近日，国际著名杂志《国家科学院院刊》PNAS在线版上刊登了由哈佛大学公共卫生学院和布洛德研究所共同组成的一个研究小组研究的最新成果，研究者利用全基因组测序已经追查到去年在欧洲大范围致病的大肠杆菌（E.coli）暴发路径。这是第一个采用基因组测序的方法来研究食源性暴发的动态，由此为了解未来疫情和传染病的出现和蔓延提供了新途径。
据美国物理学家组织网近日报道，由哈佛大学公共卫生学院和布洛德研究所共同组成的一个研究小组，利用全基因组测序已经追查到去年在欧洲大范围致病的大肠杆菌（E.coli）暴发路径。
这是第一个采用基因组测序的方法来研究食源性暴发的动态，由此为了解未来疫情和传染病的出现和蔓延提供了新途径。这项研究的合作者还包括法国巴斯德研究所、丹麦国立血清研究所等。
在生物学中，一个生物体的基因组是指包含在该生物的DNA（部分病毒是RNA）中的全部遗传信息。确定哪些DNA变异导致特定性状或疾病则需要进行个体间比较。该研究的主要作者、传染性疾病动态中心研究者永纳坦·格拉德说，寻找疫情暴发的多种细菌的基因组之间的差异，即可得到疫情发生的线索。像做侦探工作一样，研究人员通过这种方式跟踪疫情，可了解未来疾病暴发路径。
去年夏天在德国，因大肠杆菌病毒的肆虐成千上万人生病，50多人死亡，之后在法国也引起了小范围的暴发。研究人员将这两国的致病大肠杆菌株对比分析，发现菌株相同。然而，利用全基因组测序分析菌株之间的差异时，研究人员发现：所有与德国当地相关暴发的菌株都几乎是相同的，而出现在法国菌株表现出更大的多样性，显示出是从德国菌株分离出来的一个子集。
随着基因组测序成本的下降，未来将其与传统的流行病学方法相结合，可以为人们对传染病的出现及蔓延提供更深入的了解，将有助于指导公共卫生预防措施。（生物谷Bioon.com）
doi:10.1073/pnas.1121491109
PMC:
PMID:
Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011
Grad, Yonatan H.; Lipsitch, Marc; Feldgarden, Michael; Arachchi, Harindra M.; Cerqueira, Gustavo C.; FitzGerald, Michael; Godfrey, Paul; Haas, Brian J.; Murphy, Cheryl I.; Russ, Carsten; Sykes, Sean; Walker, Bruce J.; Wortman, Jennifer R.; Young, Sarah; Zeng, Qiandong; Abouelleil, Amr; Bochicchio, James; Chauvin, Sara; DeSmet, Timothy; Gujja, Sharvari; McCowan, Caryn; Montmayeur, Anna; Steelman, Scott; Frimodt-M?ller, Jakob; Petersen, Andreas M.; Struve, Carsten; Krogfelt, Karen A.; Bingen, Edou
The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia coli O104:H4 from the outbreak centered in Germany in May–July 2011, and the much smaller outbreak in southwest France in June 2011, were indistinguishable by standard tests. We report a molecular epidemiological analysis using multiplatform whole-genome sequencing and analysis of multiple isolates from the German and French outbreaks. Isolates from the German outbreak showed remarkably little diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in isolates from seven individuals infected in the French outbreak. The German isolates form a clade within the more diverse French outbreak strains. Moreover, five isolates derived from a single infected individual from the French outbreak had extremely limited diversity. The striking difference in diversity between the German and French outbreak samples is consistent with several hypotheses, including a bottleneck that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak.
