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Schaumburg F, Schuler F, Fobker M, Esser J. Integrated decentralized blood culture incubation: A step towards a 24/7 microbiology service? J Microbiol Methods 2024; 223:106973. [PMID: 38880388 DOI: 10.1016/j.mimet.2024.106973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]
Abstract
To have an impact on the mortality of bloodstream infections, microbiological diagnostics of blood cultures (BC) should provide first results within 12 h. Here, we show how a decentralized BC incubation connected to the central BC incubators via a browser-based application significantly reduces turnaround times.
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Affiliation(s)
- Frieder Schaumburg
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.
| | - Franziska Schuler
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Manfred Fobker
- Central facility for laboratory medicine, University Hospital Münster, Münster, Germany
| | - Jutta Esser
- Central facility for laboratory medicine, University Hospital Münster, Münster, Germany
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2
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Vidal-García M, Urrutikoetxea-Gutiérrez M, Forero Niampira JC, Basaras M, Cisterna R, Díaz de Tuesta Del Arco JL. Ultrafast detection of β-lactamase resistance in Klebsiella pneumoniae from blood culture by nanopore sequencing. Future Microbiol 2023; 18:1309-1317. [PMID: 37850345 DOI: 10.2217/fmb-2023-0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/25/2023] [Indexed: 10/19/2023] Open
Abstract
Aim: This study aimed to assess the ultra-fast method using MinION™ sequencing for rapid identification of β-lactamase-producing Klebsiella pneumoniae clinical isolates from positive blood cultures. Methods: Spiked-blood positive blood cultures were extracted using the ultra-fast method and automated DNA extraction for MinION sequencing. Raw reads were analyzed for β-lactamase resistance genes. Multilocus sequence typing and β-lactamase variant characterization were performed after assembly. Results: The ultra-fast method identified clinically relevant β-lactamase resistance genes in less than 1 h. Multilocus sequence typing and β-lactamase variant characterization required 3-6 h. Sequencing quality showed no direct correlation with pore number or DNA concentration. Conclusion: Nanopore sequencing, specifically the ultra-fast method, is promising for the rapid diagnosis of bloodstream infections, facilitating timely identification of multidrug-resistant bacteria in clinical samples.
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Affiliation(s)
- Matxalen Vidal-García
- Clinical Microbiology Department, Basurto University Hospital, 480132
- Clinical Microbiology & Infection Control, ISS Biocruces Bizkaia, 489033
| | - Mikel Urrutikoetxea-Gutiérrez
- Clinical Microbiology Department, Basurto University Hospital, 480132
- Clinical Microbiology & Infection Control, ISS Biocruces Bizkaia, 489033
| | - Juan C Forero Niampira
- Inmunology, Microbiology & Parasitology Department, University of the Basque Country, 48940
| | - Miren Basaras
- Inmunology, Microbiology & Parasitology Department, University of the Basque Country, 48940
| | - Ramón Cisterna
- Inmunology, Microbiology & Parasitology Department, University of the Basque Country, 48940
| | - José L Díaz de Tuesta Del Arco
- Clinical Microbiology Department, Basurto University Hospital, 480132
- Clinical Microbiology & Infection Control, ISS Biocruces Bizkaia, 489033
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3
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Blondeau JM, Coetzee J. Has coronavirus disease 2019 changed clinical microbiology laboratories forever? Future Microbiol 2023; 18:1211-1215. [PMID: 37750782 DOI: 10.2217/fmb-2023-0187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 08/31/2023] [Indexed: 09/27/2023] Open
Affiliation(s)
- Joseph M Blondeau
- Division of Clinical Microbiology, Royal University Hospital & Saskatchewan Health Authority, 103 Hospital Drive, Saskatoon, Saskatchewan, S7N 0W8, Canada
