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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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Al-Sarawi HA, Habibi N, Uddin S, Jha AN, Al-Sarawi MA, Lyons BP. Antibiotic Resistance Mediated by Escherichia coli in Kuwait Marine Environment as Revealed through Genomic Analysis. Antibiotics (Basel) 2023; 12:1366. [PMID: 37760663 PMCID: PMC10525739 DOI: 10.3390/antibiotics12091366] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Antibiotic-resistance gene elements (ARGEs) such as antibiotic-resistance genes (ARGs), integrons, and plasmids are key to the spread of antimicrobial resistance (AMR) in marine environments. Kuwait's marine area is vulnerable to sewage contaminants introduced by numerous storm outlets and indiscriminate waste disposal near recreational beaches. Therefore, it has become a significant public health issue and warrants immediate investigation. Coliforms, especially Gram-negative Escherichia coli, have been regarded as significant indicators of recent fecal pollution and carriers of ARGEs. In this study, we applied a genome-based approach to identify ARGs' prevalence in E. coli isolated from mollusks and coastal water samples collected in a previous study. In addition, we investigated the plasmids and intl1 (class 1 integron) genes coupled with the ARGs, mediating their spread within the Kuwait marine area. Whole-genome sequencing (WGS) identified genes resistant to the drug classes of beta-lactams (blaCMY-150, blaCMY-42, blaCTX-M-15, blaDHA-1, blaMIR-1, blaOKP-B-15, blaOXA-1, blaOXA-48, blaTEM-1B, blaTEM-35), trimethoprim (dfrA14, dfrA15, dfrA16, dfrA1, dfrA5, dfrA7), fluroquinolone (oqxA, oqxB, qnrB38, qnrB4, qnrS1), aminoglycoside (aadA2, ant(3'')-Ia, aph(3'')-Ib, aph(3')-Ia, aph(6)-Id), fosfomycin (fosA7, fosA_6, fosA, fosB1), sulfonamide (sul1, sul2, sul3), tetracycline (tet-A, tet-B), and macrolide (mph-A). The MFS-type drug efflux gene mdf-A is also quite common in E. coli isolates (80%). The plasmid ColRNAI was also found to be prevalent in E. coli. The integron gene intI1 and gene cassettes (GC) were reported to be in 36% and 33%, respectively, of total E. coli isolates. A positive and significant (p < 0.001) correlation was observed between phenotypic AMR-intl1 (r = 0.311) and phenotypic AMR-GC (r = 0.188). These findings are useful for the surveillance of horizontal gene transfer of AMR in the marine environments of Kuwait.
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Affiliation(s)
- Hanan A. Al-Sarawi
- Environment Public Authority, Fourth Ring Road, Shuwaikh Industrial 70050, Kuwait
| | - Nazima Habibi
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait;
| | - Saif Uddin
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait;
| | - Awadhesh N. Jha
- School of Biological Sciences, Plymouth University, Drake Circus, Plymouth PL4 8AA, UK;
| | - Mohammed A. Al-Sarawi
- Department of Earth & Environmental Sciences, Kuwait University, Faculty of Science, P.O. Box 5969, Safat 13060, Kuwait;
| | - Brett P. Lyons
- Research & Monitoring Coordination Nature Conservation Department, Neom 49625, Saudi Arabia;
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Relich RF, Abbott AN. Syndromic and Point-of-Care Molecular Testing. Clin Lab Med 2022; 42:507-531. [PMID: 36368779 DOI: 10.1016/j.cll.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ryan F Relich
- Division of Clinical Microbiology, Indiana University Health Pathology Laboratory, Indiana University Health and Indiana University School of Medicine, Suite 6027E, 350 West 11th Street, Indianapolis, IN 46202, USA.
| | - April N Abbott
- Department of Laboratory Medicine, Deaconess Hospital, 600 Mary Street, Evansville, IN 47747, USA
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Ojha SC, Chen K, Yuan Y, Ahmed S, Malik AA, Nisha M, Sheng YJ, Sun C, Wu G, Deng CL. Clinical relevance of molecular testing methods in the diagnosis and guidance of therapy in patients with staphylococcal empyema: a systematic review and meta-analysis. Front Cell Infect Microbiol 2022; 12:758833. [PMID: 35967859 PMCID: PMC9372472 DOI: 10.3389/fcimb.2022.758833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 07/05/2022] [Indexed: 12/14/2022] Open
Abstract
BackgroundEfficient detection tools for determining staphylococcal pleural infection are critical for its eradication. The objective of this meta-analysis was to assess the diagnostic utility of nucleic acid amplification tests (NAAT) in suspected empyema cases to identify staphylococcal strains and avoid unnecessary empiric methicillin-resistant Staphylococcus aureus (MRSA) therapy.MethodsFrom inception to July 24, 2021, relevant records were retrieved from PubMed, Embase, Scopus, Web of Science, and the Cochrane Library. The quality of studies was determined using the QUADAS-2 tool. The pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and hierarchical summary receiver operating characteristic (HSROC) curve for NAAT’s diagnostic performance were evaluated using an HSROC model.ResultsEight studies comprising 424 samples evaluated NAAT accuracy for Staphylococcus aureus (SA) identification, while four studies comprising 317 samples evaluated methicillin-resistant Staphylococcus aureus (MRSA) identification. The pooled NAAT summary estimates for detection of both SA (sensitivity: 0.35 (95% CI 0.19–0.55), specificity: 0.95 (95% CI 0.92–0.97), PLR: 7.92 (95% CI 4.98–12.59), NLR: 0.44 (95% CI 0.14–1.46), and DOR: 24.0 (95% CI 6.59–87.61) ) and MRSA (sensitivity: 0.45 (95% CI 0.15–0.78), specificity: 0.93 (95% CI 0.89–0.95), PLR: 10.06 (95% CI 1.49–67.69), NLR: 0.69 (95% CI 0.41–1.15), and DOR: 27.18 (95% CI 2.97–248.6) ) were comparable. The I2 statistical scores for MRSA and SA identification sensitivity were 13.7% and 74.9%, respectively, indicating mild to substantial heterogeneity. PCR was frequently used among NAA tests, and its diagnostic accuracy coincided well with the overall summary estimates. A meta-regression and subgroup analysis of country, setting, study design, patient selection, and sample condition could not explain the heterogeneity (meta-regression P = 0.66, P = 0.46, P = 0.98, P = 0.68, and P = 0.79, respectively) in diagnostic effectiveness.ConclusionsOur study suggested that the diagnostic accuracy of NAA tests is currently inadequate to substitute culture as a principal screening test. NAAT could be used in conjunction with microbiological culture due to the advantage of faster results and in situations where culture tests are not doable.
