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Duta TF, Iqhrammullah M. Can bacterial culture be used as a golden standard for diagnostic research of multiplex PCR? Implications to its reporting in meta-analysis. Anaesth Crit Care Pain Med 2024; 43:101399. [PMID: 38821158 DOI: 10.1016/j.accpm.2024.101399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 06/02/2024]
Affiliation(s)
- Teuku Fais Duta
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
| | - Muhammad Iqhrammullah
- Postgraduate Program of Public Health, Universitas Muhammadiyah Aceh, Banda Aceh, Indonesia.
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2
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Srivastava S, Sharad N, Kiro VV, Ningombam A, Shrivastava S, Farooque K, Mathur P. Utility of a multiplex pathogen detection system directly from respiratory specimens for treatment and diagnostic stewardship. Microbiol Spectr 2024; 12:e0375923. [PMID: 38712971 PMCID: PMC11237763 DOI: 10.1128/spectrum.03759-23] [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: 10/23/2023] [Accepted: 03/29/2024] [Indexed: 05/08/2024] Open
Abstract
The availability of syndrome-based panels for various ailments has widened the scope of diagnostics in many clinical settings. These panels can detect a multitude of pathogens responsible for a particular condition, which can lead to a timely diagnosis and better treatment outcomes. In contrast to traditional identification methods based on pathogen growth on culture, syndrome-based panels offer a quicker diagnosis, which can be especially beneficial in situations requiring urgent care, such as intensive care units. One such panel is the Biofire Filmarray Pneumonia plus Panel (BFP), which we have compared against microbiological culture and identification. The lower respiratory samples from patients were tested with BFP, culture, and identification with culture considered the gold standard. The phenotypic antibiotic susceptibility results (Vitek 2) were compared with the antimicrobial resistance (AMR) genes detected in BFP. Statistical analysis was carried out using GraphPad 7.0 and MS Excel (Microsoft Inc.). The results showed a positive percent agreement of 100% and a negative percent agreement of 47.8% with an overall agreement of 76.72% compared to culture. BFP was better at identifying fastidious bacteria, and the agreement with culture was higher for high bacterial identification numbers (107 and 106). There was also a correlation between the number of pathogens detected and growth in culture. Carbapenemase genes were detected in around 80% of phenotypically resistant samples and correlated with in-house PCR 60% of the time. Hence, BFP results need to be interpreted with caution especially when multiple pathogens are detected. Similarly, the presence or absence of AMR genes should be used to guide the therapy while being watchful of unusual resistance or susceptibility. The cost constraints and low throughput call for patient selection criteria and prioritization in emergency or resource-limited conditions.IMPORTANCEApplication of syndrome-based panels in clinical microbiology is of huge support in infectious conditions requiring urgent interventions, such as pneumonia. Interpreting the results requires caution; hence, we have compared the results obtained from Biofire Filmarray Pneumonia plus Panel with standard microbiological methods.
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Affiliation(s)
| | - Neha Sharad
- Department of Microbiology, AIIMS, New Delhi, India
| | | | - Aparna Ningombam
- Department of Laboratory Medicine, JPNATC, AIIMS, New Delhi, India
| | | | | | - Purva Mathur
- Department of Laboratory Medicine, JPNATC, AIIMS, New Delhi, India
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3
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Gavalda M, Fullana MI, Ferre A, Peña RR, Armendariz J, Torrallardona O, Magraner A, Lorenzo A, García C, Mut G, Planas L, Iglesias C, Fraile-Ribot P, Macia Romero MD, Riera M, García-Gasalla M. Clinical Characteristics and Microorganisms Isolated in Community-Acquired Pneumonia in the COVID-19 Period. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2024; 2024:5948747. [PMID: 38532828 PMCID: PMC10965275 DOI: 10.1155/2024/5948747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 01/15/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
Introduction Community-acquired pneumonia is a leading cause of mortality and hospital admissions. The aetiology remains unknown in 30-65% of the cases. Molecular tests are available for multiple pathogen detection and are under research to improve the causal diagnosis. Methods We carried out a prospective study to describe the clinical characteristics and aetiology of community-acquired pneumonia during the COVID-19 pandemic and to assess the diagnostic effectivity of the microbiological tests, including a molecular test of respiratory pathogens (FilmArray™ bioMérieux). Results From the 1st of February 2021 until the 31st of March 2022, 225 patients were included. Failure in microorganism identification occurred in approximately 70% of patients. Streptococcus pneumoniae was the most common isolate. There were 5 cases of viral pneumonia. The tested FilmArray exhibited a low positivity rate of 7% and mainly aided in the diagnosis of viral coinfections. Conclusions Despite our extensive diagnostic protocol, there is still a low rate of microorganism identification. We have observed a reduction in influenza and other viral pneumoniae during the COVID-19 pandemic. Having a high NEWS2 score on arrival at the emergency department, an active oncohematological disease or chronic neurological conditions and a positive microbiological test result were related to worse outcomes. Further research is needed to determine the role of molecular tests in the microbiological diagnosis of pneumonia.
