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Koryukov MA, Oscorbin IP, Novikova LM, Gordukova MA, Turina IE, Galeeva EV, Kudlay DA, Filipenko ML. A Novel Multiplex LAMP Assay for the Detection of Respiratory Human Adenoviruses. Int J Mol Sci 2024; 25:7215. [PMID: 39000322 PMCID: PMC11241107 DOI: 10.3390/ijms25137215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Human adenoviruses (HAdVs) are common pathogens that are associated with a variety of diseases, including respiratory tract infections (RTIs). Without reliable, fast, and cost-effective detection methods for HAdVs, patients may be misdiagnosed and inappropriately treated. To address this problem, we have developed a multiplex loop-mediated isothermal amplification (LAMP) assay for the detection of the species Human adenovirus B (HAdV-B), Human adenovirus C (HAdV-C) and Human adenovirus E (HAdV-E) that cause RTIs. This multiplexing approach is based on the melting curve analysis of the amplicons with a specific melting temperature for each HAdV species. Without the need for typing of HAdVs, the LAMP results can be visually detected using colorimetric analysis. The assay reliably detects at least 375 copies of HAdV-B and -C and 750 copies of HAdV-E DNA per reaction in less than 35 min at 60 °C. The designed primers have no in silico cross-reactivity with other human respiratory pathogens. Validation on 331 nasal swab samples taken from patients with RTIs showed a 90-94% agreement rate with our in-house multiplex quantitative polymerase chain reaction (qPCR) method. Concordance between the quantitative and visual LAMP was 99%. The novel multiplexed LAMP could be an alternative to PCR for diagnostic purposes, saving personnel and equipment time, or could be used for point-of-care testing.
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Affiliation(s)
- Maksim A. Koryukov
- The Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; (M.A.K.)
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Igor P. Oscorbin
- The Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; (M.A.K.)
| | - Lidiya M. Novikova
- The Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; (M.A.K.)
| | - Maria A. Gordukova
- G. Speransky Children’s Hospital No. 9, 29 Shmitovsky Prospect, Moscow 123317, Russia
| | - Irina E. Turina
- Department of Natural Sciences, I.M. Sechenov First Moscow State Medical University, Pogodinskaya St. 1, Moscow 119991, Russia
| | - Elena V. Galeeva
- G. Speransky Children’s Hospital No. 9, 29 Shmitovsky Prospect, Moscow 123317, Russia
| | - Dmitry A. Kudlay
- Department of Natural Sciences, I.M. Sechenov First Moscow State Medical University, Pogodinskaya St. 1, Moscow 119991, Russia
| | - Maxim L. Filipenko
- The Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; (M.A.K.)
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Gunasekaran BM, Srinivasan S, Ezhilan M, Nesakumar N. Nucleic acid-based electrochemical biosensors. Clin Chim Acta 2024; 559:119715. [PMID: 38735514 DOI: 10.1016/j.cca.2024.119715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/01/2024] [Accepted: 05/01/2024] [Indexed: 05/14/2024]
Abstract
Colorectal cancer, breast cancer, oxidative DNA damage, and viral infections are all significant and major health threats to human health, presenting substantial challenges in early diagnosis. In this regard, a wide range of nucleic acid-based electrochemical platforms have been widely employed as point-of-care diagnostics in health care and biosensing technologies. This review focuses on biosensor design strategies, underlying principles involved in the development of advanced electrochemical genosensing devices, approaches for immobilizing DNA on electrode surfaces, as well as their utility in early disease diagnosis, with a particular emphasis on cancer, leukaemia, oxidative DNA damage, and viral pathogen detection. Notably, the role of biorecognition elements and nanointerfaces employed in the design and development of advanced electrochemical genosensors for recognizing biomarkers related to colorectal cancer, breast cancer, leukaemia, oxidative DNA damage, and viral pathogens has been extensively reviewed. Finally, challenges associated with the fabrication of nucleic acid-based biosensors to achieve high sensitivity, selectivity, a wide detection range, and a low detection limit have been addressed. We believe that this review will provide valuable information for scientists and bioengineers interested in gaining a deeper understanding of the fabrication and functionality of nucleic acid-based electrochemical biosensors for biomedical diagnostic applications.
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Affiliation(s)
- Balu Mahendran Gunasekaran
- School of Chemical & Biotechnology (SCBT), SASTRA Deemed University, Thanjavur 613 401, Tamil Nadu, India; Center for Nanotechnology & Advanced Biomaterials (CENTAB), SASTRA Deemed University, Thanjavur 613401, Tamil Nadu, India
| | - Soorya Srinivasan
- Department of Chemistry, A.V.V.M Sri Pushpam College (Autonomous), (Affiliated to Bharathidasan University, Tiruchirappalli), Poondi, Thanjavur, Tamil Nadu 613 503, India
| | - Madeshwari Ezhilan
- Department of biomedical engineering, Vel Tech Rangarajan Dr. Sagunthala R & D Institute of Science and Technology, Vel Nagar, Avadi, Chennai 600062, Tamil Nadu, India
| | - Noel Nesakumar
- School of Chemical & Biotechnology (SCBT), SASTRA Deemed University, Thanjavur 613 401, Tamil Nadu, India; Center for Nanotechnology & Advanced Biomaterials (CENTAB), SASTRA Deemed University, Thanjavur 613401, Tamil Nadu, India.
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AlFulayyih SF, Al Baridi SS, Alomar SA, Alshammari AN, Uddin MS. Impact of Respiratory Viruses and SARS-CoV-2 on Febrile Seizures in Saudi Children: Insights into Etiologies, Gender, and Familial Associations. Med Sci Monit 2024; 30:e942478. [PMID: 38192092 PMCID: PMC10787381 DOI: 10.12659/msm.942478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Childhood febrile seizures occur between 5 months and 6 years of age in children without a previous history of seizure and are associated with high temperature in the absence of intracranial infection. This retrospective study identified 71 children aged 6 months to 5 years with febrile seizures between 2017 and 2021 at a single center in Saudi Arabia and aimed to identify an association between common respiratory virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. MATERIAL AND METHODS Pediatric nasopharyngeal specimens were tested using a multiplex PCR respiratory panel detecting human coronaviruses (NL63, 229E, OC43, HKU1), influenza A/B, human adenovirus, parainfluenza viruses 1-4, respiratory syncytial virus, human metapneumovirus, rhinovirus/enterovirus, Middle East respiratory syndrome coronavirus, and, as of September 2021, SARS-CoV-2, confirmed using the Cepheid Xpert Xpress SARS-CoV2 RT-PCR kit. RESULTS In a cohort of 71 pediatric patients (median age, 19 months; 54.9% female), dominant pathogens included human rhinovirus/enterovirus (23.9%), influenza A/B (26.8%), and SARS-CoV-2 (14.1%). Concurrent infections were noted in 28.2%. Simple seizures occurred in 69%, and complex seizures in 31%. Females exhibited an 8.18-fold increased risk for complex seizures. Each additional fever day reduced complex seizure risk by 36%. Familial seizure history increased risk 8.76-fold. Human rhinovirus/enterovirus or parainfluenza infections inversely affected complex seizure likelihood compared with adenovirus. CONCLUSIONS In Saudi children with febrile seizures, distinct viral etiologies, sex, and familial links play pivotal roles. Given regional viral variations, region-tailored diagnostic and therapeutic strategies are paramount. A multicenter prospective cohort study is essential for comprehensive understanding.
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Affiliation(s)
- Saleh Fahad AlFulayyih
- Department of Pediatrics, Ministry of National Guard Health Affairs, Dammam, Saudi Arabia
| | - Sarah Saleh Al Baridi
- Department of Pediatrics, Ministry of National Guard Health Affairs, Dammam, Saudi Arabia
| | - Sara Amer Alomar
- Department of Pediatrics, Ministry of National Guard Health Affairs, Dammam, Saudi Arabia
| | | | - Mohammed Shahab Uddin
- Department of Pediatrics, Ministry of National Guard Health Affairs, Dammam, Saudi Arabia
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Fang W, Wu J, Cheng M, Zhu X, Du M, Chen C, Liao W, Zhi K, Pan W. Diagnosis of invasive fungal infections: challenges and recent developments. J Biomed Sci 2023; 30:42. [PMID: 37337179 DOI: 10.1186/s12929-023-00926-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/13/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND The global burden of invasive fungal infections (IFIs) has shown an upsurge in recent years due to the higher load of immunocompromised patients suffering from various diseases. The role of early and accurate diagnosis in the aggressive containment of the fungal infection at the initial stages becomes crucial thus, preventing the development of a life-threatening situation. With the changing demands of clinical mycology, the field of fungal diagnostics has evolved and come a long way from traditional methods of microscopy and culturing to more advanced non-culture-based tools. With the advent of more powerful approaches such as novel PCR assays, T2 Candida, microfluidic chip technology, next generation sequencing, new generation biosensors, nanotechnology-based tools, artificial intelligence-based models, the face of fungal diagnostics is constantly changing for the better. All these advances have been reviewed here giving the latest update to our readers in the most orderly flow. MAIN TEXT A detailed literature survey was conducted by the team followed by data collection, pertinent data extraction, in-depth analysis, and composing the various sub-sections and the final review. The review is unique in its kind as it discusses the advances in molecular methods; advances in serology-based methods; advances in biosensor technology; and advances in machine learning-based models, all under one roof. To the best of our knowledge, there has been no review covering all of these fields (especially biosensor technology and machine learning using artificial intelligence) with relevance to invasive fungal infections. CONCLUSION The review will undoubtedly assist in updating the scientific community's understanding of the most recent advancements that are on the horizon and that may be implemented as adjuncts to the traditional diagnostic algorithms.
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Affiliation(s)
- Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Junqi Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Mingrong Cheng
- Department of Anorectal Surgery, The Third Affiliated Hospital of Guizhou Medical University, Guizhou, 558000, China
| | - Xinlin Zhu
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Mingwei Du
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Wanqing Liao
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Kangkang Zhi
- Department of Vascular and Endovascular Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
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Alsulami AO, Chahine R, Kong M, Kimberlin DW, Whitley RJ, James SH. Impact of human coronavirus infections on paediatric patients at a tertiary paediatric hospital: a retrospective study of the prepandemic era. J Hosp Infect 2023; 134:27-34. [PMID: 36682627 PMCID: PMC9850843 DOI: 10.1016/j.jhin.2022.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/08/2022] [Accepted: 12/22/2022] [Indexed: 01/20/2023]
Abstract
BACKGROUND Human coronaviruses (HCoVs) are important respiratory pathogens in humans and animals. Most HCoVs are emerging pathogens, with five known human pathogens identified in the last two decades. AIM To examine the clinical course of HCoV infection in children to improve understanding of severity and outcomes. METHODS A retrospective review was undertaken of all encounters of children with known HCoV infection at a tertiary paediatric hospital from January 2015 to January 2018. Electronic medical records were reviewed for demographic data, HCoV type, viral co-pathogens, time to testing, need for hospitalization, requirement for higher-level care (HLC) including intensive care unit management and requirement for oxygen support, radiographic findings suggestive of lower respiratory tract (LRT) disease, and length of stay (LOS). FINDINGS In total, 450 encounters for 430 different patients were identified, with the majority (85%) being inpatient. OC43 was the most common HCoV. Younger patients (age <5 years) had higher probability of hospitalization [adjusted odds ratio (aOR) 2.2, 95% confidence interval (CI) 1.2-4.1], requirement for HLC (aOR 1.8, 95% CI 1.0-3.1) and presence of LRT findings on chest radiographs (aOR 1.7, 95% CI 1.01-2.9). Clinical outcomes did not differ between HCoV types, except LOS which was longer for 229E. Fifty-two (11%) encounters were detected after 3 days of hospitalization (median 25.5 days), suggesting possible nosocomial infection. CONCLUSION HCoVs are important respiratory pathogens in the paediatric population, especially among patients aged <5 years who are at increased risk for severe disease. The role of HCoVs as hospital-acquired pathogens may be underappreciated.
