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Wang K, Zhang T, Jiao T, Pang F, Dai F, Zhang Z, Li X, Chen Y, Zhang H, Chen Z, Song J. Mini-Program Enabled IoT Intelligent Molecular Diagnostic Device for Co-Detection and Spatiotemporal Mapping of Infectious Disease Pathogens. Anal Chem 2024. [PMID: 39082644 DOI: 10.1021/acs.analchem.4c01762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Effective detection of infectious pathogens is crucial for disease prevention and control. We present an innovative Internet of Things (IoT) molecular diagnostic device featuring a WeChat mini-program for simultaneous detection and spatiotemporal mapping of respiratory pathogens. Leveraging social software's widespread usage, our device integrates seamlessly with WeChat, eliminating the need for app downloads and installations. Through a comprehensive detection system, including a user-friendly mini-program, a portable Point-of-Care fluorescence detector, and a diagnostic information management platform (EzDx Cloud), we demonstrate high sensitivity and specificity in detecting common respiratory viruses. Our SARS-CoV-2/H1N1 combo test kit, developed using a novel one-tube/one-step loop-mediated isothermal amplification-CRISPR method, shows remarkable performance. We address challenges in at-home nucleic acid testing by providing a cost-effective solution capable of detecting multiple pathogens simultaneously. Our system's versatility accommodates various assays operating at different temperatures and fluorescence intensities, offering significant advantages over traditional methods. Moreover, integration with EzDx Cloud facilitates disease monitoring and early warning systems, enhancing public health management. This study highlights the potential of our IoT molecular diagnostic device in revolutionizing infectious disease detection and control, with wide-ranging applications in both human and animal population.
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Affiliation(s)
- Kaizheng Wang
- Academy of Medical Engineering and Translational Medicine, Medical College, Tianjin University, Tianjin 300072, China
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Tao Zhang
- Academy of Medical Engineering and Translational Medicine, Medical College, Tianjin University, Tianjin 300072, China
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Tianjiao Jiao
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
| | - Feibiao Pang
- Hangzhou EzDx Technology Co., Ltd., Hangzhou, Zhejiang 311231, China
| | - Fengyi Dai
- Academy of Medical Engineering and Translational Medicine, Medical College, Tianjin University, Tianjin 300072, China
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Zhanfang Zhang
- Academy of Medical Engineering and Translational Medicine, Medical College, Tianjin University, Tianjin 300072, China
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Xiang Li
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
| | - Yao Chen
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Hongyu Zhang
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Zhiguang Chen
- Hangzhou EzDx Technology Co., Ltd., Hangzhou, Zhejiang 311231, China
| | - Jinzhao Song
- Hangzhou Institute of Medicine, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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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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Chen W, Liu G, Cui L, Tian F, Zhang J, Zhao J, Lv Y, Du J, Huan X, Wu Y, Zhang Y. Evaluation of metagenomic and pathogen-targeted next-generation sequencing for diagnosis of meningitis and encephalitis in adults: A multicenter prospective observational cohort study in China. J Infect 2024; 88:106143. [PMID: 38548243 DOI: 10.1016/j.jinf.2024.106143] [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: 11/26/2023] [Revised: 02/17/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Next-generation sequencing (NGS) might aid in the identification of causal pathogens. However, the optimal approaches applied to cerebrospinal fluid (CSF) for detection are unclear, and studies evaluating the application of different NGS workflows for the diagnosis of intracranial infections are limited. METHODS In this multicenter, prospective observational cohort study, we described the diagnostic efficacy of pathogen-targeted NGS (ptNGS) and metagenomic NGS (mNGS) compared to that of composite microbiologic assays, for infectious meningitis/encephalitis (M/E). RESULTS In total, 152 patients diagnosed with clinically suspected M/E at four tertiary hospitals were enrolled; ptNGS and mNGS were used in parallel for pathogen detection in CSF. Among the 89 patients who were diagnosed with definite infectious M/E, 57 and 39 patients had causal microbial detection via ptNGS and mNGS, respectively. The overall accuracy of ptNGS was 65.1%, with a positive percent agreement (PPA) of 64% and a negative percent agreement (NPA) of 66.7%; and the overall accuracy of mNGS was 47.4%, with a PPA of 43.8% and an NPA of 52.4% after discrepancy analysis. There was a significant difference in the detection efficiency between these two methods both for PPA (sensitivity) and overall accuracy for pathogen detection (P < 0.05). CONCLUSIONS NGS tests have provided new information in addition to conventional microbiologic tests. ptNGS seems to have superior performance over mNGS for common causative pathogen detection in CSF for infectious M/E.
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Affiliation(s)
- Weibi Chen
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Gang Liu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Lili Cui
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Fei Tian
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jiatang Zhang
- Department of Neurology, the First Medical Center of People's Liberation Army General Hospital, Beijing, China
| | - Jiahua Zhao
- Department of Neurology, the First Medical Center of People's Liberation Army General Hospital, Beijing, China
| | - Ying Lv
- Department of Neurology & Psychiatry, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jianxin Du
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China; Department of Neurosurgery, Beijing Fengtai Youanmen Hospital, Beijing, China
| | - Xinyu Huan
- Department of Neurosurgery, Beijing Fengtai Youanmen Hospital, Beijing, China
| | - Yingfeng Wu
- Department of Vascular Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China.
| | - Yan Zhang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China; Department of Sleep and Consciousness Disorders, Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China.
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Challen R, Chatzilena A, Qian G, Oben G, Kwiatkowska R, Hyams C, Finn A, Tsaneva-Atanasova K, Danon L. Combined multiplex panel test results are a poor estimate of disease prevalence without adjustment for test error. PLoS Comput Biol 2024; 20:e1012062. [PMID: 38669293 PMCID: PMC11078360 DOI: 10.1371/journal.pcbi.1012062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/08/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Multiplex panel tests identify many individual pathogens at once, using a set of component tests. In some panels the number of components can be large. If the panel is detecting causative pathogens for a single syndrome or disease then we might estimate the burden of that disease by combining the results of the panel, for example determining the prevalence of pneumococcal pneumonia as caused by many individual pneumococcal serotypes. When we are dealing with multiplex test panels with many components, test error in the individual components of a panel, even when present at very low levels, can cause significant overall error. Uncertainty in the sensitivity and specificity of the individual tests, and statistical fluctuations in the numbers of false positives and false negatives, will cause large uncertainty in the combined estimates of disease prevalence. In many cases this can be a source of significant bias. In this paper we develop a mathematical framework to characterise this issue, we determine expressions for the sensitivity and specificity of panel tests. In this we identify a counter-intuitive relationship between panel test sensitivity and disease prevalence that means panel tests become more sensitive as prevalence increases. We present novel statistical methods that adjust for bias and quantify uncertainty in prevalence estimates from panel tests, and use simulations to test these methods. As multiplex testing becomes more commonly used for screening in routine clinical practice, accumulation of test error due to the combination of large numbers of test results needs to be identified and corrected for.
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Affiliation(s)
- Robert Challen
- Bristol Vaccine Centre, Schools of Population Health Sciences and of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Anastasia Chatzilena
- Bristol Vaccine Centre, Schools of Population Health Sciences and of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - George Qian
- Bristol Vaccine Centre, Schools of Population Health Sciences and of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Glenda Oben
- Bristol Vaccine Centre, Schools of Population Health Sciences and of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Rachel Kwiatkowska
- Population Health Sciences, University of Bristol, United Kingdom
- NIHR Health Protection Unit in Behavioural Science and Evaluation, University of Bristol, United Kingdom
| | - Catherine Hyams
- Bristol Vaccine Centre, Schools of Population Health Sciences and of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Adam Finn
- Bristol Vaccine Centre, Schools of Population Health Sciences and of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | | | - Leon Danon
- Bristol Vaccine Centre, Schools of Population Health Sciences and of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
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Craney A, Miller S. Present and Future Non-Culture-Based Diagnostics: Stewardship Potentials and Considerations. Clin Lab Med 2024; 44:109-122. [PMID: 38280793 DOI: 10.1016/j.cll.2023.10.003] [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] [Indexed: 01/29/2024]
Abstract
The medical microbiologist plays a key role in the transition from culture-based to molecular test methods for diagnosis of infectious diseases. They must understand the scientific and technical bases underlying these tests along with their associated benefits and limitations and be able to educate administrators and patient providers on their proper use. Coordination of testing practices between clinical departments and the spectrum of public health and research laboratories is essential to optimize health care delivery.
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Affiliation(s)
- Arryn Craney
- Center for Infectious Disease Diagnostics and Research, Diagnostic Medicine Institute, Geisinger Health System, 100 North Academy Avenue, Danville, PA 17822, USA
| | - Steve Miller
- Delve Bio, Inc. and Department of Laboratory Medicine, University of California San Francisco, 953 Indiana Street, San Francisco, CA 94107, USA.
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Marcelo RZ, Lustik MB, Jones MU. Seasonality and Climatic Factors Associated With Human Rhinovirus/Enterovirus Nasopharyngeal Sample Positivity on Oahu, Hawai'i, 2016-2019. Mil Med 2024; 189:e34-e39. [PMID: 37151191 DOI: 10.1093/milmed/usad125] [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: 01/24/2023] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 05/09/2023] Open
Abstract
INTRODUCTION Globally, human rhinoviruses/enteroviruses (HRVs/ENTs), indistinguishable on many widely available molecular platforms, are among the leading causes of the common cold. Geographic and climatic factors impact the peak activity of these viruses. In temperate climates, the peak activity of HRV occurs during autumn and spring whereas that of ENT occurs during autumn and summer. Both viruses are thought to peak during the rainy season in tropical climates like Hawai'i; however, data remain limited. We describe HRV/ENT seasonality and evaluate the climatic factors associated with peak activity among respiratory viral samples processed on Oahu, Hawai'i. MATERIALS AND METHODS We conducted a retrospective analysis of all respiratory specimens submitted to Tripler Army Medical Center for multiplex polymerase chain reaction testing between May 2016 and May 2019. Among HRV/ENT-positive samples, we recorded the month and year of positivity. Summative monthly positive detection was calculated with peak months above the mean. Associations between temperature, precipitation levels, relative humidity, and wind speed by week and the number of positive samples for HRV/ENT were evaluated using Poisson regression. This analysis was conducted via IRB exempt protocol number 19R18. RESULTS During our study period, there were 7,143 nasopharyngeal respiratory samples sent for multiplex polymerase chain reaction testing, with 1,572 positive for HRV/ENT (22%). Nineteen percent of respiratory samples positive for HRV/ENT were additionally positive for one or more respiratory pathogens. The majority of HRV/ENT-positive samples arose from children < 5 years of age (n = 959, 61%). Peak months were February, March, May, August, November, and December. After controlling for lagged count and year, average wind speed was the only climatic factor significantly associated with HRV/ENT sample positivity. CONCLUSIONS The peak monthly activity of HRV/ENT was similar to temperate climates with the exception of peak activity in February. Unlike other tropical climates, lower wind speed was associated with increased weekly HRV/ENT positivity and should be further explored as a transmission factor. Our study contributes to understanding the annual variability of HRV/ENT activity in tropical environments, which can inform clinician expectations regarding respiratory viral symptomatology in this region.
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Affiliation(s)
- Raymundo Z Marcelo
- Department of Pediatrics, Tripler Army Medical Center, Honolulu, HI 96859, USA
| | - Michael B Lustik
- Department of Clinical Investigations, Tripler Army Medical Center, Honolulu, HI 96859, USA
| | - Milissa U Jones
- Department of Pediatrics, Tripler Army Medical Center, Honolulu, HI 96859, USA
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
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Jones MU, Montgomery AS, Coskun JD, Marcelo RZ, Sutton AB, Raiciulescu S. Comparing the Clinical Courses of Children With Human Rhinovirus/Enterovirus to Children With Other Respiratory Viruses in the Outpatient Setting. Pediatr Infect Dis J 2023; 42:e432-e439. [PMID: 37725805 DOI: 10.1097/inf.0000000000004097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
BACKGROUND While infections caused by rhinoviruses and enteroviruses are common among children, the entirety of their clinical impact remains elusive. We compared the clinical outcomes of children with rhinovirus/enterovirus infections to other common respiratory viruses in outpatient settings. METHODS We conducted a retrospective analysis of nasopharyngeal samples singly positive for human rhinovirus/enterovirus (HRV/ENT), influenza A/B (FLU) or respiratory syncytial virus (RSV) from patients ≤17 years submitted for clinical testing via multiplex polymerase chain reaction between 2016 and 2019. We evaluated the following outpatient outcomes: days of respiratory symptoms before testing; visits for respiratory symptoms; receipt of a breathing treatment; receipt of antibiotics and hospital admission. Statistical analyses were conducted controlling for age and comorbid conditions. RESULTS There were 1355 positive samples included in this analysis (HRV/ENT: n = 743, FLU: n = 303 and RSV: n = 309). Compared to HRV/ENT, children with FLU had 28% fewer days of respiratory symptoms (β: -0.32; 95% confidence interval: -0.46 to -0.18; P < 0.001), fewer visits for respiratory symptoms, and significantly decreased odds of receiving a breathing treatment or antibiotics, and admission to the hospital. Children with RSV had a similar number of days of respiratory symptoms, outpatient visits and odds of hospital admission, but significantly increased odds of receiving a breathing treatment and antibiotics compared to those with HRV/ENT. CONCLUSION Clinicians should have a high level of vigilance when managing children with positive respiratory viral testing for HRV/ENT given the potential for clinical outcomes similar to and, in some instances, worse than known highly pathogenic viruses.
