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Luštrek M, Cesar Z, Suljič A, Kogoj R, Knap N, Virant MJ, Uršič T, Petrovec M, Avšič-Županc T, Korva M. Influenza A, Influenza B, human respiratory syncytial virus and SARSCoV-2 molecular diagnostics and epidemiology in the post COVID-19 era. Respir Res 2024; 25:234. [PMID: 38840154 PMCID: PMC11151539 DOI: 10.1186/s12931-024-02862-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND The concurrent circulation of SARS-CoV-2 with other respiratory viruses is unstoppable and represents a new diagnostic reality for clinicians and clinical microbiology laboratories. Multiplexed molecular testing on automated platforms that focus on the simultaneous detection of multiple respiratory viruses in a single tube is a useful approach for current and future diagnosis of respiratory infections in the clinical setting. METHODS Two time periods were included in the study: from February to April 2022, an early 2022 period, during the gradual lifting of COVID-19 prevention measures in the country, and from October 2022 to April 2023, the 2022/23 respiratory infections season. We analysed a total of 1,918 samples in the first period and 18,131 respiratory samples in the second period using a multiplex molecular assay for the simultaneous detection of Influenza A (Flu-A), Influenza B (Flu-B), Human Respiratory Syncytial Virus (HRSV) and SARS-CoV-2. RESULTS The results from early 2022 showed a strong dominance of SARS-CoV-2 infections with 1,267/1,918 (66.1%) cases. Flu-A was detected in 30/1,918 (1.6%) samples, HRSV in 14/1,918 (0.7%) samples, and Flu-B in 2/1,918 (0.1%) samples. Flu-A/SARS-CoV-2 co-detections were observed in 11/1,267 (0.9%) samples, and HRSV/SARS-CoV-2 co-detection in 5/1,267 (0.4%) samples. During the 2022/23 winter respiratory season, SARS-CoV-2 was detected in 1,738/18,131 (9.6%), Flu-A in 628/18,131 (3.5%), Flu-B in 106/18,131 (0.6%), and HRSV in 505/18,131 (2.8%) samples. Interestingly, co-detections were present to a similar extent as in early 2022. CONCLUSION The results show that the multiplex molecular approach is a valuable tool for the simultaneous laboratory diagnosis of SARS-CoV-2, Flu-A/B, and HRSV in hospitalized and outpatients. Infections with Flu-A/B, and HRSV occurred shortly after the COVID-19 control measures were lifted, so a strong reoccurrence of various respiratory infections and co-detections in the post COVID-19 period was to be expected.
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Affiliation(s)
- Manca Luštrek
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Zala Cesar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Alen Suljič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Rok Kogoj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Nataša Knap
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Monika Jevšnik Virant
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Tina Uršič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Miša Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia.
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Levin S, Mayer D, Puius YA, Arora S, Gileles-Hillel A. Things We Do for No Reason™: Routine respiratory pathogen panels for emergency department and hospitalized patients. J Hosp Med 2024. [PMID: 38599820 DOI: 10.1002/jhm.13365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 03/20/2024] [Accepted: 03/31/2024] [Indexed: 04/12/2024]
Affiliation(s)
- Samara Levin
- Division of General Internal Medicine, Section of Hospital Medicine, Weill Cornell Medicine, New York, New York, USA
| | - David Mayer
- Pediatric Division, Hadassah Medical Center, & Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Yoram A Puius
- Division of Infectious Diseases, Department of Internal Medicine, Montefiore Medical Center, Bronx, New York, USA
| | - Shitij Arora
- Division of Hospital Medicine, Department of Internal Medicine, Montefiore Medical Center, Bronx, New York, USA
| | - Alex Gileles-Hillel
- Pediatric Division, Hadassah Medical Center, & Faculty of Medicine, The Hebrew University, Jerusalem, Israel
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Lewinski MA, Alby K, Babady NE, Butler-Wu SM, Bard JD, Greninger AL, Hanson K, Naccache SN, Newton D, Temple-Smolkin RL, Nolte F. Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology. J Mol Diagn 2023; 25:857-875. [PMID: 37757952 DOI: 10.1016/j.jmoldx.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/08/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The use of clinical molecular diagnostic methods for detecting microbial pathogens continues to expand and, in some cases, supplant conventional identification methods in various scenarios. Analytical and clinical benefits of multiplex molecular panels for the detection of respiratory pathogens have been demonstrated in various studies. The use of these panels in managing different patient populations has been incorporated into clinical guidance documents. The Association for Molecular Pathology's Infectious Diseases Multiplex Working Group conducted a review of the current benefits and challenges to using multiplex PCR for the detection of pathogens from gastrointestinal tract, central nervous system, lower respiratory tract, and joint specimens. The Working Group also discusses future directions and novel approaches to detection of pathogens in alternate specimen types, and outlines challenges associated with implementation of these multiplex PCR panels.
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Affiliation(s)
- Michael A Lewinski
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Roche Molecular Systems, San Clemente, California.
| | - Kevin Alby
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - N Esther Babady
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Clinical Microbiology Service, Departments of Laboratory Medicine and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan M Butler-Wu
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jennifer Dien Bard
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alexander L Greninger
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Kimberly Hanson
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; University of Utah School of Medicine and ARUP Laboratories, Salt Lake City, Utah
| | - Samia N Naccache
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Microbiology, LabCorp Seattle, Seattle, Washington
| | - Duane Newton
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Bio-Rad Laboratories, Irvine, California
| | | | - Frederick Nolte
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
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Measuring clinical outcomes of highly multiplex molecular diagnostics for respiratory infections: A systematic review and conceptual framework. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e9. [PMID: 36714285 PMCID: PMC9879901 DOI: 10.1017/ash.2022.362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/22/2022] [Accepted: 11/26/2022] [Indexed: 01/11/2023]
Abstract
Objectives To review methodologies and outcomes reporting among these studies and to develop a conceptual framework of outcomes to assist in guiding studies and production of clinical metrics. Data sources PubMed and Embase from January 1, 2012, thru December 1, 2021. Study eligibility criteria Studies evaluating highly multiplex molecular respiratory diagnostics and their impact on either clinical or economic outcomes. Methods A systematic literature review (SLR) of methodologies and outcomes reporting was performed. A qualitative synthesis of identified SLRs and associated primary studies was conducted to develop conceptual framework for outcomes. Results Ultimately, 4 systemic literature reviews and their 12 associated primary studies were selected for review. Most primary studies included patient outcomes focusing on antimicrobial exposure changes such as antibiotic (80%) and antiviral use (50%) or occupancy changes such as hospital length of stay (60%). Economic outcomes were infrequently reported, and societal outcomes, such as antibiotic resistance impact, were absent from the reviewed literature. Qualitative evidence synthesis of reported outcomes yielded a conceptual framework of outcomes to include operational, patient, economic, and societal domains. Conclusions Our review highlights the significant heterogeneity in outcomes reporting among clinical impact studies for highly multiplex molecular respiratory diagnostics. Furthermore, we developed a conceptual framework of outcomes domains that may act as a guide to improve considerations in outcomes selection and reporting when evaluating clinical impact of these tests. These improvements may be important in synthesizing the evidence for informing clinical decision making, guidelines, and financial reimbursement.
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5
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Clinical impact of rapid viral respiratory panel testing on pediatric critical care of patients with acute lower respiratory infection. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2022; 40:53-58. [PMID: 35120650 DOI: 10.1016/j.eimce.2020.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/05/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND We aimed to determine the impact of utilizing a rapid panel test of respiratory viral and atypical bacteria (FilmArray® Respiratory Panel, FA RP) on etiological diagnosis of acute lower respiratory infection (ALRI) and antimicrobial stewardship in critical care pediatric patients. METHODS Prospective cohort study of patients aged<18 years with clinical diagnosis of ALRI that were admitted to the Pediatric Intensive Care Unit (PICU) of Hospital Sant Joan de Deu (Barcelona, Spain) during December 2015-February 2017. Patients were diagnosed by FA RP and by a bundle of routine microbiological assays. RESULTS ALRI viral and bacterial etiology was confirmed by a composite reference standard of routine microbiological assays in 72 (55.4%) and 15 (11.5%) respiratory samples, respectively, that were collected from 130 children (median age, 3.5 months, IQR 1.1-14.8 months; 54.6% male). Comparatively, FA RP use increased etiological confirmation of ALRI in up to 123 (94.6%) samples (p<0.001) but only determined a bacterial origin in 2 (1.5%). Availability of diagnostic results before patient discharge from the PICU rose from 65.4 to 38.5% (p<0.001). Use of the new panel test directly influenced antimicrobial stewardship in 11 (8.4%) episodes, leading to discontinuation of antiviral drugs (n=5), administration of targeted antibiotics (n=3), antiviral therapy start (n=2) and both targeted antibiotic administration and discontinuation of antiviral drugs (n=1). CONCLUSION FA RP contributed to improve etiological diagnosis of ALRI in a timely manner while enhancing a more rational use of antimicrobial drugs in critical care pediatric patients.
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Hill JA, Dalai SC, Hong DK, Ahmed AA, Ho C, Hollemon D, Blair L, Maalouf J, Keane-Candib J, Stevens-Ayers T, Boeckh M, Blauwkamp TA, Fisher CE. Liquid Biopsy for Invasive Mold Infections in Hematopoietic Cell Transplant Recipients With Pneumonia Through Next-Generation Sequencing of Microbial Cell-Free DNA in Plasma. Clin Infect Dis 2021; 73:e3876-e3883. [PMID: 33119063 PMCID: PMC8664431 DOI: 10.1093/cid/ciaa1639] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/22/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Noninvasive diagnostic options are limited for invasive mold infections (IMIs). We evaluated the performance of a plasma microbial cell-free DNA sequencing (mcfDNA-Seq) test for diagnosing pulmonary IMI after hematopoietic cell transplant (HCT). METHODS We retrospectively assessed the diagnostic performance of plasma mcfDNA-Seq next-generation sequencing in 114 HCT recipients with pneumonia after HCT who had stored plasma obtained within 14 days of diagnosis of proven/probable Aspergillus IMI (n = 51), proven/probable non-Aspergillus IMI (n = 24), possible IMI (n = 20), and non-IMI controls (n = 19). Sequences were aligned to a database including >400 fungi. Organisms above a fixed significance threshold were reported. RESULTS Among 75 patients with proven/probable pulmonary IMI, mcfDNA-Seq detected ≥1 pathogenic mold in 38 patients (sensitivity, 51% [95% confidence interval {CI}, 39%-62%]). When restricted to samples obtained within 3 days of diagnosis, sensitivity increased to 61%. McfDNA-Seq had higher sensitivity for proven/probable non-Aspergillus IMI (sensitivity, 79% [95% CI, 56%-93%]) compared with Aspergillus IMI (sensitivity, 31% [95% CI, 19%-46%]). McfDNA-Seq also identified non-Aspergillus molds in an additional 7 patients in the Aspergillus subgroup and Aspergillus in 1 patient with possible IMI. Among 19 non-IMI pneumonia controls, mcfDNA-Seq was negative in all samples, suggesting a high specificity (95% CI, 82%-100%) and up to 100% positive predictive value (PPV) with estimated negative predictive values (NPVs) of 81%-99%. The mcfDNA-Seq assay was complementary to serum galactomannan index testing; in combination, they were positive in 84% of individuals with proven/probable pulmonary IMI. CONCLUSIONS Noninvasive mcfDNA-Seq had moderate sensitivity and high specificity, NPV, and PPV for pulmonary IMI after HCT, particularly for non-Aspergillus species.
