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2.
Biomedical and Environmental Sciences ; (12): 459-462, 2018.
Article in English | WPRIM | ID: wpr-690635

ABSTRACT

A retrospective analysis was performed in two major HIV/AIDS referral hospitals in Beijing to evaluate the prevalence of Mycobacterium tuberculosis (MTB) and non-tuberculous mycobacterial (NTM) infections in HIV-infected patients. A total of 627 patients' data were reviewed, and 102 (16.3%) patients were diagnosed with culture-confirmed mycobacterial infection, including 84 with MTB, 16 with NTM, and 2 with both MTB and NTM. The most frequent clinical complication by mycobacterial infection was pulmonary infection (48/102, 47.1%). The overall rates of multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB) were 11.9% and 3.4%, respectively. This study underlines the urgent need to intensify screening for mycobacteria coinfection with HIV and to prevent the spread of drug-resistant TB among HIV-infected patients.


Subject(s)
Adult , Female , Humans , Male , AIDS-Related Opportunistic Infections , Epidemiology , Microbiology , Beijing , Coinfection , Extensively Drug-Resistant Tuberculosis , Epidemiology , Microbiology , HIV Infections , Epidemiology , Microbiology , Hospitals, Urban , Mycobacterium Infections, Nontuberculous , Epidemiology , Microbiology , Mycobacterium tuberculosis , Nontuberculous Mycobacteria , Prevalence , Retrospective Studies , Sputum , Microbiology , Tuberculosis, Multidrug-Resistant , Epidemiology , Microbiology , Tuberculosis, Pulmonary , Epidemiology , Microbiology
3.
Biomedical and Environmental Sciences ; (12): 25-35, 2015.
Article in English | WPRIM | ID: wpr-264623

ABSTRACT

<p><b>OBJECTIVE</b>A PCR-reverse dot blot hybridization (RDBH) assay was developed for rapid detection of rpoB gene mutations in 'hot mutation region' of Mycobacterium tuberculosis (M. tuberculosis).</p><p><b>METHODS</b>12 oligonucleotide probes based on the wild-type and mutant genotype rpoB sequences of M. tuberculosis were designed to screen the most frequent wild-type and mutant genotypes for diagnosing RIF resistance. 300 M. tuberculosis clinical isolates were detected by RDBH, conventional drug-susceptibility testing (DST) and DNA sequencing to evaluate the RDBH assay.</p><p><b>RESULTS</b>The sensitivity and specificity of the RDBH assay were 91.2% (165/181) and 98.3% (117/119), respectively, as compared to DST. When compared with DNA sequencing, the accuracy, positive predictive value (PPV) and negative predictive value (NPV) of the RDBH assay were 97.7% (293/300), 98.2% (164/167), and 97.0% (129/133), respectively. Furthermore, the results indicated that the most common mutations were in codons 531 (48.6%), 526 (25.4%), 516 (8.8%), and 511 (6.6%), and the combinative mutation rate was 15 (8.3%). One and two strains of insertion and deletion were found among all strains, respectively.</p><p><b>CONCLUSION</b>Our findings demonstrate that the RDBH assay is a rapid, simple and sensitive method for diagnosing RIF-resistant tuberculosis.</p>


Subject(s)
Antitubercular Agents , Pharmacology , Drug Resistance, Bacterial , Genotype , Immunoblotting , Methods , Microbial Sensitivity Tests , Mycobacterium tuberculosis , Genetics , Polymerase Chain Reaction , Methods , Rifampin , Pharmacology , Sensitivity and Specificity , Time Factors
4.
Biomedical and Environmental Sciences ; (12): 222-226, 2015.
Article in English | WPRIM | ID: wpr-264596

ABSTRACT

70 clinical Mycobacterium tuberculosis strains isolated from AIDS patients in two HIV/AIDS referral hospitals in Beijing were used in this study. M. tuberculosis and non-tuberculosis mycobacterium (NTM) were identified by using multi-locus PCR. M. tuberculosis was genotyped by using 15-locus MIRU-VNTR technique and spoligotyping afterwards. Meanwhile, the drug susceptibilities of the strains to the four first-line anti TB drugs (rifampin, isoniazid, streptomycin, and ethambutol) and the four second-line anti-TB drugs (capreomycin, kanamycin, ofloxacin, and ethionanide) were tested with proportional method. In this study, M. tuberculosis and NTM strains isolated from AIDS patients with TB-like symptoms were identified and genotyping analysis indicated that Beijing genotype was the predominant genotype. In addition, the prevalence of drug-resistant TB, especially the prevalence of XDR-TB, was higher than that in TB patients without HIV infection.


