导读与评议（2017年第6期）

精准医疗概念的提出开启了一个医学新时代,其实质包括精准诊断和精准治疗。张文宏课题组围绕结核病治疗中的精准医疗进行了阐述,涉及结核病的精准诊断,包括结核病的临床诊断及结核分枝杆菌的检测(分子检测及耐药检测技术等)、特殊人群的药理学参数与药物代谢相关的分子标记、针对病原体生命周期分子靶点的直接作用药物研发、通过正向调控或负向调控药物的使用实现宿主导向抗结核精准治疗。本期刊登了3篇关于结核病耐药的综述。鉴于耐药结核分枝杆菌的补偿性进化是其传播与流行的基础,高谦课题组从结核分枝杆菌的耐药分子机制、耐药突变的适应性代价与补偿性进化,以及补偿性进化如何影响耐药结核病传播等方面进行了综述。袁莉课题组就近年来结核分枝杆菌“毒素-抗毒素系统”(TAS)与生物膜的研究及抗结核药物对生物膜形成的影响进行综述......     

结核分枝杆菌的耐药基因及其相关分子机制

结核分枝杆菌原发性和继发性耐药是当前控帝】和治疗结核病面临的重要问题,随着分子遗传学的发展,已经阐明了结核分枝杆菌耐药的分子基础是染色体的突变,影响了药靶本身或激活了药物前体的细菌酶,造成MTB的耐药。本文主要就MTB对其常用药物的耐药机制展开讨论,以便正确认识MTB对不同药物的耐药机制,建立快速检测耐药结核分枝杆菌基因型的分子生物学方法。     

结核分枝杆菌的耐药基因及其相关分子机制

结核分枝杆菌原发性和继发性耐药是当前控制和治疗结核病面临的重要问题,随着分子遗传学的发展,已经阐明了结核分枝杆菌耐药的分子基础是染色体的突变,影响了药靶本身或激活了药物前体的细菌酶,造成MTB的耐药。本文主要就MTB对其常用药物的耐药机制展开讨论,以便正确认识MTB对不同药物的耐药机制,建立快速检测耐药结核分枝杆菌基因型的分子生物学方法。     

结核分枝杆菌耐药性的分子生物学研究进展

结核病一直是世界性问题,我国其发病情况尤为严重,是亚洲的第二大结核病发病国家。结核病治疗方面常使用抗生素作为首选药物,随着抗菌药的滥用,结核杆菌对多种抗菌药产生耐药性,结核病耐药患者增多,治疗难度增加。因此,结核杆菌耐药分子机制的研究更加重要,新型抗结核药物研制更加迫切。结核分枝杆菌的基因突变是引起耐药的主要分子学依据,因此基于结核分枝杆菌耐药性相关基因的深入探索,对于预防结核病的传播及治疗皆具有深远影响。本文从分子生物学角度分析了近年来结核分枝杆菌耐药性产生的原因及相关研究进展。     

结核分枝杆菌毒素-抗毒素系统与生物膜

结核分枝杆菌(Mycobacterium tuberculosis)是引起结核病的病原菌。其处于持续生存的休眠状态时,可导致长期无症状感染,称为结核潜伏感染。研究显示,结核分枝杆菌染色体中存在大量 “毒素-抗毒素系统”(toxin-antitoxin system,TAS),某些TAS在潜伏感染中发挥作用,可调节细菌生长和诱导细菌进入休眠状态;某些TAS参与生物膜形成和应激反应,但其影响生物膜形成的机制尚未阐明。生物膜中的结核分枝杆菌对多种抗结核药物耐药,且能抵抗宿主免疫系统防御;休眠状态的结核分枝杆菌对抗结核药物通常也是耐受的,给结核病治疗带来了巨大挑战。本文就近年来结核分枝杆菌TAS与生物膜的研究及抗结核药物对生物膜形成的影响进行综述。     

二代测序技术在结核分枝杆菌研究中的应用进展

结核病是由结核分枝杆菌引起的全球第二大传染病。二代测序技术为从基因组水平研究结核分枝杆菌提供了重要的研究方法。本文从结核病流行病学、结核分枝杆菌耐药和进化及相关生物信息学等方面,介绍二代测序技术在结核分枝杆菌研究中的应用进展。     

