Logue Catherine M, Wannemuehler Yvonne, Nicholson Bryon A, Doetkott Curt, Barbieri Nicolle L, Nolan Lisa K
Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames IA, USA.
Department of Statistics, North Dakota State University, Fargo ND, USA.
Front Microbiol. 2017 Feb 23;8:283. doi: 10.3389/fmicb.2017.00283. eCollection 2017.
The Clermont scheme has been used for subtyping of since it was initially described in early 2000. Since then, researchers have used the scheme to type and sub-type commensal and pathogenic , such as extraintestinal pathogenic (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 using the old and revised Clermont schemes to determine if the new scheme provides a refined snapshot of isolate classification. 1,996 from human hosts and poultry, including 84 human neonatal meningitis isolates, 88 human vaginal , 696 human uropathogenic , 197 healthy human fecal , 452 avian pathogenic (APEC), 200 retail poultry , 80 crop and gizzard from healthy poultry at slaughter and 199 fecal from healthy birds at slaughter. All isolates were subject to phylogenetic analysis using the Clermont et al. (2000, 2013) 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 ( < 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.
自2000年初首次被描述以来，克莱蒙分类法一直用于[未提及的微生物]的分型。从那时起，研究人员已使用该分类法对共生[未提及的微生物]和致病性[未提及的微生物]进行分型和亚型划分，如肠外致病性未提及的微生物，并通过致病性、血清群、在不同宿主物种的ExPEC中的分布以及毒力和抗性特征的互补性来比较它们的系统发育归属。在这里，我们使用旧的和修订后的克莱蒙分类法比较人类和禽类ExPEC以及共生[未提及的微生物]的归属，以确定新分类法是否能提供更精确的菌株分类概况。来自人类宿主和家禽的1996株[未提及的微生物]，包括84株人类新生儿脑膜炎[未提及的微生物]分离株、88株人类阴道[未提及的微生物]、696株人类尿路致病性[未提及的微生物]、197株健康人类粪便[未提及的微生物]、452株禽致病性未提及的微生物、200株零售家禽[未提及的微生物]、80株屠宰时健康家禽的嗉囊和砂囊[未提及的微生物]以及199株屠宰时健康鸟类的粪便[未提及的微生物]。所有分离株均使用克莱蒙等人(2000年、2013年)的分类法进行系统发育分析，并进行比较以确定新分类对菌株命名的影响。大多数分离株的菌株命名仍保持在最初指定的位置。最大的命名变化发生在APEC中，53.8%的分离株被重新分类；而人类菌株的分类率在8%至14%之间。然而，观察到与UPEC相关的菌株有一些显著变化，从A到C以及从D到E或F系统发育类型观察到显著的( < 0.05)命名变化；在NMEC中也注意到从D到F命名变化的类似情况。在APEC中，观察到从A到C以及从D到E和F的显著命名变化。这些研究表明，新分类法对一些ExPEC提供了更严格和更有意义的定义；而新的分型分类法对APEC分类有显著影响。对APEC中毒力、抗性、复制子和致病岛基因含量的系统发育组归属进行比较表明，致病岛插入基因组似乎与修订后的系统发育归属密切相关。