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Affiliation(s)
- Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Jiangyang District, Luzhou, China
- *Correspondence: Ke Chen, ; Suvash Chandra Ojha,
| | - Ke Chen
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Jiangyang District, Luzhou, China
- *Correspondence: Ke Chen, ; Suvash Chandra Ojha,
| | - Yue Yuan
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Sarfraz Ahmed
- Department of Basic Sciences, University of Veterinary and Animal Sciences Lahore, Narowal, Pakistan
| | - Aijaz Ahmad Malik
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Mehru Nisha
- Investigative Biomedical Science Research Cluster, Institute of Medical Science Technology, Universiti Kuala Lumpur, Kajang, Selangor, Malaysia
| | - Yun-Jian Sheng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Jiangyang District, Luzhou, China
| | - Changfeng Sun
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Jiangyang District, Luzhou, China
| | - Gang Wu
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Jiangyang District, Luzhou, China
| | - Cun-Liang Deng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Boyd S, Nseir S, Rodriguez A, Martin-Loeches I. Ventilator-associated pneumonia in critically ill patients with COVID-19 infection, a narrative review. ERJ Open Res 2022; 8:00046-2022. [PMID: 35891621 PMCID: PMC9080287 DOI: 10.1183/23120541.00046-2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/24/2022] [Indexed: 01/08/2023] Open
Abstract
COVID pneumonitis can cause patients to become critically ill. They may require intensive care and mechanical ventilation. Ventilator-associated pneumonia is a concern. This review aims to discuss the topic of ventilator-associated pneumonia in this group. Several reasons have been proposed to explain the elevated rates of VAP in critically ill COVID patients compared to non-COVID patients. Extrinsic factors include understaffing, lack of PPE and use of immunomodulating agents. Intrinsic factors include severe parenchymal damage, immune dysregulation, along with pulmonary vascular endothelial inflammation and thrombosis. The rate of VAP has been reported at 45.4%, with an ICU mortality rate of 42.7%. Multiple challenges to diagnosis exist. Other conditions such as acute respiratory distress syndrome, pulmonary oedema and atelectasis can present with similar features. Frequent growth of gram-negative bacteria has been shown in multiple studies, with particularly high rates of pseudomonas aeruginosa. The rate of invasive pulmonary aspergillosis has been reported at 4–30%. We would recommend the use of invasive techniques when possible. This will enable de-escalation of antibiotics as soon as possible, decreasing overuse. It is also important to keep other possible causes of ventilator-associated pneumonia in mind, such as COVID-19 associated pulmonary aspergillosis, cytomegalovirus, etc. Diagnostic tests such as galactomannan and B-D-glucan should be considered. These patients may face a long treatment course, with risk of re-infection, along with prolonged weaning, which carries its own long-term consequences.
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Comparison of a novel lateral-flow device to galactomannan assay at different time periods for detections of invasive aspergillosis. J Formos Med Assoc 2022; 121:2123-2129. [DOI: 10.1016/j.jfma.2022.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/25/2022] [Accepted: 04/11/2022] [Indexed: 11/21/2022] Open
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Fromentin M, Ricard JD, Roux D. Lung Microbiome in Critically Ill Patients. Life (Basel) 2021; 12:life12010007. [PMID: 35054400 PMCID: PMC8778861 DOI: 10.3390/life12010007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/11/2022] Open
Abstract
The historical hypothesis of sterility of the lungs was invalidated over a decade ago when studies demonstrated the existence of sparse but very diverse bacterial populations in the normal lung and the association between pulmonary dysbiosis and chronic respiratory diseases. Under mechanical ventilation, dysbiosis occurs rapidly with a gradual decline in diversity over time and the progressive predominance of a bacterial pathogen (mainly Proteobacteria) when lung infection occurs. During acute respiratory distress syndrome, an enrichment in bacteria of intestinal origin, mainly Enterobacteriaceae, is observed. However, the role of this dysbiosis in the pathogenesis of ventilator-associated pneumonia and acute respiratory distress syndrome is not yet fully understood. The lack of exploration of other microbial populations, viruses (eukaryotes and prokaryotes) and fungi is a key issue. Further analysis of the interaction between these microbial kingdoms and a better understanding of the host−microbiome interaction are necessary to fully elucidate the role of the microbiome in the pathogenicity of acute diseases. The validation of a consensual and robust methodology in order to make the comparison of the different studies relevant is also required. Filling these different gaps should help develop preventive and therapeutic strategies for both acute respiratory distress syndrome and ventilator-associated pneumonia.
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Affiliation(s)
- Mélanie Fromentin
- Anesthesiology and Intensive Care Department, AP-HP, Hôpital Cochin, 75014 Paris, France;
- UMR1137 IAME, Université de Paris, INSERM, 75018 Paris, France;
| | - Jean-Damien Ricard
- UMR1137 IAME, Université de Paris, INSERM, 75018 Paris, France;
- Médecine Intensive Réanimation, AP-HP, Hôpital Louis Mourier, DMU ESPRIT, 92700 Colombes, France
| | - Damien Roux
- Médecine Intensive Réanimation, AP-HP, Hôpital Louis Mourier, DMU ESPRIT, 92700 Colombes, France
- Institut Necker-Enfants Malades, Université de Paris, INSERM U1151, CNRS UMR 8253, 75015 Paris, France
- Correspondence: ; Tel.: +33-1-47-60-63-29
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Clark JA, Kean IRL, Curran MD, Khokhar F, White D, Daubney E, Conway Morris A, Navapurkar V, Bartholdson Scott J, Maes M, Bousfield R, Gouliouris T, Agrawal S, Inwald D, Zhang Z, Török ME, Baker S, Pathan N. Rapid Assay for Sick Children with Acute Lung infection Study (RASCALS): diagnostic cohort study protocol. BMJ Open 2021; 11:e056197. [PMID: 34845080 PMCID: PMC8634010 DOI: 10.1136/bmjopen-2021-056197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/11/2021] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION Lower respiratory tract infection (LRTI) is the most commonly treated infection in critically ill children. Pathogens are infrequently identified on routine respiratory culture, and this is a time-consuming process. A syndromic approach to rapid molecular testing that includes a wide range of bacterial and fungal targets has the potential to aid clinical decision making and reduce unnecessary broad spectrum antimicrobial prescribing. Here, we describe a single-centre prospective cohort study investigating the use of a 52-pathogen TaqMan array card (TAC) for LRTI in the paediatric intensive care unit (PICU). METHODS AND ANALYSIS Critically ill children with suspected LRTI will be enrolled to this 100 patient single-centre prospective observational study in a PICU in the East of England. Samples will be obtained via routine non-bronchoscopic bronchoalveolar lavage which will be sent for standard microbiology culture in addition to TAC. A blood draw will be obtained via any existing vascular access device. The primary outcomes of the study will be (1) concordance of TAC result with routine culture and 16S rRNA gene sequencing and (2) time of diagnostic result from TAC versus routine culture. Secondary outcomes will include impact of the test on total antimicrobial prescriptions, a description of the inflammatory profile of the lung and blood in response to pneumonia and a description of the clinical experience of medical and nursing staff using TAC. ETHICS AND DISSEMINATION This study has been approved by the Yorkshire and the Humber-Bradford Leeds Research Ethics Committee (REC reference 20/YH/0089). Informed consent will be obtained from all participants. Results will be published in peer-reviewed publications and international conferences. TRIAL REGISTRATION NUMBER NCT04233268.
