Whole-genome sequencing enhances existing pathogen and antimicrobial-resistance surveillance schemes within a neonatal unit.
Whole-genome sequencing enhances existing pathogen and antimicrobial-resistance surveillance schemes within a neonatal unit.
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DOI：
10.1099/mgen.0.000841
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发表时间：
2022-06
影响因子：
3.9
通讯作者：
McNally, Alan
中科院分区：
文献类型：
--
作者：
Price, Vivien;Dunn, Steven J.;Moran, Robert A.;Swindells, Jonathan;McNally, Alan
在一些新生儿病房，筛选耐抗生素微生物的分离株是一项常规工作，其理论上的好处包括预防或早期发现疫情。本研究旨在回顾性地使用全基因组测序（WGS）来表征从英国伯明翰城市医院提供密集，高依赖性和特殊护理的32张病床单位的筛查计划中获得的革兰氏阴性菌的基因组流行病学，确定隐匿性传播事件和临床重要的抗菌素耐药（AMR）基因。对44名新生儿在2个月内从直肠和脐带筛查拭子中收集的155株分离株进行WGS。基因组流行病学分析显示，可能的传播事件涉及 大肠杆菌、 阴沟肠杆菌， 酸克雷伯菌 和 肺炎克雷伯菌 常规筛查未检测到，8个推定的集群涉及不同的个人确定。在系统发生簇中，生物体的相关性-由SNP的丰度确定-变化很大，表明可能涉及多种传播途径。虽然临床上重要的AMR基因不存在于假定的传播集群中，但我们对个体内bla CTX-M-15的疑似种间水平转移的观察突出了其在该环境中在生物体和个体之间传播的潜力，并对监测产生影响。我们的数据表明，WGS可以揭示隐匿性革兰氏阴性传播事件，证明了基于测序的医院病原体监测系统的潜力。在理解如何在现实世界中最大限度地利用WGS监测方面仍然存在挑战。
In some neonatal units, the screening of isolates for antimicrobial-resistant organisms is a matter of routine, with theoretical benefits including the prevention or early detection of outbreaks. This study sought to use whole-genome sequencing (WGS) retrospectively to characterize the genomic epidemiology of Gram-negative organisms obtained from a screening programme in a 32-bed unit providing intensive, high-dependency and special care at City Hospital, Birmingham, UK, identifying occult transmission events and clinically important antimicrobial-resistance (AMR) genes. WGS was performed for 155 isolates collected from rectal and umbilical screening swabs over a 2 month period from 44 individual neonates. Genomic epidemiological analysis showed possible transmission events involving Escherichia coli , Enterobacter cloacae , Klebsiella oxytoca and Klebsiella pneumoniae not detected by routine screening, with eight putative clusters involving different individuals identified. Within phylogenetic clusters, the relatedness of organisms – as determined by the abundance of SNPs – varied widely, indicating that a variety of transmission routes may be implicated. While clinically important AMR genes were not present in the putative transmission clusters, our observation of suspected interspecies horizontal transfer of bla CTX-M-15 within individuals highlights the potential for their spread between organisms as well as individuals in this environment, with implications for surveillance. Our data show that WGS may reveal occult Gram-negative transmission events, demonstrating the potential of sequencing-based surveillance systems for nosocomial pathogens. Challenges remain in understanding how to utilize WGS surveillance to maximum effect in real-world settings.
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DOI：
10.1016/j.jhin.2020.11.001
发表时间：
2021-03
期刊：
The Journal of hospital infection
影响因子：
--
作者：
Parcell BJ;Gillespie SH;Pettigrew KA;Holden MTG
通讯作者：
Holden MTG
DOI：
10.1093/bioinformatics/btx610
发表时间：
2018-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Hadfield J;Croucher NJ;Goater RJ;Abudahab K;Aanensen DM;Harris SR
通讯作者：
Harris SR
影响因子：
13.8
作者：
Nurjadi D;Eichel VM;Tabatabai P;Klein S;Last K;Mutters NT;Pöschl J;Zanger P;Heeg K;Boutin S
通讯作者：
Boutin S
DOI：
10.3390/antibiotics9100705
发表时间：
2020-10-16
期刊：
Antibiotics (Basel, Switzerland)
影响因子：
--
作者：
Frenk S;Rakovitsky N;Temkin E;Schechner V;Cohen R;Kloyzner BS;Schwaber MJ;Solter E;Cohen S;Stepansky S;Carmeli Y
通讯作者：
Carmeli Y
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.