WA PHL participation in GenomeTrakr Network for foodborne disease investigations using whole genome sequencing

1应用简介 华盛顿州公共卫生实验室(WA PHL)是首批四个实验室之一 3通过与FDA签订研究合作协议(RCA)形成了GenomeTrakr网络- 4 CFSAN于2012年末。2013年，WAPHL获得了MiSeq仪器，获得了李珍博士的支持 5通过ORISE联谊会，开始接受食品/环境测序的试剂支持 细菌分离物6株。 7在西澳PHL为GenomeTrakr执行的全基因组测序(WGS)工作总体上 8建立更强大的国际病原体追溯样本快速监测系统的目标 9通过可公开获得的食品和环境病原体数据库收集和编目序列 10株分离物。通过这项工作，WAPHL将继续扩大和改进疾病聚集性跟踪的结果 11返回具体来源，并将有助于监督遵守FDA关于 12安全食品处理做法，以加强食品安全的预防性控制。这个项目的具体目标是 13个是1.对多达400个食源性相关细菌、病毒和/或寄生虫病原体进行测序 14个分离物，2.根据要求加强合作和分享活的分离物培养3.积极参与 15在GenomeTrakr网络活动中。这项工作的总体目标只有在整个 16 GenomeTrakr网络继续为这一目标作出贡献(通过西澳PHL的参与以及 17个其他实验室)。此外，当前食源性疾病集群和/或暴发之间的成功联系 18一种食品或一种环境来源取决于从食品/环境来源获得WGS数据 19株和临床分离株。作为PulseNet西部地区实验室；WA PHL还在临床上执行WGS 因此，从食源性疾病患者那里获得的20个分离株；作为联系临床的管道 21个有源的星团。WAPHL主动在本地与适当的协作者共享集群信息，并 22全国加快食源性疾病暴发调查，预防更多食源性疾病和 23人死亡。 24 GenomeTrakr的工作正在彻底改变西澳PHL和WAPHL进行微生物学研究的方式 25个其他公共卫生实验室，在分子流行病学方面提供更高的分辨率和确定性 26对疾病聚集性的调查；进一步建立耐药标记基因组数据库； 27提供病原体传统表征方式的替代方法 28份(血清分型、毒力标记、耐药性分型等)。该项目的参与者拥有 29共同生成了大量数据，可供其他研究人员利用 30个额外的申请。

1 Introduction to Application 2 The Washington State Public Health Laboratories (WA PHL) were among of the first four laboratories 3 that formed the GenomeTrakr network by entering into a Research Cooperative Agreement (RCA) with FDA- 4 CFSAN in late 2012. In 2013, the WA PHL received a MiSeq instrument, obtained the support of Dr. Zhen Li 5 through the ORISE Fellowship and started receiving reagent support for the sequencing of food/environmental 6 bacterial isolates. 7 The whole genome sequencing (WGS) work performed at WA PHL for GenomeTrakr has the overall 8 objective of building a stronger international rapid surveillance system for pathogen trace back sample 9 collection and sequence cataloging through a publicly available database of food and environmental pathogen 10 isolates. Through this work, WA PHL will continue to expand and improve the outcome of disease cluster trace 11 back to specific sources and will contribute towards the effort of monitoring compliance with FDA’s rules on 12 safe food-handling practices to enhance preventive controls for food safety. The specific aims of this project 13 are 1. To sequence up to four hundred (400) foodborne related bacterial, viral and/or parasite pathogen 14 isolates, 2. To increase collaboration and share live isolate cultures upon request and 3. To actively participate 15 in GenomeTrakr network activities. The overall objective of this work will be possible only if the entire 16 GenomeTrakr network continues to contribute to this goal (through the participation of WA PHL as well as 17 other laboratories). In addition, the successful linkage of current foodborne disease clusters and/or outbreaks 18 to a food or an environmental source hinges upon obtaining WGS data from both food/environmental sources 19 and clinical isolates. As a PulseNet Western Region Area Laboratory; WA PHL also perform WGS on clinical 20 isolates obtained from patients with foodborne disease, therefore; serving as a conduit for the linking of clinical 21 clusters with a source. WA PHL actively shares cluster information with appropriate collaborators locally and 22 nationally to speed foodborne illness outbreak investigations and prevent additional foodborne illnesses and 23 deaths. 24 The GenomeTrakr work is revolutionizing the way in which microbiology is performed at WA PHL and 25 other public health laboratories by providing higher resolution and certainty in molecular epidemiology 26 investigations of disease clusters; by furthering the database of genomic antibiotic resistant markers; and by 27 providing alternative methodologies for the way in which pathogens have traditionally been characterized 28 (serotyping, virulence markers, resistance typing, etc) in the laboratory. Participants of this project have 29 collectively generated massive amounts of data that is publicly available for other researchers to harness for 30 additional applications.