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Affiliation(s)
- John Alexander Clark
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, Cambridge, UK
| | - Fahad Khokhar
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Deborah White
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Esther Daubney
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Vilas Navapurkar
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Josefin Bartholdson Scott
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Rachel Bousfield
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Shruti Agrawal
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David Inwald
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Zhenguang Zhang
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - M Estée Török
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Nazima Pathan
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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Abstract
PURPOSE OF REVIEW Pneumonia represents a major burden in clinical practice. A rapid etiological diagnosis is critical for optimizing the antibiotic use. Owing to the variety of possible pathogens and the time needed for bacterial cultures or usual polymerase chain reaction (PCR) assays, timely and precise diagnosis is a huge challenge. Several new rapid multiplex assays have been developed in the last decade to resolve these issues. This review aims to provide an overview of recent evidence on improvements and limitations of new rapid molecular assays for pneumonia. RECENT FINDINGS Several rapid multiplex-PCR assays are commercially available for upper or lower respiratory tract samples, allowing detection of a wide range of respiratory viruses, bacteria, and, in some cases, of several antibiotic resistance genes. Clinical evaluations demonstrated their good correlation with gold-standard assays but their lack of exhaustiveness, especially for hospital-acquired pneumonia. Studies that evaluated their potential benefits on antibiotic use suffered from important weaknesses with conflicting and limited results. SUMMARY New molecular assays may enable improvements in patient management and antibiotic use. Available studies highlight several benefits and the strong interrelations needed between microbiologists and physicians for their implementation and interpretation according to the clinical and epidemiological context.
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Accuracy of Molecular Amplification Assays for Diagnosis of Staphylococcal Pneumonia: a Systematic Review and Meta-analysis. J Clin Microbiol 2021; 59:e0300320. [PMID: 33568465 DOI: 10.1128/jcm.03003-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Rapid and accurate identification of staphylococcal pneumonia is crucial for effective antimicrobial stewardship. We performed a meta-analysis to evaluate the diagnostic value of nucleic acid amplification tests (NAAT) from lower respiratory tract (LRT) samples from suspected pneumonia patients to avoid superfluous empirical methicillin-resistant Staphylococcus aureus (MRSA) treatment. PubMed, Scopus, Embase, Web of Science, and the Cochrane Library Database were searched from inception to 2 September 2020. Data analysis was carried out using a bivariate random-effects model to estimate pooled sensitivity, specificity, positive likelihood ratio (PLR), and negative likelihood ratio (NLR). Of 1,808 citations, 24 publications comprising 32 data sets met our inclusion criteria. Twenty-two studies (n = 4,630) assessed the accuracy of the NAAT for methicillin-sensitive S. aureus (MSSA) detection, while 10 studies (n = 2,996) demonstrated the accuracy of the NAAT for MRSA detection. The pooled NAAT sensitivity and specificity (with 95% confidence interval [CI]) for all MSSA detection were higher (sensitivity of 0.91 [95% CI, 0.89 to 0.94], specificity of 0.94 [95% CI, 0.94 to 0.95]) than those of MRSA (sensitivity of 0.75 [95% CI, 0.69 to 0.80], specificity of 0.88 [95% CI, 0.86 to 0.89]) in lower respiratory tract (LRT) samples. NAAT pooled sensitivities differed marginally among different LRT samples, including sputum, endotracheal aspirate (ETA), and bronchoalveolar lavage (BAL) fluid. Noticeably, NAAT pooled specificity against microbiological culture was consistently ≥88% across various types of LRT samples. A meta-regression and subgroup analysis of study design, sample condition, and patient selection method could not explain the heterogeneity (P > 0.05) in the diagnostic efficiency. This meta-analysis has demonstrated that the NAAT can be applied as the preferred initial test for timely diagnosis of staphylococcal pneumonia in LRT samples for successful antimicrobial therapy.
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An evaluation of the Unyvero pneumonia system for rapid detection of microorganisms and resistance markers of lower respiratory infections-a multicenter prospective study on ICU patients. Eur J Clin Microbiol Infect Dis 2021; 40:2113-2121. [PMID: 33934275 DOI: 10.1007/s10096-021-04259-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
Rapid diagnosis of microorganisms and antibiotic resistance is vital for the appropriate treatment of patients with lower respiratory infections, especially for patients in Intensive Care Unit. We conducted a multicenter prospective study to evaluate the ability of the Unyvero pneumonia system for rapid detection from bronchoalveolar lavage fluid (BALF) in China. Eighty-four patients with lower respiratory infections were enrolled, and their BALF samples were collected, and Unyvero, a rapid molecular diagnostic sample-to-answer solution based on multiple PCRs, was applied to detect 21 types of pathogens and 19 types of resistance markers, compared to a routine bacterial culture method. The overall concordance of Unyvero and routine culture was 69/84 (82.1%). Unyvero detected more microorganisms than routine culture (38.1% vs 27.4%, P<0.05) and reported multi-pathogens in more patients than routine culture (10.7% vs 2.4%, P=0.01). The overall sensitivity and specificity of Unyvero for bacteria detection were 84.0% and 98.0%. Besides, Unyvero showed a good performance for antibiotic-resistant bacteria, except Pseudomonas aeruginosa. The concordance was 87.5-100% for methicillin-resistant Staphylococcus aureus and carbapenem-resistant isolates but was only 20-33.3% for Pseudomonas aeruginosa. The high-level semi-quantitative signal intensity of microorganisms detected positive by Unyvero correlates well with positive bacterial cultures. For specimens that were exposed to antibiotic treatment, the Unyvero pneumonia system showed a high concordance with routine bacterial culture and performs well for the detection of antibiotic-resistant bacteria, especially, carbapenem-resistant Klebsiella pneumoniae. It shows promise in guiding the clinical use of antibiotics, such as ceftazidime/avibactam. However, the system needs improvement in detecting resistance markers of Pseudomonas aeruginosa.
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13
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Multicenter Evaluation of the Unyvero Platform for Testing Bronchoalveolar Lavage Fluid. J Clin Microbiol 2021; 59:JCM.02497-20. [PMID: 33328178 DOI: 10.1128/jcm.02497-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/10/2020] [Indexed: 01/08/2023] Open
Abstract
Bronchoalveolar lavage (BAL) culture is a standard, though time-consuming, approach for identifying microorganisms in patients with severe lower respiratory tract (LRT) infections. The sensitivity of BAL culture is relatively low, and prior antimicrobial therapy decreases the sensitivity further, leading to overuse of empirical antibiotics. The Unyvero LRT BAL Application (Curetis GmbH, Germany) is a multiplex molecular panel that detects 19 bacteria, 10 antibiotic resistance markers, and a fungus, Pneumocystis jirovecii, in BAL fluid in ∼4.5 h. Its performance was evaluated using 1,016 prospectively collected and 392 archived specimens from 11 clinical trial sites in the United States. Overall positive and negative percent agreements with culture results for identification of bacteria that grow in routine cultures were 93.4% and 98.3%, respectively, with additional potential pathogens identified by Unyvero in 21.7% of prospectively collected specimens. For detection of P. jirovecii, the positive percent agreement with standard testing was 87.5%. Antibiotic resistance marker results were compared to standard antibiotic susceptibility test results to determine positive predictive values (PPVs). PPVs ranged from 80 to 100%, based on the microorganism and specific resistance marker(s). The Unyvero LRT BAL Application provides accurate detection of common agents of bacterial pneumonia and of P. jirovecii The sensitivity and rapidity of this panel suggest significant clinical value for choosing appropriate antibiotics and for antibiotic stewardship.
