Genotipificación de aislamientos del complejo Mycobacterium tuberculosis mediante MIRU-VNTR, Cali, Colombia, 2013-2015 / MIRU-VNTR genotyping of Mycobacterium tuberculosis in a population of patients in Cali, Colombia, 2013-2015

Resumen Introducción. La tuberculosis continúa siendo uno de los problemas de salud más importantes a nivel mundial y, con la infección por el virus de la inmunodeficiencia humana (HIV), constituye la principal causa de muerte por infecciones. En el 2016, se notificaron 6,3 millones de casos nuevos de la enfermedad. Objetivo. Describir los patrones genéticos determinados mediante la genotipificación del número variable de repeticiones en tándem de unidades repetitivas interespaciadas de micobacterias (Mycobacterial Interspersed Repetitive Units - Variable Number of Tandem Repeats, MIRU-VNTR) en la población de estudio y compararlos con los hallados en otros estudios locales e internacionales. Materiales y métodos. Mediante MIRU-VNTR, entre el 2013 y el 2015 se hizo la genotipificación de 105 muestras de ADN extraídas del esputo o de aislamientos en cultivo de M. tuberculosis provenientes de pacientes residentes en Cali con diagnóstico de tuberculosis pulmonar. La amplificación de 24 loci MIRU-VNTR se hizo por medio de la reacción en cadena de la polimerasa (PCR). Los amplicones resultantes se visualizaron por electroforesis en geles de agarosa (2 %) teñidos con SYBR Safe™. La asignación de los alelos se hizo con un análisis gráfico con el programa GelAnalyzer 2010. Los resultados obtenidos se analizaron con el algoritmo UPGMA y se compararon con las bases de datos internacionales MIRU-VNTRplus y SITVITWEB. Resultados. Se genotipificaron por completo 62 de las muestras y se obtuvieron 58 perfiles diferentes de MIRU-VNTR. Al comparar con las bases de datos internacionales, su distribución por linajes fue la siguiente: 54,8 % para el LAM, 25,8 % para el Haarlem, 14,5 % para el S, 3,2 % para el Beijing y 1,6 % para el Cameroon. Los patrones MIRU-VNTR correspondieron a 20 tipos internacionales de MIRU (MIRU International Types, MIT) diferentes, y los más frecuentes fueron el MIT 190 y el MIT 110, con 22,6 y 6,5 %, respectivamente. Conclusión. Estos resultados confirmaron hallazgos previos sobre el predominio de los linajes LAM y Haarlem en la ciudad y la presencia de los MIT encontrados en otra ciudad de Colombia.

Abstract Introduction: Tuberculosis continues to be one of the main public health problems in the world. Together with the HIV infection, it is one of the main causes of death due to infections worldwide. In 2016, 6.3 million new cases of the disease were reported. Objective: To describe the genetic patterns determined by genotyping using variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) in the study population and compare them with other studies carried out in Cali, Colombia, and the world. Materials and methods: We genotyped a total of 105 DNA samples extracted from sputum or culture isolates of the Mycobacterium tuberculosis complex, which were obtained from pulmonary tuberculosis diagnosed patients over the period 2013-2015, in Cali. We performed PCR amplification of 24 loci by MIRU-VNTR on the DNA extracted from the samples. The amplicons were visualized in agarose gel electrophoresis (2%) with SYBR Safe™ staining. Then, the alleles were designated by graphical analysis using the GelAnalyzer 2010 software. These results were analyzed using the UPGMA logarithm and compared with the registers from the MIRU-VNTR plus and SITVITWEB databases. Results: We genotyped 62 of the samples completely and we obtained 58 different MIRU-VNTR profiles. By comparing with the international databases, we determined the following distributions per lineage: LAM, 54.8%; Haarlem,25.8%; S, 14.5%; Beijing, 3.2%, and Cameroon, 1.6%. The MIRU-VNTR patterns corresponded to 17 different MITs; the most frequent were MIT 190 and MIT 110, with 22.6% and 6.5%, respectively. Conclusions: These results demonstrated previous observations about the predominance of the LAM and Haarlem lineages in the city, and the presence of the MITs found in another city of Colombia.

