Evaluation of alternatives to RFLP for the analysis of clustered cases of tuberculosis

Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) analysis is a recently developed method which could be suitable as a 'real-time' genotyping tool for Mycobacterium tuberculosis.

One hundred and thirty-four M. tuberculosis isolates were analysed using the reference method, IS6110-restriction fragment length polymorphism (RFLP), and by MIRU, alone and together with spoligotyping.

MIRU reduced the genotyping turnaround time by 21 days. The discriminatory power (HGDI) for MIRU and RFLP was 0.978 and 0.989, respectively. RFLP clustered 41.8% of the isolates (17 clusters; 2-9 representatives), whereas MIRU increased the number and size of the clusters (57.5% of the isolates in 20 clusters; 2-14 representatives). With respect to the RFLP clusters, MIRU data showed full correlation in only 7/ 17 (41%) clusters and low correlation in 8/17 (47%) clusters. When MIRU and spoligotyping were considered together, the analysis fitted better with RFLP data: 1) 42.5% of the isolates were grouped in 20 clusters of 2-6 representatives, and 2) the number of clusters with full correlation with RFLP data increased to 11/17 and those with low correlation decreased to 2/17.

MIRU-VNTR analysis showed low correlation with RFLP. The addition of spoligotyping to MIRU analysis fitted much better with RFLP analysis, although full correlation was still not achieved.