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Thomas JK, Clark J, Arora V, Burgess DS, Burgess DR, Mynatt RP, VanHoose JD, Wallace KL, Cotner SE. Performance of ePlex® blood culture identification panels in clinical isolates and characterization of antimicrobial stewardship opportunities. Diagn Microbiol Infect Dis 2024; 109:116269. [PMID: 38692201 DOI: 10.1016/j.diagmicrobio.2024.116269] [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: 08/03/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 05/03/2024]
Abstract
We assessed the performance of GenMark's ePlex® Blood Culture Identification (BCID) Panels for overall agreement of organism identification and resistance mechanism detection with standard microbiologic methods. This study included patients with a positive blood culture from May 2020 to January 2021. The primary outcomes were to assess concordance of ePlex® organism identification with standard identification methods and concordance of ePlex® genotypic resistance mechanism detection with standard phenotypic susceptibility testing. Secondary outcomes included panel specific performance and characterization of antimicrobial stewardship opportunities. The overall identification concordance rate in 1276 positive blood cultures was 98.1%. The overall concordance for the presence of resistance markers was 98.2% and concordance for the absence of resistance markers was 100%. A majority of ePlex® results (69.5%) represented opportunities for potential antimicrobial stewardship intervention. High concordance rates between the ePlex® BCID panels and standard identification and susceptibility methods enable utilization of results to guide rapid antimicrobial optimization.
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Affiliation(s)
- Jenni K Thomas
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA
| | - Justin Clark
- University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Vaneet Arora
- University of Kentucky College of Medicine, Lexington, KY, USA; Department of Pathology and Laboratory Medicine, University of Kentucky HealthCare, Lexington, KY, USA
| | - David S Burgess
- University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Donna R Burgess
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA; University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Ryan P Mynatt
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA
| | - Jeremy D VanHoose
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA
| | - Katie L Wallace
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA; University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Sarah E Cotner
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA; University of Kentucky College of Pharmacy, Lexington, KY, USA.
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Pina-Vaz C, Silva-Dias A, Martins-Oliveira I, Gomes R, Perez-Viso B, Cruz S, Rodrigues AG, Sarmento A, Cantón R. A multisite validation of a two hours antibiotic susceptibility flow cytometry assay directly from positive blood cultures. BMC Microbiol 2024; 24:187. [PMID: 38802760 PMCID: PMC11131321 DOI: 10.1186/s12866-024-03341-1] [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: 07/25/2023] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Rapid antimicrobial susceptibility testing (AST) is urgently needed to provide safer treatment to counteract antimicrobial resistance. This is critical in septic patients, because resistance increases empiric therapy uncertainty and the risk of a poor outcome. We validate a novel 2h flow cytometry AST assay directly from positive blood cultures (PBC) by using a room temperature stable FASTgramneg and FASTgrampos kits (FASTinov® Porto, Portugal) in three sites: FASTinov (site-1), Hospital Ramon y Cajal, Madrid, Spain (site-2) and Centro Hospitalar S. João, Porto, Portugal (site-3). A total of 670 PBC were included: 333 spiked (site-1) and 337 clinical PBC (151 site-2 and 186 site-3): 367 gram-negative and 303 gram-positive. Manufacturer instructions were followed for sample preparation, panel inoculation, incubation (1h/37ºC) and flow cytometry analysis using CytoFlex (Site-1 and -2) or DxFlex (site-3) both instruments from Beckman-Coulter, USA. RESULTS A proprietary software (bioFAST) was used to immediately generate a susceptibility report in less than 2 h. In parallel, samples were processed according to reference AST methods (disk diffusion and/or microdilution) and interpreted with EUCAST and CLSI criteria. Additionally, ten samples were spiked in all sites for inter-laboratory reproducibility. Sensitivity and specificity were >95% for all antimicrobials. Reproducibility was 96.8%/95.0% for FASTgramneg and 95.1%/95.1% for FASTgrampos regarding EUCAST/CLSI criteria, respectively. CONCLUSION FASTinov® kits consistently provide ultra-rapid AST in 2h with high accuracy and reproducibility on both Gram-negative and Gram-positive bacteria. This technology creates a new paradigm in bacterial infection management and holds the potential to significantly impact septic patient outcomes and antimicrobial stewardship.
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Affiliation(s)
- C Pina-Vaz
- FASTinov SA, UPTEC Science and Technology Campus, Porto, Portugal.
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal.
- CINTESIS/RISE-Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, Porto, Portugal.
| | - A Silva-Dias
- FASTinov SA, UPTEC Science and Technology Campus, Porto, Portugal
- CINTESIS/RISE-Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, Porto, Portugal
| | - I Martins-Oliveira
- FASTinov SA, UPTEC Science and Technology Campus, Porto, Portugal
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - R Gomes
- FASTinov SA, UPTEC Science and Technology Campus, Porto, Portugal
| | - B Perez-Viso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - S Cruz
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - A G Rodrigues
- FASTinov SA, UPTEC Science and Technology Campus, Porto, Portugal
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
- CINTESIS/RISE-Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, Porto, Portugal
| | - A Sarmento
- Department of Infectious Diseases, Centro Hospitalar de São João, Porto, Portugal
| | - R Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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Gopikrishnan M, Haryini S, C GPD. Emerging strategies and therapeutic innovations for combating drug resistance in Staphylococcus aureus strains: A comprehensive review. J Basic Microbiol 2024; 64:e2300579. [PMID: 38308076 DOI: 10.1002/jobm.202300579] [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: 10/03/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 02/04/2024]
Abstract
In recent years, antibiotic therapy has encountered significant challenges due to the rapid emergence of multidrug resistance among bacteria responsible for life-threatening illnesses, creating uncertainty about the future management of infectious diseases. The escalation of antimicrobial resistance in the post-COVID era compared to the pre-COVID era has raised global concern. The prevalence of nosocomial-related infections, especially outbreaks of drug-resistant strains of Staphylococcus aureus, have been reported worldwide, with India being a notable hotspot for such occurrences. Various virulence factors and mutations characterize nosocomial infections involving S. aureus. The lack of proper alternative treatments leading to increased drug resistance emphasizes the need to investigate and examine recent research to combat future pandemics. In the current genomics era, the application of advanced technologies such as next-generation sequencing (NGS), machine learning (ML), and quantum computing (QC) for genomic analysis and resistance prediction has significantly increased the pace of diagnosing drug-resistant pathogens and insights into genetic intricacies. Despite prompt diagnosis, the elimination of drug-resistant infections remains unattainable in the absence of effective alternative therapies. Researchers are exploring various alternative therapeutic approaches, including phage therapy, antimicrobial peptides, photodynamic therapy, vaccines, host-directed therapies, and more. The proposed review mainly focuses on the resistance journey of S. aureus over the past decade, detailing its resistance mechanisms, prevalence in the subcontinent, innovations in rapid diagnosis of the drug-resistant strains, including the applicants of NGS and ML application along with QC, it helps to design alternative novel therapeutics approaches against S. aureus infection.
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Affiliation(s)
- Mohanraj Gopikrishnan
- Department of Integrative Biology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Sree Haryini
- Department of Biomedical Sciences, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - George Priya Doss C
- Department of Integrative Biology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
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Chastain DB, White BP, Tu PJ, Chan S, Jackson BT, Kubbs KA, Bandali A, McDougal S, Henao-Martínez AF, Cluck DB. Candidemia in Adult Patients in the ICU: A Reappraisal of Susceptibility Testing and Antifungal Therapy. Ann Pharmacother 2024; 58:305-321. [PMID: 37272474 DOI: 10.1177/10600280231175201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
OBJECTIVE To provide updates on the epidemiology and recommendations for management of candidemia in patients with critical illness. DATA SOURCES A literature search using the PubMed database (inception to March 2023) was conducted using the search terms "invasive candidiasis," "candidemia," "critically ill," "azoles," "echinocandin," "antifungal agents," "rapid diagnostics," "antifungal susceptibility testing," "therapeutic drug monitoring," "antifungal dosing," "persistent candidemia," and "Candida biofilm." STUDY SELECTION/DATA EXTRACTION Clinical data were limited to those published in the English language. Ongoing trials were identified through ClinicalTrials.gov. DATA SYNTHESIS A total of 109 articles were reviewed including 25 pharmacokinetic/pharmacodynamic studies and 30 studies including patient data, 13 of which were randomized controlled clinical trials. The remaining 54 articles included fungal surveillance data, in vitro studies, review articles, and survey data. The current 2016 Infectious Diseases Society of America (IDSA) Clinical Practice Guideline for the Management of Candidiasis provides recommendations for selecting empiric and definitive antifungal therapies for candidemia, but data are limited regarding optimized dosing strategies in critically ill patients with dynamic pharmacokinetic changes or persistent candidemia complicated. RELEVANCE TO PATIENT CARE AND CLINICAL PRACTICE Outcomes due to candidemia remain poor despite improved diagnostic platforms, antifungal susceptibility testing, and antifungal therapy selection for candidemia in critically ill patients. Earlier detection and identification of the species causing candidemia combined with recognition of patient-specific factors leading to dosing discrepancies are crucial to improving outcomes in critically ill patients with candidemia. CONCLUSIONS Treatment of candidemia in critically ill patients must account for the incidence of non-albicans Candida species and trends in antifungal resistance as well as overcome the complex pathophysiologic changes to avoid suboptimal antifungal exposure.
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Affiliation(s)
- Daniel B Chastain
- Department of Clinical & Administrative Pharmacy, University of Georgia College of Pharmacy, Albany, GA, USA
| | - Bryan P White
- University of Oklahoma Health Medical Center, Oklahoma City, OK, USA
| | - Patrick J Tu
- Charlie Norwood VA Medical Center, Augusta, GA, USA
| | - Sophea Chan
- Department of Clinical & Administrative Pharmacy, University of Georgia College of Pharmacy, Albany, GA, USA
- Department of Pharmacy, Phoebe Putney Memorial Hospital, Albany, GA, USA
| | | | - Kara A Kubbs
- University of Oklahoma Health Medical Center, Oklahoma City, OK, USA
| | - Aiman Bandali
- Overlook Medical Center, Atlantic Health System, Summit, NJ, USA
| | | | - Andrés F Henao-Martínez
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - David B Cluck
- Department of Pharmacy Practice, Bill Gatton College of Pharmacy, East Tennessee State University, Johnson City, TN, USA
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Chang KM, Haghamad A, Saunders-Hao P, Shaffer A, Mirsaidi N, Zimilover A, Epstein M, Jain S, Streva V, Juretschko S, Demissie S, Gautam-Goyal P. The clinical impact of early detection of ESBL-producing Enterobacterales with PCR-based blood culture assays. Am J Infect Control 2024; 52:73-80. [PMID: 37544512 DOI: 10.1016/j.ajic.2023.08.001] [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: 06/03/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/08/2023]
Abstract
BACKGROUND Starting January 4, 2021, our health system core microbiology laboratory changed blood culture identification (BCID) platforms to ePlex BCID from BioFire BCID1 with the additional capability to detect the blaCTX-M-Type gene of ESBL-producing organisms. Clinical outcomes of ESBL bloodstream infections (BSI) after implementing ePlex BCID were unknown. METHODS Patients with ESBL BSI were compared pre and postimplementation of ePlex BCID in this 11-hospital retrospective analysis (BioFire BCID1 in 2019 vs ePlex BCID in 2021). The primary outcome was time from the Gram stain result to escalation to a carbapenem. Secondary outcomes included in-hospital mortality, 30-day readmission rate, length of stay (LOS), and the duration of antimicrobial therapy. RESULTS A total of 275 patients were analyzed. The median time of Gram stain result to escalation to carbapenem was reduced from 44.5 hours with BioFire BCID1 to 7.9 hours with ePlex BCID (P < .001). There were no significant differences in mortality, 30-day readmission, or LOS. The duration of antimicrobial therapy for ESBL BSI was lower in the ePlex BCID group (from 14.4 days to 12.7 days, P = .014). CONCLUSIONS Timely detection of the blaCTX-M-Type gene by BCID provides valuable information for the early initiation of appropriate and effective antimicrobial therapy. Although it was not associated with lower mortality, 30-day readmission, or LOS, it may have benefits such as decreasing antimicrobial exposure to patients.
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Affiliation(s)
- Kai-Ming Chang
- Division of Infectious Diseases, Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA; Division of Infectious Diseases, Department of Medicine, Koo Foundation Sun Yat-Sen Cancer Center, Taipei, Taiwan.
| | - Aya Haghamad
- Pathology and Laboratory Medicine, Northwell Health Laboratories, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | | | - Alexander Shaffer
- Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - Niloofar Mirsaidi
- Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - Adam Zimilover
- Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - Marcia Epstein
- Division of Infectious Diseases, Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - Sumeet Jain
- Department of Pharmacy, North Shore University Hospital, Manhasset, NY, USA
| | - Vincent Streva
- Pathology and Laboratory Medicine, Northwell Health Laboratories, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - Stefan Juretschko
- Pathology and Laboratory Medicine, Northwell Health Laboratories, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - Seleshi Demissie
- Biostatistics Unit, Feinstein Institutes for Medical Research, Staten Island University Hospital, Staten Island, NY, USA
| | - Pranisha Gautam-Goyal
- Division of Infectious Diseases, Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
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Otto C, Babady NE. Epidemiology and Outcomes of Non-albicans Candida Bloodstream Infections in Transplant Recipients and Cancer Patients. Mycopathologia 2023; 188:863-871. [PMID: 37365379 DOI: 10.1007/s11046-023-00765-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/10/2023] [Indexed: 06/28/2023]
Abstract
We performed a retrospective survey of non-Candida albicans candidemia in patients with cancer, including those with solid tumors and those with hematological malignancies as well as transplants patients both, solid-organ transplant recipients and hematopoietic stem cell transplant recipients. The study was performed at two healthcare centers in New York City and covered the years 2018-2022. A total of 292 patients (318 isolates) were included in the study. In order of frequency, C. glabrata (38%) was the most common species recovered, followed by C. parapsilosis (19.2%), C. tropicalis (12.6%), C. krusei (10.7%), C. lusitaniae (5.7%), and C. guilliermondii (4.4%). Micafungin was the most common antifungal treatment and 18.5% of patients were on antifungal prophylaxis. The 30-day crude mortality was 40%. 4.5% of patients had more than one non-albicans species detected. In conclusion, this study represents one of the largest surveys of non-albicans species in cancer and transplant patients and provides data on the current epidemiology of these Candida species in this patient population.
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Affiliation(s)
- Caitlin Otto
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | - N Esther Babady
- Department of Pathology and Laboratory Medicine, Department of Medicine, Memorial Sloan Kettering Cancer Center, 327 East 64th Street CLM 522, New York, NY, 10065, USA.