- Departments of Biochemistry, Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Departments of Pathology & Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Ophthalmology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Jennifer Coetzee
- Clinical Microbiology, Ampath Laboratories, 166 Witch-Hazel Avenue, Technopart, Centurion, 0157, Johannesburg, South Africa
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Chirio D, Demonchy E, Le Marechal M, Gaudart A, Lotte R, Carles M, Ruimy R. 24/7 workflow for bloodstream infection diagnostics in microbiology laboratories: the first step to improve clinical management. Clin Chem Lab Med 2023; 61:349-355. [PMID: 36326696 DOI: 10.1515/cclm-2022-0667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVES We aimed to evaluate the impact of an uninterrupted workflow regarding blood cultures on turnaround time and antibiotic prescription. METHODS Monomicrobial episodes of bacteremia were retrospectively evaluated before and after a continuous 24/7 workflow was implemented in our clinical microbiology laboratory (pre- and post-intervention periods; PREIP and POSTIP). Primary outcome was the time from specimen collection to the first change in antibiotic therapy. Secondary outcomes included the time from specimen collection to effective antibiotic therapy and to antibiotic susceptibility testing results (or turnaround time), as well as hospital length of stay and all-cause mortality at 30 days. RESULTS A total of 548 episodes of bacteremia were included in the final analysis. There was no difference in PREIP and POSTIP regarding patient characteristics and causative bacteria. In POSTIP, the mean time to the first change in antibiotic therapy was reduced by 10.4 h (p<0.001). The time to effective antibiotic therapy and the turnaround time were respectively reduced by 4.8 h (p<0.001) and 5.1 h (p=0.006) in POSTIP. There was no difference in mean hospital length of stay or mortality between the two groups. CONCLUSIONS Around the clock processing of blood cultures allows for a reduction in turnaround time, which in turn reduces the delay until effective antibiotic therapy prescription.
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Affiliation(s)
- David Chirio
- Service de Maladies infectieuses et Tropicales, Hôpital l'Archet 1, CHU de Nice, Nice, France
- Université Côte d'Azur, Nice, France
| | - Elisa Demonchy
- Service de Maladies infectieuses et Tropicales, Hôpital l'Archet 1, CHU de Nice, Nice, France
| | - Marion Le Marechal
- Service de Maladies infectieuses et Tropicales, Hôpital l'Archet 1, CHU de Nice, Nice, France
- Département de santé publique, CHU de Nice, Nice, France
| | - Alice Gaudart
- Laboratoire de Bactériologie, CHU de Nice, Hôpital de l'Archet, Nice, France
| | - Romain Lotte
- Université Côte d'Azur, Nice, France
- Laboratoire de Bactériologie, CHU de Nice, Hôpital de l'Archet, Nice, France
- INSERM U1065, C3M, Equipe 6 "Virulence microbienne et signalisation inflammatoire", Bâtiment Universitaire Archimed, Nice, France
| | - Michel Carles
- Service de Maladies infectieuses et Tropicales, Hôpital l'Archet 1, CHU de Nice, Nice, France
- Université Côte d'Azur, Nice, France
| | - Raymond Ruimy
- Université Côte d'Azur, Nice, France
- Laboratoire de Bactériologie, CHU de Nice, Hôpital de l'Archet, Nice, France
- INSERM U1065, C3M, Equipe 6 "Virulence microbienne et signalisation inflammatoire", Bâtiment Universitaire Archimed, Nice, France
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5
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Bou G, Calbo E, Crespo M, Cantón R, Álvarez de Luna FF, García Rodríguez J, Ángel Goenaga M, González-García J, Gonzàlez J, Larrosa N, Martínez-Martínez L, Navarro D, Ramón Paño J, Rivero A, Carlos Rodríguez J, Tomás M, Vilaj J. Justification for 24/7 clinical microbiology services. Enferm Infecc Microbiol Clin 2022. [DOI: 10.1016/j.eimc.2021.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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6