Subject(s)
Humans , AIDS-Related Opportunistic Infections , Microbiology , Antitubercular Agents , Pharmacology , China , Microbial Sensitivity Tests , Mycobacterium tuberculosis , Classification , Phylogeny , Tuberculosis , Microbiology
5.
Biomedical and Environmental Sciences ; (12): 960-964, 2014.
Article in English | WPRIM | ID: wpr-264631

ABSTRACT

To understand the genetic diversity and drug resistance status of Mycobacterium tuberculosis (M. tuberculosis) circulating in Xuzhou of China, the spacer-oligonucleotide typing (Spoligotyping) and multi-loci VNTRs (variable number tandem repeats) analysis (MLVA) were utilized for the genotyping of the isolates. Drug susceptibility test (DST) was performed by the proportion method on the Lowenstein-Jensen (L-J) medium using isoniazid, rifampicin, ethambutol, and streptomycin. By Spoligotyping, 287 M. tuberculosis isolates were differentiated into 14 clusters. Then with 15-loci MLVA, these strains could be divided into 32 clusters, 228 genotypes. Of 15 VNTRs, 6 loci had the highly discriminatory powers, 6 loci presented moderate discrimination and 3 loci demonstrated less polymorphism. The DST results showed that 46 strains were resistant to at least one first-line anti-tuberculosis agent. There was a difference in the isoniazid resistance between Beijing and non-Beijing genotype strains. We concluded that the combination of Spoligotyping and 15 VNTR loci as the genotyping in our study was applicable for this region, the drug resistant isolates were identified, and the Beijing family was the most prevalent genotype in the rural counties of Xuzhou.


Subject(s)
China , Drug Resistance, Bacterial , Genetics , Genotyping Techniques , Mycobacterium tuberculosis , Genetics
6.
Biomedical and Environmental Sciences ; (12): 894-901, 2013.
Article in English | WPRIM | ID: wpr-247115

ABSTRACT

<p><b>OBJECTIVE</b>To identify the novel species 'Mycobacterium fukienense' sp. nov of Mycobacterium chelonae/abscessus complex from tuberculosis patients in Fujian Province, China.</p><p><b>METHODS</b>Five of 27 clinical Mycobacterium isolates (Cls) were previously identified as M. chelonae/abscessus complex by sequencing the hsp65, rpoB, 16S-23S rRNA internal transcribed spacer region (its), recA and sodA house-keeping genes commonly used to describe the molecular characteristics of Mycobacterium. Clinical Mycobacterium isolates were classified according to the gene sequence using a clustering analysis program. Sequence similarity within clusters and diversity between clusters were analyzed.</p><p><b>RESULTS</b>The 5 isolates were identified with distinct sequences exhibiting 99.8% homology in the hsp65 gene. However, a complete lack of homology was observed among the sequences of the rpoB, 16S-23S rRNA internal transcribed spacer region (its), sodA, and recA genes as compared with the M. abscessus. Furthermore, no match for rpoB, sodA, and recA genes was identified among the published sequences.</p><p><b>CONCLUSION</b>The novel species, Mycobacterium fukienense, is identified from tuberculosis patients in Fujian Province, China, which does not belong to any existing subspecies of M. chelonea/abscessus complex.</p>


