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Robinson JL, Kellner JD, Crotts J, Travassos G, Chen G, Kirk VG, Pusic M, Reed M, Reid S, Weinstein M, Bhargava R, Bhatt M, Boutis K, Curtis S, Gouin S, Lynch T, van Wylick R, Johnson DW. Accuracy of the diagnosis of pneumonia in Canadian pediatric emergency departments: A prospective cohort study. PLoS One 2024; 19:e0311201. [PMID: 39661638 PMCID: PMC11633949 DOI: 10.1371/journal.pone.0311201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 09/06/2024] [Indexed: 12/13/2024] Open
Abstract
BACKGROUND The diagnosis of pediatric pneumonia and determination of the likely pathogen are complicated as the clinical picture overlaps with other respiratory illnesses, interpretation of radiographs is subjective, and laboratory results are rarely diagnostic. This study was designed to describe the relative rates of bacterial and viral pneumonia in the pediatric Emergency Department (ED), determine the accuracy of pediatric ED physicians' ability to diagnose pneumonia and distinguish bacterial from viral etiology, and to determine clinical and laboratory predictors of bacterial pneumonia. METHODS Children 3 months to 16 years of age presenting to seven Canadian pediatric EDs before the COVID-19 pandemic with fever and cough who had a chest radiograph performed for possible pneumonia were enrolled and underwent standardized clinical investigations. An expert panel was convened and reached a Consensus Diagnosis of typical or atypical bacterial pneumonia, viral pneumonia or not pneumonia for each case. RESULTS The expert panel assessed 247 cases with the Consensus Diagnosis being typical bacterial pneumonia (N = 44(18%)), atypical bacterial pneumonia (N = 18(7%)), viral pneumonia (N = 46(19%)) and no pneumonia (N = 139(56%)). Treating ED physician diagnoses were typical bacterial pneumonia (N = 126(51%)), atypical bacterial pneumonia (N = 3(1%)), viral pneumonia (N = 10(4%)) and no pneumonia (N = 108(44%)) with low agreement between a diagnosis of bacterial pneumonia by the ED physician and the panel's Consensus Diagnosis (Kappa 0.15 (95% CI 0.08, 0.21)). Cut off values that predicted bacterial pneumonia as the Consensus Diagnosis were ESR ≥ 47 mm/hour, CRP ≥ 42 mg/L and procalcitonin ≥0.85 ng/m. Age greater than 5 years and cough for 5 or more days also predict bacterial pneumonia. CONCLUSION In this cohort, pediatric ED physicians over-diagnosed typical bacterial pneumonia and underdiagnosed viral and atypical bacterial pneumonia. Bacterial pneumonia is most likely in children over 5 years of age, with cough for 5 or more days and/or with elevated inflammatory markers.
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Affiliation(s)
- Joan L. Robinson
- Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - James D. Kellner
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jennifer Crotts
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Gabino Travassos
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Valerie G. Kirk
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Martin Pusic
- Pediatrics, Harvard Medical School, Boston, MA, United States of America
| | - Martin Reed
- University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sarah Reid
- Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Ravi Bhargava
- Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Maala Bhatt
- Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Sarah Curtis
- Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Serge Gouin
- Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Tim Lynch
- Department of Pediatrics, Schulich School of Medicine, Western University, London, Ontario, Canada
| | | | - David W. Johnson
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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Tian J, Pinto JM, Li L, Zhang S, Sun Z, Wei Y. Identification of Viruses in Patients With Postviral Olfactory Dysfunction by Multiplex Reverse-Transcription Polymerase Chain Reaction. Laryngoscope 2020; 131:158-164. [PMID: 32786080 PMCID: PMC7436707 DOI: 10.1002/lary.28997] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 12/29/2022]
Abstract
Objectives/Hypothesis To investigate causative viruses in patients with postviral olfactory disorders (PVOD). Study Design Case‐control study. Methods One hundred fifty‐one consecutive patients diagnosed with PVOD were enrolled, and samples from 38 patients who visited the doctor within 3 months of symptom onset were collected and analyzed. Thirty‐two individuals who underwent surgery for nasal septal deviation during the same time period were collected as the control group. The Sniffin' Sticks psychophysical olfactory test was used to evaluate olfactory function. Olfactory cleft specimens were collected using nasopharyngeal flocked swabs (COPAN FLOQSwabs). Eighteen viruses were tested for with the Luminex xTAG RVP FAST v2 Assay Kit. Results Out of the 38 patients with PVOD, rhinoviruses were detected in 13 patients, and coronavirus OC43 was detected in one patient. The frequency of positive virus detection in the patients with anosmia was higher than in those with hyposmia (58.8% vs. 19.0%, P = 0.018). In control group, rhinovirus was identified in one patient (3.1%). Nasal obstruction was the most common symptom and was experienced by 71.0% of patients. Conclusions Rhinovirus and coronavirus are more commonly identified in PVOD. Our methods represent an approach to screen for viruses that may be involved in PVOD. Level of Evidence 4 Laryngoscope, 131:158–164, 2021
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Affiliation(s)
- Jun Tian
- Department of Otolaryngology-Head and Neck Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jayant M Pinto
- Section of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of Chicago, Chicago, Illinois, U.S.A
| | - Li Li
- Department of Otolaryngology-Head and Neck Surgery, Hospital of Renmin University of China, Beijing, China
| | - Sanmei Zhang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Zhifu Sun
- Department of Otolaryngology-Head and Neck Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Yongxiang Wei
- Department of Otolaryngology-Head and Neck Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
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On R, Matsumoto T, Kushima H, Hirano R, Fujita M. Prevalence of viral infection in acute exacerbation of interstitial lung diseases in Japan. Respir Investig 2020; 58:473-478. [PMID: 32753313 PMCID: PMC7395810 DOI: 10.1016/j.resinv.2020.06.006] [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: 02/07/2020] [Revised: 06/24/2020] [Accepted: 06/28/2020] [Indexed: 01/08/2023]
Abstract
Background Fatal acute exacerbation of interstitial lung diseases is often accompanied by indicators of infection such as fever, cough, and sputum. Although viral infection can contribute to acute exacerbation of interstitial lung diseases, few studies have identified a relationship between acute exacerbations and viral infections. The present study aimed to prospectively clarify the role of viral infection in patients showing acute exacerbation of interstitial lung disease in Japan. Methods Nasopharyngeal swab specimens were collected from patients with acute exacerbation of interstitial lung disease between May 2017 and February 2019. Respiratory viruses were detected by the Luminex xTAG Respiratory Viral Panel FAST v2 RUO kit and the BioFire FilmArray Respiratory Panel assay. Results Three of 29 patients demonstrated respiratory viral infection during acute exacerbation of interstitial lung diseases. The infectious agents were identified as respiratory syncytial virus, respiratory syncytial virus and influenza A virus, and influenza A virus and rhino/enterovirus in the three patients, respectively. Conclusions These results suggest that viral infection did not frequently induce acute exacerbation of interstitial lung diseases in Japan.
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Affiliation(s)
- Rintaro On
- Department of Respiratory Medicine, Fukuoka University Hospital, Japan.
| | | | - Hisako Kushima
- Department of Respiratory Medicine, Fukuoka University Hospital, Japan.
| | - Ryosuke Hirano
- Department of Respiratory Medicine, Fukuoka University Hospital, Japan.
| | - Masaki Fujita
- Department of Respiratory Medicine, Fukuoka University Hospital, Japan.
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Pham HT, Nguyen PTT, Tran ST, Phung TTB. Clinical and Pathogenic Characteristics of Lower Respiratory Tract Infection Treated at the Vietnam National Children's Hospital. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2020; 2020:7931950. [PMID: 32256905 PMCID: PMC7086417 DOI: 10.1155/2020/7931950] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/15/2019] [Accepted: 02/14/2020] [Indexed: 01/17/2023]
Abstract
Lower respiratory tract infections are commonly caused by viruses and cause significant morbidity and mortality among children. Early identification of the pathological agent causing these infections is essential to avoid unnecessary antibiotic use and improve patient management. Multiplex PCR techniques were recently developed to detect multiple viral pathogens using a single PCR reaction. In this study, we identify viral pathogens in children with respiratory infections. We collected 194 nasopharyngeal aspirates from infants (2-24 months old) with lower respiratory tract infections treated at the Vietnam National Children's Hospital between November 2014 and June 2015 and assessed the presence of 16 virus types and subtypes by multiplex PCR using the xTAG Respiratory Viral Panel (RVP) assay. Overall, 73.7% of the samples were positive for at least one virus, and 24.2% corresponded to infections with multiple viruses. The most common viruses were respiratory syncytial virus and enterovirus/rhinovirus. These viruses were more frequent among younger patients (2-5 months old) and caused symptoms similar to those of bronchiolitis and pneumonia. The most common clinical manifestation caused by respiratory tract infection was bronchiolitis. Elevated neutrophils levels were associated with adenovirus infection. Our results showed that the xTAG Respiratory Viral Panel (RVP) can effectively detect multiple viruses causing respiratory infections in children and that the nasopharyngeal aspirates are a good sample choice to detect respiratory viruses in children. Applying this approach in the clinical setting would improve patient management and allow early diagnosis, thus avoiding the unnecessary use of antibiotics.