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Bou G, Calbo E, Crespo M, Cantón R, Álvarez de Luna FF, García Rodríguez J, Ángel Goenaga M, González-García J, Gonzàlez J, Larrosa N, Martínez-Martínez L, Navarro D, Ramón Paño J, Rivero A, Carlos Rodríguez J, Tomás M, Vilaj J. Justification for 24/7 clinical microbiology services. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2022; 40:1-4. [PMID: 34991847 DOI: 10.1016/j.eimce.2021.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/12/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Germán Bou
- Servicio de Microbiología, Complejo Hospitalario Universitario La Coruña e Instituto Investigación Biomédica A Coruña (INIBIC), La Coruña, Spain
| | - Esther Calbo
- Unidad de Enfermedades Infecciosas, Hospital Mutua de Terrassa, Universidad Internacional de Cataluña, Barcelona, Spain
| | - Manuel Crespo
- Servicio de Medicina Interna, Instituto de Investigación Galicia Sur, Hospital Universitario Álvaro Cunqueiro, Vigo, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal e Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | | | - Julio García Rodríguez
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPaz, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Miguel Ángel Goenaga
- Servicio Enfermedades Infecciosas, Hospital Donostia, OSI Donostialdea, Donostia, Spain
| | - Juan González-García
- Servicio de Medicina Interna, Hospital Universitario La Paz, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain; Instituto de Investigación Hospital Universitario La Paz (IdiPaz), Madrid, Spain
| | - Julià Gonzàlez
- Servicio de Microbiología, Hospital Clínic, Facultad de Medicina, Universidad de Barcelona, Barcelona, Spain; Instituto de Salud Global (ISGlobal) de Barcelona, Barcelona, Spain
| | - Nieves Larrosa
- Servicio de Microbiología, Hospital Universitario Vall d'Hebron, VHIR, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Luis Martínez-Martínez
- Unidad de Microbiología Clínica, Hospital Universitario Reina Sofía, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Departamento de Química Agrícola, Edafología y Microbiología, Universidad de Córdoba, Córdoba, Spain
| | - David Navarro
- Servicio de Microbiología, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - José Ramón Paño
- Servicio de Enfermedades Infecciosas, Hospital Clínico Universitario "Lozano Blesa", IIS Aragón, Zaragoza, Spain
| | - Antonio Rivero
- Servicio de Enfermedades Infecciosas, Hospital Universitario Reina Sofía, Universidad de Córdoba, IMIBIC, Córdoba, Spain
| | - Juan Carlos Rodríguez
- Servicio de Microbiología, Hospital General Universitario de Alicante-ISABIAL, Universidad Miguel Hernández, Alicante, Spain
| | - María Tomás
- Servicio de Microbiología, Complejo Hospitalario Universitario La Coruña e Instituto Investigación Biomédica A Coruña (INIBIC), La Coruña, Spain
| | - Jordi Vilaj
- Instituto de Salud Global (ISGlobal) de Barcelona, Barcelona, Spain.
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Méndez L, Ferreira J, Caneiras C. Hafnia alvei Pneumonia: A Rare Cause of Infection in a Patient with COVID-19. Microorganisms 2021; 9:microorganisms9112369. [PMID: 34835494 PMCID: PMC8620350 DOI: 10.3390/microorganisms9112369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 01/08/2023] Open
Abstract
Herein, we describe a case report of a critically ill patient, a 48-year-old man without comorbidities admitted to the hospital with a serious type 1 (hypoxemic) respiratory insufficiency and confirmed diagnosis of COVID-19. After 5 days with invasive mechanical ventilation, the patient developed a bacterial co-infection, namely a pneumonia by Hafnia alvei, requiring the last line of respiratory support: extracorporeal membrane oxygenation (ECMO). Subsequently, his clinical situation gradually stabilized, until he was discharged from the hospital on day 61, being accompanied in ambulatory consultation by the physical medicine and pulmonology department during the post-COVID-19 recovery. H. alvei is a Gram-negative bacterium that is rarely isolated from human specimens and is rarely considered to be pathogenic. However, COVID-19 disease can cause substantial organ dysfunction and can be associated with bacterial secondary infections which can favor the emergence of rare infectious diseases by uncommon microorganisms.