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Affiliation(s)
- Meritxell Gavalda
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Maria Isabel Fullana
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Adrià Ferre
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Rebecca Rowena Peña
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Julen Armendariz
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Orla Torrallardona
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Aina Magraner
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Alejandro Lorenzo
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Carles García
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Gemma Mut
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Lluís Planas
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Carla Iglesias
- Microbiology Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Pablo Fraile-Ribot
- Microbiology Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
- Fundació Institut d'Investigació Sanitària Illes Balears (IdISBa), Illes Balears, Palma, Spain
| | - Maria Dolores Macia Romero
- Microbiology Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
- Fundació Institut d'Investigació Sanitària Illes Balears (IdISBa), Illes Balears, Palma, Spain
- Universitat de les Illes Balears, Illes Balears, Palma, Spain
| | - Melchor Riera
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
- Fundació Institut d'Investigació Sanitària Illes Balears (IdISBa), Illes Balears, Palma, Spain
- Universitat de les Illes Balears, Illes Balears, Palma, Spain
| | - Mercedes García-Gasalla
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
- Fundació Institut d'Investigació Sanitària Illes Balears (IdISBa), Illes Balears, Palma, Spain
- Universitat de les Illes Balears, Illes Balears, Palma, Spain
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4
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Søgaard KK, Hinic V, Goldenberger D, Gensch A, Schweitzer M, Bättig V, Siegemund M, Bassetti S, Bingisser R, Tamm M, Battegay M, Weisser M, Stolz D, Khanna N, Egli A. Evaluation of the clinical relevance of the Biofire © FilmArray pneumonia panel among hospitalized patients. Infection 2024; 52:173-181. [PMID: 37572241 PMCID: PMC10810975 DOI: 10.1007/s15010-023-02080-1] [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: 04/04/2023] [Accepted: 07/27/2023] [Indexed: 08/14/2023]
Abstract
PURPOSE Panel PCR tests provide rapid pathogen identification. However, their diagnostic performance is unclear. We assessed the performance of the Biofire© FilmArray pneumonia (PN)-panel against standard culture in broncho-alveolar lavage (BAL) samples. METHODS Setting: University Hospital Basel (February 2019 to July 2020), including hospitalized patients with a BAL (± pneumonia). We determined sensitivity and specificity of the PN-panel against standard culture. Using univariate logistic regression, we calculated odds ratios (OR) for pneumonia according to PN-panel and culture status, stratifying by chronic pulmonary disease. We calculated ORs for pneumonia for different pathogens to estimate the clinical relevance. RESULTS We included 840 adult patients, 60% were males, median age was 68 years, 35% had chronic pulmonary disease, 21% had pneumonia, and 36% had recent antibiotic use. In 1078 BAL samples, bacterial pathogens were detected in 36% and 16% with PN-panel and culture, respectively. The overall sensitivity and specificity of the PN-panel was high, whereas the positive predictive value was low. The OR of pneumonia was 1.1 (95% CI 0.7-1.6) for PN-panel-positive only; 2.6 (95% CI 1.3-5.3) for culture-positive only, and 1.6 (95% CI 1.0-2.4) for PN-panel and culture-positive. The detection rate of Haemophilus influenzae, Staphylococcus aureus, and Moraxella catarrhalis in the PN-panel was high but not associated with pneumonia. CONCLUSION While sensitivity and specificity of PN-panel are high compared to culture, pathogen detection did not correlate well with a pneumonia diagnosis. Patients with culture-positive BAL had the highest OR for pneumonia-thus the impact of the PN-panel on clinical management needs further evaluation in randomized controlled trials.
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Affiliation(s)
- Kirstine K Søgaard
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031, Basel, Switzerland
- Department of Biomedicine, Applied Microbiology Research, University of Basel, Basel, Switzerland
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - Vladimira Hinic
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30 8006, Zurich, Switzerland
| | - Daniel Goldenberger
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031, Basel, Switzerland
| | - Alexander Gensch
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031, Basel, Switzerland
- Department of Biomedicine, Applied Microbiology Research, University of Basel, Basel, Switzerland
| | - Michael Schweitzer
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031, Basel, Switzerland
- Department of Biomedicine, Applied Microbiology Research, University of Basel, Basel, Switzerland
| | - Veronika Bättig
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Martin Siegemund
- Intensive Care Medicine, University Hospital Basel, Basel, Switzerland
| | - Stefano Bassetti
- Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Roland Bingisser
- Emergency Medicine, University Hospital Basel, Basel, Switzerland
| | - Michael Tamm
- Pneumology, University Hospital Basel, Basel, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Maja Weisser
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Daiana Stolz
- Pneumology, University Hospital Basel, Basel, Switzerland
| | - Nina Khanna
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031, Basel, Switzerland.
- Department of Biomedicine, Applied Microbiology Research, University of Basel, Basel, Switzerland.
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30 8006, Zurich, Switzerland.
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5
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Dessajan J, Timsit JF. Impact of Multiplex PCR in the Therapeutic Management of Severe Bacterial Pneumonia. Antibiotics (Basel) 2024; 13:95. [PMID: 38247654 PMCID: PMC10812737 DOI: 10.3390/antibiotics13010095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024] Open
Abstract
Pneumonia is a common and severe illness that requires prompt and effective management. Advanced, rapid, and accurate tools are needed to diagnose patients with severe bacterial pneumonia, and to rapidly select appropriate antimicrobial therapy, which must be initiated within the first few hours of care. Two multiplex molecular tests, Unyvero HPN and FilmArray Pneumonia+ Panel, have been developed using the multiplex polymerase chain reaction (mPCR) technique to rapidly identify pathogens and their main antibiotic resistance mechanisms from patient respiratory specimens. Performance evaluation of these tests showed strong correlations with reference techniques. However, good knowledge of their indications, targets, and limitations is essential. Collaboration with microbiologists is, therefore, crucial for their appropriate use. Under these conditions, and with standardized management, these rapid tests can improve the therapeutic management of severe pneumonia faster, more precisely, and with narrow-spectrum antibiotic therapy. Further randomized controlled trials are needed to address the many unanswered questions about multiplex rapid molecular testing during the diagnosis and the management of severe pneumonia. This narrative review will address the current knowledge, advantages, and disadvantages of these tests, and propose solutions for their routine use.
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Affiliation(s)
- Julien Dessajan
- Assistance Publique Hôpitaux de Paris (AP-HP), Medical and Infectious Diseases Intensive Care Unit, Bichat Claude-Bernard Hospital, Paris Cité University, 46 Rue Henri Huchard, 75018 Paris, France;
| | - Jean-François Timsit
- Assistance Publique Hôpitaux de Paris (AP-HP), Medical and Infectious Diseases Intensive Care Unit, Bichat Claude-Bernard Hospital, Paris Cité University, 46 Rue Henri Huchard, 75018 Paris, France;
- Mixt Research Unit (UMR) 1137, Infection, Antimicrobials, Modelization, Epidemiology (IAME), Institut National de la Recherche Médicale (INSERM), Paris Cité University, 75018 Paris, France
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Falsey AR, Branche AR, Croft DP, Formica MA, Peasley MR, Walsh EE. Real-life Assessment of BioFire FilmArray Pneumonia Panel in Adults Hospitalized With Respiratory Illness. J Infect Dis 2024; 229:214-222. [PMID: 37369370 PMCID: PMC10786250 DOI: 10.1093/infdis/jiad221] [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: 04/03/2023] [Revised: 06/09/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Inability to identify the microbial etiology of lower respiratory tract infection leads to unnecessary antibiotic use. We evaluated the utility of the BioFire FilmArray Pneumonia Panel (BioFire PN) to inform microbiologic diagnosis. METHODS Hospitalized adults with respiratory illness were recruited; sputa and clinical/laboratory data were collected. Sputa were cultured for bacteria and tested with BioFire PN. Microbial etiology was adjudicated by 4 physicians. Bacterial polymerase chain reaction (PCR) was compared with culture and clinical adjudication. RESULTS Of 298 sputa tested, BioFire PN detected significantly more pathogens (350 bacteria, 16 atypicals, and 164 viruses) than sputum culture plus any standard-of-care testing (91% vs 60%, P < .0001). When compared with culture, the sensitivity of BioFire PN for individual bacteria was 46% to 100%; specificity, 61% to 100%; and negative predictive value, 92% to 100%. Cases were adjudicated as viral (n = 58) and bacterial (n = 100). PCR detected bacteria in 55% of viral cases and 95% of bacterial (P < .0001). High serum procalcitonin and bacterial adjudication were more often associated with sputa with 106 or 107 copies detected. CONCLUSIONS Multiplex PCR testing of sputa for bacteria is useful to rule out bacterial infection with added value to detect viruses and atypical bacteria.