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Affiliation(s)
- Milissa U Jones
- From the Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, Maryland
- Department of Pediatrics, Tripler Army Medical Center, Honolulu, Hawaii
| | - Agnes S Montgomery
- From the Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, Maryland
- Department of Pediatrics, Children's National Hospital, Washington, DC
| | - Jennifer D Coskun
- Department of Pediatrics, Tripler Army Medical Center, Honolulu, Hawaii
| | | | - Alyssa B Sutton
- Department of Pediatrics, Tripler Army Medical Center, Honolulu, Hawaii
| | - Sorana Raiciulescu
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, Marylan
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Murray HC, Smith BJ, Putland M, Irving L, Johnson D, Williamson DA, Tong SYC. The impact of rapid diagnostic testing on hospital administrative coding accuracy for influenza. Infect Dis Health 2023; 28:271-275. [PMID: 37316338 DOI: 10.1016/j.idh.2023.05.003] [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: 11/08/2022] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND Hospital administrative coding may underestimate the true incidence of influenza-associated hospitalisation. Earlier availability of test results could lead to improved accuracy of administrative coding. METHODS In this study we evaluated International Classification of Diseases 10 (ICD-10) coding for influenza (with [J09-J10] or without [J11] virus identified) in adult inpatients who underwent testing in the year prior, compared to those in the 2.5 years after, the introduction of rapid PCR testing in 2017. Other factors associated with influenza coding were evaluated using logistic regression. Discharge summaries were audited to assess the impact of documentation and result availability on coding accuracy. RESULTS Influenza was confirmed by laboratory testing in 862 of 5755 (15%) patients tested after rapid PCR introduction compared with 170 of 926 (18%) prior. Following the introduction of rapid testing there was a significant increase in patients allocated J09 or J10 ICD-10 codes (768 of 860 [89%] vs 107 of 140 [79%], P = 0.001). On multivariable analysis, factors independently associated with correct coding were rapid PCR testing (aOR 4.36 95% CI [2.75-6.90]) and increasing length of stay (aOR 1.01, 95% CI [1.00-1.01]). Correctly coded patients were more likely to have documentation of influenza in their discharge summaries (95 of 101 [89%] vs 11 of 101 [10%], P < 0.001) and less likely to have pending results at discharge (8 of 101 [8%] vs 65 of 101 [61%], P < 0.001). CONCLUSION The introduction of rapid PCR testing for influenza was associated with more accurate hospital coding. One possible explanation is faster test turnaround leading to improvement in clinical documentation.
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Affiliation(s)
- Hugh C Murray
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, At the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, VIC, 3000, Australia.
| | - Benjamin J Smith
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, At the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
| | - Mark Putland
- Royal Melbourne Hospital, 300 Grattan St, Parkville, VIC, 3050, Melbourne, Australia
| | - Lou Irving
- Royal Melbourne Hospital, 300 Grattan St, Parkville, VIC, 3050, Melbourne, Australia
| | - Douglas Johnson
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, At the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
| | - Deborah A Williamson
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia; Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, At the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Steven Y C Tong
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, At the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, VIC, 3000, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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Bălan AM, Bodolea C, Trancă SD, Hagău N. Trends in Molecular Diagnosis of Nosocomial Pneumonia Classic PCR vs. Point-of-Care PCR: A Narrative Review. Healthcare (Basel) 2023; 11:healthcare11091345. [PMID: 37174887 PMCID: PMC10177880 DOI: 10.3390/healthcare11091345] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/23/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Nosocomial pneumonia is one of the most frequent hospital-acquired infections. One of the types of nosocomial pneumonia is ventilator-associated pneumonia, which occurs in endotracheally intubated patients in intensive care units (ICU). Ventilator-associated pneumonia may be caused by multidrug-resistant pathogens, which increase the risk of complications due to the difficulty in treating them. Pneumonia is a respiratory disease that requires targeted antimicrobial treatment initiated as early as possible to have a good outcome. For the therapy to be as specific and started sooner, diagnostic methods have evolved rapidly, becoming quicker and simpler to perform. Polymerase chain reaction (PCR) is a rapid diagnostic technique with numerous advantages compared to classic plate culture-based techniques. Researchers continue to improve diagnostic methods; thus, the newest types of PCR can be performed at the bedside, in the ICU, so-called point of care testing-PCR (POC-PCR). The purpose of this review is to highlight the benefits and drawbacks of PCR-based techniques in managing nosocomial pneumonia.
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Affiliation(s)
- Andrei-Mihai Bălan
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Anaesthesia and Intensive Care, Municipal Clinical Hospital, 400139 Cluj-Napoca, Romania
| | - Constantin Bodolea
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Anaesthesia and Intensive Care, Municipal Clinical Hospital, 400139 Cluj-Napoca, Romania
| | - Sebastian Daniel Trancă
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Emergency Department, The Emergency County Hospital Cluj, 400347 Cluj-Napoca, Romania
| | - Natalia Hagău
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Anaesthesia and Intensive Care, "Regina Maria" Hospital, 400221 Cluj-Napoca, Romania
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Nakamura T, Imai R, Kitamura A, So C, Ro S, Okafuji K, Tomishima Y, Jinta T, Nishimura N. Investigating Viral Involvement in Immunocompromised Patients Using Comprehensive Infectious Disease Testing Including FilmArray Respiratory Panel 2.1 on Bronchoscopy: A Retrospective Study. Cureus 2023; 15:e38820. [PMID: 37303378 PMCID: PMC10256251 DOI: 10.7759/cureus.38820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Reports are rare on the usefulness of the FilmArray Respiratory Panel 2.1 (FARP) using lower respiratory tract specimens. This retrospective study assessed its use, as part of a comprehensive infectious disease panel, to detect the viral causes of pneumonia using bronchoalveolar lavage samples from immunosuppressed patients. Methods This study included immunocompromised patients who underwent bronchoalveolar lavage or bronchial washing by bronchoscopy between April 1, 2021, and April 30, 2022. The collected samples were submitted for comprehensive testing, including FARP test; reverse transcription polymerase chain reaction (RT-PCR) for cytomegalovirus, varicella-zoster virus DNA, and herpes simplex virus; PCR for Pneumocystis jirovecii DNA; antigen testing for Aspergillus and Cryptococcus neoformans; and loop-mediated isothermal amplification method for Legionella. Results Out of 23 patients, 16 (70%) showed bilateral infiltrative shadows on computed tomography and three (13%) were intubated. The most common causes of immunosuppression were anticancer drug use (n=12, 52%) and hematologic tumors (n=11, 48%). Only two (9%) patients tested positive for severe acute respiratory syndrome coronavirus 2 and adenovirus by FARP. Four patients (17%) tested positive for cytomegalovirus by RT-PCR, but no inclusion bodies were identified cytologically. Nine (39%) patients tested positive for Pneumocystis jirovecii by PCR, but cytology confirmed the organism in only one case. Conclusions Comprehensive infectious disease testing, performed using bronchoalveolar lavage samples collected from lung lesions in immunosuppressed patients, showed low positive detection by FARP. The viruses currently detectable by FARP may be less involved in viral pneumonia diagnosed in immunocompromised patients.
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Affiliation(s)
- Tomoaki Nakamura
- Department of Pulmonary Medicine, Thoracic Center, St. Luke's International Hospital, Tokyo, JPN
| | - Ryosuke Imai
- Department of Pulmonary Medicine, Thoracic Center, St. Luke's International Hospital, Tokyo, JPN
| | - Atsushi Kitamura
- Department of Pulmonary Medicine, Thoracic Center, St. Luke's International Hospital, Tokyo, JPN
| | - Clara So
- Department of Pulmonary Medicine, Thoracic Center, St. Luke's International Hospital, Tokyo, JPN
| | - Shosei Ro
- Department of Pulmonary Medicine, Thoracic Center, St. Luke's International Hospital, Tokyo, JPN
| | - Kohei Okafuji
- Department of Pulmonary Medicine, Thoracic Center, St. Luke's International Hospital, Tokyo, JPN
| | - Yutaka Tomishima
- Department of Pulmonary Medicine, Thoracic Center, St. Luke's International Hospital, Tokyo, JPN
| | - Torahiko Jinta
- Department of Pulmonary Medicine, Thoracic Center, St. Luke's International Hospital, Tokyo, JPN
| | - Naoki Nishimura
- Department of Pulmonary Medicine, Thoracic Center, St. Luke's International Hospital, Tokyo, JPN
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11
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Hayotte A, Mariani-Kurkdjian P, Boizeau P, Dauger S, Riaud C, Lacarra B, Bourmaud A, Levy M. Viral Identification Using Multiplex Polymerase Chain Reaction Testing Does Not Reduce Antibiotic Prescribing in Paediatric Intensive Care Units. Microorganisms 2023; 11:microorganisms11040884. [PMID: 37110306 PMCID: PMC10143589 DOI: 10.3390/microorganisms11040884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/07/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023] Open
Abstract
PCR tests for viral identification, performed on nasopharyngeal secretions, have experienced a major boom in the last few years. Their use is very frequent, but their indications are still not well defined, especially in Paediatric Intensive Care Units (PICU). These tests are used for the microbiological diagnosis of lower respiratory infections but can be used in other situations. The aim of the study was to investigate the effect of viral identification on antibiotic therapy management. We conducted a single-centre retrospective study from 1 October 2017 to 31 December 2019. This study included all consecutive FilmArray® Respiratory Panel tests performed in patients hospitalised in a PICU. Patients were identified using the microbiology laboratory prospective database and data were extracted from the medical record. 544 tests corresponding to 408 patients were included. The main reasons for testing were pneumonia (34%) and bronchiolitis (24%). In 70% of cases, at least one virus was identified, with Human Rhinovirus (56%) and Respiratory Syncytial Virus (28%) being the two predominant. Bacterial co-infection was present in 25% of cases. Viral identification was not associated with reduced antibiotic therapy. On multivariate analysis, antibiotic management was significantly associated with clinical gravity, CRP value or radiology findings regardless of virus identification. Viral identification has an epidemiological value, but antibiotic prescription relies on other factors.
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12
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Suzuki Y, Kusama Y, Ito Y. Negative effects of pre-admission screening with simplified multiplex PCR. Pediatr Int 2023; 65:e15629. [PMID: 37804060 DOI: 10.1111/ped.15629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/12/2023] [Accepted: 07/19/2023] [Indexed: 10/08/2023]
Affiliation(s)
- Yumiko Suzuki
- Division of General Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Yoshiki Kusama
- Division of General Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
- Division of Pediatric Infectious Diseases, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
- Department of Infection Control and Prevention, Graduate School of Medicine/Faculty of Medicine, Osaka University, Suita, Japan
| | - Yusuke Ito
- Division of Pediatric Infectious Diseases, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
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13
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Chiu YT, Tien N, Lin HC, Wei HM, Lai HC, Chen JA, Low YY, Lin HH, Hsu YL, Hwang KP. Detection of respiratory pathogens by application of multiplex PCR panel during early period of COVID-19 pandemic in a tertiary hospital in Central Taiwan. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1144-1150. [PMID: 34674956 PMCID: PMC8493640 DOI: 10.1016/j.jmii.2021.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND Respiratory tract infections (RTIs) represent a major cause of clinical visits worldwide. Viral epidemiology of RTIs in adults has been less studied compared to children. FilmArray respiratory panel (FA-RP), a multiplex, real time polymerase chain reaction method can simultaneously detect the nucleic acids of multiple pathogens. The purpose of this study is to analyze the epidemiology and clinical presentations of an RTI cohort. METHODS This retrospective cohort study was conducted at China Medical University Hospital (CMUH) and China Medical University Children's Hospital (CMUCH), from January 2020 to June 2020. The FA-RP results were collected and analyzed according to upper versus lower RTIs. RESULTS Among 253 respiratory samples tested, 135 (53.4%) were from adults and 118 (46.6%) from children. A total positive rate of 33.9% (86/253) was found, with 21.48% (29/135) in adults and 48.31% (57/118) in children. Human rhinovirus/Enterovirus (HRV/EV) was detected in most of the age groups and was more common in URIs. HRV/EV was found as a frequent co-detection virus. Among children, HRV/EV was the most detected pathogen of URIs, while the most predominant pathogen in LRIs was Mycoplasma pneumoniae. CONCLUSIONS FA-RP has the potential to improve the detection rate of respiratory pathogens. The positive rate of FA-RP was higher in children compared to adults, which likely corresponds to the higher incidence of viral RTIs in children. Different pathogens may lead to different types of respiratory infections.