Optimal Combination of VNTR Typing for Discrimination of Isolated Mycobacterium tuberculosis in Korea / 결핵및호흡기질환

BACKGROUND: Variable-number tandem repeat (VNTR) typing is a promising method to discriminate the Mycobacterium tuberculosis isolates in molecular epidemiology. The purpose of this study is to determine the optimal VNTR combinations for discriminating isolated M. tuberculosis strains in Korea. METHODS: A total of 317 clinical isolates collected throughout Korea were genotyped by using the IS6110 restriction fragment length polymorphism (RFLP), and then analysed for the number of VNTR copies from 32 VNTR loci. RESULTS: The results of discriminatory power according to diverse combinations were as follows: 25 clusters in 83 strains were yielded from the internationally standardized 15 VNTR loci (Hunter-Gaston discriminatory index [HGDI], 0.9958), 25 clusters in 65 strains by using IS6110 RFLP (HGDI, 0.9977), 14 clusters in 32 strains in 12 hyper-variable VNTR loci (HGDI, 0.9995), 6 clusters in 13 strains in 32 VNTR loci (HDGI, 0.9998), and 7 clusters in 14 strains of both the 12 hyper-variable VNTR and IS6110 RFLP (HDGI, 0.9999). CONCLUSION: The combination of 12 hyper-variable VNTR typing can be an effective tool for genotyping Korean M. tuberculosis isolates where the Beijing strains are predominant.

Allele-related Variation in Minisatellite Repeats Involved in Transcription of the ABO Gene in Korean Blood Donors / 대한혈액학회지

BACKGROUND: The CBF/NF-Y enhancer region of ABO gene reported to contain 43bp minisatellite tandem repeats has been rarely reported. We describe here the relationship between minisatellite tandem repeats and ABO alleles in samples from Korean population with common ABO blood group and rare ABO subgroup. METHODS: Sixty one cases of ABO subgroup (14 A2, 12 A2B, 1 Aweak, 7 AweakB, 11 B3, 5 A1B3, 1 A1Bweak, 2 Bweak, and 8 cis-AB) and 41 cases of common ABO blood group (13 A, 6 AB, 11 B, and 11 O) were obtained from healthy donors at the Gwangju-Chonnam Red Cross Blood Center between Sep 2004 and Aug 2005. Red cells were phenotyped by standard serologic tests and genotyped by direct DNA sequencing exon 6 and 7 of the ABO gene. The minisatellite repeats were analyzed by PCR method. RESULTS: The ABO*A101 and *A102 had only one repeat, *B101, *O01 and *O02 had 4 repeats in common ABO blood group, while the *A102, *cis-AB01, and *Aw10 had only one minisatellite repeat and *A201, *A204, *B101, *Bw03, *B306, *O01, and *O02 alleles had 4 repeats and unexpectedly 3 A2 cases with *A102 had 4 repeats in the rare ABO subgroup. CONCLUSION: The minisatellite repeats found in Koreans correlate well with ABO alleles in sample common ABO phenotype, but do not completely correlate with those of ABO subgroup. We revealed here a pattern of the minisatellite repeats in various ABO subgroup in Korea.

Evaluation of multiple locus variable number tandem repeat analysis (15-locus set) in genotyping of Mycobacterium tuberculosis strains of the Beijing genotype / 中华检验医学杂志

Objective To evaluate the application of multiple locus variable number tandem repeat analysis (MLVA, 15-locus set)for genotyping of Mycobacterium tuberculosis (MTB) strains of Beijing genotype. Methods Total 72 Beijing genotype MTB strains obtained from Beijing Thoracic Hospital were genotyped by MLVA (15-locus set). The results were compared with that generated from "gold standard"IS6110-RFLP. Results After genotyped by MLVA ( 15-locus set), 72 strains were grouped into 59 types,of which 53 were unique types. The Hunter-Gaston index (HGI) of MLVA ( 15-locus set) was 0.990. The loci QUB-11b, Mtub 21 and QUB-26 were polymorphic in selected Beijing genotype strains. Genotyping by IS6110-RFLP generated 69 types, of which 66 were unique types. The HGI of IS6110-RFLP was up to 0.999, and the MLVA (15-locus set) clustered strains could be further subdivided. Conclusion MLVA(15-locus set) showed better discriminatory ability in Beijing genotype MTB strains, though secondary typing of clustered strains by IS6110-RFLP is needed.

