PCR but not by RPII). Conclusions Both multiplex NATs were promising, but had notable limitations.
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Sampath R, Mulholland N, Blyn LB, Massire C, Whitehouse CA, Waybright N, Harter C, Bogan J, Miranda MS, Smith D, Baldwin C, Wolcott M, Norwood D, Kreft R, Frinder M, Lovari R, Yasuda I, Matthews H, Toleno D, Housley R, Duncan D, Li F, Warren R, Eshoo MW, Hall TA, Hofstadler SA, Ecker DJ. Comprehensive biothreat cluster identification by PCR/electrospray-ionization mass spectrometry. PLoS One 2012; 7:e36528. [PMID: 22768032 PMCID: PMC3387173 DOI: 10.1371/journal.pone.0036528] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 04/02/2012] [Indexed: 11/18/2022] Open
Abstract
Technology for comprehensive identification of biothreats in environmental and clinical specimens is needed to protect citizens in the case of a biological attack. This is a challenge because there are dozens of bacterial and viral species that might be used in a biological attack and many have closely related near-neighbor organisms that are harmless. The biothreat agent, along with its near neighbors, can be thought of as a biothreat cluster or a biocluster for short. The ability to comprehensively detect the important biothreat clusters with resolution sufficient to distinguish the near neighbors with an extremely low false positive rate is required. A technological solution to this problem can be achieved by coupling biothreat group-specific PCR with electrospray ionization mass spectrometry (PCR/ESI-MS). The biothreat assay described here detects ten bacterial and four viral biothreat clusters on the NIAID priority pathogen and HHS/USDA select agent lists. Detection of each of the biothreat clusters was validated by analysis of a broad collection of biothreat organisms and near neighbors prepared by spiking biothreat nucleic acids into nucleic acids extracted from filtered environmental air. Analytical experiments were carried out to determine breadth of coverage, limits of detection, linearity, sensitivity, and specificity. Further, the assay breadth was demonstrated by testing a diverse collection of organisms from each biothreat cluster. The biothreat assay as configured was able to detect all the target organism clusters and did not misidentify any of the near-neighbor organisms as threats. Coupling biothreat cluster-specific PCR to electrospray ionization mass spectrometry simultaneously provides the breadth of coverage, discrimination of near neighbors, and an extremely low false positive rate due to the requirement that an amplicon with a precise base composition of a biothreat agent be detected by mass spectrometry.
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Affiliation(s)
- Rangarajan Sampath
- Ibis Biosciences, Abbott, Carlsbad, California, United States of America.
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Wolk DM, Kaleta EJ, Wysocki VH. PCR-electrospray ionization mass spectrometry: the potential to change infectious disease diagnostics in clinical and public health laboratories. J Mol Diagn 2012; 14:295-304. [PMID: 22584138 PMCID: PMC7106027 DOI: 10.1016/j.jmoldx.2012.02.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 02/04/2012] [Accepted: 02/09/2012] [Indexed: 12/18/2022] Open
Abstract
During the past 20 years, microbial detection methods that are genetically based, such as real-time PCR and peptide nucleic acid fluorescent hybridization, coexisted with traditional microbiological methods and were typically based on the identification of individual genetic targets. For these methods to be successful, a potential cause of infection must be suspected. More recently, multiplex PCR and multiplex RT-PCR were used to enable more broad-range testing based on panels of suspected pathogens. PCR–electrospray ionization mass spectrometry (PCR-ESI/MS) has emerged as a technology that is capable of identifying nearly all known human pathogens either from microbial isolates or directly from clinical specimens. Assay primers are strategically designed to target one or more of the broad pathogen categories: bacterial, mycobacterial, fungal, or viral. With broad-range amplification followed by detection of mixed amplicons, the method can identify genetic evidence of known and unknown pathogens. This unique approach supports a higher form of inquiry, asking the following question: What is the genetic evidence of known or unknown pathogens in the patient sample? This approach has advantages over traditional assays that commonly target the presence or absence of one or more pathogens with known genetic composition. This review considers the breadth of the published literature and explores the possibilities, advantages, and limitations for implementation of PCR-ESI/MS in diagnostic laboratories.
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Affiliation(s)
- Donna M Wolk
- Division of Clinical Microbiology, Department of Pathology/BIO5 Institute, University of Arizona, Tucson, AZ 85724, USA.
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Cordey S, Thomas Y, Suter P, Kaiser L. Pilot Evaluation of RT-PCR/Electrospray Ionization Mass Spectrometry (PLEX-ID/Flu assay) on Influenza-Positive Specimens. Open Virol J 2012; 6:64-7. [PMID: 22611461 PMCID: PMC3355350 DOI: 10.2174/1874357901206010064] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 03/12/2012] [Accepted: 03/22/2012] [Indexed: 12/27/2022] Open
Abstract
The PLEX-ID/Flu assay has been recently developed to enable the detection and typing of influenza viruses based on the RT-PCR/electrospray ionization mass spectrometry technology.This novel assay was evaluated for typing performance on 201 positive influenza A or B nasopharyngeal swab specimens (NPS) detected by real-time RT-PCR during the 2010-2011 season. The PLEX-ID/Flu assay detected and characterized 91.3% and 95.3% of all influenza A and B samples, respectively. All non-typeable influenza A and B specimens by the assay showed low viral loads with threshold cycle values ≥ 33. Taken together, and although our results need to be confirmed by further prospective studies, the PLEX-ID/Flu assay detected positively and gave a typing result for 93% of all NPS detected positively by real-time RT-PCR, thus suggesting a potential role for influenza virus surveillance among other techniques.