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Affiliation(s)
| | | | - Daniel P Croft
- Department of Pulmonary and Critical Medicine, University of Rochester
| | - Maria A Formica
- Infectious Disease Unit, Rochester General Hospital, Rochester, New York, USA
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Clark JA, Curran MD, Gouliouris T, Conway Morris A, Bousfield R, Navapurkar V, Kean IRL, Daubney E, White D, Baker S, Pathan N. Rapid Detection of Antimicrobial Resistance Genes in Critically Ill Children Using a Custom TaqMan Array Card. Antibiotics (Basel) 2023; 12:1701. [PMID: 38136735 PMCID: PMC10740637 DOI: 10.3390/antibiotics12121701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Bacteria are identified in only 22% of critically ill children with respiratory infections treated with antimicrobial therapy. Once an organism is isolated, antimicrobial susceptibility results (phenotypic testing) can take another day. A rapid diagnostic test identifying antimicrobial resistance (AMR) genes could help clinicians make earlier, informed antimicrobial decisions. Here we aimed to validate a custom AMR gene TaqMan Array Card (AMR-TAC) for the first time and assess its feasibility as a screening tool in critically ill children. An AMR-TAC was developed using a combination of commercial and bespoke targets capable of detecting 23 AMR genes. This was validated using isolates with known phenotypic resistance. The card was then tested on lower respiratory tract and faecal samples obtained from mechanically ventilated children in a single-centre observational study of respiratory infection. There were 82 children with samples available, with a median age of 1.2 years. Major comorbidity was present in 29 (35%) children. A bacterial respiratory pathogen was identified in 13/82 (16%) of children, of which 4/13 (31%) had phenotypic AMR. One AMR gene was detected in 49/82 (60%), and multiple AMR genes were detected in 14/82 (17%) children. Most AMR gene detections were not associated with the identification of phenotypic AMR. AMR genes are commonly detected in samples collected from mechanically ventilated children with suspected respiratory infections. AMR-TAC may have a role as an adjunct test in selected children in whom there is a high suspicion of antimicrobial treatment failure.
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Affiliation(s)
- John A. Clark
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
| | - Martin D. Curran
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge CB2 0QQ, UK;
| | - Theodore Gouliouris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge CB2 0QQ, UK;
| | - Andrew Conway Morris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge CB2 2QQ, UK
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Rachel Bousfield
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge CB2 0QQ, UK;
| | - Vilas Navapurkar
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
| | - Iain R. L. Kean
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
| | - Esther Daubney
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
| | - Deborah White
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK;
| | - Nazima Pathan
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
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Lewinski MA, Alby K, Babady NE, Butler-Wu SM, Bard JD, Greninger AL, Hanson K, Naccache SN, Newton D, Temple-Smolkin RL, Nolte F. Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology. J Mol Diagn 2023; 25:857-875. [PMID: 37757952 DOI: 10.1016/j.jmoldx.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/08/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The use of clinical molecular diagnostic methods for detecting microbial pathogens continues to expand and, in some cases, supplant conventional identification methods in various scenarios. Analytical and clinical benefits of multiplex molecular panels for the detection of respiratory pathogens have been demonstrated in various studies. The use of these panels in managing different patient populations has been incorporated into clinical guidance documents. The Association for Molecular Pathology's Infectious Diseases Multiplex Working Group conducted a review of the current benefits and challenges to using multiplex PCR for the detection of pathogens from gastrointestinal tract, central nervous system, lower respiratory tract, and joint specimens. The Working Group also discusses future directions and novel approaches to detection of pathogens in alternate specimen types, and outlines challenges associated with implementation of these multiplex PCR panels.
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Affiliation(s)
- Michael A Lewinski
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Roche Molecular Systems, San Clemente, California.
| | - Kevin Alby
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - N Esther Babady
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Clinical Microbiology Service, Departments of Laboratory Medicine and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan M Butler-Wu
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jennifer Dien Bard
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alexander L Greninger
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Kimberly Hanson
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; University of Utah School of Medicine and ARUP Laboratories, Salt Lake City, Utah
| | - Samia N Naccache
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Microbiology, LabCorp Seattle, Seattle, Washington
| | - Duane Newton
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Bio-Rad Laboratories, Irvine, California
| | | | - Frederick Nolte
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
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9
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Moy AC, Kimmoun A, Merkling T, Berçot B, Caméléna F, Poncin T, Deniau B, Mebazaa A, Dudoignon E, Dépret F. Performance evaluation of a PCR panel (FilmArray® Pneumonia Plus) for detection of respiratory bacterial pathogens in respiratory specimens: A systematic review and meta-analysis. Anaesth Crit Care Pain Med 2023; 42:101300. [PMID: 37709201 DOI: 10.1016/j.accpm.2023.101300] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/31/2023] [Accepted: 08/16/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Accuracy and timing of antibiotic therapy remain a challenge for lower respiratory tract infections. New molecular techniques using Multiplex Polymerase Chain Reaction, including the FilmArray® Pneumonia Plus Panel [FAPP], have been developed to address this. The aim of this study is to evaluate the FAPP diagnostic performance for the detection of the 15 typical bacteria of the panel from respiratory samples in a meta-analysis from a systematic review. METHODS We searched PubMed and EMBASE from January 1, 2010, to December 31, 2022, and selected any study on the FAPP diagnostic performance on respiratory samples compared to the reference standard, bacterial culture. The main outcome was the overall diagnostic accuracy with sensitivity and specificity. We calculated the log Diagnostic Odds Ratio and analyzed performance for separate bacteria, antimicrobial resistance genes, and according to the sample type. We also reported the FAPP turnaround time and the out-of-panel bacteria number and species. This study is registered with PROSPERO (CRD42021226280). RESULTS From 10 317 records, we identified 30 studies including 8 968 samples. Twenty-one were related to intensive care. The overall sensitivity and specificity were 94% [95% Confidence Interval (CI) 91-95] and 98% [95%CI 97-98], respectively. The log Diagnostic Odds Ratio was 6.35 [95%CI 6.05-6.65]. 9.3% [95%CI 9.2-9.5] of bacteria detected in culture were not included in the FAPP panel. CONCLUSION This systematic review reporting the FAPP evaluation revealed a high accuracy. This test may represent an adjunct tool for pulmonary bacterial infection diagnostic and antimicrobial stewardship. Further evidence is needed to assess the impact on clinical outcome.