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Affiliation(s)
- Hien T. Pham
- International Outpatient Department of Vietnam National Children's Hospital (VNCH), Hanoi 100000, Vietnam
| | - Phuc T. T. Nguyen
- International Outpatient Department of Vietnam National Children's Hospital (VNCH), Hanoi 100000, Vietnam
| | - Sinh T. Tran
- Research Biomolecular for Infectious Disease Department of Vietnam National Children's Hospital (VNCH), Hanoi 100000, Vietnam
| | - Thuy T. B. Phung
- Research Biomolecular for Infectious Disease Department of Vietnam National Children's Hospital (VNCH), Hanoi 100000, Vietnam
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Scott AN, Buchan SA, Kwong JC, Drews SJ, Simmonds KA, Svenson LW. Using population-wide administrative and laboratory data to estimate type- and subtype-specific influenza vaccine effectiveness: a surveillance protocol. BMJ Open 2019; 9:e029708. [PMID: 31575570 PMCID: PMC6773297 DOI: 10.1136/bmjopen-2019-029708] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION The appropriateness of using routinely collected laboratory data combined with administrative data for estimating influenza vaccine effectiveness (VE) is still being explored. This paper outlines a protocol to estimate influenza VE using linked laboratory and administrative data which could act as a companion to estimates derived from other methods. METHODS AND ANALYSIS We will use the test-negative design to estimate VE for each influenza type/subtype and season. Province-wide individual-level records of positive and negative influenza tests at the Provincial Laboratory for Public Health in Alberta will be linked, by unique personal health numbers, to administrative databases and vaccination records held at the Ministry of Health in Alberta to determine covariates and influenza vaccination status, respectively. Covariates of interests include age, sex, immunocompromising chronic conditions and healthcare setting. Cases will be defined based on an individual's first positive influenza test during the season, and potential controls will be defined based on an individual's first negative influenza test during the season. One control for each case will be randomly selected based on the week the specimen was collected. We will estimate VE using multivariable logistic regression. ETHICS AND DISSEMINATION Ethics approval was obtained from the University of Alberta's Health Research Ethics Board-Health Panel under study ID Pro00075997. Results will be disseminated by public health officials in Alberta.
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Affiliation(s)
- Allison Nicole Scott
- Ministry of Health, Government of Alberta, Edmonton, Alberta, Canada
- Department of Public Health, Concordia University of Edmonton, Edmonton, Alberta, Canada
| | - Sarah A Buchan
- Populations and Public Health Research Program, ICES, Toronto, Ontario, Canada
- Public Health Sciences, Public Health Ontario, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey C Kwong
- Populations and Public Health Research Program, ICES, Toronto, Ontario, Canada
- Public Health Sciences, Public Health Ontario, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Family and Community Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | - Kimberley A Simmonds
- Ministry of Health, Government of Alberta, Edmonton, Alberta, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Lawrence W Svenson
- Ministry of Health, Government of Alberta, Edmonton, Alberta, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Division of Preventive Medicine, University of Alberta, Edmonton, Alberta, Canada
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
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Opportunities Revealed for Antimicrobial Stewardship and Clinical Practice with Implementation of a Rapid Respiratory Multiplex Assay. J Clin Microbiol 2019; 57:JCM.00861-19. [PMID: 31413077 PMCID: PMC6760939 DOI: 10.1128/jcm.00861-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/05/2019] [Indexed: 12/18/2022] Open
Abstract
Few studies assess the utility of rapid multiplex molecular respiratory panels in adult patients. Previous multiplex PCR assays took hours to days from order time to result. We analyze the clinical impact of switching to a molecular assay with a 3-h test-turnaround-time (TAT). We performed a retrospective review of adult patients who presented to our emergency departments with respiratory symptoms and had a respiratory viral panel (xTAG RVP; RVP) or respiratory pathogen panel (ePlex RP; RPP) within 48 h of presentation. The average TATs for the RVP and RPP were 27.9 and 3.0 h, respectively (P < 0.0001). In RVP-positive and RPP-positive patients, 68.9 and 44.5% of those with normal chest imaging received antibiotics (P = 0.013), while 95.4 and 89.6% of those with abnormal imaging received antibiotics, respectively (P = 0.187). There was no difference in antibiotic duration in RVP-positive and RPP-positive patients with abnormal chest imaging (6.2 and 6.0 days, respectively; P = 0.923) and normal chest imaging (4.5 and 4.3 days, respectively; P = 0.922). Fewer patients were admitted in the RPP-positive compared to the RVP-positive group (76.9 and 88.6%, respectively; P = 0.013), while the proportion of admissions were similar among RPP-negative and RVP-negative patients (85.3 and 87.1%, P = 0.726). Switching to a multiplex respiratory panel with a clinically actionable TAT is associated with reduced hospital admissions and, in admitted adults without focal radiographic findings, reduced antibiotic initiation. Opportunities to further mitigate inappropriate antibiotic use may be realized by combining rapid multiplex PCR with provider education, clinical decision-care algorithms, and active antibiotic stewardship.
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Wen S, Lv F, Chen X, Zhu L, Li H, Lin L, Zhang H. Application of a nucleic acid-based multiplex kit to identify viral and atypical bacterial aetiology of lower respiratory tract infection in hospitalized children. J Med Microbiol 2019; 68:1211-1218. [PMID: 31225788 DOI: 10.1099/jmm.0.001006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Shunhang Wen
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Fangfang Lv
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Xiaofang Chen
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Lili Zhu
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Haiyan Li
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Li Lin
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Hailin Zhang
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
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Xu L, Jiang X, Zhu Y, Duan Y, Huang T, Huang Z, Liu C, Xu B, Xie Z. A Multiplex Asymmetric Reverse Transcription-PCR Assay Combined With an Electrochemical DNA Sensor for Simultaneously Detecting and Subtyping Influenza A Viruses. Front Microbiol 2018; 9:1405. [PMID: 30013525 PMCID: PMC6036258 DOI: 10.3389/fmicb.2018.01405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/07/2018] [Indexed: 12/21/2022] Open
Abstract
The reliable and rapid detection of viral pathogens that cause respiratory infections provide physicians several advantages in treating patients and managing outbreaks. The Luminex respiratory virus panel (RVP) assay has been shown to be comparable to or superior to culture/direct fluorescent-antibody assays (DFAs) and nucleic acid tests that are used to diagnose respiratory viral infections. We developed a multiplex asymmetric reverse transcription (RT)-PCR assay that can simultaneously differentiate all influenza A virus epidemic subtypes. The amplified products were hybridized with an electrochemical DNA sensor, and the results were automatically acquired. The limits of detection (LoDs) of both the Luminex RVP assay and the multiplex RT-PCR-electrochemical DNA sensor were 101 TCID50 for H1N1 virus and 102 TCID50 for H3N2 virus. The specificity assessment of the multiplex RT-PCR-electrochemical DNA sensor showed no cross-reactivity among different influenza A subtypes or with other non-influenza respiratory viruses. In total, 3098 respiratory tract specimens collected from padiatric patients diagnosed with pneumonia were tested. More than half (43, 53.75%) of the specimens positive for influenza A viruses could not be further subtyped using the Luminex RVP assay. Among the remaining 15 specimens that were not subtyped, not degraded, and in sufficient amounts for the multiplex RT-PCR-electrochemical DNA sensor test, all (100%) were H3N2 positive. Therefore, the sensitivity of the Luminex RVP assay for influenza A virus was 46.25%, whereas the sensitivity of the multiplex RT-PCR-electrochemical DNA sensor for the clinical H1N1 and H3N2 specimens was 100%. The sensitivities of the multiplex RT-PCR-electrochemical DNA sensor for the avian H5N1, H5N6, H9N2, and H10N8 viruses were 100%, whereas that for H7N9 virus was 85.19%. We conclude that the multiplex RT-PCR-electrochemical DNA sensor is a reliable method for the rapid and accurate detection of highly variable influenza A viruses in respiratory infections with greater detection sensitivity than that of the Luminex xTAG assay. The high mutation rate of influenza A viruses, particularly H3N2 during the 2014 to 2016 epidemic seasons, has a strong impact on diagnosis. A study involving more positive specimens from all influenza A virus epidemic subtypes is required to fully assess the performance of the assay.
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Affiliation(s)
- Lili Xu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Xiwen Jiang
- DAAN Gene Co., Ltd., Sun Yat-sen University, Guangzhou, China
- The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, China
| | - Yun Zhu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Yali Duan
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Taosheng Huang
- DAAN Gene Co., Ltd., Sun Yat-sen University, Guangzhou, China
- The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, China
| | - Zhiwen Huang
- DAAN Gene Co., Ltd., Sun Yat-sen University, Guangzhou, China
- The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, China
| | - Chunyan Liu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Baoping Xu
- National Clinical Research Center for Respiratory Diseases, Department of Respiratory, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
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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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10
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Amini R, Gilca R, Douville-Fradet M, Boulianne N, De Serres G. Evaluation of the New World Health Organization Case Definition of Severe Acute Respiratory Infection for Influenza Surveillance During the Peak Weeks of Two Influenza Seasons in Quebec, Canada. J Pediatric Infect Dis Soc 2017; 6:297-300. [PMID: 27496537 DOI: 10.1093/jpids/piw044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 07/11/2016] [Indexed: 12/21/2022]
Abstract
During the peak of the 2012-2013 and 2014-2015 influenza seasons in Quebec, Canada, the sensitivity of the new World Health Organization (WHO) case definition of severe acute respiratory infection (SARI) in <5-year-old children was 65% for polymerase chain reaction-confirmed influenza and 79% for other respiratory viruses (ORVs), whereas its specificity and positive predictive value were approximately 2- and 4-fold lower for influenza than ORVs (25% vs 40% and 18% vs 76%, respectively). The use of the WHO SARI definition for influenza surveillance in children should be interpreted with caution according to the specific surveillance goals.
