The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia.
Microb Genom. 2019 Mar;5(3). doi: 10.1099/mgen.0.000225. Epub 2018 Oct 10.
We recently identified clonal complex 10 (CC10) Escherichia coli as the predominant clonal group in two populations of healthy Australian food-production pigs. CC10 are highly successful, colonizing humans, food-production animals, fresh produce and environmental niches. Furthermore, E. coli within CC10 are frequently drug resistant and increasingly reported as human and animal extra-intestinal pathogens. In order to develop a high-resolution global phylogeny and determine the repertoire of antimicrobial-resistance genes, virulence-associated genes and plasmid types within this clonal group, we downloaded 228 publicly available CC10 short-read genome sequences for comparison with 20 porcine CC10 we have previously described. Core genome single nucleotide polymorphism phylogeny revealed a highly diverse global phylogeny consisting of multiple lineages that did not cluster by geography or source of the isolates. Australian porcine strains belonged to several of these divergent lineages, indicative that CC10 is present in these animals due to multiple colonization events. Differences in resistance gene and plasmid carriage between porcine strains and the global collection highlighted the role of lateral gene transfer in the evolution of CC10 strains. Virulence profiles typical of extra-intestinal pathogenic E. coli were present in both Australian porcine strains and the broader collection. As both the core phylogeny and accessory gene characteristics appeared unrelated to the geography or source of the isolates, it is likely that the global expansion of CC10 is not a recent event and may be associated with faecal carriage in humans.
我们最近发现，克隆复合体 10（CC10）大肠杆菌是澳大利亚两个健康的食品生产猪群中的主要克隆群。CC10 是高度成功的，定植于人类、食品生产动物、新鲜农产品和环境小生境中。此外，CC10 中的大肠杆菌经常具有耐药性，并越来越多地被报道为人类和动物肠道外病原体。为了开发高分辨率的全球系统发育，并确定该克隆群中的抗生素耐药基因、毒力相关基因和质粒类型，我们下载了 228 个公开的 CC10 短读基因组序列，与我们之前描述的 20 个猪 CC10 进行比较。核心基因组单核苷酸多态性系统发育显示，全球系统发育高度多样化，由多个不按地理或分离物来源聚类的谱系组成。澳大利亚猪株属于其中的几个不同谱系，表明 CC10 由于多次定植事件而存在于这些动物中。猪株与全球分离株之间在耐药基因和质粒携带方面的差异突出了水平基因转移在 CC10 菌株进化中的作用。肠道外致病性大肠杆菌的典型毒力谱存在于澳大利亚猪株和更广泛的分离株中。由于核心系统发育和辅助基因特征似乎与分离物的地理或来源无关，因此 CC10 的全球扩张不太可能是最近发生的事件，可能与人类粪便携带有关。