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Affiliation(s)
- Anne-Clotilde Moy
- Department of Anesthesiology, Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Antoine Kimmoun
- Intensive Care Medicine Brabois, CHRU de Nancy, INSERM U1116, Université de Lorraine, Nancy, France; INSERM UMR-S 942, MASCOT, Université de Paris, Paris, France
| | - Thomas Merkling
- Nancy Clinical Investigation Centre, INSERM 1433, CHRU Nancy, Université de Lorraine, Nancy, France
| | - Béatrice Berçot
- Department of Microbiology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 1137, IAME, Paris, France
| | - François Caméléna
- Department of Microbiology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 1137, IAME, Paris, France
| | - Thibaut Poncin
- Department of Microbiology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 1137, IAME, Paris, France
| | - Benjamin Deniau
- Department of Anesthesiology, Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, FHU PROMICE, INSERM 942, INI-CRCT Network, Paris, France
| | - Alexandre Mebazaa
- Department of Anesthesiology, Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, FHU PROMICE, INSERM 942, INI-CRCT Network, Paris, France
| | - Emmanuel Dudoignon
- Department of Anesthesiology, Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, FHU PROMICE, INSERM 942, INI-CRCT Network, Paris, France.
| | - François Dépret
- Department of Anesthesiology, Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, FHU PROMICE, INSERM 942, INI-CRCT Network, Paris, France
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10
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Cojuc-Konigsberg G, Moscona-Nissan A, Guijosa A, Mireles Dávalos CD, Martínez MEJ, Mújica Sánchez MA, Hernández Huizar VF, Durán Barrón MA, Gómez KV, Andrade-Galindo R, Ordóñez-Oviedo M, Brito GD, Vargas EB. Diagnostic accuracy of the BioFire® FilmArray® pneumonia panel in COVID-19 patients with ventilator-associated pneumonia. BMC Infect Dis 2023; 23:524. [PMID: 37559032 PMCID: PMC10413519 DOI: 10.1186/s12879-023-08486-4] [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: 05/19/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Ventilator-Associated pneumonia (VAP) is one of the leading causes of morbidity and mortality in critically ill COVID-19 patients in lower-and-middle-income settings, where timely access to emergency care and accurate diagnostic testing is not widely available. Therefore, rapid microbiological diagnosis is essential to improve effective therapy delivery to affected individuals, preventing adverse outcomes and reducing antimicrobial resistance. METHODS We conducted a cross-sectional study of patients with suspected VAP and COVID-19, evaluating the diagnostic performance of the BioFire® FilmArray® Pneumonia Panel (FA-PP). Respiratory secretion samples underwent standard microbiological culture and FA-PP assays, and the results were compared. RESULTS We included 252 samples. The traditional culture method detected 141 microorganisms, and FA-PP detected 277, resulting in a sensitivity of 95% and specificity of 60%, with a positive predictive value of 68% and negative predictive value of 93%. In samples with high levels of genetic material (> 10^5 copies/mL), the panel had a sensitivity of 94% and specificity of 86%. In addition, 40% of the culture-negative samples had positive FA-PP® results, of which 35% had > 10^5 copies/mL of genetic material. The most prevalent bacteria were Gram-negative bacilli, followed by Gram-positive cocci. The panel identified 98 genes associated with antimicrobial resistance, predominantly extended-spectrum beta-lactamases (28%). CONCLUSION The FA-PP is a sensitive assay for identifying bacteria causing VAP in patients with COVID-19, with a greater capacity to detect bacteria than the conventional method. The timely microbiological recognition offered by this panel could lead to optimized decision-making processes, earlier tailored treatment initiation, and improved antibiotic stewardship practices.
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Affiliation(s)
- Gabriel Cojuc-Konigsberg
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
- Health Sciences Faculty, Universidad Anahuac Mexico, Mexico City, Mexico
| | - Alberto Moscona-Nissan
- School of Medicine, Universidad Panamericana, Insurgentes Mixcoac, Donatello 59, 03920, Mexico City, Mexico
| | - Alberto Guijosa
- School of Medicine, Universidad Panamericana, Insurgentes Mixcoac, Donatello 59, 03920, Mexico City, Mexico
| | | | - María E Jiménez Martínez
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Mario A Mújica Sánchez
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
| | | | - Martha A Durán Barrón
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Karen Villarreal Gómez
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
| | | | - Montserrat Ordóñez-Oviedo
- School of Medicine, Universidad Panamericana, Insurgentes Mixcoac, Donatello 59, 03920, Mexico City, Mexico
| | - Grecia Deloya Brito
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Eduardo Becerril Vargas
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico.
- Health Sciences Faculty, Universidad Anahuac Mexico, Mexico City, Mexico.