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Affiliation(s)
- Yu-Ting Chiu
- Division of Pediatric Infectious Diseases, China Medical University Children's Hospital, China Medical University, Taichung, Taiwan
| | - Ni Tien
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Hsiao-Chuan Lin
- Division of Pediatric Infectious Diseases, China Medical University Children's Hospital, China Medical University, Taichung, Taiwan,School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
| | - Hsiu-Mei Wei
- Division of Pediatric Infectious Diseases, China Medical University Children's Hospital, China Medical University, Taichung, Taiwan
| | - Huan-Cheng Lai
- Division of Pediatric Infectious Diseases, China Medical University Children's Hospital, China Medical University, Taichung, Taiwan
| | - Jiun-An Chen
- Division of Pediatric Infectious Diseases, China Medical University Children's Hospital, China Medical University, Taichung, Taiwan
| | - Yan-Yi Low
- Division of Pediatric Infectious Diseases, China Medical University Children's Hospital, China Medical University, Taichung, Taiwan
| | - Hsiu-Hsien Lin
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Yu-Lung Hsu
- Division of Pediatric Infectious Diseases, China Medical University Children's Hospital, China Medical University, Taichung, Taiwan,Corresponding author. Division of Pediatric Infectious Diseases, China Medical University Children's Hospital, China Medical University, No. 2, Yude Rd., North Dist., Taichung City, 40447, Taiwan. Fax: +886 4 22032798
| | - Kao-Pin Hwang
- Division of Pediatric Infectious Diseases, China Medical University Children's Hospital, China Medical University, Taichung, Taiwan,School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan,Corresponding author. Division of Pediatric Infectious Diseases, China Medical University Children's Hospital, China Medical University, No. 2, Yude Rd., North Dist., Taichung City, 40447, Taiwan. Fax: +886 4 22064008
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14
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Banerjee D, Hassan F, Avadhanula V, Piedra PA, Boom J, Sahni LC, Weinberg GA, Lindstrom S, Rha B, Harrison CJ, Selvarangan R. Comparative analysis of three multiplex platforms for the detection of respiratory viral pathogens. J Clin Virol 2022; 156:105274. [PMID: 36099751 DOI: 10.1016/j.jcv.2022.105274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 08/24/2022] [Accepted: 08/27/2022] [Indexed: 10/31/2022]
Abstract
BACKGROUND Acute viral respiratory infections are a major health burden in children worldwide. In recent years, rapid and sensitive multiplex nucleic acid amplification tests (NAATs) have replaced conventional methods for routine virus detection in the clinical laboratory. OBJECTIVE/STUDY DESIGN We compared BioFire® FilmArray® Respiratory Panel (FilmArray V1.7), Luminex NxTag® Respiratory Pathogen Panel (NxTag RPP) and Applied Biosystems TaqMan Array Card (TAC) for the detection of eight viruses in pediatric respiratory specimens. Results from the three platforms were analyzed with a single-plex real-time RT-PCR (rRT-PCR) assay for each virus. RESULTS Of the 170/210 single-plex virus-positive samples, FilmArray detected a virus in 166 (97.6%), TAC in 163 (95.8%) and NxTag RPP in 160 (94.1%) samples. The Positive Percent Agreement (PPA) of FilmArray, NxTag RPP and TAC was highest for influenza B (100%, 100% and 95.2% respectively) and lowest for seasonal coronaviruses on both FilmArray (90.2%) and NxTag RPP (81.8%), and for parainfluenza viruses 1- 4 on TAC (84%). The Negative Percent Agreement (NPA) was lowest for rhinovirus/enterovirus (92.9%, 96.7% and 97.3%) on FilmArray, NxTag RPP and TAC respectively. NPA for all three platforms was highest (100%) for both parainfluenza viruses 1- 4 and influenza A and B, and 100% for human metapneumovirus with TAC as well. CONCLUSION All three multiplex platforms displayed high overall agreement (>90%) and high NPA (>90%), while PPA was pathogen dependent and varied among platforms; high PPA (>90%) was observed for FilmArray for all eight viruses, TAC for six viruses and NxTag RPP for 4 viruses.
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Affiliation(s)
- Dithi Banerjee
- Children's Mercy Hospital, Kansas City, MO, United States of America
| | - Ferdaus Hassan
- Children's Mercy Hospital, Kansas City, MO, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America; Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States of America
| | - Julie Boom
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States of America; Texas Children's Hospital, Immunization Project, Baylor College of Medicine, Houston, TX, United States of America
| | - Leila C Sahni
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States of America; Texas Children's Hospital, Immunization Project, Baylor College of Medicine, Houston, TX, United States of America
| | - Geoffrey A Weinberg
- University of Rochester School of Medicine & Dentistry, Rochester, NY, United States of America
| | - Stephen Lindstrom
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Brian Rha
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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15
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Mike TB, Rajbhandari P. Persistent Tachycardia in a 10-year-old. Pediatr Rev 2022; 43:590-592. [PMID: 36180537 DOI: 10.1542/pir.2021-004930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Affiliation(s)
- Thomas B Mike
- Division of Pediatric Hospital Medicine, Department of Pediatrics, Akron Children's Hospital, Akron, OH
| | - Prabi Rajbhandari
- Division of Pediatric Hospital Medicine, Department of Pediatrics, Akron Children's Hospital, Akron, OH
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16
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Neopane P, Nypaver J, Shrestha R, Beqaj S. Performance Evaluation of TaqMan SARS-CoV-2, Flu A/B, RSV RT-PCR Multiplex Assay for the Detection of Respiratory Viruses. Infect Drug Resist 2022; 15:5411-5423. [PMID: 36119638 PMCID: PMC9480588 DOI: 10.2147/idr.s373748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/24/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose To detect and differentiate co-infection with influenza and respiratory syncytial virus during the COVID pandemic, a rapid method that can detect multiple pathogens in a single test is a significant diagnostic advance to analyze the outcomes and clinical implications of co-infection. Therefore, we validated and evaluated the performance characteristics of TaqMan SARS-CoV-2, Flu A/B, RSV RT-PCR multiplex assay for the detection of SARS-CoV-2, Flu A/B, and RSV using nasopharyngeal and saliva samples. Materials and Methods The method validation was performed by using culture fluids of Influenza A virus (H3N2) (A/Wisconsin/67/2005), Influenza B virus (B/Virginia/ATCC4/2009), RSV A2 cpts-248, SARS-CoV-2 (USA-WA1/2020) and quantitative RNA controls of Influenza A virus (H1N1) strain A/PR/8/34 (VR-95DQ), RSV A2 (VR-1540DQ) and SARS-CoV-2 (MN908947.3 Wuhan-Hu-1) from ATCC and Zeptometrix, NY, USA. A total of 110 nasopharyngeal specimens and 70 saliva samples were used for the SARS-CoV-2 detection, and a total of 70 nasopharyngeal specimens were used for Influenza and RSV detection. Total RNA was extracted from all the samples and multiplex PCR was performed using TaqMan SARS-CoV-2, Flu A/B, RSV RT-PCR multiplex assay. The assay was used for SARS-CoV-2 variant (B.1.1.7_601443, B.1.617.1_1662307, P.1_792683, B.1.351_678597, B.1.1.529/BA.1). Results Validation controls showed accurate and precise results. The correlation study found the accuracy of 96.38 to 100% (95% CI) in nasopharyngeal and 94.87 to 100% (95% CI) in saliva for SARS-CoV-2 and 91.1 to 100% (95% CI) for both Influenza A/B and RSV. The diagnostic efficiency of this assay was not affected by SARS-CoV-2 variant, including Omicron. Conclusion The TaqMan SARS-CoV-2, Flu A/B, RSV RT-PCR multiplex assay is a rapid method to detect and differentiate SAR-CoV-2, Flu A and B, and RSV in nasopharyngeal and saliva samples. It has a significant role in the diagnosis and management of respiratory illnesses and the clinical implications of co-infection.
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Affiliation(s)
- Puja Neopane
- Patients Choice Laboratories, Indianapolis, IN, 46278, USA
| | - Jerome Nypaver
- Patients Choice Laboratories, Indianapolis, IN, 46278, USA
| | | | - Safedin Beqaj
- Patients Choice Laboratories, Indianapolis, IN, 46278, USA
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17
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Huang AH, Hsu WT, Lee CC. Respiratory Virus Burden in the Community: More Than What Meets the Eye. Clin Infect Dis 2022; 75:551. [PMID: 35148382 DOI: 10.1093/cid/ciac132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Amy Huaishiuan Huang
- Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Wan Ting Hsu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Chien Chang Lee
- Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan
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18
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Schwellnus M, Adami PE, Bougault V, Budgett R, Clemm HH, Derman W, Erdener U, Fitch K, Hull JH, McIntosh C, Meyer T, Pedersen L, Pyne DB, Reier-Nilsen T, Schobersberger W, Schumacher YO, Sewry N, Soligard T, Valtonen M, Webborn N, Engebretsen L. International Olympic Committee (IOC) consensus statement on acute respiratory illness in athletes part 1: acute respiratory infections. Br J Sports Med 2022; 56:bjsports-2022-105759. [PMID: 35863871 DOI: 10.1136/bjsports-2022-105759] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2022] [Indexed: 11/04/2022]
Abstract
Acute illnesses affecting the respiratory tract are common and form a significant component of the work of Sport and Exercise Medicine (SEM) clinicians. Acute respiratory illness (ARill) can broadly be classified as non-infective ARill and acute respiratory infections (ARinf). The aim of this consensus is to provide the SEM clinician with an overview and practical clinical approach to ARinf in athletes. The International Olympic Committee (IOC) Medical and Scientific Commission appointed an international consensus group to review ARill (non-infective ARill and ARinf) in athletes. Six subgroups of the IOC Consensus group were initially established to review the following key areas of ARill in athletes: (1) epidemiology/risk factors for ARill, (2) ARinf, (3) non-infective ARill including ARill due to environmental exposure, (4) acute asthma and related conditions, (5) effects of ARill on exercise/sports performance, medical complications/return-to-sport and (6) acute nasal/vocal cord dysfunction presenting as ARill. Several systematic and narrative reviews were conducted by IOC consensus subgroups, and these then formed the basis of sections in the consensus documents. Drafting and internal review of sections were allocated to 'core' members of the consensus group, and an advanced draft of the consensus document was discussed during a meeting of the main consensus core group in Lausanne, Switzerland on 11 to 12 October 2021. Final edits were completed after the meeting. This consensus document (part 1) focusses on ARinf, which accounts for the majority of ARill in athletes. The first section of this consensus proposes a set of definitions and classifications of ARinf in athletes to standardise future data collection and reporting. The remainder of the consensus paper examines a wide range of clinical considerations related to ARinf in athletes: epidemiology, risk factors, pathology/pathophysiology, clinical presentation and diagnosis, management, prevention, medical considerations, risks of infection during exercise, effects of infection on exercise/sports performance and return-to-sport guidelines.