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Affiliation(s)
- Lucía Méndez
- Microbiology Research Laboratory on Environmental Health (EnviHealthMicro Lab), Institute of Environmental Health (ISAMB), Faculty of Medicine, Universidade de Lisboa, 1649-028 Lisboa, Portugal;
- Pulmonology Department, Centro Hospitalar Entre o Douro e Vouga, 4520-221 Santa Maria da feira, Portugal;
| | - Jorge Ferreira
- Pulmonology Department, Centro Hospitalar Entre o Douro e Vouga, 4520-221 Santa Maria da feira, Portugal;
| | - Cátia Caneiras
- Microbiology Research Laboratory on Environmental Health (EnviHealthMicro Lab), Institute of Environmental Health (ISAMB), Faculty of Medicine, Universidade de Lisboa, 1649-028 Lisboa, Portugal;
- Institute of Preventive Medicine and Public Health, Faculty of Medicine, Universidade de Lisboa, 1649-028 Lisboa, Portugal
- Microbiology and Immunology Department, Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
- Correspondence:
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Blondeau J. Clinical microbiology laboratories and COVID-19: an interview with Joseph Blondeau. Future Microbiol 2021; 16:615-618. [PMID: 34082568 PMCID: PMC8186473 DOI: 10.2217/fmb-2021-0113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
This interview was conducted by Atiya Henry, Commissioning Editor of Future Microbiology. Joseph M Blondeau, MSc, PhD, RSM(CCM), SM(AAM), SM(ASCP), FCCP is a Clinical Microbiologist and Head of Clinical Microbiology at Royal University Hospital (Saskatoon Health Region) and the University of Saskatchewan in Saskatoon, Canada. He is also the Provincial Clinical Lead for Microbiology in Saskatchewan, Canada. He holds a Masters of Sciences in Microbiology from Dalhousie University (1985) and a Doctor of Philosophy in Medical Microbiology from the University of Manitoba (1989). Following completion of his PhD, he completed a 1 and a half year post-doctoral training in an infectious diseases research laboratory at Dalhousie University and following which he completed a 2 year post-doctoral residency training program in Clinical Microbiology, also at Dalhousie University. He holds appointments as a Clinical Associate Professor of Pathology, Adjunct Professor of Microbiology and Immunology and Clinical Associate Professor of Ophthalmology. He teaches to undergraduate and graduate students in the areas of microbiology, infectious diseases, antimicrobial agents and pharmacology. Dr Blondeau’s main research interests are in the area of antimicrobial agents and antimicrobial resistance, clinical microbiology and clinical outcomes associated with antimicrobial therapy in both human and veterinary medicine.
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Affiliation(s)
- Joseph Blondeau
- Division of Clinical Microbiology, Royal University Hospital & Saskatchewan Health Authority, Saskatoon, SK, Canada.,Department of Microbiology & Immunology, Pathology & Laboratory Medicine, Ophthalmology, University of Saskatchewan, Saskatoon, SK, Canada
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9
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Blondeau JM, Rankin SC. Diagnostic clinical microbiology. J Vet Pharmacol Ther 2021; 44:250-269. [PMID: 33686661 DOI: 10.1111/jvp.12962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/27/2021] [Accepted: 02/09/2021] [Indexed: 01/07/2023]
Abstract
Technological advancements have changed the way clinical microbiology laboratories are detecting and identifying bacterial, viral, parasitic, and yeast/fungal pathogens. Such advancements have improved sensitivity and specificity and reduce turnaround time to reporting of clinically important results. This article discusses and reviews some traditional methodologies along with some of the technological innovations introduced into diagnostic microbiology laboratories. Some insight to what might be available in the coming years is also discussed.
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Affiliation(s)
- Joseph M Blondeau
- Division of Clinical Microbiology, Royal University Hospital and Saskatchewan Health Authority, Saskatoon, SK, Canada.,Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Ophthalmology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Shelley C Rankin
- Department of Pathobiology, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, USA
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Princess I, Vadala R. Clinical Microbiology in the Intensive Care Unit: Time for Intensivists to Rejuvenate this Lost Art. Indian J Crit Care Med 2021; 25:566-574. [PMID: 34177177 PMCID: PMC8196372 DOI: 10.5005/jp-journals-10071-23810] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We live in an era of evolving microbial infections and equally evolving drug resistance among microorganisms. In any healthcare facility, intensivists play the most pivotal role with critically ill patients under their direct care. Majority of the critically ill patients already harbor a microorganism at admission or acquire one in the form of healthcare-associated infections during their course of intensive care unit stay. It is therefore rather imperative for intensivists to possess sound knowledge in clinical microbiology. On a negative note, most clinicians have very meager and remote knowledge acquired during their undergraduate years. This knowledge is rather theoretical than applied and wanes over the years becoming nonbeneficial in intensive patient care. We, therefore, intend to explore important concepts in applied microbiology and infection control that intensivists should know and implement in their clinical practice on a day-to-day basis. How to cite this article: Princess I, Vadala R. Clinical Microbiology in the Intensive Care Unit: Time for Intensivists to Rejuvenate this Lost Art. Indian J Crit Care Med 2021;25(5):566–574.
