Mycobacterium tuberculosis Beijing genotype emerging in Vietnam

To assess whether the Mycobacterium tuberculosis Beijing genotype is emerging in Vietnam, we analyzed 563 isolates from new cases by spoligotyping and examined the association between the genotype and age, resistance, and BCG vaccination status. Three hundred one (54%) patients were infected with Beijing genotype strains. The genotype was associated with younger age (and hence with active transmission) and with isoniazid and streptomycin resistance, but not with BCG vaccination.     

Association of Mycobacterium tuberculosis Beijing genotype with tuberculosis relapse in Singapore

The relationship of Mycobacterium tuberculosis Beijing genotype with tuberculosis relapse was examined. Beijing strains were detected from 32 out of 45 (71%) relapsed cases and 148 out of 290 (51%) non-relapsed cases. Multivariate logistic regression analysis revealed that Beijing genotype was significantly associated with tuberculosis relapse (OR 2.64, 95% CI 1.30-5.34, P=0.005).     

Beijing/W genotype Mycobacterium tuberculosis and drug resistance

Beijing/W genotype Mycobacterium tuberculosis is widespread, may be increasing, and may have a predilection for drug resistance. Individual-level data on >29,000 patients from 49 studies in 35 countries were combined to assess the Beijing genotype's prevalence worldwide, trends over time and with age, and associations with drug resistance. We found 4 patterns for Beijing/W genotype tuberculosis (TB): 1) endemic, not associated with drug resistance (high level in most of East Asia, lower level in parts of the United States); 2) epidemic, associated with drug resistance (high level in Cuba, the former Soviet Union, Vietnam, and South Africa, lower level in parts of Western Europe); 3) epidemic but drug sensitive (Malawi, Argentina); and 4) very low level or absent (parts of Europe, Africa). This study confirms that Beijing/W genotype TB is an emerging pathogen in several areas and a predominant endemic strain in others; it is frequently associated with drug resistance.     

天津市北京基因型结核分枝杆菌流行特征及与耐药表型关系研究

目的 了解北京基因型结核分枝杆菌在天津市人群中的分布、流行特征及其与耐药表型的关系.方法 收集2008年1月至2009年6月天津市结核病控制中心和10个区(县)结核病防治机构肺结核患者中初次分离培养的结核分枝杆菌656株及患者管理信息、临床信息和实验室信息.菌株对利福平、异烟肼、链霉素和乙胺丁醇的药物敏感性试验采用比例...     

Genetic geography of Mycobacterium tuberculosis Beijing genotype: A multifacet mirror of human history?

The Beijing genotype of Mycobacterium tuberculosis has been shown in many settings to be hypervirulent and associated with multi-drug resistance. Its presently global and rapid dissemination makes it an important issue of public health. Here, I present a significantly enlarged update of the MIRU-VNTR global database of the M. tuberculosis Beijing genotype (11 loci). I further attempted to link the observed mycobacterial diversity with relevant events of the known human history. Large water masses have been the most efficient and drastic generators of the genetic divergence between human populations. The same situation appears true also for M. tuberculosis, which general diversity pattern amazingly resembles that of its human host. At the same time, less expected affinities observed between distant populations of M. tuberculosis may reflect hidden patterns of human migrations or yet unknown epidemiological links between distant regions.     

Penitentiary population of Mycobacterium tuberculosis in Kyrgyzstan: Exceptionally high prevalence of the Beijing genotype and its Russia-specific subtype

Here, we present results of the first study of the Mycobacterium tuberculosis genotypes circulating in Kyrgyzstan. We focused on the incarcerated population known to be at high-risk for tuberculosis (TB) and with a significant impact on TB incidence in the general population. Beijing genotype was detected in 42 of 56 M. tuberculosis sputum-extracted DNA samples from newly-diagnosed adult pulmonary TB patients. RIF and INH resistance was genotypically detected in 28% and 55% samples; 13 of 15 MDR strains belonged to Beijing genotype. 12-locus MIRU-VNTR typing showed 8 of 56 samples to be mixed cases; 7 of them contained a Beijing strain. MIRU analysis demonstrated a high homogeneity of the studied collection (HGI = 0.66) while 28 of 56 strains had a profile 223325153533 corresponding to Beijing/M2 subtype highly prevalent in different Russian settings. Three hypervariable loci, QUB-3232, VNTR-3820 and VNTR-4120, permitted to further subdivide 28 Beijing/M2 strains into 11 subtypes shared by 1 to 9 strains. To conclude, all markers taken together, the penitentiary population of M. tuberculosis in Kyrgyzstan exhibited a strong genetic affinity to Russia and a weak relatedness to East Asia.     

