全基因组测序在暴发调查中的应用的一些见解。
Selected insights from application of whole-genome sequencing for outbreak investigations.
机构信息
aDivision of Infectious Diseases, Department of Medicine, University of California, San Francisco, California bDivision of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA.
出版信息
Curr Opin Crit Care. 2013 Oct;19(5):432-9. doi: 10.1097/MCC.0b013e3283636b8c.
Abstract
PURPOSE OF REVIEW
The advent of high-throughput whole-genome sequencing has the potential to revolutionize the conduct of outbreak investigation. Because of its ultimate resolution power for differentiating between closely related pathogen strains, whole-genome sequencing could augment the traditional epidemiologic investigations of infectious disease outbreaks.
RECENT FINDINGS
The combination of whole-genome sequencing and intensive epidemiologic analysis provided new insights on the sources and transmission dynamics of large-scale epidemics caused by Escherichia coli and Vibrio cholerae, nosocomial outbreaks caused by methicillin-resistant Staphylococcus aureus, Klebsiella pneumoniae, Mycobacterium abscessus, community-centered outbreaks caused by Mycobacterium tuberculosis, and natural disaster-associated outbreaks caused by environmentally acquired molds.
SUMMARY
When combined with traditional epidemiologic investigation, whole-genome sequencing has proven useful for elucidating the sources and transmission dynamics of disease outbreaks. Development of a fully automated bioinformatics pipeline for the analysis of whole-genome sequence data is much needed to make this powerful tool more widely accessible.
摘要
目的综述
高通量全基因组测序的出现有可能彻底改变暴发调查的实施方式。由于其在区分密切相关的病原体菌株方面具有最终的分辨率，全基因组测序可以增强传染病暴发的传统流行病学调查。
最近的发现
全基因组测序与密集的流行病学分析相结合，为大肠杆菌和霍乱弧菌引起的大规模流行、耐甲氧西林金黄色葡萄球菌、肺炎克雷伯菌、脓肿分枝杆菌、社区为中心的结核分枝杆菌引起的医院感染暴发以及与自然灾害相关的环境获得性霉菌引起的暴发的来源和传播动态提供了新的见解。
总结
当与传统的流行病学调查相结合时，全基因组测序已被证明有助于阐明疾病暴发的来源和传播动态。非常需要开发一个全自动的生物信息学管道来分析全基因组序列数据，以使这个强大的工具更广泛地被使用。
相似文献
1
Selected insights from application of whole-genome sequencing for outbreak investigations.全基因组测序在暴发调查中的应用的一些见解。
Curr Opin Crit Care. 2013 Oct;19(5):432-9. doi: 10.1097/MCC.0b013e3283636b8c.
2
Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study.全基因组测序分析耐甲氧西林金黄色葡萄球菌爆发：一项描述性研究。
Lancet Infect Dis. 2013 Feb;13(2):130-6. doi: 10.1016/S1473-3099(12)70268-2. Epub 2012 Nov 14.
3
Whole genome sequencing reveals a prolonged and spatially spread nosocomial outbreak of Panton-Valentine leucocidin-positive meticillin-resistant Staphylococcus aureus (USA300).全基因组测序揭示了耐甲氧西林金黄色葡萄球菌（USA300）泛耐药、携带杀白细胞素 Panton-Valentine 的医院感染的长时间和空间扩散暴发。
J Hosp Infect. 2019 Mar;101(3):327-332. doi: 10.1016/j.jhin.2018.09.007. Epub 2018 Sep 18.
4
Tracking a hospital outbreak of KPC-producing ST11 Klebsiella pneumoniae with whole genome sequencing.利用全基因组测序追踪产 KPC 的 ST11 型肺炎克雷伯菌引起的医院感染暴发。
Clin Microbiol Infect. 2015 Nov;21(11):1001-7. doi: 10.1016/j.cmi.2015.07.001. Epub 2015 Jul 10.