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Affiliation(s)
- Joshua A Hill
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- University of Washington, Seattle, Washington, USA
| | - Sudeb C Dalai
- Karius, Inc, Redwood City, California, USA
- Stanford University School of Medicine, Stanford, California, USA
| | | | | | - Carine Ho
- Karius, Inc, Redwood City, California, USA
| | | | - Lily Blair
- Karius, Inc, Redwood City, California, USA
| | - Joyce Maalouf
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | - Michael Boeckh
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- University of Washington, Seattle, Washington, USA
| | | | - Cynthia E Fisher
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- University of Washington, Seattle, Washington, USA
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Liu YL, Xie TA, Lin GL, Deng W, Lin QR, Pan ZY, Fan SJ, Li ZX, Ouyang S, Zhu GD, Ji TX, Wu LJ, Xia Y, Guo XG. Diagnostic accuracy of Xpert Xpress Flu/RSV for detection of Influenza and Respiratory syncytial virus. Jpn J Infect Dis 2021; 75:183-191. [PMID: 34053954 DOI: 10.7883/yoken.jjid.2020.987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Xpert Xpress Flu/RSV is a fast and automated real-time nucleic acid amplification tool for detecting influenza virus and respiratory syncytial virus (RSV). The aim of this study was to verify the accuracy of Xpert Xpress Flu/RSV in detecting influenza virus and RSV. PubMed, EMBASE, Cochrane Library, and Web of Science were searched up to October 2020. The quality of original research was assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 guidelines. Meta-DiSc 1.4 software was used to analyze the sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and Summary receiver operating characteristic curve. Deek's funnel plot asymmetry test was used to evaluate the publication bias by Stata 12.0. Ten studies with 25 fourfold tables were included in this analysis. The sensitivity of Xpert Xpress Flu/RSV in detecting influenza A, influenza B, and RSV was 0.97, 0.98, 0.96, respectively, and the specificity was 0.97, 1.00, 1.00, respectively. Compared with other common clinical real-time reverse transcriptase PCR (RT-PCR), Xpert Xpress Flu/RSV is a valuable tool for diagnosing influenza virus and RSV with high sensitivity and specificity.
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Affiliation(s)
- Ye-Ling Liu
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, China
| | - Tian-Ao Xie
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, China
| | - Geng-Ling Lin
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, China
| | - Wei Deng
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, China
| | - Qin-Rong Lin
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, China
| | - Zhi-Yong Pan
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, China
| | - Shu-Jin Fan
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, China
| | - Zhen-Xing Li
- Department of Respiratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, China
| | - Shi Ouyang
- Department of Infectious Disease, The Fifth Affiliated Hospital of Guangzhou Medical University, China
| | - Guo-Dong Zhu
- Department of Geriatrics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, China
| | - Tian-Xing Ji
- Department of Clinical Medicine, The Second Affiliated Hospital of Guangzhou Medical University, China
| | - Li-Juan Wu
- Baoan Maternal and Child Health Hospital of Jinan University, China
| | - Yong Xia
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, China.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, China
| | - Xu-Guang Guo
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, China.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, China
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Risk factors for seasonal human coronavirus lower respiratory tract infection after hematopoietic cell transplantation. Blood Adv 2021; 5:1903-1914. [PMID: 33792629 PMCID: PMC8015796 DOI: 10.1182/bloodadvances.2020003865] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/08/2021] [Indexed: 12/25/2022] Open
Abstract
We demonstrate risk factors for HCoV LRTI in allogeneic HCT recipients and significance of virologic documentation by BAL on mortality. Hyperglycemia associated with steroid use appears to be a strong predictor of HCoV disease progression.
Data are limited regarding risk factors for lower respiratory tract infection (LRTI) caused by seasonal human coronaviruses (HCoVs) and the significance of virologic documentation by bronchoalveolar lavage (BAL) on outcomes in hematopoietic cell transplant (HCT) recipients. We retrospectively analyzed patients undergoing allogeneic HCT (4/2008-9/2018) with HCoV (OC43/NL63/HKU1/229E) detected by polymerase chain reaction during conditioning or post-HCT. Risk factors for all manifestations of LRTI and progression to LRTI among those presenting with HCoV upper respiratory tract infection (URTI) were analyzed by logistic regression and Cox proportional hazard models, respectively. Mortality rates following HCoV LRTI were compared according to virologic documentation by BAL. A total of 297 patients (61 children and 236 adults) developed HCoV infection as follows: 254 had URTI alone, 18 presented with LRTI, and 25 progressed from URTI to LRTI (median, 16 days; range, 2-62 days). Multivariable logistic regression analyses showed that male sex, higher immunodeficiency scoring index, albumin <3 g/dL, glucose >150 mg/dL, and presence of respiratory copathogens were associated with occurrence of LRTI. Hyperglycemia with steroid use was associated with progression to LRTI (P < .01) in Cox models. LRTI with HCoV detected in BAL was associated with higher mortality than LRTI without documented detection in BAL (P < .01). In conclusion, we identified factors associated with HCoV LRTI, some of which are less commonly appreciated to be risk factors for LRTI with other respiratory viruses in HCT recipients. The association of hyperglycemia with LRTI might provide an intervention opportunity to reduce the risk of LRTI.
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Rader TS, Stevens MP, Bearman G. Syndromic Multiplex Polymerase Chain Reaction (mPCR) Testing and Antimicrobial Stewardship: Current Practice and Future Directions. Curr Infect Dis Rep 2021; 23:5. [PMID: 33679252 PMCID: PMC7909367 DOI: 10.1007/s11908-021-00748-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2021] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW Syndromic multiplex polymerase chain reaction (mPCR) panels offer the antimicrobial steward a rapid tool for optimizing and de-escalating antimicrobials. In this review, we analyze the role of syndromic mPCR in respiratory, gastrointestinal, and central nervous system infections within the context of antimicrobial stewardship efforts. RECENT FINDINGS For all mPCR syndromic panels, multiple studies analyzed the pre-and-post implementation impact of mPCR on antimicrobial utilization. Prospective studies and trials of respiratory mPCR stewardship interventions, including diagnostic algorithms, educational efforts, co-testing with procalcitonin, and targeted provider feedback currently exist. For gastrointestinal and cerebrospinal fluid mPCR, fewer peer-reviewed reports exist for the use of mPCR in antimicrobial stewardship. These studies demonstrated an inconsistent trend towards decreasing antibiotic use with mPCR. This is further limited by a lack of statistical significance, the absence of controlled, prospective trials, and issues with data generalizability. SUMMARY Antibiotic overuse may improve when mPCR is coupled with electronic medical record algorithm-based approaches and direct provider feedback by an antimicrobial stewardship professional. mPCR may prove a useful tool for antimicrobial stewardship but future studies are needed to define the best practice for its utilization.
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Affiliation(s)
- Theodore S. Rader
- Department of Internal Medicine, Virginia Commonwealth University Health System, 1250 E MARSHALL ST # 980509, Richmond, VA 23298-0019 USA
| | - Michael P. Stevens
- Division of Infectious Diseases, Virginia Commonwealth University Health System, Richmond, VA USA
| | - Gonzalo Bearman
- Division of Infectious Diseases, Virginia Commonwealth University Health System, Richmond, VA USA
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Impact of clinical guidance and rapid molecular pathogen detection on evaluation and outcomes of febrile or hypothermic infants. Infect Control Hosp Epidemiol 2020; 41:1285-1291. [PMID: 32880255 DOI: 10.1017/ice.2020.317] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To quantify the impact of clinical guidance and rapid respiratory and meningitis/encephalitis multiplex polymerase chain reaction (mPCR) testing on the management of infants. DESIGN Before-and-after intervention study. SETTING Tertiary-care children's hospital. PATIENTS Infants ≤90 days old presenting with fever or hypothermia to the emergency department (ED). METHODS The study spanned 3 periods: period 1, January 1, 2011, through December 31, 2014; period 2, January 1, 2015, through April 30, 2018; and period 3, May 1, 2018, through June 15, 2019. During period 1, no standardized clinical guideline had been established and no rapid pathogen testing was available. During period 2, a clinical guideline was implemented, but no rapid testing was available. During period 3, a guideline was in effect, plus mPCR testing using the BioFire FilmArray respiratory panel 2 (RP 2) and the meningitis encephalitis panel (MEP). Outcomes included antimicrobial and ancillary test utilization, length of stay (LOS), admission rate, 30-day mortality. Outcomes were compared across periods using Kruskal-Wallis and Pearson tests and interrupted time series analysis. RESULTS Overall 5,317 patients were included: 2,514 in period 1, 2,082 in period 2, and 721 in period 3. Over the entire study period, we detected reductions in the use of chest radiographs, lumbar punctures, LOS, and median antibiotic duration. After adjusting for temporal trends, we observed that the introduction of the guideline was associated with reductions in ancillary tests and lumbar punctures. Use of mPCR testing with the febrile infant clinical guideline was associated with additional reductions in ancillary testing for all patients and a higher proportion of infants 29-60 days old being managed without antibiotics. CONCLUSIONS Use of mPCR testing plus a guideline for young infant evaluation in the emergency department was associated with less antimicrobial and ancillary test utilization compared to the use of a guideline alone.
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Brotons P, Villaronga M, Henares D, Armero G, Launes C, Jordan I, Muñoz-Almagro C. Clinical impact of rapid viral respiratory panel testing on pediatric critical care of patients with acute lower respiratory infection. Enferm Infecc Microbiol Clin 2020; 40:S0213-005X(20)30285-8. [PMID: 33041081 PMCID: PMC7544565 DOI: 10.1016/j.eimc.2020.08.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND We aimed to determine the impact of utilizing a rapid panel test of respiratory viral and atypical bacteria (FilmArray® Respiratory Panel, FA RP) on etiological diagnosis of acute lower respiratory infection (ALRI) and antimicrobial stewardship in critical care pediatric patients. METHODS Prospective cohort study of patients aged<18 years with clinical diagnosis of ALRI that were admitted to the Pediatric Intensive Care Unit (PICU) of Hospital Sant Joan de Deu (Barcelona, Spain) during December 2015-February 2017. Patients were diagnosed by FA RP and by a bundle of routine microbiological assays. RESULTS ALRI viral and bacterial etiology was confirmed by a composite reference standard of routine microbiological assays in 72 (55.4%) and 15 (11.5%) respiratory samples, respectively, that were collected from 130 children (median age, 3.5 months, IQR 1.1-14.8 months; 54.6% male). Comparatively, FA RP use increased etiological confirmation of ALRI in up to 123 (94.6%) samples (p<0.001) but only determined a bacterial origin in 2 (1.5%). Availability of diagnostic results before patient discharge from the PICU rose from 65.4 to 38.5% (p<0.001). Use of the new panel test directly influenced antimicrobial stewardship in 11 (8.4%) episodes, leading to discontinuation of antiviral drugs (n=5), administration of targeted antibiotics (n=3), antiviral therapy start (n=2) and both targeted antibiotic administration and discontinuation of antiviral drugs (n=1). CONCLUSION FA RP contributed to improve etiological diagnosis of ALRI in a timely manner while enhancing a more rational use of antimicrobial drugs in critical care pediatric patients.
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Affiliation(s)
- Pedro Brotons
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain; CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain; Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain.
| | | | - Desirée Henares
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain; CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Georgina Armero
- Pediatric Department, Hospital Sant Joan de Deu, Barcelona, Spain
| | - Cristian Launes
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain; CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Iolanda Jordan
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain; CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain; CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain; Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
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12
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Anand M, Nimmala P. Seasonal incidence of respiratory viral infections in Telangana, India: utility of a multiplex PCR assay to bridge the knowledge gap. Trop Med Int Health 2020; 25:1503-1509. [PMID: 32996228 DOI: 10.1111/tmi.13501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE The diagnosis of acute viral respiratory tract infections (RTI) is a challenge due to overlapping clinical presentations and lack of availability of robust diagnostic methods. This in turn leads to lack of data regarding incidence and seasonality of viral RTIs which could potentially help to implement efficient strategies of antimicrobial stewardship as well as vaccine administration. Here we utilise a commercial Multiplex PCR assay for the early diagnosis of acute respiratory tract infections and discuss their epidemiology. METHODS A prospective, observational study was conducted over a period of 3 years (2017-2019). Respiratory samples received from outpatients and inpatients with suspected acute RTIs from three multispeciality hospitals located in the twin cities of Hyderabad-Secunderabad were subjected to FilmArray Respiratory Panel (RP) (BioFire Diagnostics, Salt Lake City, Utah, USA). Results were tabulated and statistically analysed. RESULTS Of 513 samples, 261 (50.9%) were positive for one or more pathogens. The viruses detected included influenza A H1 2009 (26.0%), human rhinovirus/enterovirus (21.5%), influenza A H3N2 (17.0%), human metapneumovirus (9.4%), influenza B (6.6%), coronavirus (4.9%), parainfluenza virus (4.5%), respiratory syncytial virus (3.1%) and adenovirus (2.1%). The largest number of samples was positive during the monsoon season (43.8%). Influenza A H1 2009 peaked in the monsoon season with another, smaller peak in February. CONCLUSIONS There is a bimodal peak of respiratory infections relative to the seasons, and vaccine administration should take place in April-May before the advent of the monsoons in this part of the country. Multiplexed PCR may be used as first line for diagnosis of viral infections so that infection control measures can be prioritised and antibiotic administration can be avoided in those who do not require it.
