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
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 MIRU-VNTR 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.
Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil;Multidisciplinary Research Laboratory, University Hospital Clementino Fraga Filho – HUCFF, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil;Laboratory of Cellular Microbiology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil;Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil;Instituto Evandro Chagas, Section of Bacteriology and Mycology, Belém, Pará, Brazil;Instituto Evandro Chagas, Section of Bacteriology and Mycology, Belém, Pará, Brazil;Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil;Hospital Municipal Rafael de Paula Souza, Municipal Secretary of Health, Rio de Janeiro, Rio de Janeiro, Brazil;Hospital Municipal Rafael de Paula Souza, Municipal Secretary of Health, Rio de Janeiro, Rio de Janeiro, Brazil;Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Publica Sergio Arouca, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil;Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil;Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil;CNRS–Université Paris–Sud, Institut de Génétique et Microbiologie–Infection Genetics Emerging Pathogens Evolution Team, Orsay, France;CNRS–Université Paris–Sud, Institut de Génétique et Microbiologie–Infection Genetics Emerging Pathogens Evolution Team, Orsay, France;Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France;Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France;Multidisciplinary Research Laboratory, University Hospital Clementino Fraga Filho – HUCFF, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil;Graduate Program in Clinical Medicine, Faculty of Medicine, University Hospital Clementino Fraga Filho, Rio de Janeiro, Rio de Janeiro, Brazil;Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
Recommended Citation:
Sidra E. G. Vasconcellos,Chyntia Carolina Acosta,Lia Lima Gomes,et al. 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[J]. PLOS ONE,2014-01-01,9(10)