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Affiliation(s)
- R Amini
- Institut National de Santé Publique du Québec
| | - R Gilca
- Institut National de Santé Publique du Québec.,Centre Hospitalier Universitaire de Quebec.,Laval University, Quebec, Quebec City, Canada
| | - M Douville-Fradet
- Institut National de Santé Publique du Québec.,Centre Hospitalier Universitaire de Quebec
| | - N Boulianne
- Institut National de Santé Publique du Québec.,Centre Hospitalier Universitaire de Quebec
| | - G De Serres
- Institut National de Santé Publique du Québec.,Centre Hospitalier Universitaire de Quebec.,Laval University, Quebec, Quebec City, Canada
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Li Y, Yang X, Zhao W. Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing. SLAS Technol 2017; 22:585-608. [PMID: 28850804 DOI: 10.1177/2472630317727519] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Rapid bacterial identification (ID) and antibiotic susceptibility testing (AST) are in great demand due to the rise of drug-resistant bacteria. Conventional culture-based AST methods suffer from a long turnaround time. By necessity, physicians often have to treat patients empirically with antibiotics, which has led to an inappropriate use of antibiotics, an elevated mortality rate and healthcare costs, and antibiotic resistance. Recent advances in miniaturization and automation provide promising solutions for rapid bacterial ID/AST profiling, which will potentially make a significant impact in the clinical management of infectious diseases and antibiotic stewardship in the coming years. In this review, we summarize and analyze representative emerging micro- and nanotechnologies, as well as automated systems for bacterial ID/AST, including both phenotypic (e.g., microfluidic-based bacterial culture, and digital imaging of single cells) and molecular (e.g., multiplex PCR, hybridization probes, nanoparticles, synthetic biology tools, mass spectrometry, and sequencing technologies) methods. We also discuss representative point-of-care (POC) systems that integrate sample processing, fluid handling, and detection for rapid bacterial ID/AST. Finally, we highlight major remaining challenges and discuss potential future endeavors toward improving clinical outcomes with rapid bacterial ID/AST technologies.
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Affiliation(s)
- Yiyan Li
- 1 Sue and Bill Gross Stem Cell Research Center, University of California-Irvine, Irvine, CA, USA.,7 Department of Physics and Engineering, Fort Lewis College, Durango, Colorado, USA
| | | | - Weian Zhao
- 1 Sue and Bill Gross Stem Cell Research Center, University of California-Irvine, Irvine, CA, USA.,6 Department of Biological Chemistry, University of California-Irvine, Irvine, CA, USA
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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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Evaluation of a TaqMan Array Card for Detection of Central Nervous System Infections. J Clin Microbiol 2017; 55:2035-2044. [PMID: 28404679 DOI: 10.1128/jcm.02469-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/06/2017] [Indexed: 11/20/2022] Open
Abstract
Infections of the central nervous system (CNS) are often acute, with significant morbidity and mortality. Routine diagnosis of such infections is limited in developing countries and requires modern equipment in advanced laboratories that may be unavailable to a number of patients in sub-Saharan Africa. We developed a TaqMan array card (TAC) that detects multiple pathogens simultaneously from cerebrospinal fluid. The 21-pathogen CNS multiple-pathogen TAC (CNS-TAC) assay includes two parasites (Balamuthia mandrillaris and Acanthamoeba), six bacterial pathogens (Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, Mycoplasma pneumoniae, Mycobacterium tuberculosis, and Bartonella), and 13 viruses (parechovirus, dengue virus, Nipah virus, varicella-zoster virus, mumps virus, measles virus, lyssavirus, herpes simplex viruses 1 and 2, Epstein-Barr virus, enterovirus, cytomegalovirus, and chikungunya virus). The card also includes human RNase P as a nucleic acid extraction control and an internal manufacturer control, GAPDH (glyceraldehyde-3-phosphate dehydrogenase). This CNS-TAC assay can test up to eight samples for all 21 agents within 2.5 h following nucleic acid extraction. The assay was validated for linearity, limit of detection, sensitivity, and specificity by using either live viruses (dengue, mumps, and measles viruses) or nucleic acid material (Nipah and chikungunya viruses). Of 120 samples tested by individual real-time PCR, 35 were positive for eight different targets, whereas the CNS-TAC assay detected 37 positive samples across nine different targets. The CNS-TAC assays showed 85.6% sensitivity and 96.7% specificity. Therefore, the CNS-TAC assay may be useful for outbreak investigation and surveillance of suspected neurological disease.
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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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Reslova N, Michna V, Kasny M, Mikel P, Kralik P. xMAP Technology: Applications in Detection of Pathogens. Front Microbiol 2017; 8:55. [PMID: 28179899 PMCID: PMC5263158 DOI: 10.3389/fmicb.2017.00055] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/09/2017] [Indexed: 12/14/2022] Open
Abstract
xMAP technology is applicable for high-throughput, multiplex and simultaneous detection of different analytes within a single complex sample. xMAP multiplex assays are currently available in various nucleic acid and immunoassay formats, enabling simultaneous detection and typing of pathogenic viruses, bacteria, parasites and fungi and also antigen or antibody interception. As an open architecture platform, the xMAP technology is beneficial to end users and therefore it is used in various pharmaceutical, clinical and research laboratories. The main aim of this review is to summarize the latest findings and applications in the field of pathogen detection using microsphere-based multiplex assays.
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Affiliation(s)
- Nikol Reslova
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Botany and Zoology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Veronika Michna
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Martin Kasny
- Department of Botany and Zoology, Faculty of Science, Masaryk University Brno, Czechia
| | - Pavel Mikel
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Petr Kralik
- Department of Food and Feed Safety, Veterinary Research Institute Brno, Czechia
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Esposito S, Principi N. The role of the NxTAG® respiratory pathogen panel assay and other multiplex platforms in clinical practice. Expert Rev Mol Diagn 2016; 17:9-17. [PMID: 27899038 DOI: 10.1080/14737159.2017.1266260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
INTRODUCTION The advent of nucleic acid amplification tests has significantly improved the aetiologic diagnosis of respiratory infections. However, multiplex real-time polymerase chain reaction (PCR) can be technologically challenging. Areas covered: This paper reports the results of the main published studies on the NxTAG Respiratory Pathogen Panel (RPP) and discusses the advantages and disadvantages of extensive use of multiplex assays in clinical practice. Expert commentary: Currently available data seem to indicate that routine use of multiplex assays, including NxTAG RPP Assay, should be recommended only when epidemiological data concerning circulation of viruses and bacteria have to be collected. Their use in clinical practice seems debatable. They have limited sensitivity and specificity at least in the identification of some infectious agents or, as in the case of NxTAG RPP, they have not been evaluated in a sufficient number of patients to allow definitive conclusions. In the future, the clinical relevance of multiplex assays, including NxTAG RPP, could significantly increase, mainly because a number of new antiviral agents effective against several respiratory viruses for which no drug is presently available will be marketed. In addition, it is highly likely that the efficiency of multiplex assays will be significantly improved.
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Affiliation(s)
- Susanna Esposito
- a Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation , Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milan , Italy
| | - Nicola Principi
- a Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation , Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milan , Italy
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Accurate Detection of Avian Respiratory Viruses by Use of Multiplex PCR-Based Luminex Suspension Microarray Assay. J Clin Microbiol 2016; 54:2716-2725. [PMID: 27558184 DOI: 10.1128/jcm.00610-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 08/18/2016] [Indexed: 02/07/2023] Open
Abstract
A novel oligonucleotide suspension microarray (Luminex microsphere system) was developed for the rapid detection of avian respiratory viruses of major clinical importance. This test was optimized and validated with 70 clinical samples. The developed tool was accurate for high-throughput detection and differentiation of the most important avian respiratory viruses: avian influenza virus (AIV), Newcastle disease virus (NDV), infection bronchitis virus (IBV), and infectious laryngotracheitis virus (ILTV) in single- and mixed-virus infections. A multiplex reverse transcriptase PCR (RT-PCR), followed by a monoplex or a multiplex Luminex assays, were realized using a Luminex 200 analyzer instrument. The sensitivity, specificity, and reproducibility of the multiplex DNA suspension microarray system were evaluated. The results showed no significant differences in the median fluorescence intensity (MFI) value in monoplex and multiplex Luminex assays. The sensitivity and specificity proved to be completely concordant with monoplex real-time RT-PCR. We demonstrated that the multiplex DNA suspension microarray system is an accurate, high-throughput, and relatively simple method for the rapid detection of the main respiratory viruses of poultry.
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Choudhary ML, Anand SP, Tikhe SA, Walimbe AM, Potdar VA, Chadha MS, Mishra AC. Comparison of the conventional multiplex RT-PCR, real time RT-PCR and Luminex xTAG® RVP fast assay for the detection of respiratory viruses. J Med Virol 2016; 88:51-7. [PMID: 26100490 PMCID: PMC7166673 DOI: 10.1002/jmv.24299] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2015] [Indexed: 02/02/2023]
Abstract
Detection of respiratory viruses using polymerase chain reaction (PCR) is sensitive, specific and cost effective, having huge potential for patient management. In this study, the performance of an in‐house developed conventional multiplex RT–PCR (mRT–PCR), real time RT–PCR (rtRT–PCR) and Luminex xTAG® RVP fast assay (Luminex Diagnostics, Toronto, Canada) for the detection of respiratory viruses was compared. A total 310 respiratory clinical specimens predominantly from pediatric patients, referred for diagnosis of influenza A/H1N1pdm09 from August 2009 to March 2011 were tested to determine performance characteristic of the three methods. A total 193 (62.2%) samples were detected positive for one or more viruses by mRT–PCR, 175 (56.4%) samples by real time monoplex RT‐PCR, and 138 (44.5%) samples by xTAG® RVP fast assay. The overall sensitivity of mRT–PCR was 96.9% (95% CI: 93.5, 98.8), rtRT–PCR 87.9% (95% CI: 82.5, 92.1) and xTAG® RVP fast was 68.3% (95% CI: 61.4, 74.6). Rhinovirus was detected most commonly followed by respiratory syncytial virus group B and influenza A/H1N1pdm09. The monoplex real time RT–PCR and in‐house developed mRT‐PCR are more sensitive, specific and cost effective than the xTAG® RVP fast assay. J. Med. Virol. 88:51–57, 2016. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
| | | | - Shamal A Tikhe
- National Institute of Virology, Human Influenza Group, Pune, India
| | - Atul M Walimbe
- National Institute of Virology, Human Influenza Group, Pune, India
| | - Varsha A Potdar
- National Institute of Virology, Human Influenza Group, Pune, India
| | - Mandeep S Chadha
- National Institute of Virology, Human Influenza Group, Pune, India
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Abstract
Human parainfluenza viruses (HPIVs) are single-stranded, enveloped RNA viruses of the Paramyoviridaie family. There are four serotypes which cause respiratory illnesses in children and adults. HPIVs bind and replicate in the ciliated epithelial cells of the upper and lower respiratory tract and the extent of the infection correlates with the location involved. Seasonal HPIV epidemics result in a significant burden of disease in children and account for 40% of pediatric hospitalizations for lower respiratory tract illnesses (LRTIs) and 75% of croup cases. Parainfluenza viruses are associated with a wide spectrum of illnesses which include otitis media, pharyngitis, conjunctivitis, croup, tracheobronchitis, and pneumonia. Uncommon respiratory manifestations include apnea, bradycardia, parotitis, and respiratory distress syndrome and rarely disseminated infection. Immunity resulting from disease in childhood is incomplete and reinfection with HPIV accounts for 15% of respiratory illnesses in adults. Severe disease and fatal pneumonia may occur in elderly and immunocompromised adults. HPIV pneumonia in recipients of hematopoietic stem cell transplant (HSCT) is associated with 50% acute mortality and 75% mortality at 6 months. Though sensitive molecular diagnostics are available to rapidly diagnose HPIV infection, effective antiviral therapies are not available. Currently, treatment for HPIV infection is supportive with the exception of croup where the use of corticosteroids has been found to be beneficial. Several novel drugs including DAS181 appear promising in efforts to treat severe disease in immunocompromised patients, and vaccines to decrease the burden of disease in young children are in development.