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Affiliation(s)
- Martin Schwellnus
- Sport, Exercise Medicine and Lifestyle Institute (SEMLI), Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- International Olympic Committee Research Centre, Pretoria, South Africa
| | - Paolo Emilio Adami
- Health and Science Department, World Athletics, Monaco, Monaco Principality
| | - Valerie Bougault
- Laboratoire Motricité Humaine Expertise Sport Santé, Université Côte d'Azur, Nice, France
| | - Richard Budgett
- Medical and Scientific Department, International Olympic Committee, Lausanne, Switzerland
| | - Hege Havstad Clemm
- Department of Pediatric and Adolescent Medicine, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Wayne Derman
- International Olympic Committee Research Centre, Pretoria, South Africa
- Institute of Sport and Exercise Medicine (ISEM), Department of Sport Science, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Uğur Erdener
- Medical and Scientific Department, International Olympic Committee, Lausanne, Switzerland
| | - Ken Fitch
- School of Human Science; Sports, Exercise and Health, University of Western Australia, Perth, Western Australia, Australia
| | - James H Hull
- Department of Respiratory Medicine, Royal Brompton Hospital, London, UK
- Institute of Sport, Exercise and Health (ISEH), University College London (UCL), London, UK
| | | | - Tim Meyer
- Institute of Sports and Preventive Medicine, Saarland University, Saarbrucken, Germany
| | - Lars Pedersen
- Department of Respiratory Medicine, Bispebjerg Hospital, Copenhagen, Denmark
| | - David B Pyne
- Research Institute for Sport and Exercise, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Tonje Reier-Nilsen
- The Norwegian Olympic Sports Centre, Oslo, Norway
- Trauma Research Center, Department of Sports Medicine, Norwegian School of Sport Sciences, Oslo, Norway
| | - Wolfgang Schobersberger
- Institute for Sports Medicine, Alpine Medicine & Health Tourism (ISAG), University Hospital - Tirol Kliniken Innsbruck and Private University UMIT Tirol, Hall, Austria
| | | | - Nicola Sewry
- Sport, Exercise Medicine and Lifestyle Institute (SEMLI), Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- International Olympic Committee Research Centre, Pretoria, South Africa
| | - Torbjørn Soligard
- Medical and Scientific Department, International Olympic Committee, Lausanne, Switzerland
| | | | - Nick Webborn
- Centre for Sport and Exercise Science and Medicine, University of Brighton, Brighton, UK
| | - Lars Engebretsen
- Medical and Scientific Department, International Olympic Committee, Lausanne, Switzerland
- Trauma Research Center, Department of Sports Medicine, Norwegian School of Sport Sciences, Oslo, Norway
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19
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Ye Q, Lu D, Zhang T, Mao J, Shang S. Recent advances and clinical application in point-of-care testing of SARS-CoV-2. J Med Virol 2022; 94:1866-1875. [PMID: 35080017 PMCID: PMC9015580 DOI: 10.1002/jmv.27617] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/14/2022] [Accepted: 01/19/2022] [Indexed: 01/09/2023]
Abstract
The novel coronavirus 2019 (COVID-19) caused by SARS-CoV-2 spread rapidly worldwide, posing a severe threat to public life and health. It is significant to realize rapid testing and timely control of epidemic situations under the condition of limited resources. However, laboratory-based standardized nucleic acid detection methods have a long turnaround time and high cost, so it is urgent to develop convenient methods for detecting COVID-19. This paper summarizes the point-of-care testing (POCT) developed for novel coronavirus from three aspects: nucleic acid extraction, nucleic acid amplification, and detection methods. This paper introduces a commercial real-time detection system that integrates the abovementioned three steps and the matters needing attention in use. The primary purpose of this review is to provide a reference for emergency response and rapid deployment of COVID-19 and some other emerging infectious diseases.
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Affiliation(s)
- Qing Ye
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Dezhao Lu
- School of Life ScienceZhejiang Chinese Medical UniversityHangzhouChina
| | - Ting Zhang
- School of Medical Technology and Information EngineeringZhejiang Chinese Medical UniversityHangzhouChina
| | - Jianhua Mao
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Shiqiang Shang
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
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20
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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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21
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Ye Q, Lu D, Zhang T, Mao J, Shang S. Application experience of a rapid nucleic acid detection system for COVID-19. Microbes Infect 2022; 24:104945. [PMID: 35093551 PMCID: PMC8801965 DOI: 10.1016/j.micinf.2022.104945] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 12/29/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is raging worldwide. The COVID-19 outbreak caused severe threats to the life and health of all humans caused by SARS-CoV-2. Clinically, there is an urgent need for an in vitro diagnostic product to detect SARS-CoV-2 nucleic acid quickly. Under this background, commercial SARS-CoV-2 nucleic acid POCT products came into being. However, how to choose these products and how to use these products in a standardized way have brought new puzzles to clinical laboratories. This paper focuses on evaluating the performance of these commercial SARS-CoV-2 nucleic acid POCT products and helps the laboratory make the correct choice. At the same time, to standardize the use of this kind of product, this paper also puts forward corresponding suggestions from six elements of total quality management, namely, human, machine, material, method, environment, and measurement. In addition, this paper also puts forward some ideas on the future development direction of POCT products.
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Affiliation(s)
- Qing Ye
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou 310052, China
| | - Dezhao Lu
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Ting Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Jianhua Mao
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou 310052, China.
| | - Shiqiang Shang
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou 310052, China.
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22
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Yoshida K, Hatachi T, Okamoto Y, Aoki Y, Kyogoku M, Moon Miyashita K, Inata Y, Shimizu Y, Fujiwara F, Takeuchi M. Application of Multiplex Polymerase Chain Reaction for Pathogen Identification and Antibiotic Use in Children With Respiratory Infections in a PICU. Pediatr Crit Care Med 2021; 22:e644-e648. [PMID: 34224509 DOI: 10.1097/pcc.0000000000002794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVES To compare the pathogen identification rate and use of antibiotics before and after the implementation of multiplex polymerase chain reaction testing in children with respiratory infections in a PICU. DESIGN Single-center, pre-post study. SETTING PICU of Osaka Women's and Children's Hospital, Osaka, Japan. PATIENTS Consecutive children with respiratory infections who were admitted to the PICU between December 2017 and November 2018 (premultiplex polymerase chain reaction period) and between March 2019 and February 2020 (postmultiplex polymerase chain reaction period). INTERVENTIONS Conventional rapid antigen tests and bacterial culture tests were performed throughout the study period. Multiplex polymerase chain reaction testing using the FilmArray respiratory panel (BioFire Diagnostics, Salt Lake City, UT) was conducted to detect 17 viruses and three bacterial pathogens. During the postmultiplex polymerase chain reaction period, we did not recommend prescribing antibiotics for stable children, depending on the virus species and laboratory test results. MEASUREMENTS AND MAIN RESULTS Ninety-six and 85 children were enrolled during the pre- and postmultiplex polymerase chain reaction periods, respectively. Rapid antigen tests identified pathogens in 22% of the children (n = 21) during the premultiplex polymerase chain reaction period, whereas rapid antigen tests and/or multiplex polymerase chain reaction testing identified pathogens in 67% of the children (n = 57) during the postmultiplex polymerase chain reaction period (p < 0.001). The most commonly identified pathogen using multiplex polymerase chain reaction testing was human rhino/enterovirus. Bacterial pathogens were identified in 50% of the children (n = 48) and 60% of the children (n = 51) during the pre- and postmultiplex polymerase chain reaction periods (p = 0.18). There were no differences in antibiotic use (84% vs 75%; p = 0.14), broad-spectrum antibiotic use (33% vs 34%; p = 0.91), or the duration of antibiotic use within 14 days of admission (6.0 vs 7.0 d; p = 0.45) between the pre- and postmultiplex polymerase chain reaction periods. CONCLUSIONS Although the pathogen identification rate, especially for viral pathogens, increased using multiplex polymerase chain reaction testing, antibiotic use did not reduce in children with respiratory infections in the PICU. Definitive identification of bacterial pathogens and implementation of evidence-based antimicrobial stewardship programs employing multiplex polymerase chain reaction testing are warranted.
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Affiliation(s)
- Kota Yoshida
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Takeshi Hatachi
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Yuya Okamoto
- Department of Laboratory Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Yoshihiro Aoki
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
- Department of Emergency and Critical Care Medicine, Aizawa Hospital, Nagano, Japan
| | - Miyako Kyogoku
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Kazue Moon Miyashita
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Yu Inata
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Yoshiyuki Shimizu
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Futoshi Fujiwara
- Department of Laboratory Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Muneyuki Takeuchi
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
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23
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Almansa R, Herrero-Rodríguez C, Martínez-Huélamo M, Vicente-Andres MDP, Nieto-Barbero JA, Martín-Ballesteros M, Rodilla-Carvajal MDM, de la Fuente A, Ortega A, Alonso-Ramos MJ, Wacker J, Liesenfeld O, Sweeney TE, Bermejo-Martin JF, García-Ortiz L. A host transcriptomic signature for identification of respiratory viral infections in the community. Eur J Clin Invest 2021; 51:e13626. [PMID: 34120332 DOI: 10.1111/eci.13626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Fever-7 is a test evaluating host mRNA expression levels of IFI27, JUP, LAX, HK3, TNIP1, GPAA1 and CTSB in blood able to detect viral infections. This test has been validated mostly in hospital settings. Here we have evaluated Fever-7 to identify the presence of respiratory viral infections in a Community Health Center. METHODS A prospective study was conducted in the "Servicio de Urgencias de Atención Primaria" in Salamanca, Spain. Patients with clinical signs of respiratory infection and at least one point in the National Early Warning Score were recruited. Fever-7 mRNAs were profiled on a Nanostring nCounter® SPRINT instrument from blood collected upon patient enrolment. Viral diagnosis was performed on nasopharyngeal aspirates (NPAs) using the Biofire-RP2 panel. RESULTS A respiratory virus was detected in the NPAs of 66 of the 100 patients enrolled. Median National Early Warning Score was 7 in the group with no virus detected and 6.5 in the group with a respiratory viral infection (P > .05). The Fever-7 score yielded an overall AUC of 0.81 to predict a positive viral syndromic test. The optimal operating point for the Fever-7 score yielded a sensitivity of 82% with a specificity of 71%. Multivariate analysis showed that Fever-7 was a robust marker of viral infection independently of age, sex, major comorbidities and disease severity at presentation (OR [CI95%], 3.73 [2.14-6.51], P < .001). CONCLUSIONS Fever-7 is a promising host immune mRNA signature for the early identification of a respiratory viral infection in the community.
