Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, University of Sydney, Sydney, Australia Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research-Pathology West, Westmead Hospital, Sydney, NSW 2145, Australia
Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, University of Sydney, Sydney, Australia School of Biological Sciences, Charles Perkins Centre, University of Sydney, Sydney, Australia.
BMJ. 2015 May 11;350:h1314. doi: 10.1136/bmj.h1314.
Whole genome sequencing (WGS) of pathogens enables the sources and patterns of transmission to be identified during specific disease outbreaks and promises to transform epidemiological research on communicable diseases. This review discusses new insights into disease spread and transmission that have come from the use of WGS, particularly when combined with genomic scale phylogenetic analyses. These include elucidation of the mechanisms of cross species transmission, the potential modes of pathogen transmission, and which people in the population contribute most to transmission. Particular attention is paid to the ability of WGS to resolve individual patient to patient transmission events. Importantly, WGS data seem to be sufficiently discriminatory to target cases linked to community or hospital contacts and hence prevent further spread, and to investigate genetically related cases without a clear epidemiological link. Approaches to combine evidence from epidemiological with genomic sequencing observations are summarised. Ongoing genomic surveillance can identify determinants of transmission, monitor pathogen evolution and adaptation, ensure the accurate and timely diagnosis of infections with epidemic potential, and refine strategies for their control.
全基因组测序（WGS）可用于鉴定特定疾病暴发期间病原体的来源和传播模式，并有望改变传染病的流行病学研究。本文综述了 WGS 在疾病传播和传播方面的新见解，特别是与基因组规模的系统发育分析相结合时。这些见解包括阐明跨物种传播的机制、病原体传播的潜在模式以及人群中哪些人对传播的贡献最大。特别关注 WGS 解析个体患者之间传播事件的能力。重要的是，WGS 数据似乎具有足够的区分能力，可以针对与社区或医院接触相关的病例进行靶向治疗，从而防止进一步传播，并调查没有明确流行病学联系的遗传相关病例。总结了将流行病学证据与基因组测序观察结果相结合的方法。正在进行的基因组监测可以识别传播决定因素，监测病原体的进化和适应，确保对具有流行潜力的感染进行准确和及时的诊断，并改进其控制策略。