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14
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Jones NK, Conway Morris A, Curran MD, Parmar S, Sule O, Enoch DA, Aliyu SH, Zhang H, Jalal H, Navapurkar V, Murphy ME. Evaluating the use of a 22-pathogen TaqMan array card for rapid diagnosis of respiratory pathogens in intensive care. J Med Microbiol 2020; 69:971-978. [PMID: 32552987 DOI: 10.1099/jmm.0.001218] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Introduction. Pneumonia is highly prevalent in intensive care units (ICUs), with high associated mortality. Empirical treatment prioritizes breadth of coverage while awaiting laboratory diagnosis, often at the expense of antimicrobial stewardship. Microarrays use multiple parallel polymerase chain reactions to enable a rapid syndromic approach to laboratory diagnosis.Aim. To evaluate the clinical and laboratory implications of introducing a bespoke 22-pathogen TaqMan Array Card (TAC) for rapid pathogen detection in deep respiratory samples from adult ICUs.Methodology. TAC results from all ICU patients prospectively tested over a 9-month period at Cambridge's Clinical Microbiology and Public Health Laboratory were compared to those of corresponding conventional microbiological assays (culture-, PCR- or serology-based) in terms of result agreement and time-to-result availability. Clinical impact was assessed by retrospective review of medical records.Results. Seventy-one patients were included [45 (63 %) male, median age 59). Overall result agreement was 94 %, with TAC detecting more pathogens than conventional methods. TAC detected Streptococcus pneumoniae more readily than culture (7 vs 0 cases; P=0.02). TAC did not detect Aspergillus spp. in eight culture- or galactomannan-positive cases. The median turnaround time (1 day) was significantly shorter than that of bacterial/fungal culture, Pneumocystis jirovecii PCR and galactomannan testing (each 3 days; P<0.001), atypical bacteria serology (13 days; P<0.001) and Mycobacterium tuberculosis culture (46 days; P<0.001). Earlier result availability prompted discontinuation of unnecessary antimicrobials in 15/71 (21 %) cases, but had no bearing on patient isolation/deisolation.Conclusion. TAC provided greater overall yield of pathogen detection and faster turnaround times, permitting earlier discontinuation of unnecessary antimicrobials.
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Affiliation(s)
- Nick K Jones
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew Conway Morris
- The John Farman Intensive Care Unit, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Surendra Parmar
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Olajumoke Sule
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - David A Enoch
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Sani H Aliyu
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Hongyi Zhang
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Hamid Jalal
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Vilas Navapurkar
- The John Farman Intensive Care Unit, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Michael E Murphy
- NHS GGC, Glasgow Royal Infirmary, Department of Clinical Microbiology, New Lister Building, Alexandra Parade, Glasgow, UK.,Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
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15
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Luyt CE, Hékimian G, Bonnet I, Bréchot N, Schmidt M, Robert J, Combes A, Aubry A. Usefulness of point-of-care multiplex PCR to rapidly identify pathogens responsible for ventilator-associated pneumonia and their resistance to antibiotics: an observational study. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2020; 24:378. [PMID: 32586347 PMCID: PMC7316635 DOI: 10.1186/s13054-020-03102-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/17/2020] [Indexed: 01/07/2023]
Abstract
Background The use of multiplex PCR to shorten time to identification of pathogens and their resistance mechanisms for patients with ventilator-associated pneumonia (VAP) is attractive, but poorly studied. The multiplex PCR–based Unyvero pneumonia cartridge assay can directly identify 20 bacteria and one fungus, amongst the most frequently causing VAP, and 19 of their resistance markers in clinical specimens (bronchoalveolar lavage or tracheal aspirate), with a turnaround time of 4–5 h. We performed this study to evaluate the concordance between the multiplex PCR–based Unyvero pneumonia cartridge assay and conventional microbiological techniques to identify pathogens and their resistance mechanisms in patients with VAP. Methods All patients suspected of having VAP (January 2016 to January 2019), who underwent fiberoptic bronchoscopy with bronchoalveolar lavage fluid (BALF) and whose BALF microscopy examination revealed intracellular bacteria, were included. BALF conventional cultures (gold standard), antimicrobial susceptibility testing and processing for the Unyvero pneumonia cartridge were done. Culture and Unyvero results were compared. Results Compared to cultures of the 93 samples processed for both techniques, Unyvero correctly identified pathogens in 68 (73%) proven VAP episodes, was discordant for 25 (27%), detected no pathogen in 11 and overdetected a not otherwise found pathogen in six. For the eight remaining discordant results, the pathogen responsible for VAP was not included in the Unyvero cartridge panel or it grew at a non-significant level in culture. Amongst the 31 (33%) resistance mechanism discordances observed, 22 were resistance detection failures and 24 concerned Pseudomonas aeruginosa. Conclusions Compared to conventional microbiological cultures, the Unyvero pneumonia cartridge had poor diagnostic performance: it correctly identified pathogens and their resistance mechanisms in 73% and 67% of VAP cases, respectively. The lack of performance on the resistance mechanism was more pronounced when the pathogen detected was a Pseudomonas aeruginosa.
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Affiliation(s)
- Charles-Edouard Luyt
- Service de Médecine Intensive Réanimation, Institut de Cardiologie, Hospital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (APHP), Sorbonne Université, 47-83, Boulevard de l'Hôpital, 75651, Paris Cedex 13, France. .,Sorbonne Université, INSERM, UMRS_1166-ICAN Institute of Cardiometabolism and Nutrition, Paris, France.