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Affiliation(s)
- A O Alsulami
- Division of Pediatric Infectious Disease, Department of Pediatrics, University of Alabama at Birmingham, AL, USA; Department of Paediatrics, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - R Chahine
- Research Triangle Institute International, Raleigh, NC, USA
| | - M Kong
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, University of Alabama at Birmingham, AL, USA
| | - D W Kimberlin
- Division of Pediatric Infectious Disease, Department of Pediatrics, University of Alabama at Birmingham, AL, USA
| | - R J Whitley
- Division of Pediatric Infectious Disease, Department of Pediatrics, University of Alabama at Birmingham, AL, USA
| | - S H James
- Division of Pediatric Infectious Disease, Department of Pediatrics, University of Alabama at Birmingham, AL, USA
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Chen N, Li G, Si Y, Ye Y, Zhang T, Chi D, Zhang W, Pan L, Qu G, Lu Y, Zong M, Sui G, Fan L. Development and evaluation of a centrifugal disk system for the rapid detection of multiple pathogens and their antibiotic resistance genes in urinary tract infection. Front Microbiol 2023; 14:1157403. [PMID: 37200917 PMCID: PMC10187633 DOI: 10.3389/fmicb.2023.1157403] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/08/2023] [Indexed: 05/20/2023] Open
Abstract
Background Urinary tract infections (UTIs) are some of the most common bacterial infections in the world. Nevertheless, as uncomplicated UTIs are treated empirically without culturing the urine, adequate knowledge of the resistance pattern of uropathogens is essential. Conventional urine culture and identification take at least 2 days. Here, we developed a platform based on LAMP and centrifugal disk system (LCD) to simultaneously detect the main pathogens and antibiotic resistant genes (ARGs) of urgent concern multidrug-resistant among UTIs. Methods We designed specific primers to detect the target genes above and evaluated their sensitivity and specificity. We also assessed the result of our preload LCD platform on 645 urine specimens with a conventional culturing method and Sanger sequencing. Results The results obtained with the 645 clinical samples indicated that the platform has high specificity (0.988-1) and sensitivity (0.904-1) for the studied pathogens and ARGs. Moreover, the kappa value of all pathogens was more than 0.75, revealing an excellent agreement between the LCD and culture method. Compared to phenotypic tests, the LCD platform is a practical and fast detection approach for methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococci, carbapenem-resistant Enterobacteriaceae, carbapenem-resistant Acinetobacter, carbapenem-resistant Pseudomonas aeruginosa (kappa value of all >0.75), and non-extended-spectrum β-lactamase producers. Conclusion We developed a detection platform that has high accuracy and that meets the need for rapid diagnosis, which can be completed within 1.5 h from specimen collection. It may be a powerful tool for evidence-based UTIs diagnosis, which has essential support for the rational use of antibiotics. More high-quality clinical studies are required to prove the effectiveness of our platform.
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Affiliation(s)
- Nianzhen Chen
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Gen Li
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuying Si
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yangqin Ye
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tong Zhang
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, China
| | - Dali Chi
- Fosun Diagnostics Co., Ltd., Shanghai, China
| | - Wenyan Zhang
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lifeng Pan
- Department of Microbiology, Pudong New Area Center for Disease Control and Prevention, Shanghai, China
| | - Guoying Qu
- Weifang Community Health Service Center, Shanghai, China
| | - Yun Lu
- Huamu Community Health Service Center, Shanghai, China
| | - Ming Zong
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Ming Zong,
| | - Guodong Sui
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, China
- Guodong Sui,
| | - Lieying Fan
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Lieying Fan,
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Relich RF, Abbott AN. Syndromic and Point-of-Care Molecular Testing. Clin Lab Med 2022; 42:507-531. [PMID: 36368779 DOI: 10.1016/j.cll.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ryan F Relich
- Division of Clinical Microbiology, Indiana University Health Pathology Laboratory, Indiana University Health and Indiana University School of Medicine, Suite 6027E, 350 West 11th Street, Indianapolis, IN 46202, USA.
| | - April N Abbott
- Department of Laboratory Medicine, Deaconess Hospital, 600 Mary Street, Evansville, IN 47747, USA
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Recent Advances in Early Diagnosis of Viruses Associated with Gastroenteritis by Biosensors. BIOSENSORS 2022; 12:bios12070499. [PMID: 35884302 PMCID: PMC9313180 DOI: 10.3390/bios12070499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 11/29/2022]
Abstract
Gastroenteritis, as one of the main worldwide health challenges, especially in children, leads to 3–6 million deaths annually and causes nearly 20% of the total deaths of children aged ˂5 years, of which ~1.5 million gastroenteritis deaths occur in developing nations. Viruses are the main causative agent (~70%) of gastroenteritis episodes and their specific and early diagnosis via laboratory assays is very helpful for having successful antiviral therapy and reduction in infection burden. Regarding this importance, the present literature is the first review of updated improvements in the employing of different types of biosensors such as electrochemical, optical, and piezoelectric for sensitive, simple, cheap, rapid, and specific diagnosis of human gastroenteritis viruses. The Introduction section is a general discussion about the importance of viral gastroenteritis, types of viruses that cause gastroenteritis, and reasons for the combination of conventional diagnostic tests with biosensors for fast detection of viruses associated with gastroenteritis. Following the current laboratory detection tests for human gastroenteritis viruses and their limitations (with subsections: Electron Microscope (EM), Cell Culture, Immunoassay, and Molecular Techniques), structural features and significant aspects of various biosensing methods are discussed in the Biosensor section. In the next sections, basic information on viruses causing gastroenteritis and recent developments for fabrication and testing of different biosensors for each virus detection are covered, and the prospect of future developments in designing different biosensing platforms for gastroenteritis virus detection is discussed in the Conclusion and Future Directions section as well.
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Babaei A, Pouremamali A, Rafiee N, Sohrabi H, Mokhtarzadeh A, de la Guardia M. Genosensors as an alternative diagnostic sensing approaches for specific detection of various certain viruses: a review of common techniques and outcomes. Trends Analyt Chem 2022; 155:116686. [PMID: 35611316 PMCID: PMC9119280 DOI: 10.1016/j.trac.2022.116686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/08/2022] [Accepted: 05/15/2022] [Indexed: 12/19/2022]
Abstract
Viral infections are responsible for the deaths of millions of people throughout the world. Since outbreak of highly contagious and mutant viruses such as contemporary sars-cov-2 pandemic, has challenged the conventional diagnostic methods, the entity of a thoroughly sensitive, specific, rapid and inexpensive detecting technique with minimum level of false-positivity or -negativity, is desperately needed more than any time in the past decades. Biosensors as minimized devices could detect viruses in simple formats. So far, various nucleic acid, immune- and protein-based biosensors were designed and tested for recognizing the genome, antigen, or protein level of viruses, respectively; however, nucleic acid-based sensing techniques, which is the foundation of constructing genosensors, are preferred not only because of their ultra-sensitivity and applicability in the early stages of infections but also for their ability to differentiate various strains of the same virus. To date, the review articles related to genosensors are just confined to particular pathogenic diseases; In this regard, the present review covers comprehensive information of the research progress of the electrochemical, optical, and surface plasmon resonance (SPR) genosensors that applied for human viruses' diseases detection and also provides a well description of viruses' clinical importance, the conventional diagnosis approaches of viruses and their disadvantages. This review would address the limitations in the current developments as well as the future challenges involved in the successful construction of sensing approaches with the functionalized nanomaterials and also allow exploring into core-research works regarding this area.
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Affiliation(s)
- Abouzar Babaei
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Amir Pouremamali
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Nastaran Rafiee
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hessamaddin Sohrabi
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain
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Almannaei L, Alsaadoon E, AlbinAli S, Taha M, Lambert I. A retrospective study examining the clinical significance of testing respiratory panels in children who presented to a tertiary hospital in 2019. Access Microbiol 2022; 4:000332. [PMID: 35693466 PMCID: PMC9175981 DOI: 10.1099/acmi.0.000332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/19/2022] [Indexed: 11/08/2022] Open
Abstract
Background. Respiratory tract infections are a leading cause of hospital visits in the paediatric population and carry significant associated morbidity and mortality in this population. The introduction of respiratory panel testing has been said to guide clinicians in the overall management of patients. Methods. We conducted a retrospective study examining all respiratory panels carried out in our hospital during 2019 on paediatric patients. Patients included were those who had symptoms indicative of respiratory infections who presented acutely, including those with chronic respiratory conditions. A total of 188 respiratory panel results were obtained along with collected patient data. These were analysed using SPSS V. 25.0 to get the below mentioned results. Results. The majority (76.6 %) of patients were less than 3 years with 59 % of total population being males. The majority (80.9 %) had mild clinical severity score. The most common pathogen that was detected on the respiratory panel was Enterovirus Human Rhinovirus spp, followed by the influenza viruses. Only four cases were positive for bacterial pathogens (two Mycoplasma pneumoniae, one Bordetella pertussis and one Chlamydia pneumoniae), which accounts for 2.1 % of all panels analysed. The significance of respiratory panels in influencing treatment were analysed in the forms of change of management plans before and after results of respiratory panels. This was observed in 14.4 % of patients who were not on any empiric medication and then based on panel results were started on medications, as well as 11.7 % who were on medications already, and the medications were altered based on the result of the panel (Chi square P=0.057). This was mainly seen with cases of influenza A H1N1 patients and to a lesser extent, Mycoplasma pneumonia. Conclusion. The use of respiratory panels in our hospital had little impact on patient care and management. The main organisms that influenced clinician decision in treatment were influenza A viruses and bacterial organisms (Mycoplasma pneumoniae, Chlamydia pneumoniae and Bordetella pertussis). Other than that, the use of clinical judgement proved more beneficial. We recommend use of specific testing for these organisms rather than the whole panel as case to case bases, which would be more cost-effective and consistent with patient management.
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Affiliation(s)
- Lulwa Almannaei
- Pediatrics Department, King Hamad University Hospital, Busaiteen, Bahrain
| | - Ebrahim Alsaadoon
- Pediatrics Department, King Hamad University Hospital, Busaiteen, Bahrain
| | - Sultan AlbinAli
- Pediatrics Department, King Hamad University Hospital, Busaiteen, Bahrain
| | - Mohammed Taha
- Pediatrics Department, King Hamad University Hospital, Busaiteen, Bahrain
| | - Imelda Lambert
- Pediatrics Department, King Hamad University Hospital, Busaiteen, Bahrain
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van Asten SAV, Boers SA, de Groot JDF, Schuurman R, Claas ECJ. Evaluation of the Genmark ePlex® and QIAstat-Dx® respiratory pathogen panels in detecting bacterial targets in lower respiratory tract specimens. BMC Microbiol 2021; 21:236. [PMID: 34445973 PMCID: PMC8390116 DOI: 10.1186/s12866-021-02289-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 07/30/2021] [Indexed: 11/26/2022] Open
Abstract
Background The ePlex® and QIAstat-Dx® respiratory pathogen panels detect multiple respiratory pathogens, mainly viruses but also Legionella pneumophila, Mycoplasma pneumoniae and Bordetella pertussis. The assays have been marketed for use in nasopharyngeal swab specimens. For diagnosing bacterial pneumonia, lower respiratory tract (LRT) specimens are indicated. Aim of this study was to evaluate the performance of these syndromic panels for these three bacterial targets in samples from the LRT. Fifty-six specimens were collected from our repositories, five negative samples and fifty-one samples which had been previously tested positive with the routine diagnostic real-time PCR assays for Legionella spp. (N = 20), Bordetella spp. (N = 16) or M. pneumoniae (N = 15). Results The QIAstat-Dx Respiratory Panel V2 (RP) assay detected all of the L. pneumophila and B. pertussis positive samples but only 11/15 (73.3 %) of the M. pneumoniae targets. The ePlex Respiratory Pathogen Panel (RPP) assay detected 10/14 (71.4 %) of the L. pneumophila targets, 8/12 (66.7 %) of the B. pertussis positive samples and 13/15 (86.7 %) of the M. pneumoniae targets. Conclusions No false-positive results were reported for all three bacterial pathogens by both assays. The clinical performance of both assays depended highly on the bacterial load in the sample and the type of specimen under investigation.