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Affiliation(s)
- Samuel Cordey
- Swiss National Reference Centre for Emerging Viral Diseases, University of Geneva Hospitals, Geneva, Switzerland
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Sibley CD, Peirano G, Church DL. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology. INFECTION GENETICS AND EVOLUTION 2012; 12:505-21. [PMID: 22342514 PMCID: PMC7106020 DOI: 10.1016/j.meegid.2012.01.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 12/25/2022]
Abstract
Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.
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Affiliation(s)
- Christopher D. Sibley
- Department of Microbiology, Immunology & Infectious Diseases, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
| | - Gisele Peirano
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
| | - Deirdre L. Church
- Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Department of Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
- Corresponding author. Address: c/o Calgary Laboratory Services, 9-3535 Research Rd. N.W., Calgary, Alta, Canada T2L 2K8. Tel.: +1 403 770 3281; fax: +1 403 770 3347.
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Pabbaraju K, Wong S, Drews SJ. Rethinking approaches to improve the utilization of nucleic acid amplification tests for detection and characterization of influenza A in diagnostic and reference laboratories. Future Microbiol 2011; 6:1443-60. [PMID: 22122441 DOI: 10.2217/fmb.11.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Influenza A virus (IFVA) is a significant cause of respiratory infections worldwide and was also responsible for a recent pandemic in 2009. Laboratory identification of IFVA can guide antiviral therapy, assist in cohorting of patients and prevent antibiotic use. Characterization of the virus can track the emergence of novel strains, identify resistance and determine how circulating strains match with vaccine components. The gold standard for detection and characterization of IFVA is nucleic acid amplification technology (e.g., reverse transcriptase PCR [RT-PCR]), which must contend with a constantly evolving viral genome. Although molecular technology has been available for over two decades, there is still an operational gap between assay design and utilization of these tests for the diagnosis and characterization of IFVA. This review will discuss issues surrounding the implementation and use of RT-PCR for the identification and characterization of IFVA, and speculate on why RT-PCR has not been used more widely in clinical laboratories or moved closer to the patient. Newer, less widely used technologies that may change our laboratory practices will be identified and the authors will close with an attempt to identify some future applications of RT-PCR-based technologies for the detection and characterization of IFVA.
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Affiliation(s)
- Kanti Pabbaraju
- Provincial Laboratory for Public Health, Microbiology, 3030 Hospital Drive NW, Calgary, Alberta T2N 4W4, Canada
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Falchi A, Turbelin C, Andreoletti L, Arena C, Blanchon T, Bonmarin I, Hanslik T, Leruez-Ville M, De Lamballerie X, Carrat F. Nationwide surveillance of 18 respiratory viruses in patients with influenza-like illnesses: a pilot feasibility study in the French Sentinel Network. J Med Virol 2011; 83:1451-7. [PMID: 21638286 PMCID: PMC7166811 DOI: 10.1002/jmv.22113] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2011] [Indexed: 11/28/2022]
Abstract
The aim of the present study was to test the feasibility of integrating the diagnosis of 18 respiratory viruses into clinical surveillance of influenza‐like illness using a PCR‐DNA microarray detection assay. The study took place in the French Sentinel Network, a nationwide surveillance network of General Practitioners (GPs) representative of French GPs in terms age, location, and type of practice (urban/rural). Three virological laboratories also participated in the study. The study was planned for 5 weeks from January 25, 2010 to February 27, 2010. A subset of 150 Sentinel GPs, located in mainland France, was enrolled to collect clinical data and nasopharyngeal samples from every first patient of the week having a medical visit for influenza‐like illness defined as a sudden fever of 39°C or more with respiratory symptoms and myalgia. Sixty‐three GPs (42%) collected 103 samples while 87 GPs (58%) did not. GPs did not differ with respect to their age, gender, urban/rural distribution, or years of inscription in the Sentinel Network. Patients included were of a similar age and had similar vaccination characteristics, but were more frequently men than influenza‐like illness patients reported to the network during the study period. Sixty‐one viruses were detected from 56 of 96 (58%) interpretable samples. The respiratory viruses detected most frequently were metapneumovirus and respiratory syncytial virus. This study showed that virological diagnosis of 18 respiratory viruses can be combined with surveillance of clinical influenza‐like illness in general practice. Although feasibility has not been demonstrated yet, it will be evaluated over the winter of 2010–2011. J. Med. Virol. 83:1451–1457, 2011. © 2011 Wiley‐Liss, Inc.
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