Multidrug-resistant tuberculosis, People's Republic of China, 2007-2009

We conducted a case-control study to investigate risk factors for multidrug-resistant tuberculosis (MDR TB) in the People's Republic of China. Genotyping analysis was used to estimate the percentage of cases from recent transmission among 100 MDR TB case-patients hospitalized during April 2007-July 2009. Molecular subtyping of isolates showed that 41% of MDR TB strains clustered. Beijing genotype was found in 94% of the MDR TB isolates and 79% of the pan-susceptible isolates. In multivariate analysis, MDR TB was independently associated with Beijing genotype, retreatment for TB, symptoms lasting >3 months before first evaluation at the hospital, lack of health insurance, and being a farmer (vs. being a student). MDR TB was associated with Beijing genotype and lower socioeconomic status. A large percentage of MDR TB cases seemed to result from recent transmission. Early detection, effective treatment, and infection control measures for MDR TB are needed to reduce transmission.     

'Lethal' combination of Mycobacterium tuberculosis Beijing genotype and human CD209 -336G allele in Russian male population

An interaction of different human alleles and endemic bacterial strains may be clinically manifested as different outcome of the disease in different hosts infected with the same genotype. The primary objective of this study was to investigate this issue in the model of Mycobacterium tuberculosis and human DC-SIGN encoding CD209 promoter SNP (rs4804803) in Russian Siberian population. We sought to find a possible combination of M. tuberculosis lineage and human host allele/genotype correlating with unfavorable outcome of the disease. The 101 paired DNA samples from patients with pulmonary TB (human and M. tuberculosis DNA) were studied by 12-loci MIRU-VNTR typing (M. tuberculosis strains) and CD209 -336 A/G typing (human DNA). Ninety autopsy DNA samples as a source of human and mycobacterial nucleic acids from persons who died from TB were also subjected to the same genotyping procedures. A human control group consisted of 177 healthy individuals. The Beijing genotype was more frequently identified in autopsy versus patient samples, in 70.0% and 51.5%, respectively (χ(2)=6.06, P=0.01). Regarding other M. tuberculosis genetic families, no significant difference in LAM family distribution among patient strains and autopsy samples has been found. In contrast, Ural genotype was significantly less frequently detected in the autopsy samples (χ(2)=6.12, P=0.01). Allelic and genotypic frequencies of the CD209 -336A/G did not differ significantly under global comparison when contrasting controls versus patients versus autopsy samples. However intriguing and contrasting significant associations were found in the male subgroup under M. tuberculosis genotype-stratified comparisons. Firstly, male carriers of -336AA genotype were more frequently infected with Beijing genotype (χ(2)=5.2, P=0.02). Secondly and remarkably, this association was inverted in the autopsy sample: male carriers of -336AA genotype died less frequently due to TB caused by a Beijing rather than a non-Beijing strain (χ(2)=5.37, P=0.02). In conclusion, we hypothesize that although carriers of CD209 -336A allele are more sensitive to infection with a Beijing strain, a combination of human CD209 -336G allele and M. tuberculosis Beijing genotype leads more frequently to the lethal outcome in pulmonary TB male patients in Russian (Caucasian) population.     

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.     

Clusters of Multidrug-Resistant Mycobacterium tuberculosis Cases, Europe

Molecular surveillance of multidrug-resistant tuberculosis (MDR TB) was implemented in Europe as case reporting in 2005. For all new MDR TB cases detected from January 2003 through June 2007, countries reported case-based epidemiologic data and DNA fingerprint patterns of MDR TB strains when available. International clusters were detected and analyzed. From 2003 through mid-2007 in Europe, 2,494 cases of MDR TB were reported from 24 European countries. Epidemiologic and molecular data were linked for 593 (39%) cases, and 672 insertion sequence 6110 DNA fingerprint patterns were reported from 19 countries. Of these patterns, 288 (43%) belonged to 18 European clusters; 7 clusters (242/288 cases, 84%) were characterized by strains of the Beijing genotype family, including the largest cluster (175/288 cases, 61%). Both clustering and the Beijing genotype were associated with strains originating in eastern European countries. Molecular cluster detection contributes to identification of transmission profile, risk factors, and control measures.     