5
Whole genome sequence revealed the fine transmission map of carbapenem-resistant isolates within a nosocomial outbreak.全基因组序列揭示了医院感染爆发中耐碳青霉烯类 分离株的精细传播图谱。
Antimicrob Resist Infect Control. 2018 Jun 1;7:70. doi: 10.1186/s13756-018-0363-8. eCollection 2018.
6
Pan-genome multilocus sequence typing and outbreak-specific reference-based single nucleotide polymorphism analysis to resolve two concurrent Staphylococcus aureus outbreaks in neonatal services.泛基因组多位点序列分型和基于爆发特异性参考的单核苷酸多态性分析，解决新生儿科中两起同时发生的金黄色葡萄球菌爆发事件。
Clin Microbiol Infect. 2016 Jun;22(6):520-6. doi: 10.1016/j.cmi.2016.01.024. Epub 2016 Feb 17.
7
Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation.实施全国范围的实时全基因组测序以加强李斯特菌病暴发的检测与调查。
Clin Infect Dis. 2016 Aug 1;63(3):380-6. doi: 10.1093/cid/ciw242. Epub 2016 Apr 18.
8
Whole-genome sequencing data-based modeling for the investigation of an outbreak of community-associated methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit in Hong Kong.基于全基因组测序数据的建模用于调查香港一家新生儿重症监护病房发生的社区相关性耐甲氧西林金黄色葡萄球菌爆发。
Eur J Clin Microbiol Infect Dis. 2019 Mar;38(3):563-573. doi: 10.1007/s10096-018-03458-y. Epub 2019 Jan 24.
9
Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis.细菌病原体的全基因组测序：医院感染暴发分析的未来
Clin Microbiol Rev. 2017 Oct;30(4):1015-1063. doi: 10.1128/CMR.00016-17.
10
Two listeria outbreaks caused by smoked fish consumption-using whole-genome sequencing for outbreak investigations.两起因食用熏鱼导致的李斯特菌病暴发——应用全基因组测序进行暴发调查。
Clin Microbiol Infect. 2016 Jul;22(7):620-4. doi: 10.1016/j.cmi.2016.04.017. Epub 2016 May 1.
引用本文的文献
1
RUBICON: a framework for designing efficient deep learning-based genomic basecallers.RUBICON：一种用于设计高效深度学习基因组碱基调用器的框架。
Genome Biol. 2024 Feb 16;25(1):49. doi: 10.1186/s13059-024-03181-2.
2
An Automated Strategy to Handle Antigenic Variability in Immunisation Protocols, Part I: Nanopore Sequencing of Infectious Agent Variants.免疫协议中抗原变异性处理的自动化策略，第一部分：传染性病原体变异的纳米孔测序。
Methods Mol Biol. 2023;2575:305-321. doi: 10.1007/978-1-0716-2716-7_16.
3
From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures.从分子到基因组变异：通过智能算法和架构加速基因组分析
Comput Struct Biotechnol J. 2022 Aug 18;20:4579-4599. doi: 10.1016/j.csbj.2022.08.019. eCollection 2022.
4
Development and validation of a high throughput SARS-CoV-2 whole genome sequencing workflow in a clinical laboratory.开发并验证一种临床实验室高通量 SARS-CoV-2 全基因组测序工作流程。
Sci Rep. 2022 Feb 8;12(1):2054. doi: 10.1038/s41598-022-06091-0.
5
The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks.实时全基因组测序在控制医疗保健相关 SARS-CoV-2 爆发中的影响。
J Infect Dis. 2022 Jan 5;225(1):10-18. doi: 10.1093/infdis/jiab483.
6
Thompson outbreak associated with consumption of chicken shawarma and the usefulness of genome sequencing in the investigation.与食用鸡肉沙瓦玛相关的汤普森疫情以及基因组测序在调查中的作用
Can Commun Dis Rep. 2017 Sep 7;43(9):186-192. doi: 10.14745/ccdr.v43i09a05.
7
Bayesian reconstruction of transmission within outbreaks using genomic variants.利用基因组变异对暴发疫情中的传播进行贝叶斯重建。
PLoS Comput Biol. 2018 Apr 18;14(4):e1006117. doi: 10.1371/journal.pcbi.1006117. eCollection 2018 Apr.