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Affiliation(s)
- Suzanne A V van Asten
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, Leiden, 2300 RC, The Netherlands.
| | - Stefan A Boers
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, Leiden, 2300 RC, The Netherlands
| | - Jolanda D F de Groot
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - R Schuurman
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, Leiden, 2300 RC, The Netherlands
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12
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Mizusawa M. Updates on Rapid Diagnostic Tests in Infectious Diseases. MISSOURI MEDICINE 2020; 117:328-337. [PMID: 32848269 PMCID: PMC7431065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In the last two decades there have been dramatic advances in development of rapid diagnostic tests. Turnaround time of the assays have significantly been shortened which led to reductions in time to appropriate antimicrobial therapy and improvement of patient clinical outcomes. Molecular-based assays generally have better sensitivity than conventional methods, but the cost is higher. The results need to be interpreted cautiously as detection of colonized organisms, pathogen detection in asymptomatic patients, and false negative/positive can occur. Indications and cost-effectiveness need to be considered for appropriate utilization of rapid diagnostic tests.
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Affiliation(s)
- Masako Mizusawa
- Section of Infectious Diseases, Department of Internal Medicine, University of Missouri - Kansas City, Kansas City, Missouri
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13
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Dynamics and predisposition of respiratory viral co-infections in children and adults. Clin Microbiol Infect 2020; 27:631.e1-631.e6. [PMID: 32540470 DOI: 10.1016/j.cmi.2020.05.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/26/2020] [Accepted: 05/30/2020] [Indexed: 01/06/2023]
Abstract
OBJECTIVES The epidemiology of respiratory co-infection pairings is poorly understood. Here we assess the dynamics of respiratory viral co-infections in children and adults and determine predisposition for or against specific viral pairings. METHODS Over five respiratory seasons from 30 November 2013 through 6 June 2018, the mono-infection and co-infection prevalence of 13 viral pathogens was tabulated at The Cleveland Clinic. Employing a model to proportionally distribute viral pairs using individual virus co-infection rate with prevalence patterns of concurrent co-circulating viruses, we compared predicted occurrence with observed occurrence of 132 viral pairing permutations using binomial analysis. RESULTS Of 30 535 respiratory samples, 9843 (32.2%) were positive for at least one virus and 1018 (10.8%) of these were co-infected. Co-infected samples predominantly originated from children. Co-infection rate in paediatric population was 35.0% (2068/5906), compared with only 5.8% (270/4591) in adults. Adenovirus C (ADVC) had the highest co-infection rate (426/623, 68.3%) while influenza virus B had the lowest (55/546, 10.0%). ADVC-rhinovirus (HRV), respiratory syncytial virus A (RSVA)-HRV and RSVB-HRV pairings occurred at significantly higher frequencies than predicted by the proportional distribution model (p < 0.05). Additionally, several viral pairings had fewer co-infections than predicted by our model: notably metapneumovirus (hMPV)-parainfluenza virus 3, hMPV-RSVA and RSVA-RSVB. CONCLUSIONS This is one of the largest studies on respiratory viral co-infections in children and adults. Co-infections are substantially more common in children, especially under 5 years of age, and the most frequent pairings occurred at a higher frequency than would be expected by random. Specific pairings occur at altered rates compared with those predicted by proportional distribution, suggesting either direct or indirect interactions result between specific viral pathogens.
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14
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Evaluation of Commercial Molecular Diagnostic Methods for Detection and Determination of Macrolide Resistance in Mycoplasma pneumoniae. J Clin Microbiol 2020; 58:JCM.00242-20. [PMID: 32269102 DOI: 10.1128/jcm.00242-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/01/2020] [Indexed: 12/11/2022] Open
Abstract
We evaluated six commercial molecular tests targeting Mycoplasma pneumoniae, namely, the BioFire FilmArray respiratory panel (RP), the Meridian Alethia Mycoplasma Direct, the GenMark ePlex respiratory pathogen panel (RPP), the Luminex NxTAG RPP, the ELITech ELITe InGenius Mycoplasma MGB research use only (RUO) PCR, and the SpeeDx Resistance Plus MP assays. Laboratory-developed PCR assays at the University of Alabama at Birmingham and the Centers for Disease Control and Prevention were used as reference standards. Among 428 specimens, 212 were designated confirmed positives for M. pneumoniae The highest clinical sensitivities were found with the InGenius PCR (99.5%) and the FilmArray RP (98.1%). The Resistance Plus MP identified 93.3% of the confirmed-positive specimens, whereas 83.6, 64.6, and 55.7% were identified by the ePlex RPP, NxTAG RPP, and Mycoplasma Direct assays, respectively. There was no significant difference between the sensitivity of the reference methods and that of the FilmArray RP and InGenius assays, but the remaining four assays detected significantly fewer positive specimens (P < 0.05). Specificities of all assays were 99.5 to 100%. The Resistance Plus MP assay detected macrolide resistance in 27/33 specimens, resulting in a sensitivity of 81.8%. This study provides the first large-scale comparison of commercial molecular assays for detection of M. pneumoniae in the United States and identified clear differences among their performance. Additional studies are necessary to explore the impact of various test performances on patient outcome.
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15
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Trotter M, Borst N, Thewes R, von Stetten F. Review: Electrochemical DNA sensing – Principles, commercial systems, and applications. Biosens Bioelectron 2020; 154:112069. [DOI: 10.1016/j.bios.2020.112069] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/28/2020] [Accepted: 02/01/2020] [Indexed: 02/06/2023]
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16
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Viruses of Respiratory Tract: an Observational Retrospective Study on Hospitalized Patients in Rome, Italy. Microorganisms 2020; 8:microorganisms8040501. [PMID: 32244685 PMCID: PMC7232519 DOI: 10.3390/microorganisms8040501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/28/2020] [Accepted: 03/30/2020] [Indexed: 12/12/2022] Open
Abstract
Respiratory tract infections account for high morbidity and mortality around the world. Fragile patients are at high risk of developing complications such as pneumonia and may die from it. Limited information is available on the extent of the circulation of respiratory viruses in the hospital setting. Most knowledge relates to influenza viruses (FLU) but several other viruses produce flu-like illness. The study was conducted at the University Hospital Policlinico Tor Vergata, Rome, Italy. Clinical and laboratory data from hospitalized patients with respiratory tract infections during the period October 2016-March 2019 were analysed. The retrospective analysis included 17 viral agents detected by FilmArray test and clinical data from medical records and hospital discharge sheets. Models were adjusted for relevant confounders such as clinical severity and risk of death, socio-demographic characteristics and surgical procedures. From a total of 539 specimens analysed, 180 (33.39%) were positive for one or more respiratory viruses. Among them, 83 (46.1 %) were positive for influenza viruses (FLU), 36 (20%) rhino/enteroviruses (RHV/EV), 17 (9.44%) human coronaviruses (HCOV-229E, -HKU1, -NL63, and -OC43), 17 (9.44%) respiratory syncytial virus, 15 (8.33%) human metapneumovirus (HMPV), 8 (4.44%) parainfluenza viruses (PIV) and 4 (2.22%) adenoviruses (ADV). The distribution of viral agents varied across age groups and month of detection. The positive specimens were from 168 patients [102 M, 66 F; median age (range): 64 years (19-93)]. Overall, 40% of them had a high-grade clinical severity and a 27% risk of death; 27 patients died and 22 of them (81.5%) had received a clinical diagnosis of pneumonia. Respiratory viral infections may have a severe course and a poor prognosis in hospitalized patients, due to underlying comorbidities. Monitoring the circulation of respiratory viruses in hospital settings is important to improve diagnosis, prevention and treatment.
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17
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Randolph AG, Xu R, Novak T, Newhams MM, Bubeck Wardenburg J, Weiss SL, Sanders RC, Thomas NJ, Hall MW, Tarquinio KM, Cvijanovich N, Gedeit RG, Truemper EJ, Markovitz B, Hartman ME, Ackerman KG, Giuliano JS, Shein SL, Moffitt KL. Vancomycin Monotherapy May Be Insufficient to Treat Methicillin-resistant Staphylococcus aureus Coinfection in Children With Influenza-related Critical Illness. Clin Infect Dis 2020; 68:365-372. [PMID: 29893805 PMCID: PMC6336914 DOI: 10.1093/cid/ciy495] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/08/2018] [Indexed: 12/28/2022] Open
Abstract
Background Coinfection with influenza virus and methicillin-resistant Staphylococcus aureus (MRSA) causes life-threatening necrotizing pneumonia in children. Sporadic incidence precludes evaluation of antimicrobial efficacy. We assessed the clinical characteristics and outcomes of critically ill children with influenza–MRSA pneumonia and evaluated antibiotic use. Methods We enrolled children (<18 years) with influenza infection and respiratory failure across 34 pediatric intensive care units 11/2008–5/2016. We compared baseline characteristics, clinical courses, and therapies in children with MRSA coinfection, non-MRSA bacterial coinfection, and no bacterial coinfection. Results We enrolled 170 children (127 influenza A, 43 influenza B). Children with influenza–MRSA pneumonia (N = 30, 87% previously healthy) were older than those with non-MRSA (N = 61) or no (N = 79) bacterial coinfections. Influenza–MRSA was associated with increased leukopenia, acute lung injury, vasopressor use, extracorporeal life support, and mortality than either group (P ≤ .0001). Influenza-related mortality was 40% with MRSA compared to 4.3% without (relative risk [RR], 9.3; 95% confidence interval [CI], 3.8–22.9). Of 29/30 children with MRSA who received vancomycin within the first 24 hours of hospitalization, mortality was 12.5% (N = 2/16) if treatment also included a second anti-MRSA antibiotic compared to 69.2% (N = 9/13) with vancomycin monotherapy (RR, 5.5; 95% CI, 1.4, 21.3; P = .003). Vancomycin dosing did not influence initial trough levels; 78% were <10 µg/mL. Conclusions Influenza–MRSA coinfection is associated with high fatality in critically ill children. These data support early addition of a second anti-MRSA antibiotic to vancomycin in suspected severe cases.