RD105基因缺失法鉴定95株结核分枝杆菌北京基因型及其耐药相关性分析

目的鉴定吉林省结核分枝杆菌(MTB)中的北京基因型及其与耐药性的关联。方法 95株结核分枝杆菌分离自2008-2009年吉林省临床肺结核病人的痰液标本,培养方法为改良酸性罗氏(L-J)培养基。分离出的抗酸杆菌经对硝基苯甲酸(PNB)培养基初步鉴定后选出结核分枝杆菌复合群并应用比例法进行药敏试验(DST)。北京基因型的鉴定采用RD105基因缺失法。实验结果应用Epi Info统计软件和卡方检验进行分析。结果 95株结核分枝杆菌中,北京基因型占88.4%(84/95)。北京基因型中,异烟肼、利福平、乙胺丁醇、链霉素、卡那霉素和氧氟沙星的耐药率分别为31.7%、23.2%、15.9%、31.7%、13.4%和18.3%,均位于非北京基因型菌株耐药率的95%置信区间内。北京基因型中的多重耐药(MDR)结核(TB)率占19.5%,通过卡方检验与非北京基因型中的MDRMTB进行比较,差异无统计学意义(P>0.05)。结论 RD105基因缺失法是鉴定MTB北京基因型的简便、有效方法;北京基因型为吉林省结核分枝杆菌的优势株;北京基因型与非北京基因型耐药率无统计学意义上的差别。     

北京市昌平地区2011-2015年结核分枝杆菌的流行特征

目的 了解昌平地区结核分枝杆菌不同基因型流行特征,以及不同基因型和耐药性的关系,探讨基因分型用于评价本地区结核病控制中的应用价值。方法 选取北京市昌平区2011-2015年所有培养阳性结核分枝杆菌1 099株,采用Spoligotyping和Gao等推荐的12位点VNTR进行基因分型,同时检测上述菌株对利福平、异烟肼、乙胺丁醇、链霉素、阿米卡星和氧氟沙星的耐药性。结果 2011-2015年,昌平地区结核对氧氟沙星耐药率提高（2.9%比8.9%,P=0.01）。在所有菌株中,北京基因型菌株总计976株,占88.8%,非北京基因型菌株总计123株,占11.2%,其中北京基因型菌株中还包括189株（17.2%）古代北京基因型和787株（71.6%）现代北京基因型。北京基因型所占比例在5年期间无显著性变化,从2011年的81.1%到2015年的82.0%。采用VNTR基因分型后,仅有2株菌成簇,成簇率为0.1%。北京基因型对阿米卡星的耐药率（1.7%）低于非北京基因型（4.9%,P=0.02）;而古代北京基因型对链霉素耐药率（28.0%）高于现代北京基因型（15.7%,P=0.01）。结论 近5年来,昌平地区结核对氧氟沙星耐药率提高。北京基因型所占比例在5年期间无明显变化,且菌株成簇率较低,提示近期传播率低。     

