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Kremser M, Weiss N, Kaufmann-Stoeck A, Vierbaum L, Kappler S, Schellenberg I, Hiergeist A, Fingerle V, Baier M, Reischl U. Longitudinal analysis of 20 Years of external quality assurance schemes for PCR/NAAT-based bacterial genome detection in diagnostic testing. Front Mol Biosci 2024; 11:1373114. [PMID: 38601324 PMCID: PMC11004257 DOI: 10.3389/fmolb.2024.1373114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 02/28/2024] [Indexed: 04/12/2024] Open
Abstract
Background Quality control (QC), quality assurance, and standardization are crucial for modern diagnostic testing in the field of medical microbiology. The need for efficient QC to ensure accurate laboratory results, treatment, and infection prevention has led to significant efforts in standardizing assay reagents and workflows. External quality assessment (EQA) schemes, like those offered by INSTAND, play a vital role in evaluating in-house and commercial routine diagnostic assays, regarded as mandatory by national and global guidelines. The recent impact of polymerase chain reaction/nucleic acid amplification technology (PCR/NAAT) assays in medical microbiology requires that high-performing assays be distinguished from inadequately performing ones, especially those made by inexperienced suppliers. Objectives The study assesses the evolving diagnostic performance trends over 2 decades for the detection of EHEC/STEC, Borrelia (B.) burgdorferi, and MRSA/cMRSA. It explores the historical context of assay utilization, participant engagement, and rates of correct results in EQA schemes. The research seeks to identify patterns in assay preferences, participant proficiency, and the challenges encountered in detecting emerging variants or clinical strains. Results The study highlights the decline in in-house PCR assay usage, the emergence of new diagnostic challenges, and educational aspects within EQA schemes. Specific examples, such as the inclusion, in certain EQA surveys, of EHEC strains carrying stx-2f or B. miyamotoi, highlight the role of EQAs in increasing awareness and diagnostic capabilities. Advancements in MRSA detection, especially through the adoption of commercial assays, demonstrate the impact that technology evolution has had on diagnostic performance. Conclusion Achieving excellence in diagnostic molecular microbiology involves a multifaceted approach, including well-evaluated assays, careful instrumentation selection, and structured training programs. EQA schemes contribute significantly to this pursuit by providing insights into the evolving diagnostic landscape and identifying areas for improvement in the diagnostic workflow as well as in PCR/NAAT assay design.
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Affiliation(s)
- Marcel Kremser
- INSTAND e.V., Society for Promoting Quality Assurance in Medical Laboratories, Duesseldorf, Germany
| | - Nathalie Weiss
- INSTAND e.V., Society for Promoting Quality Assurance in Medical Laboratories, Duesseldorf, Germany
| | - Anne Kaufmann-Stoeck
- INSTAND e.V., Society for Promoting Quality Assurance in Medical Laboratories, Duesseldorf, Germany
| | - Laura Vierbaum
- INSTAND e.V., Society for Promoting Quality Assurance in Medical Laboratories, Duesseldorf, Germany
| | - Silke Kappler
- INSTAND e.V., Society for Promoting Quality Assurance in Medical Laboratories, Duesseldorf, Germany
| | - Ingo Schellenberg
- INSTAND e.V., Society for Promoting Quality Assurance in Medical Laboratories, Duesseldorf, Germany
- Institute of Bioanalytical Sciences (IBAS), Center of Life Sciences, Anhalt University of Applied Sciences, Bernburg, Germany
| | - Andreas Hiergeist
- INSTAND e.V., Society for Promoting Quality Assurance in Medical Laboratories, Duesseldorf, Germany
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Volker Fingerle
- INSTAND e.V., Society for Promoting Quality Assurance in Medical Laboratories, Duesseldorf, Germany
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Michael Baier
- Institute of Medical Microbiology, University Hospital Jena, Jena, Germany
| | - Udo Reischl
- INSTAND e.V., Society for Promoting Quality Assurance in Medical Laboratories, Duesseldorf, Germany
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
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Misquitta K, Miller BM, Malecek K, Gleason E, Martin K, Walesky CM, Foley K, Copeland DS, Saavedra EA, Kraves S. A fluorescence viewer for rapid molecular assay readout in space and low-resource terrestrial environments. PLoS One 2024; 19:e0291158. [PMID: 38489299 PMCID: PMC10942025 DOI: 10.1371/journal.pone.0291158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/07/2023] [Indexed: 03/17/2024] Open
Abstract
Fluorescence-based assays provide sensitive and adaptable methods for point of care testing, environmental monitoring, studies of protein abundance and activity, and a wide variety of additional applications. Currently, their utility in remote and low-resource environments is limited by the need for technically complicated or expensive instruments to read out fluorescence signal. Here we describe the Genes in Space Fluorescence Viewer (GiS Viewer), a portable, durable viewer for rapid molecular assay readout that can be used to visualize fluorescence in the red and green ranges. The GiS Viewer can be used to visualize any assay run in standard PCR tubes and contains a heating element. Results are visible by eye or can be imaged with a smartphone or tablet for downstream quantification. We demonstrate the capabilities of the GiS Viewer using two case studies-detection of SARS-CoV-2 RNA using RT-LAMP and quantification of drug-induced changes in gene expression via qRT-PCR on Earth and aboard the International Space Station. We show that the GiS Viewer provides a reliable method to visualize fluorescence in space without the need to return samples to Earth and can further be used to assess the results of RT-LAMP and qRT-PCR assays on Earth.
