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Clodi-Seitz T, Baumgartner S, Turner M, Mader T, Hind J, Wenisch C, Zoufaly A, Presterl E. Point-of-Care Method T2Bacteria ®Panel Enables a More Sensitive and Rapid Diagnosis of Bacterial Blood Stream Infections and a Shorter Time until Targeted Therapy than Blood Culture. Microorganisms 2024; 12:967. [PMID: 38792796 PMCID: PMC11124434 DOI: 10.3390/microorganisms12050967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 04/25/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Rapid diagnosis and identification of pathogens are pivotal for appropriate therapy of blood stream infections. The T2Bacteria®Panel, a culture-independent assay for the detection of Escherichia coli, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa in blood, was evaluated under real-world conditions as a point-of-care method including patients admitted to the internal medicine ward due to suspected blood stream infection. METHODS Patients were assigned to two groups (standard of care-SOC vs. T2). In the SOC group 2 × 2 blood culture samples were collected, in the T2 group the T2Bacteria®Panel was performed additionally for pathogen identification. RESULTS A total of 94 patients were included. Pathogens were detected in 19 of 50 patients (38%) in the T2 group compared to 16 of 44 patients (36.4%) in the SOC group. The median time until pathogen detection was significantly shorter in the T2 group (4.5 h vs. 60 h, p < 0.001), as well as the time until targeted therapy (antibiotic with the narrowest spectrum and maximal effectiveness) (6.4 h vs. 42.2 h, p = 0.043). CONCLUSIONS The implementation of the T2Bacteria®Panel for patients with sepsis leads to an earlier targeted antimicrobial therapy resulting in earlier sufficient treatment and decreased excessive usage of broad-spectrum antimicrobials.
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Affiliation(s)
- Tamara Clodi-Seitz
- Department of Infectious Diseases and Tropical Medicine, Klinik Favoriten, 1100 Vienna, Austria
| | - Sebastian Baumgartner
- Department of Infectious Diseases and Tropical Medicine, Klinik Favoriten, 1100 Vienna, Austria
| | - Michael Turner
- Department of Rheumatology and Osteology, Klinik Favoriten, 1100 Vienna, Austria
| | - Theresa Mader
- Department of Infectious Diseases and Tropical Medicine, Klinik Favoriten, 1100 Vienna, Austria
| | - Julian Hind
- Department of Infectious Diseases and Tropical Medicine, Klinik Favoriten, 1100 Vienna, Austria
| | - Christoph Wenisch
- Department of Infectious Diseases and Tropical Medicine, Klinik Favoriten, 1100 Vienna, Austria
| | - Alexander Zoufaly
- Department of Infectious Diseases and Tropical Medicine, Klinik Favoriten, 1100 Vienna, Austria
- Faculty of Medicine, Sigmund Freud University Vienna, 1020 Vienna, Austria
| | - Elisabeth Presterl
- Department of Hospital Epidemiology and Infection Control, Medical University of Vienna, 1090 Vienna, Austria
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Song J, Lin S, Zhu L, Lin Y, An W, Zhang J, Wang H, Yang Z, Liao Y, Xu Y, Li Q. Direct identification of pathogens via microbial cellular DNA in whole blood by MeltArray. Microb Biotechnol 2024; 17:e14380. [PMID: 38084800 PMCID: PMC10832520 DOI: 10.1111/1751-7915.14380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/27/2023] [Accepted: 11/16/2023] [Indexed: 02/03/2024] Open
Abstract
Rapid identification of pathogens is critical for early and appropriate treatment of bloodstream infections. The various culture-independent assays that have been developed often have long turnaround times, low sensitivity and narrow pathogen coverage. Here, we propose a new multiplex PCR assay, MeltArray, which uses intact microbial cells as the source of genomic DNA (gDNA). The successive steps of the MeltArray assay, including selective lysis of human cells, microbial cell sedimentation, microbial cellular DNA extraction, target-specific pre-amplification and multiplex PCR detection, allowed the detection of 35 major bloodstream infectious pathogens in whole blood within 5.5 h. The limits of detection varied depending on the pathogen and ranged from 1 to 5 CFU/mL. Of 443 blood culture samples, including 373 positive blood culture samples and 70 negative blood culture samples, the MeltArray assay showed a sensitivity of 93.8% (350/373, 95% confidence interval [CI] = 90.7%-96.0%), specificity of 98.6% (69/70, 95% CI = 91.2%-99.9%), positive predictive value of 99.7% (95% CI = 98.1%-99.9%), and negative predictive value of 75.0% (95% CI = 64.7%-83.2%). The MeltArray detection results of 16 samples differed from MALDI-TOF and were confirmed by Sanger sequencing. Further testing of 110 whole blood samples from patients with suspected bloodstream infections using blood culture results revealed that the MeltArray assay had a clinical sensitivity of 100% (9/9, 95% CI = 62.8%-100.0%), clinical specificity of 74.5% (70/94, 95% CI = 64.2%-82.7%), positive predictive value of 27.3% (95% CI = 13.9%-45.8%), and negative predictive value of 100.0% (95% CI = 93.5%-100.0%). Compared with metagenomic next-generation sequencing, the MeltArray assay displayed a positive agreement of 85.7% (6/7, 95% CI = 42.0%-99.2%) and negative agreement of 100.0% (4/4, 95% CI = 39.6%-100.0%). We conclude that the MeltArray assay can be used as a rapid and reliable tool for direct identification of pathogens in bloodstream infections.
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Affiliation(s)
- Jiabao Song
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
| | - Su Lin
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
| | - Lin Zhu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
| | - Yong Lin
- Zhongshan HospitalXiamen UniversityXiamenChina
| | - Wenbin An
- Xiang'an HospitalXiamen UniversityXiamenChina
| | - Jinding Zhang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
| | - Haohao Wang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
| | - Zhuan Yang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
| | - Yiqun Liao
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life SciencesXiamen UniversityXiamenChina
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Jenks JD, White PL, Kidd SE, Goshia T, Fraley SI, Hoenigl M, Thompson GR. An update on current and novel molecular diagnostics for the diagnosis of invasive fungal infections. Expert Rev Mol Diagn 2023; 23:1135-1152. [PMID: 37801397 PMCID: PMC10842420 DOI: 10.1080/14737159.2023.2267977] [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: 07/07/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND Invasive fungal infections cause millions of infections annually, but diagnosis remains challenging. There is an increased need for low-cost, easy to use, highly sensitive and specific molecular assays that can differentiate between colonized and pathogenic organisms from different clinical specimens. AREAS COVERED We reviewed the literature evaluating the current state of molecular diagnostics for invasive fungal infections, focusing on current and novel molecular tests such as polymerase chain reaction (PCR), digital PCR, high-resolution melt (HRM), and metagenomics/next generation sequencing (mNGS). EXPERT OPINION PCR is highly sensitive and specific, although performance can be impacted by prior/concurrent antifungal use. PCR assays can identify mutations associated with antifungal resistance, non-Aspergillus mold infections, and infections from endemic fungi. HRM is a rapid and highly sensitive diagnostic modality that can identify a wide range of fungal pathogens, including down to the species level, but multiplex assays are limited and HRM is currently unavailable in most healthcare settings, although universal HRM is working to overcome this limitation. mNGS offers a promising approach for rapid and hypothesis-free diagnosis of a wide range of fungal pathogens, although some drawbacks include limited access, variable performance across platforms, the expertise and costs associated with this method, and long turnaround times in real-world settings.
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Affiliation(s)
- Jeffrey D Jenks
- Durham County Department of Public Health, Durham, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, North Carolina, USA
| | - P Lewis White
- Public Health Wales Microbiology Cardiff, UHW, United Kingdom and Centre for trials research/Division of Infection/Immunity, Cardiff University, Cardiff, UK
| | - Sarah E Kidd
- National Mycology Reference Centre, SA Pathology, Adelaide, Australia
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, Australia
| | - Tyler Goshia
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Stephanie I Fraley
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Martin Hoenigl
- Division of Infectious Diseases, Medical University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - George R Thompson
- University of California Davis Center for Valley Fever, Sacramento, CA, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of California Davis Medical Center, Sacramento, CA, USA
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
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Effective Rapid Diagnosis of Bacterial and Fungal Bloodstream Infections by T2 Magnetic Resonance Technology in the Pediatric Population. J Clin Microbiol 2022; 60:e0029222. [PMID: 36069557 PMCID: PMC9580347 DOI: 10.1128/jcm.00292-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Children are prone to bloodstream infections (BSIs), the rapid and accurate diagnosis of which is an unmet clinical need. The T2MR technology is a direct molecular assay for identification of BSI pathogens, which can help to overcome the limits of blood culture (BC) such as diagnostic accuracy, blood volumes required, and turnaround time. We analyzed results obtained with the T2Bacteria (648) and T2Candida (106) panels in pediatric patients of the Bambino Gesù Children's Hospital between May 2018 and September 2020 in order to evaluate the performance of the T2Dx instrument with respect to BC. T2Bacteria and T2Candida panels showed 84.2% and 100% sensitivity with 85.9% and 94.1% specificity, respectively. The sensitivity and specificity of the T2Bacteria panel increased to 94.9% and 98.7%, respectively, when BC was negative but other laboratory data supported the molecular result. T2Bacteria sensitivity was 100% with blood volumes <2 mL in neonates and infants. T2Bacteria and T2Candida provided definitive microorganism identification in a mean time of 4.4 and 3.7 h, respectively, versus 65.7 and 125.5 h for BCs (P < 0.001). T2 panels rapidly and accurately enable a diagnosis of a pediatric BSI, even in children under 1 year of age and for very small blood volumes. These findings support their clinical use in life-threatening pediatric infections, where the time to diagnosis is of utmost importance, in order to improve survival and minimize the long-term sequalae of sepsis. The T2 technology could be further developed to include more bacteria and fungi species that are involved in the etiology of sepsis.