多位点可变串联重复序列技术用于西藏地区结核分枝杆菌基因分型的初步研究

目的初步探讨多位点数目可变串联重复序列(MLVA)技术在西藏地区结核分枝杆菌基因分型中的应用和初步了解西藏地区结核分枝杆菌数目可变串联重复序列(VNTR)基因型种类及其分布。方法在拉萨、山南、林芝、日喀则、那曲、昌都6个地区结核病防治中心收集结核分枝杆菌临床分离菌株,设计引物,采用PCR和琼脂糖凝胶电泳技术对结核分枝杆菌20个VNTR位点进行检测,并通过BioNumerics 4.5软件进行DNA指纹图谱多态性分析。结果共收集到217株结核分枝杆菌,分为19个不同的VNTR基因型,其中以Ⅺ型为主要基因型占87.6%(属于北京家族),其次Ⅵ型、ⅩⅤ型、ⅩⅥ型各占1.38%,Ⅰ型、Ⅶ型、ⅩⅢ型各占0.92%,12株结核分枝杆菌为单一的基因型。不同地区之间,以Ⅺ型为主要基因型,分别占各地区的86.8%、91.3%、78.95%、88.2%、95.05、89.3%。结论西藏地区的结核分枝杆菌存在明显的基因多态性,主要流行型为VNTRⅪ型(即北京家族基因型),初步研究结果显示北京家族基因型与卡介苗接种和耐药性无相关性。MLVA分型方法简单、快速,可以有效地用于结核分枝杆菌的基因分型和病原监测。     

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.     

Multidrug-resistant tuberculosis in prison inmates, Azerbaijan.

In a tuberculosis (TB) program in the Central Penitentiary Hospital of Azerbaijan, we analyzed 65 isolates of Mycobacterium tuberculosis by IS6110-based restriction fragment-length polymorphism (RFLP) and spoligotyping. From 11 clusters associated with 33 patients, 31 isolates had an IS6110-based banding pattern characteristic of the Beijing genotype of M. tuberculosis. In addition, 15 M. tuberculosis isolates with similar RFLP patterns constituted a single group by spoligotyping, matching the Beijing genotype. Multidrug resistance, always involving isoniazid and rifampin, was seen in 34 (52.3%) of 65 isolates, with 28 belonging to the Beijing genotype.     

Molecular epidemiology and drug-resistance of tuberculosis in Luodian revealed by whole genome sequencing

In this study, we aimed to investigate the molecular epidemiology and drug-resistance profiles of tuberculosis (TB) in Luodian, an area with highest TB incidence and limited healthcare resources in Guizhou, China. The passive case finding strategy was used to identify suspected pulmonary TB with symptoms, and individuals with positive Mycobacterium tuberculosis (MTB) culture were enrolled from May 22, 2018 to April 21, 2019. All the 107 cases except three came from nine towns, including 55.1% from Longping and Bianyang. The phylogeny tree showed that 53.3% of strains were Lineage 2 (Beijing genotype), while 46.7% were Lineage 4 (Euro-American genotype). Among Lineage 2 strains, 66.7% were of “modern” Beijing type. Seven clusters with genomic distance within 12 SNPs were identified. The clusters included 14 strains, accounting for a clustering rate of 13.1%. The distance separating the clustered cases was between 2.1 and 71.0 km (Km), with an average paired distance of 21.8 Km (interquartile range, 2.8–38.0 Km). Based on the gene mutations associated with drug-resistance, we predicted that 4.8% of strains were resistant to isoniazid, 3.7% to rifampicin, and 3.7% to streptomycin; only one strain (0.9%) had multidrug resistance (MDR). This study found low drug-resistance rates in Luodian, and the sub-lineage of the “modern” Beijing branch has recent expansion in Luodian. This work may also serve as a genomic baseline to assess the evolution and spread of MTB in Guizhou.     

Molecular typing and drug susceptibility of Mycobacterium tuberculosis isolates from Chongqing Municipality,China

