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AlQahtani H, Alqahtani FY, Aleanizy FS, Baloch S, Tabb D. Impact of Rapid Identification of Staphylococcus Species in Positive Blood Culture Using GeneXpert Methicillin-Resistant Staphylococcus aureus/ Staphylococcus aureus Blood Culture Assay Combined with Antibiotic Stewardship. Microb Drug Resist 2021; 27:1037-1043. [PMID: 33544027 DOI: 10.1089/mdr.2020.0347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus aureus bacteremia is a life-threatening condition associated with a substantial financial burden on the health care system. The use of the GeneXpert® methicillin-resistant S. aureus (MRSA)/S. aureus blood culture (BC) test for the identification of S. aureus may influence antibiotic stewardship and clinical outcomes. This study assessed the clinical and financial impact of utilizing GeneXpert MRSA/SA in combination with criterion-based testing. The outcomes between October 1, 2018, and June 30, 2019, were evaluated in 65 adult patients who had positive BCs with Gram-positive cocci in clusters. GeneXpert MRSA/SA significantly shortened the time to optimal antimicrobial therapy by 1.7 days (2.5 vs. 44 hr, p < 0.0001). The cost saved because of interventions based on GeneXpert testing results was $4,121. GeneXpert testing has shortened the time to optimal therapy and positively impacted cost, although it had no significant effect on length of hospital stay and mortality rate.
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Affiliation(s)
- Hajar AlQahtani
- Department of Pharmacy Services, King Abdul-Aziz Medical City, Ministry of National Guard, Health Affairs, Riyadh, Saudi Arabia.,Department of Infectious Diseases, Piedmont Columbus Regional Healthcare System, Columbus, Georgia, USA
| | - Fulwah Yahya Alqahtani
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Fadilah Sfouq Aleanizy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Saeed Baloch
- Department of Infectious Diseases, Piedmont Columbus Regional Healthcare System, Columbus, Georgia, USA
| | - Deanne Tabb
- Department of Infectious Diseases, Piedmont Columbus Regional Healthcare System, Columbus, Georgia, USA
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Evaluation of EUCAST rapid antimicrobial susceptibility testing (RAST) for positive blood cultures in clinical practice using a total lab automation. Eur J Clin Microbiol Infect Dis 2020; 39:1305-1313. [PMID: 32112163 PMCID: PMC7303068 DOI: 10.1007/s10096-020-03846-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/10/2020] [Indexed: 11/07/2022]
Abstract
Our objective was to evaluate EUCAST’s ‘rapid antimicrobial susceptibility testing’ (RAST) directly from positive blood culture that delivers antimicrobial results within 6 h for Staphylococcus aureus, Enterococcus spp., Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa, using total lab automation. Zone diameters from RAST were compared with MIC results. Furthermore, its influence on time to report was investigated. RAST was performed to all positive aerobic and anaerobic blood culture bottles by subculturing them, i.e. onto Mueller-Hinton agar and adding six antibiotic discs covering Gram-negative and Gram-positive therapy (cefoxitin, ampicillin, vancomycin, piperacillin/tazobactam, meropenem and ciprofloxacin). RAST was automatically imaged after 6 h. Zone sizes were measured using a TLA software tool and interpreted according to EUCAST clinical breakpoints. Bacteria were identified using MALDI-TOF MS and MIC results were determined using Vitek2 panels. Categorial agreement between agar diffusion and MIC results was investigated. Additionally, time to RAST and time to Vitek were compared for 100 isolates (20 per species). Between November 2018 and April 2019, 3313 positive mono-bacterial blood culture bottles were collected of which 894 bottles with RAST-validated species were investigated. Among these bottles, 2029 individual antibiotic measurements were compared with MIC results from Vitek2 and 14 very major, 28 major and 12 minor errors were found. A median reduction of 17:30 h in time to report was observed. Introduction of RAST with automatic TLA imaging function could reduce time to report by 17:30 h. Excellent accordance between zone diameter and MIC results, particularly for cefoxitin, vancomycin and meropenem, was observed, but drawbacks due to ATU were seen.