Subject(s)
Humans , Bacterial Proteins , Genetics , Base Sequence , China , Epidemiology , Cluster Analysis , DNA, Bacterial , Genetics , Molecular Sequence Data , Mycobacterium , Classification , Genetics , Mycobacterium Infections, Nontuberculous , Epidemiology , Microbiology , Mycobacterium chelonae , Classification , Genetics , Phylogeny , Sequence Alignment , Tuberculosis , Epidemiology , Microbiology
7.
Chinese Journal of Epidemiology ; (12): 379-384, 2013.
Article in Chinese | WPRIM | ID: wpr-318393

ABSTRACT

Objective To detect the changes on the expression of putative drug effiux genes caused by isoniazid-inducement in single resistance to the isoniazid Mycobacterium tuberculosis (M.tuberculosis) clinical isolates,for exploring the putative effiux genes which causing M.tuberculosis isoniazid resistance as well as the mechanism related to high expression of the putative effiux genes.Methods We selected 35 M.tuberculosis clinical isolates which were only resistant to isoniazid as well as 10 sensitive M.tuberculosis clinical isolates and using H37Rv as control.Each strain was cultured in 7H9 liquid medium without isoniazid and with subinhibitory isoniazid concentration (1/4 MIC) induction.After RNA extraction and reverse transcription,real-time PCR was conducted to assess the expression changes of 27 putative drug effiux pump genes with formula 2-△△CT to calculate the expression of each putative drug efflux pump genes.Results Of the 27 putative genes,13 of them were expressed at high level.High expression of Rv1258c gene had the maximum number of 6strains,followed by high expression of Rv0849 and Rv2265 which both had 5 strains.Fourteen strains (40.00%) out of the 35 strains had high expression pump genes.Six strains (17.14%) had only one highly expressed putative efflux pump gene.Eight strains (22.86%) had two or more highly expressed putative effiux pump genes,including two,four,five,seven genes that highly expressed in 4,2,1,1strains respectively.For the 27 putative genes,ten sensitive strains and H37Rv did not show highly expressed genes.Conclusion Rv1258c,Rv2265,Rv0849,etc.genes might be the putative effiux pumps genes of M.tuberculosis resistant to isoniazid.Isoniazid might serve as the inducer of M.tuberculosis part putative effiux pump genes,inducing activation and causing high expression of these putative effiux pump genes.

8.
Biomedical and Environmental Sciences ; (12): 620-629, 2012.
Article in English | WPRIM | ID: wpr-320389

ABSTRACT

<p><b>OBJECTIVE</b>Tuberculosis remains one of the most serious infectious diseases in the world. In this study, a scheme of Mycobacterium tuberculosis (M. tuberculosis) multilocus sequence analysis (MLSA) was established for the phylogenetic and epidemiology analysis.</p><p><b>METHODS</b>To establish the scheme of M. tuberculosis MLSA, the genome of H37Rv, CCDC5079 and CCDC5180 were compared, and some variable genes were chosen to be the MLSA typing scheme. 44 M. tuberculosis clinical isolates were typed by MLSA, IS6110-RFLP, and soligotyping, to evaluate the MLSA methods.</p><p><b>RESULTS</b>After comparison of the genome, seven high discrimination gene loci (recX, rpsL, rmlC, rpmG1, mprA, gcvH, ideR) were chosen to be the MLSA typing scheme finally. 11 variable SNP sites of those seven genes were found among the 44 M. tuberculosis isolate strains and 11 sequence types (STs) were identified. Based on the Hunter-Gaston Index (HGI), MLSA typing was not as good for discrimination at the strain level as IS6110-RFLP, but the HGI was much better than that of spoligotyping. In addition, the MEGA analysis result of MLSA data was similar to spoligotyping/PGG lineage, showing a strong phylogenetic signal in the modern strains of M. tuberculosis. The MLSA data analysis by eBURST revealed that 4 sequence types (ST) came into a main cluster, showing the major clonal complexes in those 44 strains.</p><p><b>CONCLUSION</b>MLSA genotyping not only can be used for molecular typing, but also is an ideal method for the phylogenetic analysis for M. tuberculosis.</p>