| | - Guillaume Hékimian
- Service de Médecine Intensive Réanimation, Institut de Cardiologie, Hospital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (APHP), Sorbonne Université, 47-83, Boulevard de l'Hôpital, 75651, Paris Cedex 13, France
| | - Isabelle Bonnet
- Service de Bactériologie-Hygiène, Hospital Pitié-Salpêtrière, APHP, Sorbonne Université, Paris, France.,Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, équipe 2, Paris, France
| | - Nicolas Bréchot
- Service de Médecine Intensive Réanimation, Institut de Cardiologie, Hospital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (APHP), Sorbonne Université, 47-83, Boulevard de l'Hôpital, 75651, Paris Cedex 13, France.,Sorbonne Université, INSERM, UMRS_1166-ICAN Institute of Cardiometabolism and Nutrition, Paris, France
| | - Matthieu Schmidt
- Service de Médecine Intensive Réanimation, Institut de Cardiologie, Hospital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (APHP), Sorbonne Université, 47-83, Boulevard de l'Hôpital, 75651, Paris Cedex 13, France.,Sorbonne Université, INSERM, UMRS_1166-ICAN Institute of Cardiometabolism and Nutrition, Paris, France
| | - Jérôme Robert
- Service de Bactériologie-Hygiène, Hospital Pitié-Salpêtrière, APHP, Sorbonne Université, Paris, France.,Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, équipe 2, Paris, France
| | - Alain Combes
- Service de Médecine Intensive Réanimation, Institut de Cardiologie, Hospital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (APHP), Sorbonne Université, 47-83, Boulevard de l'Hôpital, 75651, Paris Cedex 13, France.,Sorbonne Université, INSERM, UMRS_1166-ICAN Institute of Cardiometabolism and Nutrition, Paris, France
| | - Alexandra Aubry
- Service de Bactériologie-Hygiène, Hospital Pitié-Salpêtrière, APHP, Sorbonne Université, Paris, France.,Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, équipe 2, Paris, France
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16
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Peiffer-Smadja N, Bouadma L, Mathy V, Allouche K, Patrier J, Reboul M, Montravers P, Timsit JF, Armand-Lefevre L. Performance and impact of a multiplex PCR in ICU patients with ventilator-associated pneumonia or ventilated hospital-acquired pneumonia. Crit Care 2020; 24:366. [PMID: 32560662 PMCID: PMC7303941 DOI: 10.1186/s13054-020-03067-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Early appropriate antibiotic therapy reduces morbidity and mortality of severe pneumonia. However, the emergence of bacterial resistance requires the earliest use of antibiotics with the narrowest possible spectrum. The Unyvero Hospitalized Pneumonia (HPN, Curetis) test is a multiplex PCR (M-PCR) system detecting 21 bacteria and 19 resistance genes on respiratory samples within 5 h. We assessed the performance and the potential impact of the M-PCR on the antibiotic therapy of ICU patients. METHODS In this prospective study, we performed a M-PCR on bronchoalveolar lavage (BAL) or plugged telescoping catheter (PTC) samples of patients with ventilated HAP or VAP with Gram-negative bacilli or clustered Gram-positive cocci. This study was conducted in 3 ICUs in a French academic hospital: the medical and infectious diseases ICU, the surgical ICU, and the cardio-surgical ICU. A multidisciplinary expert panel simulated the antibiotic changes they would have made if the M-PCR results had been available. RESULTS We analyzed 95 clinical samples of ventilated HAP or VAP (72 BAL and 23 PTC) from 85 patients (62 males, median age 64 years). The median turnaround time of the M-PCR was 4.6 h (IQR 4.4-5). A total of 90/112 bacteria were detected by the M-PCR system with a global sensitivity of 80% (95% CI, 73-88%) and specificity of 99% (95% CI 99-100). The sensitivity was better for Gram-negative bacteria (90%) than for Gram-positive cocci (62%) (p = 0.005). Moreover, 5/8 extended-spectrum beta-lactamases (CTX-M gene) and 4/4 carbapenemases genes (3 NDM, one oxa-48) were detected. The M-PCR could have led to the earlier initiation of an effective antibiotic in 20/95 patients (21%) and to early de-escalation in 37 patients (39%) but could also have led to one (1%) inadequate antimicrobial therapy. Among 17 empiric antibiotic treatments with carbapenems, 10 could have been de-escalated in the following hours according to the M-PCR results. The M-PCR also led to 2 unexpected diagnosis of severe legionellosis confirmed by culture methods. CONCLUSIONS Our results suggest that the use of a M-PCR system for respiratory samples of patients with VAP and ventilated HAP could improve empirical antimicrobial therapy and reduce the use of broad-spectrum antibiotics.
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Affiliation(s)
- Nathan Peiffer-Smadja
- Université de Paris, IAME, INSERM, Paris, F-75018, France.
- Infectious and Tropical Diseases Department, Bichat-Claude Bernard Hospital, AP-HP, Paris, 75018, France.
| | - Lila Bouadma
- Université de Paris, IAME, INSERM, Paris, F-75018, France
- Medical and Infectious Diseases ICU (MI2), Bichat-Claude Bernard Hospital, AP-HP, 75018, Paris, France
| | - Vincent Mathy
- Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Kahina Allouche
- Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Juliette Patrier
- Medical and Infectious Diseases ICU (MI2), Bichat-Claude Bernard Hospital, AP-HP, 75018, Paris, France
| | - Martin Reboul
- Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Philippe Montravers
- Département d'Anesthésie Réanimation, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
- INSERM UMR 1152, Physiopathologie et Epidémiologie des Maladies respiratoires, Paris, France
| | - Jean-François Timsit
- Université de Paris, IAME, INSERM, Paris, F-75018, France
- Medical and Infectious Diseases ICU (MI2), Bichat-Claude Bernard Hospital, AP-HP, 75018, Paris, France
| | - Laurence Armand-Lefevre
- Université de Paris, IAME, INSERM, Paris, F-75018, France
- Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
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17
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Mizusawa M, Carroll KC. Novel strategies for rapid identification and susceptibility testing of MRSA. Expert Rev Anti Infect Ther 2020; 18:759-778. [PMID: 32329637 DOI: 10.1080/14787210.2020.1760842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Methicillin-resistant Staphylococcus aureus (MRSA) is associated with adverse clinical outcomes and increased morbidity, mortality, length of hospital stay, and health-care costs. Rapid diagnosis of MRSA infections has been associated with positive impact on clinical outcomes. AREAS COVERED We searched relevant papers in PubMed for the last 10 years. In major papers, we scanned the bibliographies to ensure that important articles were included. This review describes screening and diagnostic test methods for MRSA and their analytical performances with a focus on rapid molecular-based assays including those that are on the horizon. Future novel technologies will allow more rapid detection of phenotypic resistance. In the case of whole-genome sequencing, detection of mutations may predict resistance, transmission, and virulence. EXPERT OPINION Currently there are many diagnostic options for the detection of MRSA in surveillance and clinical samples. In general, these are highly accurate and have resulted in improvements in targeted management and reduction in hospital or intensive care unit length of stay for both MSSA and MRSA. Impact on mortality has been variable. Promising novel technologies will not only accurately identify pathogens and detect their resistance markers but will allow discovery of virulence determinants that might further affect patient management.
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Affiliation(s)
- Masako Mizusawa
- Section of Infectious Diseases, Department of Internal Medicine, University of Missouri , Kansas, MO, USA
| | - Karen C Carroll
- Department of Pathology, Division of Medical Microbiology, The Johns Hopkins University School of Medicine , Baltimore, MD, USA
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18
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Dhesi Z, Enne VI, O'Grady J, Gant V, Livermore DM. Rapid and Point-of-Care Testing in Respiratory Tract Infections: An Antibiotic Guardian? ACS Pharmacol Transl Sci 2020; 3:401-417. [PMID: 32551433 PMCID: PMC7233852 DOI: 10.1021/acsptsci.0c00027] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Indexed: 12/15/2022]
Abstract
![]()
This
is a narrative review on the potential of rapid and point-of-care
microbiological testing in pneumonia patients, focusing particularly
on hospital-acquired and ventilator-associated pneumonia, which have
substantial mortality and diverse microbiology. This work is written
from a United Kingdom perspective, but much of it is generalizable
internationally. In a world where antimicrobial resistance is a major
international threat, the use of rapid molecular diagnostics has great
potential to improve both the management of pneumonia patients and
the stewardship of antibiotics. Rapid tests potentially can distinguish
patients with bacterial versus viral infection and can swiftly identify
bacterial pathogens and their resistances. We seek to answer the question:
“Can such tests be used as an antibiotic guardian?”