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11
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Ferrer J, Clari MÁ, Giménez E, Carbonell N, Torres I, Blasco ML, Albert E, Navarro D. The Biofire® Filmarray® Pneumonia Plus panel for management of lower respiratory tract infection in mechanically-ventilated patients in the COVID-19 era: a diagnostic and cost-benefit evaluation. Diagn Microbiol Infect Dis 2023; 105:115847. [PMID: 36403558 PMCID: PMC9625846 DOI: 10.1016/j.diagmicrobio.2022.115847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/04/2022] [Accepted: 10/27/2022] [Indexed: 11/07/2022]
Abstract
We assessed the diagnostic performance of the Biofire® Filmarray® Pneumonia Plus panel (FA-PP) compared to standard culture in Intensive Care Unit patients with suspected ventilator-associated lower respiratory tract infection in the COVID-19 era. We determined whether its implementation in routine diagnostic algorithms would be cost-beneficial from a hospital perspective. Of 163 specimens, 96 (59%) returned negative results with FA-PP and conventional culture, and 29 specimens (17.8%) were positive with both diagnostic methods and yielded concordant qualitative bacterial identification/isolation. Thirty-nine specimens (23.9%) gave discordant results (positive via FA-PP and negative via culture). Real-life adjustments of empirical antimicrobial therapy (EAT) after FA-PP results resulted in additional costs beyond EAT alone of 1868.7 €. Adequate EAT adjustments upon FA-PP results would have resulted in a saving of 6675.8 €. In conclusion, the data presented supports the potential utility of FA-PP for early EAT adjustment in patients with ventilator-associated lower respiratory tract infection.
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Affiliation(s)
- Josep Ferrer
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - María Ángeles Clari
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Estela Giménez
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Nieves Carbonell
- Medical Intensive Care Unit, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Ignacio Torres
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - María Luisa Blasco
- Medical Intensive Care Unit, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Eliseo Albert
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain,Corresponding author. Tel.: +34-9-6197-3500; fax: +34-9-6386-4173
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12
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Van Der Westhuyzen M, Samodien N, Brink AJ, Moodley C. Utility of the BioFire ® FilmArray ® Pneumonia Panel plus assay for syndromic testing of lower respiratory tract infections in a low/middle-income setting. JAC Antimicrob Resist 2023; 5:dlac139. [PMID: 36628341 PMCID: PMC9825243 DOI: 10.1093/jacamr/dlac139] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/15/2022] [Indexed: 01/09/2023] Open
Abstract
Background Determining lower respiratory tract infection (LRTI) aetiology is complex. Culture-based methods are laborious with poor sensitivity. Molecular assays improve detection of potential pathogens, but incorrect interpretation of results may lead to inappropriate antimicrobial therapy. Methods The utility of the BioFire® FilmArray® Pneumonia Panel plus (FA-PP) to detect LRTI pathogens, and the potential impact on antimicrobial stewardship in a low-resource setting, were assessed. Routine LRT samples were included from adult patients with clinically suspected LRTI or with a concomitant blood culture at Groote Schuur Hospital and referring facilities. Culture and FA-PP results were compared, and pharmacy data analysed to determine appropriateness of antibiotic therapy. Results There was an 80% correlation between cultured LRTI pathogens and the FA-PP bin ≥107 results. Compared with culture, the FA-PP detected substantially more pathogens (86.6% versus 17.9%) and produced a combined 100% positive percent agreement, and 88% negative percent agreement. The FA-PP detected bacterial/viral coinfections in 27% of samples. Correlation of FA-PP results with pharmacy data (n = 69) indicated a potential antibiotic change in 75% of cases, but this is difficult to accurately characterize without a 'gold standard' for treatment or complete clinical data. Conclusions The FA-PP increased the number of positive samples with typical bacteria, but the semi-quantitative reporting algorithm does not describe the correlation between the different bin values and colonization versus infection. This complicates result interpretation and may lead to inappropriate antimicrobial treatment. This study highlights the potential positive impact of rapid molecular assays for routine care in lower-income settings, but also underscores the interpretive challenges associated with these tests.
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Affiliation(s)
| | - N Samodien
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa,National Health Laboratory Service, Microbiology, Groote Schuur Hospital, Cape Town, South Africa
| | - A J Brink
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa,National Health Laboratory Service, Microbiology, Groote Schuur Hospital, Cape Town, South Africa
| | - C Moodley
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa,National Health Laboratory Service, Microbiology, Groote Schuur Hospital, Cape Town, South Africa
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13
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Jitmuang A, Puttinad S, Hemvimol S, Pansasiri S, Horthongkham N. A multiplex pneumonia panel for diagnosis of hospital-acquired and ventilator-associated pneumonia in the era of emerging antimicrobial resistance. Front Cell Infect Microbiol 2022; 12:977320. [PMID: 36310855 PMCID: PMC9597303 DOI: 10.3389/fcimb.2022.977320] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022] Open
Abstract
Background Antimicrobial resistance (AMR), including multidrug (MDR) and extensively drug-resistant (XDR) bacteria, is an essential consideration in the prevention and management of hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP). In the AMR era, the clinical utility of the BioFire FilmArray Pneumonia Panel Plus (BFPP) to diagnose HAP/VAP has not been thoroughly evaluated. Methods We enrolled adult hospitalized patients with HAP or VAP at Siriraj Hospital and Saraburi Hospital from July 2019–October 2021. Respiratory samples were collected for standard microbiological assays, antimicrobial susceptibility testing (AST), and the BFPP analysis. Results Of 40 subjects, 21 were men. The median duration of HAP/VAP diagnoses was 10.5 (5, 21.5) days, and 36 endotracheal aspirate and 4 sputum samples were collected. Standard cultures isolated 54 organisms—A. baumannii (37.0%), P. aeruginosa (29.6%), and S. maltophilia (16.7%). 68.6% of Gram Negatives showed an MDR or XDR profile. BFPP detected 77 bacterial targets—A. baumannii 32.5%, P. aeruginosa 26.3%, and K. pneumoniae 17.5%. Of 28 detected AMR gene targets, CTX-M (42.5%), OXA-48-like (25%), and NDM (14.3%) were the most common. Compared with standard testing, the BFPP had an overall sensitivity of 98% (88-100%), specificity of 81% (74-87%), positive predictive value of 60% (47-71%), negative predictive value of 99% (96-100%), and kappa (κ) coefficient of 0.64 (0.53-0.75). The concordance between phenotypic AST and detected AMR genes in Enterobacterales was 0.57. There was no concordance among A. baumannii, P. aeruginosa, and S. aureus Conclusions The BFPP has excellent diagnostic sensitivity to detect HAP/VAP etiology. The absence of S. maltophilia and discordance of AMR gene results limit the test performance.