结核分枝杆菌持续感染相关基因及其调控网络分析

结核分枝杆菌是结核病的致病菌, 也是迄今最成功的人类致病菌之一. 结核分枝杆菌能逃避宿主免疫攻击, 在人体内持续感染或呈休眠状态. 当人体免疫功能低下时, 持续感染或休眠的致病菌可能被重新激活. 结核分枝杆菌的持续感染是制约结核病控制计划成功的主要障碍之一. 揭示结核分枝杆菌持续感染的分子机制、寻找其中薄弱环节、发现适当的药物靶标并开发全新药物及免疫干预措施, 被认为是遏制结核病蔓延的关键. 结核分枝杆菌持续感染和再激活是众多基因协同的系统适应过程. 本文在全面分析全球结核分枝杆菌持续感染相关基因研究文献的基础上, 通过文本挖掘, 综合本实验室前期研究结果, 提出了结核分枝杆菌持续感染相关基因的调控网络, 为揭示结核分枝杆菌持续感染的机制, 筛选控制结核病的新靶标和免疫干预节点提供研究基础.     

抗结核药物及其耐药相关突变位点的研究进展

结核病是结核分枝杆菌复合物引起的传染性疾病,致死率、致残率高,在全球传染病中居第2位。近年来耐药结核病所占比例逐年升高,成为消灭结核病面临的巨大挑战之一。传统的耐药诊断方法基于培养,费时费力,所需技术要求高;而现有分子检测方法仅能检测少量抗结核药物的少数耐药基因。因此,更好地理解抗结核药物的耐药机制有助于全面耐药诊断。本文对临床中使用频率较高的11类一线和二线抗结核药物及其相应耐药相关基因、突变位点的研究进展进行总结,尤其是对环丝氨酸、利奈唑胺、氯法齐明等二线药物的近期研究做了系统描述,为全面耐药诊断、精准治疗指导、新药研发及耐药机制深入研究提供了前期工作基础。     

结核分枝杆菌耐药性的分子机理研究进展

结核分枝杆菌内,抗结核药物的作用靶编码基因已在细菌染色体上定位,使人们能在分子水平上研究耐药结核分枝杆菌,并对其耐药机理有了深刻了解,本文就结核分枝杆菌对几种主要抗结核药物耐药性的分子机理相关的基因等方面的研究作一综述。     

耐药结核分枝杆菌潜伏-复发感染动物模型的研究进展

潜伏结核感染(latent tuberculosis infection,LTBI)复发是新发结核病的主要来源,其中耐药结核病所占比例较大,使耐药LTBI复发的防控成为结核病研究的重点。耐药结核分枝杆菌潜伏-复发感染动物模型是开展耐药结核病防控相关机制研究、抗耐药结核分枝杆菌药物和疫苗研究的基础。目前耐药结核分枝杆菌感染动物模型缺乏,而已有的结核分枝杆菌标准株H37Rv潜伏-复发感染模型存在缺陷,如小鼠模型的潜伏期荷菌量偏高、复发期变异大,而猴模型的潜伏期和复发期不可预测。模型的可控性差使其应用困难,且缺乏可用的免疫学评价指标,导致远期复发无法预测。因此,基于现有H37Rv潜伏-复发感染动物模型的制备方法,展望耐药结核分枝杆菌潜伏-复发感染动物模型可能存在的缺陷,通过选用新的抑菌剂和诱导剂,制备有稳定潜伏期、潜伏时长适中、复发起点和复发水平变异小的动物模型,是未来耐药结核分枝杆菌潜伏-复发感染动物模型研究的方向。     

Directed mutagenesis of Mycobacterium smegmatis 16S rRNA to reconstruct the in vivo evolution of aminoglycoside resistance in Mycobacterium tuberculosis

Drug resistance in Mycobacterium tuberculosis is a global problem, with major consequences for treatment and public health systems. As the emergence and spread of drug‐resistant tuberculosis epidemics is largely influenced by the impact of the resistance mechanism on bacterial fitness, we wished to investigate whether compensatory evolution occurs in drug‐resistant clinical isolates of M. tuberculosis. By combining information from molecular epidemiology studies of drug‐resistant clinical M. tuberculosis isolates with genetic reconstructions and measurements of aminoglycoside susceptibility and fitness in Mycobacterium smegmatis, we have reconstructed a plausible pathway for how aminoglycoside resistance develops in clinical isolates of M. tuberculosis. Thus, we show by reconstruction experiments that base changes in the highly conserved A‐site of 16S rRNA that: (i) cause aminoglycoside resistance, (ii) confer a high fitness cost and (iii) destabilize a stem‐loop structure, are associated with a particular compensatory point mutation that restores rRNA secondary structure and bacterial fitness, while maintaining to a large extent the drug‐resistant phenotype. The same types of resistance and associated mutations can be found in M. tuberculosis in clinical isolates, suggesting that compensatory evolution contributes to the spread of drug‐resistant tuberculosis disease.     