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An Evaluation of the OLM CandID Real-Time PCR to Aid in the Diagnosis of Invasive Candidiasis When Testing Serum Samples. J Fungi (Basel) 2022; 8:jof8090935. [PMID: 36135660 PMCID: PMC9505555 DOI: 10.3390/jof8090935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Treatment for invasive candidiasis (IC) is time-critical, and culture-based tests can limit clinical utility. Nonculture-based methods such as Candida PCR represent a promising approach to improving patient management but require further evaluation to understand their optimal role and incorporation into clinical algorithms. This study determined the performance of the commercially available OLM CandID real-time PCR when testing serum and developed a diagnostic algorithm for IC. Methods: The study comprised a retrospective performance evaluation of the CandID real-time PCR assay when testing surplus serum (n = 83 patients, 38 with IC), followed by a prospective consecutive cohort evaluation (n = 103 patients, 24 with IC) post incorporation into routine service. A combined diagnostic algorithm, also including (1-3)-β-D-Glucan testing, was generated. Results: Prospective CandID testing generated a sensitivity/specificity of 88%/82%, respectively. Specificity was improved (>95%) when both PCR replicates were positive and/or the patient had multiple positive samples. When combining CandID with (1-3)-β-D-Glucan testing, the probability of IC when both were positive or negative was >69% or <1%, respectively. Conclusions: The CandID provides excellent performance and a rapid time-to-result using methods widely available in generic molecular diagnostic laboratories. By combining nonculture diagnostics, it may be possible to accurately confirm or exclude IC.
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Giacobbe DR, Asperges E, Cortegiani A, Grecchi C, Rebuffi C, Zuccaro V, Scudeller L, Bassetti M. Performance of existing clinical scores and laboratory tests for the diagnosis of invasive candidiasis in critically ill, nonneutropenic, adult patients: a systematic review with qualitative evidence synthesis. Mycoses 2022; 65:1073-1111. [PMID: 35938455 DOI: 10.1111/myc.13515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/03/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND The Fungal Infections Definitions in Intensive Care Unit (ICU) patients (FUNDICU) project aims to provide standard sets of definitions for invasive fungal diseases in critically ill, adult patients. OBJECTIVES To summarize the available evidence on the diagnostic performance of clinical scores and laboratory tests for invasive candidiasis (IC) in nonneutropenic, adult critically ill patients. METHODS A systematic review was performed to evaluate studies assessing the diagnostic performance for IC of clinical scores and/or laboratory tests vs. a reference standard or a reference definition in critically ill, nonneutropenic, adult patients in ICU. RESULTS Clinical scores, despite the heterogeneity of study populations and IC prevalences, constantly showed a high negative predictive value (NPV) and a low positive predictive value (PPV) for the diagnosis of IC in the target population. Fungal antigen-based biomarkers (with most studies assessing serum beta-D-glucan) retained a high NPV similar to that of clinical scores, with a higher PPV, although the latter showed important heterogeneity across studies, possibly reflecting the targeted or untargeted use of these tests in patients with a consistent clinical picture and risk factors for IC. CONCLUSIONS Both clinical scores and laboratory tests showed high NPV for the diagnosis of IC in nonneutropenic critically ill patients. The PPV of laboratory tests varies significantly according to the baseline patients' risk of IC. This qualitative synthesis will provide the FUNDICU panel with baseline evidence to be considered during the development of definitions of IC in critically ill, nonneutropenic adult patients in ICU.
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Affiliation(s)
- Daniele Roberto Giacobbe
- Department of Health Sciences, University of Genoa, Genoa, Italy.,Clinica Malattie Infettive, Ospedale Policlinico San Martino - IRCCS, Genoa, Italy
| | - Erika Asperges
- Infectious Diseases Unit, IRCCS San Matteo, Pavia, Italy
| | - Andrea Cortegiani
- Department of Surgical, Oncological and Oral Science (Di.Chir.On.S.), University of Palermo, Palermo, Italy.,Department of Anesthesia, Intensive Care and Emergency, Policlinico Paolo Giaccone, Palermo, Italy
| | | | - Chiara Rebuffi
- Scientific Direction, IRCCS Istituto Giannina Gaslini, Scientific Direction, Italy
| | | | - Luigia Scudeller
- Research and Innovation Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Matteo Bassetti
- Department of Health Sciences, University of Genoa, Genoa, Italy.,Clinica Malattie Infettive, Ospedale Policlinico San Martino - IRCCS, Genoa, Italy
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7
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Costa SP, Carvalho CM. Burden of bacterial bloodstream infections and recent advances for diagnosis. Pathog Dis 2022; 80:6631550. [PMID: 35790126 DOI: 10.1093/femspd/ftac027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/07/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
Bloodstream infections (BSIs) and subsequent organ dysfunction (sepsis and septic shock) are conditions that rank among the top reasons for human mortality and have a great impact on healthcare systems. Their treatment mainly relies on the administration of broad-spectrum antimicrobials since the standard blood culture-based diagnostic methods remain time-consuming for the pathogen's identification. Consequently, the routine use of these antibiotics may lead to downstream antimicrobial resistance and failure in treatment outcomes. Recently, significant advances have been made in improving several methodologies for the identification of pathogens directly in whole blood especially regarding specificity and time to detection. Nevertheless, for the widespread implementation of these novel methods in healthcare facilities, further improvements are still needed concerning the sensitivity and cost-effectiveness to allow a faster and more appropriate antimicrobial therapy. This review is focused on the problem of BSIs and sepsis addressing several aspects like their origin, challenges, and causative agents. Also, it highlights current and emerging diagnostics technologies, discussing their strengths and weaknesses.
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Affiliation(s)
- Susana P Costa
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.,International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal.,Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Rua Alves Redol, 9 1000-029 Lisbon, Portugal
| | - Carla M Carvalho
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
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Thompson GR, Boulware DR, Bahr NC, Clancy CJ, Harrison TS, Kauffman CA, Le T, Miceli MH, Mylonakis E, Nguyen MH, Ostrosky-Zeichner L, Patterson TF, Perfect JR, Spec A, Kontoyiannis DP, Pappas PG. Noninvasive Testing and Surrogate Markers in Invasive Fungal Diseases. Open Forum Infect Dis 2022; 9:ofac112. [PMID: 35611348 PMCID: PMC9124589 DOI: 10.1093/ofid/ofac112] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/02/2022] [Indexed: 02/04/2023] Open
Abstract
Invasive fungal infections continue to increase as at-risk populations expand. The high associated morbidity and mortality with fungal diseases mandate the continued investigation of novel antifungal agents and diagnostic strategies that include surrogate biomarkers. Biologic markers of disease are useful prognostic indicators during clinical care, and their use in place of traditional survival end points may allow for more rapid conduct of clinical trials requiring fewer participants, decreased trial expense, and limited need for long-term follow-up. A number of fungal biomarkers have been developed and extensively evaluated in prospective clinical trials and small series. We examine the evidence for these surrogate biomarkers in this review and provide recommendations for clinicians and regulatory authorities.
