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Comparative Analysis of Phylogenetic Assignment of Human and Avian ExPEC and Fecal Commensal Escherichia coli Using the (Previous and Revised) Clermont Phylogenetic Typing Methods and its Impact on Avian Pathogenic Escherichia coli (APEC) Classification

机译:使用(先前和修订的)Clermont系统发生分型方法对人和禽ExPEC和粪便共生大肠杆菌的系统发生分配进行比较分析及其对禽致病性大肠杆菌(APEC)分类的影响

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摘要

The Clermont scheme has been used for subtyping of Escherichia coli since it was initially described in early 2000. Since then, researchers have used the scheme to type and sub-type commensal E. coli and pathogenic E. coli, such as extraintestinal pathogenic E. coli (ExPEC), and compare their phylogenetic assignment by pathogenicity, serogroup, distribution among ExPEC of different host species and complement of virulence and resistance traits. Here, we compare assignments of human and avian ExPEC and commensal E. coli using the old and revised Clermont schemes to determine if the new scheme provides a refined snapshot of isolate classification. 1,996 E. coli from human hosts and poultry, including 84 human neonatal meningitis E. coli isolates, 88 human vaginal E. coli, 696 human uropathogenic E. coli, 197 healthy human fecal E. coli, 452 avian pathogenic E. coli (APEC), 200 retail poultry E. coli, 80 crop and gizzard E. coli from healthy poultry at slaughter and 199 fecal E. coli from healthy birds at slaughter. All isolates were subject to phylogenetic analysis using the , ) schemes and compared to determine the effect of the new classification on strain designation. Most of the isolates’ strain designation remained where they were originally assigned. Greatest designation change occurred in APEC where 53.8% of isolates were reclassified; while classification rates among human strains ranged from 8 to 14%. However, some significant changes were observed for UPEC associated strains with significant (P < 0.05) designation changes observed from A to C and D to E or F phylogenetic types; a similar designation change was noted among NMEC for D to F designation change. Among the APEC significant designation changes were observed from A to C and D to E and F. These studies suggest that the new scheme provides a tighter and more meaningful definition of some ExPEC; while the new typing scheme has a significant impact on APEC classification. A comparison of phylogenetic group assignment by content of virulence, resistance, replicon and pathogenicity island genes in APEC suggests that insertion of pathogenicity islands into the genome appears to correlate closely with revised phylogenetic assignment.
机译:自从2000年初就开始使用Clermont方案对大肠杆菌进行亚型分析。此后,研究人员就使用该方案对普通大肠杆菌和致病性大肠杆菌(如肠外致病性大肠杆菌)进行分型和分型。大肠杆菌(ExPEC),并通过致病性,血清群,不同宿主物种的ExPEC之间的分布以及毒力和抗性性状的互补性来比较它们的系统发育分配。在这里,我们使用旧的和修订的Clermont方案比较人和禽ExPEC和普通大肠杆菌的分配,以确定新方案是否提供了分离株分类的精确快照。来自人宿主和家禽的1,996大肠杆菌,包括84例人类新生儿脑膜炎大肠杆菌分离物,88例人类阴道大肠杆菌,696例尿毒症性大肠杆菌,197例健康人粪便大肠杆菌,452例禽病原性大肠杆菌(APEC) ),200头零售家禽大肠杆菌,80头健康家禽的屠宰场和izz大肠杆菌,以及199头来自健康家禽的粪便大肠杆菌。使用)方案对所有分离株进行系统发育分析,并进行比较以确定新分类对菌株名称的影响。大多数分离株的菌株名称仍保留在最初分配的位置。 APEC中最大的名称变化发生在53.8%的分离株中。而人类菌株的分类率介于8%至14%之间。但是,观察到UPEC相关菌株发生了一些显着变化,从A到C和D到E或F的系统发生类型,显着(P <0.05)命名变化;在NMEC中,对于D到F的名称更改也注意到了类似的名称更改。在APEC中,从A到C以及从D到E和F都有明显的名称变化。这些研究表明,新方案为某些ExPEC提供了更为严格和有意义的定义;而新的打字方案对APEC的分类有重大影响。通过在APEC中通过毒力,抗性,复制子和致病岛基因的含量对系统发生群分配进行比较,表明将致病岛插入基因组似乎与修订的系统发生分配密切相关。

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