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Affiliation(s)
- Angela R Branche
- Department of Medicine, University of Rochester, Rochester, New York
| | - Ann R Falsey
- Department of Medicine, University of Rochester, Rochester, New York
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20
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Partial comparison of the NxTAG Respiratory Pathogen Panel Assay with the Luminex xTAG Respiratory Panel Fast Assay V2 and singleplex real-time polymerase chain reaction for detection of respiratory pathogens. Diagn Microbiol Infect Dis 2016; 86:53-7. [PMID: 27401400 PMCID: PMC7132749 DOI: 10.1016/j.diagmicrobio.2016.06.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 06/18/2016] [Accepted: 06/20/2016] [Indexed: 11/24/2022]
Abstract
In this study, 185 nasopharyngeal swabs were tested to compare the sensitivity and specificity of the Luminex NxTAG (NxTAG) Respiratory Pathogen Panel (RPP) Assay with those of the Luminex Respiratory Virus Panel (RVP) Fast Assay v2 and singleplex real-time polymerase chain reaction (PCR). The NxTAG Assay identified at least one infectious agent in 164 (88.7%) of the swabs. In 91 (6.2%) tests with negative results with the RVP Fast Assay v2, a virus was identified by the NxTAG (P < 0.001). With the NxTAG Assay, the detection rates were significantly higher for respiratory syncytial virus (P = 0.003), human metapneumovirus (P < 0.001), human rhinovirus/human enterovirus (P = 0.009) and human adenovirus (P < 0.001). Finally, the NxTAG Assay identified M. pneumoniae in 32 of 44 (72.7%) PCR-positive samples. However, the concordance with real-time PCR results was low for both assays. In conclusion, the results indicate that the NxTAG Assay overcomes some of the limitations of previous Luminex assays, although further studies are needed for a more complete evaluation of the new assay. NxTAG Respiratory Pathogen Panel Assay was developed to improve viral detection and to simultaneously identify atypical bacteria. NxTAG Assay has overcome some of the limitations of the previous Luminex assays. NxTAG Assay remains generally less sensitive and specific than singleplex real-time polymerase chain reaction. Further studies on more samples collected during the whole year are needed for a complete evaluation of the NxTAG Assay.
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21
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Luchsinger V, Prades Y, Ruiz M, Pizarro R, Rossi P, Lizama L, Garmendia ML, Meza A, Larrañaga C, Avendaño LF. Comparison of Luminex xTAG® RVP fast assay and real time RT-PCR for the detection of respiratory viruses in adults with community-acquired pneumonia. J Med Virol 2016; 88:1173-9. [PMID: 27061405 PMCID: PMC7166572 DOI: 10.1002/jmv.24463] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/26/2015] [Indexed: 11/18/2022]
Abstract
Community‐acquired pneumonia (CAP) is the third cause of death worldwide. Viruses are frequently detected in adult CAP. Highly sensitive diagnostic techniques should be used due to poor viral shedding. Different sampling methods can affect viral detection, being necessary to establish the optimal type of sample for identifying respiratory viruses in adults. The detection rates of respiratory viruses by Luminex xTAG® RVP fast assay, real time RT‐PCR (rtRT‐PCR) (Sacace®), and immunofluorescence assay (IFA) in adult CAP were performed in nasopharyngeal swabs (NPS) and aspirates (NPA) from 179 hospitalized adults. Positivity was 47.5% for Luminex®, 42.5% for rtRT‐PCR (P = 0.3), and 2.7% for IFA (2.7%) (P < 0.0). The sensitivity, specificity, and kappa coefficient of xTAG® RVP compared with rtRT‐PCR were 84.2%, 79.6%, and 0.62%, respectively. Luminex® and rtRT‐PCR detected 65 (58.0%) and 57 (50.9%) viruses in 112 NPA and 35 (34.3%) and 31 (30.4%) in 102 NPS, respectively (P < 0.01). xTAG® RVP is appropriate for detecting respiratory viruses in CAP adults. Both molecular techniques yielded better results with nasopharyngeal aspirate than swabs. J. Med. Virol. 88:1173–1179, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Vivian Luchsinger
- Program of Virology, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Yara Prades
- Program of Virology, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Mauricio Ruiz
- Clinical Hospital of the University of Chile, Santiago, Chile
| | - Rolando Pizarro
- Dr. Lucio Cordova Hospital of Infectious Diseases, Santiago, Chile
| | | | - Luis Lizama
- Program of Virology, Faculty of Medicine, University of Chile, Santiago, Chile
| | | | | | - Carmen Larrañaga
- Program of Virology, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Luis F Avendaño
- Program of Virology, Faculty of Medicine, University of Chile, Santiago, Chile
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22
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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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23
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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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García‐Arroyo L, Prim N, Martí N, Roig MC, Navarro F, Rabella N. Benefits and drawbacks of molecular techniques for diagnosis of viral respiratory infections. Experience with two multiplex PCR assays. J Med Virol 2016; 88:45-50. [PMID: 26100363 PMCID: PMC7166422 DOI: 10.1002/jmv.24298] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2015] [Indexed: 11/08/2022]
Abstract
Molecular techniques have represented a major step forward in the diagnosis of viral respiratory infections. They are considered highly sensitive and specific compared to conventional techniques. In this study two nucleic acid amplification tests (NAATs) were compared to conventional methods (immunofluorescence and viral culture). The aim of this work was to discuss the clinical interpretation of the results obtained by NAATs on the basis of the two-decade experience of our group and the literature. Eighty nasopharyngeal aspirates were collected from children under six years attended for acute respiratory illness at the pediatric emergency room of a third level Hospital. Both NAATs tested (Seeplex(®) and Clart(®)) showed an overall higher performance regarding sensitivity (76% and 90%, respectively). Compared to Seeplex(®), the Clart(®) system tripled the number of multiple detections (8 by Seeplex(®) vs. 25 by Clart(®)). In some specimens both NAATs detected different viruses. Given these discrepancies and the fact that detection of viral nucleic acids is not necessarily related to the current clinical syndrome, the interpretation of molecular results may not always be so straightforward. The pros and cons of NAATs should always be taken into account when giving a result.
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Affiliation(s)
| | - Núria Prim
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
| | - Neus Martí
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
| | - Maria Carme Roig
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Núria Rabella
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de BarcelonaBarcelonaSpain
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Gorse GJ, Donovan MM, Patel GB, Balasubramanian S, Lusk RH. Coronavirus and Other Respiratory Illnesses Comparing Older with Young Adults. Am J Med 2015; 128:1251.e11-20. [PMID: 26087047 PMCID: PMC7093847 DOI: 10.1016/j.amjmed.2015.05.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 05/13/2015] [Accepted: 05/19/2015] [Indexed: 11/01/2022]
Abstract
BACKGROUND Study of human coronavirus and other virus-associated respiratory illnesses is needed to describe their clinical effects on chronically ill, older adults. METHODS A prospective study during 2009 to 2013 clinically assessed acute respiratory illnesses soon after onset and 3 to 4 weeks later in patients aged ≥60 years with chronic lung and heart diseases (group 1, 100 subjects) and healthy adults aged 18 to 40 years (group 2, 101 subjects). Respiratory secretions were tested for nucleic acids of a panel of respiratory viruses. An increase in antibody titer was assessed for 4 coronavirus strains. RESULTS Virus-associated illnesses (29 [39.1%] of 74 illnesses in group 1 and 59 [48.7%] of 121 illnesses in group 2) occurred in all calendar quarters, most commonly in the first and fourth quarters. Coronaviruses (group 1: 14 [18.9%] illnesses; group 2: 26 [21.5%] illnesses) and enteroviruses/rhinoviruses (group 1: 14 [18.9%] illnesses; group 2: 37 [30.6%] illnesses) were most common. Virus co-infections occurred in 10 illnesses. Illnesses with 9 to 11 symptoms were more common in group 1 (17 [23.0%]) than in group 2 (15 [12.4%]) (P < .05). Compared with group 2, more group 1 subjects reported dyspnea, more severe disease of longer duration, and treatment for acute illness with prednisone and antibiotics. Coronavirus-associated illnesses (percent of illnesses, group 1 vs group 2) were characterized by myalgias (21% vs 68%, P < .01), chills (50% vs 52%), dyspnea (71% vs 24%, P < .01), headache (64% vs 72%), malaise (64% vs 84%), cough (86% vs 68%), sputum production (86% vs 60%), sore throat (64% vs 80%), and nasal congestion (93% vs 96%). CONCLUSIONS Respiratory illnesses were commonly associated with coronaviruses and enteroviruses/rhinoviruses affecting chronically ill, older patients more than healthy, young adults.
