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Correlations between major risk factors and closely related Mycobacterium tuberculosis isolates grouped by three current genotyping procedures: a population-based study in northeast Mexico.

Peñuelas-Urquides K, Martínez-Rodríguez HG, Enciso-Moreno JA, Molina-Salinas GM, Silva-Ramírez B, Padilla-Rivas GR, Vera-Cabrera L, Torres-de-la-Cruz VM, Martínez-Martínez YB, Ortega-García JL, Garza-Treviño EN, Enciso-Moreno L, Saucedo-Cárdenas O, Becerril-Montes P, Said-Fernández S - Mem. Inst. Oswaldo Cruz (2014)

Bottom Line: SMR exhibited a significant correlation (p < 0.05) with visits to clinics, municipalities and comorbidities (primarily diabetes mellitus).S correlated with drug consumption and M with comorbidities.SMR is needed to identify a social network in metropolitan areas for PTB transmission and S and M are able to detect risk factors as secondary components of a transmission chain of TB.

View Article: PubMed Central - PubMed

Affiliation: División de Biología Celular y Molecular, Centro de Investigación Biomédica del Noreste, Zacatecas, ZC, México.

ABSTRACT
The characteristics of tuberculosis (TB) patients related to a chain of recent TB transmissions were investigated. Mycobacterium tuberculosis (MTB) isolates (120) were genotyped using the restriction fragment length polymorphism-IS6110 (R), spacer oligotyping (S) and mycobacterial interspersed repetitive units-variable number of tandem repeats (M) methods. The MTB isolates were clustered and the clusters were grouped according to the similarities of their genotypes. Spearman's rank correlation coefficients between the groups of MTB isolates with similar genotypes and those patient characteristics indicating a risk for a pulmonary TB (PTB) chain transmission were ana- lysed. The isolates showing similar genotypes were distributed as follows: SMR (5%), SM (12.5%), SR (1.67%), MR (0%), S (46.67%), M (5%) and R (0%). The remaining 35 cases were orphans. SMR exhibited a significant correlation (p < 0.05) with visits to clinics, municipalities and comorbidities (primarily diabetes mellitus). S correlated with drug consumption and M with comorbidities. SMR is needed to identify a social network in metropolitan areas for PTB transmission and S and M are able to detect risk factors as secondary components of a transmission chain of TB.

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Related in: MedlinePlus

: restriction fragment length polymorphism (RFLP)-IS6110diagram and dendrogram. These were generated by the BioNumerics software andshow the relationships of clusters and groups of clusters using theRFLP-IS6110 method exclusively. Numbers on the right sideare case-identifiers.
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f01: : restriction fragment length polymorphism (RFLP)-IS6110diagram and dendrogram. These were generated by the BioNumerics software andshow the relationships of clusters and groups of clusters using theRFLP-IS6110 method exclusively. Numbers on the right sideare case-identifiers.

Mentions: Analysis of genotyping data - Based on the findings of Lindquist et al. (2013), we defined clusters asthose PTB cases with indistinguishable MTB genotypes. The spoligotypes were converted totheir corresponding octal codes as described by Dale etal. (2001) and clusters and unique patterns were identified using SPSSsoftware, v.10.0. The RFLP-IS6110 data were analysed with BioNumericssoftware, v.2.0 (Applied Maths, Belgium) using the unweighted pair group method with anarithmetical mean and Dice’s coefficient. The running differences in the gels werenormalised using the relative position of the λ/Hind III and φX174/Hae III molecularweight markers (Sigma-Aldrich) using BioNumerics software. To determine the besttolerance, a DNA sample from the reference strain H37Rv was included in each assay. Whenthe alignments of all of the reference RFLP-IS6110 patterns from allthe agarose gels matched, the tolerance value was set at 1.9%. The genotypes wereconsidered identical according to the results from the analyses performed by theBioNumerics program. Because RFLP-IS6110 codes have not been previouslydescribed, we designed a code using the relative migration of each IS6110band (Rf) of every MTB isolate DNA sample (Fig. 1). The description of the RFLP-IS6110 codesis as follows: the RFLP-IS6110 codes have two arms of numbers,separated by a dot. The left arm is composed of one or two digits and includesinformation regarding the number of bands found in each MTB isolate. The right armcontains the Rf of each DNA band with an IS-6110 element.Each Rf is represented by three numbers. From left to right, theRf values were placed in descending order of DNA-molecular weight. TheRf values were calculated by dividing the distance between the origin andfront of the electrophoresis by the distance travelled by eachIS6110-band and multiplying by 1 × 103. The MIRU-VNTRpatterns were analysed with Microsoft Excel 2002 software (Microsoft Co, USA). Thecorresponding codes were constructed according to Cowanet al. (2002) and Supply et al. (2006).The cluster groups with comparable codes were named as follows to differentiate theclusters from the genotyping methods: spoligotypes, MIRU-VNTR andRFLP-IS6110, SMR, spoligotypes and RFLP-IS6110, SR,spoligotypes and MIRU-VNTR, SM, MIRU-VNTR and RFLP-IS6110, MR,spoligotypes, S, RFLP-IS6110, R, and MIRU-VNTR, M. The methods arereferred to by their corresponding shortened names (spoligotyping, MIRU-VNTR andRFLP-IS6110).