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Affiliation(s)
- Anupop Jitmuang
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- *Correspondence: Anupop Jitmuang,
| | - Soravit Puttinad
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Siri Pansasiri
- Saraburi Hospital Research Center, Saraburi Hospital, Saraburi, Thailand
| | - Navin Horthongkham
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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14
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Multiplex PCR in the empirical antibiotic treatment of patients with SARS-CoV-2 and bacterial respiratory superinfection. Infect Prev Pract 2022; 4:100227. [PMID: 35784092 PMCID: PMC9238185 DOI: 10.1016/j.infpip.2022.100227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/14/2022] [Indexed: 11/20/2022] Open
Abstract
Background The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic led to overuse of antimicrobials, which increased concerns regarding antimicrobial resistance. Objective To measure the impact of a multiplex polymerase chain reaction (PCR) pneumonia panel on empirical antibiotic treatment for patients with critical coronavirus disease 2019 (COVID-19) with suspected bacterial respiratory superinfection. Methods This descriptive, prospective study was undertaken in a 36-bed intensive care unit from June 2020 to July 2021. Patients with severe COVID-19 who were ventilated and under suspicion of bacterial respiratory superinfection were included in the study. The intervention was a semi-quantitative multiplex PCR alongside concurrent standard cultures. When PCR panel results were expected to be obtained within 3 h of sampling, empirical antibiotic treatment was not administered while awaiting the results. Otherwise, empirical treatment was initiated. Patients classified as 'avoided empirical treatment' avoided 48-72 h of empirical antibiotic therapy. For those patients who received empirical treatment, the PCR panel results were used to decide whether treatment should be escalated, de-escalated, maintained or stopped. Positive and negative predictive values, and 'avoided empirical treatment' were calculated. Medical conduct and panel results were analysed for patients who received empirical treatment. Results Eighty-two patients (71% male, 29% female) were included in this study. The mean age was 57.5 years, and the mean APACHE II score was 16. Ninety PCR panels were performed, and the negative and positive predictive values were 99.9% and 66.7%, respectively. Empirical treatment was avoided in 61% of episodes. Of those patients who were receiving antibiotics when the PCR panel was performed, treatment was de-escalated in 71%, escalated in 14%, stopped in 9% and maintained in 6%. A diagnosis of bacterial respiratory superinfection was ruled out in 19% of cases. Conclusions PCR panels prevented the initiation of empirical antibiotic treatment in two-thirds of patients, and led to de-escalation in more than two-thirds of those who had started empirical antibiotic treatment. The high negative predictive value of the PCR panel allowed the diagnosis of bacterial respiratory superinfection to be ruled out. This tool represents a significant contribution to diagnostic stewardship in order to avoid the unnecessary use of antibiotics.
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15
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Tellapragada C, Ydsten KA, Ternhag A, Giske CG. Evaluation of a pneumonia multiplex PCR panel for detection of bacterial respiratory tract pathogens from serial specimens collected from hospitalized COVID-19 patients. Eur J Clin Microbiol Infect Dis 2022; 41:1093-1098. [PMID: 35727430 PMCID: PMC9210330 DOI: 10.1007/s10096-022-04466-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022]
Abstract
We investigated the concordance between the Unyvero Hospitalized Pneumonia (HPN) application and quantitative culture for detection of bacterial pathogens from serial lower respiratory tract (LRT) specimens collected from the same subject. Comparison of results from HPN application and culture was evaluated using 69 LRT samples from 27 subjects, using two evaluation approaches. False positive detections by the HPN application was 29% (20/69) in Evaluation I vs 10% (7/68) in Evaluation II. Additional pathogens detected by the HPN application could be confirmed in many instances by culture positivity for the same organism from previous or subsequent samples from the same subject.
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Affiliation(s)
- Chaitanya Tellapragada
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Allé 8, 14183, Stockholm, Sweden.
| | | | - Anders Ternhag
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Medicine, Solna, Karolinska Institute, Stockholm, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Allé 8, 14183, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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16
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Gerace E, Mancuso G, Midiri A, Poidomani S, Zummo S, Biondo C. Recent Advances in the Use of Molecular Methods for the Diagnosis of Bacterial Infections. Pathogens 2022; 11:pathogens11060663. [PMID: 35745518 PMCID: PMC9229729 DOI: 10.3390/pathogens11060663] [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: 04/28/2022] [Revised: 05/31/2022] [Accepted: 06/05/2022] [Indexed: 12/14/2022] Open
Abstract
Infections caused by bacteria have a major impact on public health-related morbidity and mortality. Despite major advances in the prevention and treatment of bacterial infections, the latter continue to represent a significant economic and social burden worldwide. The WHO compiled a list of six highly virulent multidrug-resistant bacteria named ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) responsible for life-threatening diseases. Taken together with Clostridioides difficile, Escherichia coli, Campylobacter spp., (C. jejuni and C. coli), Legionella spp., Salmonella spp., and Neisseria gonorrhoeae, all of these microorganisms are the leading causes of nosocomial infections. The rapid and accurate detection of these pathogens is not only important for the early initiation of appropriate antibiotic therapy, but also for resolving outbreaks and minimizing subsequent antimicrobial resistance. The need for ever-improving molecular diagnostic techniques is also of fundamental importance for improving epidemiological surveillance of bacterial infections. In this review, we aim to discuss the recent advances on the use of molecular techniques based on genomic and proteomic approaches for the diagnosis of bacterial infections. The advantages and limitations of each of the techniques considered are also discussed.
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Affiliation(s)
| | - Giuseppe Mancuso
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Angelina Midiri
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Stefano Poidomani
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Sebastiana Zummo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Carmelo Biondo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
- Correspondence: ; Tel.: +39-090-2213322
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17
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Buchan BW, Armand-Lefevre L, Anderson N. Molecular Diagnosis of Pneumonia (Including Multiplex Panels). Clin Chem 2021; 68:59-68. [DOI: 10.1093/clinchem/hvab143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022]
Abstract
Abstract
Background
Pneumonia is a common illness, accounting for a staggering amount of worldwide morbidity and mortality. The diagnosis of pneumonia is challenging given the variety of responsible pathogens. Diagnostic testing for bacterial pneumonia has traditionally relied on time-consuming culture-based methods, though recently multiplexed molecular approaches have been described. Multiplexed molecular assays for pneumonia have the potential to provide broad diagnostic information in a rapid timeframe. Much has yet to be learned about these assays regarding analytical performance, potential impact, and optimal implementation strategy.
Content
Herein we provide a summary of what is known and what has yet to be learned about multiplexed molecular pneumonia assays. We provide a comparison of the different commercially available assays and summarize the most current performance data for each. We further describe outcome data and lessons learned from those who have implemented these assays worldwide. Finally, based on the current state of performance and outcome data, we provide informed strategies and considerations for laboratories contemplating implementation.