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Affiliation(s)
- Geoffrey J Gorse
- Section of Infectious Diseases, VA St Louis Health Care System, and Division of Infectious Diseases, Allergy & Immunology, Saint Louis University School of Medicine, St Louis, Mo.
| | - Mary M Donovan
- Research Service, VA St Louis Health Care System, and Division of Infectious Diseases, Allergy & Immunology, Saint Louis University School of Medicine, St Louis, Mo
| | - Gira B Patel
- Research Service, VA St Louis Health Care System, and Division of Infectious Diseases, Allergy & Immunology, Saint Louis University School of Medicine, St Louis, Mo
| | - Sumitra Balasubramanian
- Research Service, VA St Louis Health Care System, and Washington University in St Louis, St Louis, Mo
| | - Rodney H Lusk
- Section of Infectious Diseases, VA St Louis Health Care System, and Division of Infectious Diseases, Allergy & Immunology, Saint Louis University School of Medicine, St Louis, Mo
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Kabir MS, Clements MO, Atkins M, Kimmitt PT. Application of RT-Bst to enhance detection of pathogenic viruses of the respiratory tract. Br J Biomed Sci 2015; 72:128-34. [PMID: 26510269 DOI: 10.1080/09674845.2015.11666809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Inefficiency of RT-PCR can be associated with the suboptimal process of reverse transcription as only 40-80% of RNA is converted to cDNA. We employed a novel method, RT-Bst, to enrich the concentration of cDNA for subsequent multiplex PCR detection of selected RNA viruses. The RT-Bst method amplifies cDNA through reverse transcription of viral RNA using reverse transcriptase and amplification of cDNA using Bst DNA polymerase. Viral RNA was extracted from 25 nasopharyngeal samples for detection of influenza A, B and C; parainfluenza 1-4; human coronaviruses 229E and OC43; respiratory syncytial virus (RSV) and rhinovirus. Both multiplex one-step RT-PCR and RT-Bst PCR were used to compare their performances for detection of virus sequences. These findings were compared with routine laboratory detection. When using RT-Bst PCR, 28% of samples yielded a viral pathogen compared to 20% with RT-PCR and 12% using routine diagnostic tests. RT-Bst PCR was shown to have particular utility in the detection of RSV RNA as this was present in 20% of the samples studied compared to 8% when using RT-PCR. For one patient, RT-Bst PCR was able to detect RSV five days earlier than conventional hospital diagnostic testing. RT-Bst and RT-Bst PCR can be used as alternative approaches to reverse transcription and one-step RT-PCR, respectively, for sequence-independent amplification of RNA virus sequences and a larger scale analysis of this new diagnostic approach is warranted.
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Arvia R, Corcioli F, Ciccone N, Della Malva N, Azzi A. Detection of 12 respiratory viruses by duplex real time PCR assays in respiratory samples. Mol Cell Probes 2015; 29:408-413. [PMID: 26334289 PMCID: PMC7127684 DOI: 10.1016/j.mcp.2015.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 08/25/2015] [Accepted: 08/25/2015] [Indexed: 11/25/2022]
Abstract
Different viruses can be responsible for similar clinical manifestations of respiratory infections. Thus, the etiological diagnosis of respiratory viral diseases requires the detection of a large number of viruses. In this study, 6 duplex real-time PCR assays, using EvaGreen intercalating dye, were developed to detect 12 major viruses responsible for respiratory diseases: influenza A and B viruses, enteroviruses (including enterovirus spp, and rhinovirus spp), respiratory syncytial virus, human metapneumovirus, coronaviruses group I (of which CoV 229E and CoV NL63 are part) and II (including CoV OC43 and CoV HKU1), parainfluenza viruses type 1, 2, 3 and 4, human adenoviruses and human bocaviruses. The 2 target viruses of each duplex reaction were distinguishable by the melting temperatures of their amplicons. The 6 duplex real time PCR assays were applied for diagnostic purpose on 202 respiratory samples from 157 patients. One hundred fifty-seven samples were throat swabs and 45 were bronchoalveolar lavages. The results of the duplex PCR assays were confirmed by comparison with a commercial, validated, assay; in addition, the positive results were confirmed by sequencing. The analytical sensitivity of the duplex PCR assays varied from 103 copies/ml to 104 copies/ml. For parainfluenza virus 2 only it was 105 copies/ml. Seventy clinical samples (35%) from 55 patients (30 children and 25 adults) were positive for 1 or more viruses. In adult patients, influenza A virus was the most frequently detected respiratory virus followed by rhinoviruses. In contrast, respiratory syncytial virus was the most common virus in children, followed by enteroviruses, influenza A virus and coronavirus NL63. The small number of samples/patients does not allow us to draw any epidemiological conclusion. Altogether, the results of this study indicate that the 6 duplex PCR assays described in this study are sensitive, specific and cost-effective. Thus, this assay could be particularly useful to identify the main respiratory viruses directly from clinical samples, after nucleic acid extraction, and, also, to screen a large number of patients for epidemiological studies. We developed 6 real time PCRs to detect 12 respiratory viruses. The amplicons of each duplex were distinguishable by the melting temperatures. Altogether, the assay can be performed in about 2 h. The cost of each duplex-PCR is about 3 euros. 202 clinical samples have been analyzed for the detection of 12 respiratory viruses.
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Affiliation(s)
- Rosaria Arvia
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, 50134 Florence, Italy.
| | - Fabiana Corcioli
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, 50134 Florence, Italy.
| | - Nunziata Ciccone
- Careggi Teaching Hospital, Largo Brambilla 3, 50134 Florence, Italy.
| | | | - Alberta Azzi
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, 50134 Florence, Italy.
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Gilca R, Skowronski DM, Douville-Fradet M, Amini R, Boulianne N, Rouleau I, Martineau C, Charest H, De Serres G. Mid-Season Estimates of Influenza Vaccine Effectiveness against Influenza A(H3N2) Hospitalization in the Elderly in Quebec, Canada, January 2015. PLoS One 2015; 10:e0132195. [PMID: 26200655 PMCID: PMC4511737 DOI: 10.1371/journal.pone.0132195] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/10/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The 2014/15 influenza season in Canada was characterized by an early epidemic due to vaccine-mismatched influenza A(H3N2) viruses, disproportionately affecting elderly individuals ≥65-years-old. We assessed vaccine effectiveness (VE) against A(H3N2) hospitalization among elderly individuals during the peak weeks of the 2014/15 epidemic in Quebec, Canada. METHODS Nasal specimens and clinical/epidemiological data were collected within 7 days of illness onset from elderly patients admitted with respiratory symptoms to one of four participating hospitals between November 30, 2014 and January 13, 2015. Cases tested RT-PCR positive for influenza A(H3N2) and controls tested negative for any influenza. VE was assessed by test-negative case-control design. RESULTS There were 314 participants including 186 cases (62% vaccinated) and 128 controls (59% vaccinated) included in primary VE analysis. Median age was 81.5 years, two-thirds were admitted from the community and 91% had underlying comorbidity. Crude VE against A(H3N2) hospitalization was -17% (95%CI: -86% to 26%), decreasing to -23% (95%CI: -99 to 23%) with adjustment for age and comorbidity, and to -39% (95%CI: -142 to 20%) with additional adjustment for specimen collection interval, calendar time, type of residence and hospital. In sensitivity analyses, VE estimates were improved toward the null with restriction to participants admitted from the community (-2%; 95%CI: -105 to 49%) or with specimen collection ≤4 days since illness onset (- 8%; 95%CI: -104 to 43%) but further from the null with restriction to participants with comorbidity (-51%; 95%CI: -169 to 15%). CONCLUSION The 2014/15 mismatched influenza vaccine provided elderly patients with no cross-protection against hospitalization with the A(H3N2) epidemic strain, reinforcing the need for adjunct protective measures among high-risk individuals and improved vaccine options.
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Affiliation(s)
- Rodica Gilca
- Biological, Environmental and Occupational Risks, Institut National de Santé Publique du Québec, Quebec, QC, Canada
- CHU de Quebec, Quebec, QC, Canada
- Laval University, Quebec, QC, Canada
| | - Danuta M. Skowronski
- Influenza & Emerging Respiratory Pathogens, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Monique Douville-Fradet
- Biological, Environmental and Occupational Risks, Institut National de Santé Publique du Québec, Quebec, QC, Canada
| | - Rachid Amini
- Biological, Environmental and Occupational Risks, Institut National de Santé Publique du Québec, Quebec, QC, Canada
| | - Nicole Boulianne
- Biological, Environmental and Occupational Risks, Institut National de Santé Publique du Québec, Quebec, QC, Canada
- CHU de Quebec, Quebec, QC, Canada
| | - Isabelle Rouleau
- Bureau de surveillance et de vigie, Ministère de la Santé et des Services sociaux du Québec, Quebec, QC, Canada
| | - Christine Martineau
- Laboratoire de santé publique du Québec, Institut National de Santé Publique du Québec, Montreal, Canada
| | - Hugues Charest
- Laboratoire de santé publique du Québec, Institut National de Santé Publique du Québec, Montreal, Canada
| | - Gaston De Serres
- Biological, Environmental and Occupational Risks, Institut National de Santé Publique du Québec, Quebec, QC, Canada
- CHU de Quebec, Quebec, QC, Canada
- Laval University, Quebec, QC, Canada
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Development of multiplexed bead arrays for the simultaneous detection of nucleic acid from multiple viruses in bat samples. J Virol Methods 2015; 223:5-12. [PMID: 26190638 PMCID: PMC7113788 DOI: 10.1016/j.jviromet.2015.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 07/08/2015] [Accepted: 07/14/2015] [Indexed: 11/21/2022]
Abstract
Virus surveillance of wildlife populations is important for identifying, monitoring, and predicting the emergence of pathogens that pose a potential threat to animal and human health. Bats are identified as important wildlife hosts of many viruses capable of causing fatal human disease, including members of the henipaviruses, coronaviruses, rhabdoviruses and filoviruses. As global warming and habitat change are thought to impact upon pathogen transmission dynamics and increase the risk of spillover, virus surveillance in bat populations remains a significant component of efforts to improve the prediction and control of potential future disease outbreaks caused by bat-borne viruses. In this study we have developed two fluid bead array assays containing customized panels that target multiple bat-borne viruses. These assays detect up to 11 viral RNA's simultaneously in urine samples collected from wild bat populations in Australia and Bangladesh. The assays developed show high specificity for the target viruses and the analytical sensitivity compares favorably to qRT-PCR. These assays enhance the ability to monitor multi-pathogen dynamics and identify patterns of virus shedding from bat populations, thus informing key approaches to outbreak response and control.