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Affiliation(s)
- George R Thompson
- Division of Infectious Diseases, Department of Internal Medicine, University of California-Davis Medical Center, Sacramento California, USA
- Department of Medical Microbiology and Immunology, University of California-Davis, Davis, California, USA
| | - David R Boulware
- Division of Infectious Diseases, Department of Internal Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Nathan C Bahr
- Division of Infectious Diseases, Department of Medicine, University of Kansas, Kansas City, Kansas, USA
| | - Cornelius J Clancy
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Thomas S Harrison
- Centre for Global Health, Institute of Infection and Immunity, St George’s University of London, London, United Kingdom
- Clinical Academic Group in Infection, St George’s Hospital NHS Trust, London, United Kingdom
- MRC Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Carol A Kauffman
- VA Ann Arbor Healthcare System and University of Michigan, Ann Arbor, Michigan, USA
| | - Thuy Le
- Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, North Carolina, USA
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Eleftherios Mylonakis
- Division of Infectious Diseases, Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | - M Hong Nguyen
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | | | - Thomas F Patterson
- Division of Infectious Diseases, Department of Medicine, The University of Texas Health Science Center, San Antonio, Texas, USA
| | - John R Perfect
- Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, North Carolina, USA
- Division of Infectious Diseases, Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Andrej Spec
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Dimitrios P Kontoyiannis
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Peter G Pappas
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Burillo A, Bouza E. Faster infection diagnostics for intensive care unit (ICU) patients. Expert Rev Mol Diagn 2022; 22:347-360. [PMID: 35152813 DOI: 10.1080/14737159.2022.2037422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION : The patient admitted to intensive care units (ICU) is critically ill, to some extent immunosuppressed, with a high risk of infection, sometimes by multidrug-resistant microorganisms. In this context, the intensivist expects from the microbiology service quick and understandable information so that appropriate antimicrobial treatment for that particular patient and infection can be initiated. AREAS COVERED : In this review of recent literature (2015-2021), we identified diagnostic methods for the most prevalent infections in these patients through a search of the databases Pubmed, evidence-based medicine online, York University reviewers group, Cochrane, MBE-Trip, and Sumsearch using the terms: adult, clinical laboratory techniques, critical care, early diagnosis, microbiology, molecular diagnostic techniques, spectrometry and metagenomics. EXPERT OPINION : There has been an exponential surge in diagnostic systems used directly on blood and other samples to expedite microbial identification and antimicrobial susceptibility testing of pathogens. Few studies have thus far assessed their clinical impact; final outcomes will also depend on preanalytical and post-analytical factors. Besides, many of the resistance mechanisms cannot yet be detected with molecular techniques, which impairs the prediction of the actual resistance phenotype. Nonetheless, this is an exciting field with much yet to explore.
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Affiliation(s)
- Almudena Burillo
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Doctor Esquerdo 46, 28007 Madrid, Spain.,Medicine Department, School of Medicine, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n, Ciudad Universitaria, 28040 Madrid, Spain.,Gregorio Marañón Health Research Institute, Doctor Esquerdo 46, 28007, Madrid, Spain
| | - Emilio Bouza
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Doctor Esquerdo 46, 28007 Madrid, Spain.,Medicine Department, School of Medicine, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n, Ciudad Universitaria, 28040 Madrid, Spain.,Gregorio Marañón Health Research Institute, Doctor Esquerdo 46, 28007, Madrid, Spain.,CIBER of Respiratory Diseases (CIBERES CB06/06/0058), Av. Monforte de Lemos 3-5, Pabellón 11, Planta, 28029 Madrid, Spain
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10
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White PL, Alanio A, Brown L, Cruciani M, Hagen F, Gorton R, Lackner M, Millon L, Morton CO, Rautemaa-Richardson R, Barnes RA, Donnelly JP, Loffler J. An overview of using fungal DNA for the diagnosis of invasive mycoses. Expert Rev Mol Diagn 2022; 22:169-184. [PMID: 35130460 DOI: 10.1080/14737159.2022.2037423] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Fungal PCR has undergone considerable standardization and together with the availability of commercial assays, external quality assessment schemes and extensive performance validation data, is ready for widespread use for the screening and diagnosis of invasive fungal disease (IFD). AREAS COVERED Drawing on the experience and knowledge of the leads of the various working parties of the Fungal PCR initiative, this review will address general considerations concerning the use of molecular tests for the diagnosis of IFD, before focussing specifically on the technical and clinical aspects of molecular testing for the main causes of IFD and recent technological developments. EXPERT OPINION For infections caused by Aspergillus, Candida and Pneumocystis jirovecii, PCR testing is recommended, combination with serological testing will likely enhance the diagnosis of these diseases. For other IFD (e.g. Mucormycosis) molecular diagnostics, represent the only non-classical mycological approach towards diagnoses and continued performance validation and standardization has improved confidence in such testing. The emergence of antifungal resistance can be diagnosed, in part, through molecular testing. Next-generation sequencing has the potential to significantly improve our understanding of fungal phylogeny, epidemiology, pathogenesis, mycobiome/microbiome and interactions with the host, while identifying novel and existing mechanisms of antifungal resistance and novel diagnostic/therapeutic targets.
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Affiliation(s)
- P Lewis White
- Public Health Wales Microbiology Cardiff, UHW, Cardiff, UK CF14 4XW
| | - Alexandre Alanio
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Université de Paris, Paris, France.,Institut Pasteur, CNRS UMR2000, Unité de Mycologie Moléculaire, Centre National de Reference Mycoses invasives et Antifongiques, Paris, France
| | - Lottie Brown
- NHS Mycology Reference Centre Manchester, ECMM Centre of Excellence, Manchester University NHS Foundation Trust, Wythenshawe Hospital; and Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | | | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands & Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rebecca Gorton
- Dept. of Infection Sciences, Health Services Laboratories (HSL) LLP, London, UK
| | - Michaela Lackner
- Institute of Hygiene and Medical Microbiology, Department of Hygiene, Medical Microbiology and Publics Health, Medical University Innsbruck, Innsbruck, Austria
| | - Laurence Millon
- Parasitology-Mycology Department, University Hospital of Besançon, 25000 Besançon, France.,UMR 6249 CNRS Chrono-Environnement, University of Bourgogne Franche-Comté, 25000 Besançon, France
| | - C Oliver Morton
- Western Sydney University, School of Science, Campbelltown, NSW 2560, Australia
| | - Riina Rautemaa-Richardson
- NHS Mycology Reference Centre Manchester, ECMM Centre of Excellence, Manchester University NHS Foundation Trust, Wythenshawe Hospital; and Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | | | | | - Juergen Loffler
- Department of Internal Medicine II, WÜ4i, University Hospital Wuerzburg, Wuerzburg, Germany
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Helweg-Larsen J, Steensen M, Møller Pedersen F, Bredahl Jensen P, Perch M, Møller K, Riis Olesen B, Søderlund M, Cavling Arendrup M. Intensive Care Antifungal Stewardship Programme Based on T2Candida PCR and Candida Mannan Antigen: A Prospective Study. J Fungi (Basel) 2021; 7:jof7121044. [PMID: 34947026 PMCID: PMC8705527 DOI: 10.3390/jof7121044] [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] [Received: 11/21/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 12/17/2022] Open
Abstract
Non-culture-based biomarkers may improve diagnosis and antifungal treatment (AFT) of invasive candidiasis (IC). We evaluated an antifungal stewardship programme (AFSP) in a prospective intensive care unit (ICU) study, which included T2Candida and Candida mannan antigen (MAg) screening of patients with sepsis and a high risk of IC. Patients with non-neutropenic sepsis and a high risk of IC from two large tertiary ICUs were prospectively included, during a one-year period. IC was classified as proven, likely, possible or unlikely. The AFSP, diagnostic values of T2Candida and MAg, and the consumption of antifungals were evaluated. An amount of 219 patients with 504 T2Candida/MAg samples were included. IC was classified as proven in 29 (13.2%), likely in 7 (3.2%) and possible in 10 (5.5%) patients. Sensitivity/specificity/PPV/NPV values, comparing proven/likely versus unlikely IC, were 47%/100%/94%/90% for BC alone, 50%/97%/75%/90% for T2Candida alone, and 39%/96%/67%/88% for MAg alone. For the combination of T2Candida/MAg taken ≤3 days after AFT initiation, sensitivity/specificity/PPV/NPV was 70%/90%/63%/93%. T2Candida/MAg contributed to early (<3 days) AFT initiation in 13%, early AFT discontinuation in 25% and abstaining from AFT in 24% of patients. No reduction in overall use of AFT during the study period compared with the previous year was observed. An AFSP based on T2Candida and MAg screening contributed to a reduction of unnecessary treatment, but not overall AFT use. The diagnostic performance of T2Candida was lower than previously reported, but increased if T2Candida was combined with MAg.