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Affiliation(s)
- Mridu Anand
- Department of Clinical Microbiology, Yashoda Hospital, Secunderabad, Telangana, 500003, India
| | - Pavani Nimmala
- Department of Clinical Microbiology, Yashoda Hospital, Secunderabad, Telangana, 500003, India
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13
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Qavi AJ, McMullen A, Burnham CAD, Anderson NW. Repeat Molecular Testing for Respiratory Pathogens: Diagnostic Gain or Diminishing Returns? J Appl Lab Med 2020; 5:897-907. [PMID: 32674131 PMCID: PMC7454602 DOI: 10.1093/jalm/jfaa029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/02/2020] [Indexed: 01/05/2023]
Abstract
BACKGROUND Upper respiratory tract infections are common, and the ability to accurately and rapidly diagnose the causative pathogen has important implications for patient management. METHODS We evaluated the test-ordering practices for 2 commonly utilized nucleic acid amplification tests (NAATs) for the detection of respiratory pathogens: the Xpert Flu Assay for influenza A/B (Flu assay) and the Biofire FilmArray respiratory panel assay (RP assay), which detects 20 different targets. Our study examined repeat testing; that is, testing within 7 days from an initial test. RESULTS Our study found that repeat testing is common for each of the individual assays: 3.0% of all Flu assays and 10.0% of all RP assays were repeat testing. Of repeat testing, 8/293 (2.7%) of repeat Flu assays and 75/1257 (6.0%) of RP assays resulted diagnostic gains, i.e., new detections. However, for the RP assay, these new detections were not always clinically actionable. The most frequently discrepant organisms were rhinovirus/enterovirus (28/102, 27.5%), followed by respiratory syncytial virus (12/102, 11.8%) and coronavirus OC43 (11/102, 10.8%). Furthermore, there were 3,336 instances in which a patient was tested using both a Flu assay and RP assay, of which only 44 (1.3%) had discrepant influenza results. CONCLUSIONS Our findings suggest opportunities exist to better guide ordering practices for respiratory pathogen testing, including limiting repeat testing, with the goal of optimization of clinical yield, and diagnostic stewardship.
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Affiliation(s)
- Abraham J Qavi
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Allison McMullen
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Carey-Ann D Burnham
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Neil W Anderson
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
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14
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Impact of a Point-of-care Respiratory PCR Panel in a Pediatric Clinic on Postvisit Communication and Follow-up Visits. Pediatr Infect Dis J 2020; 39:e282-e283. [PMID: 32502126 DOI: 10.1097/inf.0000000000002782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
While the FilmArray Respiratory Panel EZ has been proven to reduce inappropriate antibiotic use in the outpatient pediatric setting, it is unclear whether its implementation will also reduce downstream health costs such as provider visits and telephone calls. This analysis will help pediatricians make more informed decisions on the implementation and judicious use of the Respiratory Panel EZ in their clinical practice.
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15
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Multiplex Tests for Respiratory Tract Infections: The Direct Utility of the FilmArray Respiratory Panel in Emergency Department. Can Respir J 2020; 2020:6014563. [PMID: 32774562 PMCID: PMC7397412 DOI: 10.1155/2020/6014563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/29/2020] [Indexed: 12/31/2022] Open
Abstract
Background The FilmArray Respiratory Panel with multiplex targets for respiratory pathogens has been widely used and verified in clinical trials in special test settings. However, it is necessary to evaluate the panel's performance at the point of care directly, in nonspecific test settings. Methods Patients with respiratory tract infections were enrolled from among emergency department visitors, and all steps, including the collection of specimens and testing, were performed by our clinicians. Results Among 270 patients, 196 (72.6%) patients were found to have one or more pathogens. For signal pathogen detection, influenza A virus had the highest rate of detection; 45 (16.7%) of the patients had two or more respiratory pathogens codetected, and most of the multiplex pathogens were rhinovirus/enterovirus codetected with Bordetella pertussis (17.8%). The information provided by the FilmArray had an impact on the prescription of antimicrobials, and there were differences in the rates of antibiotic prescriptions and anti-influenza prescriptions among patients. Conclusions Use of the FilmArray by clinical staff was successfully implemented in the emergency department for the first time in China. The FilmArray has the potential for point-of-care testing in nonspecific settings.
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16
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Lhommet C, Garot D, Grammatico-Guillon L, Jourdannaud C, Asfar P, Faisy C, Muller G, Barker KA, Mercier E, Robert S, Lanotte P, Goudeau A, Blasco H, Guillon A. Predicting the microbial cause of community-acquired pneumonia: can physicians or a data-driven method differentiate viral from bacterial pneumonia at patient presentation? BMC Pulm Med 2020; 20:62. [PMID: 32143620 PMCID: PMC7060632 DOI: 10.1186/s12890-020-1089-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/17/2020] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Community-acquired pneumonia (CAP) requires urgent and specific antimicrobial therapy. However, the causal pathogen is typically unknown at the point when anti-infective therapeutics must be initiated. Physicians synthesize information from diverse data streams to make appropriate decisions. Artificial intelligence (AI) excels at finding complex relationships in large volumes of data. We aimed to evaluate the abilities of experienced physicians and AI to answer this question at patient admission: is it a viral or a bacterial pneumonia? METHODS We included patients hospitalized for CAP and recorded all data available in the first 3-h period of care (clinical, biological and radiological information). For this proof-of-concept investigation, we decided to study only CAP caused by a singular and identified pathogen. We built a machine learning model prediction using all collected data. Finally, an independent validation set of samples was used to test the pathogen prediction performance of: (i) a panel of three experts and (ii) the AI algorithm. Both were blinded regarding the final microbial diagnosis. Positive likelihood ratio (LR) values > 10 and negative LR values < 0.1 were considered clinically relevant. RESULTS We included 153 patients with CAP (70.6% men; 62 [51-73] years old; mean SAPSII, 37 [27-47]), 37% had viral pneumonia, 24% had bacterial pneumonia, 20% had a co-infection and 19% had no identified respiratory pathogen. We performed the analysis on 93 patients as co-pathogen and no-pathogen cases were excluded. The discriminant abilities of the AI approach were low to moderate (LR+ = 2.12 for viral and 6.29 for bacterial pneumonia), and the discriminant abilities of the experts were very low to low (LR+ = 3.81 for viral and 1.89 for bacterial pneumonia). CONCLUSION Neither experts nor an AI algorithm can predict the microbial etiology of CAP within the first hours of hospitalization when there is an urgent need to define the anti-infective therapeutic strategy.
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Affiliation(s)
- Claire Lhommet
- CHRU Tours, Service de Médecine Intensive Réanimation, 2 Bd Tonnellé, F-37044, Tours Cedex 9, France
| | - Denis Garot
- CHRU Tours, Service de Médecine Intensive Réanimation, 2 Bd Tonnellé, F-37044, Tours Cedex 9, France
| | - Leslie Grammatico-Guillon
- CHRU Tours, Service d'Information Médicale, d'Epidémiologie et d'Economie de la Santé, Tours, France
| | | | - Pierre Asfar
- CHRU Angers, Service médecine intensive et réanimation, Angers, France
| | - Christophe Faisy
- UPRES EA220, Laboratoire de recherche en pharmacologie respiratoire, Université Versailles Saint-Quentin, Suresnes, France
| | - Grégoire Muller
- CHR Orléans, Service de Médecine Intensive Réanimation, Orléans, France
| | - Kimberly A Barker
- Pulmonary Center, Boston University School of Medicine, Boston, MA, USA
| | - Emmanuelle Mercier
- CHRU Tours, Service de Médecine Intensive Réanimation, 2 Bd Tonnellé, F-37044, Tours Cedex 9, France
| | - Sylvie Robert
- CHRU Tours, Service de bactériologie, virologie et hygiène hospitalière, Tours, France
| | - Philippe Lanotte
- CHRU Tours, Service de bactériologie, virologie et hygiène hospitalière, Tours, France
| | - Alain Goudeau
- CHRU Tours, Service de bactériologie, virologie et hygiène hospitalière, Tours, France
| | - Helene Blasco
- CHRU Tours, Laboratoire de Biochimie et Biologie Moléculaire, Tours, France.,INSERM U 930, Université de Tours, Tours, France
| | - Antoine Guillon
- CHRU Tours, Service de Médecine Intensive Réanimation, 2 Bd Tonnellé, F-37044, Tours Cedex 9, France. .,INSERM, centre d'étude des pathologies respiratoires (CEPR), U1100, Université de Tours, Tours, France.
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17
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Qian Y, Ai J, Wu J, Yu S, Cui P, Gao Y, Jin J, Weng X, Zhang W. Rapid detection of respiratory organisms with FilmArray respiratory panel and its impact on clinical decisions in Shanghai, China, 2016-2018. Influenza Other Respir Viruses 2019; 14:142-149. [PMID: 31786832 PMCID: PMC7040966 DOI: 10.1111/irv.12701] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/15/2019] [Accepted: 10/18/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND In this study, we evaluated the diagnostic potential and clinical impact of an automated multiplex PCR platform (the FilmArray Respiratory Panel; FA-RP), specially designed for pathogen detection in respiratory tract infections in adults with unexplained pneumonia (UP). METHODS A total of 112 UP patients in Shanghai, China, were enrolled prospectively and assessed using the FA-RP from October 2016 to March 2018. We examined the test results and their influence on clinical decisions. Furthermore, as a control group, we retrospectively obtained the clinical data of 70 UP patients between October 2014 and March 2016 (before the FA-RP was available). The two patient groups were compared with respect to factors, including general antimicrobial use and defined daily dose (DDD) numbers. RESULTS Between October 2016 and March 2018, the positive rate obtained using FA-RP for UP was 76.8%. The primary pathogens in adults with UP were Influenza A/B (47.3%, 53/112). Compared with the patients before FA-RP was available, patients who underwent FA-RP testing had higher rates of antiviral drug use and antibiotic de-escalation during clinical treatment. FA-RP significantly decreased the total DDDs of antibiotic or antifungal drugs DDDs by 7 days after admission (10.6 ± 2.5 vs 14.1 ± 8.8, P < .01). CONCLUSIONS The FA-RP is a rapid and sensitive nucleic acid amplification test method for UP diagnosis in adults. The application of FA-RP may lead to a more accurately targeted antimicrobial treatment and reduced use of antibiotic/antifungal drugs.
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Affiliation(s)
- Yiyi Qian
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jingwen Ai
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jing Wu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Shenglei Yu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Peng Cui
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yan Gao
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jialin Jin
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinhua Weng
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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18
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May L, Tatro G, Poltavskiy E, Mooso B, Hon S, Bang H, Polage C. Rapid Multiplex Testing for Upper Respiratory Pathogens in the Emergency Department: A Randomized Controlled Trial. Open Forum Infect Dis 2019; 6:ofz481. [PMID: 32128326 PMCID: PMC7043218 DOI: 10.1093/ofid/ofz481] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/04/2019] [Indexed: 01/10/2023] Open
Abstract
Background Acute upper respiratory tract infections are a common cause of emergency department (ED) visits and often result in unnecessary antibiotic treatment. Methods We conducted a randomized clinical trial to evaluate the impact of a rapid, multipathogen respiratory panel (RP) test vs usual care (control). Patients were eligible if they were ≥12 months old, had symptoms of upper respiratory infection or influenza-like illness, and were not on antibiotics. The primary outcome was antibiotic prescription; secondary outcomes included antiviral prescription, disposition, and length of stay (ClinicalTrials.gov# NCT02957136). Results Of 191 patients enrolled, 93 (49%) received RP testing; 98 (51%) received usual care. Fifty-three (57%) RP and 7 (7%) control patients had a virus detected and reported during the ED visit (P = .0001). Twenty (22%) RP patients and 33 (34%) usual care patients received antibiotics during the ED visit (–12%; 95% confidence interval, –25% to 0.4%; P = .06/0.08); 9 RP patients received antibiotics despite having a virus detected. The magnitude of antibiotic reduction was greater in children (–19%) vs adults (–9%, post hoc analysis). There was no difference in antiviral use, length of stay, or disposition. Conclusions Rapid RP testing was associated with a trend toward decreased antibiotic use, suggesting a potential benefit from more rapid viral tests in the ED. Future studies should determine if specific groups are more likely to benefit from testing and evaluate the relative cost and effectiveness of broad testing, focused testing, and a combined diagnostic and antimicrobial stewardship approach.
