Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya.
Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya.
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DOI：
10.1186/s12916-022-02677-7
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发表时间：
2022-12-08
期刊：
影响因子：
9.3
通讯作者：
Woolhouse, Mark E. J.
中科院分区：
文献类型：
--
作者：
Muloi, Dishon M.;Hassell, James M.;Wee, Bryan A.;Ward, Melissa J.;Bettridge, Judy M.;Kivali, Velma;Kiyong'a, Alice;Ndinda, Christine;Gitahi, Nduhiu;Ouko, Tom;Imboma, Titus;Akoko, James;Murungi, Maurice K.;Njoroge, Samuel M.;Muinde, Patrick;Alumasa, Lorren;Kaitho, Titus;Amanya, Fredrick;Ogendo, Allan;van Bunnik, Bram A. D.;Kiiru, John;Robinson, Timothy P.;Kang'ethe, Erastus K.;Kariuki, Samuel;Pedersen, Amy B.;Fevre, Eric M.;Woolhouse, Mark E. J.
畜牧系统被认为是耐药性细菌和耐药性遗传决定因素的储存库，这些细菌和遗传决定因素可能会感染或定植人类，但仍然缺乏关于其流行病学作用的定量证据。在这里，我们使用了基因组学，流行病学和生态学相结合，以调查模式的AMR基因携带大肠杆菌，被视为一个哨兵生物。我们对肯尼亚内罗毕的99个家庭进行了结构化流行病学调查，并对E.从311份人、606份牲畜和399份野生动物粪便样品中分离出大肠杆菌。我们使用统计模型来调查AMR携带的患病率和AMR基因的多样性和AMR基因在整个城市的不同宿主人群的结构。我们还调查了同域人类和牲畜之间AMR基因交换的家庭水平风险因素。我们检测到了56个独特的获得性基因沿着13个点突变，这些点突变以不同的比例存在于人类和动物分离株中，已知这些基因赋予对9种抗生素的耐药性。我们发现AMR基因群落组成与宿主物种无关，但AMR基因经常共存，可能使多药耐药的获得和分散在一个步骤。我们发现，虽然饲养牲畜对人类AMR基因携带没有影响，但当粪便处理不当和家庭规模较大时，AMR在人畜界面传播的潜力最大。在人类和动物群体中广泛携带AMR细菌的发现，包括在远距离野生动物物种中，在社区环境中强调了循证监测在全球范围内解决抗菌素耐药性的价值。我们的基因组分析提供了一个深入的了解AMR决定因素在一个卫生部门的接口，将告知AMR预防和控制。在线版本包含补充材料，可通过10.1186/s12916-022-02677-7获得。
Livestock systems have been proposed as a reservoir for antimicrobial-resistant (AMR) bacteria and AMR genetic determinants that may infect or colonise humans, yet quantitative evidence regarding their epidemiological role remains lacking. Here, we used a combination of genomics, epidemiology and ecology to investigate patterns of AMR gene carriage in Escherichia coli, regarded as a sentinel organism. We conducted a structured epidemiological survey of 99 households across Nairobi, Kenya, and whole genome sequenced E. coli isolates from 311 human, 606 livestock and 399 wildlife faecal samples. We used statistical models to investigate the prevalence of AMR carriage and characterise AMR gene diversity and structure of AMR genes in different host populations across the city. We also investigated household-level risk factors for the exchange of AMR genes between sympatric humans and livestock. We detected 56 unique acquired genes along with 13 point mutations present in variable proportions in human and animal isolates, known to confer resistance to nine antibiotic classes. We find that AMR gene community composition is not associated with host species, but AMR genes were frequently co-located, potentially enabling the acquisition and dispersal of multi-drug resistance in a single step. We find that whilst keeping livestock had no influence on human AMR gene carriage, the potential for AMR transmission across human-livestock interfaces is greatest when manure is poorly disposed of and in larger households. Findings of widespread carriage of AMR bacteria in human and animal populations, including in long-distance wildlife species, in community settings highlight the value of evidence-based surveillance to address antimicrobial resistance on a global scale. Our genomic analysis provided an in-depth understanding of AMR determinants at the interfaces of One Health sectors that will inform AMR prevention and control. The online version contains supplementary material available at 10.1186/s12916-022-02677-7.
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影响因子：
2.8
作者：
Muloi D;Ward MJ;Pedersen AB;Fèvre EM;Woolhouse MEJ;van Bunnik BAD
通讯作者：
van Bunnik BAD
影响因子：
4.8
作者：
Chao, Anne;Jost, Lou
通讯作者：
Jost, Lou
DOI：
10.1016/s0140-6736(21)02724-0
发表时间：
2022-02-12
期刊：
Lancet (London, England)
影响因子：
--
作者：
Antimicrobial Resistance Collaborators
通讯作者：
Antimicrobial Resistance Collaborators
影响因子：
4.6
作者：
Graham DW;Knapp CW;Christensen BT;McCluskey S;Dolfing J
通讯作者：
Dolfing J
影响因子：
4.9
作者：
Aworh MK;Kwaga J;Okolocha E;Harden L;Hull D;Hendriksen RS;Thakur S
通讯作者：
Thakur S