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Affiliation(s)
| | - Bess M. Miller
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Kathryn Malecek
- Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Emily Gleason
- miniPCR bio, Cambridge, MA, United States of America
| | | | - Chad M. Walesky
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Kevin Foley
- Boeing Defense, Space & Security, Berkeley, MO, United States of America
| | - D. Scott Copeland
- Boeing Defense, Space & Security, Berkeley, MO, United States of America
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3
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Makhlouf J, Valkonen A, Smirani Sta W. Growth, single crystal investigation and physico-chemical properties of thiocyanate coordination compounds based on 1,4-dimethylpiperazine. J COORD CHEM 2022. [DOI: 10.1080/00958972.2022.2102905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Jawher Makhlouf
- Laboratory of Material Chemistry, Faculty of Sciences of Bizerte, University of Carthage, Bizerte Zarzouna, Tunisia
| | - Arto Valkonen
- Department of Chemistry, University of Jyvaskyla, Jyvaskyla, Finland
| | - Wajda Smirani Sta
- Laboratory of Material Chemistry, Faculty of Sciences of Bizerte, University of Carthage, Bizerte Zarzouna, Tunisia
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Lephart P, LeBar W, Newton D. Behind Every Great Infection Prevention Program is a Great Microbiology Laboratory: Key Components and Strategies for an Effective Partnership. Infect Dis Clin North Am 2021; 35:789-802. [PMID: 34362544 DOI: 10.1016/j.idc.2021.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A great clinical microbiology laboratory supporting a great infection prevention program requires focusing on the following services: rapid and accurate identification of pathogens associated with health care-associated infections; asymptomatic surveillance for health care-acquired pathogens before infections arise; routine use of broad and flexible antimicrobial susceptibility testing to direct optimal therapy; implementation of epidemiologic tracking tools to identify outbreaks; development of clear result communication with interpretative comments for clinicians. These goals are best realized in a collaborative relationship with the infection prevention program so that both can benefit from the shared priorities of providing the best patient care.
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Affiliation(s)
- Paul Lephart
- Clinical Microbiology Laboratory, Department of Pathology, University of Michigan Medical School, 2800 Plymouth Road Building 36-1221-52, Ann Arbor, MI 48109-2800, USA.
