Evaluation of Five User-Friendly Whole Genome Sequencing Software for Mycobacterium tuberculosis in Clinical Application

BackgroundWhole genome sequencing (WGS) is an increasingly useful tool for tuberculosis (TB) diagnosis and disease management. In this study, we evaluated the utility of user-friendly WGS tools in reporting resistance profiles and identifying lineages of clinical TB isolates from South Korea.MethodsForty clinical samples from TB patients showing discrepancies between their rapid molecular and conventional drug susceptibility tests were used in this study. Among these clinical isolates, 37 strains were successfully evaluated via WGS software, using the GenTB, TB Profiler, PhyResSE, CASTB, and Mykrobe.ResultsMore accurate and faster susceptibility results could be obtained with isoniazid than with rifampin. Using the phenotypic test as the gold standard, the isoniazid concordance rate between phenotypic drug susceptibility test (DST) and WGS (GenTB: 45.9%, TB profiler: 40.5%, PhyResSE: 40.5%, CASTB: 48.6%, and Mykrobe: 43.2%) was much higher than between phenotypic DST and rapid molecular genotypic DST (18.9%) among the 37 strains. In contrast, the rifampin concordance rate between phenotypic DST and WGS and that between phenotypic DST and rapid molecular genotypic DST was similar (81.1–89.2%). We also found novel mutations associated with INH in katG and ahpC gene region, not covered by the line probe assay. In addition, lineage analysis identified 81.1% of these samples as L2 East Asian lineage strains, and 18.9% as L4 Euro-American lineage strains.ConclusionWGS may play a pivotal role in TB diagnosis and the detection of drug resistance, genetic diversity, and transmission dynamics in the near future because of its accuracy, speed, and extensibility.     

间充质干细胞治疗结核分枝杆菌感染的基础研究进展

间充质干细胞(MSCs)是一群具有高度自我更新能力和多向分化潜能的多能干细胞,已有多项研究证明其对结核分枝杆菌感染的治疗潜力。MSCs可通过抗菌肽与关键酶的分泌、细胞表面受体的表达,直接或间接地介导受宿主细胞由免疫抑制状态向激活状态转化,进而作为细胞治疗的一种手段,在足量抗菌药物覆盖的基础上,辅助杀灭以结核分枝杆菌为主的分枝杆菌感染,并抑制过度的炎症反应,减少不必要的组织损伤。本文就间充质干细胞治疗结核分枝杆菌感染的基础及临床前研究进展作一概述。     

Antitubercular activity of Arctium lappa and Tussilago farfara extracts and constituents

Ethnopharmacological relevance

Arctium lappa and Tussilago farfara (Asteraceae) are two plant species used traditionally as antitubercular remedies. The aim of this study was (i) to screen Arctium lappa and Tussilago farfara extracts for activity against Mycobacterium tuberculosis and (ii) to isolate and identify the compound(s) responsible for this reputed anti-TB effect.

Materials and methods

The activity of extracts and isolated compounds was determined against Mycobacterium tuberculosis H₃₇R_v using a high throughput spot culture growth inhibition (HT-SPOTi) assay.

Results

The n-hexane extracts of both plants, the ethyl acetate extract of Tussilago farfara and the dichloromethane phase derived from the methanol extract of Arctium lappa displayed antitubercular activity (MIC 62.5 μg/mL). Further chemical investigation of Arctium lappa led to the isolation of n-nonacosane (1), taraxasterol acetate (2), taraxasterol (3), a (1:1) mixture of β sitosterol/stigmasterol (4), isololiolide (5), melitensin (6), trans-caffeic acid (7), kaempferol (8), quercetin (9), kaempferol-3-O-glucoside (10). Compounds isolated from Tussilago farfara were identified as a (1:1) mixture of β sitosterol/stigmasterol (4), trans-caffeic acid (7), kaempferol (8), quercetin (9), kaempferol-3-O-glucoside (10), loliolide (11), a (4:1) mixture of p-coumaric acid/4-hydroxybenzoic acid (12), p-coumaric acid (13). All compounds were identified following analyses of their physicochemical and spectroscopic data (MS, ¹H and ¹³C-NMR) and by comparison with published data. This is the first report of the isolation of n-nonacosane (1), isololiolide (5), melitensin (6) and kaempferol-3-O-glucoside (10) from Arctium lappa, and of loliolide (11) from Tussilago farfara. Amongst the isolated compounds, the best activity was observed for p-coumaric acid (13) (MIC 31.3 μg/mL or 190.9 μM) alone and in mixture with 4-hydroxybenzoic acid (12) (MIC 62.5 μg/mL).