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30
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Emerging technologies for the clinical microbiology laboratory. Clin Microbiol Rev 2015; 27:783-822. [PMID: 25278575 DOI: 10.1128/cmr.00003-14] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory.
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Costa E, Rodríguez-Domínguez M, Clari MÁ, Giménez E, Galán JC, Navarro D. Comparison of the performance of 2 commercial multiplex PCR platforms for detection of respiratory viruses in upper and lower tract respiratory specimens. Diagn Microbiol Infect Dis 2015; 82:40-3. [PMID: 25724853 PMCID: PMC7132747 DOI: 10.1016/j.diagmicrobio.2015.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 02/06/2015] [Accepted: 02/07/2015] [Indexed: 11/18/2022]
Abstract
The performance of the CLART® PneumoVir system with that of the Luminex xTAG RVP Fast v1 assay for detection of most common respiratory viruses in upper and lower tract respiratory specimens (n=183) from unique patients with influenza-like syndrome or lower tract respiratory infection. Nested PCR coupled to automated sequencing was used for resolution of discrepancies. Fully concordant results were obtained for a total of 122 specimens, whereas 56 specimens gave partially (n=21) or fully discordant (n=35) results (Kappa coefficient, 0.62). The overall specificity of the Luminex xTAG RVP Fast v1 assay was slightly higher than that of the CLART® PneumoVir assay for human bocavirus, influenza A virus/H3N2, influenza B virus, human metapneumovirus, and parainfluenza virus, whereas the sensitivity of the latter was higher for most targeted viruses except, notably, for picornaviruses. This was irrespective of either the origin of the respiratory specimen or the age group to which the patients belonged.
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Affiliation(s)
- Elisa Costa
- Servicio de Microbiología, Hospital Clínico Universitario, Fundación INCLIVA, Valencia, Spain
| | - Mario Rodríguez-Domínguez
- Servicio de Microbiología, Hospital Ramón y Cajal, and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Red Española para la Investigación en Enfermedades Infecciosas (REIPI), Madrid, Spain
| | - María Ángeles Clari
- Servicio de Microbiología, Hospital Clínico Universitario, Fundación INCLIVA, Valencia, Spain
| | - Estela Giménez
- Servicio de Microbiología, Hospital Clínico Universitario, Fundación INCLIVA, Valencia, Spain
| | - Juan Carlos Galán
- Servicio de Microbiología, Hospital Ramón y Cajal, and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - David Navarro
- Servicio de Microbiología, Hospital Clínico Universitario, Fundación INCLIVA, Valencia, Spain; Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain.
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Mengelle C, Mansuy JM, Pierre A, Claudet I, Grouteau E, Micheau P, Sauné K, Izopet J. The use of a multiplex real-time PCR assay for diagnosing acute respiratory viral infections in children attending an emergency unit. J Clin Virol 2014; 61:411-7. [PMID: 25223920 PMCID: PMC7185773 DOI: 10.1016/j.jcv.2014.08.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/21/2014] [Accepted: 08/26/2014] [Indexed: 11/18/2022]
Abstract
Evaluate the use of multiplex real-time PCR for diagnosing respiratory infections. 857/966 samples from 914 children were positive for one or multiple viruses. Respiratory syncytial virus and rhinovirus were the most prevalent. Co-infections were associated with severe respiratory symptoms. The spread of respiratory viruses returned to the one it was before the flu outbreak.
Background The use of a multiplex molecular technique to identify the etiological pathogen of respiratory viral infections might be a support as clinical signs are not characteristic. Objectives The aim of the study was to evaluate a multiplex molecular real-time assay for the routine diagnosis of respiratory viruses, to analyze the symptoms associated with the pathogens detected and to determine the spread of virus during the period. Study design Respiratory samples were collected from children presenting with respiratory symptoms and attending the emergency unit during the 2010–2011 winter seasons. Samples were tested with the multiplex RespiFinder® 15 assay (PathoFinder™) which potentially detects 15 viruses. Results 857 (88.7%) of the 966 samples collected from 914 children were positive for one (683 samples) or multiple viruses (174 samples). The most prevalent were the respiratory syncytial virus (39.5%) and the rhinovirus (24.4%). Influenza viruses were detected in 139 (14.4%) samples. Adenovirus was detected in 93 (9.6%) samples, coronaviruses in 88 (9.1%), metapneumovirus in 51 (5.3%) and parainfluenzae in 47 (4.9%). Rhinovirus (40%) was the most prevalent pathogen in upper respiratory tract infections while respiratory syncytial virus (49.9%) was the most prevalent in lower respiratory tract infections. Co-infections were associated with severe respiratory symptoms. Conclusion The multiplex assay detected clinically important viruses in a single genomic test and thus will be useful for detecting several viruses causing respiratory tract disorders.
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Affiliation(s)
- C Mengelle
- Department of Virology, Toulouse University Hospital, Toulouse, France.
| | - J M Mansuy
- Department of Virology, Toulouse University Hospital, Toulouse, France
| | - A Pierre
- Department of Virology, Toulouse University Hospital, Toulouse, France
| | - I Claudet
- Children Emergency Unit, Toulouse University Hospital, Toulouse, France
| | - E Grouteau
- Children Emergency Unit, Toulouse University Hospital, Toulouse, France
| | - P Micheau
- Children Emergency Unit, Toulouse University Hospital, Toulouse, France
| | - K Sauné
- Department of Virology, Toulouse University Hospital, Toulouse, France; Department of Physiopathology, Toulouse Purpan, Unité Inserm U563, Toulouse, France
| | - J Izopet
- Department of Virology, Toulouse University Hospital, Toulouse, France; Department of Physiopathology, Toulouse Purpan, Unité Inserm U563, Toulouse, France
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Hwang SM, Lim MS, Han M, Hong YJ, Kim TS, Lee HR, Song EY, Park KU, Song J, Kim EC. Comparison of xTAG respiratory virus panel and Verigene Respiratory Virus Plus for detecting influenza virus and respiratory syncytial virus. J Clin Lab Anal 2014; 29:116-21. [PMID: 24796703 PMCID: PMC6807105 DOI: 10.1002/jcla.21738] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 12/12/2013] [Indexed: 11/21/2022] Open
Abstract
Background Nucleic acid amplification tests have allowed simultaneous detection of multiple respiratory viruses. Methods We compared the results of a liquid bead array xTAG Respiratory Virus Panel (RVP; (Luminex Corporation, Toronto, Canada) and a solid microarray Verigene Respiratory Virus Plus (RV+; Nanosphere, Northbrook, IL) for the detection of influenza A virus (INF A), influenza B virus (INF B), and respiratory syncytial virus (RSV) in 170 respiratory specimens from hospitalized patients. Results Overall, xTAG RVP demonstrated sensitivities and specificities of 97.6 and 100% for INF A, 100 and 99.4% for INF B, and 100 and 100% for RSV, while the Verigene RV+ test sensitivities and specificities were 95.1 and 98.5%, 100.0 and 99.4%, and 97.1 and 100%, respectively. There were no significant differences in the area under the curves between the two assays for each virus (P = 0.364 for INF A, P = 1.000 for INF B, P = 0.317 for RSV). Comparing the results of two assays, discordant results were present mostly due to subtype assignments and identification of coinfections. The detection of viruses was not significantly different (P = 1.000) and the virus/subtype assignment showed good agreement with kappa coefficients of 0.908. Conclusion The xTAG RVP and Verigene RV+ showed high sensitivities and specificities, and good overall agreement in detection and identification of INF and RSV. These assays can be used in clinical settings for a reliable detection of respiratory viruses found commonly in hospitalized patients.
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Affiliation(s)
- Sang Mee Hwang
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea; Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
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Cho HJ, Jang JW, Ko SY, Choi SH, Lim CS, An SSA. Evaluation and verification of the nanosphere Verigene RV+ assay for detection of influenza A/B and H1/H3 subtyping. J Med Virol 2014; 87:18-24. [DOI: 10.1002/jmv.23970] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Han Jin Cho
- Department of Emergency Medicine; Korea University; Seoul Republic of Korea
| | - Jin Woo Jang
- Department of Laboratory Medicine; College of Medicine; Korea University; Seoul Republic of Korea
| | - Sun Young Ko
- Department of Laboratory Medicine; College of Medicine; Korea University; Seoul Republic of Korea
| | - Sung Hyuk Choi
- Department of Emergency Medicine; Korea University; Seoul Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine; College of Medicine; Korea University; Seoul Republic of Korea
| | - Seong Soo A. An
- College of Bionanotechnology & Gachon Medical Research Institute; Gachon University & Gil Medical Center; Seongnam-si Gyeonggi Do Republic of Korea
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Abstract
Over the past several years a wide variety of molecular assays for the detection of respiratory viruses has reached the market. The tests described herein range from kits containing primers and probes detecting specific groups of viruses, to self-contained systems requiring specialized instruments that extract nucleic acids and perform the polymerase chain reaction with little operator input. Some of the tests target just the viruses involved in large yearly epidemics such as influenza, or specific groups of viruses such as the adenoviruses or parainfluenza viruses; others can detect most of the known respiratory viruses and some bacterial agents.
