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STRAIN CLASSIFICATION OF MYCOBACTERIUM TUBERCULOSIS ISOLATES IN BRAZIL BASED ON GENOTYPES OBTAINED BY SPOLIGOTYPING, MYCOBACTERIAL INTERSPERSED REPETITIVE UNIT TYPING AND THE PRESENCE OF LARGE SEQUENCE AND SINGLE NUCLEOTIDE POLYMORPHISM
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Rio de Janeiro is endemic for tuberculosis (TB) and presents the second largest prevalence of the disease in Brazil. Here, we
present the bacterial population structure of 218 isolates of Mycobacterium tuberculosis, derived from 186 patients that were
diagnosed between January 2008 and December 2009. Genotypes were generated by means of spoligotyping, 24 MIRUVNTR
typing and presence of fbpC103, RDRio and RD174. The results confirmed earlier data that predominant genotypes in
Rio de Janeiro are those of the Euro American Lineages (99%). However, we observed differences between the classification
by spoligotyping when comparing to that of 24 MIRU-VNTR typing, being respectively 43.6% vs. 62.4% of LAM, 34.9% vs.
9.6% of T and 18.3% vs. 21.5% of Haarlem. Among isolates classified as LAM by MIRU typing, 28.0% did not present the
characteristic spoligotype profile with absence of spacers 21 to 24 and 32 to 36 and we designated these conveniently as
‘‘LAM-like’’, 79.3% of these presenting the LAM-specific SNP fbpC103. The frequency of RDRio and RD174 in the LAM strains, as
defined both by spoligotyping and 24 MIRU-VNTR loci, were respectively 11% and 15.4%, demonstrating that RD174 is not
always a marker for LAM/RDRio strains. We conclude that, although spoligotyping alone is a tool for classification of strains of
the Euro-American lineage, when combined with MIRU-VNTRs, SNPs and RD typing, it leads to a much better understanding
of the bacterial population structure and phylogenetic relationships among strains of M. tuberculosis in regions with high
incidence of TB.
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