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Witt LS, Page A, Burd EM, Ozturk T, Weiss DS, Ray SM, Satola S, Gottlieb LB. Discordant antimicrobial susceptibility and polymerase chain reaction (PCR) testing in a Klebsiella pneumoniae isolate with a carbapenemase gene. Infect Control Hosp Epidemiol 2023; 44:2100-2102. [PMID: 37652898 DOI: 10.1017/ice.2023.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Affiliation(s)
- Lucy S Witt
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia
- Georgia Emerging Infections Program, Atlanta Veterans' Affairs Medical Center, Decatur, Georgia
| | - Alex Page
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia
- Georgia Emerging Infections Program, Atlanta Veterans' Affairs Medical Center, Decatur, Georgia
| | - Eileen M Burd
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
- Emory Antibiotic Resistance Center, Atlanta, Georgia
| | - Tugba Ozturk
- Emory Antibiotic Resistance Center, Atlanta, Georgia
| | - David S Weiss
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia
- Emory Antibiotic Resistance Center, Atlanta, Georgia
| | - Susan M Ray
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia
- Georgia Emerging Infections Program, Atlanta Veterans' Affairs Medical Center, Decatur, Georgia
| | - Sarah Satola
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia
- Georgia Emerging Infections Program, Atlanta Veterans' Affairs Medical Center, Decatur, Georgia
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
- Emory Antibiotic Resistance Center, Atlanta, Georgia
| | - Lindsey B Gottlieb
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia
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Smith RD, Johnson JK, Ernst RK. Comparison of 3 diagnostic platforms for identification of bacteria and yeast from positive blood culture bottles. Diagn Microbiol Infect Dis 2023; 107:116018. [PMID: 37478505 DOI: 10.1016/j.diagmicrobio.2023.116018] [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: 02/23/2023] [Revised: 04/26/2023] [Accepted: 07/03/2023] [Indexed: 07/23/2023]
Abstract
Managing bloodstream infections requires fast and accurate diagnostics. Culture-based diagnostic methods for identification from positive blood culture require 24-hour subculture, potentially delaying time to appropriate therapy. Positive blood cultures were collected (n = 301) from September 2021 to August 2022 at the University of Maryland Medical Center. Platforms compared were BioFire® BCID2, Sepsityper®, and short-term culture. For monomicrobial cultures, FilmArray® BCID2 identified 88.3% (241/273) of pathogens. Rapid Sepsityper® identified 76.9% (210/273) of pathogens. Sepsityper® extraction identified 82.4% (225/273) of pathogens. Short-term culture identified 83.5% (228/273) of pathogens. For polymicrobial cultures, Sepsityper®, short-term culture, and BioFire® BCID2 had complete identifications at 10.7% (3/28), 0%, and 92.9% (26/28), respectively. Time-to-results for Rapid Sepsityper®, Sepsityper® extraction, BioFire® BCID2, and Short-term culture were 35, 52, 65, and 306 minutes, respectively. Performance of these platforms can reduce time-to-results and may help effectively treat bloodstream infections faster. Accuracy, time-to-result, and hands-on time are important factors when evaluation diagnostic platforms.
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Affiliation(s)
- Richard D Smith
- Department of Pathology, School of Medicine, University of Maryland, Baltimore, MD, USA; Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA.
| | - J Kristie Johnson
- Department of Pathology, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Robert K Ernst
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA
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Chatelard PA, Rousseau N, Parmeland L, Metral P, Pariset C, Vivier E. Shortening identification times: comparative observational study of three early blood culture testing protocols. Front Cell Infect Microbiol 2023; 13:1192002. [PMID: 37533929 PMCID: PMC10390722 DOI: 10.3389/fcimb.2023.1192002] [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: 03/22/2023] [Accepted: 06/27/2023] [Indexed: 08/04/2023] Open
Abstract
Background While early appropriate antibiotic therapy is a proven means of limiting the progression of infections, especially bacteremia, empirical antibiotic therapy in sepsis is ineffective up to 30%. The aim of this study was to compare early blood culture testing protocols in terms of their ability to shorten the delay between blood sampling and appropriate antibiotic therapy. Methods In this french observational study, we compared three blood culture testing protocols. Positive blood cultures were tested using either GenMark ePlex panels (multiplex PCR period), a combination of MRSA/SA PCR, β-Lacta and oxidase tests (multitest period), or conventional identification and susceptibility tests only (reference period). Conventional identification and susceptibility tests were performed in parallel for all samples, as the gold standard. Results Among the 270 patients with positive blood cultures included, early and conventional results were in good agreement, especially for the multitest period. The delay between a blood culture positivity and initial results was 3.8 (2.9-6.9) h in the multiplex PCR period, 2.6 (1.3-4.5) h in the multitest period and 3.7 (1.8-8.2) h in the reference period (p<0.01). Antibiotic therapy was initiated or adjusted in 68 patients based on early analysis results. The proportion of patients receiving appropriate antibiotic therapy within 48 h of blood sampling was higher in the multiplex PCR and multitest periods, (respectively 90% and 88%) than in the reference period (71%). Conclusion These results suggest rapid bacterial identification and antibiotic resistance tests are feasible, efficient and can expedite appropriate antibiotic therapy.
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Affiliation(s)
| | - Nathalie Rousseau
- Centre Hospitalier Saint Joseph Saint Luc, Laboratoire de biologie médicale, Lyon, France
| | - Laurence Parmeland
- Centre Hospitalier Saint Joseph Saint Luc, Laboratoire de biologie médicale, Lyon, France
| | - Pierre Metral
- Centre Hospitalier Saint Joseph Saint Luc, Département d’Information Médicale, Lyon, France
| | - Caroline Pariset
- Centre Hospitalier Saint Joseph Saint Luc, Maladies Infectieuses, Lyon, France
| | - Emmanuel Vivier
- Centre Hospitalier Saint Joseph Saint Luc, Médecine Intensive Réanimation, Lyon, France
- Centre Hospitalier Saint Joseph Saint Luc, Unité de Recherche Clinique, Lyon, France
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Fang W, Wu J, Cheng M, Zhu X, Du M, Chen C, Liao W, Zhi K, Pan W. Diagnosis of invasive fungal infections: challenges and recent developments. J Biomed Sci 2023; 30:42. [PMID: 37337179 DOI: 10.1186/s12929-023-00926-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/13/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND The global burden of invasive fungal infections (IFIs) has shown an upsurge in recent years due to the higher load of immunocompromised patients suffering from various diseases. The role of early and accurate diagnosis in the aggressive containment of the fungal infection at the initial stages becomes crucial thus, preventing the development of a life-threatening situation. With the changing demands of clinical mycology, the field of fungal diagnostics has evolved and come a long way from traditional methods of microscopy and culturing to more advanced non-culture-based tools. With the advent of more powerful approaches such as novel PCR assays, T2 Candida, microfluidic chip technology, next generation sequencing, new generation biosensors, nanotechnology-based tools, artificial intelligence-based models, the face of fungal diagnostics is constantly changing for the better. All these advances have been reviewed here giving the latest update to our readers in the most orderly flow. MAIN TEXT A detailed literature survey was conducted by the team followed by data collection, pertinent data extraction, in-depth analysis, and composing the various sub-sections and the final review. The review is unique in its kind as it discusses the advances in molecular methods; advances in serology-based methods; advances in biosensor technology; and advances in machine learning-based models, all under one roof. To the best of our knowledge, there has been no review covering all of these fields (especially biosensor technology and machine learning using artificial intelligence) with relevance to invasive fungal infections. CONCLUSION The review will undoubtedly assist in updating the scientific community's understanding of the most recent advancements that are on the horizon and that may be implemented as adjuncts to the traditional diagnostic algorithms.
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Affiliation(s)
- Wenjie Fang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Junqi Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Mingrong Cheng
- Department of Anorectal Surgery, The Third Affiliated Hospital of Guizhou Medical University, Guizhou, 558000, China
| | - Xinlin Zhu
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Mingwei Du
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
- Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Wanqing Liao
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China
| | - Kangkang Zhi
- Department of Vascular and Endovascular Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Second Affiliated Hospital of Naval Medical University, Shanghai, 200003, China.
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Test Performance and Potential Clinical Utility of the GenMark Dx ePlex Blood Culture Identification Gram-Negative Panel. Microbiol Spectr 2023; 11:e0409222. [PMID: 36688641 PMCID: PMC9927486 DOI: 10.1128/spectrum.04092-22] [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] [Indexed: 01/24/2023] Open
Abstract
The test performance and potential clinical utility of the ePlex blood culture identification Gram-negative (BCID-GN) panel was evaluated relative to matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry on bacterial isolates and conventional antimicrobial susceptibility testing. The majority (106/108, 98.1%) of GN bacteria identified by MALDI were on the BCID-GN panel, and valid tests (107/108, 99.1%) yielded results on average 26.7 h earlier. For all valid tests with on-panel organisms, the positive percent agreement was 102/105 (97.2%) with 3 false negatives and the negative percent agreement was 105/105. Chart review (n = 98) showed that in conjunction with Gram stain results, negative pan-Gram-positive (GP) markers provided the opportunity to discontinue GP antibiotic coverage in 63/98 (64.3%) cases on average 26.2 h earlier. Only 8/12 (66.7%) Enterobacterales isolates with resistance to third-generation cephalosporins harbored the CTX-M gene. In contrast, 8/8 CTX-M+ samples yielded a resistant isolate. Detection of 1 Stenotrophomonas maltophilia (18 h), 1 OXA23/48+ Acinetobacter baumannii (52.4 h), and 3 CTX-M+ Enterobacterales isolates on ineffective treatment (47.1 h) and 1 on suboptimal therapy (72.6 h) would have additionally enabled early antimicrobial optimization in 6/98 (6.1%) patients. IMPORTANCE The GenMark Dx ePlex rapid blood culture diagnostic system enables earlier time to identification of antimicrobial-resistant Gram-negative bacteria causing bloodstream infections. Its ability to rule out Gram-positive bacteria enabled early discontinuation of unnecessary antibiotics in 63/98 (64.3%) cases on average 26.2 h earlier. Detection of bacteria harboring the CTX-M gene as well as early identification of highly resistant bacteria such as Stenotrophomonas maltophilia and Acinetobacter baumannii enabled optimization of ineffective therapy in 6/98 (6.1%) patients. Its implementation in clinical microbiology laboratories optimizes therapy and improves patient care.
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Caméléna F, Péan de Ponfilly G, Pailhoriès H, Bonzon L, Alanio A, Poncin T, Lafaurie M, Dépret F, Cambau E, Godreuil S, Chenouard R, Le Monnier A, Jacquier H, Berçot B. Multicenter Evaluation of the FilmArray Blood Culture Identification 2 Panel for Pathogen Detection in Bloodstream Infections. Microbiol Spectr 2023; 11:e0254722. [PMID: 36519852 PMCID: PMC9927563 DOI: 10.1128/spectrum.02547-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
The FilmArray Blood Culture Identification 2 panel (BCID2; bioMérieux) is a fully automated PCR-based assay for identifying bacteria, fungi, and bacterial resistance markers in positive blood cultures (BC) in about 1 h. In this multicenter study, we evaluated the performance of the BCID2 panel for pathogen detection in positive BC. Conventional culture and BCID2 were performed in parallel at four tertiary-care hospitals. We included 152 positive BC-130 monomicrobial and 22 polymicrobial cultures-in this analysis. The BCID2 assay correctly identified 90% (88/98) of Gram-negative and 89% (70/79) of Gram-positive bacteria. Five bacterial isolates targeted by the BCID2 panel and recovered from five positive BC, including three polymicrobial cultures, were missed by the BCID2 assay. Fifteen isolates were off-panel organisms, accounting for 8% (15/182) of the isolates obtained from BC. The mean positive percent agreement between the BCID2 assay and standard culture was 97% (95% confidence interval, 95 to 99%), with agreement ranging from 67% for Candida albicans to 100% for 17 targets included in the BCID2 panel. BCID2 also identified the blaCTX-M gene in seven BC, including one for which no extended-spectrum β-lactamase (ESBL)-producing isolate was obtained in culture. However, it failed to detect ESBL-encoding genes in three BC. Two of the 18 mecA/C genes detected by the BCID2 were not confirmed. No carbapenemase, mecA/C, or MREJ targets were detected. The median turnaround time was significantly shorter for BCID2 than for culture. The BCID2 panel may facilitate faster pathogen identification in bloodstream infections. IMPORTANCE Rapid molecular diagnosis combining the identification of pathogens and the detection of antibiotic resistance genes from positive blood cultures (BC) can improve the outcome for patients with bloodstream infections. The FilmArray BCID2 panel, an updated version of the original BCID, can detect 11 Gram-positive bacteria, 15 Gram-negative bacteria, 7 fungal pathogens, and 10 antimicrobial resistance genes directly from a positive BC. Here, we evaluated the real-life microbiological performance of the BCID2 assay in comparison to the results of standard methods used in routine practice at four tertiary care hospitals.
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Affiliation(s)
- François Caméléna
- Département de Bactériologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Gauthier Péan de Ponfilly
- Service de Microbiologie clinique, Groupe hospitalier Paris Saint Joseph, Paris, France
- Institut Micalis UMR 1319, Université Paris-Saclay, INRAe, AgroParisTech, Châtenay Malabry, France
| | - Hélène Pailhoriès
- Laboratoire de Bactériologie, Institut de Biologie en Santé, Centre Hospitalier Universitaire d’Angers, Laboratoire HIFIH, UPRES EA3859, SFR ICAT 4208, Université d’Angers, Angers, France
| | - Lucas Bonzon
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier et MIVEGEC, UMR IRD-CNRS-Université de Montpellier, Montpellier, France
| | - Alexandre Alanio
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS, Unité de Mycologie Moléculaire, UMR2000, Paris, France
| | - Thibaut Poncin
- Département de Bactériologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Matthieu Lafaurie
- Département des Maladies Infectieuses et Tropicales, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - François Dépret
- Département d’Anesthésie et Réanimation chirurgicale et brûlés, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Emmanuel Cambau
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
- Laboratoire de mycobactériologie spécialisée et de référence, Laboratoire associé du Centre National de Référence des mycobactéries et résistance des mycobactéries aux antituberculeux, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier et MIVEGEC, UMR IRD-CNRS-Université de Montpellier, Montpellier, France
| | - Rachel Chenouard
- Laboratoire de Bactériologie, Institut de Biologie en Santé, Centre Hospitalier Universitaire d’Angers, Laboratoire HIFIH, UPRES EA3859, SFR ICAT 4208, Université d’Angers, Angers, France
| | - Alban Le Monnier
- Service de Microbiologie clinique, Groupe hospitalier Paris Saint Joseph, Paris, France
- Institut Micalis UMR 1319, Université Paris-Saclay, INRAe, AgroParisTech, Châtenay Malabry, France
| | - Hervé Jacquier
- Département de Bactériologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Béatrice Berçot
- Département de Bactériologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
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Fast Track Diagnostic Tools for Clinical Management of Sepsis: Paradigm Shift from Conventional to Advanced Methods. Diagnostics (Basel) 2023; 13:diagnostics13020277. [PMID: 36673087 PMCID: PMC9857847 DOI: 10.3390/diagnostics13020277] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/24/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Sepsis is one of the deadliest disorders in the new century due to specific limitations in early and differential diagnosis. Moreover, antimicrobial resistance (AMR) is becoming the dominant threat to human health globally. The only way to encounter the spread and emergence of AMR is through the active detection and identification of the pathogen along with the quantification of resistance. For better management of such disease, there is an essential requirement to approach many suitable diagnostic techniques for the proper administration of antibiotics and elimination of these infectious diseases. The current method employed for the diagnosis of sepsis relies on the conventional culture of blood suspected infection. However, this method is more time consuming and generates results that are false negative in the case of antibiotic pretreated samples as well as slow-growing microbes. In comparison to the conventional method, modern methods are capable of analyzing blood samples, obtaining accurate results from the suspicious patient of sepsis, and giving all the necessary information to identify the pathogens as well as AMR in a short period. The present review is intended to highlight the culture shift from conventional to modern and advanced technologies including their limitations for the proper and prompt diagnosing of bloodstream infections and AMR detection.