China’s tuberculosis (TB) burden is second only to that of India worldwide. In Chongqing, the largest municipality in southwestern China, although the prevalence of both TB and drug-resistant TB is higher than in other municipalities, the molecular characteristics and drug susceptibility phenotypes are poorly known. In this study, 297 Mycobacterium tuberculosis isolates from Chongqing were genotyped with spacer oligonucleotide typing (spoligotyping) and 28-locus MIRU-VNTR (24-locus MIRU-VNTR scheme and 4 other loci). Spoligotyping results were compared with drug-resistant profiles. Patients who showed clustering by both spoligotyping and 28-locus MIRU-VNTR were interviewed to investigate their detailed contact history. Our data demonstrated that the Beijing genotype was the most prevalent genotype, and ST1 was the most predominant lineage in Chongqing. The Beijing genotype was significantly associated with ethambutol resistance and multidrug-resistant phenotypes. A combination of the 10 most polymorphic loci permitted to achieve higher discriminatory power than 24-VNTR. In addition, a presumed transmission pathway was observed in a cluster of patients with the same MIRU-VNTR profile. The 10-VNTR locus set is suitable for genotyping of Mycobacterium tuberculosis in Chongqing.     

Genotypic diversity of multidrug-, quinolone- and extensively drug-resistant Mycobacterium tuberculosis isolates in Thailand

Drug-resistant tuberculosis (TB), which includes multidrug-resistant (MDR-TB), quinolone-resistant (QR-TB) and extensively drug-resistant tuberculosis (XDR-TB), is a serious threat to TB control. We aimed to characterize the genotypic diversity of drug-resistant TB clinical isolates collected in Thailand to establish whether the emergence of drug-resistant TB is attributable to transmitted resistance or acquired resistance. We constructed the first molecular phylogeny of MDR-TB (n = 95), QR-TB (n = 69) and XDR-TB (n = 28) in Thailand based on spoligotyping and proposed 24-locus multilocus variable-number of tandem repeat analysis (MLVA). Clustering analysis was performed using the unweighted pair group method with arithmetic mean. Spoligotyping identified the Beijing strain (SIT1) as the most predominant genotype (n = 139; 72.4%). The discriminatory power of 0.9235 Hunter–Gaston Discriminatory Index (HGDI) with the 15-locus variable-number tandem repeats of mycobacterial interspersed repetitive units typing was improved to a 0.9574 HGDI with proposed 24-locus MLVA, thereby resulting in the subdivision of a large cluster of Beijing strains (SIT1) into 17 subclusters. We identified the spread of drug-resistant TB clones caused by three different MLVA types in the Beijing strain (SIT1) and a specific clone of XDR-TB caused by a rare genotype, the Manu-ancestor strain (SIT523). Overall, 49.5% of all isolates were clustered. These findings suggest that a remarkable transmission of drug-resistant TB occurred in Thailand. The remaining 50% of drug-resistant TB isolates were unique genotypes, which may have arisen from the individual acquisition of drug resistance. Our results suggest that transmitted and acquired resistance have played an equal role in the emergence of drug-resistant TB. Further characterization of whole genome sequences of clonal strains could help to elucidate the mycobacterial genetic factors relevant for drug resistance, transmissibility and virulence.     

Genetic biodiversity of Mycobacterium tuberculosis isolates from patients with pulmonary tuberculosis in India.

Spoligotyping was performed on 540 Mycobacterium tuberculosis isolates in order to evaluate the genetic biodiversity of tubercle bacilli in India. One hundred and forty seven patterns were unique and 393 were grouped in 48 clusters. Comparison with an international spoligotype database showed that the most predominant clades among tuberculosis (TB) isolates were Central Asian (CAS) and East-African Indian (EAI) with shared-types (ST) ST26 and ST11 alone being responsible for 34% of all TB cases. Twenty one (3.8%) isolates belonged to the Beijing genotype. Marked variations were observed among circulating strains, STs belonging to CAS family predominated in the North, whereas the EAI family was more common in the Southern India. TB in India is predominantly caused by strains belonging to the principal genetic group 1 (PGG1), suggesting that most of the TB burden in India may be traced to ancestral clones of the tubercle bacilli. This study gives an insight into the global M. tuberculosis genetic biodiversity in India, the predominant spoligotypes and their impact on disease transmission.     