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Affiliation(s)
- Adrienne G Randolph
- Department of Anesthesia, Critical Care, and Pain Medicine, Boston Children's Hospital, Boston, Massachusetts.,Department of Anesthesia, Harvard Medical School, Boston, Massachusetts.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Ruifei Xu
- Department of Anesthesia, Critical Care, and Pain Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Tanya Novak
- Department of Anesthesia, Critical Care, and Pain Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Margaret M Newhams
- Department of Anesthesia, Critical Care, and Pain Medicine, Boston Children's Hospital, Boston, Massachusetts
| | | | - Scott L Weiss
- Department of Pediatrics, Children's Hospital of Philadelphia, Pennsylvania
| | - Ronald C Sanders
- Section of Pediatric Critical Care, Department of Pediatrics, Arkansas Children's Hospital, Little Rock
| | - Neal J Thomas
- Division of Pediatric Critical Care Medicine, Penn State Hershey Children's Hospital, Pennsylvania
| | - Mark W Hall
- Department of Pediatrics, Nationwide Children's Hospital, Columbus, Ohio
| | - Keiko M Tarquinio
- Division of Critical Care Medicine, Children's Healthcare of Atlanta at Egleston, Emory University School of Medicine, Georgia
| | - Natalie Cvijanovich
- Department of Critical Care Medicine, University of California-San Francisco, Benioff Children's Hospital Oakland
| | - Rainer G Gedeit
- Department of Pediatrics, Children's Hospital of Wisconsin, Milwaukee
| | - Edward J Truemper
- Department of Pediatrics, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Barry Markovitz
- Department of Anesthesiology Critical Care Medicine, Children's Hospital Los Angeles, California
| | - Mary E Hartman
- Department of Pediatrics, St. Louis Children's Hospital, Missouri
| | - Kate G Ackerman
- Department of Pediatrics, Golisano Children's Hospital, Rochester, New York
| | - John S Giuliano
- Department of Pediatrics, Yale-New Haven Children's Hospital, Connecticut
| | - Steven L Shein
- Division of Pediatric Critical Care Medicine, Rainbow Babies and Children's Hospital, Cleveland, Ohio
| | - Kristin L Moffitt
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts.,Division of Infectious Diseases, Department of Medicine, Boston Children's Hospital, Massachusetts
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18
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Meyers L, Dien Bard J, Galvin B, Nawrocki J, Niesters HGM, Stellrecht KA, St George K, Daly JA, Blaschke AJ, Robinson C, Wang H, Cook CV, Hassan F, Dominguez SR, Pretty K, Naccache S, Olin KE, Althouse BM, Jones JD, Ginocchio CC, Poritz MA, Leber A, Selvarangan R. Enterovirus D68 outbreak detection through a syndromic disease epidemiology network. J Clin Virol 2020; 124:104262. [PMID: 32007841 DOI: 10.1016/j.jcv.2020.104262] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 01/08/2020] [Accepted: 01/14/2020] [Indexed: 02/04/2023]
Abstract
BACKGROUND In 2014, enterovirus D68 (EV-D68) was responsible for an outbreak of severe respiratory illness in children, with 1,153 EV-D68 cases reported across 49 states. Despite this, there is no commercial assay for its detection in routine clinical care. BioFire® Syndromic Trends (Trend) is an epidemiological network that collects, in near real-time, deidentified. BioFire test results worldwide, including data from the BioFire® Respiratory Panel (RP). OBJECTIVES Using the RP version 1.7 (which was not explicitly designed to differentiate EV-D68 from other picornaviruses), we formulate a model, Pathogen Extended Resolution (PER), to distinguish EV-D68 from other human rhinoviruses/enteroviruses (RV/EV) tested for in the panel. Using PER in conjunction with Trend, we survey for historical evidence of EVD68 positivity and demonstrate a method for prospective real-time outbreak monitoring within the network. STUDY DESIGN PER incorporates real-time polymerase chain reaction metrics from the RPRV/EV assays. Six institutions in the United States and Europe contributed to the model creation, providing data from 1,619 samples spanning two years, confirmed by EV-D68 gold-standard molecular methods. We estimate outbreak periods by applying PER to over 600,000 historical Trend RP tests since 2014. Additionally, we used PER as a prospective monitoring tool during the 2018 outbreak. RESULTS The final PER algorithm demonstrated an overall sensitivity and specificity of 87.1% and 86.1%, respectively, among the gold-standard dataset. During the 2018 outbreak monitoring period, PER alerted the research network of EV-D68 emergence in July. One of the first sites to experience a significant increase, Nationwide Children's Hospital, confirmed the outbreak and implemented EV-D68 testing at the institution in response. Applying PER to the historical Trend dataset to determine rates among RP tests, we find three potential outbreaks with predicted regional EV-D68 rates as high as 37% in 2014, 16% in 2016, and 29% in 2018. CONCLUSIONS Using PER within the Trend network was shown to both accurately predict outbreaks of EV-D68 and to provide timely notifications of its circulation to participating clinical laboratories.
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Affiliation(s)
- Lindsay Meyers
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA 90027, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA 90039, United States.
| | - Ben Galvin
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Jeff Nawrocki
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Hubert G M Niesters
- The University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Division of Clinical Virology, Groningen, The Netherlands.
| | - Kathleen A Stellrecht
- Department of Pathology and Laboratory Medicine, Albany Medical Center, Albany, NY 12208, United States.
| | - Kirsten St George
- New York State Department of Health, Albany, NY, 12202, United States.
| | - Judy A Daly
- Department of Pathology, University of Utah, Salt Lake City, UT 84132, United States; Division of Inpatient Medicine, Primary Children's Hospital, Salt Lake City, UT 84132, United States.
| | - Anne J Blaschke
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84132, United States.
| | - Christine Robinson
- Department of Pathology and Laboratory Medicine, Children's Colorado, Aurora, CO 80045, United States.
| | - Huanyu Wang
- Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH 43205, United States.
| | - Camille V Cook
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Ferdaus Hassan
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 64108, United States.
| | - Sam R Dominguez
- Department of Pathology and Laboratory Medicine, Children's Colorado, Aurora, CO 80045, United States.
| | - Kristin Pretty
- Department of Pathology and Laboratory Medicine, Children's Colorado, Aurora, CO 80045, United States.
| | - Samia Naccache
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA 90027, United States.
| | | | - Benjamin M Althouse
- Information School, University of Washington, Seattle, WA, 98105, United States; Department of Biology, New Mexico State University, Las Cruces, NM, 88003, United States.
| | - Jay D Jones
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Christine C Ginocchio
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States; Global Medical Affairs, bioMérieux, Durham, NC 27712, United States; Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, United States.
| | - Mark A Poritz
- BioFire Defense, Salt Lake City, UT 84107, United States.
| | - Amy Leber
- Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH 43205, United States.
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 64108, United States.
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Shaman J, Morita H, Birger R, Boyle M, Comito D, Lane B, Ligon C, Smith H, Desalle R, Planet P. Asymptomatic Summertime Shedding of Respiratory Viruses. J Infect Dis 2019; 217:1074-1077. [PMID: 29300926 PMCID: PMC7107397 DOI: 10.1093/infdis/jix685] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/29/2017] [Indexed: 11/17/2022] Open
Abstract
To determine rates of both symptomatic and asymptomatic infection among ambulatory adults, we collected nasopharyngeal swab specimens, demographic characteristics, and survey information from 1477 adult visitors to a New York City tourist attraction during April–July 2016. Multiplex polymerase chain reaction analysis was used to identify specimens positive for common respiratory viruses. A total of 7.2% of samples tested positive for respiratory viruses; among positive samples, 71.0% contained rhinovirus, and 21.5% contained coronavirus. Influenza virus, respiratory syncytial virus, and parainfluenza virus were also detected. Depending on symptomatologic definition, 57.7%–93.3% of positive samples were asymptomatic. These findings indicate that significant levels of asymptomatic respiratory viral shedding exist during summer among the ambulatory adult population.
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Affiliation(s)
- Jeffrey Shaman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University.,Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, New York
| | - Haruka Morita
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University
| | - Ruthie Birger
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University
| | - Mary Boyle
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University
| | - Devon Comito
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University
| | - Benjamin Lane
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University
| | - Chanel Ligon
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University
| | - Hannah Smith
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University
| | - Rob Desalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, New York
| | - Paul Planet
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, New York.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania.,Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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20
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Schmitz JE, Tang YW. The GenMark ePlex ®: another weapon in the syndromic arsenal for infection diagnosis. Future Microbiol 2018; 13:1697-1708. [PMID: 30547684 DOI: 10.2217/fmb-2018-0258] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
As one of the most recent additions to the syndromic testing landscape, the ePlex® platform by GenMark Diagnostics is a system that combines the manufacturer's signature electrochemical detection technology with updated microfluidics, providing a new option for multiplex testing that is both rapid and requires minimal hands-on steps. In this review, we detail the ePlex platform and its current/future syndromic panels, with a particular focus on the respiratory pathogen panel - the platform's first assay to undergo clinical trials and receive regulatory approval in the USA. By keeping informed of these ever-expanding laboratory options, clinicians and microbiologists can stay positioned at the forefront of infectious disease diagnosis.
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Affiliation(s)
- Jonathan E Schmitz
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center & School of Medicine, Nashville, TN 37232, USA
| | - Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA.,Department of Pathology & Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065 USA
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21
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Falsey AR, Walsh EE, Esser MT, Shoemaker K, Yu L, Griffin MP. Respiratory syncytial virus-associated illness in adults with advanced chronic obstructive pulmonary disease and/or congestive heart failure. J Med Virol 2018; 91:65-71. [PMID: 30132922 PMCID: PMC6900175 DOI: 10.1002/jmv.25285] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 08/07/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is recognized as a serious pathogen in people with chronic cardiopulmonary conditions. Immunoprophylaxis might be considered for adults at high-risk for frequent and severe RSV infection. Thus, we studied the incidence of RSV-related medically attended acute respiratory illness (MARI) in adults with severe chronic obstructive pulmonary disease (COPD) and/or congestive heart failure (CHF). METHODS Subjects ≥50 years of age with Gold Class III/IV COPD and/or American Heart Association class III/IV CHF and exposure to children ≥once per month were recruited. Subjects were evaluated over 1.5 to 2.5 years for RSV-associated MARI, defined as polymerase chain reaction (PCR) and/or seroresponse. RESULTS Four hundred forty-five subjects were enrolled between October 2011 and May 2012. Overall, 99 RSV infections were documented by PCR or serology for a cumulative incidence of 22.2%. Of these, 42 (9.4%) subjects had protocol-specified RSV-MARI for an incidence of 4.68/100 patient-seasons. All-cause MARI was common (63.85/100 patient-seasons) with rhinovirus most commonly identified. CONCLUSION RSV infection was common in adults with severe COPD and/or advanced CHF. Given the severity of underlying cardiopulmonary diseases in the study population, most illnesses were surprisingly mild. Thus, active immunization rather than passive immunoprophylaxis with monoclonal antibodies may be a more cost-effective strategy.
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Affiliation(s)
- Ann R Falsey
- Department of Medicine, Infectious Diseases Division, University of Rochester, Rochester, New York
| | - Edward E Walsh
- Department of Medicine, Infectious Diseases Division, University of Rochester, Rochester, New York
| | | | | | - Li Yu
- MedImmune, Gaithersburg, Maryland
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22
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Meyers L, Ginocchio CC, Faucett AN, Nolte FS, Gesteland PH, Leber A, Janowiak D, Donovan V, Dien Bard J, Spitzer S, Stellrecht KA, Salimnia H, Selvarangan R, Juretschko S, Daly JA, Wallentine JC, Lindsey K, Moore F, Reed SL, Aguero-Rosenfeld M, Fey PD, Storch GA, Melnick SJ, Robinson CC, Meredith JF, Cook CV, Nelson RK, Jones JD, Scarpino SV, Althouse BM, Ririe KM, Malin BA, Poritz MA. Automated Real-Time Collection of Pathogen-Specific Diagnostic Data: Syndromic Infectious Disease Epidemiology. JMIR Public Health Surveill 2018; 4:e59. [PMID: 29980501 PMCID: PMC6054708 DOI: 10.2196/publichealth.9876] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/29/2018] [Accepted: 04/12/2018] [Indexed: 12/22/2022] Open
Abstract
Background Health care and public health professionals rely on accurate, real-time monitoring of infectious diseases for outbreak preparedness and response. Early detection of outbreaks is improved by systems that are comprehensive and specific with respect to the pathogen but are rapid in reporting the data. It has proven difficult to implement these requirements on a large scale while maintaining patient privacy. Objective The aim of this study was to demonstrate the automated export, aggregation, and analysis of infectious disease diagnostic test results from clinical laboratories across the United States in a manner that protects patient confidentiality. We hypothesized that such a system could aid in monitoring the seasonal occurrence of respiratory pathogens and may have advantages with regard to scope and ease of reporting compared with existing surveillance systems. Methods We describe a system, BioFire Syndromic Trends, for rapid disease reporting that is syndrome-based but pathogen-specific. Deidentified patient test results from the BioFire FilmArray multiplex molecular diagnostic system are sent directly to a cloud database. Summaries of these data are displayed in near real time on the Syndromic Trends public website. We studied this dataset for the prevalence, seasonality, and coinfections of the 20 respiratory pathogens detected in over 362,000 patient samples acquired as a standard-of-care testing over the last 4 years from 20 clinical laboratories in the United States. Results The majority of pathogens show influenza-like seasonality, rhinovirus has fall and spring peaks, and adenovirus and the bacterial pathogens show constant detection over the year. The dataset can also be considered in an ecological framework; the viruses and bacteria detected by this test are parasites of a host (the human patient). Interestingly, the rate of pathogen codetections, on average 7.94% (28,741/362,101), matches predictions based on the relative abundance of organisms present. Conclusions Syndromic Trends preserves patient privacy by removing or obfuscating patient identifiers while still collecting much useful information about the bacterial and viral pathogens that they harbor. Test results are uploaded to the database within a few hours of completion compared with delays of up to 10 days for other diagnostic-based reporting systems. This work shows that the barriers to establishing epidemiology systems are no longer scientific and technical but rather administrative, involving questions of patient privacy and data ownership. We have demonstrated here that these barriers can be overcome. This first look at the resulting data stream suggests that Syndromic Trends will be able to provide high-resolution analysis of circulating respiratory pathogens and may aid in the detection of new outbreaks.