Fitness-compensatory mutations in rifampicin-resistant RNA polymerase

Mutations in rpoB (RNA polymerase β-subunit) can cause high-level resistance to rifampicin, an important first-line drug against tuberculosis. Most rifampicin-resistant (Rif(R)) mutants selected in vitro have reduced fitness, and resistant clinical isolates of M. tuberculosis frequently carry multiple mutations in RNA polymerase genes. This supports a role for compensatory evolution in global epidemics of drug-resistant tuberculosis but the significance of secondary mutations outside rpoB has not been demonstrated or quantified. Using Salmonella as a model organism, and a previously characterized Rif(R) mutation (rpoB R529C) as a starting point, independent lineages were evolved with selection for improved growth in the presence and absence of rifampicin. Compensatory mutations were identified in every lineage and were distributed between rpoA, rpoB and rpoC. Resistance was maintained in all strains showing that increased fitness by compensatory mutation was more likely than reversion. Genetic reconstructions demonstrated that the secondary mutations were responsible for increasing growth rate. Many of the compensatory mutations in rpoA and rpoC individually caused small but significant reductions in susceptibility to rifampicin, and some compensatory mutations in rpoB individually caused high-level resistance. These findings show that mutations in different components of RNA polymerase are responsible for fitness compensation of a Rif(R) mutant.     

Impact of bacterial genetics on the transmission of isoniazid-resistant Mycobacterium tuberculosis

Understanding the ecology of drug-resistant pathogens is essential for devising rational programs to preserve the effective lifespan of antimicrobial agents and to abrogate epidemics of drug-resistant organisms. Mathematical models predict that strain fitness is an important determinant of multidrug-resistant Mycobacterium tuberculosis transmission, but the effects of strain diversity have been largely overlooked. Here we compared the impact of resistance mutations on the transmission of isoniazid-resistant M. tuberculosis in San Francisco during a 9-y period. Strains with a KatG S315T or inhA promoter mutation were more likely to spread than strains with other mutations. The impact of these mutations on the transmission of isoniazid-resistant strains was comparable to the effect of other clinical determinants of transmission. Associations were apparent between specific drug resistance mutations and the main M. tuberculosis lineages. Our results show that in addition to host and environmental factors, strain genetic diversity can influence the transmission dynamics of drug-resistant bacteria.     

Compensatory evolution of pbp mutations restores the fitness cost imposed by β-lactam resistance in Streptococcus pneumoniae

The prevalence of antibiotic resistance genes in pathogenic bacteria is a major challenge to treating many infectious diseases. The spread of these genes is driven by the strong selection imposed by the use of antibacterial drugs. However, in the absence of drug selection, antibiotic resistance genes impose a fitness cost, which can be ameliorated by compensatory mutations. In Streptococcus pneumoniae, β-lactam resistance is caused by mutations in three penicillin-binding proteins, PBP1a, PBP2x, and PBP2b, all of which are implicated in cell wall synthesis and the cell division cycle. We found that the fitness cost and cell division defects conferred by pbp2b mutations (as determined by fitness competitive assays in vitro and in vivo and fluorescence microscopy) were fully compensated by the acquisition of pbp2x and pbp1a mutations, apparently by means of an increased stability and a consequent mislocalization of these protein mutants. Thus, these compensatory combinations of pbp mutant alleles resulted in an increase in the level and spectrum of β-lactam resistance. This report describes a direct correlation between antibiotic resistance increase and fitness cost compensation, both caused by the same gene mutations acquired by horizontal transfer. The clinical origin of the pbp mutations suggests that this intergenic compensatory process is involved in the persistence of β-lactam resistance among circulating strains. We propose that this compensatory mechanism is relevant for β-lactam resistance evolution in Streptococcus pneumoniae.     

Drug resistance-conferring mutations in Mycobacterium tuberculosis from Madang, Papua New Guinea