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GRAY J, COUPLAND LJ. The increasing application of multiplex nucleic acid detection tests to the diagnosis of syndromic infections. Epidemiol Infect 2014; 142:1-11. [PMID: 24093495 PMCID: PMC9152551 DOI: 10.1017/s0950268813002367] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 08/30/2013] [Accepted: 08/30/2013] [Indexed: 02/04/2023] Open
Abstract
On 14 January 2013, the US Food and Drug Administration (FDA) announced permission for a multiplex nucleic acid test, the xTAG® Gastrointestinal Pathogen Panel (GPP) (Luminex Corporation, USA), which simultaneously detects 11 common viral, bacterial and parasitic causes of infectious gastroenteritis, to be marketed in the USA. This announcement reflects the current move towards the development and commercialization of detection technologies based on nucleic acid amplification techniques for diagnosis of syndromic infections. We discuss the limitations and advantages of nucleic acid amplification techniques and the recent advances in Conformité Européene - in-vitro diagnostic (CE-IVD)-approved multiplex real-time PCR kits for the simultaneous detection of multiple targets within the clinical diagnostics market.
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Affiliation(s)
- J. GRAY
- Norwich Medical School, University of East Anglia, NRP Innovation Centre, Norwich Research Park, Norwich, Norfolk, UK
- Specialist Virology Centre, Department of Microbiology, Norfolk and Norwich University Hospitals NHS Foundation Trust, NRP Innovation Centre, Norwich Research Park, Norwich, Norfolk, UK
| | - L. J. COUPLAND
- Specialist Virology Centre, Department of Microbiology, Norfolk and Norwich University Hospitals NHS Foundation Trust, NRP Innovation Centre, Norwich Research Park, Norwich, Norfolk, UK
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Abstract
Since the last Handbook of Clinical Neurology volume on this topic, viral diagnosis has made tremendous strides, moving from the margin to the mainstream of clinical care. For many years, conventional virus isolation was the mainstay of viral diagnosis since it was sensitive and “open-minded.” However, growth in conventional cell culture entails an inherent delay that limits its clinical impact. Although rapid culture and viral antigen methods detect fewer pathogens and are less sensitive than conventional culture, both require less expertise and have greatly reduced time to result. Polymerase chain reaction has ushered in a new era in virology, especially in the diagnosis of neurologic diseases. Molecular amplification methods are rapid, highly sensitive, can be automated, quantitative, and detect viruses not amenable to routine culture. User-friendly, walk-away tests with results in an hour, as well as multiplex tests that can detect 20 viruses in a single reaction, are now a reality. As the variety of test methods and commercial products proliferate, the challenges for clinicians and laboratories are selecting which tests to utilize in which clinical scenarios, and understanding how to interpret the results. The advantages and limitations of each method are discussed in this chapter, with special attention to neurologic disease.
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Christopher-Hennings J, Araujo KPC, Souza CJH, Fang Y, Lawson S, Nelson EA, Clement T, Dunn M, Lunney JK. Opportunities for bead-based multiplex assays in veterinary diagnostic laboratories. J Vet Diagn Invest 2013; 25:671-91. [DOI: 10.1177/1040638713507256] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bead-based multiplex assays (BBMAs) are applicable for high throughput, simultaneous detection of multiple analytes in solution (from several to 50–500 analytes within a single, small sample volume). Currently, few assays are commercially available for veterinary applications, but they are available to identify and measure various cytokines, growth factors and their receptors, inflammatory proteins, kinases and inhibitors, neurobiology proteins, and pathogens and antibodies in human beings, nonhuman primates, and rodent species. In veterinary medicine, various nucleic acid and protein-coupled beads can be used in, or for the development of, antigen and antibody BBMAs, with the advantage that more data can be collected using approximately the same amount of labor as used for other antigen and antibody assays. Veterinary-related BBMAs could be used for detection of pathogens, genotyping, measurement of hormone levels, and in disease surveillance and vaccine assessment. It will be important to evaluate whether BBMAs are “fit for purpose,” how costs and efficiencies compare between assays, which assays are published or commercially available for specific veterinary applications, and what procedures are involved in the development of the assays. It is expected that many veterinary-related BBMAs will be published and/or become commercially available in the next few years. The current review summarizes the BBMA technology and some of the currently available BBMAs developed for veterinary settings. Some of the human diagnostic BBMAs are also described, providing an example of possible templates for future development of new veterinary-related BBMAs.
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Affiliation(s)
- Jane Christopher-Hennings
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Karla P. C. Araujo
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Carlos J. H. Souza
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Ying Fang
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Steven Lawson
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Eric A. Nelson
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Travis Clement
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Michael Dunn
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Joan K. Lunney
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
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Brownback KR, Simpson SQ. Association of bronchoalveolar lavage yield with chest computed tomography findings and symptoms in immunocompromised patients. Ann Thorac Med 2013; 8:153-9. [PMID: 23922610 PMCID: PMC3731857 DOI: 10.4103/1817-1737.114302] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 03/17/2013] [Indexed: 11/15/2022] Open
Abstract
INTRODUCTION: Fiber-optic bronchoscopy (FOB) with bronchoalveolar lavage (BAL) is a common procedure performed in immunocompromised patients with undiagnosed pulmonary pathology. Identifying patients with the highest potential diagnostic yield may help to avoid morbidity in patients unlikely to benefit from the procedure. We sought to determine which patient factors, specifically chest computed tomography (CT) findings, affected diagnostic yield of BAL. METHODS: Retrospective chart review of immunocompromised patients who underwent FOB with BAL from 01/01/2010 to 12/31/2011 at an academic medical center was performed. The lung lobe lavaged, characteristics of pulmonary infiltrate on radiograph, patient symptoms, and diagnostic yield were collected. A positive diagnostic yield was defined as a positive microbiological culture, finding on cytopathologic staining, diffuse alveolar hemorrhage, alveolar eosinophilia or a positive immunologic or nucleic acid assay. RESULTS: The overall diagnostic yield was 52.6%. Infiltrates that were predominantly reticular or nodular by CT had a lower diagnostic yield than predominantly consolidated, ground-glass, or tree-in-bud infiltrates (36.5% vs. 61.2%, P = 0.0058). The diagnostic yield was significantly improved in patients with both fever and chest symptoms compared to patients without symptoms (61.3% vs. 29.6%, P = 0.0066). CONCLUSION: CT findings of reticular and nodular infiltrates portend a worse diagnostic yield from BAL than those that are alveolar in nature. Symptomatic patients are more likely to have diagnostic FOB with BAL than asymptomatic patients.
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Affiliation(s)
- Kyle R Brownback
- Division of Pulmonary and Critical Care Medicine, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, USA
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A two-tube multiplex reverse transcription PCR assay for simultaneous detection of sixteen human respiratory virus types/subtypes. BIOMED RESEARCH INTERNATIONAL 2013; 2013:327620. [PMID: 23984344 PMCID: PMC3747601 DOI: 10.1155/2013/327620] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 06/25/2013] [Indexed: 11/17/2022]
Abstract
There is a need for the development of a rapid and sensitive diagnosis of respiratory viral pathogens. With an intended application in provincial Centers for Diseases Control and Prevention, in this study, we present a two-tube multiplex RT-PCR assay (two-tube assay) using automatic electrophoresis to simultaneously detect sixteen common respiratory viruses. The specificity and the sensitivity of the assay were tested. The assay could detect 20-200 copies per reaction when each viral type was assayed individually, 2000 copies with 9 premixed viral targets in the multiplexed assay in tube 1, and 200 copies with 8 premixed templates in tube 2. A total of 247 specimens were used to evaluate the two-tube assay, and the results were compared with those obtained from the Luminex xTAG RVP Fast assay. The discordant results were confirmed by sequencing or by the Seeplex RV15 ACE detection kit. There were no false positives, but six false negatives occurred with the two-tube assay. In conclusion, the two-tube assay is demonstrated to have great potential for routine surveillance of respiratory virus infection in China.
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Abstract
Community-acquired pneumonia (CAP) accounts for major morbidity and mortality in the United States. With improved broad-spectrum antibiotics, the implementation of diagnostic studies has declined and most patients do not have an etiologic pathogen of CAP identified. To enhance the appropriate use of antiviral agents and prevent overuse of antibiotics, the successful management of CAP requires rapid and accurate diagnosis of the etiologic agent of CAP. This article provides an overview of the new rapid molecular tests for the diagnosis of influenza, other respiratory viruses, and bacteria compared with nonmolecular tests and how their use for directed therapy can enhance and improve the management of CAP.
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Affiliation(s)
- Charlotte A Gaydos
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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Duplex molecular assay intended for point-of-care diagnosis of influenza A/B virus infection. J Clin Microbiol 2013; 51:3031-8. [PMID: 23850955 PMCID: PMC3754654 DOI: 10.1128/jcm.00740-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Early diagnosis and management of influenza virus infection directly correlates with the effectiveness in disease control. Current molecular influenza virus tests were designed for use in diagnostic testing facilities, where sophisticated equipment and highly trained technicians are available. A longer turnaround time for the centralized testing than when testing near the sample source could delay the initiation of medical intervention, thereby reducing the efficacy of antiviral treatment. The new assay, the SAMBA (simple amplification-based assay) Flu duplex test, is a dipstick-based molecular assay developed to provide a simple, accurate, and cost-effective solution for the diagnosis of influenza A/B viruses intended for near-patient testing. The test presents an alternative format of influenza virus molecular testing that utilizes isothermal amplification and visual detection of nucleic acid on a test strip. The entire test procedure (extraction, amplification, and detection) is integrated into an enclosed semiautomated system. Analytically, the SAMBA Flu duplex test detects 95 and 85 copies of viral genomes for influenza A and B viruses, respectively, with no cross-reactivity observed against other common respiratory pathogens. The clinical performance was established by blind testing of 328 nasal/throat and nasopharyngeal swab specimens from the United Kingdom and Belgium and comparing the results with the quantitative reverse transcription-PCR method routinely used in two public health laboratories. The SAMBA Flu duplex test showed a clinical sensitivity and specificity of 100% and 97.9% for influenza virus A and 100% and 100% for influenza virus B. The test provides a new technology that could facilitate simple and timely identification of influenza virus infection, potentially resulting in more efficient control measures.