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Affiliation(s)
| | - Christine C Ginocchio
- BioFire Diagnostics, Salt Lake City, UT, United States.,bioMérieux USA, Durham, NC, United States.,Hofstra Northwell School of Medicine, Hempstead, NY, United States
| | | | - Frederick S Nolte
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Per H Gesteland
- Departments of Pediatrics and Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Amy Leber
- Laboratory of Microbiology and Immunoserology, Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, United States
| | - Diane Janowiak
- Department of Lab Operations, South Bend Medical Foundation, South Bend, IN, United States
| | - Virginia Donovan
- Department of Pathology, New York University Winthrop Hospital, Mineola, NY, United States
| | - Jennifer Dien Bard
- Clinical Microbiology and Virology Laboratory, Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA, United States.,Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Silvia Spitzer
- Molecular Genetics Laboratory, Stony Brook University Medical Center, Stony Brook, NY, United States
| | - Kathleen A Stellrecht
- Department of Pathology and Laboratory Medicine, Albany Medical Center, Albany, NY, United States
| | - Hossein Salimnia
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Rangaraj Selvarangan
- Clinical Microbiology, Virology and Molecular Infectious Diseases Laboratory, Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, United States
| | - Stefan Juretschko
- Department of Pathology and Laboratory Medicine, Division of Infectious Disease Diagnostics, Northwell Health, Lake Success, NY, United States
| | - Judy A Daly
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Jeremy C Wallentine
- Department of Pathology, Intermountain Medical Center, Murray, UT, United States
| | - Kristy Lindsey
- Laboratory of Microbiology, University of Massachusetts Medical School-Baystate, Springfield, MA, United States
| | - Franklin Moore
- Laboratory of Microbiology, University of Massachusetts Medical School-Baystate, Springfield, MA, United States
| | - Sharon L Reed
- Department of Pathology and Medicine, Divisions of Clinical Pathology and Infectious Diseases, UC San Diego, San Diego, CA, United States
| | - Maria Aguero-Rosenfeld
- Department of Clinical Laboratories, New York University Langone Health, New York, NY, United States
| | - Paul D Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Gregory A Storch
- Department of Pediatrics, Washington University, St. Louis, MO, United States
| | - Steve J Melnick
- Department of Pathology and Clinical Laboratories, Nicklaus Children's Hospital, Miami, FL, United States
| | - Christine C Robinson
- Department of Pathology and Laboratory Medicine, Microbiology/Virology Laboratory Section, Children's Hospital Colorado, Aurora, CO, United States
| | - Jennifer F Meredith
- Department of Laboratory Services, Microbiology Section, Greenville Health System, Greenville, SC, United States
| | | | | | - Jay D Jones
- BioFire Diagnostics, Salt Lake City, UT, United States
| | | | - Benjamin M Althouse
- University of Washington, Seattle, WA, United States.,New Mexico State University, Las Cruces, NM, United States
| | | | - Bradley A Malin
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN, United States
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Diaz-Decaro JD, Green NM, Godwin HA. Critical evaluation of FDA-approved respiratory multiplex assays for public health surveillance. Expert Rev Mol Diagn 2018; 18:631-643. [PMID: 29886764 PMCID: PMC7103694 DOI: 10.1080/14737159.2018.1487294] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Introduction: Clinical management and identification of respiratory diseases has become more rapid and increasingly specific due to widespread use of PCR(polymerase chain reaction) multiplex technologies. Although significantly improving clinical diagnosis, multiplexed PCR assays could have a greater impact on local and global disease surveillance. The authors wish to propose methods of evaluating respiratory multiplex assays to maximize diagnostic yields specifically for surveillance efforts. Areas covered: The authors review multiplexed assays and critically assess what barriers have limited these assays for disease surveillance and how these barriers might be addressed. The manuscript focuses specifically on the case study of using multiplexed assays for surveillance of respiratory pathogens. The authors also provide a method of validation of specific surveillance measures. Expert commentary: Current commercially available respiratory multiplex PCR assays are widely used for clinical diagnosis; however, specific barriers have limited their use for surveillance. Key barriers include differences in testing phase requirements and diagnostic performance evaluation. In this work the authors clarify phase testing requirements and introduce unique diagnostic performance measures that simplify the use of these assays on a per target basis for disease surveillance.
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Affiliation(s)
- John D Diaz-Decaro
- a Los Angeles County Public Health Laboratories , Research & Training Unit , Downey , CA , USA.,b UCLA Fielding School of Public Health , Environmental Health Sciences , Los Angeles , CA , USA
| | - Nicole M Green
- a Los Angeles County Public Health Laboratories , Research & Training Unit , Downey , CA , USA
| | - Hilary A Godwin
- b UCLA Fielding School of Public Health , Environmental Health Sciences , Los Angeles , CA , USA
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Multicenter Evaluation of the ePlex Respiratory Pathogen Panel for the Detection of Viral and Bacterial Respiratory Tract Pathogens in Nasopharyngeal Swabs. J Clin Microbiol 2018; 56:JCM.01658-17. [PMID: 29212701 PMCID: PMC5786739 DOI: 10.1128/jcm.01658-17] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 11/20/2017] [Indexed: 12/20/2022] Open
Abstract
The performance of the new ePlex Respiratory Pathogen (RP) panel (GenMark Diagnostics) for the simultaneous detection of 19 viruses (influenza A virus; influenza A H1 virus; influenza A 2009 H1 virus; influenza A H3 virus; influenza B virus; adenovirus; coronaviruses [HKU1, OC43, NL63, and 229E]; human rhinovirus/enterovirus; human metapneumovirus; parainfluenza viruses 1, 2, 3, and 4; and respiratory syncytial virus [RSV] [RSV subtype A and RSV subtype B]) and 2 bacteria (Mycoplasma pneumoniae and Chlamydia pneumoniae) was evaluated. Prospectively and retrospectively collected nasopharyngeal swab (NPS) specimens (n = 2,908) were evaluated by using the ePlex RP panel, with the bioMérieux/BioFire FilmArray Respiratory Panel (BioFire RP) as the comparator method. Discordance analysis was performed by using target-specific PCRs and bidirectional sequencing. The reproducibility of the assay was evaluated by using reproducibility panels comprised of 6 pathogens. The overall agreement between the ePlex RP and BioFire RP results was >95% for all targets. Positive percent agreement with the BioFire RP result for viruses ranged from 85.1% (95% confidence interval [CI], 80.2% to 88.9%) to 95.1% (95% CI, 89.0% to 97.9%), while negative percent agreement values ranged from 99.5% (95% CI, 99.1% to 99.7%) to 99.8% (95% CI, 99.5% to 99.9%). Additional testing of discordant targets (12%; 349/2,908) confirmed the results of ePlex RP for 38% (131/349) of samples tested. Reproducibility was 100% for all targets tested, with the exception of adenovirus, for which reproducibilities were 91.6% at low virus concentrations and 100% at moderate virus concentrations. The ePlex RP panel offers a new, rapid, and sensitive “sample-to-answer” multiplex panel for the detection of the most common viral and bacterial respiratory pathogens.
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Abstract
PURPOSE OF REVIEW We aim to review the epidemiology of respiratory viral infections and the strengths and limitations of multiplex respiratory pathogen panels that are currently available along with their respective features and differences. RECENT FINDINGS We give particular emphasis to the pathogens included on each test and evaluate their performance in the hospital setting. SUMMARY We conclude with a discussion on the evidence for the clinical utility of respiratory pathogen multiplex panels in hospitalized patients, including the potential for coinfection with viral and bacterial pathogens.
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Iroh Tam PY, Zhang L, Cohen Z. Clinical characteristics and outcomes of human rhinovirus positivity in hospitalized children. Ann Thorac Med 2018; 13:230-236. [PMID: 30416595 PMCID: PMC6196663 DOI: 10.4103/atm.atm_291_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND: The clinical relevance of positive human rhinovirus (HRV) in hospitalized patients is unclear. Our objective was to describe the clinical characteristics and outcomes of HRV positivity in a heterogeneous population of hospitalized children, compared to those positive for another respiratory virus and those where no respiratory virus was detected. METHODS: A retrospective case–control study of children hospitalized between January 2014 to April 2015 who had a respiratory viral specimen collected. Clinical and laboratory data were collected, and baseline characteristics and clinical variables were compared. RESULTS: During the study period, there were 671 specimens obtained from 577 patients that were processed for the respiratory viral polymerase chain reaction assay, of which 198 were positive for HRV, 167 positive for another respiratory virus, and 306 where no respiratory virus was detected. A history of asthma was significantly associated with HRV-positive patients (odds ratio [OR] 3.71; P < 0.001). On multivariate analysis, HRV-positive patients had a higher requirement for mechanical ventilation (OR 1.44), lower rates of readmission (OR 0.53), and lower mortality (OR 0.35) compared to patients with no respiratory virus isolated; however, none were statistically significant. HRV-positive patients did have a significantly shorter length of stay (LOS) compared with patients with no respiratory virus isolated (difference–0.35; P = 0.001). Similar outcomes were seen in patients positive for other respiratory viruses. CONCLUSIONS: HRV-positive hospitalized pediatric patients with a heterogeneous set of clinical diagnoses had higher association with asthma compared to patients who had another, or no, respiratory virus isolated. HRV-positive patients had shorter LOS compared to patients who had no respiratory viruses isolated. These findings suggest that HRV positivity in hospitalized pediatric patients may not lead to adverse clinical outcomes, although asthma is a risk factor regardless of clinical comorbidities and diagnoses. Further research is warranted to understand the predisposition of asthma to HRV positivity.
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Affiliation(s)
- Pui-Ying Iroh Tam
- Division of Pediatric Infectious Diseases, University of Minnesota Masonic Children's Hospital, Minneapolis, MN, USA.,Paediatric and Child Health Research Group, Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Lei Zhang
- Biostatistical Design and Analysis Center, Clinical and Translational Science Institute, University of Minnesota, Minneapolis, MN, USA
| | - Zohara Cohen
- Biostatistical Design and Analysis Center, Clinical and Translational Science Institute, University of Minnesota, Minneapolis, MN, USA
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Tang YW, Stratton CW. Multiplex PCR for Detection and Identification of Microbial Pathogens. ADVANCED TECHNIQUES IN DIAGNOSTIC MICROBIOLOGY 2018. [PMCID: PMC7121544 DOI: 10.1007/978-3-319-95111-9_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Multiplexed nucleic acid-based tests for infectious disease have become a standard part of clinical laboratory practice. These tests provide a comprehensive syndrome-based approach to determine the etiological agent of disease. The technology underlying these different systems is reviewed here with a special focus on the BioFire FilmArray® platform. The literature on the clinical utility and cost-effectiveness of these platforms for respiratory, blood culture, and gastrointestinal infections is discussed. Although there are reports showing a clear benefit to the patient or to the healthcare system from adopting a syndromic molecular approach, it is also apparent that clinical laboratories and healthcare providers are still learning how to take full advantage of the new systems. Finally, some improvements to this technology that should appear in the next few years are discussed. These include automated pathogen-specific surveillance based on aggregating the data from these systems, a move toward point-of-care syndromic testing, and further decreases in time to result of the tests.
