Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape.
Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape.
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DOI：
10.1038/s41564-022-01079-y
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发表时间：
2022-04
影响因子：
28.3
通讯作者：
Fèvre EM
中科院分区：
文献类型：
--
作者：
Muloi DM;Wee BA;McClean DMH;Ward MJ;Pankhurst L;Phan H;Ivens AC;Kivali V;Kiyong'a A;Ndinda C;Gitahi N;Ouko T;Hassell JM;Imboma T;Akoko J;Murungi MK;Njoroge SM;Muinde P;Nakamura Y;Alumasa L;Furmaga E;Kaitho T;Öhgren EM;Amanya F;Ogendo A;Wilson DJ;Bettridge JM;Kiiru J;Kyobutungi C;Tacoli C;Kang'ethe EK;Davila JD;Kariuki S;Robinson TP;Rushton J;Woolhouse MEJ;Fèvre EM
人畜共患病风险和抗菌素耐药性传播的定量证据仍然缺乏。在这里，作为UrbanZoo项目的一部分，我们从肯尼亚内罗毕的99个家庭中的人类，牲畜和围家养野生动物中采集了大肠杆菌样本，以调查其在这个快速发展的城市景观中宿主物种之间的分布。我们对1,338株E.大肠杆菌菌株的多样性和共享模式。大肠杆菌的家庭结构和宿主类型的强烈塑造。我们还发现了家庭间和宿主间共享的证据，更重要的是，人类和动物之间的共享，尽管这种情况发生得不那么频繁。耐药基因组相似性在宿主和家庭中分布不同，这与共同暴露于抗菌药物的驱动一致。我们的研究结果表明，需要一个大的，流行病学结构化的采样框架结合WGS来揭示复杂环境中不同宿主人群之间的菌株共享事件，以及最终可能导致人畜共患病出现和抗生素耐药性传播的主要途径。E.从内罗毕99个家庭的人类、家养动物和野生动物中收集的大肠杆菌分离株显示出强烈的家庭内、较低但可检测的家庭间和宿主间菌株共享模式。
Quantitative evidence for the risk of zoonoses and the spread of antimicrobial resistance remains lacking. Here, as part of the UrbanZoo project, we sampled Escherichia coli from humans, livestock and peri-domestic wildlife in 99 households across Nairobi, Kenya, to investigate its distribution among host species in this rapidly developing urban landscape. We performed whole-genome sequencing of 1,338 E. coli isolates and found that the diversity and sharing patterns of E. coli were heavily structured by household and strongly shaped by host type. We also found evidence for inter-household and inter-host sharing and, importantly, between humans and animals, although this occurs much less frequently. Resistome similarity was differently distributed across host and household, consistent with being driven by shared exposure to antimicrobials. Our results indicate that a large, epidemiologically structured sampling framework combined with WGS is needed to uncover strain-sharing events among different host populations in complex environments and the major contributing pathways that could ultimately drive the emergence of zoonoses and the spread of antimicrobial resistance. Phylogeography and phylogenomic analyses of E. coli isolates collected from humans and domesticated and wild animals across 99 households in Nairobi reveal strong intra-household, and lower but detectable inter-household and inter-host, strain-sharing patterns.
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影响因子：
16.8
作者：
Hassell, James M.;Begon, Michael;Ward, Melissa J.;Fevre, Eric M.
通讯作者：
Fevre, Eric M.
影响因子：
3.2
作者：
Alarcon, Pablo;Fevre, Eric M.;Rushton, Jonathan
通讯作者：
Rushton, Jonathan
影响因子：
2.2
作者：
Ahmed, Sahel;Haklay, Muki;Fevre, Eric
通讯作者：
Fevre, Eric
影响因子：
28.3
作者：
Brito, Ilana L.;Gurry, Thomas;Alm, Eric J.
通讯作者：
Alm, Eric J.
影响因子：
6.4
作者：
Liu CM;Stegger M;Aziz M;Johnson TJ;Waits K;Nordstrom L;Gauld L;Weaver B;Rolland D;Statham S;Horwinski J;Sariya S;Davis GS;Sokurenko E;Keim P;Johnson JR;Price LB
通讯作者：
Price LB