One Health genomic epidemiology of antimicrobial resistant Escherichia coli carriage in sympatric humans and livestock in Nairobi, Kenya
One Health genomic epidemiology of antimicrobial resistant Escherichia coli carriage in sympatric humans and livestock in Nairobi, Kenya
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肯尼亚内罗毕同域人类和牲畜中携带抗菌药物耐药性大肠杆菌的 One Health 基因组流行病学
DOI：
10.1016/j.jiph.2020.01.043
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发表时间：
2020
影响因子：
6.7
通讯作者：
Muloi D
中科院分区：
文献类型：
--
作者：
Muloi D
牲畜被认为是抗生素耐药（AMR）细菌和可能感染人类的AMR遗传决定因素的储存库，但仍然缺乏关于其流行病学作用的定量证据。我们使用基因组学，流行病学和生态学相结合，调查模式AMR携带大肠杆菌，被视为一个前哨生物。我们对肯尼亚内罗毕的99户家庭进行了结构化流行病学调查，并培养了E. 315份人类和594份牲畜粪便样本中检出大肠杆菌。我们检测到高比率的AMR基因携带，60种不同的获得性基因和14个点突变，并发现10/74的基因在人类中比在家畜分离株中更常见。此外，AMR基因与宿主类型或家庭位置无关，AMR基因经常共存，可能使多药耐药性的获得在一个步骤。我们发现，虽然人类AMR基因携带与家庭中牲畜的存在没有直接关系，但饲养牲畜对人类AMR基因携带的影响反而受到牲畜饲养实践的影响，特别是家庭中存在或不存在动物粪便。总之，我们没有发现任何证据支持这一假设，即在这种情况下，饲养牲畜是AMR基因出现和传播给人类的风险因素。我们对人类和牲畜共存人群进行系统采样的AMR模式的表征为复杂和相互关联的城市环境中AMR的更广泛流行病学提供了新的见解。
Livestock have been proposed as a reservoir for antibiotic resistant (AMR) bacteria and AMR genetic determinants that may infect humans, yet quantitative evidence regarding their epidemiological role remains lacking. We used a combination of genomics, epidemiology and ecology to investigate patterns of AMR carriage in Escherichia coli, regarded as a sentinel organism. We conducted a structured epidemiological survey of 99 households across Nairobi, Kenya and cultured E. coli from 315 human and 594 livestock faecal samples. We detected high rates of AMR gene carriage, 60 different acquired genes and 14 point mutations, and found that 10/74 of the genes were significantly more common in human than in livestock isolates. Further, AMR genes were not associated with host type or household location, and AMR genes frequently co-occurred, potentially enabling the acquisition of multi-drug resistance in a single step. We found that, whilst AMR gene carriage in humans was not directly associated with the presence of livestock in the household, the impact of keeping livestock on human AMR gene carriage was instead influenced by livestock-keeping practices, in particular the presence or absence of animal manure in the household. In conclusion, we did not find any evidence to support the hypothesis that the keeping of livestock is a risk factor for emergence and dissemination of AMR genes to humans in this setting. Our characterisation of AMR patterns in which co-habiting human and livestock populations were systematically sampled provides new insight into the broader epidemiology of AMR in complex and interconnected urban environments.