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Abstract
Introduction: Successful treatment outcomes for viral respiratory tract infections presenting from primary health care to quaternary hospitals will only be achieved with rapid, sensitive and specific identification of pathogens to allow effective pathogen-specific antiviral therapy and infection control measures. Areas covered: This review aims to explore the different point-of-care tests currently available to diagnose viral respiratory tract infections, discuss the advantages and limitations of point-of-care testing, and provide insights into the future of point-of-care tests. The following databases were searched: Medline (January 1996 to 30 September 2017) and Embase (1988 to 30 September 2017), using the following keywords: ‘point of care’, ‘respiratory virus’, ‘influenza’, ‘RSV’, ‘diagnostics’, ‘nucleic acid test’ and ‘PCR’. Expert commentary: Viral respiratory tract infections cause significant morbidity and mortality worldwide, and point-of-care tests are facilitating the rapid identification of the pathogen responsible given the similarities in clinical presentation.
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Affiliation(s)
- Kerri Basile
- a Centre for Infectious Diseases and Microbiology Laboratory Services , Institute of Clinical Pathology and Medical Research, NSW Health Pathology , Westmead , Australia.,b Marie Bashir Institute for Emerging Infections and Biosecurity , University of Sydney, Westmead Hospital , Westmead , Australia
| | - Jen Kok
- a Centre for Infectious Diseases and Microbiology Laboratory Services , Institute of Clinical Pathology and Medical Research, NSW Health Pathology , Westmead , Australia.,b Marie Bashir Institute for Emerging Infections and Biosecurity , University of Sydney, Westmead Hospital , Westmead , Australia
| | - Dominic E Dwyer
- a Centre for Infectious Diseases and Microbiology Laboratory Services , Institute of Clinical Pathology and Medical Research, NSW Health Pathology , Westmead , Australia.,b Marie Bashir Institute for Emerging Infections and Biosecurity , University of Sydney, Westmead Hospital , Westmead , Australia
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2
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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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Woźniak W, Kozińska A, Ciostek P, Sitkiewicz I. Susceptibility of Vascular Implants to Colonization in vitro by Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis and Pseudomonas aeruginosa. Pol J Microbiol 2017; 66:125-129. [DOI: 10.5604/17331331.1235001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We compared association of Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas aeruginosa and Enterococcus faecalis with nine vascular implants after co-culture. Vascular implants were composed of various materials such as warp knitted polyester (with or without gelatin and silver ions), expanded polytetrafluoroethylene and biological materials – surface treated porcine pericardial patch and Omniflow II. The lowest overall number of associated bacteria was detected for polytetrafluoroethylene implants and porcine pericardial patch. The highest overall number of associated bacteria was detected for Omniflow II implant. The major source of variation, i.e. primary factor influencing colonization, is the implant type (56.22%), bacterial species is responsible for only 1.81%, and interaction of those two factors – 13.09% of variation.
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Affiliation(s)
- Witold Woźniak
- Department of General and Vascular Surgery, Second Faculty of Medicine with the English Division and the Physiotherapy Division, Medical University of Warsaw, Warszawa, Poland
| | - Aleksandra Kozińska
- Department of Epidemiology and Clinical Microbiology, National Institute of Medicines, Warszawa, Poland
| | - Piotr Ciostek
- Department of General and Vascular Surgery, Second Faculty of Medicine with the English Division and the Physiotherapy Division, Medical University of Warsaw, Warszawa, Poland
| | - Izabela Sitkiewicz
- Department of Molecular Microbiology, National Institute of Medicines, Warszawa, Poland
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Steensels D, Reynders M, Descheemaeker P, Curran MD, Jacobs F, Denis O, Delforge ML, Montesinos I. Performance evaluation of direct fluorescent antibody, Focus Diagnostics Simplexa™ Flu A/B & RSV and multi-parameter customized respiratory Taqman® array card in immunocompromised patients. J Virol Methods 2017; 245:61-65. [PMID: 28365410 PMCID: PMC7119654 DOI: 10.1016/j.jviromet.2017.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 03/25/2017] [Accepted: 03/26/2017] [Indexed: 11/29/2022]
Abstract
Limited sensitivity of direct fluorescent antibody testing in comparison to molecular methods. Simplexa™ direct assay is sensitive and specific for the detection of Flu A, B and RSV. Performing the TAC would increase the diagnostic yield and detection of co-infections significantly. Immunocompromised patient population with overall positivity rate of 62%. Co-infection rate of 15.3% found by TAC.