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Affiliation(s)
- Jannik Helweg-Larsen
- Department of Infectious Diseases, Rigshospitalet, 2100 Copenhagen, Denmark;
- Correspondence:
| | - Morten Steensen
- Department of Intensive Care, Rigshospitalet, 2100 Copenhagen, Denmark;
| | - Finn Møller Pedersen
- Department of Thoracic Anesthesiology, Rigshospitalet, 2100 Copenhagen, Denmark; (F.M.P.); (P.B.J.)
| | - Pia Bredahl Jensen
- Department of Thoracic Anesthesiology, Rigshospitalet, 2100 Copenhagen, Denmark; (F.M.P.); (P.B.J.)
| | - Michael Perch
- Department of Cardiology, Section for Lung Transplantation, Rigshospitalet, 2100 Copenhagen, Denmark;
| | - Kirsten Møller
- Department of Neuro Anesthesiology, Rigshospitalet, 2100 Copenhagen, Denmark;
- Department of Clinical Medicine, University of Copenhagen, 2100 Copenhagen, Denmark;
| | | | - Mathias Søderlund
- Department of Infectious Diseases, Rigshospitalet, 2100 Copenhagen, Denmark;
| | - Maiken Cavling Arendrup
- Department of Clinical Medicine, University of Copenhagen, 2100 Copenhagen, Denmark;
- Unit of Mycology, Statens Serum Institut, 2300 Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
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12
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Culture independent detection systems for bloodstream infection. Clin Microbiol Infect 2021; 28:195-201. [PMID: 34687856 DOI: 10.1016/j.cmi.2021.09.039] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/30/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Sepsis and bloodstream infection are associated with significant morbidity and mortality, and early effective antimicrobial therapy has been demonstrated to improve patient outcomes. Traditional culture-based methods, however, have several limitations which hamper a prompt diagnosis in bloodstream infection, including long turnaround times and limited sensitivity. In the last years, advances have been made in the development of several technologies which allow the identification of pathogens and their resistance markers directly from whole blood, possibly representing promising alternatives to conventional culture methods. OBJECTIVES To review the currently commercially available emerging assays for the diagnosis of bloodstream infections directly from whole blood, including their performance and the available data about their impact on patients' outcome. SOURCES Peer-reviewed publications relevant to the topic have been searched through PubMed; manufacturers' websites have also been consulted as a data source. CONTENT We have reviewed available data about the following technologies: multiplex real-time PCR working directly from whole blood (Magicplex Sepsis Real-Time test, Seegene), PCR combined with T2 Magnetic Resonance (T2Candida and T2Bacteria panel, T2Biosystem), and metagenomics-based assays (including SepsiTest, Molzym; iDTECT Dx Blood, PathoQuest; Karius NGS plasma Test, Karius). Performance characteristics, advantages and pitfalls of each method are described, and available data about their impact on patients' clinical outcomes are discussed. IMPLICATIONS The potential of rapid diagnostic tests applied on whole blood in improving the management of patients with bloodstream infection and sepsis is high, both in terms of reducing turnaround times and improving the sensitivity of pathogen and antimicrobial resistance detection. However, overall, there is still a scarcity of data about the real-life performance of such tests, and well-designed studies are awaited for assessing the impact of these emerging technologies on patients' outcomes.
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13
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Kollef MH, Shorr AF, Bassetti M, Timsit JF, Micek ST, Michelson AP, Garnacho-Montero J. Timing of antibiotic therapy in the ICU. Crit Care 2021; 25:360. [PMID: 34654462 PMCID: PMC8518273 DOI: 10.1186/s13054-021-03787-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 12/15/2022] Open
Abstract
Severe or life threatening infections are common among patients in the intensive care unit (ICU). Most infections in the ICU are bacterial or fungal in origin and require antimicrobial therapy for clinical resolution. Antibiotics are the cornerstone of therapy for infected critically ill patients. However, antibiotics are often not optimally administered resulting in less favorable patient outcomes including greater mortality. The timing of antibiotics in patients with life threatening infections including sepsis and septic shock is now recognized as one of the most important determinants of survival for this population. Individuals who have a delay in the administration of antibiotic therapy for serious infections can have a doubling or more in their mortality. Additionally, the timing of an appropriate antibiotic regimen, one that is active against the offending pathogens based on in vitro susceptibility, also influences survival. Thus not only is early empiric antibiotic administration important but the selection of those agents is crucial as well. The duration of antibiotic infusions, especially for β-lactams, can also influence antibiotic efficacy by increasing antimicrobial drug exposure for the offending pathogen. However, due to mounting antibiotic resistance, aggressive antimicrobial de-escalation based on microbiology results is necessary to counterbalance the pressures of early broad-spectrum antibiotic therapy. In this review, we examine time related variables impacting antibiotic optimization as it relates to the treatment of life threatening infections in the ICU. In addition to highlighting the importance of antibiotic timing in the ICU we hope to provide an approach to antimicrobials that also minimizes the unnecessary use of these agents. Such approaches will increasingly be linked to advances in molecular microbiology testing and artificial intelligence/machine learning. Such advances should help identify patients needing empiric antibiotic therapy at an earlier time point as well as the specific antibiotics required in order to avoid unnecessary administration of broad-spectrum antibiotics.
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Affiliation(s)
- Marin H Kollef
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, 660 South Euclid Avenue, MSC 8052-43-14, St. Louis, MO, 63110, USA.
| | - Andrew F Shorr
- Pulmonary and Critical Care Medicine, Medstar Washington Hospital, Washington, DC, USA
| | - Matteo Bassetti
- Infectious Diseases Unit, Department of Health Sciences, San Martino Policlinico Hospital - IRCCS, University of Genoa, Genoa, Italy
| | - Jean-Francois Timsit
- AP-HP, Bichat Claude Bernard Hospital, Medical and Infectious Diseases ICU (MI2), IAME, INSERM, Université de Paris, Paris, France
| | - Scott T Micek
- Department of Pharmacy Practice, University of Health Sciences and Pharmacy, St. Louis, MO, USA
| | - Andrew P Michelson
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, 660 South Euclid Avenue, MSC 8052-43-14, St. Louis, MO, 63110, USA
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14
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Paggi R, Cenci E, De Socio GV, Belati A, Marini D, Gili A, Camilloni B, Mencacci A. Accuracy and Impact on Patient Management of New Tools for Diagnosis of Sepsis: Experience with the T2 Magnetic Resonance Bacteria Panel. Pathogens 2021; 10:pathogens10091132. [PMID: 34578164 PMCID: PMC8465567 DOI: 10.3390/pathogens10091132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/20/2022] Open
Abstract
The rapid and accurate identification of pathogens responsible for sepsis is essential for prompt and effective antimicrobial therapy. Molecular technologies have been developed to detect the most common causative agents, with high sensitivity and short time to result (TTR). T2 Bacteria Panel (T2), based on a combination of PCR and T2 magnetic resonance, can identify directly in blood samples Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterococcus faecium, and Acinetobacter baumannii pathogens. This study evaluates the role of T2 in the diagnosis of sepsis and its impact on patient management, specifically in terms of TTR and the switch from empirical to directed therapy, comparing results of blood culture (BC) and T2 assay in 82 patients with sepsis. T2 significantly improved the detection of the causative agents of sepsis. For pathogens included in the panel, T2 sensitivity was 100% (95% CI 86.3–100.0), significantly higher than that of BC (54.8%, 95% CI 36.0–72.7). The TTR (median, IQR) of positive T2 (3.66 h, 3.59–4.31) was significantly shorter than that of the positive BC (37.58 h, 20.10–47.32). A significant reduction in the duration of empiric therapy and an increase in the percentage of patients with switched therapy was observed in patients with a positive T2 result. In conclusion, T2 can shorten and improve the etiological diagnosis of sepsis with a positive impact on patient management.
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Affiliation(s)
- Riccardo Paggi
- Medical Microbiology Section, Department of Medicine, University of Perugia, Polo Unico Sant’Andrea delle Fratte, 06132 Perugia, Italy; (R.P.); (E.C.); (A.B.); (D.M.); (B.C.)
| | - Elio Cenci
- Medical Microbiology Section, Department of Medicine, University of Perugia, Polo Unico Sant’Andrea delle Fratte, 06132 Perugia, Italy; (R.P.); (E.C.); (A.B.); (D.M.); (B.C.)
| | | | - Alessandra Belati
- Medical Microbiology Section, Department of Medicine, University of Perugia, Polo Unico Sant’Andrea delle Fratte, 06132 Perugia, Italy; (R.P.); (E.C.); (A.B.); (D.M.); (B.C.)
| | - Daniele Marini
- Medical Microbiology Section, Department of Medicine, University of Perugia, Polo Unico Sant’Andrea delle Fratte, 06132 Perugia, Italy; (R.P.); (E.C.); (A.B.); (D.M.); (B.C.)
| | - Alessio Gili
- Public Health Section, Department of Experimental Medicine, University of Perugia, Piazza Lucio Severi 1, 06132 Perugia, Italy;
| | - Barbara Camilloni
- Medical Microbiology Section, Department of Medicine, University of Perugia, Polo Unico Sant’Andrea delle Fratte, 06132 Perugia, Italy; (R.P.); (E.C.); (A.B.); (D.M.); (B.C.)
| | - Antonella Mencacci
- Medical Microbiology Section, Department of Medicine, University of Perugia, Polo Unico Sant’Andrea delle Fratte, 06132 Perugia, Italy; (R.P.); (E.C.); (A.B.); (D.M.); (B.C.)
