用于医院感染控制的全基因组测序多中心实施：一项前瞻性基因组流行病学分析。
Multi-site implementation of whole genome sequencing for hospital infection control: A prospective genomic epidemiological analysis.
作者信息
Sherry Norelle L, Gorrie Claire L, Kwong Jason C, Higgs Charlie, Stuart Rhonda L, Marshall Caroline, Ballard Susan A, Sait Michelle, Korman Tony M, Slavin Monica A, Lee Robyn S, Graham Maryza, Leroi Marcel, Worth Leon J, Chan Hiu Tat, Seemann Torsten, Grayson M Lindsay, Howden Benjamin P
机构信息
Microbiological Diagnostic Unit (MDU) Public Health Laboratory, Department of Microbiology & Immunology at the Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Victoria, Australia.
Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia.
出版信息
Lancet Reg Health West Pac. 2022 Apr 12;23:100446. doi: 10.1016/j.lanwpc.2022.100446. eCollection 2022 Jun.
BACKGROUND
Current microbiological methods lack the resolution to accurately identify multidrug-resistant organism (MDRO) transmission, however, whole genome sequencing can identify highly-related patient isolates providing opportunities for precision infection control interventions. We investigated the feasibility and potential impact of a prospective multi-centre genomics workflow for hospital infection control.
METHODS
We conducted a prospective genomics implementation study across eight Australian hospitals over 15 months (2017,2018), collecting all clinical and screening isolates from inpatients with VRE, MRSA, ESBL (ESBL-Ec), or ESBL (ESBL-Kp). Genomic and epidemiologic data were integrated to assess MDRO transmission.
FINDINGS
In total, 2275 isolates were included from 1970 patients, predominantly ESBL-Ec (40·8%) followed by MRSA (35·6%), VRE (15·2%), and ESBL-Kp (8·3%).Overall, hospital and genomic epidemiology showed 607 patients (30·8%) acquired their MDRO in hospital, including the majority of VRE (266 patients, 86·4%), with lower proportions of ESBL-Ec (186 patients, 23·0%), ESBL-Kp (42 patients, 26·3%), and MRSA (113 patients, 16·3%). Complex patient movements meant the majority of MDRO transmissions would remain undetected without genomic data.The genomics implementation had major impacts, identifying unexpected MDRO transmissions prompting new infection control interventions, and contributing to VRE becoming a notifiable condition. We identified barriers to implementation and recommend strategies for mitigation.
INTERPRETATION
Implementation of a multi-centre genomics-informed infection control workflow is feasible and identifies many unrecognised MDRO transmissions. This provides critical opportunities for interventions to improve patient safety in hospitals.
FUNDING
Melbourne Genomics Health Alliance (supported by State Government of Victoria, Australia), and National Health and Medical Research Council (Australia).
背景
目前的微生物学方法缺乏准确识别多重耐药菌（MDRO）传播的分辨率，然而，全基因组测序可以识别高度相关的患者分离株，为精准感染控制干预提供机会。我们调查了一种用于医院感染控制的前瞻性多中心基因组学工作流程的可行性和潜在影响。
方法
我们在2017年至2018年的15个月内，对澳大利亚的八家医院进行了一项前瞻性基因组学实施研究，收集了所有耐万古霉素肠球菌（VRE）、耐甲氧西林金黄色葡萄球菌（MRSA）、产超广谱β-内酰胺酶大肠杆菌（ESBL-Ec）或产超广谱β-内酰胺酶肺炎克雷伯菌（ESBL-Kp）住院患者的临床和筛查分离株。整合基因组和流行病学数据以评估MDRO传播。
研究结果
共纳入了1970例患者的2275株分离株，主要是ESBL-Ec（40.8%），其次是MRSA（35.6%）、VRE（15.2%）和ESBL-Kp（8.3%）。总体而言，医院和基因组流行病学显示，607例患者（30.8%）在医院获得了MDRO，其中大多数是VRE（266例患者，86.4%），ESBL-Ec（186例患者，23.0%）、ESBL-Kp（42例患者，26.3%）和MRSA（113例患者，16.3%）的比例较低。复杂的患者流动意味着如果没有基因组数据，大多数MDRO传播将仍未被发现。基因组学的实施产生了重大影响，识别出意想不到的MDRO传播，促使采取新的感染控制干预措施，并促使VRE成为应报告的疾病。我们确定了实施的障碍并推荐了缓解策略。
解读
实施多中心基因组学指导的感染控制工作流程是可行的，并能识别许多未被认识到的MDRO传播。这为采取干预措施改善医院患者安全提供了关键机会。
资金来源
墨尔本基因组健康联盟（由澳大利亚维多利亚州政府支持）和澳大利亚国家卫生与医学研究委员会。
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