Subject(s)
Chromosome Mapping , Chromosomes, Bacterial , Gene Expression Regulation, Bacterial , Genome, Bacterial , Genotype , Multilocus Sequence Typing , Methods , Mycobacterium tuberculosis , Genetics , Metabolism
9.
Biomedical and Environmental Sciences ; (12): 82-90, 2012.
Article in English | WPRIM | ID: wpr-235567

ABSTRACT

<p><b>OBJECTIVE</b>To evaluate four candidate variable number tandem repeat (VNTR) loci for genotyping Mycobacterium tuberculosis complex strains.</p><p><b>METHODS</b>Genomic sequences for two M. tuberculosis strains (CCDC5079 and CCDC5180) were generated, and using published sequence data, four candidate VNTR loci were identified. The VNTRs were used to genotype 225 Chinese clinical M. tuberculosis complex strains. The discriminatory power of the VNTRs was evaluated using BioNumerics 5.0 software.</p><p><b>RESULTS</b>The Hunter-Gaston Index (HGI) for BJ1, BJ2, BJ3, and BJ4 loci was 0.634, 0.917, 0.697, and 0.910, respectively. Combining all four loci gave an HGI value of 0.995, thus confirming that the genotyping had good discriminatory power. The HGI values for BJ1, BJ2, BJ3, and BJ4, obtained from Beijing family strain genotyping, were 0.447, 0.878, 0.315, and 0.850, respectively. Combining all four loci produced an HGI value of 0.988 for genotyping the Beijing family strains. We observed unique patterns for M. bovis and M. africanum strains from the four loci.</p><p><b>CONCLUSION</b>We have shown that the four VNTR loci can be successfully used for genotyping M. tuberculosis complex strains. Notably, these new loci may provide additional information about Chinese M. tuberculosis isolates than that currently afforded by established VNTR loci typing.</p>


Subject(s)
Humans , Cluster Analysis , Genotyping Techniques , Minisatellite Repeats , Mycobacterium bovis , Genetics , Mycobacterium tuberculosis , Genetics
10.
International Eye Science ; (12): 1469-1470, 2010.
Article in Chinese | WPRIM | ID: wpr-641421

ABSTRACT

A male patient,39 years old,presented with symptoms of cataract,dwarf,progeria,polydactyly and genu valgum,after the extracapusular cataract extraction and intraocular lens implantation on both eyes,the visual acuity was improved and his fundus examination was normal.As the syndrome is different from any eye syndrome we have ever known,so it maybe a new one.

11.
Chinese Journal of Epidemiology ; (12): 58-62, 2009.
Article in Chinese | WPRIM | ID: wpr-329535

ABSTRACT

Objective To evaluate the discriminatory efficiency of multiple loci of variable numbers of tandem repeats (VNTR) in Mycobacterium tuberculosis genome.Genotyping and identification on Chinese M.tuberculosis clinical strains were used to locate a series of high discriminated loci,so as to provide the basis for creating a standardized multiple loci VNTR analysis (MLVA) to distribute fast typing and identification on Chinese M.tuberculosis.Methods VNTR loci which were chosen from the website http://minisatellites.u-psud.fr/ and referenced to the genome sequence of M.tuberculosis standard strain H37Rv were tested in Chinese M.tuberculosis clinical strains and H37Rv by means of PCR.The primers were designed by DNAStar software.The repeat member of VNTR unit was estimated by the result of PCR.The discrimination power of single locus or multiple loci was confirmed by the Hunter-Gaston index.Results 45 VNTR loci were tested in 135 Chinese M.tuberculosis clinical strains and H37Rv.The discrimination power of these loci appeared different from each other,with the biggest Hunter-Gaston index as 0.814 (0.797-0.830),the smallest one as 0.015 (0.001-0.028),and there were 13 loci with which the Hunter-Gaston index was bigger than 0.5.Results showed that the discrimination power was increasing by different loci that associated with each other.The more loci that were combined,the bigger the Hunter-Gaston index was,For example,the Hunter-Gaston index of Qub11-b associated with Qub 18 was 0.936,by which 136 strains could be divided into 44 groups.With the combination of 9 loci including Qub11-b,Qub18,Mtub21,Rv2372,MIRU26,Qub26,Qub4156c,Qub11-a and Qub15,the HunterGaston index could have reached 1 and by which the 136 strains could be divided into 136 groups,also showing that the biggest discrimination power to strain identification,viz.strain level genotype were reached.Conclusion The discrimination power of different locus was different.The discrimination power of multiple loci was much more satisfied than that of single locus.It was satisfied the combine discrimination power of 9 loci including Qubll-b,Qubl8,Mtub21,Rv2372,MIRU26,Qub26,Qub4156c,Qub11-a and Qubl5,by which the qualified typing method could gain to facilitate research on molecular epidemiology with the Hunter-Gaston index analysis.

