高通量测序技术在临床病毒学领域的应用北大核心CSCD

本文总结了近几年高通量测序平台的发展现状,比较了不同测序平台的性能及特点。同时还对目前高通量测序平台在近两年临床病毒学领域的应用,包括病原学诊断、分子流行病学、宏基因组学和临床治疗转归等几个方面,逐一举例进行了阐述。籍此加深专业人员对高通量测序平台的认识,促进该技术在临床病毒学的转化与应用。     

慢性阻塞性肺疾病患者肺泡灌洗液宏基因组测序分析北大核心CSCD

目的评价PMseq病原微生物宏基因组测序检测用于慢性阻塞性肺疾病(COPD)合并肺部感染患者诊断的价值。方法以2019年11月至2022年5月在呼吸科确诊的67例稳定期COPD患者(合并肺部感染47例)为研究对象,同时采用肺泡灌洗液培养和PMseq病原微生物宏基因组测序,对培养及测序鉴定出的病原体进行描述性分析,并对检测结果进行比较分析。结果67例稳定期COPD患者中,宏基因组测序阳性65例、肺泡灌洗液培养阳性28例,差异有统计学意义(χ^(2)=48.11,P<0.01)。其中,宏基因组测序和肺泡灌洗液培养均阳性27例。该27例患者中,宏基因组测序和肺泡灌洗液培养检测结果完全一致8例、部分一致12例、不一致7例(Kappa值=0.46)。28例肺泡灌洗液培养阳性患者中以细菌感染多见,其中链球菌属及奈瑟菌感染分别为19例和17例,肠球菌感染5例,金黄色葡萄球菌、铜绿假单胞菌、肺炎克雷伯菌各1例;真菌感染以念珠菌多见(5例),土曲霉菌感染1例。65例高通量测序阳性COPD患者细菌感染以链球菌属为主,真菌感染以曲霉菌为主(5例)。高通量测序患者中,46例为2种及以上病原体感染、21例为单一病原体感染。结论COPD合并肺部感染患者病原体谱广,并存在混合感染。PMseq病原微生物宏基因组测序法敏感、特异,可用于COPD患者感染的病原体精准诊断,值得临床推广应用。     

宏基因组测序在感染性疾病病原体检测中的应用

感染性疾病的致病因素复杂,临床表现多样。快速、全面、准确地鉴别病原体,是临床医生及时、有针对性地采取治疗措施的前提。传统的病原体检测方法目标单一、耗时长、操作复杂,很难满足当今感染性疾病诊治的要求。宏基因组测序技术克服了多数病原体不能培养的弊端,能够准确高效地获得全部病原体遗传物质信息,直接检测出感染性疾病的病原体,对疑难感染性疾病的诊断具有重要参考价值。本文对宏基因组测序在感染性疾病病原体检测中的最新研究进展和应用进行综述。     

宏基因组技术在感染性疾病中的应用

宏基因组测序(mNGS)正越来越多地应用于临床实验室的诊断。该文探讨了这项诊断传染病的新技术的目前实施情况,并讨论将mNGS转变为常规诊断技术的可行性。大量研究表明,mNGS在直接从临床样本中识别常规、罕见、协同感染病原体并对解决抗生素耐药性问题,提供了新的诊断证据,可用于指导治疗方案和改进抗生素管理。mNGS是解决临床感染问题的重要手段,将在临床实践中被广泛接受。     

宏基因组学第二代测序技术辅助诊断肺新生隐球菌和卡氏肺孢菌混合感染一例

1例存在艾滋病基础且胸部计算机断层成像检查表现为肺弥漫性磨玻璃样病变的患者,入院时考虑为肺孢子菌肺炎,但治疗效果欠佳。肺泡灌洗液宏基因组学第二代测序技术检测出新生隐球菌与卡氏肺孢菌序列。经过联合抗肺孢子菌和抗隐球菌治疗,患者逐渐恢复。提示艾滋病患者需要警惕混合感染的可能性,宏基因组学第二代测序技术在该类人群病原学诊断中可能具有广阔的应用前景。     

糖尿病足感染微生物分布特点的研究进展

糖尿病足感染(DFI)致残、致死率高,是导致糖尿病患者住院和截肢率升高的主要原因。治疗DFI最重要的环节是选用合适的抗生素,准确选用抗生素的基础是明确致病菌。本文就DFI微生物分布特点进行综述,分析使用16S r RNA及宏基因组测序等高通量测序技术鉴定细菌的利弊,为临床准确选用抗生素治疗DFI提供依据。     

脑裂头蚴病1例

脑裂头蚴病临床较为少见, 由于其临床表现不典型, 影像学缺乏特异性改变, 因此容易误诊、漏诊。本文回顾性分析1例脑裂头蚴病患者的临床资料, 结合相关文献, 讨论脑裂头蚴病的临床、影像学特点及实验室检查, 并初步探讨脑脊液宏基因组学二代测序在脑裂头蚴病诊断中的应用价值。     

危重型日本斑点热1例

日本斑点热是由日本立克次体感染、经蜱虫叮咬传播的一种自然疫源性疾病。本例患者表现为发热、皮疹、头痛、焦痂溃疡,病程中出现血小板急剧下降、凝血功能异常、低血压休克、急性呼吸窘迫综合征、肝肾功能损伤、意识障碍等严重并发症,宏基因组学第二代测序检出日本立克次体,结合患者实验室检查和临床表现诊断为日本斑点热,经多西环素抗感染及...     