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A Closer Look at the Laboratory Impact of Utilizing ePlex Blood Culture Identification Panels: a Workflow Analysis Using Rapid Molecular Detection for Positive Blood Cultures. Microbiol Spectr 2022; 10:e0179622. [PMID: 36069598 PMCID: PMC9602361 DOI: 10.1128/spectrum.01796-22] [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] [Indexed: 12/31/2022] Open
Abstract
Rapid identification of pathogens is critical in bloodstream infections. We evaluated the diagnostic performance of the GenMark Dx ePlex blood culture identification (BCID) panels and the adoption of the ePlex system into the clinical laboratory workflow. Nonduplicate remnant specimens of positive blood cultures were prospectively tested using ePlex panels between January and March 2020. A total of 313 unique positive blood culture specimens were tested. The identified organisms consisted of 98 Gram-negative rods (GNR), 90 Gram-positive cocci (GPC) in clusters, 62 GPC in chains, 21 Gram-positive rods, and 20 yeasts; 22 organisms were off panel. The positive percent agreement was 100% across all organisms tested after discordancy resolution, while the negative percent agreement was 100% across all targets except Corynebacterium spp., where it was 99.7%. The ePlex BCID panels accurately detected 5 pan targets and 42 antimicrobial resistance gene markers, including 31 mecA, 4 vanA, 6 CTX-M, and 1 KPC gene. The median times to result were calculated as 2.5 h for Xpert MRSA/SA in GPC in clusters, 9.5 h for Accelerate Pheno (identification and susceptibility) in GNR, 6 h for peptide nucleic acid fluorescent in situ hybridization [PNA-FISH] in yeasts, 27 h for the latex agglutination test in S. aureus, 29 h for Lancefield serotyping in GPC in chains, and 29 h for Vitek-MS in GNR. In our laboratory, the ePlex panels could substantially reduce the time to result for bloodstream infection (BSI) caused by Streptococcus spp., Enterococcus spp., and Candida spp. The highly accurate ePlex panels can help streamline laboratory efficiency in the blood bench workflow, reducing the time to result for identification of BSI pathogens. IMPORTANCE Sepsis is a leading cause of morbidity and mortality worldwide. Rapid identification of the causative agent is of critical importance for the prompt initiation of the appropriate antibiotic treatment. In this study, we evaluated the diagnostic performance of the GenMark Dx ePlex blood culture identification (BCID) panels and their adoption into the clinical laboratory workflow. We prospectively tested 313 blood culture isolates and found that ePlex BCID panels had a positive percent agreement of 100% across all organisms tested after discordancy resolution. The negative percent agreement was 100% across all targets except Corynebacterium spp., where it was 99.7%. This new rapid technology (turnaround time of ~90 min) can help streamline laboratory efficiency in the blood bench workflow, reducing the time to result for identification of BSI pathogens. Adoption should be individualized based on the needs of the patient population and capabilities of the laboratory.
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Kuo P, LeCrone K, Chiu M, Realegeno S, Pride DT. Analysis of the FAST™ System for expedited identification and antimicrobial susceptibility testing of bloodborne pathogens. Diagn Microbiol Infect Dis 2022; 104:115783. [DOI: 10.1016/j.diagmicrobio.2022.115783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/03/2022]
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Analytical Performance and Potential Clinical Utility of the GenMark Dx ePlex® Blood Culture Identification Gram-Positive Panel. Diagn Microbiol Infect Dis 2022; 104:115762. [DOI: 10.1016/j.diagmicrobio.2022.115762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/26/2022] [Accepted: 06/27/2022] [Indexed: 11/22/2022]
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Direct Rapid Identification from Positive Blood Cultures by MALDI-TOF MS: Specific Focus on Turnaround Times. Microbiol Spectr 2021; 9:e0110321. [PMID: 34908465 PMCID: PMC8672911 DOI: 10.1128/spectrum.01103-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Early availability of pathogen identification in bloodstream infections has critical importance in patients' management. This study investigated the accuracy and feasibility of the direct rapid identification (RID) method from positive blood cultures (BCs) by MALDI-TOF MS and its impact on the turnaround time (TAT) compared to the short-term incubation routine identification (SIRID) method. Pellets prepared from 328 BCs using a serum separator tube in the RID method and colonies on agar plates in the SIRID method were identified with MALDI Biotyper. BCs on weekdays from 6 a.m. to 4 p.m. were defined as the daytime signal group (DSG); BCs from 4 p.m. to 6 a.m. were defined as the night signal group (NSG). Comparison between the two methods was performed with 310 monomicrobial BCs. Two hundred ninety-five (95.2%) monomicrobial BCs yielded an identification result with the RID method. Of the 295 BCs, 289 (97.9%) were identified correctly at the species level, 4 (1.4%) were at the genus level, and 2 (0.7%) were misidentified. In the RID method, at score cutoff values of 1.2, 1.3, 1.4 and 1.5, the rates of correct identifications at the species level were 97.9%, 98.9%, 99.3%, and 100%, respectively. The mean TAT in the DSG was significantly lower (P < 0.001) in the RID method (mean: 2.86 h; 95% CI: 2.65 to 3.07) compared to the SIRID method (mean: 19.49 h; 95% CI: 18.08 to 20.89). Correct identification rates at the species level were 100% in Gram-negative bacteria, 88.9% in Gram-positive bacteria, and 93.2% of all BCs isolates with the RID method. The TAT was improved remarkably in DSG, which might contribute to empirical antibiotic therapies of patients. IMPORTANCE Using MALDI-TOF MS directly from BCs reduces the time required for pathogen identification, and the TATs for final identification have been compared with overnight incubation from solid media in previous studies. However, identification from a short incubation of agar plates has been increasingly accepted and successfully implemented in routine laboratories, but there is no data comparing direct MALDI-TOF MS with the short-term incubated agar plates. Our study showed that the TAT improved remarkably by applying a RID method by MALDI-TOF MS twice a day periodically when compared to the SIRID method.
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Sze DTT, Lau CCY, Chan TM, Ma ESK, Tang BSF. Comparison of novel rapid diagnostic of blood culture identification and antimicrobial susceptibility testing by Accelerate Pheno system and BioFire FilmArray Blood Culture Identification and BioFire FilmArray Blood Culture Identification 2 panels. BMC Microbiol 2021; 21:350. [PMID: 34922463 PMCID: PMC8684256 DOI: 10.1186/s12866-021-02403-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 11/25/2021] [Indexed: 12/25/2022] Open
Abstract
Background
Conventional turnaround time (TAT) for positive blood culture (PBC) identification (ID) and antimicrobial susceptibility testing (AST) is 2–3 days. We evaluated the TAT and ID/AST performance using clinical and seeded samples directly from PBC bottles with different commercial approaches: (1) Accelerate Pheno® system (Pheno) for ID/AST; (2) BioFire® FilmArray® Blood Culture Identification (BCID) Panel and/ or BCID2 for ID; (3) direct AST by VITEK® 2 (direct AST); and (4) overnight culture using VITEK® 2 colony AST. Results
A total of 141 PBC samples were included in this evaluation. Using MALDI-TOF (Bruker MALDI Biotyper) as the reference method for ID, the overall monomicrobial ID sensitivity/specificity are as follows: Pheno 97.9/99.9%; BCID 100/100%; and BCID2 100/100%, respectively. For AST performance, broth microdilution (BMD) was used as the reference method. For gram-negatives, overall categorical and essential agreements (CA/EA) for each method were: Pheno 90.3/93.2%; direct AST 92.6/88.5%; colony AST 94.4/89.5%, respectively. For gram-positives, the overall CA/EAs were as follows: Pheno 97.2/98.89%; direct AST 97.2/100%; colony AST 97.2/100%, respectively. The BCID/BCID2 and direct AST TATs were around 9–20 h (1/9-19 h for ID with resistance markers/AST), with 15 min/sample hands-on time. In comparison, Pheno TATs were around 8–10 h (1.5/7 h for ID/AST) with 2 min/sample hands-on time, maintains a clinically relevant fast report of antibiotic minimal inhibitory concentration (MIC) and allows for less TAT and hands-on time. Conclusion In conclusion, to the best of our knowledge, this is the first study conducted as such in Asia; all studied approaches achieved satisfactory performance, factors such as TAT, panel of antibiotics choices and hands-on time should be considered for the selection of appropriate rapid ID and AST of PBC methods in different laboratory settings. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02403-y.
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Anton-Vazquez V, Planche T. Gram-negative blood stream infections: prospects and challenges of rapid antimicrobial susceptibility testing. Expert Rev Anti Infect Ther 2021; 20:483-485. [PMID: 34706610 DOI: 10.1080/14787210.2022.1999805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Vanesa Anton-Vazquez
- Institute of Infection and Immunity, St. George's University of London, London, UK.,Department of Medical Microbiology, Southwest London Pathology, St. George's Hospital, London, UK.,Infection Care Group, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Timothy Planche
- Institute of Infection and Immunity, St. George's University of London, London, UK.,Department of Medical Microbiology, Southwest London Pathology, St. George's Hospital, London, UK.,Infection Care Group, St George's University Hospitals NHS Foundation Trust, London, UK
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Detection of Multidrug-Resistant Enterobacterales-From ESBLs to Carbapenemases. Antibiotics (Basel) 2021; 10:antibiotics10091140. [PMID: 34572722 PMCID: PMC8465816 DOI: 10.3390/antibiotics10091140] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/03/2021] [Accepted: 09/10/2021] [Indexed: 12/16/2022] Open
Abstract
Multidrug-resistant Enterobacterales (MDRE) are an emerging threat to global health, leading to rising health care costs, morbidity and mortality. Multidrug-resistance is commonly caused by different β-lactamases (e.g., ESBLs and carbapenemases), sometimes in combination with other resistance mechanisms (e.g., porin loss, efflux). The continuous spread of MDRE among patients in hospital settings and the healthy population require adjustments in healthcare management and routine diagnostics. Rapid and reliable detection of MDRE infections as well as gastrointestinal colonization is key to guide therapy and infection control measures. However, proper implementation of these strategies requires diagnostic methods with short time-to-result, high sensitivity and specificity. Therefore, research on new techniques and improvement of already established protocols is inevitable. In this review, current methods for detection of MDRE are summarized with focus on culture based and molecular techniques, which are useful for the clinical microbiology laboratory.
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Garner CD, Brazelton de Cardenas J, Suganda S, Hayden RT. Accuracy of Broad-Panel PCR-Based Bacterial Identification for Blood Cultures in a Pediatric Oncology Population. Microbiol Spectr 2021; 9:e0022121. [PMID: 34232100 PMCID: PMC8552719 DOI: 10.1128/spectrum.00221-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/05/2021] [Indexed: 11/20/2022] Open
Abstract
Bloodstream infections are a major cause of morbidity and mortality and result in significant costs to health care systems. Rapid identification of the causative agent of bloodstream infections is critical for patient treatment and improved outcomes. Multiplex PCR systems that provide bacterial identification directly from the blood culture bottle allow for earlier detection of pathogens. The GenMark Dx ePlex blood culture identification (BCID) panels have an expanded number of targets for both identification and genotypic markers of antimicrobial resistance. The performance of the ePlex BCID Gram-negative (GN) and Gram-positive (GP) panels were evaluated in a predominantly pediatric oncology population. A total of 112 blood cultures were tested by the ePlex BCID GN and GP panels and results were compared to those from standard-of-care testing. Accuracy for on-panel organisms was 89% (CI, 76% to 95%) for the Gram-positive panel, with four misidentifications and one not detected, and 93% (CI, 82% to 98%) for the Gram-negative panel, with two misidentifications and one not detected. The results showed good overall performance of these panels for rapid, accurate detection of bloodstream pathogens in this high-risk population. IMPORTANCE Bloodstream infections are a major cause of morbidity and mortality and result in significant costs to health care systems. Rapid identification of the causative agent of bloodstream infections is critical for patient treatment and improved outcomes. Multiplex PCR systems that provide bacterial identification directly from the blood culture bottle allow for earlier characterization of pathogens. The GenMark Dx ePlex blood culture identification (BCID) panels, recently cleared by the FDA, have an expanded number of targets for both identification and resistance, much larger than other, automated, broad-panel PCR assays. The performance of the ePlex BCID Gram-negative and Gram-positive panels was evaluated in a predominantly pediatric oncology population, providing a unique look at its performance in a high-risk group, where rapid diagnostic information for bloodstream infections could be of particular value for clinical care providers.