12.
Chinese Journal of Preventive Medicine ; (12): 215-222, 2009.
Article in Chinese | WPRIM | ID: wpr-242664

ABSTRACT

<p><b>OBJECTIVE</b>To evaluate the application of different variable number tandem repeats (VNTR) locus in genotyping of Mycobacterium tuberculosis (M.tuberculosis) strains isolated from eight provinces in China, and to find the suitable locus-set of VNTR for epidemical strains in China.</p><p><b>METHODS</b>All 140 M.tuberculosis strains were randomly selected from 2800 M.tuberculosis strains isolated from eight provinces in China, 27 VNTR loci were used for typing all isolates. Discriminatory power (Hunter-Gaston Index, HGI) of every locus and different locus-set were analyzed by BioNumerics software. Meanwhile, Spoligotyping was used to identify Beijing family and non-Beijing family. Then the HGI of different locus-sets in two families was also evaluated.</p><p><b>RESULTS</b>All 140 isolates were clustered into Beijing kindred (112 strains, 80%) and non-Beijing kindred (28 strains, 20%) by Spoligotyping. The discriminatory power of Spoligotyping in 140 isolates was 0.4589. Every locus showed different polymorphism and HGI were from 0 to 0.809. The number of VNTR loci with HGI higher than 0.5 in all strains, Beijing family and non-Beijing family was 8, 7 and 14 respectively. 27 loci were combined into four groups which included 8, 12, 15 and 24 VNTR loci respectively. Four locus-sets showed different polymorphism, HGI of eight-locus, 12-locus, 15-locus, and 24-locus set in 140 strains was 0.9991, 0.9882, 0.9980 and 0.9986, and their discriminatory power were calculated in Beijing kindred (HGI: 0.9987, 0.9318, 0.9969 and 0.9975) and non-Beijing kindred (HGI: 1, 0.9894, 1 and 1).</p><p><b>CONCLUSION</b>Different VNTR locus and locus-set showed different discriminatory power in the selected M.tuberculosis strains isolated from China. Eight-locus set can be used in molecular epidemiological study of M.tuberculosis in China after standardization.</p>


Subject(s)
Bacterial Typing Techniques , DNA, Bacterial , Genetics , Mycobacterium tuberculosis , Classification , Genetics , Tandem Repeat Sequences
13.
Chinese Journal of Epidemiology ; (12): 616-618, 2009.
Article in Chinese | WPRIM | ID: wpr-261313

ABSTRACT

Objective To create and evaluate the PCR restriction fragment length polymorphism (PCR-RFLP) based on hsp65 gene as a method for rapid identification of Mycobacteria to the species level. Methods hsp65 gene was amplified from the DNA of mycobacterial reference strains and the PCR products were subjected to digestion by two restriction endonucleases Hae Ⅲ and Bstp Ⅰ, then loaded onto a 4% MetaPhor agorose. The size of the restricted fragments of each species (strains) was determined according to the position of the fragments on the gel, by which the differential DNA fingerprint was confirmed. Results A total of 40 Mycobacterium species (strains) was analyzed, in which six reference strains of Mycobacterium tuberculosis Complex had two different electrophoresis patterns, and thirty-four reference species of non-tuberculosis Mycobacteria had unique pattern. Conclusion PCR-RFLP Based upon hsp65 gene can be used for identification of Mycobacterium species, and the method is more rapid and simple and easy-to-use for mycobacterial species identification.