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Meunier D, Woodford N, Hopkins KL. Evaluation of the AusDiagnostics MT CRE EU assay for the detection of carbapenemase genes and transferable colistin resistance determinants mcr-1/-2 in MDR Gram-negative bacteria. J Antimicrob Chemother 2019; 73:3355-3358. [PMID: 30189011 DOI: 10.1093/jac/dky347] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/02/2018] [Indexed: 01/05/2023] Open
Abstract
Objectives To evaluate the AusDiagnostics MT CRE EU assay for the detection of carbapenemase and acquired colistin resistance genes in Gram-negative bacteria. Methods The assay allows the detection of blaKPC, blaOXA-48-like, blaNDM, blaVIM, blaIMP, blaSIM, blaGIM, blaSPM, blaFRI, blaIMI, blaGES (differentiating ESBL and carbapenemase variants), blaSME and mcr-1/-2. It was evaluated against a panel of isolates including Enterobacteriaceae, Pseudomonas spp. and Acinetobacter spp. retrospectively (n = 210) and prospectively (n = 182). Results The CRE EU assay was able to detect 268/268 carbapenemase genes, with 239 belonging to the 'big five' families (KPC, OXA-48-like, NDM, VIM and IMP) and 29 carbapenemase genes of the SIM, GIM, SPM, FRI, IMI, SME and GES families. It could distinguish between ESBL and carbapenemase variants of GES. It also allowed detection of mcr-1/-2 colistin resistance genes on their own or in isolates co-producing a carbapenemase. Conclusions The AusDiagnostics MT CRE EU assay offered wide coverage for detection of acquired carbapenemase genes. It required minimal hands-on time and delivered results in less than 4 h from bacterial culture.
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Affiliation(s)
- Danièle Meunier
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Katie L Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
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Shetty A, Macdonald SP, Keijzers G, Williams JM, Tang B, de Groot B, Thompson K, Fraser JF, Finfer S, Bellomo R, Iredell J. Review article: Sepsis in the emergency department - Part 2: Investigations and monitoring. Emerg Med Australas 2018; 30:4-12. [PMID: 29341498 DOI: 10.1111/1742-6723.12924] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 12/01/2017] [Indexed: 12/14/2022]
Abstract
Sepsis is characterised by organ dysfunction resulting from infection, with no reliable single objective test and current diagnosis based on clinical features and results of investigations. In the ED, investigations may be conducted to diagnose infection as the cause of the presenting illness, identify the source, distinguish sepsis from uncomplicated infection (i.e. without organ dysfunction) and/ or risk stratification. Appropriate sample collection for microbiological testing remains key for subsequent confirmation of diagnosis and rationalisation of antimicrobials. Routine laboratory investigations such as creatinine, bilirubin, platelet count and lactate are now critical elements in the diagnosis of sepsis and septic shock. With no biomarker sufficiently validated to rule out bacterial infection in the ED, there remains substantial interest in biomarkers representing various pathogenic pathways. New technologies for screening multiple genes and proteins are identifying unique network 'signatures' of clinical interest. Other future directions include rapid detection of bacterial DNA in blood, genes for antibiotic resistance and EMR-based computational biomarkers that collate multiple information sources. Reliable, cost-effective tests, validated in the ED to promptly and accurately identify sepsis, and to guide initial antibiotic choices, are important goals of current research efforts.
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Affiliation(s)
- Amith Shetty
- Emergency Department, Westmead Hospital, Sydney, New South Wales, Australia.,Westmead Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Stephen Pj Macdonald
- Centre for Clinical Research in Emergency Medicine, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia.,Department of Emergency Medicine, Royal Perth Hospital, Perth, Western Australia, Australia.,Division of Emergency Medicine, The University of Western Australia, Perth, Western Australia, Australia
| | - Gerben Keijzers
- School of Medicine, Bond University, Gold Coast, Queensland, Australia.,School of Medicine, Griffith University, Gold Coast, Queensland, Australia
| | - Julian M Williams
- Department of Emergency Medicine, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Benjamin Tang
- Immunology Department, Westmead Millennium Institute for Medical Research, Sydney, New South Wales, Australia.,Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Bas de Groot
- Department of Emergency Medicine, Leiden University Medical Centre, Leiden, The Netherlands
| | - Kelly Thompson
- Critical Care and Trauma Division, George Institute for Global Health, Sydney, New South Wales, Australia
| | - John F Fraser
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.,Critical Care Research Group, The Prince Charles Hospital, Brisbane, Queensland, Australia.,Intensive Care Unit, St Andrew's War Memorial Hospital, Brisbane, Queensland, Australia
| | - Simon Finfer
