Bacterial genome mapper: A comparative bacterial genome mapping tool

Recently, next generation sequencing (NGS) technologies have led to a revolutionary increase in sequencing speed and costefficacy. Consequently, a vast number of contigs from many recently sequenced bacterial genomes remain to be accurately mapped and annotated, requiring the development of more convenient bioinformatics programs. In this paper, we present a newly developed web-based bioinformatics program, Bacterial Genome Mapper, which is suitable for mapping and annotating contigs that have been assembled from bacterial genome sequence raw data. By constructing a multiple alignment map between target contig sequences and two reference bacterial genome sequences, this program also provides very useful comparative genomics analysis of draft bacterial genomes. AVAILABILITY: The database is available for free at http://mbgm.kribb.re.kr.     

两株超级广泛耐药结核分枝杆菌全基因组比较分析

【目的】结合现有数据,通过对两株临床超级广泛耐药的结核分枝杆菌全基因组的测序和分析,发现其型别相关的突变位点,解释发生广泛耐药的基因组突变机制。【方法】利用Solexa第二代测序技术对两株广泛耐药结核分枝杆菌(FJ05194和GuangZ0019)进行全基因组测序分析。以H37Rv为参考序列得到两株广泛耐药菌株的单核苷酸多态性(SNPs),构建系统发育树鉴定菌株型别,判断突变位点中型别相关和非型别相关的SNPs。定位SNPs所在的基因组区域,对型别相关的突变基因进行KEGG通路的富集分析,对非型别相关的突变基因和间隔区判断是否与耐药相关。【结果】两株广泛耐药菌株分别属于Lineage2和Lineage4型别,两菌株在碱基替换方面存在差异性,Lineage2型别相关的基因功能富集于ABC转运蛋白和核苷酸切除修复的通路。耐药方面,发现了已知的耐药相关基因的突变(rpoB、katG、rpsl、gyrA、gyrB、embB和ethA等),但卷曲霉素和卡那霉素相关的rrs、tlyA和eis启动子区域未发生突变,不足以解释其耐药性的产生。与最新报道的候选耐药基因比较,发现了卷曲霉素和卡那霉素相关的突变(Rv1393c、Rv0265c和narX等)和外排泵相关的pstB、Rv2333c和Rv2687c突变。【结论】结核分枝杆菌Lineage2型别相关的SNPs中含有影响结核分枝杆菌突变率和耐药性的突变。对于两株超级广泛耐药的结核菌,已知的激活药物或药靶相关的单耐药基因突变集合不能完全解释其广泛耐药性,还涉及新候选结核耐药基因、外排泵和补偿等其他潜在机制的相关基因突变。     

Tuberculosis patients co-infected with Mycobacterium bovis and Mycobacterium tuberculosis in an urban area of Brazil

In this cross-sectional study, mycobacteria specimens from 189 tuberculosis (TB) patients living in an urban area in Brazil were characterised from 2008-2010 using phenotypic and molecular speciation methods (pncA gene and oxyR pseudogene analysis). Of these samples, 174 isolates simultaneously grew on Löwenstein-Jensen (LJ) and Stonebrink (SB)-containing media and presented phenotypic and molecular profiles of Mycobacterium tuberculosis, whereas 12 had molecular profiles of M. tuberculosis based on the DNA analysis of formalin-fixed paraffin wax-embedded tissue samples (paraffin blocks). One patient produced two sputum isolates, the first of which simultaneously grew on LJ and SB media and presented phenotypic and molecular profiles of M. tuberculosis, and the second of which only grew on SB media and presented phenotypic profiles of Mycobacterium bovis. One patient provided a bronchial lavage isolate, which simultaneously grew on LJ and SB media and presented phenotypic and molecular profiles of M. tuberculosis, but had molecular profiles of M. bovis from paraffin block DNA analysis, and one sample had molecular profiles of M. tuberculosis and M. bovis identified from two distinct paraffin blocks. Moreover, we found a low prevalence (1.6%) of M. bovis among these isolates, which suggests that local health service procedures likely underestimate its real frequency and that it deserves more attention from public health officials.     

结核分枝杆菌蛋白抗原的研究进展

结核病当今世界人类致死的主要疾病之一,早期诊断发现病人、选择敏感的抗结核药物进行有效治疗是控制结核病的关键。而临床上对结核病患者检出率低,漏诊率和误诊率高,结果导致结核耐药的情况越来越严重。简便、快速、准确的免疫学检测方法在诊断结核病中起到了重要的作用。本文对用于免疫学检测的蛋白抗原作一综述。     

