The use of microbead-based spoligotyping for Mycobacterium tuberculosis complex to evaluate the quality of the conventional method: providing guidelines for Quality Assurance when working on membranes

Autor: Darío García de Viedma, Guislaine Refrégier, Kristin Kremer, Edgar Abadia, Christophe Sola, Viviana Ritacco, Voahangy Rasolofo-Razanamparany, Leen Rigouts, Nalin Rastogi, Sahal Al-Hajoj, Maryse Fauville-Dufaux, Philip Noel Suffys, Enrico Tortoli, Jian Zhang, Harrison Magdinier Gomes, Raymond Ruimy, Karolien Stoffels, Carlo Garzelli, Dick van Soolingen, Marta Herranz, Atina Ribeiro Elias
Přispěvatelé: Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Instituto Nacional de Enfermedades Infecciosas ANLIS Carlos Malbrán, Instituto Nacional de Enfermedades Infecciosas- ANLIS Carlos Malbrán [Buenos Aires] (INEI), National Institute for Public Health and the Environment, National Institute for Public Health and the Environment [Bilthoven] (RIVM), Emergence de la résistance bactérienne in vivo (EA3964), Université Paris Diderot - Paris 7 (UPD7), Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Molecular Biology Applied to Mycobacteria / Biologia Molecular Aplicada a Micobactérias [Rio de Janeiro], Instituto Oswaldo Cruz / Oswaldo Cruz Institute [Rio de Janeiro] (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centre national de Référence et Laboratoire Tuberculose et Mycobactéries = National Reference Centre of Tuberculosis and Mycobacteria [Brussels] (CNR), Institut Scientifique de Santé Publique [Belgique] - Scientific Institute of Public Health [Belgium] (WIV-ISP), Unité des Mycobactéries [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital Gregorio Marañón, CIBER Enfermedades Respiratorias (CIBERES), Department of Comparative Medicine, King Faisal Specialist Hospital and Research Center, Unité de la Tuberculose et des Mycobactéries - WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Dipartimento di Patologia Sperimentale Biotecnologie Mediche Infettivologia ed Epidemiologia, University of Pisa - Università di Pisa, Regional Reference Center for Mycobacteria, Careggi Hospital, Department of Pulmonary Diseases and Department of Microbiology, Radboud university [Nijmegen], Génétique mycobactérienne - Mycobacterial genetics, Institut Pasteur [Paris], This study was supported by the 'Excellency Chair in microbiology of the University Paris-Sud' granted to CS in September 2007 through a PhD (JZ) and a postdoctoral grant (EA). EA is a senior mycobacteriology scientist of the IVIC (Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela). The work done at Institut Pasteur de Guadeloupe was partially supported by United States National Institutes of Health - grant R01LM009731. JZ was a PhD fellow of the Université Paris-Sud through the 'Ecole Doctorale Gènes Génomes Cellules'. We are grateful to François Topin, Luminex BV, The Netherlands, and to Luminex Corporation, Austin, Texas for their support. Gilson S.A.S, Villiers-le-Bel, France, is also acknowledged for providing automated multi-pipettes., Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Radboud University [Nijmegen], Institut Pasteur [Paris] (IP)
Rok vydání: 2011
Předmět:
DNA
Bacterial
Quality Control
Genotype
Concordance
Computational biology
Polymerase Chain Reaction
Microbiology
lcsh:Infectious and parasitic diseases
Mycobacterium tuberculosis
03 medical and health sciences
Poverty-related infectious diseases Infection and autoimmunity [N4i 3]
[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases
Humans
Tuberculosis
[SDV.BBM]Life Sciences [q-bio]/Biochemistry
Molecular Biology
lcsh:RC109-216
Control de Calidad
Genotyping
030304 developmental biology
0303 health sciences
biology
030306 microbiology
Extramural
business.industry
ADN Bacteriano
biology.organism_classification
DNA extraction
Técnicas de Tipificación Bacteriana
3. Good health
Humanos
Bacterial Typing Techniques
[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology
Infectious Diseases
Mycobacterium tuberculosis complex
Reacción en Cadena de la Polimerasa
business
Quality assurance
Genotipo
Research Article
Zdroj: BMC Infectious Diseases, 11, 110
BMC Infectious Diseases, 11, pp. 110
BMC Infectious Diseases
BMC Infectious Diseases, Vol 11, Iss 1, p 110 (2011)
BMC Infectious Diseases, BioMed Central, 2011, 11 (1), pp.110. ⟨10.1186/1471-2334-11-110⟩
Bmc Infectious Diseases, 2011, (11) 110.