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Affiliation(s)
- Larissa May
- Department of Emergency Medicine, University of California Davis, Sacramento, California, USA
| | - Grant Tatro
- Department of Emergency Medicine, University of California Davis, Sacramento, California, USA
| | - Eduard Poltavskiy
- Graduate Group in Epidemiology, University of California Davis, Davis, California, USA
| | - Benjamin Mooso
- Department of Emergency Medicine, University of California Davis, Sacramento, California, USA
| | - Simson Hon
- Department of Emergency Medicine, University of California Davis, Sacramento, California, USA
| | - Heejung Bang
- Graduate Group in Epidemiology, University of California Davis, Davis, California, USA.,Department of Public Health Sciences, University of California Davis, Davis, California, USA
| | - Christopher Polage
- Department of Pathology, University of California Davis, Sacramento, California, USA.,Department of Pathology, Duke University, Durham, North Carolina, USA
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19
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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: 23] [Impact Index Per Article: 4.6] [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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20
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Vos LM, Bruning AHL, Reitsma JB, Schuurman R, Riezebos-Brilman A, Hoepelman AIM, Oosterheert JJ. Rapid Molecular Tests for Influenza, Respiratory Syncytial Virus, and Other Respiratory Viruses: A Systematic Review of Diagnostic Accuracy and Clinical Impact Studies. Clin Infect Dis 2019; 69:1243-1253. [PMID: 30689772 PMCID: PMC7108200 DOI: 10.1093/cid/ciz056] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/16/2019] [Indexed: 01/03/2023] Open
Abstract
We systematically reviewed available evidence from Embase, Medline, and the Cochrane Library on diagnostic accuracy and clinical impact of commercially available rapid (results <3 hours) molecular diagnostics for respiratory viruses as compared to conventional molecular tests. Quality of included studies was assessed using the Quality Assessment of Diagnostic Accuracy Studies criteria for diagnostic test accuracy (DTA) studies, and the Cochrane Risk of Bias Assessment and Risk of Bias in Nonrandomized Studies of Interventions criteria for randomized and observational impact studies, respectively. Sixty-three DTA reports (56 studies) were meta-analyzed with a pooled sensitivity of 90.9% (95% confidence interval [CI], 88.7%-93.1%) and specificity of 96.1% (95% CI, 94.2%-97.9%) for the detection of either influenza virus (n = 29), respiratory syncytial virus (RSV) (n = 1), influenza virus and RSV (n = 19), or a viral panel including influenza virus and RSV (n = 14). The 15 included impact studies (5 randomized) were very heterogeneous and results were therefore inconclusive. However, we suggest that implementation of rapid diagnostics in hospital care settings should be considered.
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Affiliation(s)
- Laura M Vos
- Department of Infectious Diseases, University Medical Center Utrecht, Utrecht University, The Netherlands
| | - Andrea H L Bruning
- Department of Medical Microbiology, Amsterdam University Medical Center, University of Amsterdam, The Netherlands
| | | | - Rob Schuurman
- Department of Microbiology and Virology, University Medical Center Utrecht, Utrecht University, The Netherlands
| | - Annelies Riezebos-Brilman
- Department of Microbiology and Virology, University Medical Center Utrecht, Utrecht University, The Netherlands
| | - Andy I M Hoepelman
- Department of Infectious Diseases, University Medical Center Utrecht, Utrecht University, The Netherlands
| | - Jan Jelrik Oosterheert
- Department of Infectious Diseases, University Medical Center Utrecht, Utrecht University, The Netherlands
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21
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Busson L, Bartiaux M, Brahim S, Konopnicki D, Dauby N, Gérard M, De Backer P, Van Vaerenbergh K, Mahadeb B, Mekkaoui L, De Foor M, Wautier M, Vandenberg O, Mols P, Levy J, Hallin M. Contribution of the FilmArray Respiratory Panel in the management of adult and pediatric patients attending the emergency room during 2015-2016 influenza epidemics: An interventional study. Int J Infect Dis 2019; 83:32-39. [PMID: 30926539 PMCID: PMC7110685 DOI: 10.1016/j.ijid.2019.03.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/18/2019] [Accepted: 03/21/2019] [Indexed: 11/17/2022] Open
Abstract
AIM To evaluate the contribution of a multiplex PCR for respiratory viruses on antibiotic and antiviral prescription, ancillary test prescription, admission and length of stay of patients. METHODS Two hundred ninety-one adult and pediatric patients visiting the emergency department during the 2015-2016 influenza epidemic were prospectively included and immediately tested 24/7 using the FilmArray Respiratory Panel. The results were communicated to the practitioner in charge as soon as they became available. Clinical and biological data were gathered and analyzed. FINDINGS Results from the FilmArray Respiratory Panel do not appear to impact admission or antibiotic prescription, with the exception of a lower admission rate for children who tested positive for influenza B. Parameters that account for the clinical decisions evaluated are CRP level, white blood cell count, suspected or proven bacterial infection and, for adult patients only, signs of respiratory distress. Length of stay is also not significantly different between patients with a positive and a negative result. A rapid influenza test result permits a more appropriate prescription of oseltamivir.
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Affiliation(s)
- L Busson
- Department of Microbiology, Laboratoire des Hôpitaux Universitaires Bruxellois, Brussels, Belgium.
| | - M Bartiaux
- Department of Emergency Medicine, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - S Brahim
- Department of Emergency Medicine, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - D Konopnicki
- Department of Infectious Diseases, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - N Dauby
- Department of Infectious Diseases, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - M Gérard
- Department of Infectious Diseases, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - P De Backer
- Pediatric Department, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - K Van Vaerenbergh
- Pediatric Department, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - B Mahadeb
- Department of Microbiology, Laboratoire des Hôpitaux Universitaires Bruxellois, Brussels, Belgium
| | - L Mekkaoui
- Department of Microbiology, Laboratoire des Hôpitaux Universitaires Bruxellois, Brussels, Belgium
| | - M De Foor
- Department of Microbiology, Laboratoire des Hôpitaux Universitaires Bruxellois, Brussels, Belgium
| | - M Wautier
- Department of Molecular Diagnostic, Laboratoire des Hôpitaux Universitaires Bruxellois, Brussels, Belgium
| | - O Vandenberg
- Department of Microbiology, Laboratoire des Hôpitaux Universitaires Bruxellois, Brussels, Belgium; Infectious Diseases Epidemiological Unit, Public Health School, Université Libre de Bruxelles, Brussels, Belgium
| | - P Mols
- Department of Emergency Medicine, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - J Levy
- Pediatric Department, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - M Hallin
- Department of Microbiology, Laboratoire des Hôpitaux Universitaires Bruxellois, Brussels, Belgium
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22
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Fontana L, Strasfeld L. Respiratory Virus Infections of the Stem Cell Transplant Recipient and the Hematologic Malignancy Patient. Infect Dis Clin North Am 2019; 33:523-544. [PMID: 30940462 PMCID: PMC7126949 DOI: 10.1016/j.idc.2019.02.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Respiratory virus infections in hematologic stem cell transplant recipients and patients with hematologic malignancies are increasingly recognized as a cause of significant morbidity and mortality. The often overlapping clinical presentation makes molecular diagnostic strategies imperative for rapid diagnosis and to inform understanding of the changing epidemiology of each of the respiratory viruses. Most respiratory virus infections are managed with supportive therapy, although there is effective antiviral therapy for influenza. The primary focus should remain on primary prevention infection control procedures and isolation precautions, avoidance of ill contacts, and vaccination for influenza.
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Affiliation(s)
- Lauren Fontana
- Division of Infectious Disease, Department of Medicine, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Mail Code L457, Portland, OR 97239, USA.
| | - Lynne Strasfeld
- Division of Infectious Disease, Department of Medicine, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Mail Code L457, Portland, OR 97239, USA
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Rahamat‐Langendoen J, Groenewoud H, Kuijpers J, Melchers WJ, van der Wilt GJ. Impact of molecular point-of-care testing on clinical management and in-hospital costs of patients suspected of influenza or RSV infection: a modeling study. J Med Virol 2019; 91:1408-1414. [PMID: 30950066 PMCID: PMC7166495 DOI: 10.1002/jmv.25479] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/22/2019] [Accepted: 03/19/2019] [Indexed: 01/25/2023]
Abstract
Background At hospital admission, patients suspected of infection with influenza or respiratory syncytial virus (RSV) are placed in isolation, pending the outcome of diagnostics. In a significant number, isolated care proves unnecessary. We investigated the potential impact of molecular point‐of‐care (POC) diagnostics on patient management and in‐hospital costs. Method Prospective collection of data on resource utilization within the hospital from consecutive patients 18 years or older presenting at our university medical center with symptoms of respiratory tract infection from December 2016 to April 2017. A cost analysis was conducted using Markov modeling comparing the actual course of events (on the basis of routine diagnostic tests) with two hypothetical scenarios: when POC would impact time to diagnosis only (scenario 1) or on discharge from the hospital, too (scenario 2). Results A total of 283 patients were included, of whom 217 (76.7%) were admitted. Influenza and RSV were detected in 31% and 7% of the patients, respectively. Fifty‐four percent of patients tested negative, of which 79% were kept in isolated care waiting for test results, with a median duration of 24 hours. Median length of stay was 6.0 days. Mean total in‐hospital costs per patient were € 5243. Introducing POC would lower mean costs per patient to € 4904 (scenario 1) and € 4206 (scenario 2). At the hospital level, this would result in a total cost reduction of € 95 937 to € 293 471 in a single influenza season. Conclusions Introducing POC testing for patients presenting with symptoms of viral respiratory tract infection can reduce time‐to‐diagnosis, hospital stay and, thereby, in‐hospital costs.
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Affiliation(s)
| | - Hans Groenewoud
- Department of Health EvidenceRadboud University Medical CenterNijmegenThe Netherlands
| | - Judith Kuijpers
- Department of Medical MicrobiologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Willem J.G. Melchers
- Department of Medical MicrobiologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Gert Jan van der Wilt
- Department of Health EvidenceRadboud University Medical CenterNijmegenThe Netherlands
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More targeted use of oseltamivir and in-hospital isolation facilities after implementation of a multifaceted strategy including a rapid molecular diagnostic panel for respiratory viruses in immunocompromised adult patients. J Clin Virol 2019; 116:11-17. [PMID: 30999234 PMCID: PMC7185605 DOI: 10.1016/j.jcv.2019.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/04/2019] [Accepted: 04/06/2019] [Indexed: 12/05/2022]
Abstract
Rapid molecular testing for respiratory viruses in immunocompromised adults in a hospital emergency care setting is useful. Implementation results in more targeted use of oseltamivir and a reduction in the use of in-hospital isolation facilities. No effect was seen on antibiotic use, antibiotic duration, hospital admissions and length of hospital stay.
