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Drevinek P, Hollweck R, Lorenz MG, Lustig M, Bjarnsholt T. Direct 16S/18S rRNA Gene PCR Followed by Sanger Sequencing as a Clinical Diagnostic Tool for Detection of Bacterial and Fungal Infections: a Systematic Review and Meta-Analysis. J Clin Microbiol 2023; 61:e0033823. [PMID: 37367430 PMCID: PMC10575125 DOI: 10.1128/jcm.00338-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
rRNA gene Sanger sequencing is being used for the identification of cultured pathogens. A new diagnostic approach is sequencing of uncultured samples by using the commercial DNA extraction and sequencing platform SepsiTest (ST). The goal was to analyze the clinical performance of ST with a focus on nongrowing pathogens and the impact on antibiotic therapy. A literature search used PubMed/Medline, Cochrane, Science Direct, and Google Scholar. Eligibility followed PRISMA-P criteria. Quality and risk of bias were assessed drawing on QUADAS-2 (quality assessment of diagnostic accuracy studies, revised) criteria. Meta-analyses were performed regarding accuracy metrics compared to standard references and the added value of ST in terms of extra found pathogens. We identified 25 studies on sepsis, infectious endocarditis, bacterial meningitis, joint infections, pyomyositis, and various diseases from routine diagnosis. Patients with suspected infections of purportedly sterile body sites originated from various hospital wards. The overall sensitivity (79%; 95% confidence interval [CI], 73 to 84%) and specificity (83%; 95% CI, 72 to 90%) were accompanied by large effect sizes. ST-related positivity was 32% (95% CI, 30 to 34%), which was significantly higher than the culture positivity (20%; 95% CI, 18 to 22%). The overall added value of ST was 14% (95% CI, 10 to 20%) for all samples. With 130 relevant taxa, ST uncovered high microbial richness. Four studies demonstrated changes of antibiotic treatment at 12% (95% CI, 9 to 15%) of all patients upon availability of ST results. ST appears to be an approach for the diagnosis of nongrowing pathogens. The potential clinical role of this agnostic molecular diagnostic tool is discussed regarding changes of antibiotic treatment in cases where culture stays negative.
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Affiliation(s)
- Pavel Drevinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | | | | | | | - Thomas Bjarnsholt
- Department of Clinical Microbiology, Centre for Diagnostics, Rigshospitalet, Copenhagen, Denmark
- Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
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Obermeier M, Pacenti M, Ehret R, Onelia F, Gunson R, Goldstein E, Chevaliez S, Vilas A, Glass A, Maree L, Krügel M, Knechten H, Braun P, Naeth G, Azzato F, Lucic D, Marlowe N, Palm MJ, Pfeifer K, Reinhardt B, Dhein J, Joseph AM, Martínez-García L, Galán JC. Improved molecular laboratory productivity by consolidation of testing on the new random-access analyzer Alinity m. J LAB MED 2020. [DOI: 10.1515/labmed-2020-0102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Abstract
Objectives
Automated molecular analyzers have accelerated diagnosis, allowing earlier intervention and better patient follow-up. A recently developed completely automated molecular analyzer, Alinity™ m (Abbott), offers consolidated, continuous, and random-access testing that may improve molecular laboratory workflow.
Methods
An international, multicenter study compared laboratory workflow metrics across various routine analyzers and Alinity m utilizing assays for human immunodeficiency virus type 1 (HIV-1), hepatitis C virus (HCV), hepatitis B virus (HBV), high-risk human papillomavirus (HR HPV), and sexually transmitted infection (STI) (Chlamydia trachomatis [CT]/Neisseria gonorrhoeae [NG]/Trichomonas vaginalis [TV]/Mycoplasma genitalium [MG]). Three turnaround times (TATs) were assessed: total TAT (sample arrival to result), sample onboard TAT (sample loading and test starting to result), and processing TAT (sample aspiration to result).
Results
Total TAT was reduced from days with routine analyzers to hours with Alinity m, independent of requested assays. Sample onboard TATs for standard workflow using routine analyzers ranged from 7 to 32.5 h compared to 2.75–6 h for Alinity m. The mean sample onboard TAT for STAT samples on Alinity m was 2.36 h (±0.19 h). Processing TATs for Alinity m were independent of the combination of assays, with 100% of results reported within 117 min.
Conclusions
The consolidated, continuous, random-access workflow of Alinity m reduces TATs across various assays and is expected to improve both laboratory operational efficiency and patient care.