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Affiliation(s)
- C. D. Garner
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | | | - S. Suganda
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - R. T. Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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Egi M, Ogura H, Yatabe T, Atagi K, Inoue S, Iba T, Kakihana Y, Kawasaki T, Kushimoto S, Kuroda Y, Kotani J, Shime N, Taniguchi T, Tsuruta R, Doi K, Doi M, Nakada TA, Nakane M, Fujishima S, Hosokawa N, Masuda Y, Matsushima A, Matsuda N, Yamakawa K, Hara Y, Sakuraya M, Ohshimo S, Aoki Y, Inada M, Umemura Y, Kawai Y, Kondo Y, Saito H, Taito S, Takeda C, Terayama T, Tohira H, Hashimoto H, Hayashida K, Hifumi T, Hirose T, Fukuda T, Fujii T, Miura S, Yasuda H, Abe T, Andoh K, Iida Y, Ishihara T, Ide K, Ito K, Ito Y, Inata Y, Utsunomiya A, Unoki T, Endo K, Ouchi A, Ozaki M, Ono S, Katsura M, Kawaguchi A, Kawamura Y, Kudo D, Kubo K, Kurahashi K, Sakuramoto H, Shimoyama A, Suzuki T, Sekine S, Sekino M, Takahashi N, Takahashi S, Takahashi H, Tagami T, Tajima G, Tatsumi H, Tani M, Tsuchiya A, Tsutsumi Y, Naito T, Nagae M, Nagasawa I, Nakamura K, Nishimura T, Nunomiya S, Norisue Y, Hashimoto S, Hasegawa D, Hatakeyama J, Hara N, Higashibeppu N, Furushima N, Furusono H, Matsuishi Y, Matsuyama T, Minematsu Y, Miyashita R, Miyatake Y, Moriyasu M, Yamada T, Yamada H, Yamamoto R, Yoshida T, Yoshida Y, Yoshimura J, Yotsumoto R, Yonekura H, Wada T, Watanabe E, Aoki M, Asai H, Abe T, Igarashi Y, Iguchi N, Ishikawa M, Ishimaru G, Isokawa S, Itakura R, Imahase H, Imura H, Irinoda T, Uehara K, Ushio N, Umegaki T, Egawa Y, Enomoto Y, Ota K, Ohchi Y, Ohno T, Ohbe H, Oka K, Okada N, Okada Y, Okano H, Okamoto J, Okuda H, Ogura T, Onodera Y, Oyama Y, Kainuma M, Kako E, Kashiura M, Kato H, Kanaya A, Kaneko T, Kanehata K, Kano KI, Kawano H, Kikutani K, Kikuchi H, Kido T, Kimura S, Koami H, Kobashi D, Saiki I, Sakai M, Sakamoto A, Sato T, Shiga Y, Shimoto M, Shimoyama S, Shoko T, Sugawara Y, Sugita A, Suzuki S, Suzuki Y, Suhara T, Sonota K, Takauji S, Takashima K, Takahashi S, Takahashi Y, Takeshita J, Tanaka Y, Tampo A, Tsunoyama T, Tetsuhara K, Tokunaga K, Tomioka Y, Tomita K, Tominaga N, Toyosaki M, Toyoda Y, Naito H, Nagata I, Nagato T, Nakamura Y, Nakamori Y, Nahara I, Naraba H, Narita C, Nishioka N, Nishimura T, Nishiyama K, Nomura T, Haga T, Hagiwara Y, Hashimoto K, Hatachi T, Hamasaki T, Hayashi T, Hayashi M, Hayamizu A, Haraguchi G, Hirano Y, Fujii R, Fujita M, Fujimura N, Funakoshi H, Horiguchi M, Maki J, Masunaga N, Matsumura Y, Mayumi T, Minami K, Miyazaki Y, Miyamoto K, Murata T, Yanai M, Yano T, Yamada K, Yamada N, Yamamoto T, Yoshihiro S, Tanaka H, Nishida O. The Japanese Clinical Practice Guidelines for Management of Sepsis and Septic Shock 2020 (J-SSCG 2020). J Intensive Care 2021; 9:53. [PMID: 34433491 PMCID: PMC8384927 DOI: 10.1186/s40560-021-00555-7] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/10/2021] [Indexed: 02/08/2023] Open
Abstract
The Japanese Clinical Practice Guidelines for Management of Sepsis and Septic Shock 2020 (J-SSCG 2020), a Japanese-specific set of clinical practice guidelines for sepsis and septic shock created as revised from J-SSCG 2016 jointly by the Japanese Society of Intensive Care Medicine and the Japanese Association for Acute Medicine, was first released in September 2020 and published in February 2021. An English-language version of these guidelines was created based on the contents of the original Japanese-language version. The purpose of this guideline is to assist medical staff in making appropriate decisions to improve the prognosis of patients undergoing treatment for sepsis and septic shock. We aimed to provide high-quality guidelines that are easy to use and understand for specialists, general clinicians, and multidisciplinary medical professionals. J-SSCG 2016 took up new subjects that were not present in SSCG 2016 (e.g., ICU-acquired weakness [ICU-AW], post-intensive care syndrome [PICS], and body temperature management). The J-SSCG 2020 covered a total of 22 areas with four additional new areas (patient- and family-centered care, sepsis treatment system, neuro-intensive treatment, and stress ulcers). A total of 118 important clinical issues (clinical questions, CQs) were extracted regardless of the presence or absence of evidence. These CQs also include those that have been given particular focus within Japan. This is a large-scale guideline covering multiple fields; thus, in addition to the 25 committee members, we had the participation and support of a total of 226 members who are professionals (physicians, nurses, physiotherapists, clinical engineers, and pharmacists) and medical workers with a history of sepsis or critical illness. The GRADE method was adopted for making recommendations, and the modified Delphi method was used to determine recommendations by voting from all committee members.As a result, 79 GRADE-based recommendations, 5 Good Practice Statements (GPS), 18 expert consensuses, 27 answers to background questions (BQs), and summaries of definitions and diagnosis of sepsis were created as responses to 118 CQs. We also incorporated visual information for each CQ according to the time course of treatment, and we will also distribute this as an app. The J-SSCG 2020 is expected to be widely used as a useful bedside guideline in the field of sepsis treatment both in Japan and overseas involving multiple disciplines.
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Affiliation(s)
- Moritoki Egi
- Department of Surgery Related, Division of Anesthesiology, Kobe University Graduate School of Medicine, Kusunoki-cho 7-5-2, Chuo-ku, Kobe, Hyogo, Japan.
| | - Hiroshi Ogura
- Department of Traumatology and Acute Critical Medicine, Osaka University Medical School, Yamadaoka 2-15, Suita, Osaka, Japan.
| | - Tomoaki Yatabe
- Department of Anesthesiology and Critical Care Medicine, Fujita Health University School of Medicine, Toyoake, Japan
| | - Kazuaki Atagi
- Department of Intensive Care Unit, Nara Prefectural General Medical Center, Nara, Japan
| | - Shigeaki Inoue
- Department of Disaster and Emergency Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Toshiaki Iba
- Department of Emergency and Disaster Medicine, Juntendo University, Tokyo, Japan
| | - Yasuyuki Kakihana
- Department of Emergency and Intensive Care Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Tatsuya Kawasaki
- Department of Pediatric Critical Care, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Shigeki Kushimoto
- Division of Emergency and Critical Care Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yasuhiro Kuroda
- Department of Emergency, Disaster, and Critical Care Medicine, Faculty of Medicine, Kagawa University, Kagawa, Japan
| | - Joji Kotani
- Department of Surgery Related, Division of Disaster and Emergency Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Nobuaki Shime
- Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takumi Taniguchi
- Department of Anesthesiology and Intensive Care Medicine, Kanazawa University, Kanazawa, Japan
| | - Ryosuke Tsuruta
- Acute and General Medicine, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Kent Doi
- Department of Acute Medicine, The University of Tokyo, Tokyo, Japan
| | - Matsuyuki Doi
- Department of Anesthesiology and Intensive Care Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Taka-Aki Nakada
- Department of Emergency and Critical Care Medicine, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Masaki Nakane
- Department of Emergency and Critical Care Medicine, Yamagata University Hospital, Yamagata, Japan
| | - Seitaro Fujishima
- Center for General Medicine Education, Keio University School of Medicine, Tokyo, Japan
| | - Naoto Hosokawa
- Department of Infectious Diseases, Kameda Medical Center, Kamogawa, Japan
| | - Yoshiki Masuda
- Department of Intensive Care Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Asako Matsushima
- Department of Advancing Acute Medicine, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Naoyuki Matsuda
- Department of Emergency and Critical Care Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuma Yamakawa
- Department of Emergency Medicine, Osaka Medical College, Osaka, Japan
| | - Yoshitaka Hara
- Department of Anesthesiology and Critical Care Medicine, Fujita Health University School of Medicine, Toyoake, Japan
| | - Masaaki Sakuraya
- Department of Emergency and Intensive Care Medicine, JA Hiroshima General Hospital, Hatsukaichi, Japan
| | - Shinichiro Ohshimo
- Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yoshitaka Aoki
- Department of Anesthesiology and Intensive Care Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mai Inada
- Member of Japanese Association for Acute Medicine, Tokyo, Japan
| | - Yutaka Umemura
- Division of Trauma and Surgical Critical Care, Osaka General Medical Center, Osaka, Japan
| | - Yusuke Kawai
- Department of Nursing, Fujita Health University Hospital, Toyoake, Japan
| | - Yutaka Kondo
- Department of Emergency and Critical Care Medicine, Juntendo University Urayasu Hospital, Urayasu, Japan
| | - Hiroki Saito
- Department of Emergency and Critical Care Medicine, St. Marianna University School of Medicine, Yokohama City Seibu Hospital, Yokohama, Japan
| | - Shunsuke Taito
- Division of Rehabilitation, Department of Clinical Support and Practice, Hiroshima University Hospital, Hiroshima, Japan
| | - Chikashi Takeda
- Department of Anesthesia, Kyoto University Hospital, Kyoto, Japan
| | - Takero Terayama
- Department of Psychiatry, School of Medicine, National Defense Medical College, Tokorozawa, Japan
| | | | - Hideki Hashimoto
- Department of Emergency and Critical Care Medicine/Infectious Disease, Hitachi General Hospital, Hitachi, Japan
| | - Kei Hayashida
- The Feinstein Institute for Medical Research, Manhasset, NY, USA
| | - Toru Hifumi
- Department of Emergency and Critical Care Medicine, St. Luke's International Hospital, Tokyo, Japan
| | - Tomoya Hirose
- Emergency and Critical Care Medical Center, Osaka Police Hospital, Osaka, Japan
| | - Tatsuma Fukuda
- Department of Emergency and Critical Care Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Tomoko Fujii
- Intensive Care Unit, Jikei University Hospital, Tokyo, Japan
| | - Shinya Miura
- The Royal Children's Hospital Melbourne, Melbourne, Australia
| | - Hideto Yasuda
- Department of Emergency and Critical Care Medicine, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Toshikazu Abe
- Department of Emergency and Critical Care Medicine, Tsukuba Memorial Hospital, Tsukuba, Japan
| | - Kohkichi Andoh
- Division of Anesthesiology, Division of Intensive Care, Division of Emergency and Critical Care, Sendai City Hospital, Sendai, Japan
| | - Yuki Iida
- Department of Physical Therapy, School of Health Sciences, Toyohashi Sozo University, Toyohashi, Japan
| | - Tadashi Ishihara
- Department of Emergency and Critical Care Medicine, Juntendo University Urayasu Hospital, Urayasu, Japan
| | - Kentaro Ide
- Critical Care Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Kenta Ito
- Department of General Pediatrics, Aichi Children's Health and Medical Center, Obu, Japan
| | - Yusuke Ito
- Department of Infectious Disease, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Yu Inata
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Akemi Utsunomiya
- Human Health Science, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takeshi Unoki
- Department of Acute and Critical Care Nursing, School of Nursing, Sapporo City University, Sapporo, Japan
| | - Koji Endo
- Department of Pharmacoepidemiology, Kyoto University Graduate School of Medicine and Public Health, Kyoto, Japan
| | - Akira Ouchi
- College of Nursing, Ibaraki Christian University, Hitachi, Japan
| | - Masayuki Ozaki
- Department of Emergency and Critical Care Medicine, Komaki City Hospital, Komaki, Japan
| | - Satoshi Ono
- Gastroenterological Center, Shinkuki General Hospital, Kuki, Japan
| | | | | | - Yusuke Kawamura
- Department of Rehabilitation, Showa General Hospital, Tokyo, Japan
| | - Daisuke Kudo
- Division of Emergency and Critical Care Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kenji Kubo
- Department of Emergency Medicine and Department of Infectious Diseases, Japanese Red Cross Wakayama Medical Center, Wakayama, Japan
| | - Kiyoyasu Kurahashi
- Department of Anesthesiology and Intensive Care Medicine, International University of Health and Welfare School of Medicine, Narita, Japan
| | | | - Akira Shimoyama
- Department of Emergency and Critical Care Medicine, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Takeshi Suzuki
- Department of Anesthesiology, Tokai University School of Medicine, Isehara, Japan
| | - Shusuke Sekine
- Department of Anesthesiology, Tokyo Medical University, Tokyo, Japan
| | - Motohiro Sekino
- Division of Intensive Care, Nagasaki University Hospital, Nagasaki, Japan
| | - Nozomi Takahashi
- Department of Emergency and Critical Care Medicine, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Sei Takahashi
- Center for Innovative Research for Communities and Clinical Excellence (CiRC2LE), Fukushima Medical University, Fukushima, Japan
| | - Hiroshi Takahashi
- Department of Cardiology, Steel Memorial Muroran Hospital, Muroran, Japan
| | - Takashi Tagami
- Department of Emergency and Critical Care Medicine, Nippon Medical School Musashi Kosugi Hospital, Kawasaki, Japan
| | - Goro Tajima
- Nagasaki University Hospital Acute and Critical Care Center, Nagasaki, Japan
| | - Hiroomi Tatsumi
- Department of Intensive Care Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masanori Tani
- Division of Critical Care Medicine, Saitama Children's Medical Center, Saitama, Japan
| | - Asuka Tsuchiya
- Department of Emergency and Critical Care Medicine, National Hospital Organization Mito Medical Center, Ibaraki, Japan
| | - Yusuke Tsutsumi
- Department of Emergency and Critical Care Medicine, National Hospital Organization Mito Medical Center, Ibaraki, Japan
| | - Takaki Naito
- Department of Emergency and Critical Care Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Masaharu Nagae
- Department of Intensive Care Medicine, Kobe University Hospital, Kobe, Japan
| | | | - Kensuke Nakamura
- Department of Emergency and Critical Care Medicine, Hitachi General Hospital, Hitachi, Japan
| | - Tetsuro Nishimura
- Department of Traumatology and Critical Care Medicine, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Shin Nunomiya
- Department of Anesthesiology and Intensive Care Medicine, Division of Intensive Care, Jichi Medical University School of Medicine, Shimotsuke, Japan
| | - Yasuhiro Norisue
- Department of Emergency and Critical Care Medicine, Tokyo Bay Urayasu Ichikawa Medical Center, Urayasu, Japan
| | - Satoru Hashimoto
- Department of Anesthesiology and Intensive Care Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Daisuke Hasegawa
- Department of Anesthesiology and Critical Care Medicine, Fujita Health University School of Medicine, Toyoake, Japan
| | - Junji Hatakeyama
- Department of Emergency and Critical Care Medicine, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Naoki Hara
- Department of Pharmacy, Yokohama Rosai Hospital, Yokohama, Japan
| | - Naoki Higashibeppu
- Department of Anesthesiology and Nutrition Support Team, Kobe City Medical Center General Hospital, Kobe City Hospital Organization, Kobe, Japan
| | - Nana Furushima
- Department of Anesthesiology, Kobe University Hospital, Kobe, Japan
| | - Hirotaka Furusono
- Department of Rehabilitation, University of Tsukuba Hospital/Exult Co., Ltd., Tsukuba, Japan
| | - Yujiro Matsuishi
- Doctoral program in Clinical Sciences. Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Tasuku Matsuyama
- Department of Emergency Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yusuke Minematsu
- Department of Clinical Engineering, Osaka University Hospital, Suita, Japan
| | - Ryoichi Miyashita
- Department of Intensive Care Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Yuji Miyatake
- Department of Clinical Engineering, Kakogawa Central City Hospital, Kakogawa, Japan