Background Immunocompromised adults are more vulnerable to a complicated course of viral respiratory tract infections (RTI). Objectives Provide evidence on the effect of implementation of rapid molecular diagnostics for viruses on use of in-hospital isolation facilities, oseltamivir and antibiotic usage, and other clinical outcomes in immunocompromised patients. Study design A before-after study during two consecutive respiratory viral seasons, including immunocompromised adult patients presenting at a tertiary care emergency department with clinical suspicion of RTI. During the first season (2016/2017), respiratory viruses were detected using inhouse real-time PCR. The second season (2017/2018), we implemented a diagnostic flowchart including a rapid molecular test for 15 respiratory viruses (FilmArray®). We assessed the effect of this implementation on need for isolation, antivirals and empirical antibiotics. Results We included 192 immunocompromised adult patients during the first and 378 during the second season. Respiratory viral testing was performed in 135 patients (70%) during the first and 284 (75%) during the second season (p = 0.218) of which 213 (75%) using the rapid test. After implementation, use of in-hospital isolation facilities was reduced (adjusted odds ratio 0.35, 95%CI 0.19-0.64). Furthermore, adequate use of oseltamivir improved, with fewer prescriptions in influenza negative patients (0.15, 95%CI 0.08-0.28) and more in influenza positive patients (11.13, 95%CI 1.75–70.86). No effect was observed on empirical antibiotic use, hospital admissions, length of hospital stay or safety outcomes. Conclusions Implementation of rapid molecular testing for respiratory viruses in adult immunocompromised patients results in more adequate use of oseltamivir and in-hospital isolation facilities without compromising safety.
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Eigner U, Reucher S, Hefner N, Staffa-Peichl S, Kolb M, Betz U, Holfelder M, Spier G, Pfefferle S, Lütgehetmann M. Clinical evaluation of multiplex RT-PCR assays for the detection of influenza A/B and respiratory syncytial virus using a high throughput system. J Virol Methods 2019; 269:49-54. [PMID: 30946852 DOI: 10.1016/j.jviromet.2019.03.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/14/2019] [Accepted: 03/31/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Lower respiratory tract infections are a major threat to public health systems worldwide, with RSV and influenza being the main agents causing hospitalization. In outbreak situations, high-volume respiratory testing is needed. In this study, we evaluated the analytical and clinical performance of a pre-designed primer/probe set for the simultaneous multiplex detection of both viruses on a high-throughput platform, the cobas® 6800, using the "open channel" of the system for integration of lab-developed assays for the detection of influenza and RSV. RESULTS Using the influenza/RSV qPCR Assay with swabs, LoD (95%) in TCID50/mL for influenza-A was 0.009, influenza-B 0.003, RSV-A 0.202, and RSV-B 0.009. Inter-run variability (3xLoD) was low (<1 Ct for all targets). Of 371 clinical respiratory specimens analyzed, results were concordant for 358 samples. The calculated sensitivity and specificity of the assay were 98.3% and 98.4% for Flu-A, 100% and 98.5% for Flu-B, and 98.6% and 99.7% for RSV. All quality assessment panel specimens (N = 63, including avian influenza strains) were correctly identified. None of the tested microorganisms showed cross-reactivity. CONCLUSION Compared with CE-IVD assays, the assay evaluated here showed good analytical and clinical sensitivity and specificity with broad coverage of different virus strains. It offers high-throughput capacity with low hands-on time, facilitating the laboratory management of large respiratory outbreaks.
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Affiliation(s)
- Ulrich Eigner
- MVZ Laboratory Dr. Limbach, Heidelberg, Germany; University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.
| | - Svenja Reucher
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | | | | | | | - Ulrike Betz
- MVZ Laboratory Dr. Limbach, Heidelberg, Germany
| | | | - Gene Spier
- Roche Molecular Systems, Pleasanton, CA, USA
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Zou X, Chang K, Wang Y, Li M, Zhang W, Wang C, Lu B, Xiong Z, Han J, Zhang Y, Zhao J, Cao B. Comparison of the Cepheid Xpert Xpress Flu/RSV assay and commercial real-time PCR for the detection of influenza A and influenza B in a prospective cohort from China. Int J Infect Dis 2019; 80:92-97. [PMID: 30634045 DOI: 10.1016/j.ijid.2018.12.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/14/2018] [Accepted: 12/16/2018] [Indexed: 10/27/2022] Open
Abstract
BACKGROUND The Xpert Xpress Flu/RSV assay is released by FDA for rapid detection of influenza A (FluA), influenza B (FluB), and respiratory syncytial virus (RSV). This study aimed to evaluate its clinical performance in comparison to that of the RT-PCR assay cleared by China FDA (CFDA-PCR). METHODS Nasopharyngeal specimens were collected from patients and tested by the two assays side by side. Discordant results were tested with a laboratory-developed real-time PCR for resolution. Viral load in the sample was quantified with a droplet digital PCR. RESULTS A total of 658 specimens were involved and gave 94.7%-99.1% agreement between the two assays. The Xpert assay showed higher sensitivity for FluA (100% vs. 89.8%) and FluB detection (100% vs. 95.3%), and also higher accuracy (98.9% vs. 95.7%) for FluA than the CDFA-PCR. The positive and negative predictive values (NPV) for the three viruses ranged from 90.5% to 100% in the two assays, with higher NPV for FluA and FluB in Xpert assay. Moreover, the Xpert Ct values showed a linear correlation with virus titer in specimens tested. CONCLUSION Overall, the Xpert assay is a reliable and sensitive tool for the detection of FluA, FluB and RSV in our clinical settings.
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Affiliation(s)
- Xiaohui Zou
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, China; Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
| | - Kang Chang
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, China; Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
| | - Yeming Wang
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, China; Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China
| | - Mengxue Li
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, China
| | - Wang Zhang
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, China
| | - Chunlei Wang
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, China
| | - Binghuai Lu
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, China
| | - Zhujia Xiong
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, China
| | - Jiajing Han
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, China
| | - Yulin Zhang
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, China
| | - Jiankang Zhao
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, China; Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China.
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Impact of multiplex molecular assay turn-around-time on antibiotic utilization and clinical management of hospitalized children with acute respiratory tract infections. J Clin Virol 2018; 110:11-16. [PMID: 30502640 PMCID: PMC7106386 DOI: 10.1016/j.jcv.2018.11.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 11/13/2018] [Accepted: 11/19/2018] [Indexed: 11/19/2022]
Abstract
BACKGROUND Empiric antibiotic treatment is common among children with acute respiratory tract infections (ARTI), despite infections being predominately viral. The use of molecular respiratory panel assays has become increasingly common for medical care of patients with ARTIs. STUDY DESIGN This was a 6-year retrospective, single-centered study of pediatric inpatients who tested positive for an ARTI respiratory pathogen. We examined the relationship between clinical outcomes and whether the patient was tested using the Luminex Respiratory Viral Panel ([RVP]; in-use: Dec. 2009 - Jul. 2012) or Biofire Respiratory Pathogen Panel ([RP]; in-use Aug. 2012 - Jun. 2016). The prevalence and duration of pre-test empiric antibiotics, post-test oseltamivir administration to influenza patients, chest x-rays and length of stay between the two assays was compared. RESULTS A total of 5142 patients (1264 RVP; 3878 RP) were included. The median laboratory turn-around-time for RP was significantly shorter than RVP (1.4 vs. 27.1 h, respectively; p < .001). Patients tested with RP were less likely to receive empiric antibiotics (OR: 0.45; p < .001; 95% CI: 0.39, 0.52) and had a shorter duration of empiric broad-spectrum antibiotics (6.4 h vs. 32.9 h; p < .001) compared to RVP patients. RP influenza patients had increased oseltamivir use post- test compared to RVP influenza patients (OR: 13.56; p < .001; 95% CI: 7.29, 25.20). CONCLUSIONS Rapid molecular testing positively impacts patient management of ARTIs. Adopting assays with a shorter turn-around-time improves decision making by decreasing empirical antibiotic use and duration, decreasing chest x-rays, increasing timely oseltamivir administration, and reducing length of stay.
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Madigan VM, Sinickas VG, Giltrap D, Kyriakou P, Ryan K, Chan HT, Clifford V. Health service impact of testing for respiratory pathogens using cartridge-based multiplex array versus molecular batch testing. Pathology 2018; 50:758-763. [PMID: 30389216 PMCID: PMC7111697 DOI: 10.1016/j.pathol.2018.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/18/2018] [Accepted: 08/23/2018] [Indexed: 12/26/2022]
Abstract
There is increasing demand for access to rapid microbiological testing, with a view to improving clinical outcomes. The possibility of rapid testing has been facilitated by development of cartridge-based random access molecular technologies that are now widely available. Whether the expense of cartridge-based assays is justified in terms of clinical or laboratory cost savings is controversial. This prospective study evaluated the impact of the Biofire FilmArray Respiratory Panel (‘FilmArray’), a cartridge-based random access molecular test, compared with standard batched molecular testing using an ‘in-house’ respiratory polymerase chain reaction (PCR) on laboratory and health service outcomes for adult patients at a tertiary-level adult hospital in Melbourne, Australia. Laboratory result turnaround time was significantly reduced with the FilmArray (median 4.4 h) compared to a standard validated in-house respiratory PCR assay (median 21.6 h, p < 0.0001) and there was a significant increase in diagnostic yield with the Filmarray (71/124, 57.3%) compared to in-house PCR (79/200; 39.5%; p = 0.002). Despite improved result turnaround time and increased diagnostic yield from testing, there was no corresponding reduction in hospital length of stay or use of isolation beds. Although cartridge-based molecular testing reduced turnaround time to result for respiratory pathogen testing, it did not impact on health service outcomes such as hospital length of stay. Further work is warranted to determine whether cartridge-based tests at the point of care can improve clinical and health service impacts.
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Affiliation(s)
- Victoria M Madigan
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia.
| | - Vincent G Sinickas
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Dawn Giltrap
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Peter Kyriakou
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Katherine Ryan
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Hiu-Tat Chan
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Vanessa Clifford
- Microbiology Department, Royal Melbourne Hospital, Melbourne, Vic, Australia; The University of Melbourne, Melbourne, Vic, Australia; Murdoch Children's Research Institute, Parkville, Vic, Australia
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Wenzler E, Timbrook TT, Wong JR, Hurst JM, MacVane SH. Implementation and optimization of molecular rapid diagnostic tests for bloodstream infections. Am J Health Syst Pharm 2018; 75:1191-1202. [PMID: 29970407 DOI: 10.2146/ajhp170604] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
PURPOSE The implementation and optimization of molecular rapid diagnostic tests (mRDTs) as an antimicrobial stewardship intervention for patients with bloodstream infections (BSIs) are reviewed. SUMMARY All U.S. acute care hospitals accredited by the Joint Commission are required to implement an antimicrobial stewardship program (ASP). Of the many interventions available to ASPs, mRDTs have demonstrated consistent, meaningful results on antimicrobial optimization and patient outcomes. Even among infectious diseases and antimicrobial stewardship-trained pharmacists, significant knowledge and familiarity gaps exist regarding available mRDTs and how best to implement and optimize them. Given the paucity of infectious diseases and/or antimicrobial stewardship-trained pharmacists, the mandates for establishing ASPs will require non-infectious diseases/antimicrobial stewardship-trained pharmacists to implement stewardship interventions, which may include mRDTs, within their institution. Optimization of mRDTs requires adequate diagnostic stewardship, specifically evaluating how mRDT implementation may decrease costs and assist in meeting antimicrobial stewardship regulatory requirements. Knowledge of how these technologies will augment existing microbiology and antimicrobial stewardship workflow is essential. Finally, selecting the right mRDT necessitates familiarity with the instrument's capabilities and with the institutional antibiogram. CONCLUSION mRDTs have demonstrated the ability to be one of the most powerful antimicrobial stewardship interventions. Pharmacists required to implement an ASP in their institution should consider mRDTs as standard of care for patients with BSIs.
