Genotypic drug resistance using whole-genome sequencing of Mycobacterium tuberculosis clinical isolates from North-western Tanzania
Genotypic drug resistance using whole-genome sequencing of Mycobacterium tuberculosis clinical isolates from North-western Tanzania
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DOI：
10.1016/j.tube.2018.02.004
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发表时间：
2018-03-01
期刊：
影响因子：
3.2
通讯作者：
Ocheretina, Oksana
中科院分区：
文献类型：
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作者：
Kidenya, Benson R.;Mshana, Stephen E.;Ocheretina, Oksana
背景：耐药结核病（TB）被认为是一个全球性的公共卫生威胁。全基因组测序技术是一种新的结核病诊断技术，能够为流行病学监测提供快速的耐药谱和基因型。因此，我们使用WGS来确定耐药结核分枝杆菌分离株的基因型耐药谱和遗传多样性从姆万扎，西北Tanzana.Methods：一项横断面研究进行了2014年9月至2015年6月在布甘多医疗中心（BMC）。相应地，登记了年龄>= 18岁的新诊断的涂阳结核病患者。痰液样本在Lowenstein-Jensen（LJ）斜面上培养。提取分枝杆菌基因组DNA用于WGS，以确定一线和二线药物的耐药突变以及spoligotype.Results：共纳入78例新诊断的肺结核患者，中位年龄为37 [IQR：30-46]岁。其中，57.8%（45/74）为男性，34.6%（27/78）为艾滋病毒阳性。从74例（94.9%）患者的分离株中获得了用于WGS的结核分枝杆菌基因组DNA。在74株分离株中，6株（8.1%）分离株携带至少一种药物耐药突变。耐药率依次为异烟肼3/74（4.1%）、利福平单药2/74（2.7%）、乙胺丁醇2/74（2.7%）、链霉素1/74（1.4%）。没有一个是异烟肼单一耐药的。在74名患者中，只有1名（1.4%）患者患有耐多药结核病。1例患者（1.4%）对二线药物乙硫异烟胺耐药。无一对吡嗪酰胺、氟喹诺酮类、卡那霉素、阿米卡星或卷曲霉素耐药。检测到的突变为：异烟肼的mabA-inhA启动子区C（-15）T和katG Ser 513 Thr;利福平的rpoB His 526 Leu和rpoB Ser 531 Leu;乙胺丁醇的embB Met 306 Val和embB Met 306 Ile;链霉素的rpsL Lys 43 Arg;以及乙硫异烟胺的mabA-inhA启动子区C（-15）T。结论：坦桑尼亚西北部结核分枝杆菌耐药株的耐药基因型包含了以往报道的常见突变，其耐药基因型分别为T1、T2、T3-ETH、CAS 1-DELHI、EAI 5和LAM 11-ZWE。对一线和二线药物，包括耐多药结核病的耐药性普遍较低。6株耐药菌株表现出不同的spoligotypes，表明该地区的耐药菌株有限的传播。
Background: Drug resistant Tuberculosis (TB) is considered a global public health threat. Whole-genome sequencing (WGS) is a new technology for tuberculosis (TB) diagnostics and is capable of providing rapid drug resistance profiles and genotypes for epidemiologic surveillance. Therefore, we used WGS to determine genotypic drug resistance profiles and genetic diversity of drug resistant Mycobacterium tuberculosis isolates from Mwanza, North-western Tanzania.Methods: A cross-sectional study was conducted at the Bugando Medical Center (BMC) from September 2014 to June 2015. Consecutively, smear-positive newly diagnosed TB patients aged >= 18 years were enrolled. Sputum samples were cultured on Lowenstein-Jensen (LJ) slants. Mycobacterial genomic DNA was extracted for WGS to determine drug resistant mutations for first and second line drugs as well as the spoligotypes.Results: A total of 78 newly diagnosed patients with pulmonary TB with a median age of 37 [IQR: 30-46] years were enrolled. Of these, 57.8% (45/74) were males and 34.6% (27/78) were HIV positive. Mycobacterium tuberculosis genomic DNA for WGS was obtained from isolates in 74 (94.9%) patients. Of the 74 isolates, six (8.1%) isolates harbored mutations for resistance to at least one drug. The resistance to the drugs was isoniazid 3/74 (4.1%), rifampicin mono-resistant 2/74 (2.7%), ethambutol 2/74 (2.7%) and streptomycin 1/74 (1.4%). None was isoniazid mono-resistant. Of the 74 only one (1.4%) patient had MDR-TB. The resistance to ethionamide, the second line drug, was detected in one patient (1.4%). None was resistant to pyrazinamide, fluoroquinolones, kanamycin, amikacin, or capreomycin. The mutations detected were mabA-inhA promoter region C(-15)T and katG Ser513Thr for isoniazid; rpoB His526Leu and rpoB Ser531Leu for rifampicin; embB Met306Val and embB Met306Ile for ethambutol; rpsL Lys43Arg for streptomycin; and mabA-inhA promoter region C(-15) T for ethionamide. The spoligotypes of the drug resistant Mycobacterium tuberculosis were distinct to all six isolates and belonged to T1, T2, T3-ETH, CAS1-DELHI, EAI5 and LAM11-ZWE lineages.Conclusion: The genetic drug resistance profile of Mycobacterium tuberculosis isolates from North-western Tanzania comprises of the common previously reported mutations. The prevalence of resistance to first and second line drugs including MDR-TB is low. Six drug resistant strains exhibited different spoligotypes, suggesting limited transmission of drug resistant strains in the region.