Summary
Multiplexed molecular assays for the diagnosis of pneumonia boast high accuracy though the diagnostic information gained from these assays is inherently different from culture and must be interpreted in cultural context. Despite this, these assays can be powerful and effective diagnostic tools with a potential to positively impact patient care. The extent to which this is realized varies from setting to setting, though is dependent on thoughtful implementation and a focus on delivering clear, rapid, and actionable results that can be interpreted in the appropriate context.
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Affiliation(s)
- Blake W Buchan
- Department of Pathology, The Medical College of Wisconsin, Milwaukee, WI, USA
| | - Laurence Armand-Lefevre
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Neil Anderson
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
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18
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Kayser MZ, Seeliger B, Valtin C, Fuge J, Ziesing S, Welte T, Pletz MW, Chhatwal P, Gottlieb J. Clinical decision making is improved by BioFire Pneumonia Plus in suspected lower respiratory tract infection after lung transplantation: Results of the prospective DBATE-IT * study. Transpl Infect Dis 2021; 24:e13725. [PMID: 34542213 DOI: 10.1111/tid.13725] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/20/2021] [Accepted: 08/29/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Lower respiratory tract infections (LRTIs) are a significant cause of morbidity and mortality in lung transplant (LTx) recipients. Timely and precise pathogen detection is vital to successful treatment. Multiplex PCR kits with short turnover times like the BioFire Pneumonia Plus (BFPPp) (manufactured by bioMérieux) may be a valuable addition to conventional tests. METHODS We performed a prospective observational cohort study in 60 LTx recipients with suspected LRTI. All patients received BFPPp testing of bronchoalveolar lavage fluid in addition to conventional tests including microbiological cultures and conventional diagnostics for respiratory viruses. Primary outcome was time-to-test-result; secondary outcomes included time-to-clinical-decision and BFPPp test accuracy compared to conventional tests. RESULTS BFPPp provided results faster than conventional tests (2.3 h [2-2.8] vs. 23.4 h [21-62], p < 0.001), allowing for faster clinical decisions (2.8 [2.2-44] vs. virology 28.1 h [23.1-70.6] and microbiology 32.6 h [4.6-70.9], both p < 0.001). Based on all available diagnostic modalities, 26 (43%) patients were diagnosed with viral LRTI, nine (15 %) with non-viral LRTI, and five (8 %) with combined viral and non-viral LRTI. These diagnoses were established by BFPPp in 92%, 78%, and 100%, respectively. The remaining 20 patients (33 %) received a diagnosis other than LRTI. Preliminary therapies based on BFPPp results were upheld in 90% of cases. There were six treatment modifications based on pathogen-isolation by conventional testing missed by BFPPp, including three due to fungal pathogens not covered by the BFPPp. CONCLUSION BFPPp offered faster test results compared to conventional tests with good concordance. The absence of fungal pathogens from the panel is a potential weakness in a severely immunosuppressed population.
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Affiliation(s)
- Moritz Z Kayser
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | - Benjamin Seeliger
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany.,Biomedical Research in End-Stage and Obstructive Lung Disease (BREATH), German Centre for Lung Research (DZL), Hannover, Germany
| | - Christina Valtin
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | - Jan Fuge
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany.,Biomedical Research in End-Stage and Obstructive Lung Disease (BREATH), German Centre for Lung Research (DZL), Hannover, Germany
| | - Stefan Ziesing
- Department of Microbiology and Hospital Hygiene, Hannover Medical School, Hannover, Germany
| | - Tobias Welte
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany.,Biomedical Research in End-Stage and Obstructive Lung Disease (BREATH), German Centre for Lung Research (DZL), Hannover, Germany
| | - Mathias W Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Patrick Chhatwal
- Department of Microbiology and Hospital Hygiene, Hannover Medical School, Hannover, Germany.,Department of Microbiology, MVZ Medical Laboratory Hannover, Hannover, Germany
| | - Jens Gottlieb
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany.,Biomedical Research in End-Stage and Obstructive Lung Disease (BREATH), German Centre for Lung Research (DZL), Hannover, Germany
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19
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Novy E, Goury A, Thivilier C, Guillard T, Alauzet C. Algorithm for rational use of Film Array Pneumonia Panel in bacterial coinfections of critically ill ventilated COVID-19 patients. Diagn Microbiol Infect Dis 2021; 101:115507. [PMID: 34364096 PMCID: PMC8299290 DOI: 10.1016/j.diagmicrobio.2021.115507] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/12/2021] [Accepted: 07/18/2021] [Indexed: 12/04/2022]
Abstract
The FilmArray Pneumonia Panel has proven to be an effective tool for rapid detection of main respiratory pathogens. However, its rational use needs appropriate knowledge and formation regarding its indication and interpretation. Herein, we provide some advices to help with success of its daily routine use, particularly in critically ill ventilated COVID-19 patients. Clinical Trial registration number: NCT04453540.
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Affiliation(s)
- Emmanuel Novy
- Centre Hospitalier Régional Universitaire de Nancy, Service d'Anesthésie-Réanimation et Médecine Péri-Opérative, F-54511 Vandœuvre-Lès-Nancy, France; Université de Lorraine, SIMPA, F-54000 Nancy, France
| | - Antoine Goury
- Centre Hospitalier Universitaire de Reims, Hôpital Robert Debré, Unité de Médecine Intensive et Réanimation Polyvalente, F-51092 Reims, France
| | - Carine Thivilier
- Centre Hospitalier Régional Universitaire de Nancy, Service de Réanimation Médicale Brabois, F-54511 Vandœuvre-Lès-Nancy, France
| | - Thomas Guillard
- Centre Hospitalier Universitaire de Reims, Hôpital Robert Debré, Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière-Parasitologie-Mycologie, F-51092 Reims, France; Université de Reims-Champagne-Ardenne, SFR CAP-Santé, Inserm UMR-S 1250 P3Cell, F-51097 Reims, France
| | - Corentine Alauzet
- Université de Lorraine, SIMPA, F-54000 Nancy, France; Centre Hospitalier Régional Universitaire de Nancy, Laboratoire de Microbiologie, F-54000, Nancy, France.