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Affiliation(s)
- Raquel Almansa
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Gerencia Regional de Salud, Salamanca, Spain.,Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Herrero-Rodríguez
- Servicio de Urgencias de Atención Primaria de Salamanca (SUAP). Gerencia de Atención Primaria de Salamanca, Gerencia Regional de salud de Castilla y León (SACyL), Salamanca, Spain.,Unidad de Investigación en Atención Primaria de Salamanca (APISAL), Instituto de investigación Biomédica de Salamanca (IBSAL), Gerencia de Atención Primaria de Salamanca, Gerencia Regional de salud de Castilla y León (SACyL), Salamanca, Spain
| | - Misericordia Martínez-Huélamo
- Servicio de Urgencias de Atención Primaria de Salamanca (SUAP). Gerencia de Atención Primaria de Salamanca, Gerencia Regional de salud de Castilla y León (SACyL), Salamanca, Spain
| | - Maria Del Pilar Vicente-Andres
- Servicio de Urgencias de Atención Primaria de Salamanca (SUAP). Gerencia de Atención Primaria de Salamanca, Gerencia Regional de salud de Castilla y León (SACyL), Salamanca, Spain
| | - Jose Angel Nieto-Barbero
- Servicio de Urgencias de Atención Primaria de Salamanca (SUAP). Gerencia de Atención Primaria de Salamanca, Gerencia Regional de salud de Castilla y León (SACyL), Salamanca, Spain
| | - Miryam Martín-Ballesteros
- Servicio de Urgencias de Atención Primaria de Salamanca (SUAP). Gerencia de Atención Primaria de Salamanca, Gerencia Regional de salud de Castilla y León (SACyL), Salamanca, Spain
| | - Maria Del Mar Rodilla-Carvajal
- Servicio de Urgencias de Atención Primaria de Salamanca (SUAP). Gerencia de Atención Primaria de Salamanca, Gerencia Regional de salud de Castilla y León (SACyL), Salamanca, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Gerencia Regional de Salud, Salamanca, Spain.,Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain
| | - Alicia Ortega
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Gerencia Regional de Salud, Salamanca, Spain.,Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain
| | - Maria Jesus Alonso-Ramos
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Gerencia Regional de Salud, Salamanca, Spain
| | | | | | | | - Jesús F Bermejo-Martin
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Gerencia Regional de Salud, Salamanca, Spain.,Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Luis García-Ortiz
- Unidad de Investigación en Atención Primaria de Salamanca (APISAL), Instituto de investigación Biomédica de Salamanca (IBSAL), Gerencia de Atención Primaria de Salamanca, Gerencia Regional de salud de Castilla y León (SACyL), Salamanca, Spain.,Departamento de Ciencias Biomédicas y del Diagnóstico, Universidad de Salamanca, Salamanca, Spain
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24
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Precit MR, He K, Mongkolrattanothai K, Moghimi B, Glucoft M, Bard JD. Impact of FilmArray™ Respiratory Panel testing on the clinical management of pediatric bone marrow transplant patients. Eur J Clin Microbiol Infect Dis 2021; 41:395-405. [PMID: 34816330 PMCID: PMC8610609 DOI: 10.1007/s10096-021-04382-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022]
Abstract
Viral respiratory tract infections cause significant morbidity in bone marrow transplant (BMT) patients. Speed and sensitivity of the FilmArray™ Respiratory Panel (FA-RP) can improve care but may prompt inappropriate testing. Studies describing FA-RP use in pediatric BMT patients are limited; we investigated FA-RP use, results, and clinical management to evaluate clinical significance of testing in pediatric BMT patients. Retrospective analysis of 671 respiratory specimens from 204 unique BMT patients between 01/01/2016 and 01/01/2019 was performed. Age, underlying diagnoses, FA-RP result, reason for FA-RP, and symptoms were abstracted. FA-RP impact on antimicrobial management, scheduled procedures, infection control measures, and hospital admission/discharge were investigated. Impacts of repeat testing were evaluated. Two hundred sixty-nine out of 671 specimens (40%) tested positive; human rhinovirus/enterovirus (hRV/hEV) was the most common (161/269, 60%). The primary reason for FA-RP was URI symptoms (402/671, 60%) with 54% testing positive. One hundred twenty-two out of 671 (18.2%) specimens were from asymptomatic patients; 14 (11.4%) tested positive. FA-RP informed antiviral initiation in 7/19 (36.8%), 7/8 (87.5%), and 5/30 (16.7%) of RSV, influenza, and human parainfluenza cases, respectively. In 11 cases, FA-RP informed azithromycin and ceftriaxone initiation, continuation, or discontinuation. BMT was delayed for three positives (two RSV, one hRV/hEV). In 22 instances, negative FA-RP cleared patients for BMT. In 70% of cases, repeats offered no new clinical information; all negative-to-positive cases had new or worsening respiratory symptoms. FA-RP was ordered on symptomatic and asymptomatic patients, provided rapid diagnosis in > 50% of symptomatic patients, and informed infection control measures for all inpatients and antiviral initiation in > 80% of influenza cases.
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Affiliation(s)
- Mimi R Precit
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA, USA.,Children's Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA, 90027, USA
| | - Kaidi He
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Los Angeles, Los Angeles, CA, USA
| | - Kanokporn Mongkolrattanothai
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Los Angeles, Los Angeles, CA, USA.,Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Babak Moghimi
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Department of Pediatrics, Division of Hematology and Oncology, Bone Marrow Transplant and Cell Therapy, Children's Hospital of Los Angeles, Los Angeles, CA, USA
| | - Marisa Glucoft
- Department of Quality Improvement & Patient Safety, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA, USA. .,Children's Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA, 90027, USA. .,Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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25
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Penela-Sánchez D, González-de-Audicana J, Armero G, Henares D, Esteva C, de-Sevilla MF, Ricart S, Jordan I, Brotons P, Cabrerizo M, Muñoz-Almagro C, Launes C. Lower Respiratory Tract Infection and Genus Enterovirus in Children Requiring Intensive Care: Clinical Manifestations and Impact of Viral Co-Infections. Viruses 2021; 13:2059. [PMID: 34696489 PMCID: PMC8541154 DOI: 10.3390/v13102059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/15/2022] Open
Abstract
Infection by rhinovirus (RV) and enterovirus (EV) in children ranges from asymptomatic infection to severe lower respiratory tract infection (LRTI). This cohort study evaluates the clinical impact of RV/EV species, alone or in codetection with other viruses, in young children with severe LRTI. Seventy-one patients aged less than 5 years and admitted to the Paediatric Intensive Care Unit (PICU) of a reference children's hospital with RV or EV (RV/EV) LRTI were prospectively included from 1/2018 to 3/2020. A commercial PCR assay for multiple respiratory pathogens was performed in respiratory specimens. In 22/71, RV/EV + respiratory syncytial virus (RSV) was found, and 18/71 had RV/EV + multiple viral detections. Patients with single RV/EV detection required invasive mechanical ventilation (IMV) as frequently as those with RSV codetection, whereas none of those with multiple viral codetections required IMV. Species were determined in 60 samples, 58 being RV. No EV-A, EV-C, or EV-D68 were detected. RV-B and EV-B were only found in patients with other respiratory virus codetections. There were not any associations between RV/EV species and severity outcomes. To conclude, RV/EV detection alone was observed in young children with severe disease, while multiple viral codetections may result in reduced clinical severity. Differences in pathogenicity between RV and EV species could not be drawn.
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Affiliation(s)
- Daniel Penela-Sánchez
- Paediatrics Department, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.P.-S.); (G.A.); (M.-F.d.-S.); (S.R.)
- Paediatrics Intensive Care Unit, Hospital Sant Joan de Déu, 08195 Barcelona, Spain;
| | - Jon González-de-Audicana
- Enterovirus and Viral Gastroenteritis Unit, Centro Nacional de Microbiología, Instituto Carlos III, 28222 Madrid, Spain; (J.G.-d.-A.); (M.C.)
| | - Georgina Armero
- Paediatrics Department, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.P.-S.); (G.A.); (M.-F.d.-S.); (S.R.)
- Paediatrics Intensive Care Unit, Hospital Sant Joan de Déu, 08195 Barcelona, Spain;
| | - Desiree Henares
- Grupo de Investigación en Enfermedades Infecciosas Pediátricas, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.H.); (C.E.); (P.B.); (C.M.-A.)
- Molecular Microbiology Department, Hospital Sant Joan de Déu, 08195 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Cristina Esteva
- Grupo de Investigación en Enfermedades Infecciosas Pediátricas, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.H.); (C.E.); (P.B.); (C.M.-A.)
- Molecular Microbiology Department, Hospital Sant Joan de Déu, 08195 Barcelona, Spain
| | - Mariona-Fernández de-Sevilla
- Paediatrics Department, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.P.-S.); (G.A.); (M.-F.d.-S.); (S.R.)
- Grupo de Investigación en Enfermedades Infecciosas Pediátricas, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.H.); (C.E.); (P.B.); (C.M.-A.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Paediatrics Department, Faculty of Medicine and Health Sciences, Universitat de Barcelona, 08007 Barcelona, Spain
| | - Silvia Ricart
- Paediatrics Department, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.P.-S.); (G.A.); (M.-F.d.-S.); (S.R.)
- Paediatrics Department, Faculty of Medicine and Health Sciences, Universitat de Barcelona, 08007 Barcelona, Spain
| | - Iolanda Jordan
- Paediatrics Intensive Care Unit, Hospital Sant Joan de Déu, 08195 Barcelona, Spain;
- Grupo de Investigación en Enfermedades Infecciosas Pediátricas, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.H.); (C.E.); (P.B.); (C.M.-A.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Paediatrics Department, Faculty of Medicine and Health Sciences, Universitat de Barcelona, 08007 Barcelona, Spain
| | - Pedro Brotons
- Grupo de Investigación en Enfermedades Infecciosas Pediátricas, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.H.); (C.E.); (P.B.); (C.M.-A.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Medicine, School of Medicine, Universitat Internacional de Catalunya, 08017 Barcelona, Spain
| | - María Cabrerizo
- Enterovirus and Viral Gastroenteritis Unit, Centro Nacional de Microbiología, Instituto Carlos III, 28222 Madrid, Spain; (J.G.-d.-A.); (M.C.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Carmen Muñoz-Almagro
- Grupo de Investigación en Enfermedades Infecciosas Pediátricas, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.H.); (C.E.); (P.B.); (C.M.-A.)
- Molecular Microbiology Department, Hospital Sant Joan de Déu, 08195 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Medicine, School of Medicine, Universitat Internacional de Catalunya, 08017 Barcelona, Spain
| | - Cristian Launes
- Paediatrics Department, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.P.-S.); (G.A.); (M.-F.d.-S.); (S.R.)
- Grupo de Investigación en Enfermedades Infecciosas Pediátricas, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.H.); (C.E.); (P.B.); (C.M.-A.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Paediatrics Department, Faculty of Medicine and Health Sciences, Universitat de Barcelona, 08007 Barcelona, Spain
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26
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Ahmad-Nejad P, Ashavaid T, Vacaflores Salinas A, Huggett J, Harris K, Linder MW, Baluchova K, Steimer W, Payne DA. Current and future challenges in quality assurance in molecular diagnostics. Clin Chim Acta 2021; 519:239-246. [PMID: 33971158 DOI: 10.1016/j.cca.2021.05.004] [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] [Received: 10/30/2020] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 02/08/2023]
Abstract
The development and performance of molecular genetic assays has required increasingly complex quality assurance in recent years and continues to pose new challenges. Quality management officers, as well as academic and technical personnel are confronted with new molecular genetic parameters, methods, changing regulatory environments, questions regarding appropriate validation, and quality control for these innovative assays that are increasingly applying quantification and/or multiplex formats. Yet, quality assurance and quality control guidelines are still not widely available or in some circumstances have become outdated. For these reasons, the need for solutions to provide test confidence continues to grow. In order to integrate new test procedures into existing quality assurance measures, the ISO 15189 guideline can serve as an orientation. The ISO 15189 guideline describes requirements for medical laboratories and thus includes those performing molecular diagnostics. This article gives an overview of the possibilities and challenges in quality assurance of molecular parameters and shows possible solutions.
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Affiliation(s)
- Parviz Ahmad-Nejad
- Institute for Medicine Laboratory Diagnostics, Centre for Clinical and Translational Research (CCTR), HELIOS University Hospital, Wuppertal, Witten/Herdecke University, Germany.
| | - Tester Ashavaid
- Department of Laboratory Medicine, P.D. Hinduja National Hospital and Medical Research Center, Mumbai, India
| | | | - Jim Huggett
- National Measurement Laboratory (NML) at LGC, Queens Rd, Teddington, TW11 0LY, United Kingdom; School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Kathryn Harris
- Microbiology Department, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Mark W Linder
- Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | - Katarina Baluchova
- OncoLab Diagnostics GmbH Technologie- und Forschungszentrum, Viktor-Kaplan-Straße 2, 2700 Wiener Neustadt, Austria
| | - Werner Steimer
- Institute for Clinical Chemistry and Pathobiochemistry, Munich University of Technology, Klinikum rechts der Isar, D-81675 Munich, Germany
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27
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Abstract
Community-acquired pneumonia (CAP) is the prominent cause of mortality and morbidity with important clinical impact across the globe. India accounts for 23 per cent of global pneumonia burden with case fatality rates between 14 and 30 per cent, and Streptococcus pneumoniae is considered a major bacterial aetiology. Emerging pathogens like Burkholderia pseudomallei is increasingly recognized as an important cause of CAP in Southeast Asian countries. Initial management in the primary care depends on clinical assessment while the hospitalized patients require combinations of clinical scores, chest radiography and various microbiological and biomarker assays. This comprehensive diagnostic approach together with additional sampling and molecular tests in selected high-risk patients should be practiced. Inappropriate therapy in CAP in hospitalized patients lengthens hospital stay and increases cost and mortality. In addition, emergence of multidrug-resistant organisms poses tough challenges in deciding empirical as well as definitive therapy. Developing local evidence on the cause and management should be a priority to improve health outcomes in CAP.
