被称为第三代测序技术的单分子测序是最近几年发展起来的高通量测序技术。其中,由Pacbio Bio Sciences公司开发的单分子实时测序技术(SMRT)是最先商用的技术。SMRT测序技术通过对模板序列循环测序产生环形一致序列(CCS),成功克服第三代...被称为第三代测序技术的单分子测序是最近几年发展起来的高通量测序技术。其中,由Pacbio Bio Sciences公司开发的单分子实时测序技术(SMRT)是最先商用的技术。SMRT测序技术通过对模板序列循环测序产生环形一致序列(CCS),成功克服第三代测序技术准确率低的弊病。通过SMRT测序技术,科学家可以更深入准确地探究复杂环境微生物的结构和功能。介绍SMRT测序技术在微生物16S rRNA基因测序中的优势和劣势,并就基于SMRT测序技术所得的全长16S rRNA基因序列的质量控制、错误序列排除、聚类和注释分析等重要分析环节进行概述,同时,提出利用SMRT测序技术研究复杂环境微生物可能存在的问题及其解决方法,期望能为研究人员提供参考。展开更多
BACKGROUND Infectious diseases are still one of the greatest threats to human health,and the etiology of 20%of cases of clinical fever is unknown;therefore,rapid identification of pathogens is highly important.Traditi...BACKGROUND Infectious diseases are still one of the greatest threats to human health,and the etiology of 20%of cases of clinical fever is unknown;therefore,rapid identification of pathogens is highly important.Traditional culture methods are only able to detect a limited number of pathogens and are time-consuming;serologic detection has window periods,false-positive and false-negative problems;and nucleic acid molecular detection methods can detect several known pathogens only once.Three-generation nanopore sequencing technology provides new options for identifying pathogens.CASE SUMMARY Case 1:The patient was admitted to the hospital with abdominal pain for three days and cessation of defecation for five days,accompanied by cough and sputum.Nanopore sequencing of the drainage fluid revealed the presence of orallike bacteria,leading to a clinical diagnosis of bronchopleural fistula.Cefoperazone sodium sulbactam treatment was effective.Case 2:The patient was admitted to the hospital with fever and headache,and CT revealed lung inflammation.Antibiotic treatment for Streptococcus pneumoniae,identified through nanopore sequencing of cerebrospinal fluid,was effective.Case 3:The patient was admitted to our hospital with intermittent fever and an enlarged neck mass that had persisted for more than six months.Despite antibacterial treatment,her symptoms worsened.The nanopore sequencing results indicate that voriconazole treatment is effective for Aspergillus brookii.The patient was diagnosed with mixed cell type classical Hodgkin's lymphoma with infection.CONCLUSION Three-generation nanopore sequencing technology allows for rapid and accurate detection of pathogens in human infectious diseases.展开更多
文摘被称为第三代测序技术的单分子测序是最近几年发展起来的高通量测序技术。其中,由Pacbio Bio Sciences公司开发的单分子实时测序技术(SMRT)是最先商用的技术。SMRT测序技术通过对模板序列循环测序产生环形一致序列(CCS),成功克服第三代测序技术准确率低的弊病。通过SMRT测序技术,科学家可以更深入准确地探究复杂环境微生物的结构和功能。介绍SMRT测序技术在微生物16S rRNA基因测序中的优势和劣势,并就基于SMRT测序技术所得的全长16S rRNA基因序列的质量控制、错误序列排除、聚类和注释分析等重要分析环节进行概述,同时,提出利用SMRT测序技术研究复杂环境微生物可能存在的问题及其解决方法,期望能为研究人员提供参考。
基金Supported by Research and Development Funding for Medical and Health Institutions,No.2021YL007.
文摘BACKGROUND Infectious diseases are still one of the greatest threats to human health,and the etiology of 20%of cases of clinical fever is unknown;therefore,rapid identification of pathogens is highly important.Traditional culture methods are only able to detect a limited number of pathogens and are time-consuming;serologic detection has window periods,false-positive and false-negative problems;and nucleic acid molecular detection methods can detect several known pathogens only once.Three-generation nanopore sequencing technology provides new options for identifying pathogens.CASE SUMMARY Case 1:The patient was admitted to the hospital with abdominal pain for three days and cessation of defecation for five days,accompanied by cough and sputum.Nanopore sequencing of the drainage fluid revealed the presence of orallike bacteria,leading to a clinical diagnosis of bronchopleural fistula.Cefoperazone sodium sulbactam treatment was effective.Case 2:The patient was admitted to the hospital with fever and headache,and CT revealed lung inflammation.Antibiotic treatment for Streptococcus pneumoniae,identified through nanopore sequencing of cerebrospinal fluid,was effective.Case 3:The patient was admitted to our hospital with intermittent fever and an enlarged neck mass that had persisted for more than six months.Despite antibacterial treatment,her symptoms worsened.The nanopore sequencing results indicate that voriconazole treatment is effective for Aspergillus brookii.The patient was diagnosed with mixed cell type classical Hodgkin's lymphoma with infection.CONCLUSION Three-generation nanopore sequencing technology allows for rapid and accurate detection of pathogens in human infectious diseases.