Drug susceptibility of Mycobacterium tuberculosis Beijing genotype and association with MDR TB

To determine differences in the ability of Mycobacterium tuberculosis strains to withstand antituberculosis drug treatment, we compared the activity of antituberculosis drugs against susceptible Beijing and East-African/Indian genotype M. tuberculosis strains. Beijing genotype strains showed high rates of mutation within a wide range of drug concentrations, possibly explaining this genotype's association with multidrug-resistant tuberculosis.     

宜昌地区结核分枝杆菌北京基因型菌株的鉴定及VNTR分型

 目的 研究宜昌地区结核分枝杆菌北京基因型菌株的多态性和流行特征,揭示该地区结核病的分子流行病学特征,为结核病防治提供科学依据。方法 选择2018年1月-2019年12月具有完整病例信息的结核分枝杆菌298株,进行人型结核分枝杆菌的鉴定,用扩增RD105缺失片段的多重PCR (DTM-PCR)鉴定北京基因型菌株;应用优化的9位点数目可变串联重复序列技术(VNTR)分析北京基因型菌株的多态性。结果 298株结核分枝杆菌中,260株为人型结核分枝杆菌,DTM-PCR鉴定发现北京基因型菌株140株(53.85%),非北京基因型菌株120株(46.15%)。北京基因型菌株耐药率(32.14%)高于非北京基因型菌株耐药率(10.83%),差异有统计学意义(P<0.05)。VNTR-9位点对北京基因型菌株的分辨率为0.998 5,成簇率为12.15%。结论 北京基因型菌株在宜昌地区呈较高流行趋势,且北京基因型菌株耐药率更高。VNTR-9位点基因分型方法用于该地区结核分枝杆菌北京基因型菌株的鉴别,能准确反映宜昌地区结核分枝杆菌的分子流行病学特征。     

Mycobacterium tuberculosis Beijing genotype and risk for treatment failure and relapse, Vietnam

Among 2,901 new smear-positive tuberculosis cases in Ho Chi Minh City, Vietnam, 40 cases of treatment failure and 39 relapsing cases were diagnosed. All initial and follow-up Mycobacterium tuberculosis isolates of these case-patients had (nearly) identical restriction fragment length polymorphism patterns, and the Beijing genotype was a significant risk factor for treatment failure and relapse (odds ratio 2.8, 95% confidence interval 1.5 to 5.2).     

Seventy percent of the Mycobacterium tuberculosis isolates in Hong Kong represent the Beijing genotype

We used spoligotyping to study 500 randomly selected pretreatment Mycobacterium tuberculosis (MTB) strains isolated in Hong Kong during the 2 year period 1998-9. It was found that amongst all MTB strains studied, the 'Beijing' genotype strains were highly prevalent in our geographic area, representing about 70% of the isolates. Unlike previous observations in Vietnam, no significant associations were found either between 'Beijing' genotype strains and all other anti-tuberculosis drug resistance phenotypes, or with particular patients' age groups, except for a weak association with isoniazid susceptibility. Eighteen of these strains exhibited spoligotype patterns that were similar but not identical to the 'Beijing' specific pattern. This is the first geographical area where genetic diversity among 'Beijing' genotype of MTB strains has been observed on this scale.     

Beijing clades of Mycobacterium tuberculosis are associated with differential survival in HIV-negative Russian patients

We conducted a prospective study to establish factors associated with survival in tuberculosis patients in Russia including social, clinical and pathogen-related genetic parameters. Specifically we wished to determine whether different strains/clades of the Beijing lineage exerted a differential effect of survival.HIV-negative culture-confirmed cases were recruited during 2008–2010 across Samara Oblast and censored in December 2011. Molecular characterization was performed by a combination of spoligotyping, multilocus VNTR typing and whole genome sequencing (WGS).We analyzed 2602 strains and detected a high prevalence of Beijing family (n = 1933; 74%) represented largely by two highly homogenous dominant clades A (n = 794) and B (n = 402) and non-A/non-B (n = 737). Multivariable analysis of 1366 patients with full clinical and genotyping data showed that multi- and extensive drug resistance (HR = 1.86; 95%CI: 1.52, 2.28 and HR = 2.19; 95%CI: 1.55, 3.11) had the largest impact on survival. In addition older age, extensive lung damage, shortness of breath, treatment in the past and alcohol abuse reduced survival time.After adjustment for clinical and demographic predictors there was evidence that clades A and B combined were associated with poorer survival than other Beijing strains (HR = 0.48; 95%CI 0.34, 0.67). All other pathogen-related factors (polymorphisms in genes plcA, plcB, plcC, lipR, dosT and pks15/1) had no effect on survival.In conclusion, drug resistance exerted the greatest effect on survival of TB patients. Nevertheless we provide evidence for the independent biological effect on survival of different Beijing family strains even within the same defined geographical population. Better understanding of the role of different strain factors in active disease and their influence on outcome is essential.     