| | - Megumi Moriyasu
- Division of Respiratory Care and Rapid Response System, Intensive Care Center, Kitasato University Hospital, Sagamihara, Japan
| | - Toru Yamada
- Department of Nursing, Toho University Omori Medical Center, Tokyo, Japan
| | - Hiroyuki Yamada
- Department of Primary Care and Emergency Medicine, Kyoto University Hospital, Kyoto, Japan
| | - Ryo Yamamoto
- Department of Emergency and Critical Care Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Takeshi Yoshida
- Department of Anesthesiology and Intensive Care Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yuhei Yoshida
- Nursing Department, Osaka General Medical Center, Osaka, Japan
| | - Jumpei Yoshimura
- Division of Trauma and Surgical Critical Care, Osaka General Medical Center, Osaka, Japan
| | | | - Hiroshi Yonekura
- Department of Clinical Anesthesiology, Mie University Hospital, Tsu, Japan
| | - Takeshi Wada
- Department of Anesthesiology and Critical Care Medicine, Division of Acute and Critical Care Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Eizo Watanabe
- Department of Emergency and Critical Care Medicine, Eastern Chiba Medical Center, Togane, Japan
| | - Makoto Aoki
- Department of Emergency Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Hideki Asai
- Department of Emergency and Critical Care Medicine, Nara Medical University, Kashihara, Japan
| | - Takakuni Abe
- Department of Anesthesiology and Intensive Care, Oita University Hospital, Yufu, Japan
| | - Yutaka Igarashi
- Department of Emergency and Critical Care Medicine, Nippon Medical School Hospital, Tokyo, Japan
| | - Naoya Iguchi
- Department of Anesthesiology and Intensive Care Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Masami Ishikawa
- Department of Anesthesiology, Emergency and Critical Care Medicine, Kure Kyosai Hospital, Kure, Japan
| | - Go Ishimaru
- Department of General Internal Medicine, Soka Municipal Hospital, Soka, Japan
| | - Shutaro Isokawa
- Department of Emergency and Critical Care Medicine, St. Luke's International Hospital, Tokyo, Japan
| | - Ryuta Itakura
- Department of Emergency and Critical Care Medicine, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Hisashi Imahase
- Department of Biomedical Ethics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Haruki Imura
- Department of Infectious Diseases, Rakuwakai Otowa Hospital, Kyoto, Japan
- Department of Health Informatics, School of Public Health, Kyoto University, Kyoto, Japan
| | | | - Kenji Uehara
- Department of Anesthesiology, National Hospital Organization Iwakuni Clinical Center, Iwakuni, Japan
| | - Noritaka Ushio
- Advanced Medical Emergency Department and Critical Care Center, Japan Red Cross Maebashi Hospital, Maebashi, Japan
| | - Takeshi Umegaki
- Department of Anesthesiology, Kansai Medical University, Hirakata, Japan
| | - Yuko Egawa
- Advanced Emergency and Critical Care Center, Saitama Red Cross Hospital, Saitama, Japan
| | - Yuki Enomoto
- Department of Emergency and Critical Care Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kohei Ota
- Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yoshifumi Ohchi
- Department of Anesthesiology and Intensive Care, Oita University Hospital, Yufu, Japan
| | - Takanori Ohno
- Department of Emergency and Critical Medicine, Showa University Fujigaoka Hospital, Yokohama, Japan
| | - Hiroyuki Ohbe
- Department of Clinical Epidemiology and Health Economics, School of Public Health, The University of Tokyo, Tokyo, Japan
| | | | - Nobunaga Okada
- Department of Emergency Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yohei Okada
- Department of Primary care and Emergency medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hiromu Okano
- Department of Anesthesiology, Kyorin University School of Medicine, Tokyo, Japan
| | - Jun Okamoto
- Department of ER, Hashimoto Municipal Hospital, Hashimoto, Japan
| | - Hiroshi Okuda
- Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Takayuki Ogura
- Tochigi prefectural Emergency and Critical Care Center, Imperial Gift Foundation Saiseikai, Utsunomiya Hospital, Utsunomiya, Japan
| | - Yu Onodera
- Department of Anesthesiology, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Yuhta Oyama
- Department of Internal Medicine, Dialysis Center, Kichijoji Asahi Hospital, Tokyo, Japan
| | - Motoshi Kainuma
- Anesthesiology, Emergency Medicine, and Intensive Care Division, Inazawa Municipal Hospital, Inazawa, Japan
| | - Eisuke Kako
- Department of Anesthesiology and Intensive Care Medicine, Nagoya-City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Masahiro Kashiura
- Department of Emergency and Critical Care Medicine, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Hiromi Kato
- Department of Anesthesiology and Intensive Care Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Akihiro Kanaya
- Department of Anesthesiology, Sendai Medical Center, Sendai, Japan
| | - Tadashi Kaneko
- Emergency and Critical Care Center, Mie University Hospital, Tsu, Japan
| | - Keita Kanehata
- Advanced Medical Emergency Department and Critical Care Center, Japan Red Cross Maebashi Hospital, Maebashi, Japan
| | - Ken-Ichi Kano
- Department of Emergency Medicine, Fukui Prefectural Hospital, Fukui, Japan
| | - Hiroyuki Kawano
- Department of Gastroenterological Surgery, Onga Hospital, Fukuoka, Japan
| | - Kazuya Kikutani
- Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hitoshi Kikuchi
- Department of Emergency and Critical Care Medicine, Seirei Mikatahara General Hospital, Hamamatsu, Japan
| | - Takahiro Kido
- Department of Pediatrics, University of Tsukuba Hospital, Tsukuba, Japan
| | - Sho Kimura
- Division of Critical Care Medicine, Saitama Children's Medical Center, Saitama, Japan
| | - Hiroyuki Koami
- Center for Translational Injury Research, University of Texas Health Science Center at Houston, Houston, USA
| | - Daisuke Kobashi
- Advanced Medical Emergency Department and Critical Care Center, Japan Red Cross Maebashi Hospital, Maebashi, Japan
| | - Iwao Saiki
- Department of Anesthesiology, Tokyo Medical University, Tokyo, Japan
| | - Masahito Sakai
- Department of General Medicine Shintakeo Hospital, Takeo, Japan
| | - Ayaka Sakamoto
- Department of Emergency and Critical Care Medicine, University of Tsukuba Hospital, Tsukuba, Japan
| | - Tetsuya Sato
- Tohoku University Hospital Emergency Center, Sendai, Japan
| | - Yasuhiro Shiga
- Department of Orthopaedic Surgery, Center for Advanced Joint Function and Reconstructive Spine Surgery, Graduate school of Medicine, Chiba University, Chiba, Japan
| | - Manabu Shimoto
- Department of Primary care and Emergency medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shinya Shimoyama
- Department of Pediatric Cardiology and Intensive Care, Gunma Children's Medical Center, Shibukawa, Japan
| | - Tomohisa Shoko
- Department of Emergency and Critical Care Medicine, Tokyo Women's Medical University Medical Center East, Tokyo, Japan
| | - Yoh Sugawara
- Department of Anesthesiology, Yokohama City University, Yokohama, Japan
| | - Atsunori Sugita
- Department of Acute Medicine, Division of Emergency and Critical Care Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Satoshi Suzuki
- Department of Intensive Care, Okayama University Hospital, Okayama, Japan
| | - Yuji Suzuki
- Department of Anesthesiology and Intensive Care Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tomohiro Suhara
- Department of Anesthesiology, Keio University School of Medicine, Tokyo, Japan
| | - Kenji Sonota
- Department of Intensive Care Medicine, Miyagi Children's Hospital, Sendai, Japan
| | - Shuhei Takauji
- Department of Emergency Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Kohei Takashima
- Critical Care Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Sho Takahashi
- Department of Cardiology, Fukuyama City Hospital, Fukuyama, Japan
| | - Yoko Takahashi
- Department of General Internal Medicine, Koga General Hospital, Koga, Japan
| | - Jun Takeshita
- Department of Anesthesiology, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Yuuki Tanaka
- Fukuoka Prefectural Psychiatric Center, Dazaifu Hospital, Dazaifu, Japan
| | - Akihito Tampo
- Department of Emergency Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Taichiro Tsunoyama
- Department of Emergency Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Kenichi Tetsuhara
- Emergency and Critical Care Center, Kyushu University Hospital, Fukuoka, Japan
| | - Kentaro Tokunaga
- Department of Intensive Care Medicine, Kumamoto University Hospital, Kumamoto, Japan
| | - Yoshihiro Tomioka
- Department of Anesthesiology and Intensive Care Unit, Todachuo General Hospital, Toda, Japan
| | - Kentaro Tomita
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Naoki Tominaga
- Department of Emergency and Critical Care Medicine, Nippon Medical School Hospital, Tokyo, Japan
| | - Mitsunobu Toyosaki
- Department of Emergency and Critical Care Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yukitoshi Toyoda
- Department of Emergency and Critical Care Medicine, Saiseikai Yokohamashi Tobu Hospital, Yokohama, Japan
| | - Hiromichi Naito
- Department of Emergency, Critical Care, and Disaster Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Isao Nagata
- Intensive Care Unit, Yokohama City Minato Red Cross Hospital, Yokohama, Japan
| | - Tadashi Nagato
- Department of Respiratory Medicine, Tokyo Yamate Medical Center, Tokyo, Japan
| | - Yoshimi Nakamura
- Department of Emergency and Critical Care Medicine, Japanese Red Cross Kyoto Daini Hospital, Kyoto, Japan
| | - Yuki Nakamori
- Department of Clinical Anesthesiology, Mie University Hospital, Tsu, Japan
| | - Isao Nahara
- Department of Anesthesiology and Critical Care Medicine, Nagoya Daini Red Cross Hospital, Nagoya, Japan
| | - Hiromu Naraba
- Department of Emergency and Critical Care Medicine, Hitachi General Hospital, Hitachi, Japan
| | - Chihiro Narita
- Department of Emergency Medicine and Intensive Care Medicine, Shizuoka General Hospital, Shizuoka, Japan
| | - Norihiro Nishioka
- Department of Preventive Services, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomoya Nishimura
- Advanced Medical Emergency Department and Critical Care Center, Japan Red Cross Maebashi Hospital, Maebashi, Japan
| | - Kei Nishiyama
- Division of Emergency and Critical Care Medicine Niigata University Graduate School of Medical and Dental Science, Niigata, Japan
| | - Tomohisa Nomura
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Tokyo, Japan
| | - Taiki Haga
- Department of Pediatric Critical Care Medicine, Osaka City General Hospital, Osaka, Japan
| | - Yoshihiro Hagiwara
- Department of Emergency and Critical Care Medicine, Saiseikai Utsunomiya Hospital, Utsunomiya, Japan
| | - Katsuhiko Hashimoto
- Research Associate of Minimally Invasive Surgical and Medical Oncology, Fukushima Medical University, Fukushima, Japan
| | - Takeshi Hatachi
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Toshiaki Hamasaki
- Department of Emergency Medicine, Japanese Red Cross Society Wakayama Medical Center, Wakayama, Japan
| | - Takuya Hayashi
- Division of Critical Care Medicine, Saitama Children's Medical Center, Saitama, Japan
| | - Minoru Hayashi
- Department of Emergency Medicine, Fukui Prefectural Hospital, Fukui, Japan
| | - Atsuki Hayamizu
- Department of Emergency Medicine, Saitama Saiseikai Kurihashi Hospital, Kuki, Japan
| | - Go Haraguchi
- Division of Intensive Care Unit, Sakakibara Heart Institute, Tokyo, Japan
| | - Yohei Hirano
- Department of Emergency and Critical Care Medicine, Juntendo University Urayasu Hospital, Urayasu, Japan
| | - Ryo Fujii
- Department of Emergency Medicine and Critical Care Medicine, Tochigi Prefectural Emergency and Critical Care Center, Imperial Foundation Saiseikai Utsunomiya Hospital, Utsunomiya, Japan
| | - Motoki Fujita
- Acute and General Medicine, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Naoyuki Fujimura
- Department of Anesthesiology, St. Mary's Hospital, Our Lady of the Snow Social Medical Corporation, Kurume, Japan
| | - Hiraku Funakoshi
- Department of Emergency and Critical Care Medicine, Tokyo Bay Urayasu Ichikawa Medical Center, Urayasu, Japan
| | - Masahito Horiguchi
- Department of Emergency and Critical Care Medicine, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Jun Maki
- Department of Critical Care Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Naohisa Masunaga
- Department of Healthcare Epidemiology, School of Public Health in the Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yosuke Matsumura
- Department of Intensive Care, Chiba Emergency Medical Center, Chiba, Japan
| | - Takuya Mayumi
- Department of Internal Medicine, Kanazawa Municipal Hospital, Kanazawa, Japan
| | - Keisuke Minami
- Ishikawa Prefectual Central Hospital Emergency and Critical Care Center, Kanazawa, Japan
| | - Yuya Miyazaki
- Department of Emergency and General Internal Medicine, Saiseikai Kawaguchi General Hospital, Kawaguchi, Japan
| | - Kazuyuki Miyamoto
- Department of Emergency and Disaster Medicine, Showa University, Tokyo, Japan
| | - Teppei Murata
- Department of Cardiology, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo, Japan
| | - Machi Yanai
- Department of Emergency Medicine, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Takao Yano
- Department of Critical Care and Emergency Medicine, Miyazaki Prefectural Nobeoka Hospital, Nobeoka, Japan
| | - Kohei Yamada
- Department of Traumatology and Critical Care Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Naoki Yamada
- Department of Emergency Medicine, University of Fukui Hospital, Fukui, Japan
| | - Tomonori Yamamoto
- Department of Intensive Care Unit, Nara Prefectural General Medical Center, Nara, Japan
| | - Shodai Yoshihiro
- Pharmaceutical Department, JA Hiroshima General Hospital, Hatsukaichi, Japan
| | - Hiroshi Tanaka
- Department of Emergency and Critical Care Medicine, Juntendo University Urayasu Hospital, Urayasu, Japan
| | - Osamu Nishida
- Department of Anesthesiology and Critical Care Medicine, Fujita Health University School of Medicine, Toyoake, Japan
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A Multicenter Clinical Study To Demonstrate the Diagnostic Accuracy of the GenMark Dx ePlex Blood Culture Identification Gram-Negative Panel. J Clin Microbiol 2021; 59:e0248420. [PMID: 34232066 PMCID: PMC8373019 DOI: 10.1128/jcm.02484-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bacteremia can progress to septic shock and death without appropriate medical intervention. Increasing evidence supports the role of molecular diagnostic panels in reducing the clinical impact of these infections through rapid identification of the infecting organism and associated antimicrobial resistance genes. We report the results of a multicenter clinical study assessing the performance of the GenMark Dx ePlex investigational-use-only blood culture identification Gram-negative panel (BCID-GN), a rapid diagnostic assay for detection of bloodstream pathogens in positive blood culture (PBC) bottles. Prospective, retrospective, and contrived samples were tested. Results from the BCID-GN were compared to standard-of-care bacterial identification methods. Antimicrobial resistance genes (ARGs) were identified using PCR and sequence analysis. The final BCID-GN analysis included 2,444 PBC samples, of which 926 were clinical samples with negative Gram stain results. Of these, 109 samples had false-negative and/or -positive results, resulting in an overall sample accuracy of 88.2% (817/926). After discordant resolution, overall sample accuracy increased to 92.9% (860/926). Pre- and postdiscordant resolution sample accuracy excludes 37 Gram-negative organisms representing 20 uncommon genera, 10 Gram-positive organisms, and 1 Candida species present in 5% of samples that are not targeted by the BCID-GN. The overall weighted positive percent agreement (PPA), which averages the individual PPAs from the 27 targets (Gram-negative and ARG), was 94.9%. The limit of detection ranged from 104 to 107 CFU/ml, except for one strain of Fusobacterium necrophorum at 108 CFU/ml.