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Affiliation(s)
- Eric Wenzler
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL.
| | | | - Jordan R Wong
- Department of Pharmacy, Grady Health System, Atlanta, GA
| | - John M Hurst
- Department of Antibiotic Stewardship, St. Anthony Hospital, Oklahoma City, OK
| | - Shawn H MacVane
- Department of Pharmacy and Division of Infectious Diseases, Medical University of South Carolina, Charleston, SC
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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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Parallel Validation of Three Molecular Devices for Simultaneous Detection and Identification of Influenza A and B and Respiratory Syncytial Viruses. J Clin Microbiol 2018; 56:JCM.01691-17. [PMID: 29263204 DOI: 10.1128/jcm.01691-17] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/14/2017] [Indexed: 11/20/2022] Open
Abstract
Rapid identification of respiratory pathogens, such as influenza virus A (FluA), influenza virus B (FluB), and respiratory syncytial virus (RSV), reduces unnecessary antimicrobial use and enhances infection control practice. We performed a comparative evaluation of three molecular methods: (i) the Aries Flu A/B & RSV, (ii) the Xpert Xpress Flu/RSV, and (iii) the Cobas Flu A/B & RSV assays. The clinical performances of the three methods were evaluated using 200 remnant nasopharyngeal swab (NPS) specimens against a combined reference standard. The limits of detection (LODs) were determined using FluA, FluB, and RSV control strains with known titers. The 95% LODs were between 1.702 and 0.0003 50% tissue culture infective dose (TCID50), with no significant differences revealed among the three assays. Perfect qualitative detection agreement was obtained in the reproducibility study. The Cobas assay failed at the first run on 13 clinical specimens, resulting in an invalid rate of 6.5%. The sensitivities and specificities for all assays were 96.0 to 100.0% and 99.3 to 100% for all three viruses. For on-demand single-specimen and batched 12-specimen workflows, the test turnaround times were 115.5 and 128.8 min for the Aries assay (12 sample capacity), 34.2 and 44.2 min for the Xpress assay (16 sample capacity), and 21.0 and 254.4 min for the Cobas assay (one instrument), respectively. In summary, the Aries, Xpress, and Cobas Liat assays demonstrated excellent sensitivities and specificities for simultaneous detection and identification of FluA, FluB, and RSV from NPS specimens in cancer patients. Test turnaround time was significantly shorter on the Xpress when instrument scalability is unlimited.
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Hansen GT, Moore J, Herding E, Gooch T, Hirigoyen D, Hanson K, Deike M. Clinical decision making in the emergency department setting using rapid PCR: Results of the CLADE study group. J Clin Virol 2018; 102:42-49. [PMID: 29494950 PMCID: PMC7106512 DOI: 10.1016/j.jcv.2018.02.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 11/06/2022]
Abstract
The influence of an influenza diagnosis on patient managed during ED visits is examined. An influenza diagnosis in the ED is actionable, impacting empiric management in 61% of cases. The clinical diagnosis of influenza, based on presenting symptoms, lacks sensitivity at 36%. A 30 min result from collection to report could be achieved in the ED for 91.7%, of cases tested. ED testing resulted in savings of $200.40/ED visit but is dependent on avoiding planned admissions.
Background Emergency Departments (ED) are challenged during influenza season by patients who present acutely during sporadic ED visits. ED management is largely empiric, often occurring without reliable diagnostics needed for targeted therapies, safe outpatient discharge, or hospital admissions. Objective To evaluate the impact of the influenza diagnosis on physician decision making during ED visits using the Cobas Liat® influenza A + B assay. Study design Prospective study assessing the impact of rapid (<30 min), reverse-transcriptase polymerase chain reaction (RT-PCR) influenza testing on physician decision making in the ED. Physician responses established pre-and post-diagnosis management courses which required confirmation via secondary documentation in the medical record. Changes in physician decision making were analyzed across four clinical touchpoints: (i) admission/discharge status, (ii) medical procedures, (iii) antiviral and antibiotic prescribing, and (iv) laboratory studies. Results An influenza diagnosis changed patient management courses, relative to empiric, pre-diagnosis plans, in in 61% of the cases resulting in cost savings of $49,420-to-$42,270 over 143 patients and 104 days during influenza season resulting in a cost savings of $200.40/ED visit. Evaluation over 2000 ED patient visits projects cost savings > $578,000 due to deferred admissions, and reduction in antiviral prescribing. Sensitivity of ED-based influenza testing using the Cobas Liat® assay was equivalent to centralized lab testing at 98.8% sensitivity and 98.5% specificity respectively. Conclusion Providing rapid, RT-PCR influenza testing to ED settings is actionable and used to guide patient care decisions. Understanding the cascade of events linked to the influenza diagnosis in the ED provides overall cost savings which offset the cost of providing ED-based testing.
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Affiliation(s)
- Glen T Hansen
- Department of Pathology & Laboratory Medicine, Hennepin County Medical Center, 701 Park Ave, Minneapolis, MN 55415, United States; Department of Pathology & Laboratory Medicine, University of Minnesota, United States; University of Minnesota, Department of Infectious Disease, Hennepin County Medical Center, 701 Park Ave, Minneapolis, MN 55415, United States.
| | - Johanna Moore
- Department of Emergency Medicine, Hennepin County Medical Center, 701 Park Ave, Minneapolis, MN 55415, United States.
| | - Emily Herding
- Minneapolis Medical Research Foundation, Hennepin County Medical Center, 701 Park Ave, Minneapolis, MN 55415, United States.
| | - Tami Gooch
- Department of Pathology & Laboratory Medicine, Hennepin County Medical Center, 701 Park Ave, Minneapolis, MN 55415, United States.
| | - Diane Hirigoyen
- Department of Pathology & Laboratory Medicine, Hennepin County Medical Center, 701 Park Ave, Minneapolis, MN 55415, United States.
| | - Kevan Hanson
- Department of Pathology & Laboratory Medicine, Hennepin County Medical Center, 701 Park Ave, Minneapolis, MN 55415, United States.
| | - Marcia Deike
- Department of Pathology & Laboratory Medicine, Hennepin County Medical Center, 701 Park Ave, Minneapolis, MN 55415, United States.
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Ogimi C, Englund JA, Bradford MC, Qin X, Boeckh M, Waghmare A. Characteristics and Outcomes of Coronavirus Infection in Children: The Role of Viral Factors and an Immunocompromised State. J Pediatric Infect Dis Soc 2018; 8:21-28. [PMID: 29447395 PMCID: PMC6437838 DOI: 10.1093/jpids/pix093] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 01/23/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Immunocompromised children might be predisposed to serious infections from human coronaviruses (HCoVs), including strains OC43, NL63, HKU1, and 229E; however, the virologic and clinical features of HCoV infection in immunocompromised children have not been compared to those in nonimmunocompromised children. METHODS We retrospectively analyzed a cohort of children who presented to Seattle Children's Hospital and in whom HCoV was detected by a multiplex respiratory polymerase chain reaction assay of a nasal sample between October 2012 and March 2016. Lower respiratory tract disease (LRTD) was defined as possible or definite infiltrate seen in chest imaging, need for oxygen, or abnormal lung examination in conjunction with a physician diagnosis of LRTD. We used logistic regression modeling to evaluate risk factors for LRTD and LRTD that necessitated oxygen use (severe LRTD), including an immunocompromised state, in children with HCoV infection. RESULTS The median ages of 85 immunocompromised and 1152 nonimmunocompromised children with HCoV infection were 6.3 and 1.6 years, respectively. The prevalence of LRTD and of severe LRTD did not differ greatly between the immunocompromised and nonimmunocompromised patients (22% vs 26% [LRTD] and 15% vs 11% [severe LRTD], respectively); however, in a multivariable model, an immunocompromised state was associated with an increased likelihood of severe LRTD (adjusted odds ratio, 2.5 [95% confidence interval, 1.2-4.9]; P = .01). Younger age, having an underlying pulmonary disorder, and the presence of respiratory syncytial virus were also associated with LRTD or severe LRTD in multivariable models. The risks of LRTD or severe LRTD did not differ among the children with different HCoV strains. CONCLUSIONS The presence of a copathogen and host factors, including an immunocompromised state, were associated with increased risk for severe LRTD. Recognizing risk factors for severe respiratory illness might assist in risk stratification.
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Affiliation(s)
- Chikara Ogimi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington,Department of Pediatrics, University of Washington, Seattle,Pediatric Infectious Diseases Division, Seattle Children’s Hospital, Washington
| | - Janet A Englund
- Department of Pediatrics, University of Washington, Seattle,Pediatric Infectious Diseases Division, Seattle Children’s Hospital, Washington
| | - Miranda C Bradford
- Children’s Core for Biomedical Statistics, Center for Clinical and Translational Research, Seattle Children’s Research Institute, Washington
| | - Xuan Qin
- Department of Laboratory Medicine, University of Washington, Seattle,Microbiology Laboratory, Seattle Children’s Hospital, Washington
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington,Department of Medicine, University of Washington, Seattle,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Alpana Waghmare
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington,Department of Pediatrics, University of Washington, Seattle,Pediatric Infectious Diseases Division, Seattle Children’s Hospital, Washington,Correspondence: A. Waghmare, MD, Pediatric Infectious Diseases Division, Seattle Children’s Hospital, 4800 Sand Point Way NE, MA 7.226, Seattle, WA 98105 ()
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Tang YW, Stratton CW. Multiplex PCR for Detection and Identification of Microbial Pathogens. ADVANCED TECHNIQUES IN DIAGNOSTIC MICROBIOLOGY 2018. [PMCID: PMC7121544 DOI: 10.1007/978-3-319-95111-9_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Multiplexed nucleic acid-based tests for infectious disease have become a standard part of clinical laboratory practice. These tests provide a comprehensive syndrome-based approach to determine the etiological agent of disease. The technology underlying these different systems is reviewed here with a special focus on the BioFire FilmArray® platform. The literature on the clinical utility and cost-effectiveness of these platforms for respiratory, blood culture, and gastrointestinal infections is discussed. Although there are reports showing a clear benefit to the patient or to the healthcare system from adopting a syndromic molecular approach, it is also apparent that clinical laboratories and healthcare providers are still learning how to take full advantage of the new systems. Finally, some improvements to this technology that should appear in the next few years are discussed. These include automated pathogen-specific surveillance based on aggregating the data from these systems, a move toward point-of-care syndromic testing, and further decreases in time to result of the tests.
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Affiliation(s)
- Yi-Wei Tang
- Departments of Laboratory Medicine and Internal Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Charles W. Stratton
- Department of Pathology, Microbiology and Immunology and Medicine, Vanderbilt University Medical Center, Nashville, TN USA
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Andrews D, Chetty Y, Cooper BS, Virk M, Glass SK, Letters A, Kelly PA, Sudhanva M, Jeyaratnam D. Multiplex PCR point of care testing versus routine, laboratory-based testing in the treatment of adults with respiratory tract infections: a quasi-randomised study assessing impact on length of stay and antimicrobial use. BMC Infect Dis 2017; 17:671. [PMID: 29017451 PMCID: PMC5635493 DOI: 10.1186/s12879-017-2784-z] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 10/03/2017] [Indexed: 02/04/2023] Open
Abstract
Background Laboratory-based respiratory pathogen (RP) results are often available too late to influence clinical decisions such as hospitalisation or antibiotic treatment due to time delay in transport of specimens and testing schedules. Ward-based i.e. point of care (POC) testing providing rapid results may alter the clinical management pathway. Methods FilmArray® RP polymerase chain reaction (PCR) systems were placed in three in-patient and out-patient medical areas. Patients presenting with influenza-like illness /upper respiratory tract infection +/− lower RTI were recruited between January–July 2015. FilmArray® POC testing occurred on even days of the month (intervention) or routine, laboratory-based RP PCR testing +/− atypical serology on odd days (control). The primary outcome was length of hospital stay. The secondary outcomes were impact on the use of antimicrobials, readmissions, all-cause mortality, length of ward stay and turn-around time (TAT) (time to result from admission). Results Of 606 eligible patients, 545 (89.9%) were included; 211 in the control arm and 334 in the intervention arm. 20% of control arm patients and 24% of intervention arm patients had an RP detected. POC testing was not associated with the primary outcome measure, length of stay, but reduced the TAT from 39.5 h to 19.0 h, p < 0.001. Only the prescribing decision differed between study arms, p < 0.001. When antivirals were given, the intervention was associated with a reduction in the median time to the first dose of 36 h and allowed appropriate treatment of mycoplasma infection. Conclusions We found no association between respiratory PCR POC testing and length of stay or most of the secondary outcomes except the antimicrobial prescribing decision. This was probably due to a delay in initiating FilmArray® testing. Despite this, POC testing allowed time-critical antivirals to be given significantly faster, appropriate mycoplasma treatment and results were available considerably faster than routine, laboratory-based testing. Ward-staff of all grades performed POC testing without difficulty suggesting potential use across many divergent healthcare settings. Further studies evaluating the implementation of rapid respiratory PCR POC testing and the effect on length of stay and antimicrobial use are required. Trial registration ISRCTN10470967, Retrospectively Registered, 30/6/2015.