8
Routine Whole-Genome Sequencing for Outbreak Investigations of in a National Reference Center.国家参考中心用于疫情调查的常规全基因组测序
Front Microbiol. 2018 Mar 20;9:511. doi: 10.3389/fmicb.2018.00511. eCollection 2018.
9
Epidemiological aspects of healthcare-associated infections and microbial genomics.医疗保健相关感染和微生物基因组学的流行病学方面。
Eur J Clin Microbiol Infect Dis. 2018 May;37(5):823-831. doi: 10.1007/s10096-017-3170-x. Epub 2018 Jan 17.
10
Development of a rapid MALDI-TOF MS based epidemiological screening method using MRSA as a model organism.利用耐甲氧西林金黄色葡萄球菌（MRSA）作为模式生物，开发一种快速基质辅助激光解吸电离飞行时间质谱（MALDI-TOF MS）的流行病学筛查方法。
Eur J Clin Microbiol Infect Dis. 2018 Jan;37(1):57-68. doi: 10.1007/s10096-017-3101-x. Epub 2017 Sep 18.
本文引用的文献
1
Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study.全基因组测序鉴定囊性纤维化患者分枝杆菌脓肿之间的传播：一项回顾性队列研究。
Lancet. 2013 May 4;381(9877):1551-60. doi: 10.1016/S0140-6736(13)60632-7. Epub 2013 Mar 29.
2
Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK.回顾性分析全基因组测序与前瞻性分型数据，进一步为英国一起宋内志贺菌爆发的流行病学调查提供信息。
Epidemiol Infect. 2013 Dec;141(12):2568-75. doi: 10.1017/S0950268813000137. Epub 2013 Feb 21.
3
Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.全基因组测序与传统基因分型在结核分枝杆菌暴发调查中的比较：一项纵向分子流行病学研究。
PLoS Med. 2013;10(2):e1001387. doi: 10.1371/journal.pmed.1001387. Epub 2013 Feb 12.
4
Necrotizing cutaneous mucormycosis after a tornado in Joplin, Missouri, in 2011.2011 年美国密苏里州乔普林龙卷风后的坏死性皮肤毛霉菌病。
N Engl J Med. 2012 Dec 6;367(23):2214-25. doi: 10.1056/NEJMoa1204781.
5
Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study.全基因组测序分析耐甲氧西林金黄色葡萄球菌爆发：一项描述性研究。
Lancet Infect Dis. 2013 Feb;13(2):130-6. doi: 10.1016/S1473-3099(12)70268-2. Epub 2012 Nov 14.
6
Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study.全基因组测序解析结核分枝杆菌暴发：一项回顾性观察研究。
Lancet Infect Dis. 2013 Feb;13(2):137-46. doi: 10.1016/S1473-3099(12)70277-3. Epub 2012 Nov 15.
7
Public health value of next-generation DNA sequencing of enterohemorrhagic Escherichia coli isolates from an outbreak.肠出血性大肠杆菌暴发分离株下一代 DNA 测序的公共卫生价值。
J Clin Microbiol. 2013 Jan;51(1):232-7. doi: 10.1128/JCM.01696-12. Epub 2012 Nov 7.
8
Carbapenemases in Klebsiella pneumoniae and other Enterobacteriaceae: an evolving crisis of global dimensions.肺炎克雷伯菌和其他肠杆菌科细菌中的碳青霉烯酶：具有全球范围的不断演变的危机。
Clin Microbiol Rev. 2012 Oct;25(4):682-707. doi: 10.1128/CMR.05035-11.
9
Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing.应用全基因组测序追踪医院碳青霉烯类耐药肺炎克雷伯菌暴发疫情
Sci Transl Med. 2012 Aug 22;4(148):148ra116. doi: 10.1126/scitranslmed.3004129.
10
Cholera.霍乱。
Lancet. 2012 Jun 30;379(9835):2466-2476. doi: 10.1016/S0140-6736(12)60436-X.
Zotero 插件