- Division of Critical Care, George Institute for Global Health, Sydney, New South Wales, Australia
| | - Rinaldo Bellomo
- Department of Intensive Care, Austin Hospital, Melbourne, Victoria, Australia.,School of Medicine, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jonathan Iredell
- Westmead Clinical School, The University of Sydney, Sydney, New South Wales, Australia.,Infectious Diseases, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia.,Institute of Clinical Pathology and Medical Research, Pathology West, Sydney, New South Wales, Australia
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Wei S, Wang C, Zhu P, Zhou G, Fu W, Wu X. A high-throughput multiplex tandem PCR assay for the screening of genetically modified maize. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2017.08.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Florio W, Morici P, Ghelardi E, Barnini S, Lupetti A. Recent advances in the microbiological diagnosis of bloodstream infections. Crit Rev Microbiol 2017; 44:351-370. [PMID: 29185372 DOI: 10.1080/1040841x.2017.1407745] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Rapid identification (ID) and antimicrobial susceptibility testing (AST) of the causative agent(s) of bloodstream infections (BSIs) are essential for the prompt administration of an effective antimicrobial therapy, which can result in clinical and financial benefits. Immediately after blood sampling, empirical antimicrobial therapy, chosen on clinical and epidemiological data, is administered. When ID and AST results are available, the clinician decides whether to continue or streamline the antimicrobial therapy, based on the results of the in vitro antimicrobial susceptibility profile of the pathogen. The aim of the present study is to review and discuss the experimental data, advantages, and drawbacks of recently developed technological advances of culture-based and molecular methods for the diagnosis of BSI (including mass spectrometry, magnetic resonance, PCR-based methods, direct inoculation methods, and peptide nucleic acid fluorescence in situ hybridization), the understanding of which could provide new perspectives to improve and fasten the diagnosis and treatment of septic patients. Although blood culture remains the gold standard to diagnose BSIs, newly developed methods can significantly shorten the turnaround time of reliable microbial ID and AST, thus substantially improving the diagnostic yield.
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Affiliation(s)
- Walter Florio
- a Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia , Università di Pisa , Pisa , Italy
| | - Paola Morici
- a Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia , Università di Pisa , Pisa , Italy
| | - Emilia Ghelardi
- a Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia , Università di Pisa , Pisa , Italy
| | - Simona Barnini
- b U.O. Microbiologia Universitaria Azienda Ospedaliero-Universitaria Pisana , Pisa , Italy
| | - Antonella Lupetti
- a Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia , Università di Pisa , Pisa , Italy
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Schulte B, Eickmeyer H, Heininger A, Juretzek S, Karrasch M, Denis O, Roisin S, Pletz MW, Klein M, Barth S, Lüdke GH, Thews A, Torres A, Cillóniz C, Straube E, Autenrieth IB, Keller PM. Detection of pneumonia associated pathogens using a prototype multiplexed pneumonia test in hospitalized patients with severe pneumonia. PLoS One 2014; 9:e110566. [PMID: 25397673 PMCID: PMC4232251 DOI: 10.1371/journal.pone.0110566] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 09/23/2014] [Indexed: 11/18/2022] Open
Abstract
Severe pneumonia remains an important cause of morbidity and mortality. Polymerase chain reaction (PCR) has been shown to be more sensitive than current standard microbiological methods – particularly in patients with prior antibiotic treatment – and therefore, may improve the accuracy of microbiological diagnosis for hospitalized patients with pneumonia. Conventional detection techniques and multiplex PCR for 14 typical bacterial pneumonia-associated pathogens were performed on respiratory samples collected from adult hospitalized patients enrolled in a prospective multi-center study. Patients were enrolled from March until September 2012. A total of 739 fresh, native samples were eligible for analysis, of which 75 were sputa, 421 aspirates, and 234 bronchial lavages. 276 pathogens were detected by microbiology for which a valid PCR result was generated (positive or negative detection result by Curetis prototype system). Among these, 120 were identified by the prototype assay, 50 pathogens were not detected. Overall performance of the prototype for pathogen identification was 70.6% sensitivity (95% confidence interval (CI) lower bound: 63.3%, upper bound: 76.9%) and 95.2% specificity (95% CI lower bound: 94.6%, upper bound: 95.7%). Based on the study results, device cut-off settings were adjusted for future series production. The overall performance with the settings of the CE series production devices was 78.7% sensitivity (95% CI lower bound: 72.1%) and 96.6% specificity (95% CI lower bound: 96.1%). Time to result was 5.2 hours (median) for the prototype test and 43.5 h for standard-of-care. The Pneumonia Application provides a rapid and moderately sensitive assay for the detection of pneumonia-causing pathogens with minimal hands-on time. Trial Registration Deutsches Register Klinischer Studien (DRKS) DRKS00005684