- Correspondence:
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15
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Honore PM, Redant S, Preseau T, Moorthamers S, Kaefer K, Barreto Gutierrez L, Attou R, Gallerani A, De Bels D. T2MR can be used as a non-culture-based test together with biomarkers to improve detection of Candida in the bloodstream and reduce time delay in treating invasive candidiasis. Expert Rev Anti Infect Ther 2021; 20:327-329. [PMID: 34357835 DOI: 10.1080/14787210.2021.1964954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Patrick M Honore
- Faculty of Medicine at the ULB University, Brussels, Belgium.,ICU Dept, Centre Hospitalier Universitaire Brugmann, Brussels, Belgium
| | - Sebastien Redant
- ICU Dept, Centre Hospitalier Universitaire Brugmann, Brussels, Belgium
| | - Thierry Preseau
- ICU Dept, Centre Hospitalier Universitaire Brugmann, Brussels, Belgium
| | - Sofie Moorthamers
- ICU Dept, Centre Hospitalier Universitaire Brugmann, Brussels, Belgium
| | - Keitiane Kaefer
- ICU Dept, Centre Hospitalier Universitaire Brugmann, Brussels, Belgium
| | | | - Rachid Attou
- ICU Dept, Centre Hospitalier Universitaire Brugmann, Brussels, Belgium
| | - Andrea Gallerani
- ICU Dept, Centre Hospitalier Universitaire Brugmann, Brussels, Belgium
| | - David De Bels
- ICU Dept, Centre Hospitalier Universitaire Brugmann, Brussels, Belgium
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16
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Mind the gaps: challenges in the clinical management of invasive candidiasis in critically ill patients. Curr Opin Infect Dis 2021; 33:441-448. [PMID: 33044240 DOI: 10.1097/qco.0000000000000684] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
PURPOSE OF REVIEW Strict adherence to clinical practice guidelines is recognized to improve outcomes but the inconvenient truth is that only a small subset of what is done in medicine has been tested in appropriate, well designed studies. In this article, we aim to review controversial aspects of the clinical management of invasive candidiasis recommended by guidelines. RECENT FINDINGS Despite still being recommended by guidelines, we fail to identify a single randomized clinical trial documenting that the use of antifungal drugs in high-risk critically ill patients without microbiologic documentation of Candida infection decreases mortality. Regarding deep-seated Candida infections, most cohort studies of patients with candidemia found less than 5% of patients developed endophthalmitis and endocarditis. In this scenario, it is reasonable to reconsider routine universal screening of both complications in candidemic patients. Finally, a large number of studies have shown that critically ill patients usually have lower echinocandin exposure when compared with other populations. We need more data on the clinical relevance of this finding. SUMMARY We need robust studies to validate new strategies for the clinical management of candidemia in ICU, including: the use of fungal biomarkers in the early initiation or interruption of antifungal therapy in high-risk patients to replace the conventional empirical antifungal therapy driven by predictive rules; validation of targeted screening of eye infection and endocarditis with the aid of fungal biomarkers only in high-risk patients; we should clarify if higher doses of candins are necessary to treat invasive candidiasis in critically ill patients, especially in the case of intra-abdominal infections where drug penetration is suboptimal.
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17
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Bassetti M, Azoulay E, Kullberg BJ, Ruhnke M, Shoham S, Vazquez J, Giacobbe DR, Calandra T. EORTC/MSGERC Definitions of Invasive Fungal Diseases: Summary of Activities of the Intensive Care Unit Working Group. Clin Infect Dis 2021; 72:S121-S127. [PMID: 33709127 DOI: 10.1093/cid/ciaa1751] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The EORTC/MSGERC recently revised and updated the consensus definitions of invasive fungal disease (IFD). These definitions primarily focus on patients with cancer and stem cell or solid-organ transplant patients. They may therefore not be suitable for intensive care unit (ICU) patients. More in detail, while the definition of proven IFD applies to a broad range of hosts, the categories of probable and possible IFD were primarily designed for classical immunocompromised hosts and may therefore not be ideal for other populations. Moreover, the scope of the possible category of IFD has been diminished in the recently revised definitions for classically immunocompromised hosts. Diagnosis of IFD in the ICU presents many challenges, which are different for invasive candidiasis and for invasive aspergillosis. The aim of this article is to review progresses made in recent years and difficulties remaining in the development of definitions applicable in the ICU setting.
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Affiliation(s)
- Matteo Bassetti
- Infectious Diseases Unit, Ospedale Policlinico San Martino-IRCCS, Genoa, Italy.,Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Elie Azoulay
- Medical ICU, APHP, Saint-Louis Hospital, Paris, France.,Université de Paris, Paris, France
| | - Bart-Jan Kullberg
- Department of Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Markus Ruhnke
- Division of Hematology, Oncology and Palliative Care, Department of Internal Medicine, Helios Klinikum Aue, Aue, Germany
| | - Shmuel Shoham
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jose Vazquez
- Department of Medicine, Division of Infectious Diseases, Medical College of Georgia/Augusta University, Augusta, Georgia, USA
| | | | - Thierry Calandra
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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18
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Monday LM, Parraga Acosta T, Alangaden G. T2Candida for the Diagnosis and Management of Invasive Candida Infections. J Fungi (Basel) 2021; 7:jof7030178. [PMID: 33802391 PMCID: PMC7999352 DOI: 10.3390/jof7030178] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/27/2021] [Accepted: 02/28/2021] [Indexed: 02/07/2023] Open
Abstract
Invasive candidiasis is a common healthcare-associated infection with high mortality and is difficult to diagnose due to nonspecific symptoms and limitations of culture based diagnostic methods. T2Candida, based on T2 magnetic resonance technology, is FDA approved for the diagnosis of candidemia and can rapidly detect the five most commonly isolated Candida sp. in approximately 5 h directly from whole blood. We discuss the preclinical and clinical studies of T2Candida for the diagnosis of candidemia and review the current literature on its use in deep-seated candidiasis, its role in patient management and prognosis, clinical utility in unique populations and non-blood specimens, and as an antifungal stewardship tool. Lastly, we summarize the strengths and limitations of this promising nonculture-based diagnostic test.
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Affiliation(s)
- Lea M Monday
- Division of Infectious Diseases, Department of Internal Medicine, Henry Ford Hospital, Detroit, MI 48202, USA; (L.MM.); (T.P.A.)
| | - Tommy Parraga Acosta
- Division of Infectious Diseases, Department of Internal Medicine, Henry Ford Hospital, Detroit, MI 48202, USA; (L.MM.); (T.P.A.)
| | - George Alangaden
- Division of Infectious Diseases, Department of Internal Medicine, Henry Ford Hospital, Detroit, MI 48202, USA; (L.MM.); (T.P.A.)
- School of Medicine, Wayne State University, Detroit, MI 48202, USA
- Correspondence: ; Tel.: 313-916-2556
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19
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Hoyt L, O'Day EM. Perspective: A potential role for NUS in metabolite-based in vitro diagnostics. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:257-263. [PMID: 32997360 DOI: 10.1002/mrc.5104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/17/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
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20
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Zurl C, Prattes J, Zollner-Schwetz I, Valentin T, Rabensteiner J, Wunsch S, Hoenigl M, Krause R. T2Candida magnetic resonance in patients with invasive candidiasis: Strengths and limitations. Med Mycol 2021; 58:632-638. [PMID: 31613367 DOI: 10.1093/mmy/myz101] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/02/2019] [Indexed: 12/12/2022] Open
Abstract
T2Candida enables detection of five Candida species in whole blood within approximately 5 hours. Routinely drawn EDTA blood samples were prospectively stored and tested with T2Candida in patients with invasive candidiasis identified by routine index blood or sterile site cultures. T2Candida was compared to diagnostic blood and sterile site cultures and also performed with samples obtained prior and after collection of index cultures. T2Candida was evaluated with 133 samples of 32 patients with candidemia and 22 patients with deep-seated invasive candidiasis. In the candidemic group 28/32 (87.5%) patients had at least one positive T2Candida result at any time point. A total of 17/25 (68%) candidemic patients had a positive T2Candida sample that was drawn concurrently to the index blood culture. In the per patient analysis 17/18 (94.4%) candidemic patients with matched T2Candida samples and peripheral blood cultures at any timepoint had a positive T2Candida test. T2Candida revealed discordant Candida species identification in two candidemic patients. Six of 22 (27.3%) deep-seated IC patients had a positive T2Candida result. Despite advanced time-to-results the clinical value of T2Candida in diagnosing candidemia seems to be limited by missing blood culture positive cases. Positivity rates of T2Candida increased when serial T2Candida samples were tested. In patients with suspected deep-seated invasive candidiasis T2Candida might act as a blood based adjunct to sterile site cultures.
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Affiliation(s)
- Christoph Zurl
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria.,Division of General Paediatrics, Department of Paediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Juergen Prattes
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Ines Zollner-Schwetz
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Thomas Valentin
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Jasmin Rabensteiner
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Austria
| | - Stefanie Wunsch
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Martin Hoenigl
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria.,Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, California, United States
| | - Robert Krause
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
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21
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Recent Advances and Novel Approaches in Laboratory-Based Diagnostic Mycology. J Fungi (Basel) 2021; 7:jof7010041. [PMID: 33440757 PMCID: PMC7827937 DOI: 10.3390/jof7010041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/31/2020] [Accepted: 01/01/2021] [Indexed: 12/16/2022] Open
Abstract
What was once just culture and microscopy the field of diagnostic mycology has significantly advanced in recent years and continues to incorporate novel assays and strategies to meet the changes in clinical demand. The emergence of widespread resistance to antifungal therapy has led to the development of a range of molecular tests that target mutations associated with phenotypic resistance, to complement classical susceptibility testing and initial applications of next-generation sequencing are being described. Lateral flow assays provide rapid results, with simplicity allowing the test to be performed outside specialist centres, potentially as point-of-care tests. Mycology has responded positively to an ever-diversifying patient population by rapidly identifying risk and developing diagnostic strategies to improve patient management. Nowadays, the diagnostic repertoire of the mycology laboratory employs classical, molecular and serological tests and should be keen to embrace diagnostic advancements that can improve diagnosis in this notoriously difficult field.