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Comparing the Clinical Utility of Rapid Diagnostics for Treatment of Bloodstream Infections Using Desirability of Outcome Ranking Approach for the Management of Antibiotic Therapy (DOOR-MAT). Antimicrob Agents Chemother 2021; 65:e0044121. [PMID: 34228533 PMCID: PMC8370220 DOI: 10.1128/aac.00441-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Decisions regarding which rapid diagnostic test (RDT) for bloodstream infections to implement remain challenging given the diversity of organisms detected by different platforms. We used the desirability of outcome ranking management of antimicrobial therapy (DOOR-MAT) as a framework to compare two RDT platforms on potential desirability of antimicrobial therapy decisions. An observational study was performed at University of Maryland Medical System comparing Verigene blood culture (BC) to GenMark Dx ePlex blood culture ID (BCID) (research use only) panels on blood cultures from adult patients. Positive percent agreement (PPA) between each RDT platform and Vitek MS was calculated for comparison of on-panel targets. Theoretical antimicrobial decisions were made based on RDT results, taking into consideration patient parameters, antimicrobial stewardship practices, and local infectious diseases epidemiology. DOOR-MAT with a partial credit scoring system was applied to these decisions, and mean scores were compared across platforms using a paired t test. The study consisted of 160 unique patients. The Verigene BC PPA was 98.6% (95% confidence interval [CI], 95.1 to 99.8), and ePlex BCID PPA was 98% (95% CI, 94.3 to 99.6). Among the 31 organisms not on the Verigene BC panels, 61% were identified by the ePlex BCID panels. The mean (standard deviation [SD]) DOOR-MAT score for Verigene BC was 86.8 (28.5), while that for ePlex BCID was 91.9 (23.1) (P = 0.01). Both RDT platforms had high PPA for on-panel targets. The ePlex BCID was able to identify more organisms than Verigene, resulting in higher mean DOOR-MAT scores.
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Holma T, Torvikoski J, Friberg N, Nevalainen A, Tarkka E, Antikainen J, Martelin JJ. Rapid molecular detection of pathogenic microorganisms and antimicrobial resistance markers in blood cultures: evaluation and utility of the next-generation FilmArray Blood Culture Identification 2 panel. Eur J Clin Microbiol Infect Dis 2021; 41:363-371. [PMID: 34350523 PMCID: PMC8831274 DOI: 10.1007/s10096-021-04314-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/09/2021] [Indexed: 11/30/2022]
Abstract
Rapid detection of pathogens causing bloodstream infections (BSI) directly from positive blood cultures is of highest importance in order to enable an adequate and timely antimicrobial therapy. In this study, the utility and performance of a recently launched next-generation fully automated test system, the Biofire FilmArray® Blood Culture Identification 2 (BCID2) panel, was evaluated using a set of 103 well-characterized microbial isolates including 29 antimicrobial resistance genes and 80 signal-positive and 23 signal-negative clinical blood culture samples. The results were compared to culture-based reference methods, MALDI-TOF, and/or 16S rDNA sequencing. Of the clinical blood culture samples, 68 were monomicrobial (85.0%) and 12 polymicrobial (15.0%). Six samples contained ESBL (blaCTX-M), two MRSA (mecA), and three MRSE (mecA) isolates. In overall, the FilmArray BCID2 panel detected well on-panel targets and resistance markers from mono- and polymicrobial samples. However, one Klebsiella aerogenes and one Bacteroides ovatus were undetected, and the assay falsely reported one Shigella flexneri as Escherichia coli. Hence, the sensitivity and specificity for detecting microbial species were 98.8% (95%CI, 95.8–99.9%) and 99.9% (95%CI, 99.8–99.9%), respectively. The sensitivity and specificity for detecting of resistance gene markers were 100%. The results were available within 70 min from signal-positive blood cultures with minimal hands-on time. In conclusion, the BCID2 test allows reliable and simplified detection of a vast variety of clinically relevant microbes causing BSI and the most common antimicrobial resistance markers present among these isolates.
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Affiliation(s)
- Tanja Holma
- HUS Diagnostic Center, HUSLAB, Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
| | - Jukka Torvikoski
- HUS Diagnostic Center, HUSLAB, Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Nathalie Friberg
- HUS Diagnostic Center, HUSLAB, Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Annika Nevalainen
- HUS Diagnostic Center, HUSLAB, Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Eveliina Tarkka
- HUS Diagnostic Center, HUSLAB, Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jenni Antikainen
- HUS Diagnostic Center, HUSLAB, Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jari J Martelin
- HUS Diagnostic Center, HUSLAB, Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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26
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Jacobs MR, Colson JD, Rhoads DD. Recent advances in rapid antimicrobial susceptibility testing systems. Expert Rev Mol Diagn 2021; 21:563-578. [PMID: 33926351 DOI: 10.1080/14737159.2021.1924679] [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: 10/21/2022]
Abstract
INTRODUCTION Until recently antimicrobial susceptibility testing (AST) methods based on the demonstration of phenotypic susceptibility in 16-24 h remained largely unchanged. AREAS COVERED Advances in rapid phenotypic and molecular-based AST systems. EXPERT OPINION AST has changed over the past decade, with many rapid phenotypic and molecular methods developed to demonstrate phenotypic or genotypic resistance, or biochemical markers of resistance such as β-lactamases associated with carbapenem resistance. Most methods still require isolation of bacteria from specimens before both legacy and newer methods can be used. Bacterial identification by MALDI-TOF mass spectroscopy is now widely used and is often key to the interpretation of rapid AST results. Several PCR arrays are available to detect the most frequent pathogens associated with bloodstream infections and their major antimicrobial resistance genes. Many advances in whole-genome sequencing of bacteria and fungi isolated by culture as well as directly from clinical specimens have been made but are not yet widely available. High cost and limited throughput are the major obstacles to uptake of rapid methods, but targeted use, continued development and decreasing costs are expected to result in more extensive use of these increasingly useful methods.
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Affiliation(s)
- Michael R Jacobs
- Emeritus Professor of Pathology and Emeritus Medical Director, Clinical Microbiology, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Jordan D Colson
- Microbiology Fellow, Department of Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Daniel D Rhoads
- Section Head of Microbiology, Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
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Prevalence of bla CTX-M Genes in Gram-Negative Bloodstream Isolates across 66 Hospitals in the United States. J Clin Microbiol 2021; 59:JCM.00127-21. [PMID: 33827899 DOI: 10.1128/jcm.00127-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/27/2021] [Indexed: 12/18/2022] Open
Abstract
Understanding bacterial species at greatest risk for harboring bla CTX-M genes is necessary to guide antibiotic treatment. We identified the species-specific prevalence of bla CTX-M genes in Gram-negative clinical isolates from the United States. Twenty-four microbiology laboratories representing 66 hospitals using the GenMark Dx ePlex blood culture identification Gram-negative (BCID-GN) panel extracted blood culture results from April 2019 to July 2020. The BCID-GN panel includes 21 Gram-negative targets. Along with identifying bla CTX-M genes, it detects major carbapenemase gene families. A total of 4,209 Gram-negative blood cultures were included. bla CTX-M genes were identified in 462 (11%) specimens. The species-specific prevalence of bla CTX-M genes was as follows: Escherichia coli (16%), Klebsiella pneumoniae (14%), Klebsiella oxytoca (6%), Salmonella spp. (6%), Acinetobacter baumannii (5%), Enterobacter species (3%), Proteus mirabilis (2%), Serratia marcescens (0.6%), and Pseudomonas aeruginosa (0.5%). bla CTX-M prevalence was 26%, 24%, and 22% among participating hospitals in the District of Columbia, New York, and Florida, respectively. Carbapenemase genes were identified in 61 (2%) organisms with the following distribution: bla KPC (59%), bla VIM (16%), bla OXA (10%), bla NDM (8%), and bla IMP (7%). The species-specific prevalence of carbapenemase genes was as follows: A. baumannii (5%), K. pneumoniae (3%), P. mirabilis (3%), Enterobacter species (3%), Citrobacter spp. (3%), P. aeruginosa (2%), E. coli (<1%), K. oxytoca (<1%), and S. marcescens (<1%). Approximately 11% of Gram-negative organisms in our US cohort contain bla CTX-M genes. bla CTX-M genes remain uncommon in organisms beyond E. coli, K. pneumoniae, and K. oxytoca Future molecular diagnostic panels would benefit from the inclusion of plasmid-mediated ampC and SHV and TEM extended-spectrum beta-lactamase (ESBL) targets.
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Johnson MD, Lewis RE, Dodds Ashley ES, Ostrosky-Zeichner L, Zaoutis T, Thompson GR, Andes DR, Walsh TJ, Pappas PG, Cornely OA, Perfect JR, Kontoyiannis DP. Core Recommendations for Antifungal Stewardship: A Statement of the Mycoses Study Group Education and Research Consortium. J Infect Dis 2021; 222:S175-S198. [PMID: 32756879 DOI: 10.1093/infdis/jiaa394] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In recent years, the global public health community has increasingly recognized the importance of antimicrobial stewardship (AMS) in the fight to improve outcomes, decrease costs, and curb increases in antimicrobial resistance around the world. However, the subject of antifungal stewardship (AFS) has received less attention. While the principles of AMS guidelines likely apply to stewarding of antifungal agents, there are additional considerations unique to AFS and the complex field of fungal infections that require specific recommendations. In this article, we review the literature on AMS best practices and discuss AFS through the lens of the global core elements of AMS. We offer recommendations for best practices in AFS based on a synthesis of this evidence by an interdisciplinary expert panel of members of the Mycoses Study Group Education and Research Consortium. We also discuss research directions in this rapidly evolving field. AFS is an emerging and important component of AMS, yet requires special considerations in certain areas such as expertise, education, interventions to optimize utilization, therapeutic drug monitoring, and data analysis and reporting.
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Affiliation(s)
- Melissa D Johnson
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina, USA
| | - Russell E Lewis
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Elizabeth S Dodds Ashley
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina, USA
| | - Luis Ostrosky-Zeichner
- Division of Infectious Diseases, Laboratory of Mycology Research, McGovern Medical School, Houston, Texas, USA
| | - Theoklis Zaoutis
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - George R Thompson
- Division of Infectious Diseases, Department of Internal Medicine, University of California, Davis, Sacramento, California, USA
| | - David R Andes
- Department of Medicine and Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Thomas J Walsh
- Transplantation-Oncology Infectious Diseases, Weill Cornell Medicine of Cornell University, New York, New York, USA
| | - Peter G Pappas
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Oliver A Cornely
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany.,German Centre for Infection Research, partner site Bonn-Cologne, Cologne, Germany.,CECAD Cluster of Excellence, University of Cologne, Cologne, Germany.,Clinical Trials Center Cologne, University Hospital of Cologne, Cologne, Germany
| | - John R Perfect
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina, USA
| | - Dimitrios P Kontoyiannis
- Department of Infectious Diseases, Infection Control and Employee Health, MD Anderson Cancer Center, Houston, Texas, USA
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29
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Banerjee R, Humphries R. Rapid Antimicrobial Susceptibility Testing Methods for Blood Cultures and Their Clinical Impact. Front Med (Lausanne) 2021; 8:635831. [PMID: 33777978 PMCID: PMC7987685 DOI: 10.3389/fmed.2021.635831] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/01/2021] [Indexed: 12/29/2022] Open
Abstract
Antimicrobial susceptibility testing (AST) of bacteria isolated in blood cultures is critical for optimal management of patients with sepsis. This review describes new and emerging phenotypic and genotypic AST methods and summarizes the evidence that implementation of these methods can impact clinical outcomes of patients with bloodstream infections.
