A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance.
A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance.
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DOI：
10.1136/bmjopen-2012-001124
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发表时间：
2012
期刊：
影响因子：
2.9
通讯作者：
Crook DW
中科院分区：
文献类型：
--
作者：
Eyre DW;Golubchik T;Gordon NC;Bowden R;Piazza P;Batty EM;Ip CL;Wilson DJ;Didelot X;O'Connor L;Lay R;Buck D;Kearns AM;Shaw A;Paul J;Wilcox MH;Donnelly PJ;Peto TE;Walker AS;Crook DW
探讨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。下一代测序有可能解决围绕卫生保健相关感染的人际传播途径和时间的不确定性，这一直是最佳管理的主要障碍。作者使用Illumina MiSeq台式测序进行案例研究，调查耐甲氧西林金黄色葡萄球菌（MRSA）和艰难梭菌的潜在爆发。分离株来自与三家英国医院相关的潜在疫情。对来自重症监护室的8个MRSA携带者和相关菌血症病例的一组、6个病例的另一组MRSA和两组艰难梭菌的分离株进行测序。此外，对来自同一家医院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。 每个流行病学聚类中分离株的全基因组遗传相关性。26个MRSA和15个艰难梭菌分离株在培养5天内成功测序和分析。 两个MRSA簇都被鉴定为爆发，每个簇中的大多数序列无法区分，并且都在三个单核苷酸变体（SNV）内。相同SPA型的流行病学无关分离株在遗传上不同（≥21个SNV）。在两个艰难梭菌群中，流行病学密切相关的病例（一例病例共享相同的菌株类型）显示具有遗传差异（≥144个SNV）。在艰难梭菌监测中应用快速测序的重建提供了早期爆发检测，并确定了以前未检测到的可能的社区传播。这种台式测序技术可广泛推广到人类细菌病原体。这些发现提供了几个很好的例子，说明快速和精确的测序如何改变医疗相关感染传播的识别，从而改善医院感染控制和常规临床实践中的患者结局。探讨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。特别是调查这种技术在查明与卫生保健有关的病原体传播事件方面的潜力。我们证明台式测序可以通过使用遗传数据的高精度支持和拒绝传播来增强医院感染控制。全基因组数据提供了额外的遗传分辨率超过现有的遗传分型策略。我们还展示了这项技术提供了一周以下的周转时间，与分子分型相比，它是独立于生物体的。这些案例研究提供了几个很好的例子，说明快速和精确的测序如何改变医疗相关感染传播的识别。鉴于这是一项试点研究，需要进一步评估这项技术对医院感染控制的影响。然而，这项研究提供了一个明确的理由，未来的工作进行正式的比较台式测序与现有的地方和国家分型计划。
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. To investigate the prospects of newly available benchtop sequencers to provide rapid whole-genome data in routine clinical practice. In particular to investigate the potential of such technology for identification of transmission events of healthcare-associated pathogens. We demonstrate benchtop sequencing can enhance hospital infection control through high precision support and rejection of transmission using genetic data. Whole-genome data provided additional genetic resolution over existing genetic typing strategies. We also show this technology offers turnaround times of under a week in a format that, in contrast to molecular typing, is organism independent. The case studies presented provide several good examples of how rapid and precise sequencing could transform identification of transmission of healthcare-associated infection. Given this is a pilot study, further evaluations of the impact of this technology on hospital infection control are required. However, this study provides a clear rationale for future work undertaking formal comparisons of benchtop sequencing with existing local and national typing schemes.
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DOI：
10.1056/nejmoa1106920
发表时间：
2011-08-25
期刊：
The New England journal of medicine
影响因子：
--
作者：
Rasko DA;Webster DR;Sahl JW;Bashir A;Boisen N;Scheutz F;Paxinos EE;Sebra R;Chin CS;Iliopoulos D;Klammer A;Peluso P;Lee L;Kislyuk AO;Bullard J;Kasarskis A;Wang S;Eid J;Rank D;Redman JC;Steyert SR;Frimodt-Møller J;Struve C;Petersen AM;Krogfelt KA;Nataro JP;Schadt EE;Waldor MK
通讯作者：
Waldor MK
影响因子：
30.8
作者：
通讯作者：
--
影响因子：
11.8
作者：
Blanc, DS;Petignat, C;Francioli, P
通讯作者：
Francioli, P
影响因子：
7
作者：
Lunter, Gerton;Goodson, Martin
通讯作者：
Goodson, Martin
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