Their availability at the bedside rather than in the laboratory should
best ensure that results are swiftly used to optimize patient management
but will raise new challenges, not the least with respect to maintaining
quality control and microbiology/infection control input. A further
challenge lies in assessing the degree of trust that treating clinicians
will place in these molecular diagnostic tests, particularly when
early de-escalation of antibiotic therapy is indicated.
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Affiliation(s)
- Zaneeta Dhesi
- University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Virve I Enne
- University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Justin O'Grady
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UA, United Kingdom
| | - Vanya Gant
- University College London Hospitals NHS Foundation Trust, London NW1 2PG, United Kingdom
| | - David M Livermore
- University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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19
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Evaluation of a Novel Multiplex PCR Panel Compared to Quantitative Bacterial Culture for Diagnosis of Lower Respiratory Tract Infections. J Clin Microbiol 2020; 58:JCM.02013-19. [PMID: 32075901 DOI: 10.1128/jcm.02013-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/11/2020] [Indexed: 11/20/2022] Open
Abstract
Quantitative bacterial culture of bronchoalveolar lavage fluids (BALF) is labor-intensive, and the delay involved in performing culture, definitive identification, and susceptibility testing often results in prolonged use of broad-spectrum antibiotics. The Unyvero lower respiratory tract (LRT) panel (Curetis, Holzgerlingen, Germany) allows the multiplexed rapid detection and identification of 20 potential etiologic agents of pneumonia within 5 h of collection. In addition, the assay includes detection of gene sequences that confer antimicrobial resistance. We retrospectively compared the performance of the molecular panel to routine quantitative bacterial culture methods on remnant BALF. Upon testing 175 BALF, we were able to analyze positive agreement of 181 targets from 129 samples, and 46 samples were negative. The positive percent agreement (PPA) among the microbial targets was 96.5%, and the negative percent agreement (NPA) was 99.6%. The targets with a PPA of <100% were Staphylococcus aureus (34/37 [91.9%]), Streptococcus pneumoniae (10/11 [90.9%]), and Enterobacter cloacae complex (2/4 [50%]). For the analyzable resistance targets, concordance with phenotypic susceptibility testing was 79% (14/18). This study found the Unyvero LRT panel largely concordant with culture results; however, no outcome or clinical impact studies were performed.
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20
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Yoo IY, Huh K, Shim HJ, Yun SA, Chung YN, Kang OK, Huh HJ, Lee NY. Evaluation of the BioFire FilmArray Pneumonia Panel for rapid detection of respiratory bacterial pathogens and antibiotic resistance genes in sputum and endotracheal aspirate specimens. Int J Infect Dis 2020; 95:326-331. [PMID: 32179139 DOI: 10.1016/j.ijid.2020.03.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/06/2020] [Accepted: 03/06/2020] [Indexed: 10/24/2022] Open
Abstract
OBJECTIVES The performance of the investigational-use-only version of the BioFire FilmArray Pneumonia Panel (FA-Pneumo), a high-order nested multiplex PCR, was evaluated for the detection of typical respiratory bacterial pathogens and antibiotic resistance genes in sputa and endotracheal aspirate (ETA) specimens. METHODS Thirty-one sputa and 69 ETA specimens were analyzed. The diagnostic performance of FA-Pneumo was assessed using routine microbiological methods as the reference standard. RESULTS Overall sensitivity and specificity for organism detection using FA-Pneumo were 98.5% and 76.5%, respectively. The sensitivity for each pathogen was 100%, except for Klebsiella aerogenes, and the range of specificity was 83.3-99.0%. FA-Pneumo detected antimicrobial resistance genes in 17 out of 18 specimens (94.4%) that were resistant by antimicrobial susceptibility testing. FA-Pneumo additionally detected 25 resistance genes in 22 specimens, and sequencing for the presence of resistance genes confirmed the majority of these results (20/25, 80%). Semi-quantitative analysis of bacterial nucleic acid amounts by FA-Pneumo revealed that 88.2% of the identified bacteria (67/76) with ≥106 copies/ml also gave culture-positive results with significant amounts of bacteria. CONCLUSIONS FA-Pneumo is a rapid test with high sensitivity for the detection of bacteria and antimicrobial resistance genes in sputum and ETA specimens and could aid in determining antibiotic therapy.
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Affiliation(s)
- In Young Yoo
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyungmin Huh
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Asia Pacific Foundation for Infectious Diseases, Seoul, Republic of Korea
| | - Hyang Jin Shim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Sun Ae Yun
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Yoo Na Chung
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - On Kyun Kang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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21
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Papazian L, Klompas M, Luyt CE. Ventilator-associated pneumonia in adults: a narrative review. Intensive Care Med 2020; 46:888-906. [PMID: 32157357 PMCID: PMC7095206 DOI: 10.1007/s00134-020-05980-0] [Citation(s) in RCA: 312] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/19/2020] [Indexed: 12/15/2022]
Abstract
Ventilator-associated pneumonia (VAP) is one of the most frequent ICU-acquired infections. Reported incidences vary widely from 5 to 40% depending on the setting and diagnostic criteria. VAP is associated with prolonged duration of mechanical ventilation and ICU stay. The estimated attributable mortality of VAP is around 10%, with higher mortality rates in surgical ICU patients and in patients with mid-range severity scores at admission. Microbiological confirmation of infection is strongly encouraged. Which sampling method to use is still a matter of controversy. Emerging microbiological tools will likely modify our routine approach to diagnosing and treating VAP in the next future. Prevention of VAP is based on minimizing the exposure to mechanical ventilation and encouraging early liberation. Bundles that combine multiple prevention strategies may improve outcomes, but large randomized trials are needed to confirm this. Treatment should be limited to 7 days in the vast majority of the cases. Patients should be reassessed daily to confirm ongoing suspicion of disease, antibiotics should be narrowed as soon as antibiotic susceptibility results are available, and clinicians should consider stopping antibiotics if cultures are negative.
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Affiliation(s)
- Laurent Papazian
- Médecine Intensive Réanimation, Hôpital Nord, Hôpitaux de Marseille, Chemin des Bourrely, 13015, Marseille, France. .,Centre d'Etudes et de Recherches sur les Services de Santé et qualité de vie EA 3279, Groupe de recherche en Réanimation et Anesthésie de Marseille pluridisciplinaire (GRAM +), Faculté de médecine, Aix-Marseille Université, 13005, Marseille, France.
| | - Michael Klompas
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, USA
| | - Charles-Edouard Luyt
- Médecine Intensive Réanimation, Institut de Cardiologie, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM, UMRS 1166, ICAN Institute of Cardiometabolism and Nutrition, Sorbonne Université, Paris, France
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22
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Poole S, Clark TW. Rapid syndromic molecular testing in pneumonia: The current landscape and future potential. J Infect 2020; 80:1-7. [PMID: 31809764 PMCID: PMC7132381 DOI: 10.1016/j.jinf.2019.11.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 12/18/2022]
Abstract
Community acquired pneumonia (CAP), hospital-acquired pneumonia (HAP) and ventilator associated pneumonia (VAP) are all associated with significant mortality and cause huge expense to health care services around the world. Early, appropriate antimicrobial therapy is crucial for effective treatment. Syndromic diagnostic testing using novel, rapid multiplexed molecular platforms represents a new opportunity for rapidly targeted antimicrobial therapy to improve patient outcomes and facilitate antibiotic stewardship. In this article we review the currently available testing platforms and discuss the potential benefits and pitfalls of rapid testing in pneumonia.