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Affiliation(s)
- Vandana Kalwaje Eshwara
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Chiranjay Mukhopadhyay
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Jordi Rello
- Department of Critical Care, Vall d'Hebron Research Institute; Clinical Research & Innovation in Pneumonia and Sepsis, Barcelona, Spain
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28
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Cassedy A, Parle-McDermott A, O’Kennedy R. Virus Detection: A Review of the Current and Emerging Molecular and Immunological Methods. Front Mol Biosci 2021; 8:637559. [PMID: 33959631 PMCID: PMC8093571 DOI: 10.3389/fmolb.2021.637559] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/01/2021] [Indexed: 12/14/2022] Open
Abstract
Viruses are ubiquitous in the environment. While many impart no deleterious effects on their hosts, several are major pathogens. This risk of pathogenicity, alongside the fact that many viruses can rapidly mutate highlights the need for suitable, rapid diagnostic measures. This review provides a critical analysis of widely used methods and examines their advantages and limitations. Currently, nucleic-acid detection and immunoassay methods are among the most popular means for quickly identifying viral infection directly from source. Nucleic acid-based detection generally offers high sensitivity, but can be time-consuming, costly, and require trained staff. The use of isothermal-based amplification systems for detection could aid in the reduction of results turnaround and equipment-associated costs, making them appealing for point-of-use applications, or when high volume/fast turnaround testing is required. Alternatively, immunoassays offer robustness and reduced costs. Furthermore, some immunoassay formats, such as those using lateral-flow technology, can generate results very rapidly. However, immunoassays typically cannot achieve comparable sensitivity to nucleic acid-based detection methods. Alongside these methods, the application of next-generation sequencing can provide highly specific results. In addition, the ability to sequence large numbers of viral genomes would provide researchers with enhanced information and assist in tracing infections.
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Affiliation(s)
- A. Cassedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | | | - R. O’Kennedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
- Hamad Bin Khalifa University, Doha, Qatar
- Qatar Foundation, Doha, Qatar
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29
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Kim YK, Lee JH, Kim SY, Ahn JY, Choi KH, Lee YH, Jang KM, Hau YS, Lee JM. Rapid Molecular Tests for Detecting Respiratory Pathogens Reduced the Use of Antibiotics in Children. Antibiotics (Basel) 2021; 10:283. [PMID: 33801828 PMCID: PMC8001485 DOI: 10.3390/antibiotics10030283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/06/2021] [Accepted: 03/07/2021] [Indexed: 12/25/2022] Open
Abstract
Multiplex polymerase chain reaction (mPCR) is increasingly being used to diagnose infections caused by respiratory pathogens in pediatric inpatient facilities. mPCR assays detect a broader array of viruses, with higher specificity and sensitivity and faster turnaround than previous assays. We adapted the FilmArray Respiratory Panel (FA-RP) for diagnosing respiratory infections. FA-RP is an in vitro mPCR assay that simultaneously and rapidly (in about 1 h) detects 20 pathogens directly from respiratory specimens. Here, we studied the clinical efficacy of FA-RP in children who underwent testing for respiratory pathogens at Yeungnam University Hospital from November 2015 to August 2018. From November 2015 to June 2016, routine mPCR testing was performed on nasopharyngeal swabs using the routine mPCR kit. From November 2016 to July 2018, mPCR testing was performed using FA-RP. A total of 321 tests by routine mPCR and 594 tests by FA-RP were included. The positive detection rates for routine mPCR and FA-RP were 71.3% and 83.3%, respectively. FA-RP reduced the lead time, waiting time, turnaround time, intravenous (IV) antibiotic use, and length of hospital stay for pediatric patients. The decreased use of antibiotics is expected to reduce antibiotic resistance in children.
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Affiliation(s)
- Yu Kyung Kim
- Department of Clinical Pathology, School of Medicine, Kyungpook National University, Daegu 41944, Korea;
| | - Jong Ho Lee
- Department of Laboratory Medicine, Yeungnam University College of Medicine, Daegu 42415, Korea;
| | - Sae Yoon Kim
- Department of Pediatrics, College of Medicine, Yeungnam University, Daegu 42415, Korea; (S.Y.K.); (J.Y.A.); (K.H.C.); (Y.H.L.); (K.M.J.)
| | - Ji Young Ahn
- Department of Pediatrics, College of Medicine, Yeungnam University, Daegu 42415, Korea; (S.Y.K.); (J.Y.A.); (K.H.C.); (Y.H.L.); (K.M.J.)
| | - Kwang Hae Choi
- Department of Pediatrics, College of Medicine, Yeungnam University, Daegu 42415, Korea; (S.Y.K.); (J.Y.A.); (K.H.C.); (Y.H.L.); (K.M.J.)
| | - Young Hwan Lee
- Department of Pediatrics, College of Medicine, Yeungnam University, Daegu 42415, Korea; (S.Y.K.); (J.Y.A.); (K.H.C.); (Y.H.L.); (K.M.J.)
| | - Kyung Mi Jang
- Department of Pediatrics, College of Medicine, Yeungnam University, Daegu 42415, Korea; (S.Y.K.); (J.Y.A.); (K.H.C.); (Y.H.L.); (K.M.J.)
| | - Yong Sauk Hau
- Department of Business Administration, School of Business, Yeungnam University, Gyeongsan 38541, Korea;
| | - Jae Min Lee
- Department of Pediatrics, College of Medicine, Yeungnam University, Daegu 42415, Korea; (S.Y.K.); (J.Y.A.); (K.H.C.); (Y.H.L.); (K.M.J.)
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Dulanto Chiang A, Dekker JP. From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics. J Infect Dis 2021; 221:S331-S340. [PMID: 31538184 DOI: 10.1093/infdis/jiz151] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Indexed: 12/13/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized multiple areas in the field of infectious diseases, from pathogen discovery to characterization of genes mediating drug resistance. Consequently, there is much anticipation that NGS technologies may be harnessed in the realm of diagnostic methods to complement or replace current culture-based and molecular microbiologic techniques. In this context, much consideration has been given to hypothesis-free, culture-independent tests that can be performed directly on primary clinical samples. The closest realizations of such universal diagnostic methods achieved to date are based on targeted amplicon and unbiased metagenomic shotgun NGS approaches. Depending on the exact details of implementation and analysis, these approaches have the potential to detect viruses, bacteria, fungi, parasites, and archaea, including organisms that were previously undiscovered and those that are uncultivatable. Shotgun metagenomics approaches additionally can provide information on the presence of virulence and resistance genetic elements. While many limitations to the use of NGS in clinical microbiology laboratories are being overcome with decreasing technology costs, expanding curated pathogen sequence databases, and better data analysis tools, there remain many challenges to the routine use and implementation of these methods. This review summarizes recent advances in applications of targeted amplicon and shotgun-based metagenomics approaches to infectious disease diagnostic methods. Technical and conceptual challenges are considered, along with expectations for future applications of these techniques.
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Affiliation(s)
- Augusto Dulanto Chiang
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
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Zhong Y, Xu F, Wu J, Schubert J, Li MM. Application of Next Generation Sequencing in Laboratory Medicine. Ann Lab Med 2021; 41:25-43. [PMID: 32829577 PMCID: PMC7443516 DOI: 10.3343/alm.2021.41.1.25] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
The rapid development of next-generation sequencing (NGS) technology, including advances in sequencing chemistry, sequencing technologies, bioinformatics, and data interpretation, has facilitated its wide clinical application in precision medicine. This review describes current sequencing technologies, including short- and long-read sequencing technologies, and highlights the clinical application of NGS in inherited diseases, oncology, and infectious diseases. We review NGS approaches and clinical diagnosis for constitutional disorders; summarize the application of U.S. Food and Drug Administration-approved NGS panels, cancer biomarkers, minimal residual disease, and liquid biopsy in clinical oncology; and consider epidemiological surveillance, identification of pathogens, and the importance of host microbiome in infectious diseases. Finally, we discuss the challenges and future perspectives of clinical NGS tests.
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Affiliation(s)
- Yiming Zhong
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
| | - Feng Xu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jinhua Wu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jeffrey Schubert
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Marilyn M. Li
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
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Liu K, Jing H, Chen Y, Zheng X, Jiang H, Kong D, Zheng Y, Chen S, Liu P, Jiang Y. Evaluation of TaqMan Array card (TAC) for the detection of 28 respiratory pathogens. BMC Infect Dis 2020; 20:820. [PMID: 33172401 PMCID: PMC7653217 DOI: 10.1186/s12879-020-05562-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/30/2020] [Indexed: 12/22/2022] Open
Abstract
Background Respiratory infections are a serious threat to human health. So, rapid detection of all respiratory pathogens can facilitate prompt treatment and prevent the deterioration of respiratory disease. Previously published primers and probes of the TaqMan array card (TAC) for respiratory pathogens are not sensitive to Chinese clinical specimens. This study aimed to develop and improve the TAC assay to detect 28 respiratory viral and bacterial pathogens in a Chinese population. Methods To improve the sensitivity, we redesigned the primers and probes, and labeled the probes with minor groove binders. The amplification efficiency, sensitivity, and specificity of the primers and probes were determined using target-gene containing standard plasmids. The detection performance of the TAC was evaluated on 754 clinical specimens and the results were compared with those from conventional methods. Results The performance of the TAC assay was evaluated using 754 clinical throat swab samples and the results were compared with those from gold-standard methods. The sensitivity and specificity were 95.4 and 96.6%, respectively. The lowest detection limit of the TAC was 10 to 100 copies/μL. Conclusions TAC is an efficient, accurate, and high-throughput approach to detecting multiple respiratory pathogens simultaneously and is a promising tool for the identification of pathogen outbreaks.
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Affiliation(s)
- Keke Liu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.,Shandong Academy of Clinical Medicine, Shandong Provincial Hospital, Jinan, 250021, China
| | - Hongbo Jing
- Department of Laboratory Medicine, Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Ying Chen
- School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing, 100048, China
| | - Xin Zheng
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Decong Kong
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yvling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Shuiping Chen
- Department of Laboratory Medicine, the Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China.
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
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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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The Evolving Role of the Clinical Microbiology Laboratory in Identifying Resistance in Gram-Negative Bacteria: An Update. Infect Dis Clin North Am 2020; 34:659-676. [PMID: 33011047 DOI: 10.1016/j.idc.2020.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The evolution of resistance to antimicrobial agents in gram-negatives has challenged the role of the clinical microbiology laboratory to implement new methods for their timely detection. Recent development has enabled the use of novel methods for more rapid pathogen identification, antimicrobial susceptibility testing, and detection of resistance markers. Commonly used methods improve the rapidity of resistance detection from both cultured bacteria and specimens. This review focuses on the commercially available systems available together with their technical performance and possible clinical impact.
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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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Jeong S, Park MJ, Song W, Kim HS. Advances in laboratory assays for detecting human metapneumovirus. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:608. [PMID: 32566634 PMCID: PMC7290561 DOI: 10.21037/atm.2019.12.42] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Human metapneumovirus (HMPV) is one of the major causes of acute respiratory tract infection (ARI) and shows high morbidity and mortality, particularly in children and immunocompromised patients. Various methods for detecting HMPV have been developed and applied in clinical laboratories. When reviewing the literature, we found that polymerase chain reaction (PCR)-based assays have been most frequently and consistently used to detect HMPV. The most commonly used method was multiplex reverse transcriptase-PCR (RT-PCR; 57.4%), followed by real-time RT-PCR (38.3%). Multiplex RT-PCR became the more popular method in 2011-2019 (69.7%), in contrast to 2001-2009 (28.6%). The advent of multiplex PCR in detecting broader viral pathogens in one run and coinfected viruses influenced the change in user preference. Further, newly developed microarray technologies and ionization mass spectrometry were introduced in 2011-2019. Viral culture (including shell vial assays) and fluorescent immunoassays (with or without culture) were once the mainstays. However, the percentage of studies employing culture and fluorescent immunoassays decreased from 21.4% in 2001-2010 to 15.2% in 2011-2019. Meanwhile, the use of PCR-based methods of HMPV detection increased from 78.6% in 2001-2010 to 84.8% in 2011-2019. The increase in PCR-based methods might have occurred because PCR methods demonstrated better diagnostic performance, shorter hands-on and run times, less hazards to laboratory personnel, and more reliable results than traditional methods. When using these assays, it is important to acquire a comprehensive understanding of the principles, advantages, disadvantages, and precautions for data interpretation. In the future, the combination of nanotechnology and advanced genetic platforms such as next-generation sequencing will benefit patients with HMPV infection by facilitating efficient therapeutic intervention. Analytical and clinical validation are required before using new techniques in clinical laboratories.