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Affiliation(s)
- Ritu Banerjee
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Romney Humphries
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
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30
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Egi M, Ogura H, Yatabe T, Atagi K, Inoue S, Iba T, Kakihana Y, Kawasaki T, Kushimoto S, Kuroda Y, Kotani J, Shime N, Taniguchi T, Tsuruta R, Doi K, Doi M, Nakada T, Nakane M, Fujishima S, Hosokawa N, Masuda Y, Matsushima A, Matsuda N, Yamakawa K, Hara Y, Sakuraya M, Ohshimo S, Aoki Y, Inada M, Umemura Y, Kawai Y, Kondo Y, Saito H, Taito S, Takeda C, Terayama T, Tohira H, Hashimoto H, Hayashida K, Hifumi T, Hirose T, Fukuda T, Fujii T, Miura S, Yasuda H, Abe T, Andoh K, Iida Y, Ishihara T, Ide K, Ito K, Ito Y, Inata Y, Utsunomiya A, Unoki T, Endo K, Ouchi A, Ozaki M, Ono S, Katsura M, Kawaguchi A, Kawamura Y, Kudo D, Kubo K, Kurahashi K, Sakuramoto H, Shimoyama A, Suzuki T, Sekine S, Sekino M, Takahashi N, Takahashi S, Takahashi H, Tagami T, Tajima G, Tatsumi H, Tani M, Tsuchiya A, Tsutsumi Y, Naito T, Nagae M, Nagasawa I, Nakamura K, Nishimura T, Nunomiya S, Norisue Y, Hashimoto S, Hasegawa D, Hatakeyama J, Hara N, Higashibeppu N, Furushima N, Furusono H, Matsuishi Y, Matsuyama T, Minematsu Y, Miyashita R, Miyatake Y, Moriyasu M, Yamada T, Yamada H, Yamamoto R, Yoshida T, Yoshida Y, Yoshimura J, Yotsumoto R, Yonekura H, Wada T, Watanabe E, Aoki M, Asai H, Abe T, Igarashi Y, Iguchi N, Ishikawa M, Ishimaru G, Isokawa S, Itakura R, Imahase H, Imura H, Irinoda T, Uehara K, Ushio N, Umegaki T, Egawa Y, Enomoto Y, Ota K, Ohchi Y, Ohno T, Ohbe H, Oka K, Okada N, Okada Y, Okano H, Okamoto J, Okuda H, Ogura T, Onodera Y, Oyama Y, Kainuma M, Kako E, Kashiura M, Kato H, Kanaya A, Kaneko T, Kanehata K, Kano K, Kawano H, Kikutani K, Kikuchi H, Kido T, Kimura S, Koami H, Kobashi D, Saiki I, Sakai M, Sakamoto A, Sato T, Shiga Y, Shimoto M, Shimoyama S, Shoko T, Sugawara Y, Sugita A, Suzuki S, Suzuki Y, Suhara T, Sonota K, Takauji S, Takashima K, Takahashi S, Takahashi Y, Takeshita J, Tanaka Y, Tampo A, Tsunoyama T, Tetsuhara K, Tokunaga K, Tomioka Y, Tomita K, Tominaga N, Toyosaki M, Toyoda Y, Naito H, Nagata I, Nagato T, Nakamura Y, Nakamori Y, Nahara I, Naraba H, Narita C, Nishioka N, Nishimura T, Nishiyama K, Nomura T, Haga T, Hagiwara Y, Hashimoto K, Hatachi T, Hamasaki T, Hayashi T, Hayashi M, Hayamizu A, Haraguchi G, Hirano Y, Fujii R, Fujita M, Fujimura N, Funakoshi H, Horiguchi M, Maki J, Masunaga N, Matsumura Y, Mayumi T, Minami K, Miyazaki Y, Miyamoto K, Murata T, Yanai M, Yano T, Yamada K, Yamada N, Yamamoto T, Yoshihiro S, Tanaka H, Nishida O. The Japanese Clinical Practice Guidelines for Management of Sepsis and Septic Shock 2020 (J-SSCG 2020). Acute Med Surg 2021; 8:e659. [PMID: 34484801 PMCID: PMC8390911 DOI: 10.1002/ams2.659] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Japanese Clinical Practice Guidelines for Management of Sepsis and Septic Shock 2020 (J-SSCG 2020), a Japanese-specific set of clinical practice guidelines for sepsis and septic shock created as revised from J-SSCG 2016 jointly by the Japanese Society of Intensive Care Medicine and the Japanese Association for Acute Medicine, was first released in September 2020 and published in February 2021. An English-language version of these guidelines was created based on the contents of the original Japanese-language version. The purpose of this guideline is to assist medical staff in making appropriate decisions to improve the prognosis of patients undergoing treatment for sepsis and septic shock. We aimed to provide high-quality guidelines that are easy to use and understand for specialists, general clinicians, and multidisciplinary medical professionals. J-SSCG 2016 took up new subjects that were not present in SSCG 2016 (e.g., ICU-acquired weakness [ICU-AW], post-intensive care syndrome [PICS], and body temperature management). The J-SSCG 2020 covered a total of 22 areas with four additional new areas (patient- and family-centered care, sepsis treatment system, neuro-intensive treatment, and stress ulcers). A total of 118 important clinical issues (clinical questions, CQs) were extracted regardless of the presence or absence of evidence. These CQs also include those that have been given particular focus within Japan. This is a large-scale guideline covering multiple fields; thus, in addition to the 25 committee members, we had the participation and support of a total of 226 members who are professionals (physicians, nurses, physiotherapists, clinical engineers, and pharmacists) and medical workers with a history of sepsis or critical illness. The GRADE method was adopted for making recommendations, and the modified Delphi method was used to determine recommendations by voting from all committee members. As a result, 79 GRADE-based recommendations, 5 Good Practice Statements (GPS), 18 expert consensuses, 27 answers to background questions (BQs), and summaries of definitions and diagnosis of sepsis were created as responses to 118 CQs. We also incorporated visual information for each CQ according to the time course of treatment, and we will also distribute this as an app. The J-SSCG 2020 is expected to be widely used as a useful bedside guideline in the field of sepsis treatment both in Japan and overseas involving multiple disciplines.
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Ponderand L, Pavese P, Maubon D, Giraudon E, Girard T, Landelle C, Maurin M, Caspar Y. Evaluation of Rapid Sepsityper® protocol and specific MBT-Sepsityper module (Bruker Daltonics) for the rapid diagnosis of bacteremia and fungemia by MALDI-TOF-MS. Ann Clin Microbiol Antimicrob 2020; 19:60. [PMID: 33298064 PMCID: PMC7727196 DOI: 10.1186/s12941-020-00403-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/28/2020] [Indexed: 12/11/2022] Open
Abstract
During bloodstream infections, rapid adaptation of empirical treatment according to the microorganism identified is essential to decrease mortality. The aim of the present study was to assess the microbiological performances of a new rapid version of the Sepsityper® kit (Bruker Daltonics) allowing identification of bacteria and yeast by MALDI-TOF mass spectrometry directly from positive blood cultures in 10 min and of the specific MBT-Sepsityper module for spectra analysis, designed to increase identification performance. Identification rates were determined prospectively on 350 bacterial and 29 fungal positive blood cultures, and compared to conventional diagnostic method. Our rapid diagnosis strategy (Rapid Sepsityper® protocol: one spot with and one without formic acid extraction step) combined to MBT-Sepsityper module provided 65.4%, 78.9% and 62% reliable identification to the species level of monomicrobial positive blood cultures growing respectively Gram-positive, Gram-negative bacteria or yeast. Importantly, identification rates of Gram-positive bacteria were higher in anaerobic than in aerobic bottles (77.8% vs 22.2%; p = 0.004), if formic acid extraction step was performed (60.8% vs 39.2%; p = 1.8e−6) and if specific MBT-Sepsityper module was used (76.2% vs 61.9%, p = 0.041) while no significant differences were observed for Gram-negative bacteria. For yeasts identification, formic acid extraction step improved rapid identification rate by 37.9% while the specific MBT-Sepsityper module increased overall performances by 38%, providing up to 89.7% reliable identification if associated with the standard Sepsityper® protocol. These performances, associated with a reduce turnaround time, may help to implement a rapid identification strategy of bloodstream infections in the routine workflow of microbiology laboratories.
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Affiliation(s)
- Léa Ponderand
- Laboratoire de Bactériologie-Hygiène Hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France.,Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France
| | - Patricia Pavese
- Service de Médecine Infectieuse et Tropicale, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France
| | - Danièle Maubon
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France.,Laboratoire de Parasitologie Mycologie, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France
| | - Emmanuelle Giraudon
- Laboratoire de Parasitologie Mycologie, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France
| | - Thomas Girard
- Laboratoire de Bactériologie-Hygiène Hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France
| | - Caroline Landelle
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France.,Service d'Hygiène Hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France
| | - Max Maurin
- Laboratoire de Bactériologie-Hygiène Hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France.,Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France
| | - Yvan Caspar
- Laboratoire de Bactériologie-Hygiène Hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France. .,Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France. .,Laboratoire de Bactériologie-Hygiène Hospitalière, Institut de Biologie et Pathologie, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043, Grenoble Cedex 9, France.
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Bryant S, Almahmoud I, Pierre I, Bardet J, Touati S, Maubon D, Cornet M, Richarme C, Maurin M, Pavese P, Caspar Y. Evaluation of Microbiological Performance and the Potential Clinical Impact of the ePlex ® Blood Culture Identification Panels for the Rapid Diagnosis of Bacteremia and Fungemia. Front Cell Infect Microbiol 2020; 10:594951. [PMID: 33324578 PMCID: PMC7726344 DOI: 10.3389/fcimb.2020.594951] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/29/2020] [Indexed: 12/18/2022] Open
Abstract
Molecular rapid diagnostic assays associated with antimicrobial stewardship have proven effective for the early adaptation of empiric therapy in bloodstream infections. The ePlex® BCID (GenMark Diagnostics) Panels allow identification of 56 bacteria and fungi and 10 resistance genes in 90 min directly from positive blood cultures. We prospectively evaluated 187 sepsis episodes at Grenoble University Hospital and retrospectively analyzed the cases to measure the potential clinical impact of the ePlex BCID results. Identification of all pathogens was obtained for 164/187 (88%) bloodstream infections with 100% detection of antimicrobial resistance genes (17 blaCTX-M , 1 vanA, and 17 mecA genes). Only 15/209 (7%) strains were not covered by the panels. Sensitivity for detection of micro-organisms targeted by the RUO BCID-GP, BCID-GN, and BCID-FP Panels was respectively 84/84 (100%), 103/107 (96%), and 14/14 (100%). Interestingly, accurate identification of all pathogens was achieved in 15/17 (88%) polymicrobial samples. Retrospective analysis of medical records showed that a modification of antimicrobial treatment would have been done in 45% of the patients. Treatment modifications would have been an optimization of empiric therapy, a de-escalation or an escalation in respectively 16, 17, and 11% of the patients. Moreover, 11% of the samples were classified as contaminants or not clinically relevant and would have led to early de-escalation or withdrawal of any antibiotic. Detection of resistance genes in addition to identification alone increased escalation rate from 4 to 11% of the patients. Absence of the ePlex result was considered a lost opportunity for therapy modification in 28% of patients.
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Affiliation(s)
- Sabrina Bryant
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Iyad Almahmoud
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Isabelle Pierre
- Service des maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Julie Bardet
- Service des maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Saber Touati
- Service des maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Daniele Maubon
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Muriel Cornet
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Claire Richarme
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Max Maurin
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France.,Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Patricia Pavese
- Service des maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Yvan Caspar
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France.,Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
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Briggs N, Campbell S, Gupta S. Advances in rapid diagnostics for bloodstream infections. Diagn Microbiol Infect Dis 2020; 99:115219. [PMID: 33059201 DOI: 10.1016/j.diagmicrobio.2020.115219] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 09/12/2020] [Accepted: 09/12/2020] [Indexed: 10/23/2022]
Abstract
Septicemia from bloodstream infections (BSI) is the second largest cause of inpatient mortality and the single most expensive condition for US hospitals to manage. There has been an explosive development of commercial diagnostic systems to accelerate the identification and antimicrobial susceptibility testing (AST) of causative pathogens. Despite adoption of advanced technologies like matrix-assisted laser desorption imaging-time-of-flight mass spectrometry and multiplex polymerase chain reaction for rapid identification, clinical impact has been variable, in part due to the persistent need for conventional AST as well as prescriber understanding of these rapidly evolving platforms. Newer technologies are expanding on rapid detection of genotypic determinants of resistance, but only recently has rapid phenotypic AST been available. Yet, improved outcomes with rapid diagnostic platforms are still most evident in conjunction with active antimicrobial stewardship. This review will outline key advancements in rapid diagnostics for BSI and the role of antimicrobial stewardship in this new era.
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Affiliation(s)
- Neima Briggs
- Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Sheldon Campbell
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Shaili Gupta
- Department of Medicine, Yale School of Medicine, New Haven, CT; Department of Medicine, Division of Infectious Diseases, VA Healthcare Systems of CT, West Haven, CT.
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Shanmugakani RK, Srinivasan B, Glesby MJ, Westblade LF, Cárdenas WB, Raj T, Erickson D, Mehta S. Current state of the art in rapid diagnostics for antimicrobial resistance. LAB ON A CHIP 2020; 20:2607-2625. [PMID: 32644060 PMCID: PMC7428068 DOI: 10.1039/d0lc00034e] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Antimicrobial resistance (AMR) is a fundamental global concern analogous to climate change threatening both public health and global development progress. Infections caused by antimicrobial-resistant pathogens pose serious threats to healthcare and human capital. If the increasing rate of AMR is left uncontrolled, it is estimated that it will lead to 10 million deaths annually by 2050. This global epidemic of AMR necessitates radical interdisciplinary solutions to better detect antimicrobial susceptibility and manage infections. Rapid diagnostics that can identify antimicrobial-resistant pathogens to assist clinicians and health workers in initiating appropriate treatment are critical for antimicrobial stewardship. In this review, we summarize different technologies applied for the development of rapid diagnostics for AMR and antimicrobial susceptibility testing (AST). We briefly describe the single-cell technologies that were developed to hasten the AST of infectious pathogens. Then, the different types of genotypic and phenotypic techniques and the commercially available rapid diagnostics for AMR are discussed in detail. We conclude by addressing the potential of current rapid diagnostic systems being developed as point-of-care (POC) diagnostic tools and the challenges to adapt them at the POC level. Overall, this review provides an insight into the current status of rapid and POC diagnostic systems for AMR.
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Affiliation(s)
- Rathina Kumar Shanmugakani
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Balaji Srinivasan
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Marshall J. Glesby
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Lars F. Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Washington B. Cárdenas
- Laboratorio para Investigaciones Biomédicas, Escuela Superior Politécnica del Litoral, Guayaquil, Guayas, Ecuador
| | - Tony Raj
- St. John’s Research Institute, Bangalore, Karnataka, India
| | - David Erickson
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, USA
| | - Saurabh Mehta
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
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Camp I, Spettel K, Willinger B. Molecular Methods for the Diagnosis of Invasive Candidiasis. J Fungi (Basel) 2020; 6:E101. [PMID: 32640656 PMCID: PMC7558065 DOI: 10.3390/jof6030101] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 12/19/2022] Open
Abstract
Invasive infections caused by members of the genus Candida are on the rise. Especially patients in intensive care units, immunocompromised patients, and those recovering from abdominal surgery are at risk for the development of candidemia or deep-seated candidiasis. Rapid initiation of appropriate antifungal therapy can increase survival rates significantly. In the past, most of these infections were caused by C. albicans, a species that typically is very susceptible to antifungals. However, in recent years a shift towards infections caused by non-albicans species displaying various susceptibly patterns has been observed and the prompt diagnosis of the underlying species has become an essential factor determining the therapeutic outcome. The gold standard for diagnosing invasive candidiasis is blood culture, even though its sensitivity is low and the time required for species identification usually exceeds 48 h. To overcome these issues, blood culture can be combined with other methods, and a large number of tests have been developed for this purpose. The aim of this review was to give an overview on strengths and limitations of currently available molecular methods for the diagnosis of invasive candidiasis.
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Affiliation(s)
| | | | - Birgit Willinger
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; (I.C.); (K.S.)
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Mizusawa M. Updates on Rapid Diagnostic Tests in Infectious Diseases. MISSOURI MEDICINE 2020; 117:328-337. [PMID: 32848269 PMCID: PMC7431065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In the last two decades there have been dramatic advances in development of rapid diagnostic tests. Turnaround time of the assays have significantly been shortened which led to reductions in time to appropriate antimicrobial therapy and improvement of patient clinical outcomes. Molecular-based assays generally have better sensitivity than conventional methods, but the cost is higher. The results need to be interpreted cautiously as detection of colonized organisms, pathogen detection in asymptomatic patients, and false negative/positive can occur. Indications and cost-effectiveness need to be considered for appropriate utilization of rapid diagnostic tests.