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Affiliation(s)
- Stephen Poole
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust Southampton, United Kingdom.
| | - Tristan W Clark
- School of Clinical and Experimental Sciences, University of Southampton and NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
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Evaluation of the Unyvero i60 ITI® multiplex PCR for infected chronic leg ulcers diagnosis. METHODS IN MICROBIOLOGY 2020; 168:105796. [DOI: 10.1016/j.mimet.2019.105796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 11/19/2022]
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Purba AK, Ascobat P, Muchtar A, Wulandari L, Rosyid AN, Purwono PB, van der Werf TS, Friedrich AW, Postma MJ. Multidrug-Resistant Infections Among Hospitalized Adults With Community-Acquired Pneumonia In An Indonesian Tertiary Referral Hospital. Infect Drug Resist 2019; 12:3663-3675. [PMID: 31819549 PMCID: PMC6883944 DOI: 10.2147/idr.s217842] [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: 05/31/2019] [Accepted: 08/12/2019] [Indexed: 01/12/2023] Open
Abstract
Objectives To evaluate the clinical and microbiological appearance among hospitalized pneumonia patients focusing on resistance and risk factors for mortality in a referral hospital. Patients and methods The study was an observational retrospective study on patients with CAP from 2014 to 2016 at Dr Soetomo referral hospital of Surabaya, Indonesia. All positive cultures with antimicrobial susceptibility results from blood and respiratory specimens were included. Patients infected with drug-susceptible pathogens and MDR organisms were also assessed in terms of clinical characteristics, day-3 clinical improvement, and 14-day mortality. Results Of 202 isolates, 181 possessed antimicrobial susceptibility data. S. pneumoniae was the most prevalent pathogen causing CAP (18.3%). Most patients were empirically treated with ceftriaxone (n=75; 41.4%). Among beta-lactam antibiotics, the susceptibility to the third-generation cephalosporins remained relatively high, between 67.4% and 82.3%, compared with the other beta-lactams such as amoxicillin/clavulanate and ampicillin/sulbactam (a sensitivity rate of 36.5% and 47.5, respectively). For carbapenem antibiotics, imipenem and meropenem susceptibility was 69.6% and 82.3% respectively. Approximately 22% of isolates were identified as MDR that showed significant differences in clinical outcomes of 14-day mortality rates (p<0.001). Notably, patients with day-3 improvement had a lower risk of mortality (OR= 0.06; 95% CI= 0.02–0.19). Conclusion One-fifth of causative agents among hospitalized CAP cases were identified as MDR organisms. The pathogens of MDR and non-MDR CAP remain susceptible to the third-generation cephalosporins. Together with additional consideration of culture findings and Pneumonia Severity Index (PSI) assessment, a 3-day clinical assessment is essential to predict the prognosis of 14-day mortality. ![]()
Point your SmartPhone at the code above. If you have a QR code reader the video abstract will appear. Or use: https://youtu.be/QzMqf278Mac
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Affiliation(s)
- Abdul Kr Purba
- Unit of Global Health, Department of Health Sciences, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Pharmacology and Therapy, Faculty of Medicine, Universitas Airlangga - Dr. Soetomo Hospital, Surabaya, Indonesia.,Department of Pharmacology and Therapeutics, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia.,Unit of PharmacoTherapy, Epidemiology and -economics (PTE2), Department of Pharmacy, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Purwantyastuti Ascobat
- Department of Pharmacology and Therapeutics, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Armen Muchtar
- Department of Pharmacology and Therapeutics, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Laksmi Wulandari
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Airlangga - Dr. Soetomo Hospital, Surabaya, Indonesia
| | - Alfian Nur Rosyid
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Airlangga - Dr. Soetomo Hospital, Surabaya, Indonesia
| | - Priyo Budi Purwono
- Department of Microbiology, Faculty of Medicine, Universitas Airlangga - Dr. Soetomo Hospital, Surabaya, Indonesia
| | - Tjip S van der Werf
- Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten J Postma
- Unit of Global Health, Department of Health Sciences, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Pharmacology and Therapy, Faculty of Medicine, Universitas Airlangga - Dr. Soetomo Hospital, Surabaya, Indonesia.,Unit of PharmacoTherapy, Epidemiology and -economics (PTE2), Department of Pharmacy, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands.,Department of Economics, Econometrics and Finance, Faculty of Economics & Business, University of Groningen, Groningen, The Netherlands
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Tschiedel E, Goralski A, Steinmann J, Rath PM, Olivier M, Mellies U, Kottmann T, Stehling F. Multiplex PCR of bronchoalveolar lavage fluid in children enhances the rate of pathogen detection. BMC Pulm Med 2019; 19:132. [PMID: 31319825 PMCID: PMC6639929 DOI: 10.1186/s12890-019-0894-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/10/2019] [Indexed: 12/23/2022] Open
Abstract
Background Culturing of bronchoalveolar lavage (BAL) fluid is a commonly used method for pathogen detection in pneumonia. However, the sensitivity is low, especially in patients pre-treated with anti-infective agents. The early detection of a pathogen is crucial for the outcome of respiratory tract infections. For bloodstream infections, a multiplex polymerase chain reaction (PCR) assay (SeptiFast®, SF) is available for improved pathogen detection from blood. Objective The aim of the present study was to determine whether the SF assay is applicable to the BAL of children with pulmonary infections and whether the frequency of pathogen detection is enhanced by the use of this multiplex PCR method. Methods We investigated 70 BAL samples of 70 children simultaneously by culture and multiplex PCR. The frequency of pathogen detection was compared. Results Pathogens were detected more frequently by SF than by culture (83% vs. 31%; p < 0.001). This advantage was shown for immunocompetent patients (p = 0.001) as well as for immunocompromised patients (p = 0.003). The majority (38/44; 86%) of the Gram positive cocci were only detected by SF. Fungal organisms were detected in 7/70 patients (10%) by SF and in 2/70 (3%) by culture (p = 0.125). Conclusion Compared to conventional culture, the use of the SF assay on the BAL of children with pneumonia increases pathogen detection rates and therefore adds important information to guide anti-infective therapy.