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Affiliation(s)
| | | | - Robert Ehret
- Medizinisches Infektiologiezentrum , Berlin , Germany
| | | | - Rory Gunson
- West of Scotland Specialist Virology Centre , Glasgow , UK
| | | | | | - Alba Vilas
- Laboratori de Referència de Catalunya , El Prat de Llobregat , Spain
| | | | - Leana Maree
- Lancet Laboratories , Johannesburg , South Africa
| | - Maria Krügel
- Lancet Laboratories , Johannesburg , South Africa
| | | | | | | | - Francesca Azzato
- Victorian Infectious Diseases Reference Laboratory , Melbourne , Australia
| | | | | | | | | | | | | | | | - Laura Martínez-García
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), CIBER en Epidemiología y Salud Pública (CIBERESP) , Madrid , Spain
| | - Juan-Carlos Galán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), CIBER en Epidemiología y Salud Pública (CIBERESP) , Madrid , Spain
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Hustá M, Ducatelle R, Haesebrouck F, Van Immerseel F, Goossens E. A comparative study on the use of selective media for the enumeration of Clostridium perfringens in poultry faeces. Anaerobe 2020; 63:102205. [PMID: 32353484 DOI: 10.1016/j.anaerobe.2020.102205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/16/2020] [Accepted: 04/18/2020] [Indexed: 01/11/2023]
Abstract
Isolation and fast detection of Clostridium perfringens is essential in veterinary medical diagnostics and veterinary research, as it allows to recommend suitable treatment options after antimicrobial resistance determination, and is essential to study pathogenesis. In this study four selective media were tested for the enumeration of, and selectivity towards C. perfringens in faecal samples from poultry. The routinely used Columbia agar with 5% sheep (CBA), Shahidi-Ferguson-perfringens agar (SFP), tryptose sulphite cycloserine agar (TSC), and a novel chromogenic medium, CHROMagar™ C. perfringens (CHCP), were tested. Overall, no difference in C. perfringens recovery could be observed between the selective media. The limit of quantification was 103 CFU/mL for all agars. CHCP showed the highest specificity, especially when low C. perfringens loads were present in the faeces, with TSC being the second most specific selective medium. Both CBA and SFP allowed considerable growth of other faecal microbiota and were not specific for C. perfringens. On CHCP, differentiation of C. perfringens from other faecal bacteria was straightforward due to the appearance of C. perfringens as orange colonies, with other bacteria being absent or appearing as blue/green colonies. On TSC, C. perfringens appeared as black colonies, but longer incubation periods were sometimes needed for the black colour to develop. Therefore, CHCP can be recommended when timely and easy identification and enumeration of C. perfringens from complex samples, such as faeces, is needed.
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Affiliation(s)
- Martina Hustá
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium.
| | - Richard Ducatelle
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium.
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium.
| | - Filip Van Immerseel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium.
| | - Evy Goossens
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium.
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Chircov C, Grumezescu AM, Holban AM. Magnetic Particles for Advanced Molecular Diagnosis. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E2158. [PMID: 31284393 PMCID: PMC6651565 DOI: 10.3390/ma12132158] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 12/17/2022]
Abstract
Molecular diagnosis is the field that aims to develop nucleic-acid-based analytical methods for biological markers and gene expression assessments by combining laboratory medicine and molecular genetics. As it gradually becomes a clinical reality, molecular diagnosis could benefit from improvements resulting from thorough studies that could enhance the accuracy of these methods. The application of magnetic particles in molecular diagnosis tools has led to tremendous breakthroughs in terms of specificity, sensitivity, and discrimination in bioassays. Therefore, the aim of this review is to highlight the principles involved in the implementation of magnetic particles for sample preparation and targeted analyte isolation, purification, and extraction. Furthermore, the most recent advancements in the area of cancer and infectious disease diagnosis are presented, with an emphasis on screening and early stage detection.
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Affiliation(s)
- Cristina Chircov
- Faculty of Applied Chemistry and Materials Science, Politehnica University of Bucharest, 011061 Bucharest, Romania
| | - Alexandru Mihai Grumezescu
- Faculty of Applied Chemistry and Materials Science, Politehnica University of Bucharest, 011061 Bucharest, Romania.
| | - Alina Maria Holban
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
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Nabal S, Mormeneo S, García-Lechuz JM. Highlights at the 28th Congress of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID), 2018. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2019; 32 Suppl 2:16-21. [PMID: 31475803 PMCID: PMC6755366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
| | | | - Juan M. García-Lechuz
- Correspondence: Juan M. García-Lechuz Servicio de Microbiología. Hospital Universitario Miguel Servet. Zaragoza E-mail:
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