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Affiliation(s)
- Seri Jeong
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Min-Jeong Park
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Hyon-Suk Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
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Edin A, Eilers H, Allard A. Evaluation of the Biofire Filmarray Pneumonia panel plus for lower respiratory tract infections. Infect Dis (Lond) 2020; 52:479-488. [PMID: 32319831 DOI: 10.1080/23744235.2020.1755053] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Background: Standard diagnostic methods for lower respiratory tract infections are currently too slow and insensitive to guide early clinical decisions concerning treatment and isolation. Syndrome-specific, diagnostic panels have potential to provide information about aetiology quickly. Available panels have been of limited use in lower respiratory tract infections due to slow turn-around-time, lack of quantification of important pathogens and lack of detection of resistance genes.Materials/methods: We evaluated the newly developed Biofire® Filmarray® Pneumonia Panel plus (Biomérieux). Eighty-eight consecutive lower respiratory tract samples were analyzed by both standard microbiological methods, as requested by the referring clinician, and by the panel. The agreement with standard methods, empirical treatment coverage and possible impact on isolation practices were assessed by comparing the results from standard diagnostic methods with the panel results in relation to clinical data and information of antimicrobial therapy.Results: Both qualitative and semi-quantitative results from the panel generally displayed good agreement with standard methods and by combining methods, a possible aetiology was detected in 73% of patients. Due to the panel approach, the panel detected viruses more frequently. In 25% of the 60 patients assessed for empirical treatment coverage, a pathogen not covered by current therapy was detected and in 30% of in-house patients the panel results were found to potentially influence clinical decisions related to isolation care.Conclusions: The new diagnostic panel shows promise in improving aetiological diagnostics of lower respiratory tract infections. Correctly applied it has potential to offer support in clinical decision-making within hours of sampling.
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Affiliation(s)
- Alicia Edin
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden.,Anesthesiology and Intensive Care Medicine, Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden
| | - Hinnerk Eilers
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Annika Allard
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
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Kutty PK, Jain S, Taylor TH, Bramley AM, Diaz MH, Ampofo K, Arnold SR, Williams DJ, Edwards KM, McCullers JA, Pavia AT, Winchell JM, Schrag SJ, Hicks LA. Mycoplasma pneumoniae Among Children Hospitalized With Community-acquired Pneumonia. Clin Infect Dis 2020; 68:5-12. [PMID: 29788037 DOI: 10.1093/cid/ciy419] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 05/14/2018] [Indexed: 12/22/2022] Open
Abstract
Background The epidemiology of Mycoplasma pneumoniae (Mp) among US children (<18 years) hospitalized with community-acquired pneumonia (CAP) is poorly understood. Methods In the Etiology of Pneumonia in the Community study, we prospectively enrolled 2254 children hospitalized with radiographically confirmed pneumonia from January 2010-June 2012 and tested nasopharyngeal/oropharyngeal swabs for Mp using real-time polymerase chain reaction (PCR). Clinical and epidemiological features of Mp PCR-positive and -negative children were compared using logistic regression. Macrolide susceptibility was assessed by genotyping isolates. Results One hundred and eighty two (8%) children were Mp PCR-positive (median age, 7 years); 12% required intensive care and 26% had pleural effusion. No in-hospital deaths occurred. Macrolide resistance was found in 4% (6/169) isolates. Of 178 (98%) Mp PCR-positive children tested for copathogens, 50 (28%) had ≥1 copathogen detected. Variables significantly associated with higher odds of Mp detection included age (10-17 years: adjusted odds ratio [aOR], 10.7 [95% confidence interval {CI}, 5.4-21.1] and 5-9 years: aOR, 6.4 [95% CI, 3.4-12.1] vs 2-4 years), outpatient antibiotics ≤5 days preadmission (aOR, 2.3 [95% CI, 1.5-3.5]), and copathogen detection (aOR, 2.1 [95% CI, 1.3-3.3]). Clinical characteristics were non-specific. Conclusions Usually considered as a mild respiratory infection, Mp was the most commonly detected bacteria among children aged ≥5 years hospitalized with CAP, one-quarter of whom had codetections. Although associated with clinically nonspecific symptoms, there was a need for intensive care in some cases. Mycoplasma pneumoniae should be included in the differential diagnosis for school-aged children hospitalized with CAP.
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Affiliation(s)
- Preeta K Kutty
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Seema Jain
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Thomas H Taylor
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Anna M Bramley
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Maureen H Diaz
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Krow Ampofo
- University of Utah Health Sciences Center, Salt Lake City
| | - Sandra R Arnold
- Le Bonheur Children's Hospital, Memphis.,University of Tennessee Health Science Center, Memphis
| | - Derek J Williams
- Vanderbilt University Medical Center, Nashville.,Monroe Carell Jr Children's Hospital at Vanderbilt, Nashville
| | - Kathryn M Edwards
- Vanderbilt University Medical Center, Nashville.,Monroe Carell Jr Children's Hospital at Vanderbilt, Nashville
| | - Jonathan A McCullers
- Le Bonheur Children's Hospital, Memphis.,University of Tennessee Health Science Center, Memphis.,St Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew T Pavia
- University of Utah Health Sciences Center, Salt Lake City
| | | | | | - Lauri A Hicks
- Centers for Disease Control and Prevention, Atlanta, Georgia
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Performance evaluation of the Panther Fusion® respiratory tract panel. J Clin Virol 2019; 123:104232. [PMID: 31869661 PMCID: PMC7172494 DOI: 10.1016/j.jcv.2019.104232] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/29/2019] [Accepted: 12/09/2019] [Indexed: 12/21/2022]
Abstract
Clinical specificity of Panther Fusion® is between 96 %–100 %, compared to LDT. Clinical sensitivity Panther Fusion® is between 71.9 %–100 %, compared to LDT. Overall linear regression showed good correlations between LDT and Panther Fusion® for all viruses, except RV and PIV-4. The Panther Fusion® provides a random-access system with continuous loading and shorter sample-to-answer times compared to LDT.
Background Respiratory tract infections are among the most common infections during winter season. Rapid diagnostics is required for clinical decision making regarding isolation of patients and appropriate therapy. Objectives The aim of this study was to evaluate the analytical and clinical performance characteristics of the Panther Fusion® respiratory panel using published laboratory-developed real-time PCR assays (LDT). Study design Analytical sensitivity of Panther Fusion® Flu A/B/RSV was assessed by testing dilutions of cell culture isolates. Clinical performance assessment included the complete Panther Fusion® respiratory panel (Flu-A/B/RSV, PIV 1-4 and AdV/hMPV/RV) and consisted of a retrospective and a prospective study-arm. The retrospective evaluation included 201, stored (−80 °C) samples collected between February 2006 and January 2017. Prospective evaluation was performed on 1045 unselected pretreated respiratory tract samples from patients presented to our hospital between November 2017 and May 2018. Results Analytical sensitivity was generally slightly lower for the Panther Fusion® assays. Clinical specificity and sensitivity was between 96 %–100 % and 71.9 %–100 %, respectively. Discrepant results were found in 146 samples of which 88 samples tested LDT positive / Panther Fusion® negative and 58 samples were LDT negative / Panther Fusion® positive. A total of ten discrepant samples with Ct-values <30 were sequenced to confirm the presence of 7 RV-C not-detected by LDT and 1 RV-A and 2 ADV-2 not detected by Panther Fusion®. Conclusions The Panther Fusion® provides a random-access system with continuous loading and much shorter sample-to-answer times compared to LDT, albeit with a slightly less clinical sensitivity compared to the LDT.
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40
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Combining Procalcitonin and Rapid Multiplex Respiratory Virus Testing for Antibiotic Stewardship in Older Adult Patients With Severe Acute Respiratory Infection. J Am Med Dir Assoc 2019; 21:62-67. [PMID: 31791902 PMCID: PMC7106143 DOI: 10.1016/j.jamda.2019.09.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 09/14/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Virus infection is underevaluated in older adults with severe acute respiratory infections (SARIs). We aimed to evaluate the clinical impact of combining point-of-care molecular viral test and serum procalcitonin (PCT) level for antibiotic stewardship in the emergency department (ED). DESIGN A prospective twin-center cohort study was conducted between January 2017 and March 2018. SETTING AND PARTICIPANTS Older adult patients who presented to the ED with SARIs received a rapid molecular test for 17 respiratory viruses and a PCT test. MEASURES To evaluate the clinical impact, we compared the outcomes of SARI patients between the experimental cohort and a propensity score-matched historical cohort. The primary outcome was the proportion of antibiotics discontinuation or de-escalation in the ED. The secondary outcomes included duration of intravenous antibiotics, length of hospital stay, and mortality. RESULTS A total of 676 patients were included, of which 169 patients were in the experimental group and 507 patients were in the control group. More than one-fourth (27.9%) of the patients in the experimental group tested positive for virus. Compared with controls, the experimental group had a significantly higher proportion of antibiotics discontinuation or de-escalation in the ED (26.0% vs 16.1%, P = .007), neuraminidase inhibitor uses (8.9% vs 0.6%, P < .001), and shorter duration of intravenous antibiotics (10.0 vs 14.5 days, P < .001). CONCLUSIONS AND IMPLICATIONS Combining rapid viral surveillance and PCT test is a useful strategy for early detection of potential viral epidemics and antibiotic stewardship. Clustered viral respiratory infections in a nursing home is common. Patients transferred from nursing homes to ED may benefit from this approach.
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Lee SH, Ruan SY, Pan SC, Lee TF, Chien JY, Hsueh PR. Performance of a multiplex PCR pneumonia panel for the identification of respiratory pathogens and the main determinants of resistance from the lower respiratory tract specimens of adult patients in intensive care units. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2019; 52:920-928. [PMID: 31806539 PMCID: PMC7185395 DOI: 10.1016/j.jmii.2019.10.009] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/27/2019] [Accepted: 10/27/2019] [Indexed: 11/16/2022]
Abstract
Background Timely diagnostic investigation to establish the microbial etiology of pneumonia is essential to ensure the administration of effective antibiotic therapy to individual patients. Methods We evaluated a multiplex PCR assay panel, the FilmArray® pneumonia panel (FilmArray PP, BioFire Diagnostics), for detection of 35 respiratory pathogens and resistance determinants and compared the performance of the standard-of-care test in intensive care unit patients with lower respiratory tract infections. Results Among the 59 endotracheal aspirates and bronchoalveolar lavage specimens obtained from 51 adult patients, FilmArray PP was effective in detecting respiratory bacterial pathogens with an overall positive percent agreement of 90% (95% confidence interval [CI], 73.5–97.9%) and negative percent agreement of 97.4% (95% CI, 96.0–98.4%). FilmArray PP semi-quantitative reporting demonstrated a concordance rate of 53.6% for the culture-positive specimens and 86.3% for the culture-negative specimens. FilmArray PP detected 16 viral targets, whereas the conventional viral isolation failed, except influenza A, which showed 100% concordance with PCR. Coinfections were detected in 42.3% of the specimens. Substantial discrepancies were observed in identifying antimicrobial resistance gene targets and in the susceptibility testing. However, FilmArray PP may still be useful at the early stage of pneumonia before culture and susceptibility test reports are available. Consequently, the results of FilmArray PP might alter the antibiotic prescription in 40.7% of the patients. Conclusions FilmArray PP offers a rapid and sensitive diagnostic method for lower respiratory tract infections. However, clinical correlation is advised to determine its significance in interpreting multiple pathogens and detection of genes involved in antimicrobial resistance.
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Affiliation(s)
- Sze Hwei Lee
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Sheng-Yuan Ruan
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Sung-Ching Pan
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tai-Fen Lee
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jung-Yien Chien
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
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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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Varon F, Torres-Caro C, Herrera-Diaz C, Ali A, Hernández-Parra A, Aguirre-Franco C, Uribe-Hernández AM. Microbiological characterization of severe exacerbations in Chronic Obstructive Pulmonary Disease (COPD) in patients admitted to the ICU with or without associated pneumonia: A retrospective cross-sectional study. INFECTIO 2019. [DOI: 10.22354/in.v23i4.803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Meena JP, Brijwal M, Seth R, Gupta AK, Jethani J, Kapil A, Jat KR, Choudhary A, Kabra SK, Dwivedi SN, Dar L. Prevalence and clinical outcome of respiratory viral infections among children with cancer and febrile neutropenia. Pediatr Hematol Oncol 2019; 36:330-343. [PMID: 31512959 DOI: 10.1080/08880018.2019.1631920] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Background: The role of respiratory viruses (RV) in children with cancer having febrile neutropenic episodes has not been well studied. The objectives of our study were to investigate the prevalence and clinical outcomes of Respiratory viral infection (RVI). Methods: Children with cancer and febrile neutropenia (FN) having acute respiratory infections (ARI) were considered as cases and febrile neutropenic cancer patients without ARI were considered as controls. A throat swab sample was obtained for the detection of 21-respiratory pathogens. Results: A total of 81 episodes of FN in cases and 37 episodes of FN in controls were included. Prevalence of RVI (at least 1 RV) was seen in 76.5% of cases and 48.6% of controls (p = 0.005). The mixed-respiratory viruses (co-infections of ≥2 viruses) were seen only in cases (26%) (p = 0.00). Rhinovirus (36.8%) and respiratory syncytial virus (13.6%) were the most frequently detected viruses. Median duration of fever before presentation was more in cases with RVI compared to without RVI [2 (1-5) days vs 1 (1-5) day (p = 0.012)]. The median total duration of febrile period was 4 (IQR, 3-6) days in cases with RVI and 3 (IQR, 1-4) days in cases without RVI (p = 0.005). The median duration of antibiotic days were longer in cases with RVI as compared to patients without RVI [9 (IQR, 7-17) days vs 7 (IQR, 6-10) days (p = 0.046)] respectively. Conclusion: There was high prevalence of RVI in children with cancer and FN; more in association with ARI. The RVI were associated with prolonged febrile period and days of antibiotics therapy.
