title: Evaluation of the new advanced 15-loci MIRU-VNTR genotyping tool in Mycobacterium tuberculosis molecular epidemiology studies.
abstract: BACKGROUND
  During the last few years, PCR-based methods have been developed to simplify and reduce the time required for genotyping Mycobacterium tuberculosis (MTB) by standard approaches based on IS6110-Restriction Fragment Length Polymorphism (RFLP). Of these, MIRU-12-VNTR (Mycobacterial interspersed repetitive units- variable number of tandem repeats) (MIRU-12) has been considered a good alternative. Nevertheless, some limitations and discrepancies with RFLP, which are minimized if the technique is complemented with spoligotyping, have been found. Recently, a new version of MIRU-VNTR targeting 15 loci (MIRU-15) has been proposed to improve the MIRU-12 format.
  
  
  RESULTS
  We evaluated the new MIRU-15 tool in two different samples. First, we analyzed the same convenience sample that had been used to evaluate MIRU-12 in a previous study, and the new 15-loci version offered higher discriminatory power (Hunter-Gaston discriminatory index [HGDI]: 0.995 vs 0.978; 34.4% of clustered cases vs 57.5%) and better correlation (full or high correlation with RFLP for 82% of the clusters vs 47%). Second, we evaluated MIRU-15 on a population-based sample and, once again, good correlation with the RFLP clustering data was observed (for 83% of the RFLP clusters). To understand the meaning of the discrepancies still found between MIRU-15 and RFLP, we analyzed the epidemiological data for the clustered patients. In most cases, splitting of RFLP-clustered patients by MIRU-15 occurred for those without epidemiological links, and RFLP-clustered patients with epidemiological links were also clustered by MIRU-15, suggesting a good epidemiological background for clustering defined by MIRU-15.
  
  
  CONCLUSIONS
  The data obtained by MIRU-15 suggest that the new design is very efficient at assigning clusters confirmed by epidemiological data. If we add this to the speed with which it provides results, MIRU-15 could be considered a suitable tool for real-time genotyping.
authors.affiliation: Servicio de Microbiología y Enfermedades Infecciosas, Hospital Gregorio Marañón, Universidad Complutense, Madrid, CIBER de Enfermedades Respiratorias (CIBERES), Spain. noelialonsor@yahoo.es
authors.forename: Noelia
authors.initials: N
authors.lastname: Alonso-Rodríguez
authors.forename: Miguel
authors.initials: M
authors.lastname: Martínez-Lirola
authors.forename: Marta
authors.initials: M
authors.lastname: Herránz
authors.forename: Marisa
authors.initials: M
authors.lastname: Sanchez-Benitez
authors.forename: Pilar
authors.initials: P
authors.lastname: Barroso
authors.forename: Emilio
authors.initials: E
authors.lastname: Bouza
authors.forename: Darío
authors.initials: D
authors.lastname: García de Viedma
mesh_terms: D016000:Cluster Analysis; D005838:Genotype; D006801:Humans; D020071:Interspersed Repetitive Sequences; D018598:Minisatellite Repeats / Q000235:genetics*; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000302:isolation & purification; D016133:Polymerase Chain Reaction / Q000379:methods*; D012150:Polymorphism, Restriction Fragment Length; D013223:Statistics as Topic; D014376:Tuberculosis / Q000453:epidemiology / Q000382:microbiology*