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Affiliation(s)
- Yi-Wei Tang
- Departments of Laboratory Medicine and Internal Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Charles W. Stratton
- Department of Pathology, Microbiology and Immunology and Medicine, Vanderbilt University Medical Center, Nashville, TN USA
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29
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Nolte FS. Molecular Microbiology. PRINCIPLES AND APPLICATIONS OF MOLECULAR DIAGNOSTICS 2018. [PMCID: PMC7150357 DOI: 10.1016/b978-0-12-816061-9.00005-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background Nucleic acid (NA) amplification techniques are now commonly used to diagnose and manage patients with infectious diseases. The growth in the number of Food and Drug Administration–approved test kits and analyte-specific reagents has facilitated the use of this technology in clinical laboratories. Technological advances in NA amplification techniques, automation, NA sequencing, and multiplex analysis have reinvigorated the field and created new opportunities for growth. Simple, sample-in, answer-out molecular test systems are now widely available that can be deployed in a variety of laboratory and clinical settings. Molecular microbiology remains the leading area in molecular pathology in terms of both the numbers of tests performed and clinical relevance. NA-based tests have reduced the dependency of the clinical microbiology laboratory on more traditional antigen detection and culture methods and created new opportunities for the laboratory to impact patient care. Content This chapter reviews NA testing as it applies to specific pathogens or infectious disease syndromes, with a focus on those diseases for which NA testing is now considered the standard of care and highlights the unique challenges and opportunities that these tests present for clinical laboratories.
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Abstract
Acute upper and lower respiratory infections are a major public health problem and a leading cause of morbidity and mortality worldwide. At greatest risk are young children, the elderly, the chronically ill, and those with suppressed or compromised immune systems. Viruses are the predominant cause of respiratory tract illnesses and include RNA viruses such as respiratory syncytial virus, influenza virus, parainfluenza virus, metapneumovirus, rhinovirus, and coronavirus. Laboratory testing is required for a reliable diagnosis of viral respiratory infections, as a clinical diagnosis can be difficult since signs and symptoms are often overlapping and not specific for any one virus. Recent advances in technology have resulted in the development of newer diagnostic assays that offer great promise for rapid and accurate detection of respiratory viral infections. This chapter emphasizes the fundamental characteristics and clinical importance of the various RNA viruses that cause upper and lower respiratory tract diseases in the immunocompromised host. It highlights the laboratory methods that can be used to make a rapid and definitive diagnosis for the greatest impact on the care and management of ill patients, and the prevention and control of hospital-acquired infections and community outbreaks.
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Multicenter Clinical Evaluation of the Luminex Aries Flu A/B & RSV Assay for Pediatric and Adult Respiratory Tract Specimens. J Clin Microbiol 2017; 55:2431-2438. [PMID: 28539342 PMCID: PMC5527421 DOI: 10.1128/jcm.00318-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/16/2017] [Indexed: 11/20/2022] Open
Abstract
Influenza A and B viruses and respiratory syncytial virus (RSV) are three common viruses implicated in seasonal respiratory tract infections and are a major cause of morbidity and mortality in adults and children worldwide. In recent years, an increasing number of commercial molecular tests have become available to diagnose respiratory viral infections. The Luminex Aries Flu A/B & RSV assay is a fully automated sample-to-answer molecular diagnostic assay for the detection of influenza A, influenza B, and RSV. The clinical performance of the Aries Flu A/B & RSV assay was prospectively evaluated in comparison to that of the Luminex xTAG respiratory viral panel (RVP) at four North American clinical institutions over a 2-year period. Of the 2,479 eligible nasopharyngeal swab specimens included in the prospective study, 2,371 gave concordant results between the assays. One hundred eight specimens generated results that were discordant with those from the xTAG RVP and were further analyzed by bidirectional sequencing. Final clinical sensitivity values of the Aries Flu A/B & RSV assay were 98.1% for influenza A virus, 98.0% for influenza B virus, and 97.7% for RSV. Final clinical specificities for all three pathogens ranged from 98.6% to 99.8%. Due to the low prevalence of influenza B, an additional 40 banked influenza B-positive specimens were tested at the participating clinical laboratories and were all accurately detected by the Aries Flu A/B & RSV assay. This study demonstrates that the Aries Flu A/B & RSV assay is a suitable method for rapid and accurate identification of these causative pathogens in respiratory infections.
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Comparison of ePlex Respiratory Pathogen Panel with Laboratory-Developed Real-Time PCR Assays for Detection of Respiratory Pathogens. J Clin Microbiol 2017; 55:1938-1945. [PMID: 28404682 PMCID: PMC5442551 DOI: 10.1128/jcm.00221-17] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 04/04/2017] [Indexed: 11/27/2022] Open
Abstract
Infections of the respiratory tract can be caused by a diversity of pathogens, both viral and bacterial. Rapid microbiological diagnosis ensures appropriate antimicrobial therapy as well as effective implementation of isolation precautions. The ePlex respiratory pathogen panel (RP panel) is a novel molecular biology-based assay, developed by GenMark Diagnostics, Inc. (Carlsbad, CA), to be performed within a single cartridge for the diagnosis of 25 respiratory pathogens (viral and bacterial). The objective of this study was to compare the performance of the RP panel with those of laboratory-developed real-time PCR assays, using a variety of previously collected clinical respiratory specimens. A total of 343 clinical specimens as well as 29 external quality assessment (EQA) specimens and 2 different Middle East respiratory syndrome coronavirus isolates have been assessed in this study. The RP panel showed an agreement of 97.4% with the real-time PCR assay regarding 464 pathogens found in the clinical specimens. All pathogens present in clinical samples and EQA samples with a threshold cycle (CT) value of <30 were detected correctly using the RP panel. The RP panel detected 17 additional pathogens, 7 of which could be confirmed by discrepant testing. In conclusion, this study shows excellent performance of the RP panel in comparison to real-time PCR assays for the detection of respiratory pathogens. The ePlex system provided a large amount of useful diagnostic data within a short time frame, with minimal hands-on time, and can therefore potentially be used for rapid diagnostic sample-to-answer testing, in either a laboratory or a decentralized setting.
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Yun SG, Kim MY, Choi JM, Lee CK, Lim CS, Cho Y, Suh IB. Comparison of three multiplex PCR assays for detection of respiratory viruses: Anyplex II RV16, AdvanSure RV, and Real-Q RV. J Clin Lab Anal 2017; 32. [PMID: 28397965 PMCID: PMC5836940 DOI: 10.1002/jcla.22230] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/10/2017] [Indexed: 12/25/2022] Open
Abstract
Background Due to its great sensitivity, the nucleic acid amplification test (NAAT) is widely used for detection of respiratory viruses (RV). However, few reports have described a direct comparison between multiplex RT‐PCR assays for RV. The objective of this study was to perform a direct comparison of three multiplex RT‐PCR assays for the detection of respiratory viruses. Methods A total of 201 respiratory samples (161 nasopharyngeal swab samples and 40 sputum samples) were tested with three commercial RV assays: Seegene Anyplex II RV16 (AP), LG AdvanSure RV (AD), and Biosewoom Real‐Q RV (RQ). The additional tests for the discrepant results were conducted by repeat RV assay or monoplex PCR coupled direct sequencing. Data analysis using percent agreement, kappa, and prevalence‐adjusted and bias‐adjusted kappa (PABAK) values was performed for comparisons among the three RV assays. Results Of the 201 samples, AP, AD, and RQ detected 105 (52.2%), 99 (49.3%), and 95 (47.3%) positive cases respectively. The overall agreement, kappa, and PABAK values for the three assays ranged between 97%‐98%, 0.76‐0.86, and 0.93‐0.96 respectively. The performance of the three assays was very similar, with 94%‐100% agreement for all comparisons, each virus types. The additional testing of samples showed discrepant results demonstrating that AD assay had the highest rate of concordance with original results. Conclusions We suggest that all multiplex assay would be suitable for the detection of for respiratory viruses in clinical setting.
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Affiliation(s)
- Seung Gyu Yun
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
| | - Min Young Kim
- Armed Forces Medical Research Institute, Daejeon, Korea
| | - Jong Moon Choi
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Chang Kyu Lee
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Yunjung Cho
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - In Bum Suh
- Department of Laboratory Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
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Zou X, Tang G, Zhao X, Huang Y, Chen T, Lei M, Chen W, Yang L, Zhu W, Zhuang L, Yang J, Feng Z, Wang D, Wang D, Shu Y. Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique. SCIENCE CHINA. LIFE SCIENCES 2017; 60:279-286. [PMID: 27921234 PMCID: PMC7088591 DOI: 10.1007/s11427-016-0244-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 09/21/2016] [Indexed: 02/02/2023]
Abstract
Many viruses can cause respiratory diseases in humans. Although great advances have been achieved in methods of diagnosis, it remains challenging to identify pathogens in unexplained pneumonia (UP) cases. In this study, we applied next-generation sequencing (NGS) technology and a metagenomic approach to detect and characterize respiratory viruses in UP cases from Guizhou Province, China. A total of 33 oropharyngeal swabs were obtained from hospitalized UP patients and subjected to NGS. An unbiased metagenomic analysis pipeline identified 13 virus species in 16 samples. Human rhinovirus C was the virus most frequently detected and was identified in seven samples. Human measles virus, adenovirus B 55 and coxsackievirus A10 were also identified. Metagenomic sequencing also provided virus genomic sequences, which enabled genotype characterization and phylogenetic analysis. For cases of multiple infection, metagenomic sequencing afforded information regarding the quantity of each virus in the sample, which could be used to evaluate each viruses' role in the disease. Our study highlights the potential of metagenomic sequencing for pathogen identification in UP cases.
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Affiliation(s)
- Xiaohui Zou
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Guangpeng Tang
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China
| | - Xiang Zhao
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Yan Huang
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China
| | - Tao Chen
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Mingyu Lei
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China
| | - Wenbing Chen
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Wenfei Zhu
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Li Zhuang
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China
| | - Jing Yang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Zhaomin Feng
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Dingming Wang
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China.
| | - Yuelong Shu
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China.
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Impact of a Transition from Respiratory Virus Shell Vial to Multiplex PCR on Clinical Outcomes and Cost in Hospitalized Children. CHILDREN-BASEL 2017; 4:children4010003. [PMID: 28067857 PMCID: PMC5296664 DOI: 10.3390/children4010003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 12/21/2016] [Accepted: 12/28/2016] [Indexed: 11/16/2022]
Abstract
While respiratory virus PCR panel (RVPP) is more expensive than shell vial (SV) cell culture, it has been shown to reduce unnecessary diagnostic procedures, decrease the inappropriate use of antimicrobials, and shorten the hospital length of stay (LOS). We therefore hypothesized that, for hospitalized children, RVPP would be associated with improved clinical outcomes but higher hospital charges than SV cell culture. We performed a retrospective cohort study of hospitalized children. Multivariate analysis was performed, and p-values were calculated. Respiratory virus testing was collected in a total of 1625 inpatient encounters, of which 156 were tested positive by RVPP (57.7%) and 112 were tested positive by SV (11.1%, p < 0.05). Excluding human rhinovirus (HRV) and human metapneumovirus (hMPV) from the analysis, patients with a positive test from SV had more comorbidities (p = 0.04) and higher mortality (p = 0.008). Patients with a positive test from RVPP had shorter LOS (p = 0.0503). Hospital charges for patients with a positive test from RVPP were lower, but not significantly so. When a multivariate analysis was performed, there were no statistically significant differences in comorbidities, mortality, LOS, or median hospital charges between those patients with a positive SV and those with a positive RVPP. Although testing with RVPP significantly increased the detection of respiratory viruses, clinical outcomes remained comparable to those tested with SV, however RVPP was found to not be associated with higher long-term hospital costs.