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Affiliation(s)
- Isabella Princess
- Department of Microbiology, Apollo Speciality Hospitals, Vanagaram Branch, Chennai, Tamil Nadu, India
| | - Rohit Vadala
- Metro Centre for Respiratory Diseases, Metro Multispeciality Hospital, Noida, Uttar Pradesh, India
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Rapid Detection of Methicillin-Resistant Staphylococcus aureus Directly from Blood for the Diagnosis of Bloodstream Infections: A Mini-Review. Diagnostics (Basel) 2020; 10:diagnostics10100830. [PMID: 33076535 PMCID: PMC7602724 DOI: 10.3390/diagnostics10100830] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/22/2020] [Accepted: 10/14/2020] [Indexed: 11/23/2022] Open
Abstract
Staphylococcus aureus represents a major human pathogen able to cause a number of infections, especially bloodstream infections (BSI). Clinical use of methicillin has led to the emergence of methicillin-resistant S. aureus (MRSA) and MRSA-BSI have been reported to be associated with high morbidity and mortality. Clinical diagnosis of BSI is based on the results from blood culture that, although considered the gold standard method, is time-consuming. For this reason, rapid diagnostic tests to identify the presence of methicillin-susceptible S. aureus (MSSA) and MRSA isolates directly in blood cultures are being used with increasing frequency to rapidly commence targeted antimicrobial therapy, also in the light of antimicrobial stewardship efforts. Here, we review and report the most common rapid non-molecular and molecular methods currently available to detect the presence of MRSA directly from blood.
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Lamy B, Sundqvist M, Idelevich EA. Bloodstream infections – Standard and progress in pathogen diagnostics. Clin Microbiol Infect 2020; 26:142-150. [DOI: 10.1016/j.cmi.2019.11.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/11/2019] [Accepted: 11/12/2019] [Indexed: 12/17/2022]
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Idelevich EA, Becker K. How to accelerate antimicrobial susceptibility testing. Clin Microbiol Infect 2019; 25:1347-1355. [PMID: 31055166 DOI: 10.1016/j.cmi.2019.04.025] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/27/2019] [Accepted: 04/18/2019] [Indexed: 02/04/2023]
Abstract
BACKGROUND Antimicrobial susceptibility testing (AST) results are crucial for timely administration of effective antimicrobial treatment, and, thus, should be made available to clinicians as fast as possible. In particular, increasing rates of multidrug-resistant organisms emphasize the need for rapid AST (rAST). OBJECTIVES This article aims to provide microbiologists and clinicians with a critical overview of the current state of possibilities to accelerate AST. We also intend to discuss technical and strategic aspects of rAST, which may be helpful to academic researchers and assay developers in the industry. SOURCES We have reviewed literature on rAST methods and their implementation in routine diagnostics. CONTENT Phenotypic rAST is universal, mechanism-independent and allows exact categorization, but it demands time for the microorganisms to start the growth and to express the response to antibiotics. Detection of selected resistance mechanisms is more rapid, but the interpretation of its clinical impact is limited. Technical challenges of phenotypic rAST include inoculum effect, delayed expression of resistance, lag phase and initial biomass increase in susceptible isolates. Criteria for a successful rAST assay are ease of use, random access, capacity for simultaneous testing of multiple specimens, affordability and financial attractiveness for industry. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based AST seems to be particularly promising, as it can optimally be combined with MALDI-TOF MS identification. Direct testing from clinical specimens provides particularly early findings, with positive blood cultures being the most suitable specimen type. Polymicrobial samples and inoculum effect are serious obstacles for direct AST from other clinical specimens. Next to the technology improvement, optimization of pre-analytics and laboratory organization is essential. IMPLICATIONS It appears feasible to generate an AST report within the same working shift; however, only affordable and easy-to-use rAST technologies have a chance to enter broad diagnostic routine. Efforts should be made by industry, authorities and academia to enable wide dissemination of rAST in clinical diagnostics.