胆道闭锁肠道菌群特征的病例对照研究

【据《J Gastroenterol Hepatol》2020年2月报道】题:胆道闭锁肠道菌群特征的病例对照研究(作者Wang JF等)胆道闭锁是一种以胆道进行性炎性纤维梗阻为特征的疾病,其病因不明。既往研究发现多种肝脏疾病与肠道菌群改变相关。然而,胆道闭锁的肠道菌群特征目前仍未知。本研究首先对34例胆道闭锁患儿和34例正常对照的肠道菌群特征进行横断面分析,并调查胆道闭锁患儿葛西术后2周的肠道菌群变化情况;采用16S核糖体RNA测序初步分析肠道菌群特征,进一步采用宏基因组测序明确16S核糖体RNA测序的结果。此外,本研究还通过超高效液相色谱检测了胆道闭锁患儿和正常对照的大便胆汁酸谱。     

宏基因组学测序诊断曼氏裂头蚴病1例

患者于2000年无明显诱因发现下腹部游走性包块，20年来多次就诊，未明确病因。2020年8月11日发现包块游走于左侧腋前，微创手术取出不完整白色虫体3段，用宏基因组学测序鉴定虫体，明确诊断为曼氏裂头蚴病。2021年10月21日经手术取出完整虫体，患者康复出院；随访患者身体状况良好，全身未发现新包块。     

Generation and molecular characterisation of monoclonal IgG4 rheumatoid factor from a patient with rheumatoid arthritis

OBJECTIVE—To characterise IgG4 rheumatoid factor (RF) at the molecular level from a patient with rheumatoid arthritis.
METHODS—B cells were cloned from the peripheral blood of a patient with rheumatoid arthritis, using EB virus transformation. The supernatants of the clones were screened for IgG RF activity by ELISA. Nucleotide sequences of the expressed immunoglobulin heavy and light chain genes of one IgG RF producing clone were determined by direct sequencing of the products of a polymerase chain reaction.
RESULTS—One clone producing monospecific IgG4 RF was obtained. Sequence analysis of the heavy and light chain genes suggested the accumulation of somatic mutations resulting in amino acid replacement in complementarity determining regions.
CONCLUSIONS—The results may suggest an antigen driven response in the generation of IgG4 RF in rheumatoid arthritis disease processes.

     

Severe upper gastrointestinal polyposis associated with sparse colonic polyposis in a familial adenomatous polyposis family with an APC mutation at codon 1520

Background—Familial adenomatouspolyposis usually results in colonic polyposis with hundredsto thousands of polyps, congenital hypertrophy of the retinal pigmentepithelium (CHRPE), and variable extracolonic features. Recent reportsindicate that patients with distal mutations between codons 1445 and1578 do not express CHRPE and have a high incidence of desmoid tumours.
Patients—The family studied has an unusualphenotype of sparse colonic polyposis but profuse uppergastrointestinal polyposis. Affected subjects do not have CHRPE.
Methods—The protein truncation testfollowed by sequencing identified a 2 base pair deletion at codon 1520 in the APC gene. This results in a frameshift creating a stop codon 13 codons downstream.
Results—This family demonstrates that sparsecolonic polyposis but severe upper tract polyposis may be associatedwith mutations between codons 1445 and 1578.
Conclusions—Study of duodenal and colonic polypsin further cases with mutations in this region is warranted. Suchmutations may preferentially cause duodenal adenomas and desmoidtumours as somatic mutations in these tumours also occur in thisregion, unlike colorectal tumours where somatic mutations occur moreproximally. This study emphasises the importance of screening the uppergastrointestinal tract even when the colonic disease is mild.

Keywords:familial adenomatous polyposis; duodenal polyps; APCmutations; colorectal polyps

     

Characterization of a Proposed Dichorhavirus Associated with the Citrus Leprosis Disease and Analysis of the Host Response

The causal agents of Citrus leprosis are viruses; however, extant diagnostic methods to identify them have failed to detect known viruses in orange, mandarin, lime and bitter orange trees with severe leprosis symptoms in Mexico, an important citrus producer. Using high throughput sequencing, a virus associated with citrus leprosis was identified, belonging to the proposed Dichorhavirus genus. The virus was termed Citrus Necrotic Spot Virus (CNSV) and contains two negative-strand RNA components; virions accumulate in the cytoplasm and are associated with plasmodesmata—channels interconnecting neighboring cells—suggesting a mode of spread within the plant. The present study provides insights into the nature of this pathogen and the corresponding plant response, which is likely similar to other pathogens that do not spread systemically in plants.     

