Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
Black Country Pathology Service, Birmingham City Hospital, Dudley Road, Birmingham, West Midlands B18 7QH, UK.
Microb Genom. 2022 Jun;8(6). doi: 10.1099/mgen.0.000841.
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 , , and 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 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.
在一些新生儿病房中，对分离物进行抗微生物药物耐药性检测是常规操作，其理论上的益处包括预防或早期发现暴发。本研究旨在使用全基因组测序（WGS）回顾性地描述英国伯明翰市立医院 32 张病床的重症监护、高度依赖和特殊护理单元中筛选计划获得的革兰氏阴性菌的基因组流行病学，以确定隐匿性传播事件和临床上重要的抗微生物药物耐药性（AMR）基因。对从 44 名新生儿的直肠和脐部筛查拭子中采集的 155 株分离株进行了 WGS。基因组流行病学分析显示，可能涉及未通过常规筛查检测到的 、 、 和 的传播事件，共确定了 8 个涉及不同个体的假定簇。在系统发育簇内，根据 SNP 的丰度确定的生物体之间的相关性差异很大，表明可能涉及多种传播途径。虽然在假定的传播簇中没有发现临床上重要的 AMR 基因，但我们观察到个体内部的 种间水平转移，这表明它们在该环境中可能在生物体之间以及个体之间传播，这对监测有影响。我们的数据表明，WGS 可能揭示隐匿性革兰氏阴性传播事件，这表明基于测序的监测系统对抗医院病原体的潜力。在理解如何在实际环境中利用 WGS 监测来最大程度地发挥作用方面仍然存在挑战。