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Affiliation(s)
- Denise Andrews
- Division of Acute Medicine, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK
| | - Yumela Chetty
- Division of Acute Medicine, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK
| | - Ben S Cooper
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Manjinder Virk
- South London Specialist Virology Centre, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK
| | - Stephen K Glass
- Department of Medical Microbiology, Cheyne Wing, King's College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK
| | - Andrew Letters
- Infection, Prevention and Control Team, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK
| | - Philip A Kelly
- Division of Acute Medicine, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK
| | - Malur Sudhanva
- South London Specialist Virology Centre, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK
| | - Dakshika Jeyaratnam
- Department of Medical Microbiology, Cheyne Wing, King's College Hospital NHS Foundation Trust, Denmark Hill, London, SE5 9RS, UK.
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Ko F, Drews SJ. The impact of commercial rapid respiratory virus diagnostic tests on patient outcomes and health system utilization. Expert Rev Mol Diagn 2017; 17:917-931. [PMID: 28841814 DOI: 10.1080/14737159.2017.1372195] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Acute respiratory tract infections due to influenza A/B and respiratory syncytial virus (RSV) are major causes of morbidity and mortality globally. Rapid tests for detection of these pathogens include antigen detection point of care tests (POC) and newer easy to use molecular tests. From experience, these assays improve both laboratory workflow and assay interpretation issues. However, the question of the benefits of using rapid test technology compared to routine laboratory testing for respiratory viral pathogens is still often asked. Areas covered: Specifically, this review aims to; 1) identify clinical/patient indicators that can be measured prior to and following the implementation of rapid diagnostic test for influenza and RSV, 2) provide multiple perspectives on the extent of impact of a rapid diagnostic test, including direct and indirect outcomes, and 3) identify the technological advancements in the development of rapid testing, demonstrating a timeline that transitions from antigen-based assays to molecular assays. Expert commentary: Key benefits to the use of either antigen-based or molecular rapid tests for patient care, patient flow within institutions, as well as laboratory utilization are identified. Due to improved test characteristics, the authors feel that rapid molecular tests have greater benefits than antigen-based detection methods.
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Affiliation(s)
- Fiona Ko
- a Diagnostic Virology, ProvLab Alberta , Edmonton , Canada
| | - Steven J Drews
- a Diagnostic Virology, ProvLab Alberta , Edmonton , Canada.,b Division of Laboratory Medicine and Pathology , University of Alberta , Edmonton , Canada
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Abbott AN, Fang FC. Clinical Impact of Multiplex Syndromic Panels in the Diagnosis of Bloodstream, Gastrointestinal, Respiratory, and Central Nervous System Infections. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.clinmicnews.2017.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Robinson ML, Manabe YC. Reducing Uncertainty for Acute Febrile Illness in Resource-Limited Settings: The Current Diagnostic Landscape. Am J Trop Med Hyg 2017; 96:1285-1295. [PMID: 28719277 DOI: 10.4269/ajtmh.16-0667] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
AbstractDiagnosing the cause of acute febrile illness in resource-limited settings is important-to give the correct antimicrobials to patients who need them, to prevent unnecessary antimicrobial use, to detect emerging infectious diseases early, and to guide vaccine deployment. A variety of approaches are yielding more rapid and accurate tests that can detect more pathogens in a wider variety of settings. After decades of slow progress in diagnostics for acute febrile illness in resource-limited settings, a wave of converging advancements will enable clinicians in resource-limited settings to reduce uncertainty for the diagnosis of acute febrile illness.
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Affiliation(s)
- Matthew L Robinson
- Division of Infectious Disease, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Yukari C Manabe
- Division of Infectious Disease, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
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Cerone JB, Santos RP, Tristram D, Lamson DM, Stellrecht KA, St George K, Horgan MJ, Rios A. Incidence of respiratory viral infection in infants with respiratory symptoms evaluated for late-onset sepsis. J Perinatol 2017; 37:922-926. [PMID: 28518131 PMCID: PMC7100264 DOI: 10.1038/jp.2017.69] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/19/2017] [Accepted: 04/06/2017] [Indexed: 12/14/2022]
Abstract
OBJECTIVE To determine the frequency, etiology and impact of respiratory viral infection (RVI) on infants evaluated for late-onset sepsis (LOS), defined as sepsis occurring >72 h of life, in the neonatal intensive care unit. STUDY DESIGN Prospective observational study conducted from 6 March 2014 to 3 May 2016 on infants evaluated for LOS. PCR viral panel performed on nasopharyngeal specimens among infants with clinical suspicion for RVI. Sequence analysis was performed to determine viral subtypes. Fisher's exact or χ2 tests were done to determine the impact of RVI. RESULTS During the 26-month study, there were 357 blood cultures obtained for LOS evaluations, 29 (8%) had a respiratory virus detected. Only 88 (25%) of infants evaluated for LOS also had clinical suspicion for a respiratory viral infection. RSV (14 of 29; 48%) was the predominant virus detected. Almost all infants (13 of 14; 93%) with RSV required increased respiratory support. Antimicrobial therapy was withheld or discontinued on most infants with a virus detected (18 of 29; 62%) and in the majority where there was no confirmed bacterial co-infection (18 of 20; 90%). CONCLUSION The incidence of RVI in infants being evaluated for LOS is about 8%. RVI should be considered in LOS evaluation to prevent unnecessary antibiotic therapy.
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Affiliation(s)
- J B Cerone
- Department of Pediatrics/Division of Neonatology, Albany Medical Center, Albany, NY, USA
| | - R P Santos
- Department of Pediatrics/Division of Infectious Disease at Albany Medical Center, Albany, NY, USA
| | - D Tristram
- Department of Pediatrics/Division of Infectious Disease at Albany Medical Center, Albany, NY, USA
| | - D M Lamson
- Laboratory of Viral Diseases at Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - K A Stellrecht
- Department of Pathology and Laboratory Medicine at Albany Medical Center, Albany, NY, USA
| | - K St George
- Laboratory of Viral Diseases at Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - M J Horgan
- Department of Pediatrics/Division of Neonatology, Albany Medical Center, Albany, NY, USA
| | - A Rios
- Department of Pediatrics/Division of Neonatology, Albany Medical Center, Albany, NY, USA
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Multicenter Clinical Evaluation of the Luminex Aries Flu A/B & RSV Assay for Pediatric and Adult Respiratory Tract Specimens. J Clin Microbiol 2017; 55:2431-2438. [PMID: 28539342 PMCID: PMC5527421 DOI: 10.1128/jcm.00318-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/16/2017] [Indexed: 11/20/2022] Open
Abstract
Influenza A and B viruses and respiratory syncytial virus (RSV) are three common viruses implicated in seasonal respiratory tract infections and are a major cause of morbidity and mortality in adults and children worldwide. In recent years, an increasing number of commercial molecular tests have become available to diagnose respiratory viral infections. The Luminex Aries Flu A/B & RSV assay is a fully automated sample-to-answer molecular diagnostic assay for the detection of influenza A, influenza B, and RSV. The clinical performance of the Aries Flu A/B & RSV assay was prospectively evaluated in comparison to that of the Luminex xTAG respiratory viral panel (RVP) at four North American clinical institutions over a 2-year period. Of the 2,479 eligible nasopharyngeal swab specimens included in the prospective study, 2,371 gave concordant results between the assays. One hundred eight specimens generated results that were discordant with those from the xTAG RVP and were further analyzed by bidirectional sequencing. Final clinical sensitivity values of the Aries Flu A/B & RSV assay were 98.1% for influenza A virus, 98.0% for influenza B virus, and 97.7% for RSV. Final clinical specificities for all three pathogens ranged from 98.6% to 99.8%. Due to the low prevalence of influenza B, an additional 40 banked influenza B-positive specimens were tested at the participating clinical laboratories and were all accurately detected by the Aries Flu A/B & RSV assay. This study demonstrates that the Aries Flu A/B & RSV assay is a suitable method for rapid and accurate identification of these causative pathogens in respiratory infections.
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Rogan DT, Kochar MS, Yang S, Quinn JV. Impact of Rapid Molecular Respiratory Virus Testing on Real-Time Decision Making in a Pediatric Emergency Department. J Mol Diagn 2017; 19:460-467. [PMID: 28341587 DOI: 10.1016/j.jmoldx.2017.01.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 01/25/2017] [Indexed: 11/24/2022] Open
Abstract
Acute respiratory illnesses (ARIs) are usually viral [influenza, respiratory syncytial virus (RSV)] and account for 25% of emergency department (ED) peak-season visits. Laboratory PCR testing is accurate albeit slow, whereas rapid antigen testing is inaccurate. We determined the impact of bedside PCR (molecular point-of-care test; mPOCT) on pediatric ARI management. This was a prospective cohort study of consecutive pediatric patients with ED-ordered respiratory PCR test, enrolled over 9 weeks during peak flu season. On ordering, ED physicians were interviewed to ascertain real-time plans if given immediate influenza/RSV PCR results for the current patient. Two groups were compared: actual management and management adjusted for mPOCT results. We compared ED length of stay (LOS), tests ordered, and antibiotic/antiviral ordering. One-hundred thirty-six respiratory PCR panels were ordered, 71 by admitting team, 61 for ED management. Of 61 ED-initiated tests, physicians indicated in 39 cases (64%) they would change patient management were bedside viral results available. Physicians would have decreased ED LOS by 33 minutes, ordered fewer tests (18%; P < 0.001) with average patient charge savings of $669, fewer antibiotics among discharged patients (17%; P = 0.043), and increased appropriate antiviral use (13%; P = 0.023). Rapid bedside ARI mPOCT PCR has the potential to decrease ED LOS, reduce diagnostic tests and patient charges, and increase appropriate use of antibiotics and antiviral agents.
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Affiliation(s)
- Daniel T Rogan
- Department of Health Research and Policy, Stanford University, Stanford, California
| | - Mohit S Kochar
- Department of Emergency Medicine, Stanford University, Stanford, California
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University, Stanford, California.
| | - James V Quinn
- Department of Emergency Medicine, Stanford University, Stanford, California.
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Parallel pathogens in the upper and lower respiratory tracts in children with a respiratory tract infection, as revealed by the Filmarray assay. FRONTIERS IN LABORATORY MEDICINE 2017. [PMCID: PMC7147191 DOI: 10.1016/j.flm.2017.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background Respiratory tract infection (RTI) is a common disease among children of all ages that causes high hospitalization and mortality rates. Infection with more than one pathogen has been reported in RTI; however, the association of the pathogen spectrum in upper and lower respiratory tract infections remains unclear. Methods A prospective study was conducted during February to October 2016. Fifty-five nasopharyngeal swabs (NPS) and 30 bronchoalveolar lavage fluid (BALF) samples from 55 hospitalized children aged less than 14 years (mean age 40 months) and diagnosed with an RTI were collected. All samples were detected for 18 respiratory pathogens using the Filmarray assay, real-time PCR, or nested PCR methods. Detection results and clinical characteristics of all cases were analyzed using chi-square and t tests. Results Forty-one of 55 (74.5%) NPS obtained from children were positive for at least one pathogen by the Filmarray assay. Of these cases, 53.7% (22/41) were co-infected. The most commonly detected pathogen was rhinovirus (RV), followed by Mycoplasma pneumoniae (MP) and respiratory syncytial virus (RSV). Infection by both RV and MP was the most frequently observed pattern of co-infection. Similar results were observed using real-time PCR. The pathogens in the NPS from 76.6% of cases detected by Filmarray and 80.0% of cases by real-time PCR included all the pathogens detected in the BALF sample from the same individual. The Filmarray assay showed an 80% concordance rate with real-time PCR and had a turnaround time of less than 1.2 h. No significant differences were observed between the association of single-infection and co-infection with clinical characteristics, neither by Filmarray nor real-time PCR. Conclusion The spectrum of pathogens is mostly concordant in the upper and lower respiratory tract. Collecting NPS for detection can be a non-invasive and more convenient option compared with BALF. Although co-infection is common in children with an RTI, the clinical significance of co-infection remains unclear and warrants further analysis.
