Metagenomics: The Next Culture-Independent Game Changer.
Metagenomics: The Next Culture-Independent Game Changer.
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DOI：
10.3389/fmicb.2017.01069
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发表时间：
2017
影响因子：
5.2
通讯作者：
Reimer A
中科院分区：
文献类型：
--
作者：
Forbes JD;Knox NC;Ronholm J;Pagotto F;Reimer A
放弃在一线实验室获得纯培养分离物的趋势正处于一个十字路口，公共卫生机构有能力履行其食源性疾病监测和应对的基本任务。对急性胃肠炎实施独立于培养的诊断试验(CIDT)，包括核酸和基于抗原的分析，使得公共卫生机构没有实验室证据来将临床病例彼此联系起来，并与食物或环境物质联系起来。这限制了公共卫生流行病学和监测以及疫情检测和调查的效力。食源性暴发有可能没有被发现或没有足够的证据来支持源头归属，并可能无意中增加食源性疾病的发病率。临床微生物学实验室的下一代纯培养分离物测序有可能给食品安全和公共卫生领域带来革命性的变化。元基因组学和其他“组学”学科可以为临床微生物学、食品安全和公共卫生领域的无文化未来提供解决方案。从元基因组学分析获得的信息的数据挖掘除了提供高分辨率的亚型数据外，还可用于临床病原体或食源性污染的鉴定、AMR和/或毒力因子的检测。因此，元基因组学分析可以为临床诊断、食源性致病菌检测、分型和调查提供一种通用的检测方法。这些信息有可能改革肠道疾病诊断和监测领域以及整个传染病领域。这项审查的目的将是介绍诊断和公共卫生实验室中与食源性疾病和食品安全有关的CIDT的现状。此外，我们还将讨论临床微生物学、食品和公共卫生实验室中元基因组学和类似检测技术的诊断和分型实用以及伴随的偏倚限制。然而，元基因组学学科的早期进展已经表明了值得注意的挑战。通过即将在测序技术和分析管道等方面的改进，我们预计在未来十年内，通过基于元基因组学的工作流程对病原体的检测和表征将在诊断和公共卫生实验室的常规使用中实施。
A trend towards the abandonment of obtaining pure culture isolates in frontline laboratories is at a crossroads with the ability of public health agencies to perform their basic mandate of foodborne disease surveillance and response. The implementation of culture-independent diagnostic tests (CIDTs) including nucleic acid and antigen-based assays for acute gastroenteritis is leaving public health agencies without laboratory evidence to link clinical cases to each other and to food or environmental substances. This limits the efficacy of public health epidemiology and surveillance as well as outbreak detection and investigation. Foodborne outbreaks have the potential to remain undetected or have insufficient evidence to support source attribution and may inadvertently increase the incidence of foodborne diseases. Next-generation sequencing of pure culture isolates in clinical microbiology laboratories has the potential to revolutionize the fields of food safety and public health. Metagenomics and other ‘omics’ disciplines could provide the solution to a cultureless future in clinical microbiology, food safety and public health. Data mining of information obtained from metagenomics assays can be particularly useful for the identification of clinical causative agents or foodborne contamination, detection of AMR and/or virulence factors, in addition to providing high-resolution subtyping data. Thus, metagenomics assays may provide a universal test for clinical diagnostics, foodborne pathogen detection, subtyping and investigation. This information has the potential to reform the field of enteric disease diagnostics and surveillance and also infectious diseases as a whole. The aim of this review will be to present the current state of CIDTs in diagnostic and public health laboratories as they relate to foodborne illness and food safety. Moreover, we will also discuss the diagnostic and subtyping utility and concomitant bias limitations of metagenomics and comparable detection techniques in clinical microbiology, food and public health laboratories. Early advances in the discipline of metagenomics, however, have indicated noteworthy challenges. Through forthcoming improvements in sequencing technology and analytical pipelines among others, we anticipate that within the next decade, detection and characterization of pathogens via metagenomics-based workflows will be implemented in routine usage in diagnostic and public health laboratories.