ABSTRACT: BACKGROUND: Monitoring drug resistance in Mycobacterium tuberculosis is essential to curb the spread of tuberculosis (TB). Unfortunately, drug susceptibility testing is currently not available in Papua New Guinea (PNG) and that impairs TB control in this country. We report for the first time M. tuberculosis mutations associated with resistance to first and second-line anti-TB drugs in Madang, PNG. A molecular cluster analysis was performed to identify M. tuberculosis transmission in that region. RESULTS: Phenotypic drug susceptibility tests showed 15.7% resistance to at least one drug and 5.2% multidrug resistant (MDR) TB. Rifampicin resistant strains had the rpoB mutations D516F, D516Y or S531L; isoniazid resistant strains had the mutations katG S315T or inhA promoter C15T; streptomycin resistant strains had the mutations rpsL K43R, K88Q, K88R), rrs A514C or gidB V77G. The molecular cluster analysis indicated evidence for transmission of resistant strain. CONCLUSIONS: We observed a substantial rate of MDR-TB in the Madang area of PNG associated with mutations in specific genes. A close monitoring of drug resistance is therefore urgently required, particularly in the presence of drug-resistant M. tuberculosis transmission. In the absence of phenotypic drug susceptibility testing in PNG, molecular assays for drug resistance monitoring would be of advantage.     

Rapid Decline of Ceftazidime Resistance in Antibiotic-Free and Sublethal Environments Is Contingent on Genetic Background

Trade-offs of antibiotic resistance evolution, such as fitness cost and collateral sensitivity (CS), could be exploited to drive evolution toward antibiotic susceptibility. Decline of resistance may occur when resistance to other drug leads to CS to the first one and when compensatory mutations, or genetic reversion of the original ones, reduce fitness cost. Here we describe the impact of antibiotic-free and sublethal environments on declining ceftazidime resistance in different Pseudomonas aeruginosa resistant mutants. We determined that decline of ceftazidime resistance occurs within 450 generations, which is caused by newly acquired mutations and not by reversion of the original ones, and that the original CS of these mutants is preserved. In addition, we observed that the frequency and degree of this decline is contingent on genetic background. Our results are relevant to implement evolution-based therapeutic approaches, as well as to redefine global policies of antibiotic use, such as drug cycling.     

Models to understand the population-level impact of mixed strain M. tuberculosis infections

Over the past decade, numerous studies have identified tuberculosis patients in whom more than one distinct strain of Mycobacterium tuberculosis is present. While it has been shown that these mixed strain infections can reduce the probability of treatment success for individuals simultaneously harboring both drug-sensitive and drug-resistant strains, it is not yet known if and how this phenomenon impacts the long-term dynamics for tuberculosis within communities. Strain-specific differences in immunogenicity and associations with drug resistance suggest that a better understanding of how strains compete within hosts will be necessary to project the effects of mixed strain infections on the future burden of drug-sensitive and drug-resistant tuberculosis. In this paper, we develop a modeling framework that allows us to investigate mechanisms of strain competition within hosts and to assess the long-term effects of such competition on the ecology of strains in a population. These models permit us to systematically evaluate the importance of unknown parameters and to suggest priority areas for future experimental research. Despite the current scarcity of data to inform the values of several model parameters, we are able to draw important qualitative conclusions from this work. We find that mixed strain infections may promote the coexistence of drug-sensitive and drug-resistant strains in two ways. First, mixed strain infections allow a strain with a lower basic reproductive number to persist in a population where it would otherwise be outcompeted if has competitive advantages within a co-infected host. Second, some individuals progressing to phenotypically drug-sensitive tuberculosis from a state of mixed drug-sensitive and drug-resistant infection may retain small subpopulations of drug-resistant bacteria that can flourish once the host is treated with antibiotics. We propose that these types of mixed infections, by increasing the ability of low fitness drug-resistant strains to persist, may provide opportunities for compensatory mutations to accumulate and for relatively fit, highly drug-resistant strains of M. tuberculosis to emerge.     

Site-directed mutagenesis of the katG gene of Mycobacterium tuberculosis: effects on catalase–peroxidase activities and isoniazid resistance

Recent studies examining the molecular mechanisms of isoniazid (INH) resistance in Mycobacterium tuberculosis have demonstrated that a significant percentage of drug-resistant strains are mutated in the katG gene which encodes a catalase–peroxidase, and the majority of these alterations are missense mutations which result in the substitution of a single amino acid. In previous reports, residues which may be critical for enzymatic activity and the drug-resistant phenotype have been identified by evaluating INH-resistant clinical isolates and in vitro mutants. In this study, site-directed mutagenesis techniques were utilized to alter the wild-type katG gene from M. tuberculosis at 13 of these codons. The effects of these mutations were determined using complementation assays in katG -defective, INH-resistant strains of Mycobacterium smegmatis and Mycobacterium bovis BCG. This mutational analysis revealed that point mutations in the katG gene at nine of the 13 codons can cause drug resistance, and that enzymatic activity and resistance to INH are inversely related. In addition, mutations in the mycobacterial catalase–peroxidase which reduce catalase activity also decrease peroxidase activity.