复治肺结核患者结核分枝杆菌L型培养结果分析

目的：了解复治肺结核患者的结核分枝杆菌L型培养情况,探讨结核分枝杆菌L型阳性与耐多药的关系。方法：选择180例肺结核患者的痰标本进行结核分枝杆菌培养和结核分枝杆菌L型培养,同时对110例复治组中培养阳性的标本行耐药监测。结果：复治组的L型阳性率为43．6％,初治组的L型阳性率为15．7％,复治组显著高于初治组（P〈0．01）;菌阳复治组的L型阳性率50％,菌阴复治组的L型阳性率39．4％,菌阳组明显高于菌阴组（P〈0．05）;L型菌阳性患者的耐药率显著高于L型菌阴性组（P〈0．05）。结论：结核分枝杆菌L型阳性是引起结核病复发、耐药的重要原因;MDR-TB与结核分枝杆菌L型感染有关。     

Non-contiguous genome sequence of Mycobacterium simiae strain DSM 44165T

Mycobacterium simiae is a non-tuberculosis mycobacterium causing pulmonary infections in both immunocompetent and imunocompromized patients. We announce the draft genome sequence of M. simiae DSM 44165^T. The 5,782,968-bp long genome with 65.15% GC content (one chromosome, no plasmid) contains 5,727 open reading frames (33% with unknown function and 11 ORFs sizing more than 5000 -bp), three rRNA operons, 52 tRNA, one 66-bp tmRNA matching with tmRNA tags from Mycobacterium avium, Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium microti, Mycobacterium marinum, and Mycobacterium africanum and 389 DNA repetitive sequences. Comparing ORFs and size distribution between M. simiae and five other Mycobacterium species M. simiae clustered with M. abscessus and M. smegmatis. A 40-kb prophage was predicted in addition to two prophage-like elements, 7-kb and 18-kb in size, but no mycobacteriophage was seen after the observation of 10⁶ M. simiae cells. Fifteen putative CRISPRs were found. Three genes were predicted to encode resistance to aminoglycosides, betalactams and macrolide-lincosamide-streptogramin B. A total of 163 CAZYmes were annotated. M. simiae contains ESX-1 to ESX-5 genes encoding for a type-VII secretion system. Availability of the genome sequence may help depict the unique properties of this environmental, opportunistic pathogen.     

Advances in antibody-mediated immunity against Mycobacterium tuberculosis: implications for a novel vaccine strategy

Cell-mediated immunity is considered to be the major component of the host response against Mycobacterium tuberculosis, whereas antibody-mediated immunity historically has been considered inconsequential. In recent years, studies from several groups have challenged the traditional dogma and demonstrated that monoclonal antibodies can modify various aspects of mycobacterial infections. This review describes the experimental evidence supporting a role for antibodies in defense against mycobacterial infections and outlines future challenges to the field of antibody-mediated immunity against M. tuberculosis, with particular emphasis on the implications of these findings for a novel vaccine strategy.     

结核分枝杆菌潜伏感染诊断方法的新进展

每年有超过8百万人感染结核,其中绝大部分没有发展为活动性结核病,而是表现为潜伏性结核感染。大多数活动性结核病是潜伏感染的结核杆菌重新被激活所致,因此结核潜伏感染者成为结核患者的重要来源。及早诊断和治疗结核潜伏感染者是控制结核传播的最有效手段之一。我们较要综述了目前国内外结核潜伏感染的诊断方法及其新进展。     

Characterisation of IS901 integration sites in the Mycobacterium avium genome

Data are presented on the identification and characterisation of 17 chromosomal integration loci of the insertion element IS901 in the Mycobacterium avium (cervine strain JD88/118) genome. Thirteen of these integration loci have been mapped to their corresponding positions on the M. avium strain 104 (an IS901(-) strain) genome (The Institute for Genome Research (TIGR) unfinished genome-sequencing project). Sequence data for both upstream and downstream sequence flanking regions were obtained for 12 insertion loci, while upstream sequence was obtained for five others. A consensus IS901 insertion target sequence compiled from all 17 integration sites was in broad agreement with earlier reports that were based on only two such loci. Analysis of IS901 integration site flanking sequences revealed that, like IS900 in M. avium subspecies paratuberculosis, IS901 inserts preferentially between a putative ribosome-binding sequence (RBS) and the translational start codon of an open reading frame (ORF). In BLAST X and BLAST P searches of the GenBank database, these ORFs were shown to share significant homologies with a number of other prokaryotic genes.     

HBHA 在结核病研究中的应用*

结核分枝杆菌hbhA编码基因是目前发现的与肺外结核转移相关的基因,其表达产物结核分枝杆菌肝素结合血凝黏附素(HBHA),是结核分枝杆菌表面表达和分泌的一种糖蛋白。HBHA具有介导肺结核和肺外结核的发生,参与实现MTB逃逸吞噬体进入细胞质中生存和繁殖,引起巨噬细胞凋亡等重要生物学功能,同时HBHA作为特异性抗原,用作免疫学检测具有较好的效果,并且动物实验证实HBHA具有明确的免疫治疗作用。因此,HBHA在结核病的免疫学诊断及免疫治疗方面,具有广阔的应用前景。     

宠物结核病的危害及其防治

随着生活水平的提高,宠物的数量和种类增长迅速。结核病是目前病死人数最多的人兽共患病,犬、猫和鸟类都能感染发病,对人类,尤其是免疫抑制人群威胁很大。监测和防治宠物结核病对人类结核根除计划具有重要意义。     

A Study of Unusual Pacemaker Infection by Mycobacterium Tuberculosis in Indian Patients

Background

The expanding clinical indications of cardiac rhythm management have led to an increased use of pacemaker implantation which is associated with increased incidence of pacemaker infections. Staphylococcus aureus and epidermidis account for the vast majority of pacemaker infections. Pacemaker infection due to Mycobacterium tuberculosis (M. tuberculosis) is very rare, only few cases having been reported till date.

