探索越南北方社区的肠道和环境耐药组与抗生素使用的关系。
An exploration of the gut and environmental resistome in a community in northern Vietnam in relation to antibiotic use.
机构信息
Oxford University Clinical Research Unit and Welcome Trust Major Asia Programme, Oxford, Vietnam.
2Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands.
出版信息
Antimicrob Resist Infect Control. 2019 Nov 28;8:194. doi: 10.1186/s13756-019-0645-9. eCollection 2019.
BACKGROUND
Antibiotic resistance is a major global public health threat. Antibiotic use can directly impact the antibiotic resistant genes (ARGs) profile of the human intestinal microbiome and consequently the environment through shedding.
METHODS
We determined the resistome of human feces, animal stools, human food and environmental (rain, well, and irrigative water) samples ( = 304) in 40 households within a community cohort and related the data to antibiotic consumption. Metagenomic DNA was isolated and qPCR was used to determine presence of mobile colistin resistance () genes, genes encoding extended-spectrum β-lactamases (ESBL), carbapenemases and quinolone resistance genes.
RESULTS
Nearly 40 % (39.5%, 120/304) of samples contained ESBL genes (most frequent were (23.7% [72/304]), (18.8% [57/304]). Quinolone resistance genes () were detected in all human and 91% (41/45) of animal stool samples. were predominantly detected in human feces at 88% (82/93) and 55% (51/93) and animal feces at 93% (42/45) and 51% (23/45), respectively. were not detected in human feces, and only sporadically (< 6%) in other samples. Carbapenemase-encoding genes were most common in water (15% [14/91]) and cooked food (13% [10/75]) samples, while their prevalence in human and animal stools was lower at 4% in both human (4/93) and animal (2/45) samples. We did not find an association between recent antibiotic consumption and ARGs in human stools. Principal component analysis showed that the resistome differs between ecosystems with a strong separation of ARGs profiles of human and animal stools on the one hand versus cooked food and water samples on the other.
CONCLUSIONS
Our study indicated that ARGs were abundant in human and animal stools in a rural Vietnamese community, including ARGs targeting last resort antibiotics. The resistomes of animal and human stools were similar as opposed to the resistomes from water and food sources. No association between antibiotic use and ARG profiles was found in a setting of high background rates of AMR.
背景
抗生素耐药性是一个主要的全球公共卫生威胁。抗生素的使用会直接影响人类肠道微生物组的抗生素耐药基因（ARG）谱，并通过脱落影响环境。
方法
我们在一个社区队列的 40 户家庭中确定了人类粪便、动物粪便、人类食物和环境（雨水、井水和灌溉水）样本（=304）的耐药组，并将数据与抗生素消费相关联。提取元基因组 DNA，并用 qPCR 确定了携带黏菌素耐药基因（mcr-1）的移动基因、编码超广谱β-内酰胺酶（ESBL）、碳青霉烯酶和喹诺酮耐药基因的存在情况。
结果
近 40%（39.5%，120/304）的样本含有 ESBL 基因（最常见的是 （23.7% [72/304]）， （18.8% [57/304]）。喹诺酮耐药基因（）在所有人类和 91%（41/45）的动物粪便样本中均有检出。在人类粪便中，mcr-1 主要检出率为 88%（82/93）和 55%（51/93），在动物粪便中检出率分别为 93%（42/45）和 51%（23/45）。在人类粪便中未检出碳青霉烯酶基因，在其他样本中也很少检出（<6%）。携带碳青霉烯酶基因的细菌在水中（15% [14/91]）和熟食（13% [10/75]）样本中最为常见，而在人类和动物粪便中的检出率较低，均为 4%（人类粪便 4/93，动物粪便 2/45）。我们没有发现人类粪便中最近的抗生素消费与 ARG 之间存在关联。主成分分析表明，耐药组在不同的生态系统中存在差异，人类和动物粪便的 ARG 谱与水和食物样本之间存在强烈的分离。
结论
我们的研究表明，越南农村社区的人类和动物粪便中存在大量的 ARG，包括针对最后一道抗生素的 ARG。动物和人类粪便的耐药组相似，而与水和食物来源的耐药组不同。在背景耐药率较高的情况下，抗生素的使用与 ARG 谱之间没有关联。
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