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The ubiquity of asymptomatic respiratory viral infections in the tonsils and adenoids of children and their impact on airway obstruction. Int J Pediatr Otorhinolaryngol 2016; 90:128-132. [PMID: 27729119 PMCID: PMC7132388 DOI: 10.1016/j.ijporl.2016.09.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 11/23/2022]
Abstract
BACKGROUND Airway obstruction due to enlargement of tonsils and adenoids is a common pediatric problem resulting in sleep disordered breathing. The cause for the relatively abnormal growth of tonsils and adenoids is poorly understood. METHODS Non-acutely ill children undergoing tonsillectomy and adenoidectomy (T&A) for various reasons were enrolled prospectively in a study to determine the frequency of asymptomatic respiratory viral infections in each lymphoid tissue and to relate the number and types of virus to the degree of airway obstruction. Molecular techniques were used to detect 9 respiratory viruses while Brodsky scores and measurements of percentages airway obstruction were used to estimate the degree of airway compromise due to the tonsil and adenoid, respectively. RESULTS Viruses were detected in 70.9% of tonsils and 94.7% of adenoids, p < 0.001. Adenovirus was the most common virus detected at 71.1%. Adenoids had an average of 2.4 viruses compared to 0.92 for tonsils, p < 0.001. Higher Brodsky scores were only associated with EBV in tonsils, p = 0.03, while greater percentages of airway obstruction in the adenoids were associated with adenovirus, EBV, corona virus, parainfluenza virus and rhinovirus, p ≤ 0.005. CONCLUSIONS Asymptomatic viral infections are common and directly related to the degree of airway obstruction significantly more often in adenoids than tonsils.
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Hanson KE, Couturier MR. Multiplexed Molecular Diagnostics for Respiratory, Gastrointestinal, and Central Nervous System Infections. Clin Infect Dis 2016; 63:1361-1367. [PMID: 27444411 PMCID: PMC5091344 DOI: 10.1093/cid/ciw494] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/11/2016] [Indexed: 02/06/2023] Open
Abstract
The development and implementation of highly multiplexed molecular diagnostic tests have allowed clinical microbiology laboratories to more rapidly and sensitively detect a variety of pathogens directly in clinical specimens. Current US Food and Drug Administration-approved multiplex panels target multiple different organisms simultaneously and can identify the most common pathogens implicated in respiratory viral, gastrointestinal, or central nervous system infections. This review summarizes the test characteristics of available assays, highlights the advantages and limitations of multiplex technology for infectious diseases, and discusses potential utilization of these new tests in clinical practice.
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Affiliation(s)
- Kimberly E Hanson
- Divisions of Infectious Diseases.,Clinical Microbiology, University of Utah and ARUP Laboratories, Salt Lake City
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Dut R, Kocagöz S. Clinical Signs and Diagnostic Tests in Acute Respiratory Infections. Indian J Pediatr 2016; 83:380-5. [PMID: 26687497 PMCID: PMC7090667 DOI: 10.1007/s12098-015-1943-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 10/28/2015] [Indexed: 11/25/2022]
Abstract
OBJECTIVES To evaluate clinical manifestations of acute respiratory system infectious diseases and specific tests for causative agents in pediatric patients. METHODS The authors evaluated children aged 0-16 y with clinical symptoms of acute respiratory tract infections who were administered rapid strep A test and/or throat culture test and/or respiratory viral panel test, from February 2012 through January 2013 at pediatric department of Acıbadem Maslak Hospital, Turkey. RESULTS A total of 1654 patients were evaluated; 45.9 % were girls, 54.1 % were boys. Absence of cough and presence of headache were higher in the patients >6 y of age (p 0.0001, p 0.002 respectively). Positive respiratory viral panel test was higher in the patients <2 y of age (p 0.002). Both positive rapid strep A test and positive throat culture test were higher in the patients >6 y of age (p 0.0001). Positivity of rapid strep A or throat culture test were not observed in children <2 y of age. CONCLUSIONS A clinician should mostly consider viral infections in the etiology of acute respiratory infections in children under 2 y of age and there is no need to rush for the use antibiotherapy. Bacterial etiology should be frequently considered after 6 y of age and rapid use of antibiotherapy is essential to avoid the complications.
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Affiliation(s)
- Raziye Dut
- Department of Pediatrics, Acıbadem Maslak Hospital, 063340, İstanbul, Turkey.
| | - Sesin Kocagöz
- Division of Infectious Diseases, University of Acıbadem, İstanbul, Turkey
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Simpson MD, Kieke BA, Sundaram ME, McClure DL, Meece JK, Sifakis F, Gasser RA, Belongia EA. Incidence of Medically Attended Respiratory Syncytial Virus and Influenza Illnesses in Children 6-59 Months Old During Four Seasons. Open Forum Infect Dis 2016; 3:ofw081. [PMID: 27419158 PMCID: PMC4943552 DOI: 10.1093/ofid/ofw081] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 04/15/2016] [Indexed: 11/12/2022] Open
Abstract
RSV was the most common viral agent causing acute respiratory illness in children 6 to 59 months old during the influenza season. Children in the 6-23 month age range had a higher incidence of RSV compared to those aged 24-59 months. Background. Respiratory syncytial virus (RSV) and influenza are significant causes of seasonal respiratory illness in children. The incidence of influenza and RSV hospitalization is well documented, but the incidence of medically attended, laboratory-confirmed illness has not been assessed in a well defined community cohort. Methods. Children aged 6–59 months with medically attended acute respiratory illness were prospectively enrolled during the 2006–2007 through 2009–2010 influenza seasons in a Wisconsin community cohort. Nasal swabs were tested for RSV and influenza by multiplex reverse-transcription polymerase chain reaction. The population incidence of medically attended RSV and influenza was estimated separately and standardized to weeks 40 through 18 of each season. Results. The cohort included 2800–3073 children each season. There were 2384 children enrolled with acute respiratory illness; 627 (26%) were positive for RSV and 314 (13%) for influenza. The mean age was 28 months (standard deviation [SD] = 15) for RSV-positive and 38 months (SD = 16) for influenza-positive children. Seasonal incidence (cases per 10 000) was 1718 (95% confidence interval [CI], 1602–1843) for RSV and 768 (95% CI, 696–848) for influenza. Respiratory syncytial virus incidence was highest among children 6–11 (2927) and 12–23 months old (2377). Influenza incidence was highest (850) in children 24–59 months old. The incidence of RSV was higher than influenza across all seasons and age groups. Conclusions. The incidence of medically attended RSV was highest in children 6–23 months old, and it was consistently higher than influenza. The burden of RSV remains high throughout the first 2 years of life.
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Optimizing Virus Identification in Critically Ill Children Suspected of Having an Acute Severe Viral Infection. Pediatr Crit Care Med 2016; 17:279-86. [PMID: 26895562 DOI: 10.1097/pcc.0000000000000661] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Multiplex rapid viral tests and nasopharyngeal flocked swabs are increasingly used for viral testing in PICUs. This study aimed at evaluating how the sampling site and the type of diagnostic test influence test results in children with suspected severe viral infection. DESIGN Prospective cohort study. SETTING PICUs at 21 tertiary pediatric referral centers in the United States. PATIENTS During the 2010-2011 and 2011-2012 influenza seasons, we enrolled children (6 mo to 17 yr old) who were suspected to have severe viral infection. INTERVENTIONS We collected samples by using a standardized protocol for nasopharyngeal aspirate and nasopharyngeal flocked swabs in nonintubated patients and for endotracheal tube aspirate and nasopharyngeal flocked swabs in intubated patients. MEASUREMENTS AND MAIN RESULTS Viral testing included a single reverse transcription-polymerase chain reaction influenza test and the GenMark Respiratory Viral Panel (20 viruses). We enrolled 90 endotracheally intubated and 133 nonintubated children. We identified influenza in 45 patients with reverse transcription-polymerase chain reaction testing; the multiplex panel was falsely negative for influenza in two patients (4.4%). Six patients (13.3%) had not been diagnosed with influenza in the PICU. Non-influenza viruses were identified in 172 of 223 children (77.1%). In nonintubated children, the same virus was identified by nasopharyngeal flocked swabs and nasopharyngeal aspirate in 133 of 183 paired samples (72.7%), with +nasopharyngeal aspirate/-nasopharyngeal flocked swabs in 32 of 183 paired samples (17.4%). In intubated children, the same virus was identified by nasopharyngeal flocked swabs and endotracheal tube aspirate in 67 of 94 paired samples (71.3%), with +nasopharyngeal flocked swabs/- endotracheal tube aspirate in 22 of 94 paired samples (23.4%). Most discrepancies were either adenovirus or rhinovirus in both groups. CONCLUSIONS Standardized specimen collection and sensitive diagnostic testing with a reverse transcription-polymerase chain reaction increased the identification of influenza in critically ill children. For most pathogenic viruses identified, results from nasopharyngeal flocked swabs agreed with those from nasopharyngeal or endotracheal aspirates.
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Abstract
OBJECTIVES To describe the strengths and limitations of the available influenza diagnostics, with a focus on rapid antigen detection assays and nucleic acid detection assays. METHODS A case-based presentation is used to illustrate the potential limitations of rapid antigen detection assays for influenza. RESULTS Influenza is a seasonal illness; estimates attribute influenza to approximately 200,000 hospitalizations and 41,000 deaths in the United States annually. Antigen detection assays for influenza are rapid and convenient, and thus are widely used in a variety of health care settings, even though the sensitivity of these assays may be suboptimal. The United States Food and Drug Administration has recently created new guidelines intended to improve the oversight and performance characteristics of influenza antigen detection assays. Molecular assays, although more costly and complex, are more sensitive and may be designed to simultaneously detect multiple respiratory pathogens within a single assay. CONCLUSIONS Diagnostic assays for influenza can vary greatly with regards to analytical performance characteristics, complexity, turnaround time and cost. This can have important patient care and infection prevention implications.
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Affiliation(s)
- Allison R McMullen
- From the Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO
| | - Neil W Anderson
- From the Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO
| | - Carey-Ann D Burnham
- From the Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO.