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Affiliation(s)
- E A Idelevich
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.
| | - K Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
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Idelevich EA, Seifert H, Sundqvist M, Scudeller L, Amit S, Balode A, Bilozor A, Drevinek P, Kocak Tufan Z, Koraqi A, Lamy B, Mareković I, Miciuleviciene J, Müller Premru M, Pascual A, Pournaras S, Saegeman V, Schønheyder HC, Schrenzel J, Strateva T, Tilley R, Wiersinga WJ, Zabicka D, Carmeli Y, Becker K. Microbiological diagnostics of bloodstream infections in Europe-an ESGBIES survey. Clin Microbiol Infect 2019; 25:1399-1407. [PMID: 30980927 DOI: 10.1016/j.cmi.2019.03.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/21/2019] [Accepted: 03/24/2019] [Indexed: 12/14/2022]
Abstract
OBJECTIVES High-quality diagnosis of bloodstream infections (BSI) is important for successful patient management. As knowledge on current practices of microbiological BSI diagnostics is limited, this project aimed to assess its current state in European microbiological laboratories. METHODS We performed an online questionnaire-based cross-sectional survey comprising 34 questions on practices of microbiological BSI diagnostics. The ESCMID Study Group for Bloodstream Infections, Endocarditis and Sepsis (ESGBIES) was the primary platform to engage national coordinators who recruited laboratories within their countries. RESULTS Responses were received from 209 laboratories in 25 European countries. Although 32.5% (68/209) of laboratories only used the classical processing of positive blood cultures (BC), two-thirds applied rapid technologies. Of laboratories that provided data, 42.2% (78/185) were able to start incubating BC in automated BC incubators around-the-clock, and only 13% (25/192) had established a 24-h service to start immediate processing of positive BC. Only 4.7% (9/190) of laboratories validated and transmitted the results of identification and antimicrobial susceptibility testing (AST) of BC pathogens to clinicians 24 h/day. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry from briefly incubated sub-cultures on solid media was the most commonly used approach to rapid pathogen identification from positive BC, and direct disc diffusion was the most common rapid AST method from positive BC. CONCLUSIONS Laboratories have started to implement novel technologies for rapid identification and AST for positive BC. However, progress is severely compromised by limited operating hours such that current practice of BC diagnostics in Europe complies only partly with the requirements for optimal BSI management.
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Affiliation(s)
- E A Idelevich
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - H Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany; German Centre for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - M Sundqvist
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - L Scudeller
- Clinical Epidemiology Unit, Scientific Direction, Fondazione IRCCS, Policlinico San Matteo Pavia Fondazione IRCCS, Pavia, Italy
| | - S Amit
- Department of Clinical Microbiology and Infectious Diseases, Hadassah Medical Centre, Jerusalem, Israel
| | - A Balode
- Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - A Bilozor
- Microbiology Laboratory, Diagnostic Clinic, East-Tallinn Central Hospital, Tallinn, Estonia
| | - P Drevinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Z Kocak Tufan
- Infectious Diseases and Clinical Microbiology Department, Medical School of Ankara Yildirim Beyazit University, Ankara, Turkey
| | - A Koraqi
- Clinical Microbiology Laboratory, University Hospital Centre 'Mother Theresa', Tirana, Albania
| | - B Lamy
- Laboratory of Clinical Microbiology, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, INSERM U1065 (C3M), Nice, France
| | - I Mareković
- Department of Clinical and Molecular Microbiology, University Hospital Centre Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | | | - M Müller Premru
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - A Pascual
- Unidad de Enfermedades Infecciosas, Microbiologia y Medicina Preventiva, Hospital Universitario Virgen Macarena, Departamento de Microbiología, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBiS), Sevilla, Spain
| | - S Pournaras
- Laboratory of Clinical Microbiology, Attikon Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - V Saegeman
- Department of Infection Control and Epidemiology, University Hospitals Leuven, Leuven, Belgium
| | - H C Schønheyder
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - J Schrenzel
- Bacteriology Laboratory, Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - T Strateva
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - R Tilley
- Department of Microbiology, University Hospitals Plymouth NHS Trust, Plymouth, UK
| | - W J Wiersinga
- Department of Infectious Diseases and Centre for Experimental Molecular Medicine, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - D Zabicka
- National Medicines Institute, Warsaw, Poland
| | - Y Carmeli
- Division of Epidemiology, Tel Aviv Sourasky Medical Centre, Tel Aviv, Israel
| | - K Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.
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