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22
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White PL, Price JS, Cordey A, Backx M. Molecular Diagnosis of Yeast Infections. CURRENT FUNGAL INFECTION REPORTS 2021; 15:67-80. [PMID: 34178207 PMCID: PMC8212580 DOI: 10.1007/s12281-021-00421-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW The use of molecular tests to aid the diagnosis of invasive yeast infection, in particular invasive candidosis, has been described for over two decades, yet widespread application is limited, and diagnosis remains heavily dependent on classical microbiology. This article will review developments from the past decade in attempt to build on existing knowledge. It will highlight clinical performance and limitations while reviewing developments on recognized procedures; it will also provide insight into novel approaches incorporated in response to clinical demand (e.g. C. auris and antifungal resistance) or technological advances (e.g. next-generation sequencing). RECENT FINDINGS Limited methodological standardization and, until recently, unavailability of commercial options have hindered the integration of molecular diagnostics for yeasts. The development of certain, novel commercial methods has received considerable evaluation allowing a greater understanding of individual assay performance, but widespread multicentre evaluation of most commercial kits is lacking. The detection of emerging pathogens (e.g. C. auris) has been enhanced by the development of molecular tests. Molecular methods are providing a better understanding of the mycobiome, mechanisms of resistance and epidemiology/phylogeny. SUMMARY Despite over two decades of use, the incorporation of molecular methods to enhance the diagnosis of yeast infections remains limited to certain specialist centres. While the development of commercial tests will provide stimulus for broader application, further validation and reduced costs are required. Over the same period of time, Aspergillus PCR has become more widely accepted driven by international efforts to standardize methodology; it is critical that yeast PCR follows suit. Next-generation sequencing will provide significant information on the mycobiome, antifungal resistance mechanism and even broad-range detection directly from the specimen, which may be critical for the molecular detection of yeasts other than Candida species, which is currently limited.
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Affiliation(s)
- P. Lewis White
- grid.241103.50000 0001 0169 7725Mycology Reference Laboratory, Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, CF14 4XW UK
| | - Jessica S. Price
- grid.241103.50000 0001 0169 7725Mycology Reference Laboratory, Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, CF14 4XW UK
| | - Alan Cordey
- grid.241103.50000 0001 0169 7725Mycology Reference Laboratory, Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, CF14 4XW UK
| | - Matthijs Backx
- grid.241103.50000 0001 0169 7725Mycology Reference Laboratory, Public Health Wales, Microbiology Cardiff, UHW, Heath Park, Cardiff, CF14 4XW UK
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23
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D'Onofrio V, Salimans L, Bedenić B, Cartuyvels R, Barišić I, Gyssens IC. The Clinical Impact of Rapid Molecular Microbiological Diagnostics for Pathogen and Resistance Gene Identification in Patients With Sepsis: A Systematic Review. Open Forum Infect Dis 2020; 7:ofaa352. [PMID: 33033730 PMCID: PMC7528559 DOI: 10.1093/ofid/ofaa352] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
Fast microbiological diagnostics (MDx) are needed to ensure early targeted antimicrobial treatment in sepsis. This systematic review focuses on the impact on antimicrobial management and patient outcomes of MDx for pathogen and resistance gene identification compared with blood cultures. PubMed was searched for clinical studies using either whole blood directly or after short-term incubation. Twenty-five articles were retrieved describing the outcomes of 8 different MDx. Three interventional studies showed a significant increase in appropriateness of antimicrobial therapy and a nonsignificant change in time to appropriate therapy. Impact on mortality was conflicting. Length of stay was significantly lower in 2 studies. A significant decrease in antimicrobial cost was demonstrated in 6 studies. The limitations of this systematic review include the low number and observed heterogeneity of clinical studies. In conclusion, potential benefits of MDx regarding antimicrobial management and some patient outcomes were reported. More rigorous intervention studies are needed focusing on the direct benefits for patients.
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Affiliation(s)
- Valentino D'Onofrio
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.,Department of Infectious Diseases and Immunity, Jessa Hospital, Hasselt, Belgium.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lene Salimans
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
| | - Branka Bedenić
- Department of Microbiology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Ivan Barišić
- Molecular diagnostics, Austrian Institute of Technology, Vienna, Austria
| | - Inge C Gyssens
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
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Abstract
PURPOSE OF REVIEW We review the performance of culture-independent diagnostic tests (CIDTs), including β-D-glucan (BDG), polymerase chain reaction (PCR) and T2Candida, in diagnosing invasive candidiasis, their potential roles in patient management, and unintended consequences of testing. RECENT FINDINGS In a recent multicenter trial, T2Candida was 90% sensitive and 98% specific for diagnosing candidemia. A new study provided the first data for T2Candida in diagnosing deep-seated candidiasis, demonstrating sensitivity/specificity of 45%/96%. Two studies showed that ongoing T2Candida-positivity is associated with poor prognosis. In several studies, serum BDG and T2Candida, targeted to patients at-risk for invasive candidiasis, were useful in guiding treatment decisions and antifungal stewardship. A randomized, multicenter trial of BDG-guided empiric antifungal treatment is underway among critically ill patients. PCR performance was highly variable for candidemia and deep-seated candidiasis in recent studies. CIDT results may overstate bloodstream infections, according to current National Healthcare Safety Network (NHSN) definitions. SUMMARY BDG and T2Candida are nearing prime-time status in the clinic. To be useful, testing must be directed to carefully chosen patients and specific clinical questions. Candida PCR is limited by a need for standardized methodologies and commercial assays. NHSN definitions of bloodstream infections must be revised in the era of CIDTs.
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Camp I, Spettel K, Willinger B. Molecular Methods for the Diagnosis of Invasive Candidiasis. J Fungi (Basel) 2020; 6:jof6030101. [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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Bassetti M, Vena A, Pincino R, Briano F, Giacobbe DR. Role of Antifungal Therapy in Complicated Intra-abdominal Infections. Curr Infect Dis Rep 2020. [DOI: 10.1007/s11908-020-00731-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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27
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Bassetti M, Vena A, Meroi M, Cardozo C, Cuervo G, Giacobbe DR, Salavert M, Merino P, Gioia F, Fernández-Ruiz M, López-Cortés LE, Almirante B, Escolà-Vergé L, Montejo M, Aguilar-Guisado M, Puerta-Alcalde P, Tasias M, Ruiz-Gaitán A, González F, Puig-Asensio M, Marco F, Pemán J, Fortún J, Aguado JM, Soriano A, Carratalá J, Garcia-Vidal C, Valerio M, Sartor A, Bouza E, Muñoz P. Factors associated with the development of septic shock in patients with candidemia: a post hoc analysis from two prospective cohorts. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2020; 24:117. [PMID: 32216822 PMCID: PMC7099832 DOI: 10.1186/s13054-020-2793-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 02/17/2020] [Indexed: 01/09/2023]
Abstract
BACKGROUND Almost one third of the patients with candidemia develop septic shock. The understanding why some patients do and others do not develop septic shock is very limited. The objective of this study was to identify variables associated with septic shock development in a large population of patients with candidemia. METHODS A post hoc analysis was performed on two prospective, multicenter cohort of patients with candidemia from 12 hospitals in Spain and Italy. All episodes occurring from September 2016 to February 2018 were analyzed to assess variables associated with septic shock development defined according to The Third International Consensus Definition for Sepsis and Septic Shock (Sepsis-3). RESULTS Of 317 candidemic patients, 99 (31.2%) presented septic shock attributable to candidemia. Multivariate logistic regression analysis identifies the following factors associated with septic shock development: age > 50 years (OR 2.57, 95% CI 1.03-6.41, p = 0.04), abdominal source of the infection (OR 2.18, 95% CI 1.04-4.55, p = 0.04), and admission to a general ward at the time of candidemia onset (OR 0.21, 95% CI, 0.12-0.44, p = 0.001). Septic shock development was independently associated with a greater risk of 30-day mortality (OR 2.14, 95% CI 1.08-4.24, p = 0.02). CONCLUSIONS Age and abdominal source of the infection are the most important factors significantly associated with the development of septic shock in patients with candidemia. Our findings suggest that host factors and source of the infection may be more important for development of septic shock than intrinsic virulence factors of organisms.