14.
Chinese Journal of Epidemiology ; (12): 384-387, 2009.
Article in Chinese | WPRIM | ID: wpr-266522

ABSTRACT

Objective To study and preliminarily evaluate the standard spacer oligonucleotide typing (Spoligotyping) method and the application on Mycobacterium tuberculosis (M.tuberculosis).Methods Spoligotyping on 224 M.tuberculosis strains was studied by the molecular biological techniques, including DNA isolation, PCR, reverse line blot hybridization, together with data analysis software BioNumerics (Version 5.0). Results Standardization on both Spoligotyping method and parameters in result analysis and the usage of the analysis software were studied. Through this method, 224 M.tuberculosis clinical strains were classified into 2 clusters including 129 Beijing family strains and 95 non-Beijing family strains. The predominant strains belonged to Beijing family. Conclusion Standard Spoligotyping method was preliminary determined in China, showing that it was a simple, rapid, and robust method for simultaneous detection and typing of M.tubereulosis. This method can be used for tracing the source of infection and understanding the epidemic trend of M.tuberculosis. Spoligotyping can also be served as a method for simultaneous detection and typing ofM.tuberculosis, and to identify Beijing family strains.

15.
Chinese Journal of Epidemiology ; (12): 801-805, 2008.
Article in Chinese | WPRIM | ID: wpr-298381

ABSTRACT

<p><b>OBJECTIVE</b>To develop a standardized IS6110-restriction fragment length polymorphism (RFLP) method, used for evaluating the capacity of genotyping.</p><p><b>METHODS</b>IS6110-RFLP of 78 Mycobacterium (M.) tuberculosis strains were studied by bio-molecular techniques including DNA isolation, PCR, restriction endonuclease enzyme analysis, southern blotting, agarose gel electrophoresis, together with data analysis by software Gel-Pro analyzer 3.1 and BioNumerics (Version 5.0).</p><p><b>RESULTS</b>IS6110-RFLP method was established and standardized successfully, including DNA isolation, PCR, restriction endonuclease enzyme analysis, southern blotting, agarose gel electrophoresis and usage of the analysis software with standard parameters. By this method, 78 M. tuberculosis isolates were classified into 75 genotypes which belonged to 11 different clusters. Of all the isolates, 66.7% (52/78) belonged to a main cluster.</p><p><b>CONCLUSION</b>Standard IS6110-RFLP method was established successfully. This method had powerful capacity for genotyping and strain level identification and could be used for the surveillance on pathogens of M. tuberculosis in China.</p>


Subject(s)
Bacterial Typing Techniques , Methods , DNA, Bacterial , Genome, Bacterial , Genotype , Molecular Sequence Data , Mycobacterium tuberculosis , Classification , Genetics , Polymorphism, Restriction Fragment Length
16.
Chinese Journal of Epidemiology ; (12): 919-924, 2008.
Article in Chinese | WPRIM | ID: wpr-298352

ABSTRACT

Objective To establish and evaluate the standardized protocol of multiple loci variable numbers tandem repeats (VNTR) analysis (MLVA) for genotyping Mycobacterium tuberculosis (M.tuberculosis).Methods 15 VNTR loci were chosen for genotyping 54 Chinese M.tuberculosis strains by PCR-electmphoresis-based VNTR analysis and the results were analyzed by software BioNumerics (Version 5.0).Results MLVA method was successfully established and standardized,including the standard protocol for bacterial culture,DNA isolation,PCR and agarose gel electrophoresis and the software analysis. 15 VNTR loci were confirmed,including ETRA,ETRB,ETRC,ETRD,ETRE,MIRU10,MIRU16,MIRU23,MIRU26,MIRU27,MIRU39,MIRU40,Mtub21,Mtub30 and Mtub39,to be suitable for MLVA analysis of M.tuberculosis.Conclusion The standardized MLVA method has been established successfully.This method is simple and has powerful capacity for genotyping and strain differentiation,can be used for the network surveillance on pathogens of M.tuberculosis,and the data are comparable between laboratories.It is valuable for tracing the source and studying the trend of prevalence during investigation of M.tuberculosis infections.

