Household Clustering of Escherichia coli Sequence Type 131 Clinical and Fecal Isolates According to Whole Genome Sequence Analysis.
Household Clustering of Escherichia coli Sequence Type 131 Clinical and Fecal Isolates According to Whole Genome Sequence Analysis.
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DOI：
10.1093/ofid/ofw129
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发表时间：
2016-09
影响因子：
4.2
通讯作者：
Price LB
中科院分区：
文献类型：
--
作者：
Johnson JR;Davis G;Clabots C;Johnston BD;Porter S;DebRoy C;Pomputius W;Ender PT;Cooperstock M;Slater BS;Banerjee R;Miller S;Kisiela D;Sokurenko EV;Aziz M;Price LB
在一个基于全基因组的遗传学中，来自6个家庭的大肠杆菌序列型131（H30 R1和H30 Rx亚克隆）的临床和粪便分离株形成了家庭特异性簇，散布在参考ST 131基因组中。这支持了粪便尿道假说，并证实了家庭内的菌株共享。背景：基于传统的分型数据，已经推断出大肠杆菌序列型131（ST 131）耐药相关的H30 R1和H30 Rx亚克隆菌株的家庭内共享，但使用全基因组序列（WGS）分析进行了最低限度的评估。 方法：对来自6个家庭的20个人和宠物的33个临床和粪便分离的ST 131-H30 R1和ST 131-H30 Rx进行WGS分析，与52个已发表的ST 131基因组进行比较。 系统发育关系的推断使用自助最大似然树的基础上核心基因组序列多态性。附属性状之间进行了比较，遗传相似的菌株。结果：在WGS为基础的基因组学中，分离株严格按家庭聚集，在基因组学中广泛分布的分支中，散布在H30 R1和H30 Rx比较基因组之间。 只有一个家庭的核心基因组同源性将流行病学上无关的分离株与家庭分离株放在一起，但即使在那里，辅助基因组内容的多重差异也清楚地区分了这两个群体。核心基因组同源性支持家庭内菌株共享、粪便-尿道尿路感染发病机制（整个家庭可能提供粪便库）和宿主特异性微进化的实例。在1例中，该家庭的指示菌株持续了6年，然后在不同的家庭成员中引起新的感染。结论：大肠杆菌ST 131菌株的家庭内共享在基因组水平上得到了广泛的证实，这是由于ST 131-H30 Rx菌株的长期定植和重复感染。 未来的监测和非殖民化工作可能不仅需要解决受影响的患者，还需要解决其他人类和动物家庭成员的问题。
In a whole genome-based phylogeny, clinical and fecal isolates of Escherichia coli sequence type 131 (H30R1 and H30Rx subclones) from six households formed household-specific clusters, interspersed among reference ST131 genomes. This supported the fecal-urethral hypothesis and confirmed within-household strain sharing. Background. Within-household sharing of strains from the resistance-associated H30R1 and H30Rx subclones of Escherichia coli sequence type 131 (ST131) has been inferred based on conventional typing data, but it has been assessed minimally using whole genome sequence (WGS) analysis. Methods. Thirty-three clinical and fecal isolates of ST131-H30R1 and ST131-H30Rx, from 20 humans and pets in 6 households, underwent WGS analysis for comparison with 52 published ST131 genomes. Phylogenetic relationships were inferred using a bootstrapped maximum likelihood tree based on core genome sequence polymorphisms. Accessory traits were compared between phylogenetically similar isolates. Results. In the WGS-based phylogeny, isolates clustered strictly by household, in clades that were distributed widely across the phylogeny, interspersed between H30R1 and H30Rx comparison genomes. For only 1 household did the core genome phylogeny place epidemiologically unlinked isolates together with household isolates, but even there multiple differences in accessory genome content clearly differentiated these 2 groups. The core genome phylogeny supported within-household strain sharing, fecal-urethral urinary tract infection pathogenesis (with the entire household potentially providing the fecal reservoir), and instances of host-specific microevolution. In 1 instance, the household's index strain persisted for 6 years before causing a new infection in a different household member. Conclusions. Within-household sharing of E coli ST131 strains was confirmed extensively at the genome level, as was long-term colonization and repeated infections due to an ST131-H30Rx strain. Future efforts toward surveillance and decolonization may need to address not just the affected patient but also other human and animal household members.
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