Methods

We describe here a study of three patients of pacemaker pocket infection with M. tuberculosis.

Conclusion

The possibility of mycobacterial pacemaker infection should always be kept in mind in patients with delayed pacemaker infection.     

Molecular Modeling of Mycobacterium Tuberculosis dUTpase: Docking and Catalytic Mechanism Studies

Abstract

Mycobacterium tuberculosis is a leading cause of infectious disease in the world today. This outlook is aggravated by a growing number of M. tuberculosis infections in individuals who are immunocompromised as a result of HIV infections. Thus, new and more potent anti-TB agents are necessary. Therefore, dUTpase was selected as a target enzyme to combat M. tuberculosis. In this work, molecular modeling methods involving docking and QM/MM calculations were carried out to investigate the binding orientation and predict binding affinities of some potential dUTpase inhibitors. Our results suggest that the best potential inhibitor investigated, among the compounds studied in this work, is the compound dUPNPP. Regarding the reaction mechanism, we concluded that the decisive stage for the reaction is the stage 1. Furthermore, it was also observed that the compounds with a ?1 electrostatic charge presented lower activation energy in relation to the compounds with a ?2 charge.     

耐药结核分枝杆菌基因组信息挖掘

<正>由于结核分枝杆菌的耐药性问题,使结核病这个古老的传染病死灰复燃,并成为全球性的严重公关问题。从1998年首个结核分枝杆菌(H37Rv)全基因组完成图的获得[1],到近年来采用新一代测序技术对多个菌株进行高通量的基因组测序与分析,对结核分枝杆菌进化及耐药机制的认识不断深入。关于结核分枝杆菌菌株的基因组比较分析有多篇报道,包括对中国12个省来源的161株结核分枝杆菌     

Corrected sequence of the wheat plastid genome

Wheat is the most important cereal in the world in terms of acreage and productivity. We sequenced and assembled the plastid genome of one Egyptian wheat cultivar using next-generation sequence data. The size of the plastid genome is 133,873 bp, which is 672 bp smaller than the published plastid genome of “Chinese Spring” cultivar, due mainly to the presence of three sequences from the rice plastid genome. The difference in size between the previously published wheat plastid genome and the sequence reported here is due to contamination of the published genome with rice plastid DNA, most of which is present in three sequences of 332, 131 and 131 bp. The corrected plastid genome of wheat has been submitted to GenBank (accession number KJ592713) and can be used in future comparisons.     

The completed genome sequence of the pathogenic ascomycete fungus Penicillium digitatum

P. digitatum, the causative agent of green mold, is one of the most destructive pathogens in the citrus industry. To facilitate basal researches on this important plant pathogen, here we report a finished genome sequence for P. digitatum strain PDW03 using a combination of Illumina, PacBio, and Hi-C sequencing technologies. The assembly comprised 6 chromosomes from telomere to telomere and encodes approximately 9000 proteins. Genomic re-analyses identified 302 Carbohydrate-active enzymes, 420 secreted proteins, and 39 secondary metabolite (SM) gene clusters. Furthermore, we found 10 fragmentary SM clusters in the P. digitatum PDW03 genome. Pangenome analysis based on 5 P. digitatum genomes available showed that conserved orthogroups account for ~68% of the species pangenome. Taken together, this fully completed P. digitatum genome will provide an optimum resource for further researches to investigate the driving forces of fungal host switch and effectors functioning in plant-pathogen interaction.     

Study on immunity of dengue virus and dengue vaccine development

In the study of vaccines for dengue viruses, which are multivalent immunization, genetically and antigenically distinct, we should have more sophisticated understanding of viral immune physiology. Because the immune response to dengue and its role in the pathophysiology of dengue fever and dengue hemorrhagic fever are multifaceted, several different efforts have been made to engineer a protective vaccine. Because of space limitations, this review is focused only on vaccines that have emerged from preclinical studies into clinical trial.     

结核分枝杆菌感染实验模型

结核分枝杆菌是引起人结核病的主要病原,全世界约有1/3人口感染结核分枝杆菌。尽管该病原可感染并引起许多动物疾病,但人类是其中心宿主。为研究结核分枝杆菌的致病机理及宿主对本病原的保护性和免疫病理学反应,选择合适的动物模型非常必要。本文阐述了结核病研究中常用的实验模型及各种模型的优缺点。实验模型的合理应用将促进我们对结核病的认识,从中获取的资料将有助于我们发现更好的预防和治疗方案。