The Association of Polymorphism of Endothelial Nitric Oxide Synthase Gene in Patients with PAH of Chronic Obstructive Pulmonary Disease / 医学研究杂志

Objective To study the variable number tandem repeats(VNTR)polymorphism in intron 4 of the endothelial nitric oxide synthase(eNos)gene and its relationship with plasma NO in patents with PAH of COPD.Methods The VNTR polymorphism in intron 4of the eNos genes of PAH COPD and healthy control were detected by PCR.The plasma level of NO3-/NO2-was measured by spectrophotometer,which was used as an index of NO synthesis.Data were analyzed according to the different genotype and allelic gene frequency.Results The COPD PAH group significant higher frequency of VNTR 4a allele and 4a/4b allele and 4a/4b+4a/4a genotype than those of the control(P=0.027,P

The distribution of platelet glycoprotein I b? variable number tande repeat polymorphism and the relationship with cerebral infarction / 中华检验医学杂志

Objective To study the distribution of variable number tande repeat(VNTR) polymorphisms of the platelet membrane glycoprotein Ⅰ b? in Han nationality at Harbin and the relationship between these polymorpbisms and cerebral infarction(CI).Methods The identification of alleles and genotypes of VNTR polymorphism of the glycoprotein Ⅰ b? gene was performed by polymerase chain reaction (PCR)in 200 healthy individuls and 200 CI patients(77 lacunar infarction patients and 123 atherosclerotic thrombotic infarction patients),to analyze The relationship between gene polymorphisms and cerebral infarction.Results(1)There were three types of alleles:B、C、D,and five types genotypes:BC,BD,CC, CD,DD in Harbin Han nationality.No person with A allele and BB genotype was found.(2)No statistically significant differences of GP Ⅰ b? gene VNTR polymorphism was found between CI patients or subtype CI patients and controls(P=0.412 and 0.572,respectively).Conclusions(1)This study indicates that the C and D alleles of VNTR polymorphisms of GP Ⅰ b? are the main alleles while the CC and CD genotypes are the main genotypes in Harbin Han people.(2)Our findings indicate that no association exists between the VNTR polymorphism of platelet GP Ⅰ b? gene and CI.

Association of the dopamine transporter gene with Parkinson's disease in Korean patients

Dopamine transporters (DAT) uptake neurotoxic substances such as 1-methyl-4-phenylpyridinium (MPP) in the dopaminergic nerve terminals and may confer susceptibility to cytotoxic effects of neurotoxic substance. The association of a variable number tandem repeat polymorphism in the DAT gene with Parkinson's disease (PD) in a Korean population was studied. The 10-copy allele was the most common, accounting for 77.2+ACU- and 81.6+ACU- of alleles in PD patients and control subjects, respectively. The rare 11-copy allele was more common in the patients (odds ratio +AD0- 2.5, 95+ACU- confidence interval +AD0- 1.1-5.7, p+ADw-0.02). It is suggested that the 11-copy allele of the DAT gene may confer susceptibility to PD for some patients in Korea.

Association of the dopamine transporter gene with Parkinson's disease in Korean patients

Dopamine transporters (DAT) uptake neurotoxic substances such as 1-methyl-4-phenylpyridinium (MPP) in the dopaminergic nerve terminals and may confer susceptibility to cytotoxic effects of neurotoxic substance. The association of a variable number tandem repeat polymorphism in the DAT gene with Parkinson's disease (PD) in a Korean population was studied. The 10-copy allele was the most common, accounting for 77.2+ACU- and 81.6+ACU- of alleles in PD patients and control subjects, respectively. The rare 11-copy allele was more common in the patients (odds ratio +AD0- 2.5, 95+ACU- confidence interval +AD0- 1.1-5.7, p+ADw-0.02). It is suggested that the 11-copy allele of the DAT gene may confer susceptibility to PD for some patients in Korea.

The association of polymorphism of endothelial nitric-oxide synthase gene in pregnancy induced hypertension / 中华围产医学杂志

Objective To study the variable number tandem repeats (VNTR) polymorphism in intron 4 of the endothelial nitric-oxide synthase (eNOS) gene and its relationship with plasma NO in pregnancy induced hypertension (PIH). Method The VNTR polymorphism in intron 4 of the eNOS genes of PIH and healthy control pregnant women were detected by PCR. The plasma level of NO~(3-)/NO~(2-) was measured by spectrophotometer, which was used as the index of NO synthesis.Data were analyzed according to the different type of genotypes and allelic gene frequency. Results The PIH group showed significant higher frequency of VNTR 4a allele and 4a/4b+4a/4a genotype than those of the control (16.00% vs 7.50%,P