2006～2008年北京市怀柔区结核病药物耐药性监测

目的了解北京市怀柔区结核病药物耐药情况,评估怀柔区结核病防治效果,为制定新的怀柔区结核病防治规划(2010～2015)提供依据。方法对怀柔区结核病防治所2006年1月1日～2008年12年31日登记的该辖区初治菌阳肺结核患者结核分枝杆菌复合群进行分离培养,培养出的菌株全部送北京市结核病控制研究所实验室进行异烟肼(H)、利福平(R)、链霉素(S)、乙胺丁醇(E)耐药性检测。结果该辖区129例初治菌阳病例为此次入选病例,初始敏感菌株113例,初始敏感菌株率为87.6%,耐药菌株22例,初始耐药率12.4%,耐多药(MDR)7例,初始耐多药率为5.4%,以上两种耐药率均低于北京市及全国平均水平[1-2]。结论由于怀柔区30年来采取的现代结核病控制策略(DOTS),使肺结核病人得到有效的规律治疗,避免乱用药现象,减少了初始耐药病例的产生,为今后更有效地控制结核病流行打下了良好的基础,并为制定新的怀柔区结核病规划提供了科学的依据。     

中国各地区结核病防治人力资源现状与工作关系分析

目的:分析各地区结核病防治人力资源数量及构成与结核病防治工作的关系,为结核病防治规划人力资源的配备及制定培训计划提供依据。方法:按照经济条件和地域分布把各省、自治区、直辖市分为东部、中部、西部和京津沪地区及按照结核病防治负担分出12个高负担省。分析各地结核病防治人员数量、人员构成与各地病人发现、治疗管理工作的关系。结果:至2003年底全国有专职结核病防治人员25 887人,兼职7 822人。专职人员本科及以上学历占9.2%;从事临床、放射、检验专职结核病人治疗管理人员17 339人,占51.4%;有中、高级职称人员占专职结防人员36.8%。计算各地区结核病防治人员与人口的比值及结核病防治人员与活动结核病人的比值发现:京津沪地区拥有的结核病防治人员最多;结核病防治高负担省最低。学历分布,以京津沪地区最高,西部地区最低。各地区病人诊断率,京津沪地区最高,高负担省最低。结论:在结核病的预防控制工作中,人力资源是一种极为重要的特殊资源,能支配、推动和利用其它资源,人力资源的状况直接影响各地结核病防治工作的质量。     

北京市2008-2018年肺结核时空分布及影响因素分析

目的 分析2008-2018年北京市肺结核报告发病率的时空分布特征及影响因素。方法 肺结核病例数据来源于2008-2018年中国疾病预防控制信息系统结核病信息管理系统,采用ArcGIS 10.2软件可视化肺结核发病率的时空分布;街道/乡镇尺度上分析（Getis''s G_i^*统计量）发病率的空间聚集性;贝叶斯时空模型分析影响其时空分布的因素包括城市化率、人均GDP、每千人口医院床位数、常住外来人口和人口密度。结果 2008-2018年北京市肺结核报告发病率呈下降趋势,从58.64/10万下降到30.43/10万。通州区、昌平区等城市发展新区的发病率较高,热点集中在其局部地区;东城区、西城区等功能核心及拓展区的发病率较低,冷点也集中在该区域。肺结核发病风险与城市化率和常住外来人口相关,其中,城市化率每增加1%,患肺结核的RR值也会增加1%;常住外来人口每增加1万人,患肺结核的RR值会增加0.6%。结论 北京市肺结核的防控重点区域需关注城市发展新区;城市化进程加快的同时,需加强常住外来人口中的结核病防控,以期降低当地结核病发病率。     

Genotypes of Mycobacterium tuberculosis in patients at risk of drug resistance in Bolivia

