Genotyping of clinical Mycobacterium tuberculosis isolates based on IS6110 and MIRU-VNTR polymorphisms.
In this study, 155 clinical Mycobacterium tuberculosis isolates were subject to genotyping with fast ligation-mediated PCR (FLiP). This typing method is a modified mixed-linker PCR, a rapid approach based on the PCR amplification of HhaI restriction fragments of genomic DNA containing the 3' end of IS6110 and resolving the amplicons by polyacrylamide gel electrophoresis. The results were compared with previous data of the more commonly used methods, 15-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and, to verify combined FLiP/MIRU-VNTR clusters, the reference IS6110 restriction fragment length polymorphism (RFLP). FLiP banding patterns were highly reproducible and polymorphic. This method differentiated 119 types among the study set compared to 108 distinct MIRU-VNTR profiles. The discriminatory power of FLiP was slightly higher than that of MIRU-VNTR analysis (Hunter-Gaston Discriminatory Index = 0.991 and 0.990, resp.). Detailed comparison of the clusters defined by each of the methods revealed, however, a more apparent difference in the discriminatory abilities that favored FLiP. Clustering of strains by using combined results of these two PCR-based methods correlated well with IS6110 RFLP-defined clusters, further confirming high discriminatory potential of FLiP typing. These results indicate that FLiP could be an attractive and valuable secondary typing technique for verification of MIRU-VNTR clusters of M. tuberculosis strains.
Department of Biochemistry and Cell Biology, Faculty of Biology and Agriculture, University of Rzeszów, Ćwiklińskiej 2, 35-601 Rzeszów, Poland.
Anna
A
Żaczek
Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Łódź, Poland.
Anna
A
Brzostek
Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Łódź, Poland ; Proteon Pharmaceuticals, Tylna 3a, 90-364 Łódź, Poland.
Arkadiusz
A
Wojtasik
Department of Biochemistry and Cell Biology, Faculty of Biology and Agriculture, University of Rzeszów, Ćwiklińskiej 2, 35-601 Rzeszów, Poland ; Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Łódź, Poland.
Jarosław
J
Dziadek
Department of Microbial Genetics, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland.
Anna
A
Sajduda
D004269:DNA, Bacterial / Q000235:genetics; D005838:Genotype; D006801:Humans; D018598:Minisatellite Repeats / Q000235:genetics*; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D012150:Polymorphism, Restriction Fragment Length / Q000235:genetics
D004269:DNA, Bacterial