Background Molecular assays for diagnosis of Flu A, Flu B, and RSV with short turn-around-time (TAT) are of considerable clinical importance. In addition, rapid and accurate diagnosis of a large panel of viral and atypical pathogens can be crucial in immunocompromised patients. Objectives First, to evaluate the performance of the Simplexa™ Direct assay system in comparison with direct fluorescent antibody (DFA) and customized Taqman® Array Card (TAC) testing for RSV, Flu A, and Flu B in immunocompromised patients. Second, to evaluate different algorithms for the detection of respiratory pathogens in terms of cost, turn-around-time (TAT) and diagnostic yield. Study design We collected 125 nasopharyngeal swabs (NTS) and 25 BAL samples from symptomatic immunocompromised patients. Samples for which Simplexa™ and TAC results were discordant underwent verification testing. The TAC assay is based on singleplex RT-PCR, targeting 24 viruses, 8 bacteria and 2 fungi simultaneously. Results The overall sensitivity was significantly lower for DFA testing than for the two molecular methods (p < 0.05). Performance characteristics of Simplexa™ testing were not significantly different compared to TAC testing (p > 0.1). For BAL samples only, the sensitivity and specificity of the Simplexa™ assay was 100%. In total, 6.7, 16 and 18% of samples were positive for Flu A, Flu B or RSV by DFA, Simplexa™ and TAC testing, respectively. When considering not only these pathogens but also all results for TAC, the method identified 93 samples with one or more respiratory pathogens (62%). A co-infection rate of 15.3% was found by TAC. The estimated costs and TAT were 8.2€ and 2 h for DFA, 31.8€ and 1.5 h for Simplexa™ and 55€ and 3 h for TAC testing. Conclusions Performing the Simplexa™ test 24 h a day/7 days a week instead of DFA would considerably improve the overall sensitivity and time-to-result, albeit at a higher cost generated in the laboratory. Performing the TAC would increase the diagnostic yield and detection of co-infections significantly.
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Affiliation(s)
- Deborah Steensels
- Department of Clinical Microbiology, CUB-Erasme, Université Libre de Bruxelles, Brussels, Belgium.
| | - Marijke Reynders
- Department of Clinical Microbiology, AZ St-Jan Brugge-Oostende Hospital, Brugge, Belgium
| | - Patrick Descheemaeker
- Department of Clinical Microbiology, AZ St-Jan Brugge-Oostende Hospital, Brugge, Belgium
| | - Martin D Curran
- Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, Cambridge, UK
| | - Frédérique Jacobs
- Department of Infectious Diseases, CUB-Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Olivier Denis
- Department of Clinical Microbiology, CUB-Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie-Luce Delforge
- Department of Clinical Microbiology, CUB-Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Isabel Montesinos
- Department of Clinical Microbiology, CUB-Erasme, Université Libre de Bruxelles, Brussels, Belgium
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Navarro-Marí JM. Rapid diagnostic methods for acute viral respiratory infections. Enferm Infecc Microbiol Clin 2016; 34:329-30. [PMID: 27156247 PMCID: PMC7103359 DOI: 10.1016/j.eimc.2016.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 04/04/2016] [Indexed: 12/11/2022]
Affiliation(s)
- José M Navarro-Marí
- Servicio de Microbiología, Complejo Hospitales Universitarios de Granada, Instituto Biosanitario Granada, Granada, Spain.
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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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Abstract
The increasing availability of nucleic acid amplification tests since the 1980s has revolutionised our understanding of the pathogenesis, epidemiology, clinical and laboratory aspects of known and novel viral respiratory pathogens. High-throughput, multiplex polymerase chain reaction is the most commonly used qualitative detection method, but utilisation of newer techniques such as next-generation sequencing will become more common following significant cost reductions. Rapid and readily accessible isothermal amplification platforms have also allowed molecular diagnostics to be used in a ‘point-of-care’ format. This review focuses on the current applications and limitations of molecular diagnosis for respiratory viruses.