绵阳地区结核分支杆菌北京基因型菌株的鉴定和感染因素分析

目的鉴定MTB北京基因型,了解北京基因型菌株在绵阳地区的分布特征,为本地结核病的防治和分子流行病学研究提供科学依据。方法随机选取绵阳涪城和江油两个区县的结核分支杆菌临床分离菌株,收集患者流行病学资料。菌株常规培养,收集菌体,提取基因组DNA,采用RD105缺失基因检测法鉴定北京基因型菌株。药物敏感性试验采用比例法。率的比较采用χ2检验。结果共对79株结核分支杆菌了进行北京基因型鉴定,北京基因型菌株33株,占41.77%;非北京基因型菌株46株,占58.23%。北京基因型菌株耐药率(36.36%)明显高于非北京基因型菌株耐药率(10.87%),差异有统计学意义(χ2=7.395,P=0.007)。患者性别、年龄组、所在地区和治疗史与感染北京基因型菌株无关。结论北京基因型菌株在绵阳地区呈一般流行趋势。北京基因型菌株感染与耐药相关,与患者性别、年龄、所在地区和治疗史无关。     

河南省结核分枝杆菌北京家族基因型及耐药分析

目的了解河南省结核分枝杆菌北京家族基因型的分布、流行特点、与耐药性的相关性。方法 2009年6月-2010年11月在河南省尉氏县结核病防治机构实验室分离培养的165株结核分枝杆菌,采用比例法进行药物敏感性检测,应用RD 105缺失基因检测法和琼脂糖凝胶电泳技术进行北京家族基因型鉴定。结果 164株结核分枝杆菌对4种一线抗结核药物,异烟肼(IN H)、利福平(RFP)、链霉素(SM)和乙胺丁醇(EMB)药敏情况:全部敏感的菌株为126株(76.8%);任意耐药菌株38株(23.2%),其中,单耐药菌株14株(8.5%),多耐药菌株24株(14.6%);结核分支杆菌对4种一线药的耐药率依次为:INH 16.5%(27/164)、SM 15.9%(26/164)、RFP 9.1%(15/164)、EMB 7.3%(12/164)。164株结核分枝杆菌中,北京家族基因型(Beijing fam ily)占89.6%(147/164),17株为非北京家族基因型,占10.4%;147株北京家族基因型菌株中,全部敏感的菌株为111株(75.5%);耐任一种药菌株36株(24.5%),其中耐多药(MDR)菌株13株(8.8%...     

High-resolution MIRU-VNTRs typing reveals the unique nature of Mycobacterium tuberculosis Beijing genotype in Okinawa,Japan

Mycobacterium tuberculosis Beijing lineage is highly prevalent in Japan. The aim of the present study was to describe the population structure of the Beijing lineage in this country based on 12-, 15-, and 21-loci MIRU-VNTR genotyping schemes. The MIRU-VNTR patterns of Beijing strains from Okinawa, Ryukyu Islands were compared to those recently published from the Osaka-Kobe megalopolis of the main island of Japan, Honshu (Wada et al., 2009). We also compared proportions of “modern/typical” vs. “ancient/atypical” Beijing strains as defined by structure of the NTF locus. Contrarily to the 12-loci Minimum Spanning Tree (MST), the 15- and 21-loci trees allowed the distinction of two groups of strains in Okinawa. A 12-loci MIRU-VNTR pattern (223325173533) corresponding to MIRU international type MIT17 was identified as the most prevalent Beijing genotype in Japan. In the SITVIT2 database, this pattern was found to be disseminated worldwide and corresponded to the most widely distributed Beijing profile in East Asia and former USSR countries. A comparison of 15- and 21-loci MIRU-VNTR patterns showed that two loci (QUB-4156 and Mtub21) were most polymorphic in our study, and could be potential candidates to distinguish between NTF locus based subclassification of Beijing strains. High-resolution VNTR typing using 15- and 21-loci underlined an evolutionarily distinct “ancient/atypical” subpopulation of the Beijing genotype in Okinawa as well as a subgroup of strains closely related to “modern/typical” Beijing strains observed in Osaka/Kobe.     

