Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak.
Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak.
复制标题
作者：
Kwong JC;Lane CR;Romanes F;Gonçalves da Silva A;Easton M;Cronin K;Waters MJ;Tomita T;Stevens K;Schultz MB;Baines SL;Sherry NL;Carter GP;Mu A;Sait M;Ballard SA;Seemann T;Stinear TP;Howden BP
直到最近，在澳大利亚很少发现产肺炎克雷伯菌碳青霉烯酶（KPC）的肠杆菌科。随着整个维多利亚州事件病例数量的增加，我们进行了实时基因组和流行病学联合调查。这项研究的范围包括确定风险因素和传播途径，并调查基因组学的效用，以加强传统的现场流行病学，为管理已确定的大范围疫情提供信息。纳入了从2012年起提交给国家参考实验室的所有产KPC肠杆菌科分离株。全基因组测序与每个病例的详细描述性流行病学调查平行进行，使用Illumina测序每个分离株。这与PacBio对选定分离株的长读测序相补充，以建立高质量的参考序列并询问编码KPC的质粒的特征。初步调查显示，这次爆发是广泛的，有86个产KPC的肠杆菌科菌株（K。在2012年至2015年期间，从维多利亚大都市和农村的35个不同地点鉴定出肺炎（92%）。对流行病学和基因组数据的初步综合分析将疫情分解为不同的医院传播网络，并确定了KPC传播中心的医疗设施。新病例被实时分配到传播网络，从而能够集中控制感染。PacBio测序证实了种间质粒传播引起的二级传播网络。贝叶斯传播推断和宿主内多样性分析的见解为全州公共卫生和感染控制指南的制定提供了信息，包括干预措施，如在新病例检测后筛查接触者的密集方法，以最大限度地减少未识别的殖民化。一个实时的流行病学和基因组相结合的调查被证明是至关重要的，以确定和定义KPC肠杆菌科的多个传输网络，而单独的调查数据是不确定的。该调查对于实时通知感染控制措施以及制定全州范围内关于产碳青霉烯酶肠杆菌科监测和管理的公共卫生指南至关重要。
Until recently, Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae were rarely identified in Australia. Following an increase in the number of incident cases across the state of Victoria, we undertook a real-time combined genomic and epidemiological investigation. The scope of this study included identifying risk factors and routes of transmission, and investigating the utility of genomics to enhance traditional field epidemiology for informing management of established widespread outbreaks. All KPC-producing Enterobacteriaceae isolates referred to the state reference laboratory from 2012 onwards were included. Whole-genome sequencing was performed in parallel with a detailed descriptive epidemiological investigation of each case, using Illumina sequencing on each isolate. This was complemented with PacBio long-read sequencing on selected isolates to establish high-quality reference sequences and interrogate characteristics of KPC-encoding plasmids. Initial investigations indicated that the outbreak was widespread, with 86 KPC-producing Enterobacteriaceae isolates (K. pneumoniae 92%) identified from 35 different locations across metropolitan and rural Victoria between 2012 and 2015. Initial combined analyses of the epidemiological and genomic data resolved the outbreak into distinct nosocomial transmission networks, and identified healthcare facilities at the epicentre of KPC transmission. New cases were assigned to transmission networks in real-time, allowing focussed infection control efforts. PacBio sequencing confirmed a secondary transmission network arising from inter-species plasmid transmission. Insights from Bayesian transmission inference and analyses of within-host diversity informed the development of state-wide public health and infection control guidelines, including interventions such as an intensive approach to screening contacts following new case detection to minimise unrecognised colonisation. A real-time combined epidemiological and genomic investigation proved critical to identifying and defining multiple transmission networks of KPC Enterobacteriaceae, while data from either investigation alone were inconclusive. The investigation was fundamental to informing infection control measures in real-time and the development of state-wide public health guidelines on carbapenemase-producing Enterobacteriaceae surveillance and management.
登录
查看更多内容
影响因子：
5.2
作者：
Carter, Glen P.;Buultjens, Andrew H.;Howden, Benjamin P.
通讯作者：
Howden, Benjamin P.
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
影响因子：
9.8
作者：
Drummond AJ;Ho SY;Phillips MJ;Rambaut A
通讯作者：
Rambaut A
影响因子：
17.1
作者：
Conlan S;Thomas PJ;Deming C;Park M;Lau AF;Dekker JP;Snitkin ES;Clark TA;Luong K;Song Y;Tsai YC;Boitano M;Dayal J;Brooks SY;Schmidt B;Young AC;Thomas JW;Bouffard GG;Blakesley RW;NISC Comparative Sequencing Program;Mullikin JC;Korlach J;Henderson DK;Frank KM;Palmore TN;Segre JA
通讯作者：
Segre JA
影响因子：
4.3
作者：
Didelot X;Wilson DJ
通讯作者：
Wilson DJ