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Affiliation(s)
- Masako Mizusawa
- Section of Infectious Diseases, Department of Internal Medicine, University of Missouri - Kansas City, Kansas City, Missouri
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Krifors A, Rådberg G, Golbob S, Omar Z, Svensson C, Heimer D, Carlander C. The clinical impact of implementing GenMark ePlex blood culture panels for around-the-clock blood culture identification; a prospective observational study. Infect Dis (Lond) 2020; 52:705-712. [PMID: 32522111 DOI: 10.1080/23744235.2020.1775882] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background: Implementing rapid molecular blood culture diagnostics in the clinical management of sepsis is essential for early pathogen identification and resistance gene testing. The GenMark ePlex blood culture panels offer a broad microbial spectrum with minimal hands-on time and approximately 1.5 h to result. Therefore, ePlex can be utilized at times when the clinical microbiology laboratory is unavailable.Methods: From 23 October 2019 to 30 December 2019, consecutive non-duplicate positive blood cultures signalling microbial growth at the 24 h/7 days-a-week available clinical chemistry laboratory between 9 pm and 7 am were analysed with ePlex. All blood cultures were transported to the microbiology laboratory the following day for conventional identification and antibiotic susceptibility testing.Results: We used ePlex to test 91 blood cultures, of which 86 had confirmed microbial growth. Eighty-one were positive for ePlex target pathogens. The ePlex results were in complete agreement with conventional methods in 72/81 (88.9%) of cases and available within a median of 10.9 h earlier. Resistance gene targets (11 mecA and 1 CTX-M) were concordant with phenotypic susceptibility in all cases. In 18/86 (20.9%) of the patient cases, there was an opportunity to optimize antimicrobial therapy based on the ePlex result. The ePlex result affected clinical decision-making in 4/86 (4.7%) of the cases and reduced the average time to effective antimicrobial therapy by 8.9 h.Conclusions: Our implementation of ePlex is a feasible option to attain around-the-clock blood culture identification in many hospitals. It can significantly reduce time-to-pathogen identification and have an impact on clinical decision-making.
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Affiliation(s)
- Anders Krifors
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.,Centre for Clinical Research Västmanland, Uppsala University, Västmanland County Hospital, Västerås, Sweden
| | - Gunilla Rådberg
- Department of Clinical Microbiology, Västmanlands Hospital, Västerås, Sweden
| | - Sultan Golbob
- Department of Clinical Microbiology, Västmanlands Hospital, Västerås, Sweden
| | - Zhino Omar
- Department of Clinical Microbiology, Västmanlands Hospital, Västerås, Sweden
| | - Camilla Svensson
- Department of Clinical Microbiology, Västmanlands Hospital, Västerås, Sweden
| | - Daniel Heimer
- Department of Clinical Microbiology, Västmanlands Hospital, Västerås, Sweden
| | - Christina Carlander
- Centre for Clinical Research Västmanland, Uppsala University, Västmanland County Hospital, Västerås, Sweden.,Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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Clinical Performance of the Novel GenMark Dx ePlex Blood Culture ID Gram-Positive Panel. J Clin Microbiol 2020; 58:JCM.01730-19. [PMID: 31996444 PMCID: PMC7098771 DOI: 10.1128/jcm.01730-19] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 01/18/2020] [Indexed: 12/14/2022] Open
Abstract
Rapid identification from positive blood cultures is standard of care (SOC) in many clinical microbiology laboratories. The GenMark Dx ePlex Blood Culture Identification Gram-Positive (BCID-GP) Panel is a multiplex nucleic acid amplification assay based on competitive DNA hybridization and electrochemical detection using eSensor technology. This multicenter study compared the investigational-use-only (IUO) BCID-GP Panel to other methods of identification of 20 Gram-positive bacteria, four antimicrobial resistance genes, and both Pan Candida and Pan Gram-Negative targets that are unique to the BCID-GP Panel. Rapid identification from positive blood cultures is standard of care (SOC) in many clinical microbiology laboratories. The GenMark Dx ePlex Blood Culture Identification Gram-Positive (BCID-GP) Panel is a multiplex nucleic acid amplification assay based on competitive DNA hybridization and electrochemical detection using eSensor technology. This multicenter study compared the investigational-use-only (IUO) BCID-GP Panel to other methods of identification of 20 Gram-positive bacteria, four antimicrobial resistance genes, and both Pan Candida and Pan Gram-Negative targets that are unique to the BCID-GP Panel. Ten microbiology laboratories throughout the United States collected residual, deidentified positive blood culture samples for analysis. Five laboratories tested both clinical and contrived samples with the BCID-GP Panel. Comparator identification methods included each laboratory’s SOC, which included matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and automated identification systems as well as targeted PCR/analytically validated real-time PCR (qPCR) with bidirectional sequencing. A total of 2,342 evaluable samples (1,777 clinical and 565 contrived) were tested with the BCID-GP Panel. The overall sample accuracy for on-panel organisms was 89% before resolution of discordant results. For pathogenic Gram-positive targets (Bacillus cereus group, Enterococcus spp., Enterococcus faecalis, Enterococcus faecium, Staphylococcus spp., Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus lugdunensis, Listeria spp., Listeria monocytogenes, Streptococcus spp., Streptococcus agalactiae, Streptococcus anginosus group, Streptococcus pneumoniae, and Streptococcus pyogenes), positive percent agreement (PPA) and negative percent agreement (NPA) ranged from 93.1% to 100% and 98.8% to 100%, respectively. For contamination rule-out targets (Bacillus subtilis group, Corynebacterium, Cutibacterium acnes, Lactobacillus, and Micrococcus), PPA and NPA ranged from 84.5% to 100% and 99.9% to 100%, respectively. Positive percent agreement and NPA for the Pan Candida and Pan Gram-Negative targets were 92.4% and 95.7% for the former and 99.9% and 99.6% for the latter. The PPAs for resistance markers were as follows: mecA, 97.2%; mecC, 100%; vanA, 96.8%; and vanB, 100%. Negative percent agreement ranged from 96.6% to 100%. In conclusion, the ePlex BCID-GP Panel compares favorably to SOC and targeted molecular methods for the identification of 20 Gram-positive pathogens and four antimicrobial resistance genes in positive blood culture bottles. This panel detects a broad range of pathogens and mixed infections with yeast and Gram-negative organisms from the same positive blood culture bottle.
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Cherkaoui A, Renzi G, Azam N, Schorderet D, Vuilleumier N, Schrenzel J. Rapid identification by MALDI-TOF/MS and antimicrobial disk diffusion susceptibility testing for positive blood cultures after a short incubation on the WASPLab. Eur J Clin Microbiol Infect Dis 2020; 39:1063-1070. [PMID: 31965365 DOI: 10.1007/s10096-020-03817-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/12/2020] [Indexed: 12/19/2022]
Abstract
The objectives of this study were to define the shortest incubation times on the WASPLab for reliable MALDI-TOF/MS-based species identification and for the preparation of a 0.5 McFarland suspension for antimicrobial disk diffusion susceptibility testing using short subcultures growing on solid culture media inoculated by positive blood cultures spiked with a wide range of pathogens associated with bloodstream infections. The 520 clinical strains (20 × 26 different species) included in this study were obtained from a collection of non-consecutive and non-duplicate pathogens identified at Geneva University Hospitals. After 4 h of incubation on the WASPLab, microorganisms' growth allowed accurate identification of 73% (380/520) (95% CI, 69.1-76.7%) of the strains included in this study. The identification rate increased to 85% (440/520) (95% CI, 81.3-87.5%) after 6-h incubation. When excluding Corynebacterium and Candida spp., the microbial growth was sufficient to permit accurate identification of all tested species (100%, 460/460) (95% CI, 99.2-100%) after 8-h incubation. With the exception of Burkholderia cepacia and Haemophilus influenzae, AST by disk diffusion could be performed for Enterobacterales and non-fermenting Gram-negative bacilli after only 4 h of growth in the WASPLab. The preparation of a 0.5 McFarland suspension for Gram-positive bacteria required incubation times ranging between 3 and 8 h according to the bacterial species. Only Corynebacterium spp. required incubation times as long as 16 h. The WASPLab enables rapid pathogen identification as well as swift comprehensive AST from positive blood cultures that can be implemented without additional costs nor hands-on time by defining optimal time points for image acquisition.
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Affiliation(s)
- Abdessalam Cherkaoui
- Department of Diagnostics, Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland.
| | - Gesuele Renzi
- Department of Diagnostics, Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
| | - Nouria Azam
- Department of Diagnostics, Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
| | - Didier Schorderet
- Department of Diagnostics, Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
| | - Nicolas Vuilleumier
- Department of Diagnostics, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland.,Department of Medical Specialities, Division of Laboratory Medicine, Faculty of Medicine, Geneva, Switzerland
| | - Jacques Schrenzel
- Department of Diagnostics, Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland.,Department of Medicine, Genomic Research Laboratory, Division of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
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Kidd SE, Chen SCA, Meyer W, Halliday CL. A New Age in Molecular Diagnostics for Invasive Fungal Disease: Are We Ready? Front Microbiol 2020; 10:2903. [PMID: 31993022 PMCID: PMC6971168 DOI: 10.3389/fmicb.2019.02903] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/02/2019] [Indexed: 12/18/2022] Open
Abstract
Invasive fungal diseases (IFDs) present an increasing global burden in immunocompromised and other seriously ill populations, including those caused by pathogens which are inherently resistant or less susceptible to antifungal drugs. Early diagnosis encompassing accurate detection and identification of the causative agent and of antifungal resistance is critical for optimum patient outcomes. Many molecular-based diagnostic approaches have good clinical utility although interpretation of results should be according to clinical context. Where an IFD is in the differential diagnosis, panfungal PCR assays allow the rapid detection/identification of fungal species directly from clinical specimens with good specificity; sensitivity is also high when hyphae are seen in the specimen including in paraffin-embedded tissue. Aspergillus PCR assays on blood fractions have good utility in the screening of high risk hematology patients with high negative predictive value (NPV) and positive predictive value (PPV) of 94 and 70%, respectively, when two positive PCR results are obtained. The standardization, and commercialization of Aspergillus PCR assays has now enabled direct comparison of results between laboratories with commercial assays also offering the simultaneous detection of common azole resistance mutations. Candida PCR assays are not as well standardized with the only FDA-approved commercial system (T2Candida) detecting only the five most common species; while the T2Candida outperforms blood culture in patients with candidemia, its role in routine Candida diagnostics is not well defined. There is growing use of Mucorales-specific PCR assays to detect selected genera in blood fractions. Quantitative real-time Pneumocystis jirovecii PCRs have replaced microscopy and immunofluorescent stains in many diagnostic laboratories although distinguishing infection may be problematic in non-HIV-infected patients. For species identification of isolates, DNA barcoding with dual loci (ITS and TEF1α) offer optimal accuracy while next generation sequencing (NGS) technologies offer highly discriminatory analysis of genetic diversity including for outbreak investigation and for drug resistance characterization. Advances in molecular technologies will further enhance routine fungal diagnostics.
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Affiliation(s)
- Sarah E. Kidd
- National Mycology Reference Centre, Microbiology and Infectious Diseases, South Australia Pathology, Adelaide, SA, Australia
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Wieland Meyer
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Research and Education Network, Westmead Hospital, Westmead, NSW, Australia
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Westmead, NSW, Australia
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Young BA, Hanson KE, Gomez CA. Molecular Diagnostic Advances in Transplant Infectious Diseases. Curr Infect Dis Rep 2019; 21:52. [PMID: 31773290 DOI: 10.1007/s11908-019-0704-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW The infectious complications of transplantation can have devastating consequences for patients. Early and accurate diagnosis is essential to good outcomes. This review describes recent advances in pathogen-directed diagnostic testing and discusses the role of new methods for transplant infectious diseases. RECENT FINDINGS Several molecular assays have been introduced into clinical practice in recent years. When the results of rapid testing are linked to patient-specific interventions, improved outcomes can be realized. Syndromic testing along with metagenomic next-generation sequencing (mNGS) represents novel approaches to infection diagnosis. However, the optimal use of these tests for transplant patients along with an overall assessment of cost-effectiveness demands further study. Molecular diagnostics are revolutionizing transplant care. Clinicians need to be aware of the current diagnostic landscape and have a working knowledge of the nuances related to test performance, result interpretation, and cost.
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Affiliation(s)
- Brittany A Young
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,Associated Regional and University Pathologists Laboratories (ARUP), Salt Lake City, UT, USA
| | - Kimberly E Hanson
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,Associated Regional and University Pathologists Laboratories (ARUP), Salt Lake City, UT, USA.,Department of Medicine, Division of Infectious Diseases, University of Utah, Salt Lake City, UT, USA
| | - Carlos A Gomez
- Department of Medicine, Division of Infectious Diseases, University of Utah, Salt Lake City, UT, USA. .,University of Utah School of Medicine, 30 North 1900 East, Room 4B319, Salt Lake City, UT, 84132, USA.
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Diagnosing and Managing Sepsis by Probing the Host Response to Infection: Advances, Opportunities, and Challenges. J Clin Microbiol 2019; 57:JCM.00425-19. [PMID: 31043466 DOI: 10.1128/jcm.00425-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Sepsis is a major source of mortality and morbidity globally. Accurately diagnosing sepsis remains challenging due to the heterogeneous nature of the disease, and delays in diagnosis and intervention contribute to high mortality rates. Measuring the host response to infection enables more rapid diagnosis of sepsis than is possible through direct detection of the causative pathogen, and recent advances in host response diagnostics and prognostics hold promise for improving outcomes. The current review discusses recent advances in the technologies used to probe the host response to infection, particularly those based on transcriptomics. These are discussed in the context of contemporary approaches to diagnosing and prognosing sepsis, and recommendations are made for successful development and validation of host response technologies.
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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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Zhang Y, Hu A, Andini N, Yang S. A 'culture' shift: Application of molecular techniques for diagnosing polymicrobial infections. Biotechnol Adv 2019; 37:476-490. [PMID: 30797092 PMCID: PMC6447436 DOI: 10.1016/j.biotechadv.2019.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/04/2019] [Accepted: 02/19/2019] [Indexed: 12/11/2022]
Abstract
With the advancement of microbiological discovery, it is evident that many infections, particularly bloodstream infections, are polymicrobial in nature. Consequently, new challenges have emerged in identifying the numerous etiologic organisms in an accurate and timely manner using the current diagnostic standard. Various molecular diagnostic methods have been utilized as an effort to provide a fast and reliable identification in lieu or parallel to the conventional culture-based methods. These technologies are mostly based on nucleic acid, proteins, or physical properties of the pathogens with differing advantages and limitations. This review evaluates the different molecular methods and technologies currently available to diagnose polymicrobial infections, which will help determine the most appropriate option for future diagnosis.
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Affiliation(s)
- Yi Zhang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore.
| | - Anne Hu
- Emergency Medicine, Stanford University, Stanford, California 94305, USA
| | - Nadya Andini
- Emergency Medicine, Stanford University, Stanford, California 94305, USA
| | - Samuel Yang
- Emergency Medicine, Stanford University, Stanford, California 94305, USA.
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Zeitler K, Narayanan N. The Present and Future State of Antimicrobial Stewardship and Rapid Diagnostic Testing: Can One Ideally Succeed Without the Other? CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2019. [DOI: 10.1007/s40506-019-00190-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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