Eyre David W, Golubchik Tanya, Gordon N Claire, Bowden Rory, Piazza Paolo, Batty Elizabeth M, Ip Camilla L C, Wilson Daniel J, Didelot Xavier, O'Connor Lily, Lay Rochelle, Buck David, Kearns Angela M, Shaw Angela, Paul John, Wilcox Mark H, Donnelly Peter J, Peto Tim E A, Walker A Sarah, Crook Derrick W
Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
BMJ Open. 2012 Jun 6;2(3). doi: 10.1136/bmjopen-2012-001124. Print 2012.
To investigate the prospects of newly available benchtop sequencers to provide rapid whole-genome data in routine clinical practice. Next-generation sequencing has the potential to resolve uncertainties surrounding the route and timing of person-to-person transmission of healthcare-associated infection, which has been a major impediment to optimal management.
The authors used Illumina MiSeq benchtop sequencing to undertake case studies investigating potential outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) and Clostridium difficile.
Isolates were obtained from potential outbreaks associated with three UK hospitals.
Isolates were sequenced from a cluster of eight MRSA carriers and an associated bacteraemia case in an intensive care unit, another MRSA cluster of six cases and two clusters of C difficile. Additionally, all C difficile isolates from cases over 6 weeks in a single hospital were rapidly sequenced and compared with local strain sequences obtained in the preceding 3 years.
Whole-genome genetic relatedness of the isolates within each epidemiological cluster.
Twenty-six MRSA and 15 C difficile isolates were successfully sequenced and analysed within 5 days of culture. Both MRSA clusters were identified as outbreaks, with most sequences in each cluster indistinguishable and all within three single nucleotide variants (SNVs). Epidemiologically unrelated isolates of the same spa-type were genetically distinct (≥21 SNVs). In both C difficile clusters, closely epidemiologically linked cases (in one case sharing the same strain type) were shown to be genetically distinct (≥144 SNVs). A reconstruction applying rapid sequencing in C difficile surveillance provided early outbreak detection and identified previously undetected probable community transmission.
This benchtop sequencing technology is widely generalisable to human bacterial pathogens. The findings provide several good examples of how rapid and precise sequencing could transform identification of transmission of healthcare-associated infection and therefore improve hospital infection control and patient outcomes in routine clinical practice.
研究新型台式测序仪在常规临床实践中提供快速全基因组数据的前景。下一代测序有潜力解决围绕医疗保健相关感染人际传播途径和时间的不确定性问题，这一直是优化管理的主要障碍。
作者使用Illumina MiSeq台式测序技术进行案例研究，调查耐甲氧西林金黄色葡萄球菌（MRSA）和艰难梭菌的潜在暴发情况。
分离株来自与英国三家医院相关的潜在暴发事件。
从重症监护病房的一组8例MRSA携带者及1例相关菌血症病例、另一组6例MRSA病例以及两组艰难梭菌病例中获取分离株进行测序。此外，对一家医院6周以上病例的所有艰难梭菌分离株进行快速测序，并与前3年获得的当地菌株序列进行比较。
每个流行病学集群内分离株的全基因组遗传相关性。
26株MRSA和15株艰难梭菌分离株在培养后5天内成功测序并分析。两个MRSA集群均被确认为暴发，每个集群中的大多数序列无法区分，且所有序列的单核苷酸变异（SNV）均在三个以内。相同spa型但流行病学上不相关的分离株在基因上是不同的（≥21个SNV）。在两个艰难梭菌集群中，流行病学上密切相关的病例（其中1例具有相同菌株类型）在基因上是不同的（≥144个SNV）。在艰难梭菌监测中应用快速测序进行的重建提供了早期暴发检测，并识别出先前未检测到的可能的社区传播。
这种台式测序技术可广泛应用于人类细菌病原体。这些发现提供了几个很好的例子，说明快速精确的测序如何能够改变医疗保健相关感染传播的识别方式，从而在常规临床实践中改善医院感染控制和患者预后。
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