唐山市人群结核分枝杆菌基因型分析

目的初步探讨唐山市结核分枝杆菌基因型特征。方法选取结核分枝杆菌基因组中的10个数目可变串联重复序列(variable number of tandem repeats,VNTRs)位点,利用聚合酶链式反应(polymerase chain reaction,PCR)、琼脂糖凝胶电泳技术和BioNumerics(Version 3.0)软件,对从2012年唐山市结核病医院确诊的肺结核患者痰液中分离培养获得的结核分枝杆菌进行基因分型。结果 125株结核分枝杆菌具有明显的多态性,共分成5个不同的基因群,最大的一个群包含87株,占69.6%,其他型别呈散在分布。结论唐山市结核分枝杆菌的基因型具有明显的多态性,且具有成簇性分布的特点。     

Improved differentiation of Mycobacterium tuberculosis strains, including many Beijing genotype strains, using a new combination of variable number of tandem repeats loci.

Variable number of tandem repeats (VNTR) typing was done on 230 Mycobacterium tuberculosis strains, including 41 strains isolated from 17 groups of epidemiologically linked patients. By PCR amplification, 185 (80.4%) of the 230 strains were Beijing genotype strains. VNTR typing was performed using the 15 loci proposed as a standard set by Supply et al. [Supply, P., Allix, C., Lesjean, S., Cardoso-Oelemann, M., Rusch-Gerdes, S., Willery, E., Savine, E., de Haas, P., van Deutekom, H., Roring, S., Bifani, P., Kurepina, N., Kreiswirth, B., Sola, C., Rastogi, N., Vatin, V., Gutierrez, M.C., Fauville, M., Niemann, S., Skuce, R., Kremer, K., Locht, C., van Soolingen, D., 2006. Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J. Clin. Microbiol. 44, 4498-4510], and cluster analyses of these data were done. By the VNTR typing with the proposed 15 loci, strains having low similarity values by restriction fragment length polymorphism (RFLP) analysis were clustered. Use of a supplemental9 loci, proposed as a high-resolution tool, with the 15 loci showed that strains with low similarity by RFLP analysis were still clustered. Twelve VNTR loci were selected based on previously reported discriminatory index (DI) values and used with the proposed 15 loci for better differentiation by VNTR typing. When eight loci with higher DI values were used with the 15 loci, there were no clusters, including strains with low RFLP similarity. The15 loci and eight additional loci decreased the numbers of clustered strains isolated from epidemiologically unlinked patients significantly compared to using only the 15 loci. Among all tested loci, obvious differences of DI values were observed for 8 loci (miru10, miru16, miru39, Mtub29, Mtub30, QUB11a, QUB26, and QUB1895) of RD105 lineage strains compared to those of other lineage strains. These results suggest that the proposed VNTR typing method cannot be used as a routine epidemiological tool in areas where Beijing genotype strains are prevalent. Several VNTR loci should be added to the proposed method based on differences in polymorphism of VNTR loci among Beijing genotype lineages.     

间隔区寡核苷酸分型和多位点可变数量串联重复序列分析在结核分枝杆菌基因分型中的应用

目的评价间隔区寡核苷酸分型(Spoligotyping)及多位点可变数量串联重复序列分析(MLVA)方法在结核分枝杆菌基因分型研究中的应用。方法收集224株结核分枝杆菌临床分离株,分别采用Spoligotyping及MLVA方法进行基因分型,比较两种方法的分型效果,评价两种方法在结核分枝杆菌基因分型中的应用。结果使用Spoligotyping方法,224株结核分枝杆菌呈现出55种基因型,39株具有独特的基因型,其余185株菌呈现出16种基因型;使用MLVA方法时,224株结核分枝杆菌呈现出160种基因型,132株具有独特的基因型,余下的92株菌呈现出28种基因型;当两种方法联合使用时,224株结核分枝杆菌呈现出179种基因型,159株结核分枝杆菌具有独特的基因型,余下的65株菌表现为20种基因型。湖南省和安徽省的菌株中北京家族菌株所占的比例差异有统计学意义(P<0.001),安徽省北京家族菌株所占的比例明显高于湖南省。结论MLVA在结核分枝杆菌株水平的鉴定方面,其分辨能力高于Spoligotyping,但是Spoligotyping在鉴定北京家族菌株和M.bovis方面有一定的优势。将Spoligotyping方法作为一线分型技术,MLVA作为二线分型技术联合应用时,将提高结核病的流行病学调查和病原学监测效果。不同地区的菌株有不同的特点。