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Affiliation(s)
- Jagdish Prasad Meena
- Department of Pediatrics, All India Institute of Medical Sciences , New Delhi , India
| | - Megha Brijwal
- Department of Microbiology, All India Institute of Medical Sciences , New Delhi , India
| | - Rachna Seth
- Department of Pediatrics, All India Institute of Medical Sciences , New Delhi , India
| | - Aditya Kumar Gupta
- Department of Pediatrics, All India Institute of Medical Sciences , New Delhi , India
| | - Jyoti Jethani
- Department of Microbiology, All India Institute of Medical Sciences , New Delhi , India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences , New Delhi , India
| | - Kana Ram Jat
- Department of Pediatrics, All India Institute of Medical Sciences , New Delhi , India
| | - Aashish Choudhary
- Department of Microbiology, All India Institute of Medical Sciences , New Delhi , India
| | - S K Kabra
- Department of Pediatrics, All India Institute of Medical Sciences , New Delhi , India
| | - S N Dwivedi
- Department of Biostatistics, All India Institute of Medical Sciences , New Delhi , India
| | - Lalit Dar
- Department of Microbiology, All India Institute of Medical Sciences , New Delhi , India
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Zhang HC, Ai JW, Cui P, Zhu YM, Hong-Long W, Li YJ, Zhang WH. Incremental value of metagenomic next generation sequencing for the diagnosis of suspected focal infection in adults. J Infect 2019; 79:419-425. [PMID: 31442461 DOI: 10.1016/j.jinf.2019.08.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/15/2019] [Accepted: 08/18/2019] [Indexed: 12/22/2022]
Abstract
OBJECTIVES Microbiological diagnosis is essential during clinical management of focal infections. Metagenomic next generation sequencing (mNGS) has been reported as a promising diagnostic tool in infectious diseases. However, little is known about the clinical utility of mNGS in focal infections. METHODS We conducted a single-center retrospective study to investigate impact of mNGS on focal infection diagnosis and compared it with conventional methods, including culture, pathological examination, Xpert MTB/RIF, etc. 98 suspected focal infections cases were enrolled, and medical records were reviewed to determine their rates of detection, time-to-identification, and clinical outcomes. RESULTS mNGS showed a satisfying diagnostic positive percent agreement of 86.30% (95% CI: 75.79-92.88%) in a variety of tissues, compared to 45.21% (95% CI: 33.68-57.24%) for culture and 57.53% (95% CI: 45.43-68.84%)f for conventional methods (p < 0.0125), and detected an extra 34 pathogenic microorganisms. Time requirement for pathogen identification using mNGS ranges from 31 h to 55 h, which showed an advantage over culture. (82.36 h; 95%CI: 65.83, 98.89; P < 0.05) CONCLUSIONS: mNGS showed promising potential in pathogenic diagnosis during focal infections and might enable clinicians to make more timely and targeted therapeutic decisions.
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Affiliation(s)
- Hao-Cheng Zhang
- Department of Infectious Disease, Huashan Hospital of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China
| | - Jing-Wen Ai
- Department of Infectious Disease, Huashan Hospital of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China
| | - Peng Cui
- Department of Infectious Disease, Huashan Hospital of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China
| | - Yi-Min Zhu
- Department of Infectious Disease, Huashan Hospital of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China
| | - Wu Hong-Long
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Yong-Jun Li
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Wen-Hong Zhang
- Department of Infectious Disease, Huashan Hospital of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China.
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Wen S, Lv F, Chen X, Zhu L, Li H, Lin L, Zhang H. Application of a nucleic acid-based multiplex kit to identify viral and atypical bacterial aetiology of lower respiratory tract infection in hospitalized children. J Med Microbiol 2019; 68:1211-1218. [PMID: 31225788 DOI: 10.1099/jmm.0.001006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Shunhang Wen
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Fangfang Lv
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Xiaofang Chen
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Lili Zhu
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Haiyan Li
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Li Lin
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Hailin Zhang
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
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Fulminant myocarditis due to the influenza B virus in adults: Report of two cases and literature review. BIOMEDICA 2019; 39:11-19. [PMID: 31529829 DOI: 10.7705/biomedica.v39i3.4645] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Indexed: 11/21/2022]
Abstract
La miocarditis es una enfermedad inflamatoria del miocardio. Las infecciones virales son la causa más común, aunque también puede deberse a reacciones de hipersensibilidad y de etiología autoinmunitaria, entre otras. El espectro clínico de la enfermedad es variado y comprende desde un curso asintomático, seguido de dolor torácico, arritmias y falla cardiaca aguda, hasta un cuadro fulminante. El término 'fulminante' se refiere al desarrollo de un shock cardiogénico con necesidad de soporte vasopresor e inotrópico o dispositivos de asistencia circulatoria, ya sea oxigenación por membrana extracorpórea o balón de contrapulsación intraaórtico. Cerca del 10 % de los casos de falla cardiaca por miocarditis corresponde a miocarditis fulminante. La miocarditis por influenza se considera una condición infrecuente; no obstante, su incidencia ha aumentado desde el 2009 a raíz de la pandemia de influenza por el virus AH1N1. Por su parte, la miocarditis por influenza de tipo B sigue siendo una condición infrecuente. Se describen aquí dos casos confirmados de miocarditis fulminante por el virus de la influenza B atendidos en un centro cardiovascular, que requirieron dispositivos de asistencia circulatoria mecánica.
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Liapikou A, Cillóniz C, Torres A. Emerging strategies for the noninvasive diagnosis of nosocomial pneumonia. Expert Rev Anti Infect Ther 2019; 17:523-533. [PMID: 31237462 PMCID: PMC7103721 DOI: 10.1080/14787210.2019.1635010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Introduction: Hospital-acquired pneumonia is a common and therapeutically challenging diagnosis that can lead to severe sepsis, critical illness, and respiratory failure. In this review, we focus on efforts to enhance microbiological diagnosis of hospital-acquired pneumonia, including ventilator-associated pneumonia. Areas covered: A systematic literature review was conducted by searching Medline from inception to December 2018, including hand-searching of the reference lists for additional studies. The search strategy comprised the following common search terms: hospital pneumonia OR nosocomial pneumonia OR noninvasive OR molecular diagnostic tests (OR point-of-care systems OR VOC [i.e. volatile organic compounds]) OR rapid (or simple or quick test), including brand names for the most common commercial tests. Expert opinion: In recent years, the microbiological diagnosis of respiratory pathogens has improved significantly by the development and implementation of molecular diagnostic tests for pneumonia. Real-time polymerase chain reaction, hybridization, and mass spectrometry-based platforms dominate the scene, with microarray-based assays, multiplex polymerase chain reaction, and MALDI-TOF mass spectrometry capable of detecting the determinants of antimicrobial resistance (mainly β-lactamase genes). Introducing these assays into routine clinical practice for rapid identification of the causative microbes and their resistance patterns could transform the care of pneumonia, improving antimicrobial selection, de-escalation, and stewardship.
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Affiliation(s)
- Adamantia Liapikou
- a 6th Respiratory Department , Sotiria Chest Diseases Hospital , Athens , Greece
| | - Catia Cillóniz
- b Servei de Pneumologia , Institut Clinic del Tòrax, Hospital Clinic, Barcelona, IDIBAPS, CIBER Enfermedades Respiratorias, University of Barcelona , Barcelona , Spain
| | - Antoni Torres
- b Servei de Pneumologia , Institut Clinic del Tòrax, Hospital Clinic, Barcelona, IDIBAPS, CIBER Enfermedades Respiratorias, University of Barcelona , Barcelona , Spain
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Kesteman T, Ghassani A, Hajjar C, Picot V, Osman M, Alnajjar Z, Komurian-Pradel F, Messaoudi M, Pouzol S, Soulaiman HG, Vanhems P, Ramilo O, Karam-Sarkis D, Najjar-Pellet J, Hamze M, Endtz H. Investigating Pneumonia Etiology Among Refugees and the Lebanese population (PEARL): A study protocol. Gates Open Res 2019; 2:19. [PMID: 33103065 PMCID: PMC7569241 DOI: 10.12688/gatesopenres.12811.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2019] [Indexed: 11/20/2022] Open
Abstract
Background: Community-acquired pneumonia (CAP), a leading cause of mortality, mainly affects children in developing countries. The harsh circumstances experienced by refugees include various factors associated with respiratory pathogen transmission, and clinical progression of CAP. Consequently, the etiology of CAP in humanitarian crisis situations may differ to that of settled populations, which would impact appropriate case management. Therefore, the Pneumonia Etiology Among Refugees and the Lebanese population (PEARL) study was initiated with the objective of identifying the causal pathogenic microorganisms in the respiratory tract of children and adults from both the refugee and host country population presenting with signs of CAP during a humanitarian crisis. Methods: PEARL, a prospective, multicentric, case-control study, will be conducted at four primary healthcare facilities in Tripoli and the Bekaa valley over 15 months (including two high-transmission seasons/winters). Sociodemographic and medical data, and biological samples will be collected from at least 600 CAP cases and 600 controls. Nasopharyngeal swabs, sputum, urine and blood samples will be analyzed at five clinical pathology laboratories in Lebanon to identify the bacterial and viral etiological agents of CAP. Transcriptomic profiling of host leukocytes will be performed. Conclusions: PEARL is an original observational study that will provide important new information on the etiology of pneumonia among refugees, which may improve case management, help design antimicrobial stewardship interventions, and reduce morbidity and mortality due to CAP in a humanitarian crisis.
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Affiliation(s)
| | | | - Crystel Hajjar
- Faculté de Pharmacie, Université Saint-Joseph, Beirut, Lebanon
| | | | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement, Lebanese University, Tripoli, Lebanon
| | | | | | | | | | | | | | - Philippe Vanhems
- Infection Control and Epidemiology Unit, Edouard Herriot Hospital, Hospices Civils de Lyon, Lyon, 69002, France
| | - Octavio Ramilo
- Nationwide Childrens' Hospital and the Ohio State University College of Medicine, Columbus, OH, 43205, USA
| | - Dolla Karam-Sarkis
- Laboratoire des Agents Pathogènes, Faculté de Pharmacie, Université Saint-Joseph, Beirut, Lebanon.,Laboratoire Rodolphe Mérieux, Université Saint-Joseph, Beirut, Lebanon
| | | | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement, Lebanese University, Tripoli, Lebanon
| | - Hubert Endtz
- Fondation Mérieux, Lyon, 69002, France.,Erasmus Medical Center, Rotterdam, The Netherlands
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Visseaux B, Armand-Lefèvre L. Approche syndromique multiplexe en réanimation. MEDECINE INTENSIVE REANIMATION 2019. [DOI: 10.3166/rea-2019-0109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Le développement récent des nouveaux tests de diagnostic rapide par PCR multiplexe à visée syndromique, capables de détecter plusieurs dizaines de pathogènes en quelques heures, a entraîné un changement de paradigme en microbiologie et en pratique clinique. Plusieurs d’entre eux, comme les panels pour détecter les germes en cause dans les bactériémies, les infections respiratoires hautes ou basses et les méningoencéphalites, sont déjà disponibles et peuvent apporter une aide dans le diagnostic des infections chez les patients de réanimation. Bien que ces nouvelles techniques présentent des avantages évidents pour le dénombrement de micro-organismes et parfois pour la détection simultanée de gènes de résistance, pour les délais d’exécution et de rendus de résultats, elles présentent cependant certains défis, comme l’évaluation de leurs performances réelles, leur coût très élevé, le choix des stratégies d’utilisation et l’interprétation clinicobiologique des résultats. Dans cet article, nous avons passé en revue les différents tests qui peuvent ou pourront aider les réanimateurs dans leur pratique quotidienne, relevé leurs limites et leur impact bénéfique potentiel sur le soin des patients.
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