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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.

Vasconcellos SE, Acosta CC, Gomes LL, Conceição EC, Lima KV, de Araujo MI, Leite Mde L, Tannure F, Caldas PC, Gomes HM, Santos AR, Gomgnimbou MK, Sola C, Couvin D, Rastogi N, Boechat N, Suffys PN - PLoS ONE (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

ABSTRACT
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.

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Related in: MedlinePlus

Confusion Matrix comparing the classifications obtained by Spoligotyping and MIRU-VNTR. 1Classification according to SITIVIT2. For unknown Spoligotypes, we used SpotClust. 2 Patterns were classified based on a VNTRplus database that allows construction of a Neighbor-Joining based phylogenetic tree, visualizing proximity of a particular genotype with that of a set of reference strains to the genotype family level.
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pone-0107747-g001: Confusion Matrix comparing the classifications obtained by Spoligotyping and MIRU-VNTR. 1Classification according to SITIVIT2. For unknown Spoligotypes, we used SpotClust. 2 Patterns were classified based on a VNTRplus database that allows construction of a Neighbor-Joining based phylogenetic tree, visualizing proximity of a particular genotype with that of a set of reference strains to the genotype family level.

Mentions: The patterns were classified based on the database tool that allows construction of a Neighbor-Joining based phylogenetic tree, visualizing proximity of a particular genotype with that of a set of reference strains to the genotype family level. One hundred thirty-six isolates (62.4%) were classified as LAM (127 patterns), 47 (21.5%) as Haarlem (45 patterns), 21 (9.6%) as T (21 patterns), 11 (5%) as S (11 patterns), and one isolate (0.45%) each as Beijing and EAI. Considerable differences were observed between Spoligotyping and 24 MIRU-VNTR loci-based classifications, even after excluding eventual small typing errors by repeating the assays. The differences observed between the two classifications are presented in the table 3 and in the Confusion Matrix (Figure 1). The precision, accuracy, sensitivity and error rate were respectively 0.74, 0.64, 0.82 and 0.36. The T lineage showed the highest incongruence rate related to classification (sensitivity = 0.26).


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.

Vasconcellos SE, Acosta CC, Gomes LL, Conceição EC, Lima KV, de Araujo MI, Leite Mde L, Tannure F, Caldas PC, Gomes HM, Santos AR, Gomgnimbou MK, Sola C, Couvin D, Rastogi N, Boechat N, Suffys PN - PLoS ONE (2014)

Confusion Matrix comparing the classifications obtained by Spoligotyping and MIRU-VNTR. 1Classification according to SITIVIT2. For unknown Spoligotypes, we used SpotClust. 2 Patterns were classified based on a VNTRplus database that allows construction of a Neighbor-Joining based phylogenetic tree, visualizing proximity of a particular genotype with that of a set of reference strains to the genotype family level.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4196770&req=5

pone-0107747-g001: Confusion Matrix comparing the classifications obtained by Spoligotyping and MIRU-VNTR. 1Classification according to SITIVIT2. For unknown Spoligotypes, we used SpotClust. 2 Patterns were classified based on a VNTRplus database that allows construction of a Neighbor-Joining based phylogenetic tree, visualizing proximity of a particular genotype with that of a set of reference strains to the genotype family level.
Mentions: The patterns were classified based on the database tool that allows construction of a Neighbor-Joining based phylogenetic tree, visualizing proximity of a particular genotype with that of a set of reference strains to the genotype family level. One hundred thirty-six isolates (62.4%) were classified as LAM (127 patterns), 47 (21.5%) as Haarlem (45 patterns), 21 (9.6%) as T (21 patterns), 11 (5%) as S (11 patterns), and one isolate (0.45%) each as Beijing and EAI. Considerable differences were observed between Spoligotyping and 24 MIRU-VNTR loci-based classifications, even after excluding eventual small typing errors by repeating the assays. The differences observed between the two classifications are presented in the table 3 and in the Confusion Matrix (Figure 1). The precision, accuracy, sensitivity and error rate were respectively 0.74, 0.64, 0.82 and 0.36. The T lineage showed the highest incongruence rate related to classification (sensitivity = 0.26).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus