全基因组测序在疫情调查中的实时应用——可实现的周转时间是多少？
Real time application of whole genome sequencing for outbreak investigation - What is an achievable turnaround time?
作者信息
McGann Patrick, Bunin Jessica L, Snesrud Erik, Singh Seema, Maybank Rosslyn, Ong Ana C, Kwak Yoon I, Seronello Scott, Clifford Robert J, Hinkle Mary, Yamada Stephen, Barnhill Jason, Lesho Emil
机构信息
Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
Department of Critical Care, Tripler Army Medical Center, Honolulu, HI, USA.
出版信息
Diagn Microbiol Infect Dis. 2016 Jul;85(3):277-282. doi: 10.1016/j.diagmicrobio.2016.04.020. Epub 2016 Apr 30.
Whole genome sequencing (WGS) is increasingly employed in clinical settings, though few assessments of turnaround times (TAT) have been performed in real-time. In this study, WGS was used to investigate an unfolding outbreak of vancomycin resistant Enterococcus faecium (VRE) among 3 patients in the ICU of a tertiary care hospital. Including overnight culturing, a TAT of just 48.5 h for a comprehensive report was achievable using an Illumina Miseq benchtop sequencer. WGS revealed that isolates from patient 2 and 3 differed from that of patient 1 by a single nucleotide polymorphism (SNP), indicating nosocomial transmission. However, the unparalleled resolution provided by WGS suggested that nosocomial transmission involved two separate events from patient 1 to patient 2 and 3, and not a linear transmission suspected by the time line. Rapid TAT's are achievable using WGS in the clinical setting and can provide an unprecedented level of resolution for outbreak investigations.
全基因组测序（WGS）在临床环境中的应用越来越广泛，不过很少有对周转时间（TAT）进行实时评估的研究。在本研究中，WGS被用于调查一家三级护理医院重症监护病房（ICU）中3例患者之间正在发生的耐万古霉素屎肠球菌（VRE）暴发情况。包括过夜培养在内，使用Illumina Miseq台式测序仪，48.5小时即可获得一份全面报告的周转时间。WGS显示，患者2和患者3的分离株与患者1的分离株存在一个单核苷酸多态性（SNP）差异，表明存在医院内传播。然而，WGS提供的无与伦比的分辨率表明，医院内传播涉及从患者1到患者2和患者3的两个独立事件，而不是时间线所怀疑的线性传播。在临床环境中使用WGS可以实现快速的周转时间，并且可为暴发调查提供前所未有的分辨率水平。
Zotero 插件