Correlations between major risk factors and closely related Mycobacterium tuberculosis isolates grouped by three current genotyping procedures: a population-based study in northeast Mexico.

Peñuelas-Urquides K, Martínez-Rodríguez HG, Enciso-Moreno JA, Molina-Salinas GM, Silva-Ramírez B, Padilla-Rivas GR, Vera-Cabrera L, Torres-de-la-Cruz VM, Martínez-Martínez YB, Ortega-García JL, Garza-Treviño EN, Enciso-Moreno L, Saucedo-Cárdenas O, Becerril-Montes P, Said-Fernández S - Mem. Inst. Oswaldo Cruz (2014)

: restriction fragment length polymorphism (RFLP)-IS6110diagram and dendrogram. These were generated by the BioNumerics software andshow the relationships of clusters and groups of clusters using theRFLP-IS6110 method exclusively. Numbers on the right sideare case-identifiers.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4238775&req=5

f01: : restriction fragment length polymorphism (RFLP)-IS6110diagram and dendrogram. These were generated by the BioNumerics software andshow the relationships of clusters and groups of clusters using theRFLP-IS6110 method exclusively. Numbers on the right sideare case-identifiers.
Mentions: Analysis of genotyping data - Based on the findings of Lindquist et al. (2013), we defined clusters asthose PTB cases with indistinguishable MTB genotypes. The spoligotypes were converted totheir corresponding octal codes as described by Dale etal. (2001) and clusters and unique patterns were identified using SPSSsoftware, v.10.0. The RFLP-IS6110 data were analysed with BioNumericssoftware, v.2.0 (Applied Maths, Belgium) using the unweighted pair group method with anarithmetical mean and Dice’s coefficient. The running differences in the gels werenormalised using the relative position of the λ/Hind III and φX174/Hae III molecularweight markers (Sigma-Aldrich) using BioNumerics software. To determine the besttolerance, a DNA sample from the reference strain H37Rv was included in each assay. Whenthe alignments of all of the reference RFLP-IS6110 patterns from allthe agarose gels matched, the tolerance value was set at 1.9%. The genotypes wereconsidered identical according to the results from the analyses performed by theBioNumerics program. Because RFLP-IS6110 codes have not been previouslydescribed, we designed a code using the relative migration of each IS6110band (Rf) of every MTB isolate DNA sample (Fig. 1). The description of the RFLP-IS6110 codesis as follows: the RFLP-IS6110 codes have two arms of numbers,separated by a dot. The left arm is composed of one or two digits and includesinformation regarding the number of bands found in each MTB isolate. The right armcontains the Rf of each DNA band with an IS-6110 element.Each Rf is represented by three numbers. From left to right, theRf values were placed in descending order of DNA-molecular weight. TheRf values were calculated by dividing the distance between the origin andfront of the electrophoresis by the distance travelled by eachIS6110-band and multiplying by 1 × 103. The MIRU-VNTRpatterns were analysed with Microsoft Excel 2002 software (Microsoft Co, USA). Thecorresponding codes were constructed according to Cowanet al. (2002) and Supply et al. (2006).The cluster groups with comparable codes were named as follows to differentiate theclusters from the genotyping methods: spoligotypes, MIRU-VNTR andRFLP-IS6110, SMR, spoligotypes and RFLP-IS6110, SR,spoligotypes and MIRU-VNTR, SM, MIRU-VNTR and RFLP-IS6110, MR,spoligotypes, S, RFLP-IS6110, R, and MIRU-VNTR, M. The methods arereferred to by their corresponding shortened names (spoligotyping, MIRU-VNTR andRFLP-IS6110).

Bottom Line: SMR exhibited a significant correlation (p < 0.05) with visits to clinics, municipalities and comorbidities (primarily diabetes mellitus).S correlated with drug consumption and M with comorbidities.SMR is needed to identify a social network in metropolitan areas for PTB transmission and S and M are able to detect risk factors as secondary components of a transmission chain of TB.

View Article: PubMed Central - PubMed

Affiliation: División de Biología Celular y Molecular, Centro de Investigación Biomédica del Noreste, Zacatecas, ZC, México.

ABSTRACT
The characteristics of tuberculosis (TB) patients related to a chain of recent TB transmissions were investigated. Mycobacterium tuberculosis (MTB) isolates (120) were genotyped using the restriction fragment length polymorphism-IS6110 (R), spacer oligotyping (S) and mycobacterial interspersed repetitive units-variable number of tandem repeats (M) methods. The MTB isolates were clustered and the clusters were grouped according to the similarities of their genotypes. Spearman's rank correlation coefficients between the groups of MTB isolates with similar genotypes and those patient characteristics indicating a risk for a pulmonary TB (PTB) chain transmission were ana- lysed. The isolates showing similar genotypes were distributed as follows: SMR (5%), SM (12.5%), SR (1.67%), MR (0%), S (46.67%), M (5%) and R (0%). The remaining 35 cases were orphans. SMR exhibited a significant correlation (p < 0.05) with visits to clinics, municipalities and comorbidities (primarily diabetes mellitus). S correlated with drug consumption and M with comorbidities. SMR is needed to identify a social network in metropolitan areas for PTB transmission and S and M are able to detect risk factors as secondary components of a transmission chain of TB.

Show MeSH
Related in: MedlinePlus