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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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Microbiologic Diagnosis of Lung Infection. MURRAY AND NADEL'S TEXTBOOK OF RESPIRATORY MEDICINE 2016. [PMCID: PMC7152380 DOI: 10.1016/b978-1-4557-3383-5.00017-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Pratt VM, Everts RE, Aggarwal P, Beyer BN, Broeckel U, Epstein-Baak R, Hujsak P, Kornreich R, Liao J, Lorier R, Scott SA, Smith CH, Toji LH, Turner A, Kalman LV. Characterization of 137 Genomic DNA Reference Materials for 28 Pharmacogenetic Genes: A GeT-RM Collaborative Project. J Mol Diagn 2015; 18:109-23. [PMID: 26621101 DOI: 10.1016/j.jmoldx.2015.08.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/24/2015] [Accepted: 08/13/2015] [Indexed: 10/22/2022] Open
Abstract
Pharmacogenetic testing is increasingly available from clinical laboratories. However, only a limited number of quality control and other reference materials are currently available to support clinical testing. To address this need, the Centers for Disease Control and Prevention-based Genetic Testing Reference Material Coordination Program, in collaboration with members of the pharmacogenetic testing community and the Coriell Cell Repositories, has characterized 137 genomic DNA samples for 28 genes commonly genotyped by pharmacogenetic testing assays (CYP1A1, CYP1A2, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP2E1, CYP3A4, CYP3A5, CYP4F2, DPYD, GSTM1, GSTP1, GSTT1, NAT1, NAT2, SLC15A2, SLC22A2, SLCO1B1, SLCO2B1, TPMT, UGT1A1, UGT2B7, UGT2B15, UGT2B17, and VKORC1). One hundred thirty-seven Coriell cell lines were selected based on ethnic diversity and partial genotype characterization from earlier testing. DNA samples were coded and distributed to volunteer testing laboratories for targeted genotyping using a number of commercially available and laboratory developed tests. Through consensus verification, we confirmed the presence of at least 108 variant pharmacogenetic alleles. These samples are also being characterized by other pharmacogenetic assays, including next-generation sequencing, which will be reported separately. Genotyping results were consistent among laboratories, with most differences in allele assignments attributed to assay design and variability in reported allele nomenclature, particularly for CYP2D6, UGT1A1, and VKORC1. These publicly available samples will help ensure the accuracy of pharmacogenetic testing.
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Affiliation(s)
- Victoria M Pratt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | | | - Praful Aggarwal
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Brittany N Beyer
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ulrich Broeckel
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | - Paul Hujsak
- Department of Research & Development, Autogenomics Inc., Vista, California
| | - Ruth Kornreich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jun Liao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rachel Lorier
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Lorraine H Toji
- Coriell Cell Repositories, Coriell Institute for Medical Research, Camden, New Jersey
| | - Amy Turner
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Lisa V Kalman
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia.
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Parker J, Fowler N, Walmsley ML, Schmidt T, Scharrer J, Kowaleski J, Grimes T, Hoyos S, Chen J. Analytical Sensitivity Comparison between Singleplex Real-Time PCR and a Multiplex PCR Platform for Detecting Respiratory Viruses. PLoS One 2015; 10:e0143164. [PMID: 26569120 PMCID: PMC4646456 DOI: 10.1371/journal.pone.0143164] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 11/02/2015] [Indexed: 01/12/2023] Open
Abstract
Multiplex PCR methods are attractive to clinical laboratories wanting to broaden their detection of respiratory viral pathogens in clinical specimens. However, multiplexed assays must be well optimized to retain or improve upon the analytic sensitivity of their singleplex counterparts. In this experiment, the lower limit of detection (LOD) of singleplex real-time PCR assays targeting respiratory viruses is compared to an equivalent panel on a multiplex PCR platform, the GenMark eSensor RVP. LODs were measured for each singleplex real-time PCR assay and expressed as the lowest copy number detected 95-100% of the time, depending on the assay. The GenMark eSensor RVP LODs were obtained by converting the TCID50/mL concentrations reported in the package insert to copies/μL using qPCR. Analytical sensitivity between the two methods varied from 1.2-1280.8 copies/μL (0.08-3.11 log differences) for all 12 assays compared. Assays targeting influenza A/H3N2, influenza A/H1N1pdm09, influenza B, and human parainfluenza 1 and 2 were most comparable (1.2-8.4 copies/μL, <1 log difference). Largest differences in LOD were demonstrated for assays targeting adenovirus group E, respiratory syncytial virus subtype A, and a generic assay for all influenza A viruses regardless of subtype (319.4-1280.8 copies/μL, 2.50-3.11 log difference). The multiplex PCR platform, the GenMark eSensor RVP, demonstrated improved analytical sensitivity for detecting influenza A/H3 viruses, influenza B virus, human parainfluenza virus 2, and human rhinovirus (1.6-94.8 copies/μL, 0.20-1.98 logs). Broader detection of influenza A/H3 viruses was demonstrated by the GenMark eSensor RVP. The relationship between TCID50/mL concentrations and the corresponding copy number related to various ATCC cultures is also reported.
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Affiliation(s)
- Jayme Parker
- Department of Health and Social Services, Division of Public Health, Alaska State Public Health Virology Laboratory, Fairbanks, Alaska, United States of America
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Nisha Fowler
- Department of Health and Social Services, Division of Public Health, Alaska State Public Health Virology Laboratory, Fairbanks, Alaska, United States of America
| | - Mary Louise Walmsley
- Department of Health and Social Services, Division of Public Health, Alaska State Public Health Virology Laboratory, Fairbanks, Alaska, United States of America
| | - Terri Schmidt
- Department of Health and Social Services, Division of Public Health, Alaska State Public Health Virology Laboratory, Fairbanks, Alaska, United States of America
| | - Jason Scharrer
- Department of Health and Social Services, Division of Public Health, Alaska State Public Health Virology Laboratory, Fairbanks, Alaska, United States of America
| | - James Kowaleski
- Department of Health and Social Services, Division of Public Health, Alaska State Public Health Virology Laboratory, Fairbanks, Alaska, United States of America
| | - Teresa Grimes
- Department of Health and Social Services, Division of Public Health, Alaska State Public Health Virology Laboratory, Fairbanks, Alaska, United States of America
| | - Shanann Hoyos
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Jack Chen
- Department of Health and Social Services, Division of Public Health, Alaska State Public Health Virology Laboratory, Fairbanks, Alaska, United States of America
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
- * E-mail:
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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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Nguyen C, Kaku S, Tutera D, Kuschner WG, Barr J. Viral Respiratory Infections of Adults in the Intensive Care Unit. J Intensive Care Med 2015; 31:427-41. [PMID: 25990273 DOI: 10.1177/0885066615585944] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 03/16/2015] [Indexed: 12/12/2022]
Abstract
Viral lower respiratory tract infections (LRTIs) are an underappreciated cause of critical illness in adults. Recent advances in viral detection techniques over the past decade have demonstrated viral LRTIs are associated with rates of morbidity, mortality, and health care utilization comparable to those of seen with bacterial community acquired and nosocomial pneumonias. In this review, we describe the relationship between viral LRTIs and critical illness, as well as discuss relevant clinical features and management strategies for the more prevalent respiratory viral pathogens.
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Affiliation(s)
- Christopher Nguyen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Shawn Kaku
- Division of Critical Care Medicine, Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Dominic Tutera
- Division of Critical Care Medicine, Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ware G Kuschner
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA Pulmonary Section, Medicine Service, VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Juliana Barr
- Division of Critical Care Medicine, Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA Anesthesiology and Perioperative Care Service, VA Palo Alto Health Care System, Palo Alto, CA, USA
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Zhang H, Morrison S, Tang YW. Multiplex polymerase chain reaction tests for detection of pathogens associated with gastroenteritis. Clin Lab Med 2015; 35:461-86. [PMID: 26004652 DOI: 10.1016/j.cll.2015.02.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A wide range of enteric pathogens can cause infectious gastroenteritis. Conventional diagnostic algorithms are time-consuming and often lack sensitivity and specificity. Advances in molecular technology have provided new clinical diagnostic tools. Multiplex polymerase chain reaction (PCR)-based testing has been used in gastroenterology diagnostics in recent years. This article presents a review of recent laboratory-developed multiplex PCR tests and current commercial multiplex gastrointestinal pathogen tests. It focuses on two commercial syndromic multiplex tests: Luminex xTAG Gastrointestinal Pathogen Panel and BioFire FilmArray gastrointestinal test. Multiplex PCR tests have shown superior sensitivity to conventional methods for detection of most pathogens.
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Affiliation(s)
- Hongwei Zhang
- Luminex Corporation, 12212 Technology Boulevard, Austin, TX 78727, USA
| | - Scott Morrison
- Luminex Corporation, 12212 Technology Boulevard, Austin, TX 78727, USA
| | - Yi-Wei Tang
- Clinical Microbiology Service, Memorial Sloan-Kettering Cancer Center, Weill Cornell Medical College, Cornell University, 1275 York Avenue, S428, New York, NY 10065, USA.
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Zimmerman RK, Rinaldo CR, Nowalk MP, Balasubramani GK, Moehling KK, Bullotta A, Eng HF, Raviotta JM, Sax TM, Wisniewski S. Viral infections in outpatients with medically attended acute respiratory illness during the 2012-2013 influenza season. BMC Infect Dis 2015; 15:87. [PMID: 25887948 PMCID: PMC4344779 DOI: 10.1186/s12879-015-0806-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/04/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While it is known that acute respiratory illness (ARI) is caused by an array of viruses, less is known about co-detections and the resultant comparative symptoms and illness burden. This study examined the co-detections, the distribution of viruses, symptoms, and illness burden associated with ARI between December 2012 and March 2013. METHODS Outpatients with ARI were assayed for presence of 18 viruses using multiplex reverse transcriptase polymerase chain reaction (MRT-PCR) to simultaneously detect multiple viruses. RESULTS Among 935 patients, 60% tested positive for a single virus, 9% tested positive for ≥1 virus and 287 (31%) tested negative. Among children (<18 years), the respective distributions were 63%, 14%, and 23%; whereas for younger adults (18-49 years), the distributions were 58%, 8%, and 34% and for older adults (≥50 years) the distributions were 61%, 5%, and 32% (P < 0.001). Co-detections were more common in children than older adults (P = 0.01), and less frequent in households without children (P = 0.003). Most frequently co-detected viruses were coronavirus, respiratory syncytial virus, and influenza A virus. Compared with single viral infections, those with co-detections less frequently reported sore throat (P = 0.01), missed fewer days of school (1.1 vs. 2 days; P = 0.04), or work (2 vs. 3 days; P = 0.03); other measures of illness severity did not vary. CONCLUSIONS Among outpatients with ARI, 69% of visits were associated with a viral etiology. Co-detections of specific clusters of viruses were observed in 9% of ARI cases particularly in children, were less frequent in households without children, and were less symptomatic (e.g., lower fever) than single infections.
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Affiliation(s)
- Richard K Zimmerman
- Department of Family Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Charles R Rinaldo
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Departments of Infectious Disease and Microbiology, and Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.
| | - Mary Patricia Nowalk
- Department of Family Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - G K Balasubramani
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.
| | - Krissy K Moehling
- Department of Family Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Arlene Bullotta
- Departments of Infectious Disease and Microbiology, and Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.
| | - Heather F Eng
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.
| | - Jonathan M Raviotta
- Department of Family Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Theresa M Sax
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.
| | - Stephen Wisniewski
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.
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Farrell JJ, Hujer AM, Sampath R, Bonomo RA. Salvage microbiology: opportunities and challenges in the detection of bacterial pathogens following initiation of antimicrobial treatment. Expert Rev Mol Diagn 2014; 15:349-60. [PMID: 25523281 DOI: 10.1586/14737159.2015.989216] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Broad-range 16S ribosomal RNA gene PCR coupled with Sanger sequencing was originally employed by soil scientists and was subsequently adapted for clinical applications. PCR coupled with electrospray ionization mass spectrometry has also progressed from initial applications in the detection of organisms from environmental samples into the clinical realm and has demonstrated promise in detection of pathogens in clinical specimens obtained from patients with suspected infection but negative cultures. We review studies of multiplex PCR, 16S ribosomal RNA gene PCR and sequencing and PCR coupled with electrospray ionization mass spectrometry for detection of bacteria in specimens that were obtained from patients during or after administration of antibiotic treatment, and examine the role of each for assisting in antimicrobial treatment and stewardship efforts. Following an exploration of the available data in this field, we discuss the opportunities that the preliminary investigations reveal, as well as the challenges faced with the implementation of these strategies in clinical practice.
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Affiliation(s)
- John J Farrell
- Department of Medicine, Division of Infectious Disease, University of Illinois College of Medicine, 723 N.E. Glen Oak Ave. Peoria, IL 61603, USA
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