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20
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Maataoui N, Chemali L, Patrier J, Tran Dinh A, Le Fèvre L, Lortat-Jacob B, Marzouk M, d'Humières C, Rondinaud E, Ruppé E, Montravers P, Timsit JF, Armand-Lefèvre L. Impact of rapid multiplex PCR on management of antibiotic therapy in COVID-19-positive patients hospitalized in intensive care unit. Eur J Clin Microbiol Infect Dis 2021; 40:2227-2234. [PMID: 33733394 PMCID: PMC7968559 DOI: 10.1007/s10096-021-04213-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/25/2021] [Indexed: 12/27/2022]
Abstract
Because the diagnosis of co/superinfection in COVID-19 patients is challenging, empirical antibiotic therapy is frequently initiated until microbiological analysis results. We evaluated the performance and the impact of the BioFire® FilmArray® Pneumonia plus Panel on 112 respiratory samples from 67 COVID-19 ICU patients suspected of co/superinfections. Globally, the sensitivity and specificity of the test were 89.3% and 99.1%, respectively. Positive tests led to antibiotic initiation or adaptation in 15% of episodes and de-escalation in 4%. When negative, 28% of episodes remained antibiotic-free (14% no initiation, 14% withdrawal). Rapid multiplex PCRs can help to improve antibiotic stewardship by administering appropriate antibiotics earlier and avoiding unnecessary prescriptions.
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Affiliation(s)
- Naouale Maataoui
- Université de Paris, INSERM, IAME, F-75006, Paris, France. .,Service de Bactériologie, Hôpital Bichat Claude Bernard, AP-HP Nord, Université de Paris, 46 rue Henri Huchard, 75877, Paris Cedex 18, France.
| | - Lotfi Chemali
- Service de Bactériologie, Hôpital Bichat Claude Bernard, AP-HP Nord, Université de Paris, 46 rue Henri Huchard, 75877, Paris Cedex 18, France
| | - Juliette Patrier
- Medical and Infectious Diseases ICU (MI2), Hôpital Bichat, AP-HP, F-75018, Paris, France
| | - Alexy Tran Dinh
- Department of Anesthesiology and Surgical Critical Care, Hôpital Bichat, AP-HP, F-75018, Paris, France.,Université de Paris, INSERM U 1148, F-75006, Paris, France
| | - Lucie Le Fèvre
- Medical and Infectious Diseases ICU (MI2), Hôpital Bichat, AP-HP, F-75018, Paris, France
| | - Brice Lortat-Jacob
- Department of Anesthesiology and Surgical Critical Care, Hôpital Bichat, AP-HP, F-75018, Paris, France
| | - Mehdi Marzouk
- Medical and Infectious Diseases ICU (MI2), Hôpital Bichat, AP-HP, F-75018, Paris, France
| | - Camille d'Humières
- Université de Paris, INSERM, IAME, F-75006, Paris, France.,Service de Bactériologie, Hôpital Bichat Claude Bernard, AP-HP Nord, Université de Paris, 46 rue Henri Huchard, 75877, Paris Cedex 18, France
| | - Emilie Rondinaud
- Université de Paris, INSERM, IAME, F-75006, Paris, France.,Service de Bactériologie, Hôpital Bichat Claude Bernard, AP-HP Nord, Université de Paris, 46 rue Henri Huchard, 75877, Paris Cedex 18, France
| | - Etienne Ruppé
- Université de Paris, INSERM, IAME, F-75006, Paris, France.,Service de Bactériologie, Hôpital Bichat Claude Bernard, AP-HP Nord, Université de Paris, 46 rue Henri Huchard, 75877, Paris Cedex 18, France
| | - Philippe Montravers
- Department of Anesthesiology and Surgical Critical Care, Hôpital Bichat, AP-HP, F-75018, Paris, France.,Université de Paris, INSERM U 1148, F-75006, Paris, France
| | - Jean-François Timsit
- Université de Paris, INSERM, IAME, F-75006, Paris, France.,Medical and Infectious Diseases ICU (MI2), Hôpital Bichat, AP-HP, F-75018, Paris, France
| | - Laurence Armand-Lefèvre
- Université de Paris, INSERM, IAME, F-75006, Paris, France.,Service de Bactériologie, Hôpital Bichat Claude Bernard, AP-HP Nord, Université de Paris, 46 rue Henri Huchard, 75877, Paris Cedex 18, France
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Multinational evaluation of the BioFire® FilmArray® Pneumonia plus Panel as compared to standard of care testing. Eur J Clin Microbiol Infect Dis 2021; 40:1609-1622. [PMID: 33655440 PMCID: PMC7924818 DOI: 10.1007/s10096-021-04195-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/09/2021] [Indexed: 02/08/2023]
Abstract
This study compared standard of care testing (SOC) to BioFire® FilmArray® Pneumonia plus Panel (PNplus). PNplus detects 15 bacteria with semiquantitative log bin values, 7 antibiotic resistance markers, three atypical bacteria (AB), and eight viral classes directly from bronchoalveolar lavage-like specimens (BLS) and sputum-like specimens (SLS). Fifty-two laboratories from 13 European countries and Israel tested 1234 BLS and 1242 SLS with PNplus and SOC. Detection rates and number of pathogens/samples were compared for PNplus pathogens. PNplus bin values and SOC quantities were compared. Three thousand two hundred sixty-two bacteria in PNplus were detected by PNplus and/or SOC. SOC detected 57.1% compared to 95.8% for PNplus (p ≤ 0.0001). PNplus semiquantitative bin values were less than SOC, equal to SOC, or greater than SOC in 5.1%, 25.4%, and 69.6% of results, respectively. PNplus bin values were on average ≥ 1 log than SOC values (58.5% 1–2 logs; 11.0% 3–4 logs). PNplus identified 98.2% of MRSA and SOC 55.6%. SOC detected 73/103 AB (70.9%) and 134/631 viruses (21.2%). PNplus detected 93/103 AB (90.3%) and 618/631 viruses (97.9%) (p ≤ 0.0001). PNplus and SOC mean number of pathogens/samples were 1.99 and 1.44, respectively. All gram-negative resistance markers were detected. PNplus and SOC results were fully or partially concordant for 49.1% and 26.4% of specimens, respectively. PNplus was highly sensitive and detected more potential pneumonia pathogens than SOC. Semiquantification may assist in understanding pathogen significance. As PNplus generates results in approximately 1 h, PNplus has potential to direct antimicrobial therapy in near real time and improve antimicrobial stewardship and patient outcomes.
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