Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical care.
Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical care.
复制标题
DOI：
10.1099/mgen.0.000530
复制
发表时间：
2021-03
影响因子：
3.9
通讯作者：
Harris PNA
中科院分区：
文献类型：
--
作者：
Roberts LW;Forde BM;Hurst T;Ling W;Nimmo GR;Bergh H;George N;Hajkowicz K;McNamara JF;Lipman J;Permana B;Schembri MA;Paterson D;Beatson SA;Harris PNA
背景资料。耐碳青霉烯类鲍曼不动杆菌(CR-Ab)感染在临床上日益普遍，由于其多药耐药(MDR)，常导致严重的发病率和死亡率。在这里，我们展示了2016-2018年间布里斯班一家医院持续爆发CR-Ab的综合全基因组测序(WGS)反应。方法：研究方法。利用Illumina平台对鲍曼不动杆菌、肺炎克雷伯菌、粘质沙雷氏菌和铜绿假单胞菌进行了测序，初步建立了基于核心基因组SNPs、MLST和耐药性基因图谱的分离株之间的关系。选择具有代表性的菌株进行PacBio测序。使用Illumina环境元基因组测序来检测暴发菌株在医院的持久性。结果。为了应对2016年5月至8月期间疑似多微生物暴发，从重症监护病房和烧伤病房患者中收集了28株CR-Ab(和其他21株耐多药革兰氏阴性杆菌)，并将其送往WGS，临床报告的周转时间为7天。所有的CR-Ab都是序列类型(ST)1050(巴斯德ST2)，并且相隔10个SNP，表明正在暴发，与同一家医院的历史CR-Ab分离株不同。根据CR-Ab和肺炎克雷伯菌SNP图谱，确定了患者之间可能的传播途径。2016年至2018年期间WGS的持续监测使疑似暴发病例得以驳斥，但2018年年中烧伤股暴发CR-Ab疫情的死灰复燃促使进一步筛查。环境元基因组测序确定医院管道是一个潜在的来源。更换管道和例行排水管维护后，迅速解决了第二次暴发，大大降低了风险，此后烧伤病区没有明显的传播。结论。我们实施了一项全面的WGS和元基因组学调查，解决了重症监护环境中持续爆发的CR-Ab。
Background. Infections caused by carbapenem-resistant Acinetobacter baumannii (CR-Ab) have become increasingly prevalent in clinical settings and often result in significant morbidity and mortality due to their multidrug resistance (MDR). Here we present an integrated whole-genome sequencing (WGS) response to a persistent CR-Ab outbreak in a Brisbane hospital between 2016–2018. Methods. A. baumannii, Klebsiella pneumoniae, Serratia marcescens and Pseudomonas aeruginosa isolates were sequenced using the Illumina platform primarily to establish isolate relationships based on core-genome SNPs, MLST and antimicrobial resistance gene profiles. Representative isolates were selected for PacBio sequencing. Environmental metagenomic sequencing with Illumina was used to detect persistence of the outbreak strain in the hospital. Results. In response to a suspected polymicrobial outbreak between May to August of 2016, 28 CR-Ab (and 21 other MDR Gram-negative bacilli) were collected from Intensive Care Unit and Burns Unit patients and sent for WGS with a 7 day turn-around time in clinical reporting. All CR-Ab were sequence type (ST)1050 (Pasteur ST2) and within 10 SNPs apart, indicative of an ongoing outbreak, and distinct from historical CR-Ab isolates from the same hospital. Possible transmission routes between patients were identified on the basis of CR-Ab and K. pneumoniae SNP profiles. Continued WGS surveillance between 2016 to 2018 enabled suspected outbreak cases to be refuted, but a resurgence of the outbreak CR-Ab mid-2018 in the Burns Unit prompted additional screening. Environmental metagenomic sequencing identified the hospital plumbing as a potential source. Replacement of the plumbing and routine drain maintenance resulted in rapid resolution of the secondary outbreak and significant risk reduction with no discernable transmission in the Burns Unit since. Conclusion. We implemented a comprehensive WGS and metagenomics investigation that resolved a persistent CR-Ab outbreak in a critical care setting.
登录
查看更多内容
DOI：
10.1093/jac/dkx322
发表时间：
2017-12-01
期刊：
The Journal of antimicrobial chemotherapy
影响因子：
--
作者：
Nowak J;Zander E;Stefanik D;Higgins PG;Roca I;Vila J;McConnell MJ;Cisneros JM;Seifert H;MagicBullet Working Group WP4
通讯作者：
MagicBullet Working Group WP4
DOI：
10.1126/science.1182395
发表时间：
2010-01-22
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Harris SR;Feil EJ;Holden MT;Quail MA;Nickerson EK;Chantratita N;Gardete S;Tavares A;Day N;Lindsay JA;Edgeworth JD;de Lencastre H;Parkhill J;Peacock SJ;Bentley SD
通讯作者：
Bentley SD
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：
5.2
作者：
Corvec, S;Caroff, N;Reynaud, A
通讯作者：
Reynaud, A
影响因子：
2
作者：
Jiang, Yushan;Resch, Stephen;Jayaraman, Sudha P.
通讯作者：
Jayaraman, Sudha P.