Three-year population-based evaluation of standardized Mycobacterial Interspersed Repetitive Unit-Variable Number of Tandem Repeat typing of Mycobacterium tuberculosis

Institut Pasteur de Bruxelles, Laboratoire Tuberculose et Mycobacteries, rue Engeland 642, 1180 Bruxelles, Belgium, Institut Pasteur de Lille and Laboratoire des Mécanismes Moléculaires de la Pathogenèse Bactérienne, INSERM U629 - 1, rue du Professeur Calmette - BP 245 - 59019 LILLE Cedex, France

	Abstract

Standardized Mycobacterial Interspersed Repetitive Unit-Variable Number of Tandem Repeat (MIRU-VNTR) typing based on 15 and 24 loci has recently been proposed for Mycobacterium tuberculosis genotyping. So far, this optimized system has been assessed in a single, one-year population-based study performed in Germany. Here, we evaluated these optimized formats in a much larger population-based study conducted over 39 months in the Brussels-capital Region. Isolates from 807 patients were genotyped. Resolution power, cluster and lineage identification by the standardized MIRU-VNTR sets were compared with those obtained using standardized IS6110-RFLP, spoligotyping and a previous 12 MIRU-VNTR-locus set. On a subset representing 77 % of the cases over a 16-month period, a high concordance was observed between unique isolates or strain-clusters defined by standardized MIRU-VNTR and IS6110-RFLP (>5 IS6110). When extended to the entire population-based collection, the discriminatory subset of 15 loci decreased the strain-clustering rate by almost two-fold as compared to the old 12-locus set. Addition of the 9 ancillary MIRU-VNTR loci and/or spoligotyping only slightly further decreased this strain-clustering rate. Familial, social or geographic proximity links were found in 48 % of clusters identified, and well-known risk factors for tuberculosis (TB) transmission were identified. Finally, excellent correspondence was determined between our MIRU-VNTR-spoligotyping strain identifications and external reference strain lineages included in the MIRU-VNTRplus database and identified e.g. by large sequence polymorphisms (LSPs). Our results reinforce the proposal of standardized MIRU-VNTR typing as a new reference genotyping method for epidemiological and phylogenetical screening of M. tuberculosis strains.