Conclusions

The above results provide for the first time some scientific evidence to support, to some extent, the ethno-medicinal use of Arctium lappa and Tussilago farfara as traditional antitubercular remedies.     

结核杆菌复苏促进因子在分枝杆菌培养中的作用观察

目的 探讨结核杆菌复苏因子(TB-RPF)在结核患者标本的分枝杆菌培养中的作用.方法 收集疑似结核患者的痰液42例,支冲液8例,胸腔积液25例,经4%NaOH液化处理后用PBS洗涤并悬浮菌体,每份标本分设对照组和RPF组,按照两组各0.5 ml菌液量接种于MGIT培养管.对照组培养基采用含Middlebrook7H9的...     

Repositioning rifamycins for Mycobacterium abscessus lung disease

ABSTRACT

Introduction: The treatment of Mycobacterium abscessus lung disease faces significant challenges due to intrinsic antibiotic resistance. New drugs are needed to cure this incurable disease. The key anti-tubercular rifamycin, rifampicin, suffers from low potency against M. abscessus and is not used clinically. Recently, another member of the rifamycin class, rifabutin, was shown to be active against the opportunistic pathogen.

Areas covered: In this review, the authors discuss the rifamycins as a reemerging drug class for treating M. abscessus infections. The authors focus on the differential potency of rifampicin and rifabutin against M. abscessus in the context of intrinsic antibiotic resistance and bacterial uptake and metabolism. Reports of rifamycin-based drug synergies and rifamycin potentiation by host-directed therapy are evaluated.

Expert opinion: While repurposing rifabutin for M. abscessus lung disease may provide some immediate relief, the repositioning (chemical optimization) of rifamycins offers long-term potential for improving clinical outcomes. Repositioning will require a multifaceted approach involving renewed screening of rifamycin libraries, medicinal chemistry to improve ‘bacterial cell pharmacokinetics’, better models of bacterial pathophysiology and infection, and harnessing of drug synergies and host-directed therapy towards the development of a better drug regimen.     

γ干扰素释放试验诊断儿童潜伏结核菌感染的Meta分析

目的以结核菌素皮肤试验(TST)为参考试验,评价QuantiFERON-TB Gold test(QFT)和T-SPOT.TB两种IFN-γ释放试验诊断儿童潜伏结核菌感染的准确性。方法计算机检索EMBASE、PubMed、Cochrane图书馆、中文科技期刊全文数据库、中国期刊全文数据库和万方数字化期刊群等数据库,检索时间均为建库至2010年3月。全面检索IFN-γ释放试验诊断儿童潜伏结核菌感染的文献,按照诊断试验的纳入标准筛选文献,提取纳入文献的特征信息(研究背景、设计信息和诊断参数信息)。根据QUADAS质量评价标准评价纳入文献的质量。采用Meta-Disc1.4软件进行Meta分析,检验异质性,并根据异质性结果选择相应的效应模型。对纳入文献予以加权定量合并,计算汇总敏感度、特异度、阳性似然比、阴性似然比和诊断优势比及其95%CI,绘制汇总受试者工作特征(SROC)曲线,并计算曲线下面积(AUC)。结果共检出相关文献285篇,按照文献纳入标准,最终纳入13篇文献(英文文献12篇和中文文献1篇)。10篇文献报道了QFT试验对儿童潜伏结核菌感染的诊断价值,汇总敏感度为0.40(95%CI:0.37~0.44)、汇总特异度为0.87(95%CI:0.85~0.88)、汇总阳性似然比为6.21(95%CI:3.07~12.54)、汇总阴性似然比为0.46(95%CI:0.31~0.68)、汇总诊断优势比为15.58(95%CI:7.47~32.48),SROC AUC为0.8931。4篇文献报道了T-SPOT.TB试验对儿童潜伏结核菌感染的诊断价值,汇总敏感度为0.74(95%CI:0.68~0.79)、汇总特异度为0.84(95%CI:0.81~0.87)、汇总阳性似然比为4.66(95%CI:1.27~17.12)、汇总阴性似然比为0.42(95%CI:0.18~0.99)、汇总诊断优势比为13.71(95%CI:3.71~50.72),SROCAUC为0.8306。结论 IFN-γ释放试验适用于进一步鉴别诊断儿童是否处于潜伏结核菌感染,不适合儿童潜伏结核菌感染的筛查。     