17.
Chinese Journal of Epidemiology ; (12): 268-272, 2007.
Article in Chinese | WPRIM | ID: wpr-232356

ABSTRACT

<p><b>OBJECTIVE</b>To access the application of spacer oligotyping (Spoligotyping) and Multiple Locus VNTR(MLVA) in epidemiological studies of Mycobacterium tuberculosis.</p><p><b>METHODS</b>224 clinical isolates of M. tuberculosis were collected and typed by Spoligotyping and MLVA respectively, to compare the results of both methods and to access their application in epidemiological studies of M. tuberculosis.</p><p><b>RESULTS</b>Data from Spoligotyping showed that 224 strains presented 55 kinds of genotypes. Of these, 39 were represented by a unique isolate, with the remaining 185 isolates being grouped in 16 clusters whereas the result of MLVA showed that 224 strains presenting 160 kinds of genotypes. Of these, 132 were represented by a unique isolate, with the remaining 92 isolates being grouped in 28 groups. Data from the combination of Spoligotyping and VNTR showed that 224 strains presenting 179 kinds of genotypes. Of these, 159 were represented by a unique isolate, with the remaining 65 isolates being grouped in 20 groups. There was significant difference noticed among M. tuberculosis between Hunan and Anhui in the proportion of Beijing family (P < 0.001). The proportion of Beijing family in Anhui was higher than that in Hunan.</p><p><b>CONCLUSION</b>Results from this direct comparison studies demonstrated that MLVA analysis was more effective than Spoligotyping in discriminating individual M. tuberculosis isolates. However, Spoligotyping had an advantage over MLVA in identifying Beijing family strains and M. bovis. Taking Spoligotyping as a first-line typing technique and VNTR as second-line typing technique, the arrangement would improve the effectiveness of epidemiological investigation and pathological inspection of tuberculosis. The strains in different regions seemed to have had different characteristics.</p>


Subject(s)
Humans , China , Epidemiology , Genotype , Mycobacterium bovis , Genetics , Mycobacterium tuberculosis , Classification , Genetics , Oligonucleotide Array Sequence Analysis , Tandem Repeat Sequences , Tuberculosis , Epidemiology
18.
Chinese Journal of Epidemiology ; (12): 705-708, 2006.
Article in Chinese | WPRIM | ID: wpr-233890

ABSTRACT

<p><b>OBJECTIVE</b>Variable Number of Tandem Repeats (VNTRs) analysis was a recently developed method which could serve as a 'real-time' genotyping tool for Mycobacterium tuberculosis. One hundred and thirteen M. tuberculosis isolates from the patients with tuberculosis in Beijing were analysed using the reference method to study the characters of genetic diversity and genotype.</p><p><b>METHODS</b>Thirteen tandem repeat loci (ETR-A, ETR-C, ETR-D, MIRU10, MIRU16, MIRU27, MIRU31, MIRU40, Mtub21, Mtub30, Mtub38, Qublla, Qubllb) in the total genome of MTB were analyzed by PCR and agarose gel electrophoresis method. The characters of the polymorphism of DNA fingerprinting of one hundred and thirteen MTB strains were analyzed with Gel-Pro analyzer 3.1 software and BioNumerics 3.0 software. Results One hundred and thirteen MTB strains were characterized and classified in to four genotype families(type I , type II , type NV, type V ) based on thirteen tandem repeat loci. One hundred and four isolates(92.0%) belonged to type I , the other three genotypes scattered, five strains(4.4%) remaining with type II , while type IV and type V having the same quantity 1.8% (2/113). M. tuberculosis H37Rv belonged to a unattached genotype(type ll ). Conclusion There was obvious length polymorphism in the M. tuberculosis isolates which implied that type I was the epidemic strain clusters in M. tuberculosis in Beijing. VNTRs analysis seemed to be a simple, rapid, sensitive and valuable tool for epidemiological studies of M. tuberculosis complex organisms.</p>