A new mutation of the cardiac troponin T gene causing familial hypertrophic cardiomyopathy without left ventricular hypertrophy

AIM—To screen for a mutation of the cardiac troponin T gene in two families where there had been sudden deaths without an increase in left ventricular mass but with myocardial disarray suggesting hypertrophic cardiomyopathy.
METHODS—DNA from affected individuals from both families was used to screen the cardiac troponin T gene on an exon by exon basis. Mutation screening was achieved by polymerase chain reaction and direct sequencing. Where appropriate, a mutation was confirmed by restriction digest.
RESULTS—A novel missense mutation of exon 9 was found in the affected individuals of one of the families. This mutation at amino acid 94 resulted in the substitution of arginine for leucine and was not found in 100 normal control samples. A mutation of the cardiac troponin T gene was excluded in the second family.
CONCLUSIONS—A mutation of the gene for the sarcomeric protein cardiac troponin T can cause familial hypertrophic cardiomyopathy with marked myocyte disarray and frequent premature sudden death in the absence of myocardial hypertrophy at clinical or macroscopic level.


Keywords: hypertrophic cardiomyopathy; troponin T     

Colony formation from mesophyll protoplasts of a cereal, oat

Differentiated leaf cells of gramineous plants, among them the cereals with their immense importance for human nutrition, are considered extremely recalcitrant to, if not incapable of, reentering the cell cycle. This recalcitrance is related to the poor wound response of the monocots—in contrast to most dicots—and the difficulties encountered in monocot tissue culture. We report here the highly reproducible induction of sustained divisions at high frequency (up to 95%) and colony formation from mesophyll protoplasts of a cereal, oat, demonstrating that—contrary to most earlier evidence—mesophyll cells of a gramineous plant have not irreversibly lost their potential for cell division.     

Use of monoclonal antibodies to detect disease associated HLA-DRB1 alleles and the shared epitope in rheumatoid arthritis

OBJECTIVE—To use a panel of monoclonal antibodies (Mab) which recognise HLA class II alleles associated with rheumatoid arthritis for fluorescence activated cell sorter (FACS) analysis of peripheral blood mononuclear cells (PBMNC) from patients with early and established rheumatoid arthritis and to compare these results against DNA oligotyping of HLA class II molecules in the same patients.
METHODS—27 patients (18 from an early arthritis clinic, nine with established rheumatoid arthritis) were studied using both techniques. PBMNC were stained with Mab which recognise the shared epitope, the HLA-DRB1*04 molecule and its *0401, *0404 subtypes in the presence of bound peptide. Mab stained cells were analysed by FACS. Genomic DNA was prepared from PBMNC and used for DNA oligotyping and sequencing by standard methods.
RESULTS—FACS analysis of Mab stained PBMNC gave identical results to those obtained by DNA oligotyping in 26/27 patients. The antibodies identified the shared epitope in 14/14 cases and the presence of an HLA-DRB1*04 molecule in 12/12 cases. HLA-DRB1*0404 was identified in 4/4 cases. HLA-DRB1*0401 was identified in 5/6 cases. One patient oligotyped as HLA-DRB1*0401, but consistently failed to react with the *0401 Mab. DNA sequencing of the second exon of the HLA-DRB1*0401 allele in this patient confirmed a normal HLA-DRB1*0401 genotype.
CONCLUSIONS—FACS analysis of PBMNC stained with Mab recognising the shared epitope and rheumatoid arthritis associated HLA susceptibility molecules provides a rapid, reliable, and more accessible alternative to DNA oligotyping. The apparent discordance between phenotypic and genetic analysis of HLA-DRB1*0401 in one patient, may reflect variability in HLA-DRB1*0401 gene expression or in class II peptide presentation.

     

Syntax processing by auditory cortical neurons in the FM–FM area of the mustached bat Pteronotus parnellii

Syntax denotes a rule system that allows one to predict the sequencing of communication signals. Despite its significance for both human speech processing and animal acoustic communication, the representation of syntactic structure in the mammalian brain has not been studied electrophysiologically at the single-unit level. In the search for a neuronal correlate for syntax, we used playback of natural and temporally destructured complex species-specific communication calls—so-called composites—while recording extracellularly from neurons in a physiologically well defined area (the FM–FM area) of the mustached bat’s auditory cortex. Even though this area is known to be involved in the processing of target distance information for echolocation, we found that units in the FM–FM area were highly responsive to composites. The finding that neuronal responses were strongly affected by manipulation in the time domain of the natural composite structure lends support to the hypothesis that syntax processing in mammals occurs at least at the level of the nonprimary auditory cortex.     

Iron-dextran antibody conjugates: General method for simultaneous staining of two components in high-resolution immunoelectron microscopy

We report the preparation and properties of an electron-dense antibody conjugate, made by the covalent bonding of an iron—dextran (Imposil) particle to an antibody molecule. Transmission electron microscopic experiments with the Imposil—antibody conjugates demonstrate their suitability as specific immunostains at high resolution, particularly for simultaneous double staining experiments in conjunction with ferritin—antibody conjugates.