Bolivia ranks among the 10 Latin American countries with the highest rates of tuberculosis (TB) and multidrug resistant (MDR) TB. In view of this, and of the lacking information on the population structure of Mycobacterium tuberculosis in the country, we explored genotype associations with drug resistance and clustering by analyzing isolates collected in 2010 from 100 consecutive TB patients at risk of drug resistance in seven of the nine departments in which Bolivia is divided. Fourteen isolates were MDR, 29 had other drug resistance profiles, and 57 were pansusceptible. Spoligotype family distribution was: Haarlem 39.4%, LAM 26.3%, T 22.2%, S 2.0%, X 1.0%, orphan 9.1%, with very low intra-family diversity and absence of Beijing genotypes. We found 66 different MIRU-VNTR patterns; the most frequent corresponded to Multiple Locus Variable Analysis (MLVA) MtbC15 patterns 860, 372 and 873. Twelve clusters, each with identical MIRU-VNTR and spoligotypes, gathered 35 patients. We found no association of genotype with drug resistant or MDR-TB. Clustering associated with SIT 50 and the H3 subfamily to which it belongs (p < 0.0001). The largest cluster involved isolates from three departments and displayed a genotype (SIT 50/MLVA 860) previously identified in Bolivian migrants into Spain and Argentina suggesting that this genotype is widespread among Bolivian patients. Our study presents a first overview of M. tuberculosis genotypes at risk of drug resistance circulating in Bolivia. However, results should be taken cautiously because the sample is small and includes a particular subset of M. tuberculosis population.     

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。     

北京地区居民肺结核防治知识知晓率现状调查

目的了解北京地区居民肺结核防治知识的知晓率,为进一步有针对性地开展肺结核防控知识宣传工作提供依据。方法采用随机抽样的方法选取北京地区部分居民进行问卷调查,问卷内容以《2006年全国公众结核病防治知识信念行为调查问卷》为主,同时增加肺结核防治知识核心信息和疑似肺结核症状相关问题。结果共收集居民调查问卷520份,其中合格问卷503份,有效率为96.73%。调查对象中,5条肺结核防治知识核心信息总知晓率为40.87%,78.93%知道肺结核是一种严重危害人们健康的慢性呼吸道传染病,48.51%知道只要坚持正规治疗,绝大多数肺结核患者是可以治愈的,仅19.68%知道在县(区)级结核病防治机构检查和治疗肺结核可享受国家免费政策。可以识别4种及以上肺结核疑似症状的居民占53.48%,能全部识别出8种症状的居民仅占7.36%。结论北京市居民肺结核防治知识的知晓率水平相对较低。患者在罹患肺结核的早期若不能够识别症状,不仅延误治疗,增加开放性肺结核传播概率,甚至诱导多耐药结核分枝杆菌的产生,给肺结核防治工作带来更多挑战。     

Predominance of modern Mycobacterium tuberculosis strains and active transmission of Beijing sublineage in Jayapura,Indonesia Papua

Mycobacterium tuberculosis genotype distribution is different between West and Central Indonesia, but there are no data on the most Eastern part, Papua. We aimed to identify the predominant genotypes of M. tuberculosis responsible for tuberculosis in coastal Papua, their transmission, and the association with patient characteristics. A total of 199 M. tuberculosis isolates were collected. Spoligotyping was applied to describe the population structure of M. tuberculosis, lineage identification was performed using a combination of lineage-specific markers, and genotypic clusters were identified using a combination of 24-locus-MIRU-VNTR and spoligotyping. A high degree of genetic diversity was observed among isolates based on their spoligopatterns. Strains from modern lineage 4 made up almost half of strains (46.9%), being more abundant than the ancient lineage 1 (33.7%), and modern lineage 2 (19.4%). Thirty-five percent of strains belonged to genotypic clusters, especially strains in the Beijing genotype. Previous TB treatment and mutations associated with drug resistance were more common in patients infected with strains of the Beijing genotype. Papua shows a different distribution of M. tuberculosis genotypes compared to other parts of Indonesia. Clustering and drug resistance of modern strains recently introduced to Papua may contribute to the high tuberculosis burden in this region.