Subject(s)
Humans , China , Epidemiology , Epidemiologic Studies , Genes, Bacterial , Genetic Variation , Genotype , Mycobacterium tuberculosis , Genetics , Polymerase Chain Reaction , Tandem Repeat Sequences , Tuberculosis , Epidemiology
19.
Chinese Journal of Epidemiology ; (12): 973-976, 2006.
Article in Chinese | WPRIM | ID: wpr-261695

ABSTRACT

<p><b>OBJECTIVE</b>To elucidate the characters of rpoB mutation in rifampin-resistant clinical isolates of Mycobacterium tuberculosis.</p><p><b>METHODS</b>286 bp DNA fragment of rpoB gene including 81 bp code region (rifampin resistance deteremination region, RRDR) was analyzed by PCR-single-strand conformation polymorphism(SSCP). The 286 bp DNA fragment of each strain which had been proved to have mutation by PCR-SSCP was then sequenced. 110 strains of M. tuberculosis, including 73 rifampin-resistant strains, 11 rifampin-susceptible drug-resistant strains and 26 drug-susceptible strains were studied.</p><p><b>RESULTS</b>47 rifampin-resistant strains were detected to have mutations by PCR-SSCP method. 76.6% rifampin-resistant strains showed that rpoB gene was carrying single point mutation analyzed by direct sequencing technique, which mainly located at 531-Ser (61.1%) and 526-His (25.0%). The combined mutation rate was 23.4%. In addition, 2 rifampin-susceptible drug-resistant strains and 1 drug-susceptible strain were mutated, detected by PCR-SSCP method. Sequencing results showed that the mutations located at 511-Leu, 526-His and 535-Pro.</p><p><b>CONCLUSION</b>Mutations in the 81 bp RRDR of rpoB were the main reasons of M. tuberculosis resistant to rifampin. 531-Ser and 526-His were the most common positions of mutations.</p>


Subject(s)
Antibiotics, Antitubercular , Pharmacology , Bacterial Proteins , Genetics , DNA Mutational Analysis , DNA-Directed RNA Polymerases , Drug Resistance, Bacterial , Mycobacterium tuberculosis , Genetics , Polymerase Chain Reaction , Polymorphism, Single-Stranded Conformational , Rifampin , Pharmacology
20.
Chinese Journal of Experimental and Clinical Virology ; (6): 312-318, 2005.
Article in Chinese | WPRIM | ID: wpr-333015

ABSTRACT

<p><b>BACKGROUND</b>To study the molecular biology of Xinjiang hemorrhagic fever (XHF) viruses, to explore its relationship with other Crimean-Congo hemorrhagic fever viruses, analyzing the epidemic origin and the tendency of geographic distribution of XHF.</p><p><b>METHODS</b>The S partial segment from the patient and tick samples collected in 2001 and 2002 was tested by RT-PCR, the positive samples were sequenced directly. The nucleotide homology of S partial segment as well as the whole segments were analyzed and the phylogenetic tree of S and M gene segments was drawn by computer.</p><p><b>RESULTS</b>All compared sequences of S partial segments from the patient and tick samples showed a high homology of nucleotide sequences. Phylogenetic tree divided all the analyzed viruses into three groups; Europe, African and Asian group. The Asian group can be divided further into another two branches: the middle Asian branch and the Chinese branch. All the Chinese isolates were clustered into one single group and was easy to be discriminated from the other isolates. The dividing of M segments seemed not completely related to the geographic origin of the viruses.</p><p><b>CONCLUSION</b>M segment classification was not consistent to the geographic distribution of the viruses. S segments analysis showed the close relationship of genetic background between the patient isolates and the tick isolates. Besides, all the Chinese isolates have the common evolution route and the gene structure characteristics displayed the regional distribution pattern.</p>


Subject(s)
Animals , Humans , China , Epidemiology , Genetic Variation , Hemorrhagic Fever Virus, Crimean-Congo , Classification , Genetics , Hemorrhagic Fever, Crimean , Epidemiology , Virology , Molecular Epidemiology , Phylogeny , RNA, Viral , Genetics , Reverse Transcriptase Polymerase Chain Reaction , Sequence Analysis, DNA , Ticks , Virology , Viral Proteins , Genetics
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