title: Mycobacterium tuberculosis complex CRISPR genotyping: improving efficiency, throughput and discriminative power of 'spoligotyping' with new spacers and a microbead-based hybridization assay.
abstract: The aims of the present study were to implement a microbead-based 'spoligotyping' technique and to evaluate improvements by the addition of a panel of 25 extra spacers that we expected to provide an increased resolution on principal genetic group 1 (PGG 1) strains. We confirmed the high sensitivity and reproducibility of the classical technique using the 43 spacer panel and we obtained perfect agreement between the membrane-based and the microbead-based techniques. We further demonstrated an increase in the discriminative power of an extended 68 spacer format for differentiation of PGG 1 clinical isolates, in particular for the East African-Indian clade. Finally, we define a limited yet highly informative reduced 10 spacer panel set which could offer a more cost-effective option for implementation in resource-limited countries and that could decrease the need for additional VNTR (variable number of tandem repeats) genotyping work in molecular epidemiological studies. We also present an economic analysis comparing membrane-based and microbead-based techniques.
authors: IGEPE Team, Institute of Genetics and Microbiology, UMR8621, Universud, CNRS Université Paris-Sud 11, Campus d'Orsay, F-91405 Orsay-Cedex, France.
authors: Jian
authors: J
authors: Zhang
authors: IGEPE Team, Institute of Genetics and Microbiology, UMR8621, Universud, CNRS Université Paris-Sud 11, Campus d'Orsay, F-91405 Orsay-Cedex, France.
authors: Edgar
authors: E
authors: Abadia
authors: IGEPE Team, Institute of Genetics and Microbiology, UMR8621, Universud, CNRS Université Paris-Sud 11, Campus d'Orsay, F-91405 Orsay-Cedex, France.
authors: Guislaine
authors: G
authors: Refregier
authors: National TB Reference Laboratory, University Hospital of Lung Diseases 'Shefqet Ndroqi', Tirana, Albania.
authors: Silva
authors: S
authors: Tafaj
authors: Agence Française de Sécurité Sanitaire des Aliments, Maisons-Alfort, France.
authors: Maria Laura
authors: ML
authors: Boschiroli
authors: Institut Pasteur du Cambodge, Pnom-Penh, Cambodia.
authors: Bertrand
authors: B
authors: Guillard
authors: Microbiology Laboratory, Bichat-Claude Bernard Hospital, Paris, France.
authors: Antoine
authors: A
authors: Andremont
authors: Microbiology Laboratory, Bichat-Claude Bernard Hospital, Paris, France.
authors: Raymond
authors: R
authors: Ruimy
authors: Unité de Génétique Mycobactérienne, Institut Pasteur, Paris, France.|IGEPE Team, Institute of Genetics and Microbiology, UMR8621, Universud, CNRS Université Paris-Sud 11, Campus d'Orsay, F-91405 Orsay-Cedex, France.
authors: Christophe
authors: C
authors: Sola
mesh_terms: D015373:Bacterial Typing Techniques / Q000191:economics / Q000379:methods*; D016172:DNA Fingerprinting / Q000191:economics / Q000379:methods*; D005838:Genotype; D006801:Humans; D008863:Microspheres; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics*; D009693:Nucleic Acid Hybridization / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D014376:Tuberculosis / Q000382:microbiology*