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Affiliation(s)
- Eva Tschiedel
- Department of Pediatrics I, University Duisburg-Essen, University Hospital Essen, Hufelandstr. 55, 45122, Essen, Germany.
| | - Arkadius Goralski
- Department of Pediatrics III, University Duisburg-Essen, University Hospital Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Jörg Steinmann
- Institute for Medical Microbiology, University of Duisburg-Essen, Essen, Germany.,Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Klinikum Nürnberg, Paracelsus Medical University, Nuremberg, Germany
| | - Peter-Michael Rath
- Institute for Medical Microbiology, University of Duisburg-Essen, Essen, Germany
| | - Margarete Olivier
- Department of Pediatrics III, University Duisburg-Essen, University Hospital Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Uwe Mellies
- Department of Pediatrics III, University Duisburg-Essen, University Hospital Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Tanja Kottmann
- Private Institute of Medical Statistics, 59077, Hamm, Westfalen, Germany
| | - Florian Stehling
- Department of Pediatrics III, University Duisburg-Essen, University Hospital Essen, Hufelandstr. 55, 45122, Essen, Germany
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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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Trotter AJ, Aydin A, Strinden MJ, O'Grady J. Recent and emerging technologies for the rapid diagnosis of infection and antimicrobial resistance. Curr Opin Microbiol 2019; 51:39-45. [PMID: 31077935 DOI: 10.1016/j.mib.2019.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/04/2019] [Accepted: 03/08/2019] [Indexed: 10/26/2022]
Abstract
The rise in antimicrobial resistance (AMR) is predicted to cause 10 million deaths per year by 2050 unless steps are taken to prevent this looming crisis. Microbiological culture is the gold standard for the diagnosis of bacterial/fungal pathogens and antimicrobial resistance and takes 48 hours or longer. Hence, antibiotic prescriptions are rarely based on a definitive diagnosis and patients often receive inappropriate treatment. Rapid diagnostic tools are urgently required to guide appropriate antimicrobial therapy, thereby improving patient outcomes and slowing AMR development. We discuss new technologies for rapid infection diagnosis including: sample-in-answer-out PCR-based tests, BioFire FilmArray and Curetis Unyvero; rapid susceptibility tests, Accelerate Pheno and microfluidic tests; and sequencing-based approaches, focusing on targeted and clinical metagenomic nanopore sequencing.
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Affiliation(s)
- Alexander J Trotter
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Alp Aydin
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Michael J Strinden
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Justin O'Grady
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.
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Comparison of Unyvero P55 Pneumonia Cartridge, in-house PCR and culture for the identification of respiratory pathogens and antibiotic resistance in bronchoalveolar lavage fluids in the critical care setting. Eur J Clin Microbiol Infect Dis 2019; 38:1171-1178. [PMID: 30859358 DOI: 10.1007/s10096-019-03526-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/28/2019] [Indexed: 10/27/2022]
Abstract
Faster respiratory pathogen detection and antibiotic resistance identification are important in critical care due to the severity of illness, significant prior antibiotic exposure and infection control implications. Our objective was to compare the performance of the commercial Unyvero P55 Pneumonia Cartridge (Curetis AG) with routine bacterial culture methods and in-house bacterial multiplex real-time PCR assays. Seventy-four bronchoalveolar lavage specimens from patients admitted to a Scottish intensive care unit (ICU) over a 33-month period were tested prospectively by routine culture and viral PCR and retrospectively by Unyvero P55 and in-house bacterial PCR. Sensitivity/specificity was 56.9%/58.5% and 63.2%/54.8% for the Unyvero P55 and in-house bacterial PCR panels respectively; sensitivity for in-panel targets was 63.5 and 83.7% respectively. Additional organisms were detected by Unyvero P55 and in-house bacterial PCR panels in 16.2% specimens. Antibiotics were changed on the basis of routine test results in 48.3% cases; of these, true-positive or true-negative results would have been obtained earlier by Unyvero P55 or in-house bacterial PCR panel in 15 (53.6%) and 17 (60.7%) cases respectively. However, a false-negative molecular test result may have been acted upon in six (21.4%) cases with either assay. Sensitivity/specificity of Unyvero P55 antibiotic resistance detection was 18.8%/94.9% respectively. Molecular testing identified a number of respiratory pathogens in this patient cohort that were not grown in culture, but resistance detection was not a reliable tool for faster antibiotic modification. In their current set-up, molecular tests may only have benefit as additional tests in the ICU pneumonia setting.
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29
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Papan C, Meyer-Buehn M, Laniado G, Huebner J. Evaluation of the multiplex PCR based assay Unyvero implant and tissue infection application for pathogen and antibiotic resistance gene detection in children and neonates. Infection 2018; 47:195-200. [PMID: 30132251 DOI: 10.1007/s15010-018-1192-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/11/2018] [Indexed: 01/31/2023]
Abstract
BACKGROUND Skin and soft tissue infections have a high disease burden in children. The emergence of multidrug-resistant bacteria over the last decades has heavily influenced hospitalization rates, morbidity and mortality. In addition, with increased survival rates in neonatology and oncology, health-care associated infections are more frequently encountered. There is a growing need for fast and feasible diagnostic tools for the recognition of microorganisms and drug resistances. METHODS In this prospective study, we compared results of routine culture with the multiplex PCR based Unyvero Implant and Tissue Infection (ITI) application. Specimens were obtained from different sources from neonates and children. RESULTS We analyzed specimens from 29 patients (72.4% male) with a median age of 8.1 years (range 0.03-15.2). Concordance between Unyvero ITI and culture was reached in 16 of 29 samples (55.2%). Unyvero ITI yielded an overall sensitivity and specificity of 76.3% and 96.5%, respectively. Accuracies were best for non-fermenting bacteria, for which sensitivity was 100% and specificity 98.2%. Detection rates were lower for Gram-positive bacteria (68.8 and 95.2%, respectively). Unyvero correctly detected one blaOXA-24/40 producing Acinetobacter baumannii, while none of the six gyrA87 had a correlate in antimicrobial susceptibility testing. CONCLUSIONS Unyvero ITI quickly provides additional information relevant for clinical decision-makers. Sensitivity of the PCR must be improved especially for Gram-positive bacteria, and further studies are needed to assess the impact on clinical decision-making and outcome.
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Affiliation(s)
- Cihan Papan
- University Children's Hospital at Dr. von Haunersches Kinderspital, Ludwig Maximilians University, Munich, Germany. .,Pediatric Infectious Diseases, University Children's Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany.
| | - Melanie Meyer-Buehn
- University Children's Hospital at Dr. von Haunersches Kinderspital, Ludwig Maximilians University, Munich, Germany
| | - Gudrun Laniado
- University Children's Hospital at Dr. von Haunersches Kinderspital, Ludwig Maximilians University, Munich, Germany
| | - Johannes Huebner
- University Children's Hospital at Dr. von Haunersches Kinderspital, Ludwig Maximilians University, Munich, Germany
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Silva ARAD, Silva TCD, Bom GJT, Vasconcelos RMB, Junior RS. Ventilator-associated pneumonia agents in Brazilian Neonatal Intensive Care Units – a systematic review. Braz J Infect Dis 2018; 22:338-344. [PMID: 30278872 PMCID: PMC9427972 DOI: 10.1016/j.bjid.2018.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/10/2018] [Accepted: 06/15/2018] [Indexed: 12/18/2022] Open
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