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Al-Siyabi T, Binkhamis K, Wilcox M, Wong S, Pabbaraju K, Tellier R, Hatchette TF, LeBlanc JJ. A cost effective real-time PCR for the detection of adenovirus from viral swabs. Virol J 2013; 10:184. [PMID: 23758993 PMCID: PMC3679997 DOI: 10.1186/1743-422x-10-184] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 05/23/2013] [Indexed: 11/25/2022] Open
Abstract
Compared to traditional testing strategies, nucleic acid amplification tests such as real-time PCR offer many advantages for the detection of human adenoviruses. However, commercial assays are expensive and cost prohibitive for many clinical laboratories. To overcome fiscal challenges, a cost effective strategy was developed using a combination of homogenization and heat treatment with an “in-house” real-time PCR. In 196 swabs submitted for adenovirus detection, this crude extraction method showed performance characteristics equivalent to viral DNA obtained from a commercial nucleic acid extraction. In addition, the in-house real-time PCR outperformed traditional testing strategies using virus culture, with sensitivities of 100% and 69.2%, respectively. Overall, the combination of homogenization and heat treatment with a sensitive in-house real-time PCR provides accurate results at a cost comparable to viral culture.
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Affiliation(s)
- Turkiya Al-Siyabi
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Capital District Health Authority, Room 404B, Mackenzie Building, 5788 University Ave, Halifax NS B3H 1V8, Canada
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Abstract
ABSTRACTNew and reemerging infectious diseases, such as pandemic viruses and resistant bacteria, pose a serious threat in the 21st century. Some of these agents represent global security threats. This review provides an overview of diagnostic challenges presented by pandemic influenza and biothreat agents. The article summarizes recent pandemics and disease outbreaks, point-of-care influenza diagnostic tests, biothreat agents, biothreat instrument systems, and technologies in development. It highlights how medical innovation and health care initiatives can help prepare health care professionals and public health personnel to handle future crises. Based on gap analysis for current point-of-care testing deficiencies, it concludes with policy recommendations that will enhance preparedness. (Disaster Med Public Health Preparedness. 2009;3(Suppl 2):S193–S202)
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Abstract
PURPOSE OF REVIEW After decades of neglect, the importance of establishing an aetiological diagnosis for community-acquired and atypical pneumonias has increased dramatically in recent years--driven by the movement towards more rational use of antibiotics, the further spread of antimicrobial resistance, and advances in point-of-care assays that circumvent the diagnostic delays that result from the centralization of laboratories. RECENT FINDINGS There have been very few developments in patient sampling, or the direct visualization, culture, and serological detection of respiratory pathogens. There has, however, been significant interest in the development of improved and more clinically useful assays for the detection of pathogen nucleic acids and proteins, and also in the potential utility of the assessment of host response for tailoring therapy. SUMMARY The majority of patients have yet to benefit from any advances. However, nucleic acid, newer protein, and possibly host-response assays have significant potential to influence patient care in the near future.
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Comparison of the Biofire FilmArray RP, Genmark eSensor RVP, Luminex xTAG RVPv1, and Luminex xTAG RVP fast multiplex assays for detection of respiratory viruses. J Clin Microbiol 2013; 51:1528-33. [PMID: 23486707 DOI: 10.1128/jcm.03368-12] [Citation(s) in RCA: 175] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There are several U.S. FDA-cleared molecular respiratory virus panels available today, each with advantages and disadvantages. This study compares four multiplex panels, the BioFire Diagnostics FilmArray RP (respiratory panel), the GenMark Dx eSensor RVP (respiratory viral panel), the Luminex xTAG RVPv1, and the Luminex xTAG RVP fast. Three hundred specimens (200 retrospective and 100 consecutive) were tested using all four platforms to determine performance characteristics. The overall sensitivity and specificity, respectively, and 95% confidence interval (CI; in parentheses) for each panel were as follows: FilmArray RP, 84.5% (79.2, 88.6) and 100% (96.2, 100); eSensor RVP, 98.3% (95.5, 99.5) and 99.2% (95.4, 100); xTAG RVPv1, 92.7% (88.5, 95.4) and 99.8% (96.0, 100); and xTAG RVP fast, 84.4% (78.5, 88.9) and 99.9% (96.1, 100). The sensitivity of each assay fluctuated by viral target, with the greatest discrepancies noted for adenovirus and influenza virus B detection. Hands-on time and time to result were recorded and ease of use was assessed to generate a complete profile of each assay.
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Jartti T, Söderlund-Venermo M, Hedman K, Ruuskanen O, Mäkelä MJ. New molecular virus detection methods and their clinical value in lower respiratory tract infections in children. Paediatr Respir Rev 2013; 14:38-45. [PMID: 23347659 PMCID: PMC7106250 DOI: 10.1016/j.prrv.2012.04.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
During the past decade, several new respiratory viruses and their subgroups have been discovered. All these new viruses, as well as previously known respiratory viruses, can be detected by sensitive PCR methods, which have become popular in the diagnostic workup of respiratory viral infections. Currently, respiratory viruses can be detected in up to 95% of children with lower respiratory tract illness. On the other hand, virus detection rates in asymptomatic children are also high (up to 68%), as are coinfection rates in symptomatic children (up to 43%) and justified concerns of causality have been raised. Imposing progress has been made in developing multiplex quantitative PCR assays; here, several primer sets are run within a single PCR mixture. These PCR assays give a better understanding of the dominant viral infection, of viral infections that may be incipient and of any waning infections than does a single-target PCR. Multiplex PCR assays are also gaining popularity due to their cost-effectiveness and short throughput time compared to multiple single-target PCRs. Our understanding of the indications of virus PCRs and our ability to interpret the results from a clinical point of view have improved. This paper reviews the progress in PCR assays and discusses their role in the diagnosis of lower respiratory tract infections in children.
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Key Words
- dna, deoxyribonucleic acid
- hbov, human bocavirus
- hmpv, human metapneumovirus
- hrv, human rhinovirus
- lrti, lower respiratory tract illness
- n, number of samples
- np, nasophryngeal
- npa, nasopharyngeal aspirate
- pcr, polymerase chain reaction
- piv, parainfluenza virus
- qpcr, quantitative pcr
- rna, ribonucleic acid
- rsv, respiratory syncytial virus
- rt, reverse transcriptase
- rvp, respiratory virus panel
- child
- infection
- lower respiratory tract
- multiplex
- pcr
- quantitative
- respiratory
- virus
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Affiliation(s)
- Tuomas Jartti
- Department of Pediatrics, Turku University Hospital, Turku, Finland.
| | | | - Klaus Hedman
- Department of Virology; University of Helsinki; Helsinki
| | - Olli Ruuskanen
- Department of Pediatrics, Turku University Hospital, Turku
| | - Mika J. Mäkelä
- Pediatric division, Department of Allergy, Skin and Allergy Hospital, University of Helsinki, Helsinki, all in Finland
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Abstract
Determining the viral etiology of respiratory tract infections (RTI) has been limited for the most part to specific primer PCR-based methods due to their increased sensitivity and specificity compared to other methods, such as tissue culture. However, specific primer approaches have limited the ability to fully understand the diversity of infecting pathogens. A pathogen chip system (PathChip), developed at the Genome Institute of Singapore (GIS), using a random-tagged PCR coupled to a chip with over 170,000 probes, has the potential to recognize all known human viral pathogens. We tested 290 nasal wash specimens from Filipino children <2 years of age with respiratory tract infections using culture and 3 PCR methods-EraGen, Luminex, and the GIS PathChip. The PathChip had good diagnostic accuracy, ranging from 85.9% (95% confidence interval [CI], 81.3 to 89.7%) for rhinovirus/enteroviruses to 98.6% (95% CI, 96.5 to 99.6%) for PIV 2, compared to the other methods and additionally identified a number of viruses not detected by these methods.
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Development of a multiplex one step RT-PCR that detects eighteen respiratory viruses in clinical specimens and comparison with real time RT-PCR. J Virol Methods 2013; 189:15-9. [PMID: 23313883 PMCID: PMC7119668 DOI: 10.1016/j.jviromet.2012.12.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 11/30/2012] [Accepted: 12/31/2012] [Indexed: 11/22/2022]
Abstract
Rapid and accurate diagnosis of viral respiratory infections is crucial for patient management. Multiplex reverse transcriptase polymerase chain reaction (mRT-PCR) is used increasingly to diagnose respiratory infections and has shown to be more sensitive than viral culture and antigen detection. Objective of the present study was to develop a one-step mRT-PCR that could detect 18 respiratory viruses in three sets. The method was compared with real time RT-PCR (rRT-PCR) for its sensitivity and specificity. Clinical specimens from 843 pediatric patients with respiratory symptoms were used in the study. 503 (59.7%) samples were detected positive by mRT-PCR. Of these 462 (54.8%) exhibited presence of a single pathogen and 41 (4.9%) had multiple pathogens. rRT-PCR detected 439 (52.1%) positive samples, where 419 (49.7%) exhibited one virus and 20 (2.4%) showed co-infections. Concordance between mRT-PCR and rRT-PCR was 91.9% and kappa correlation 0.837. Sensitivity and specificity of mRT-PCR were 99.5% and 83.7% while that of rRT-PCR was 86.9% and 99.4% respectively. Rhinovirus (17.2%) was the most frequently detected virus followed by respiratory syncytial virus B (15.4%), H1N1pdm09 (8.54%), parainfluenza virus-3 (5.8%) and metapneumovirus (5.2%). In conclusion, mRT-PCR is a rapid, cost effective, specific and highly sensitive method for detection of respiratory viruses.
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Mercer J. Arrays in clinical microbiology. MICROBIOLOGY AUSTRALIA 2013. [DOI: 10.1071/ma13063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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