中西医结合治疗多灶性匍行性脉络膜炎一例

多灶性匍行性脉络膜炎（Multifocal serpiginous choroiditis,MSC）是一种变异型的匍行性脉络膜炎（Serpiginous choroiditis,SC）,病灶呈离散分布,多不累及视盘,同样以匍行样模式扩散至融合。若病灶累及中心凹或合并脉络膜新生血管,视力将严重受损。现将由结核分枝杆菌（M.tuberculosis,MTB）感染引起的多灶性匍行性脉络膜炎1 例多模式影像下特征研究及中西医结合治疗效果报道如下。     

The Higher Incidence of COVID-19 in Patients With Non-Tuberculous Mycobacterial Pulmonary Disease: A Single Center Experience in Korea

The aim of our study was to investigate the incidence of and risk factors for coronavirus disease 2019 (COVID-19) in patients with non-tuberculous mycobacterial-pulmonary disease (NTM-PD). A total of 3,866 patients with NTM-PD were retrospectively identified from a single center. Compared to the general population of Korea, patients with NTM-PD had a substantially increased age-standardized incidence of COVID-19 from January 2020 to February 2021 (2.1% vs. 0.2%). The odds of being infected with COVID-19 was particularly higher in patients who received treatment for NTM-PD than in those who did not receive treatment for NTM-PD (adjusted odd ratio = 1.99, 95% confidence interval = 1.09–3.64, P = 0.026). Patients with NTM-PD might be regarded as a high-risk group for COVID-19 and may need a more proactive preventive strategy for COVID-19 and other pandemics in the future.     

线性探针检测技术对痰标本中耐药结核分枝杆菌快速检测的应用评价

目的 评价线性探针检测技术(LPAs)直接从痰标本中检测结核分枝杆菌复合群及其对耐多药结核病的快速检测。方法 连续收取193例临床涂片抗酸染色阳性的痰标本,直接用LPAs法从痰标本中进行结核分枝杆菌复合群及其对利福平和异烟肼耐药性的检测,结果与MGIT 960系统药物敏感性试验以及利福平、异烟肼耐药相关基因rpoB、katG、inhA和ahpC的基因测序结果进行比较,评价线性探针检测技术从痰标本中检测耐药结核分枝杆菌的灵敏度、特异度和符合率。统计学分析采用kappa检验。结果 LPAs法对涂阳痰标本结核分枝杆菌复合群检测的灵敏度为100.0%,耐利福平、耐异烟肼和耐多药结核分枝杆菌复合群检测的灵敏度分别为96.0%(48/50)、92.8%(64/69)和90.0%(45/50),特异度分别为99.3%(142/143)、100.0%(124/124)和99.3%(142/143),符合率分别为98.4%(190/193)、97.4%(188/193)和96.9%(187/193)。结论 LPAs法能够直接从涂阳痰标本中检测耐多药结核分枝杆菌,对耐利福平和耐异烟肼菌株具有较高的灵敏度和特异度,与MGIT 960系统药物敏感性试验结果的一致性较好,能够明显缩短从样本接收到得到药物敏感性试验结果的报告周期,为临床准确、快速地诊断耐多药结核病提供可靠的实验室依据,有利于耐药结核病的早期诊断。