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Riazzo C, Pérez-Ruiz M, Sanbonmatsu-Gámez S, Pedrosa-Corral I, Gutiérrez-Fernández J, Navarro-Marí JM. Analytical performance of the Alere™ i Influenza A&B assay for the rapid detection of influenza viruses. Enferm Infecc Microbiol Clin 2015; 35:438-440. [PMID: 26620605 PMCID: PMC7103361 DOI: 10.1016/j.eimc.2015.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/06/2015] [Accepted: 10/10/2015] [Indexed: 11/17/2022]
Abstract
The analytical performance of the new Alere™ i Influenza A&B kit (AL-Flu) assay, based on isothermal nucleic acids amplification, was evaluated and compared with an antigen detection method, SD Bioline Influenza Virus Antigen Test (SDB), and an automated real-time RT-PCR, Simplexa™ Flu A/B & VRS Direct assay (SPX), for detection of influenza viruses. An “in-house” RT-PCR was used as the reference method. Sensitivity of AL-Flu, SDB, and SPX was 71.7%, 34.8%, and 100%, respectively. Specificity was 100% for all techniques. The turnaround time was 13 min for AL-Flu, 15 min for SDB, and 75 min for SPX. The Alere™ i Influenza A&B assay is an optimal point-of-care assay for influenza diagnosis in clinical emergency settings, and is more sensitive and specific than antigen detection methods.
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Affiliation(s)
- Cristina Riazzo
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto Biosanitario de Granada, Granada, Spain
| | - Mercedes Pérez-Ruiz
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto Biosanitario de Granada, Granada, Spain.
| | - Sara Sanbonmatsu-Gámez
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto Biosanitario de Granada, Granada, Spain
| | - Irene Pedrosa-Corral
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto Biosanitario de Granada, Granada, Spain
| | - José Gutiérrez-Fernández
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto Biosanitario de Granada, Granada, Spain
| | - José-María Navarro-Marí
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto Biosanitario de Granada, Granada, Spain
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10
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Svensson MJ, Lind I, Wirgart BZ, Östlund MR, Albert J. Performance of the Simplexa™ Flu A/B & RSV Direct Kit on respiratory samples collected in saline solution. ACTA ACUST UNITED AC 2014; 46:825-31. [PMID: 25195649 DOI: 10.3109/00365548.2014.946444] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Molecular assays for diagnosis of influenza A, influenza B, and respiratory syncytial virus (RSV) with short turnaround time are of considerable clinical importance. We have evaluated the diagnostic performance of the Simplexa(™) Flu A/B & RSV Direct Kit, which has a run time of 60 min, using different types of respiratory samples collected from patients with a suspected respiratory tract infection, including materials not previously evaluated on this kit. METHODS In total, 210 clinical respiratory samples were analyzed using both the Simplexa direct assay and a laboratory-developed assay (LDA). The 210 clinical samples included 99 nasopharyngeal aspirates collected in 0.9% saline, 91 nasopharyngeal swabs in Σ-Virocult transport medium, 9 tracheal secretions, 8 bronchoalveolar lavages (BAL), and 3 other respiratory sample materials. RESULTS The specificity of the Simplexa assay, using the LDA as gold standard and excluding secondary viral findings, was 100% for all three viruses, whereas the sensitivity was 94.0% for influenza A (47/50), 90.7% for influenza B (49/54), and 90.1% for RSV (46/51), respectively. Discordant results were only observed for samples with cycle threshold values (Ct) > 31 in the LDA. The Simplexa assay generated higher Ct values than the LDA for all three viruses and performed equally well on nasopharyngeal swabs and aspirates. CONCLUSIONS The short run time of the Simplexa direct assay, in combination with high specificity and good sensitivity regarding the sample materials used in this study, make it an interesting option for rapid detection of these three important viral respiratory pathogens in a variety of clinical sample materials.
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Affiliation(s)
- Malin J Svensson
- From the Department of Clinical Microbiology, Karolinska University Hospital , Stockholm , Sweden
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Comparison of Simplexa Flu A/B & RSV PCR with cytospin-immunofluorescence and laboratory-developed TaqMan PCR in predominantly adult hospitalized patients. J Clin Microbiol 2014; 52:3057-9. [PMID: 24850350 DOI: 10.1128/jcm.00738-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To compare Simplexa Flu A/B & RSV PCR with cytospin-immunofluorescence and laboratory-developed TaqMan PCR methods, 445 nasopharyngeal samples were tested. Of these, 199 were positive (46 for respiratory syncytial virus [RSV], 120 for influenza A, and 33 for influenza B) and 246 were negative. The direct fluorescent-antibody assay (DFA) detected 132 (66.3%) positive samples, Simplexa direct detected 162 (81.4%), Simplexa using extracts detected 177 (88.9%), and lab-developed TaqMan PCR reference methods detected 199 (100%). The specificities were 99.6%, 100%, 100%, and 100%, respectively. The two Simplexa methods were more sensitive than the DFA (P = 0.0001) but less sensitive than the TaqMan reverse transcriptase PCR (P = 0.0001).
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