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Affiliation(s)
- Matteo Bassetti
- Infectious Diseases Clinic, Department of Medicine, University of Udine and Azienda Sanitaria Universitaria Integrata, Piazzale Santa Maria della Misericordia 15, 33010, Udine, Italy. .,Department of Health Sciences, University of Genoa, Genoa, Italy. .,Clinica Malattie Infettive, Ospedale Policlinico San Martino-IRCCS, Genoa, Italy.
| | - Antonio Vena
- Infectious Diseases Clinic, Department of Medicine, University of Udine and Azienda Sanitaria Universitaria Integrata, Piazzale Santa Maria della Misericordia 15, 33010, Udine, Italy.,Department of Health Sciences, University of Genoa, Genoa, Italy.,Clinica Malattie Infettive, Ospedale Policlinico San Martino-IRCCS, Genoa, Italy
| | - Marco Meroi
- Infectious Diseases Clinic, Department of Medicine, University of Udine and Azienda Sanitaria Universitaria Integrata, Piazzale Santa Maria della Misericordia 15, 33010, Udine, Italy
| | - Celia Cardozo
- Hospital Clínic, IDIBAPS (Institut d'Investigacions biomèdiques Agust Pi i Sunyer), Universitat de Barcelona, Barcelona, Spain
| | - Guillermo Cuervo
- Hospital Universitari de Bellvitge, IDIBELL (Institut D'Investigació Biomèdica de Bellvitge), Universitat de Barcelona, Barcelona, Spain
| | - Daniele Roberto Giacobbe
- Department of Health Sciences, University of Genoa, Genoa, Italy.,Clinica Malattie Infettive, Ospedale Policlinico San Martino-IRCCS, Genoa, Italy
| | | | - Paloma Merino
- Hospital Universitario Clínico "San Carlos", Madrid, Spain
| | | | - Mario Fernández-Ruiz
- Hospital Universitario "12 de Octubre", Instituto de Investigación Hospital "12 de Octubre" (i+12), Universidad Complutense de Madrid, Madrid, Spain
| | - Luis Eduardo López-Cortés
- Unidad Clínica de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario Virgen Macarena/Instituto de Biomedicina de Sevilla (IBiS)/Universidad de Sevilla/Centro Superior de Investigaciones Científicas, Seville, Spain
| | - Benito Almirante
- Hospital Universitari Vall d'Hebron, VHIR (Vall d'Hebron Institut de Recerca), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laura Escolà-Vergé
- Hospital Universitari Vall d'Hebron, VHIR (Vall d'Hebron Institut de Recerca), Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | | | - Pedro Puerta-Alcalde
- Hospital Clínic, IDIBAPS (Institut d'Investigacions biomèdiques Agust Pi i Sunyer), Universitat de Barcelona, Barcelona, Spain
| | - Mariona Tasias
- Hospital Universitari I Politecnic "La Fe", Valencia, Spain
| | | | | | - Mireia Puig-Asensio
- Hospital Universitari Vall d'Hebron, VHIR (Vall d'Hebron Institut de Recerca), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Francesc Marco
- Hospital Clínic, IDIBAPS (Institut d'Investigacions biomèdiques Agust Pi i Sunyer), Universitat de Barcelona, Barcelona, Spain
| | - Javier Pemán
- Hospital Universitari I Politecnic "La Fe", Valencia, Spain
| | - Jesus Fortún
- Hospital Universitario "Ramón y Cajal", Madrid, Spain
| | - Jose Maria Aguado
- Hospital Universitario "12 de Octubre", Instituto de Investigación Hospital "12 de Octubre" (i+12), Universidad Complutense de Madrid, Madrid, Spain
| | - Alejandro Soriano
- Hospital Clínic, IDIBAPS (Institut d'Investigacions biomèdiques Agust Pi i Sunyer), Universitat de Barcelona, Barcelona, Spain
| | - Jordi Carratalá
- Hospital Universitari de Bellvitge, IDIBELL (Institut D'Investigació Biomèdica de Bellvitge), Universitat de Barcelona, Barcelona, Spain
| | - Carolina Garcia-Vidal
- Hospital Clínic, IDIBAPS (Institut d'Investigacions biomèdiques Agust Pi i Sunyer), Universitat de Barcelona, Barcelona, Spain
| | - Maricela Valerio
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria, Hospital Gregorio Marañón, Madrid, Spain
| | - Assunta Sartor
- Microbiology Unit, Azienda Sanitaria Universitaria Integrata Santa Maria della Misericordia, Udine, Italy
| | - Emilio Bouza
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria, Hospital Gregorio Marañón, Madrid, Spain.,Medicine Department School of Medicine, Universidad Complutense de Madrid, Madrid, Spain.,CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), Udine, Spain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria, Hospital Gregorio Marañón, Madrid, Spain.,Medicine Department School of Medicine, Universidad Complutense de Madrid, Madrid, Spain.,CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), Udine, Spain
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What Is New in Candida Infections? T2Candida, Antifungal Stewardship, and Candida auris. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2020. [DOI: 10.1007/s40506-020-00209-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Satyanarayana G. Work-up for Fever During Neutropenia for Both the Stem Cell Transplant Recipient and the Hematologic Malignancy Patient. Infect Dis Clin North Am 2019; 33:381-397. [PMID: 31005134 DOI: 10.1016/j.idc.2019.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Fever is a common complication in patients with underlying neutropenia and is associated with significant mortality in neutropenic patients with acute myelogenous leukemia or hematopoietic cell transplant. Fever may be the only sign of infection and requires further clinical assessment, including a history, a physical examination, and additional laboratory and radiographic testing. National and international guidelines recommend initiation of empiric antimicrobial therapy in patients with fever during neutropenia. Stepwise escalation of antibacterial therapy, followed by antifungal therapy for patients with persistent fever, generally is recommended. Consideration should also be given to de-escalation of antimicrobial therapy in the appropriate clinical settings.
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Affiliation(s)
- Gowri Satyanarayana
- Division of Infectious Diseases, Vanderbilt University Medical Center, A2200 MCN, 1161 21st Avenue South, Nashville, TN 37232-2605, USA.
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31
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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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32
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Bouza E, Almirante B, García Rodríguez J, Garnacho-Montero J, Salavert M, Muñoz P, Sanguinetti M. Biomarkers of fungal infection: Expert opinion on the current situation. REVISTA ESPANOLA DE QUIMIOTERAPIA 2019. [PMID: 31729203 PMCID: PMC6987620 DOI: 10.37201/req/2260.2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The introduction of non-culture-based diagnostic techniques is revolutionizing the world of microbiological diagnosis and infection assessment. Fungi are no exception, and the introduction of biomarkers has opened up enormous expectations for better management of these entities. Biomarkers are diverse, their targets are also diverse and their evaluation has been done preferably in an individualized use and with deficient designs. Less is known about the value of the combined use of biomarkers and the impact of the negativity of two or more biomarkers on antifungal treatment decisions has been poorly studied. Given the paucity of prospective, randomized and definitive studies, we have convened experts from different fields, with an interest in invasive fungal infections, to answer some questions about the current relevant use of fungal biomarkers. This document summarizes the answers of these experts to the different questions.
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Affiliation(s)
- E Bouza
- Emilio Bouza, Instituto de Investigación Sanitaria Gregorio Marañón, Servicio de Microbiología Clínica y E. Infecciosas, C/ Dr. Esquerdo, 46, 28007 Madrid, Spain.
| | | | | | | | | | - P Muñoz
- Patricia Muñoz, Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/ Dr. Esquerdo, 46, 28007 Madrid, Spain.
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Abstract
PURPOSE OF REVIEW To outline key drivers and components of antifungal stewardship (AFS) programmes, the evidence for specific interventions, and methods to assess performance of programmes. RECENT FINDINGS Recent developments in antifungal resistance and breakthrough invasive fungal diseases have increased the urgency for effective AFS. In practice, however, few hospitals have dedicated AFS programmes. To date, AFS programmes have centred around the provision of expert bedside reviews and have reduced costs and consumption of antifungal agents. Incorporating tools such as fungal diagnostics and therapeutic drug monitoring into AFS programme models is recommended. However, the application and impact of these tools in this context have not been adequately assessed. The effectiveness of AFS programmes has been measured in multiple ways but a standardized method of evaluation remains elusive. Few studies have explored the impact of AFS interventions on patient outcomes. SUMMARY The uptake of formal AFS programmes has been slow. New initiatives integrating AFS tools in programmes, and measuring the impacts on patient outcomes are required given such data are not readily available. A comprehensive approach to evaluate AFS programmes by correlating the quantity and quality of antifungal prescribing with impacts on patient outcomes is needed. Consensus definitions for core AFS metrics are required to benchmark performance and are essential to the resourcing and sustainability of these programmes.