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Utilization Management in a Large Community Hospital. UTILIZATION MANAGEMENT IN THE CLINICAL LABORATORY AND OTHER ANCILLARY SERVICES 2017. [PMCID: PMC7123185 DOI: 10.1007/978-3-319-34199-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The utilization management of laboratory tests in a large community hospital is similar to academic and smaller community hospitals. There are numerous factors that influence laboratory utilization. Outside influences like hospitals buying physician practices, increasing numbers of hospitalists, and hospital consolidation will influence the number and complexity of the test menu that will need to be monitored for over and/or under utilization in the central laboratory and reference laboratory. CLIA’88 outlines the four test categories including point-of-care testing (waived) and provider-performed microscopy that need laboratory test utilization management. Incremental cost analysis is the most efficient method for evaluating utilization reduction cost savings. Economies of scale define reduced unit cost per test as test volume increases. Outreach programs in large community hospitals provide additional laboratory tests from non-patients in physician offices, nursing homes, and other hospitals. Disruptive innovations are changing the present paradigms in clinical diagnostics, like wearable sensors, MALDI-TOF, multiplex infectious disease panels, cell-free DNA, and others. Obsolete tests need to be universally defined and accepted by manufacturers, physicians, laboratories, and hospitals, to eliminate access to their reagents and testing platforms.
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Rappo U, Schuetz AN, Jenkins SG, Calfee DP, Walsh TJ, Wells MT, Hollenberg JP, Glesby MJ. Impact of Early Detection of Respiratory Viruses by Multiplex PCR Assay on Clinical Outcomes in Adult Patients. J Clin Microbiol 2016; 54:2096-103. [PMID: 27225406 PMCID: PMC4963510 DOI: 10.1128/jcm.00549-16] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 05/23/2016] [Indexed: 12/27/2022] Open
Abstract
Rapid and definitive diagnosis of viral respiratory infections is imperative in patient triage and management. We compared the outcomes for adult patients with positive tests for respiratory viruses at a tertiary care center across two consecutive influenza seasons (winters of 2010-2011 and 2012). Infections were diagnosed by conventional methods in the first season and by multiplex PCR (FilmArray) in the second season. FilmArray decreased the time to diagnosis of influenza compared to conventional methods (median turnaround times of 1.7 h versus 7.7 h, respectively; P = 0.015); FilmArray also decreased the time to diagnosis of non-influenza viruses (1.5 h versus 13.5 h, respectively; P < 0.0001). Multivariate logistic regression found that a diagnosis of influenza by FilmArray was associated with significantly lower odds ratios (ORs) for admission (P = 0.046), length of stay (P = 0.040), duration of antimicrobial use (P = 0.032), and number of chest radiographs (P = 0.005), when controlling for potential confounders. We conclude that the rapid turnaround time, multiplex nature of the test (allowing simultaneous detection of an array of viruses), and superior sensitivity of FilmArray may improve the evaluation and management of patients suspected of having respiratory virus infections.
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Affiliation(s)
- Urania Rappo
- Department of Medicine, Division of Clinical Epidemiology and Evaluative Sciences Research, Weill Cornell Medicine, New York, New York, USA
| | - Audrey N Schuetz
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Stephen G Jenkins
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - David P Calfee
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Thomas J Walsh
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA Departments of Pediatrics and Microbiology & Immunology, Weill Cornell Medicine, New York, New York, USA
| | - Martin T Wells
- Department of Statistical Science, Cornell University, Ithaca, New York, USA
| | - James P Hollenberg
- Department of Medicine, Division of Clinical Epidemiology and Evaluative Sciences Research, Weill Cornell Medicine, New York, New York, USA
| | - Marshall J Glesby
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
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Qin X, Zerr DM, Kronman MP, Adler AL, Berry JE, Rich S, Buccat AM, Xu M, Englund JA. Comparison of molecular detection methods for pertussis in children during a state-wide outbreak. Ann Clin Microbiol Antimicrob 2016; 15:28. [PMID: 27121506 PMCID: PMC4847268 DOI: 10.1186/s12941-016-0142-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 04/17/2016] [Indexed: 11/10/2022] Open
Abstract
A state-wide pertussis outbreak occurred in Washington during the winter–spring months of 2012, concurrent with respiratory viral season. We compared performance characteristics of a laboratory-developed pertussis PCR (LD-PCR for Bordetella pertussis, Bordetella parapertussis, and Bordetella holmesii) and rapid multiplex PCR (RM-PCR) for respiratory viruses (FilmArray™, BioFire, B. pertussis data unblinded following FDA approval post outbreak). We analyzed three cohorts of patients using physician testing orders as a proxy for clinical suspicion for pertussis or respiratory viruses: Cohort 1, tested by LD-PCR for pertussis pathogens only by nasopharyngeal swab; Cohort 2, by RM-PCR for respiratory viruses only by mid-nasal turbinate swab; and Cohort 3, by both methods. B. pertussis was detected in a total of 25 of the 490 patients in Cohort 3 in which LD-PCR detected 20/25 (80 %) cases and the RM-PCR detected 24/25 (96 %; p = 0.2). Pertussis pathogens were detected in 21/584 (3.6 %) of samples from Cohort 1 where clinicians had a relatively strong suspicion for pertussis. In contrast, B. pertussis was detected in only 4/3071 (0.1 %) specimens from Cohort 2 where suspicion for pertussis was lower (p < 0.001 for comparison with Cohort 1). In summary, the two laboratory methods were comparable for the detection of B. pertussis.
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Affiliation(s)
- X Qin
- Microbiology Laboratory, Seattle Children's Hospital, Seattle, WA, USA.
| | - D M Zerr
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - M P Kronman
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - A L Adler
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - J E Berry
- Microbiology Laboratory, Seattle Children's Hospital, Seattle, WA, USA
| | - S Rich
- Microbiology Laboratory, Seattle Children's Hospital, Seattle, WA, USA
| | - A M Buccat
- Microbiology Laboratory, Seattle Children's Hospital, Seattle, WA, USA
| | - M Xu
- Microbiology Laboratory, Seattle Children's Hospital, Seattle, WA, USA.,Department of Laboratory Medicine, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - J A Englund
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
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Clinical Evaluation of the Luminex NxTAG Respiratory Pathogen Panel. J Clin Microbiol 2016; 54:1912-1914. [PMID: 27122378 DOI: 10.1128/jcm.00482-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/22/2016] [Indexed: 11/20/2022] Open
Abstract
An evaluation of the Luminex NxTAG Respiratory Pathogen Panel was performed on 404 clinical respiratory specimens. Clinical sensitivities and specificities of the assay compared to those of the reference methods were 80.0% to 100.0% and 98.9% to 100.0%, respectively. Correct genotyping information was provided for 95.5% of influenza virus A specimens. The closed-tube format of the assay simplified the workflow and minimized carryover contamination.
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Abstract
OBJECTIVES To describe the strengths and limitations of the available influenza diagnostics, with a focus on rapid antigen detection assays and nucleic acid detection assays. METHODS A case-based presentation is used to illustrate the potential limitations of rapid antigen detection assays for influenza. RESULTS Influenza is a seasonal illness; estimates attribute influenza to approximately 200,000 hospitalizations and 41,000 deaths in the United States annually. Antigen detection assays for influenza are rapid and convenient, and thus are widely used in a variety of health care settings, even though the sensitivity of these assays may be suboptimal. The United States Food and Drug Administration has recently created new guidelines intended to improve the oversight and performance characteristics of influenza antigen detection assays. Molecular assays, although more costly and complex, are more sensitive and may be designed to simultaneously detect multiple respiratory pathogens within a single assay. CONCLUSIONS Diagnostic assays for influenza can vary greatly with regards to analytical performance characteristics, complexity, turnaround time and cost. This can have important patient care and infection prevention implications.
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Affiliation(s)
- Allison R McMullen
- From the Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO
| | - Neil W Anderson
- From the Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO
| | - Carey-Ann D Burnham
- From the Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO.
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Chu HY, Englund JA, Strelitz B, Lacombe K, Jones C, Follmer K, Martin EK, Bradford M, Qin X, Kuypers J, Klein EJ. Rhinovirus Disease in Children Seeking Care in a Tertiary Pediatric Emergency Department. J Pediatric Infect Dis Soc 2016; 5:29-38. [PMID: 26908489 PMCID: PMC4765491 DOI: 10.1093/jpids/piu099] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 09/02/2014] [Indexed: 11/14/2022]
Abstract
BACKGROUND Rhinovirus is the most common cause of viral respiratory tract infections in children. Virologic predictors of lower respiratory tract infection (LRTI), such as viral load and the presence of another respiratory virus (coinfection), are not well characterized in pediatric outpatients. METHODS Mid-nasal turbinate samples were collected from children presenting for care to the Seattle Children's Hospital emergency department (ED) or urgent care with a symptomatic respiratory infection between December 2011 and May 2013. A subset of samples was tested for rhinovirus viral load by real-time polymerase chain reaction. Clinical data were collected by chart reviews. Multivariate logistic regression was used to evaluate the relationship between viral load and coinfection and the risk for LRTI. RESULTS Rhinovirus was the most frequent respiratory virus detected in children younger than 3 years. Of 445 patients with rhinovirus infection, 262 (58.9%) had LRTIs, 231 (51.9%) required hospital admission and 52 (22.5%) were hospitalized for 3 days or longer. Children with no comorbidities accounted for 142 (54%) of 262 rhinovirus LRTIs. Higher viral load was significantly associated with LRTI among illness episodes with rhinovirus alone (OR, 2.11; 95% confidence interval [CI], 1.24-3.58). Coinfection increased the risk of LRTI (OR, 1.83; 95% CI, 1.01-3.32). CONCLUSIONS Rhinovirus was the most common pathogen detected among symptomatic young children in a pediatric ED who had respiratory viral testing performed, with the majority requiring hospitalization. Higher rhinovirus viral load and coinfection increased disease severity. Virologic data may assist clinical decision making for children with rhinovirus infections in the pediatric ED.
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Affiliation(s)
- Helen Y. Chu
- Department of Medicine, University of Washington
| | | | | | | | | | | | | | | | - Xuan Qin
- Department of Microbiology, Seattle Children's Hospital, Washington
| | - Jane Kuypers
- Department of Laboratory Medicine, University of Washington
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Seo Y, Kim JE, Jeong Y, Lee KH, Hwang J, Hong J, Park H, Choi J. Engineered nanoconstructs for the multiplexed and sensitive detection of high-risk pathogens. NANOSCALE 2016; 8:1944-1951. [PMID: 26462853 DOI: 10.1039/c5nr06230f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Many countries categorize the causative agents of severe infectious diseases as high-risk pathogens. Given their extreme infectivity and potential to be used as biological weapons, a rapid and sensitive method for detection of high-risk pathogens (e.g., Bacillus anthracis, Francisella tularensis, Yersinia pestis, and Vaccinia virus) is highly desirable. Here, we report the construction of a novel detection platform comprising two units: (1) magnetic beads separately conjugated with multiple capturing antibodies against four different high-risk pathogens for simple and rapid isolation, and (2) genetically engineered apoferritin nanoparticles conjugated with multiple quantum dots and detection antibodies against four different high-risk pathogens for signal amplification. For each high-risk pathogen, we demonstrated at least 10-fold increase in sensitivity compared to traditional lateral flow devices that utilize enzyme-based detection methods. Multiplexed detection of high-risk pathogens in a sample was also successful by using the nanoconstructs harboring the dye molecules with fluorescence at different wavelengths. We ultimately envision the use of this novel nanoprobe detection platform in future applications that require highly sensitive on-site detection of high-risk pathogens.
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Affiliation(s)
- Youngmin Seo
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, Korea.
| | - Ji-eun Kim
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, Korea.
| | - Yoon Jeong
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, Korea.
| | - Kwan Hong Lee
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, Korea. and Department of Bionano Engineering, Hanyang University ERICA, Ansan 426-791, Korea
| | - Jangsun Hwang
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, Korea.
| | - Jongwook Hong
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, Korea. and Department of Bionano Engineering, Hanyang University ERICA, Ansan 426-791, Korea
| | - Hansoo Park
- School of Integrative Engineering, Chung-Ang University, Seoul 156-756, Korea.
| | - Jonghoon Choi
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, Korea. and Department of Bionano Engineering, Hanyang University ERICA, Ansan 426-791, Korea
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