Escherichia coli Genome sequencing and assembly. Escherichia coli

A four-year surveillance diarrhea study (from January 2010 to July 2014) was conducted in 890 children <5-year-old that sought medical care for acute community-acquired diarrhea in Yucatan, Mexico. Stool samples from these children were analyzed for the presence of DEP, Campylobacter spp., Salmonella sp., Shigella spp., Vibrio cholerae sp. and rotavirus. The genomes of ten Diffusely Adherent E. coli (DAEC) and nine Enteroaggregative E. coli (EAEC) strains isolated from the most severe cases of this study were selected for whole genome sequencing, together with one EAEC strain isolated from a 56-year-old adult patient with acute diarrhea and one commensal E. coli from a healthy 2-year-old girl. These genomes were analyzed together with 85 previously sequenced E. coli genomes to study their phylogenetic distribution and the prevalence of different virulence genes among Diarrheagenic E. coli pathotypes (DEP).

本研究于墨西哥尤卡坦地区针对因急性社区获得性腹泻就诊的890名5岁以下儿童，开展了一项为期四年（2010年1月至2014年7月）的腹泻监测研究。研究人员收集上述儿童的粪便样本，检测其中是否存在致泻性大肠杆菌（Diarrheagenic E. coli, DEP）、弯曲菌属（Campylobacter spp.）、沙门氏菌属（Salmonella sp.）、志贺氏菌属（Shigella spp.）、霍乱弧菌（Vibrio cholerae sp.）以及轮状病毒。本研究从重症病例中分离得到10株弥散黏附性大肠杆菌（Diffusely Adherent E. coli, DAEC）与9株肠集聚性黏附性大肠杆菌（Enteroaggregative E. coli, EAEC），此外纳入1株从56岁急性腹泻成人患者体内分离的EAEC菌株，以及1株从健康2岁女童体内分离的共生大肠杆菌，对上述菌株的基因组进行全基因组测序。随后将该批测序基因组与85株已公开的大肠杆菌基因组开展联合分析，以探究致泻性大肠杆菌致病型的系统发育分布特征，以及不同毒力基因在各类致泻性大肠杆菌致病型中的流行情况。