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34
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Fuchs S, Lass-Flörl C, Posch W. Diagnostic Performance of a Novel Multiplex PCR Assay for Candidemia among ICU Patients. J Fungi (Basel) 2019; 5:jof5030086. [PMID: 31533333 PMCID: PMC6787705 DOI: 10.3390/jof5030086] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/11/2019] [Accepted: 09/13/2019] [Indexed: 12/16/2022] Open
Abstract
Candidemia poses a major threat to ICU patients and is routinely diagnosed by blood culture, which is known for its low sensitivity and long turnaround times. We compared the performance of a novel, Candida-specific multiplex real-time PCR assay (Fungiplex® Candida IVD Real-Time PCR Kit) with blood culture and another established diagnostic real-time PCR assay (LightCycler SeptiFast Test) with respect to Candida detection from whole blood samples. Clinical samples from 58 patients were analyzed by standard blood culture (BC) and simultaneously tested with the Fungiplex Candida PCR (FP) and the SeptiFast test (SF) for molecular detection of Candida spp. Compared to BC, the FP test showed high diagnostic power, with a sensitivity of 100% and a specificity of 94.1%. Overall diagnostic accuracy reached 94.6%. Using SF, we found a sensitivity of 60%, a specificity of 96.1%, and an overall diagnostic accuracy of 92.9%. The Fungiplex Candida PCR has shown good sensitivity and specificity on clinical samples of high-risk patients for direct detection of Candida species in whole blood samples. Together with conventional diagnostics (BC and antigen testing), this new multiplex PCR assay may contribute to a rapid and accurate diagnosis of candidiasis.
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Affiliation(s)
- Stefan Fuchs
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020 Innsbruck, Austria.
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Bassetti M, Giacobbe DR, Vena A, Brink A. Challenges and research priorities to progress the impact of antimicrobial stewardship. Drugs Context 2019; 8:212600. [PMID: 31516534 PMCID: PMC6726362 DOI: 10.7573/dic.212600] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/16/2019] [Accepted: 07/19/2019] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial stewardship programmes have been playing an important role in patient care and hospital policies. These programmes are now recognised as formal strategies for curbing the upward trend in antibiotic resistance and for improving the appropriate antimicrobial and antifungal use. The role of such programs in the era of antimicrobial resistance presents several unique challenges and opportunities, most notably in the diagnostic and therapeutic setting. Controversies remain regarding the most effective interventions and the appropriate design to evaluate their impact. In this review, based on rounds of discussion, we explain the most important challenges faced by antibiotic stewardship and antifungal stewardship programmes. We also try to suggest areas for further research.
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Affiliation(s)
- Matteo Bassetti
- Infectious Diseases Clinic, Department of Medicine, University of Udine, Italy.,Infectious Diseases Unit, Ospedale Policlinico San Martino - IRCCS per l'Oncologia, University of Genoa, Largo R. Benzi, 10, 16132, Genoa, Italy.,Department of Health Sciences, DISSAL, University of Genoa, Genoa, Italy
| | - Daniele Roberto Giacobbe
- Infectious Diseases Unit, Ospedale Policlinico San Martino - IRCCS per l'Oncologia, University of Genoa, Largo R. Benzi, 10, 16132, Genoa, Italy.,Department of Health Sciences, DISSAL, University of Genoa, Genoa, Italy
| | - Antonio Vena
- Infectious Diseases Clinic, Department of Medicine, University of Udine, Italy
| | - Adrian Brink
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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36
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Clancy CJ, Nguyen MH. T2 magnetic resonance for the diagnosis of bloodstream infections: charting a path forward. J Antimicrob Chemother 2019; 73:iv2-iv5. [PMID: 29608754 DOI: 10.1093/jac/dky050] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We discuss four studies in this issue of the Journal of Antimicrobial Chemotherapy that describe experience with T2 magnetic resonance (T2MR) nanodiagnostics for Candida and bacterial bloodstream infections, in the context of the T2MR literature. T2Candida and T2Bacteria panels use a dedicated instrument to detect amplified DNA from microbial cells directly in whole blood. T2Candida gives positive or negative results for C. albicans/C. tropicalis, C. glabrata/C. krusei, and C. parapsilosis. T2Bacteria detects Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Escherichia coli. In recent trials, T2Candida sensitivity and specificity for candidaemia were ∼90% and ∼98%, respectively. Two studies from Spanish hospitals now provide the first data on T2Candida as a prognostic tool. T2Candida was superior to cultures or serum β-d-glucan in identifying patients with complicated candidaemia, and in predicting the outcomes of empirical antifungal therapy for suspected candidiasis. In a retrospective study from US community hospitals, use of T2Candida was reported to reduce times to appropriate antifungal therapy, shorten courses of empirical therapy, and save an average of US$280 in antifungal costs per patient tested. Finally, a study from a hospital in Rome provides the first clinical data for T2Bacteria: sensitivity and specificity were 89% and 98%, respectively, among patients with positive blood cultures for bacteria detected by the panel, or fulfilling criteria for infection. We conclude that T2MR diagnostics are promising both for detecting bloodstream infections due to Candida and bacteria, and for providing prognostic information. More studies that present real-world performance data are needed.
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Affiliation(s)
- Cornelius J Clancy
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, USA
| | - M Hong Nguyen
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, USA
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Dubourg G, Raoult D, Fenollar F. Emerging methodologies for pathogen identification in bloodstream infections: an update. Expert Rev Mol Diagn 2019; 19:161-173. [DOI: 10.1080/14737159.2019.1568241] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
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Pilecky M, Schildberger A, Orth-Höller D, Weber V. Pathogen enrichment from human whole blood for the diagnosis of bloodstream infection: Prospects and limitations. Diagn Microbiol Infect Dis 2018; 94:7-14. [PMID: 30579657 DOI: 10.1016/j.diagmicrobio.2018.11.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/20/2018] [Accepted: 11/20/2018] [Indexed: 02/07/2023]
Abstract
Blood culture represents the current reference method for the detection of bacteria or fungi in the circulation. To accelerate pathogen identification, molecular diagnostic methods, mainly based on polymerase chain reaction (PCR), have been introduced to ensure early and targeted antibiotic treatment of patients suffering from bloodstream infection. Still, these approaches suffer from a lack of sensitivity and from inhibition of PCR in a number of clinical samples, leading to false negative results. To overcome these limitations, various approaches aiming at the enrichment of pathogens from larger blood volumes prior to the extraction of pathogen DNA, thereby also depleting factors interfering with PCR, have been developed. Here, we provide an overview of current systems for diagnosing bloodstream infection, with a focus on approaches for pre-analytical pathogen enrichment, and highlight emerging applications of pathogen depletion for therapeutic purposes as a potential adjunctive treatment of sepsis patients.
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Affiliation(s)
- Matthias Pilecky
- Center for Biomedical Technology, Department for Biomedical Research, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500 Krems, Austria.
| | - Anita Schildberger
- Center for Biomedical Technology, Department for Biomedical Research, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500 Krems, Austria.
| | - Dorothea Orth-Höller
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, A-6020 Innsbruck, Austria.
| | - Viktoria Weber
- Center for Biomedical Technology, Department for Biomedical Research, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500 Krems, Austria; Christian Doppler Laboratory for Innovative Therapy Approaches in Sepsis, Department for Biomedical Research, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500 Krems, Austria.
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Beganovic M, McCreary EK, Mahoney MV, Dionne B, Green DA, Timbrook TT. Interplay between Rapid Diagnostic Tests and Antimicrobial Stewardship Programs among Patients with Bloodstream and Other Severe Infections. J Appl Lab Med 2018; 3:601-616. [PMID: 31639729 DOI: 10.1373/jalm.2018.026450] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/04/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Antimicrobial stewardship programs (ASPs) aim to provide optimal antimicrobial therapy to patients quickly to improve the likelihood of overcoming infection while reducing the risk of adverse effects. Rapid diagnostic tests (RDTs) for infectious diseases have become an integral tool for ASPs to achieve these aims. CONTENT This review explored the demonstrated clinical value of longer-standing technologies and implications of newer RDTs from an antimicrobial stewardship perspective. Based on available literature, the focus was on the use of RDTs in bloodstream infections (BSIs), particularly those that perform organism identification and genotypic resistance detection, phenotypic susceptibility testing, and direct specimen testing. Clinical implications of rapid testing among respiratory, central nervous system, and gastrointestinal infections are also reviewed. SUMMARY Coupling RDTs with ASPs facilitates the appropriate and timely use of test results, translating into improved patient outcomes through optimization of antimicrobial use. These benefits are best demonstrated in the use of RDT in BSIs. Rapid phenotypic susceptibility testing offers the potential for early pharmacokinetic/pharmacodynamic optimization, and direct specimen testing on blood may allow ASPs to initiate appropriate therapy and/or tailor empiric therapy even sooner than other RDTs. RDTs for respiratory, central nervous system, and gastrointestinal illnesses have also shown significant promise, although more outcome studies are needed to evaluate their full impact.
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Affiliation(s)
- Maya Beganovic
- Advocate Lutheran General Hospital, Department of Pharmacy, Park Ridge, IL
| | - Erin K McCreary
- University of Pittsburgh Medical Center, Department of Pharmacy, Pittsburgh, PA
| | - Monica V Mahoney
- Beth Israel Deaconess Medical Center, Department of Pharmacy, Boston, MA
| | - Brandon Dionne
- Northeastern University, School of Pharmacy, Bouvé College of Health Sciences, Boston, MA.,Brigham and Women's Hospital, Department of Pharmacy, Boston, MA
| | - Daniel A Green
- Columbia University College of Physicians and Surgeons, New York, NY
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