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Affiliation(s)
- Berit Schulte
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Holm Eickmeyer
- Heart and Diabetes Center North Rhine-Westphalia, Institute for Laboratory- and Transfusion Medicine, University Hospital of the Ruhr-University Bochum, Bad Oeynhausen, Germany
- Heart and Diabetes Center North Rhine-Westphalia, Clinic for Thoracic and Cardiovascular Surgery, University Hospital of the Ruhr-University Bochum, Bad Oeynhausen, Germany
| | - Alexandra Heininger
- German Centre for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Department of Anesthesiology and Intensive Care Medicine, Tübingen University Hospital, Tübingen, Germany
| | - Stephanie Juretzek
- University Hospital Jena, Institute of Medical Microbiology, Jena, Germany
| | - Matthias Karrasch
- University Hospital Jena, Institute of Medical Microbiology, Jena, Germany
| | - Olivier Denis
- Université Libre de Bruxelles, Laboratory of Microbiology, Bruxelles, Belgium
| | - Sandrine Roisin
- Université Libre de Bruxelles, Laboratory of Microbiology, Bruxelles, Belgium
| | - Mathias W. Pletz
- University Hospital Jena, Center for Infectious Diseases and Infection Control, and Center for Sepsis Care and Control, Jena, Germany
| | | | | | | | | | - Antoni Torres
- Department of Pneumology, Institut Clinic del Tórax, Hospital Clinic of Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB) - Ciber de Enfermedades Respiratorias (Ciberes), Barcelona, Spain
| | - Catia Cillóniz
- Department of Pneumology, Institut Clinic del Tórax, Hospital Clinic of Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB) - Ciber de Enfermedades Respiratorias (Ciberes), Barcelona, Spain
| | - Eberhard Straube
- University Hospital Jena, Institute of Medical Microbiology, Jena, Germany
- University Hospital Jena, Center for Infectious Diseases and Infection Control, and Center for Sepsis Care and Control, Jena, Germany
| | - Ingo B. Autenrieth
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Peter M. Keller
- University Hospital Jena, Institute of Medical Microbiology, Jena, Germany
- University Hospital Jena, Center for Infectious Diseases and Infection Control, and Center for Sepsis Care and Control, Jena, Germany
- * E-mail:
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Gray TJ, Thomas L, Olma T, Mitchell DH, Iredell JR, Chen SCA. Rapid identification of gram negative bacteria from blood culture broth using MALDI-TOF mass spectrometry. J Vis Exp 2014. [PMID: 24893924 DOI: 10.3791/51663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
An important role of the clinical microbiology laboratory is to provide rapid identification of bacteria causing bloodstream infection. Traditional identification requires the sub-culture of signaled blood culture broth with identification available only after colonies on solid agar have matured. MALDI-TOF MS is a reliable, rapid method for identification of the majority of clinically relevant bacteria when applied to colonies on solid media. The application of MALDI-TOF MS directly to blood culture broth is an attractive approach as it has potential to accelerate species identification of bacteria and improve clinical management. However, an important problem to overcome is the pre-analysis removal of interfering resins, proteins and hemoglobin contained in blood culture specimens which, if not removed, interfere with the MS spectra and can result in insufficient or low discrimination identification scores. In addition it is necessary to concentrate bacteria to develop spectra of sufficient quality. The presented method describes the concentration, purification, and extraction of Gram negative bacteria allowing for the early identification of bacteria from a signaled blood culture broth.
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Affiliation(s)
- Timothy J Gray
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital;
| | - Lee Thomas
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital
| | - Tom Olma
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital
| | - David H Mitchell
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital
| | - Jon R Iredell
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital; Centre for Research Excellence in Critical Infection, Westmead Millennium Institute, Westmead Hospital; Sydney Emerging Infectious Diseases Institute, University of Sydney, Westmead Hospital
| | - Sharon C A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital; Sydney Emerging Infectious Diseases Institute, University of Sydney, Westmead Hospital
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The changing culture of the microbiology laboratory. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2014; 24:125-8. [PMID: 24421822 DOI: 10.1155/2013/101630] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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