| | - William LeBar
- Clinical Microbiology Laboratory, Department of Pathology, University of Michigan Medical School, 2800 Plymouth Road Building 36-1221-52, Ann Arbor, MI 48109-2800, USA
| | - Duane Newton
- NaviDx Consulting, Department of Pathology, University of Michigan Medical School, 2800 Plymouth Road Building 36-1221-52, Ann Arbor, MI 48109-2800, USA
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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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Biggel M, Heytens S, Latour K, Bruyndonckx R, Goossens H, Moons P. Asymptomatic bacteriuria in older adults: the most fragile women are prone to long-term colonization. BMC Geriatr 2019; 19:170. [PMID: 31226945 PMCID: PMC6588879 DOI: 10.1186/s12877-019-1181-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/04/2019] [Indexed: 12/31/2022] Open
Abstract
Background The diagnosis of urinary tract infections (UTIs) in institutionalized older adults is often based on vague symptoms and a positive culture. The high prevalence of asymptomatic bacteriuria (ABU), which cannot be easily discriminated from an acute infection in this population, is frequently neglected, leading to a vast over-prescription of antibiotics. This study aimed to identify subpopulations predisposed to transient or long-term ABU. Methods Residents in a long-term care facility were screened for ABU. Mid-stream urine samples were collected during two sampling rounds, separated by 10 weeks, each consisting of an initial and a confirmative follow-up sample. Results ABU occurred in approximately 40% of the participants and was mostly caused by Escherichia coli. Long-term ABU (> 3 months) was found in 30% of the subjects. The frailest women with urinary incontinence and dementia had drastically increased rates of ABU and especially long-term ABU. ABU was best predicted by a scale describing the functional independence of older adults. Conclusions Institutionalized women with incontinence have ABU prevalence rates of about 80% and are often persistent carriers. Such prevalence rates should be considered in clinical decision making as they devalue the meaning of a positive urine culture as a criterion to diagnose UTIs. Diagnostic strategies are urgently needed to avoid antibiotic overuse and to identify patients at risk to develop upper UTI. Electronic supplementary material The online version of this article (10.1186/s12877-019-1181-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael Biggel
- Laboratory of Medical Microbiology, University of Antwerp, Universiteitsplein 1, building S, 2610 Wilrijk, Antwerp, Belgium
| | - Stefan Heytens
- Department of Family Medicine and Primary Health Care, Ghent University, Ghent, Belgium
| | - Katrien Latour
- Operational Directorate Epidemiology & Public Health, Sciensano, Brussels, Belgium.,Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Robin Bruyndonckx
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BIOSTAT), Hasselt University, Hasselt, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, University of Antwerp, Universiteitsplein 1, building S, 2610 Wilrijk, Antwerp, Belgium
| | - Pieter Moons
- Laboratory of Medical Microbiology, University of Antwerp, Universiteitsplein 1, building S, 2610 Wilrijk, Antwerp, Belgium.
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Detection and prevalence of carbapenem-resistant Gram-negative bacteria among European laboratories in the COMBACTE network: a COMBACTE LAB-Net survey. Int J Antimicrob Agents 2018; 53:268-274. [PMID: 30391381 DOI: 10.1016/j.ijantimicag.2018.10.013] [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: 06/07/2018] [Revised: 09/25/2018] [Accepted: 10/23/2018] [Indexed: 12/22/2022]
Abstract
Antimicrobial resistance (AMR) represents a global public health threat that jeopardises the progress medicine has made over the last century. To confront AMR, the Innovative Medicines Initiative (IMI) has supported the development of a large network of hospitals and laboratories in Europe as part of the New Drugs for Bad Bugs (ND4BB) programme and the COMBACTE projects. COMBACTE LAB-Net conducted a pilot survey on distribution and usage of carbapenem resistance detection methods among laboratories in the COMBACTE network in two clinical trials as part of the COMBACTE-CARE project. The survey was sent out to 211 laboratories in 20 European countries between May 2015 and June 2017. Answers were collected from 165 laboratories (78%). Sixty laboratories (36%) reported an outbreak of carbapenem-resistant (CR) Enterobacteriaceae during one of the two years preceding the completion of the survey. High rates of CR Acinetobacter spp. above 50% were reported by 74 laboratories (47%), particularly in the Western Balkan countries where the rates were sometimes higher than 90%. Apart from determining the antimicrobial susceptibility of isolates, laboratories also used various methods, such as Matrix Assisted Laser Desorption Ionization - Time of Flight (MALDI-TOF), Carbapenemase Nordmann-Poirel (Carba NP) test or molecular methods, to detect CR Gram-negative bacteria. The survey resulted in the selection of sites with high resistance rates that successfully recruited many patients in the EURECA observational clinical trial.
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Manning ML, Septimus EJ, Ashley ESD, Cosgrove SE, Fakih MG, Schweon SJ, Myers FE, Moody JA. Antimicrobial stewardship and infection prevention-leveraging the synergy: A position paper update. Am J Infect Control 2018; 46:364-368. [PMID: 29592832 DOI: 10.1016/j.ajic.2018.01.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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9
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Antimicrobial Stewardship and Infection Prevention—Leveraging the Synergy: A Position Paper Update. Infect Control Hosp Epidemiol 2018; 39:467-472. [DOI: 10.1017/ice.2018.33] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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