Sistema de Gestión del Conocimiento ANLIS MALBRÁN
Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán"
instacron:ANLIS
BMC Infectious Diseases, 2011, 11 (1), pp.110. ⟨10.1186/1471-2334-11-110⟩
ISSN: 1471-2334
Popis: Background: The classical spoligotyping technique, relying on membrane reverse line-blot hybridization of the spacers of the Mycobacterium tuberculosis CRISPR locus, is used world-wide (598 references in Pubmed on April 8th, 2011). However, until now no inter-laboratory quality control study had been undertaken to validate this technique. We analyzed the quality of membrane-based spoligotyping by comparing it to the recently introduced and highly robust microbead-based spoligotyping. Nine hundred and twenty-seven isolates were analyzed totaling 39,861 data points. Samples were received from 11 international laboratories with a worldwide distribution. Methods: The high-throughput microbead-based Spoligotyping was performed on CTAB and thermolyzate DNA extracted from isolated Mycobacterium tuberculosis complex (MTC) strains coming from the genotyping participating centers. Information regarding how the classical Spoligotyping method was performed by center was available. Genotype discriminatory analyses were carried out by comparing the spoligotypes obtained by both methods. The non parametric U-Mann Whitney homogeneity test and the Spearman rank correlation test were performed to validate the observed results. Results: Seven out of the 11 laboratories (63 %), perfectly typed more than 90% of isolates, 3 scored between 80-90% and a single center was under 80% reaching 51% concordance only. However, this was mainly due to discordance in a single spacer, likely having a non-functional probe on the membrane used. The centers using thermolyzate DNA performed as well as centers using the more extended CTAB extraction procedure. Few centers shared the same problematic spacers and these problematic spacers were scattered over the whole CRISPR locus (Mostly spacers 15, 14, 18, 37, 39, 40). Conclusions: We confirm that classical spoligotyping is a robust method with generally a high reliability in most centers. The applied DNA extraction procedure (CTAB or thermolyzate) did not affect the results in this study. However performance was center-dependent, suggesting that training is a key component in quality assurance of spoligotyping. Overall, no particular spacer yielded a higher degree of deviating results, suggesting that errors. Fil: Abadia, Edgar. CNRS Université Paris-Sud 11 Universud. Institute of Genetics and Microbiology UMR8621; Francia. Fil: Zhang, Jian. CNRS Université Paris-Sud 11 Universud. Institute of Genetics and Microbiology UMR8621; Francia. Fil: Ritacco, Viviana. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina. Fil: Kremer, Kristin. National Institute for Public Health and the Environment; Paises Bajos. Fil: Ruimy, Raymond. Université Paris- Diderot & Microbiology Laboratory; Francia. Fil: Rigouts, Leen. Prince Leopold Institute of Tropical Medicine. Mycobacteriology Unit; Bélgica. Fil: Gomes, Harrison Magdinier. Oswaldo Cruz Institute. Laboratory of Molecular Biology applied to Mycobacteria; Brasil. Fil: Elias, Atina Ribeiro. Oswaldo Cruz Institute. Laboratory of Molecular Biology applied to Mycobacteria; Brasil. Fil: Fauville-Dufaux, Maryse. Scientific Institute of Public Health. National Reference Centre of Tuberculosis and Mycobacteria; Bélgica. Fil: Stoffels, Karolien. Scientific Institute of Public Health. National Reference Centre of Tuberculosis and Mycobacteria; Bélgica. Fil: Rasolofo-Razanamparany, Voahangy. Institut Pasteur de Madagascar. Unité des Mycobactéries; Madagascar. Fil: Garcia de Viedma, Dario. Hospital Gregorio Marañón. Servicio de Microbiología Clínica y Enfermedades Infecciosas; España. Fil: Herranz, Marta. Hospital Gregorio Marañón. Servicio de Microbiología Clínica y Enfermedades Infecciosas; España. Fil: Al-Hajoj, Sahal. King Faisal Specialist Hospital and Research Center. Department of Comparative Medicine; Arabia Saudita. Fil: Rastogi, Nalin. Institut Pasteur de Guadeloupe. Unité de la Tuberculose et des Mycobactéries - WHO Supranational TB Reference Laboratory; Guadalupe. Fil: Garzelli, Carlo. Università di Pisa. Dipartimento di Patologia Sperimentale Biotecnologie Mediche Infettivologia ed Epidemiologia; Italia. Fil: Tortoli, Enrico. Careggi Hospital. Regional Reference Center for Mycobacteria; Italia Fil: Suffys, Philip N. Oswaldo Cruz Institute. Laboratory of Molecular Biology applied to Mycobacteria; Brasil. Fil: van Soolingen, Dick. National Institute for Public Health and the Environment; Paises Bajos. Fil: Refregier, Guislaine. CNRS Université Paris-Sud 11 Universud. Institute of Genetics and Microbiology UMR8621; Francia. Fil: Sola, Christophe. CNRS Université Paris-Sud 11 Universud. Institute of Genetics and Microbiology UMR8621; Francia.
Databáze: OpenAIRE
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