The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain.
The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain.
复制标题
DOI：
10.3390/genes9050268
复制
发表时间：
2018-05-22
期刊：
影响因子：
3.5
通讯作者：
Alvarez-Ordóñez A
中科院分区：
文献类型：
--
作者：
Oniciuc EA;Likotrafiti E;Alvarez-Molina A;Prieto M;Santos JA;Alvarez-Ordóñez A
抗菌素耐药性监测是风险评估计划中的关键步骤，因为它是为全球战略提供信息、监测公共卫生干预措施的有效性以及发现与食品有关的新趋势和新威胁的基础。目前对AMR的监测是基于指示微生物的分离以及所分离的临床、环境和食品菌株的表型特征。然而，这种方法提供的关于驱动AMR的机制或AMR基因在整个食物链中的存在或传播的信息非常有限。细菌病原体的全基因组测序已显示出在流行病学监测、暴发检测和感染控制方面的潜力。此外，整个元基因组测序(WMS)允许对复杂的微生物群落进行独立于培养的分析，提供有关AMR基因发生的有用信息。这两种技术都可以帮助追踪AMR基因和可移动的遗传元件，为实施定量风险评估提供必要的信息，并能够确定AMR在食物链中的传播热点和途径。这篇综述文章总结了目前使用WGS和WMS监测食源性致病菌和食品相关样品中AMR的信息，并讨论了为实现这一目标而常规实施这些下一代测序方法所必须考虑的未来需求。特别是，确定了阻碍这些高通量测序(HTS)技术在全球范围内使用的方法学限制，并建议将方法和协议标准化作为升级基于HTS的AMR监测方案的一项措施。
Antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. Whole-genome sequencing (WGS) of bacterial pathogens has shown potential for epidemiological surveillance, outbreak detection, and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on AMR genes occurrence. Both technologies can assist the tracking of AMR genes and mobile genetic elements, providing the necessary information for the implementation of quantitative risk assessments and allowing for the identification of hotspots and routes of transmission of AMR across the food chain. This review article summarizes the information currently available on the use of WGS and WMS for surveillance of AMR in foodborne pathogenic bacteria and food-related samples and discusses future needs that will have to be considered for the routine implementation of these next-generation sequencing methodologies with this aim. In particular, methodological constraints that impede the use at a global scale of these high-throughput sequencing (HTS) technologies are identified, and the standardization of methods and protocols is suggested as a measure to upgrade HTS-based AMR surveillance schemes.
登录
查看更多内容
影响因子：
4.2
作者：
Berman, Hillary F.;Riley, Lee W.
通讯作者：
Riley, Lee W.
DOI：
10.1038/ismej.2014.237
发表时间：
2015-06
期刊：
The ISME journal
影响因子：
--
作者：
通讯作者：
--
影响因子：
6.4
作者：
Card RM;Cawthraw SA;Nunez-Garcia J;Ellis RJ;Kay G;Pallen MJ;Woodward MJ;Anjum MF
通讯作者：
Anjum MF
影响因子：
4
作者：
Bhatt, V. D.;Ahir, V. B.;Joshi, C. G.
通讯作者：
Joshi, C. G.
影响因子：
2
作者：
Berrang, Mark E.;Meinersmann, Richard J.;Ladely, Scott R.
通讯作者：
Ladely, Scott R.