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 (n = 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 (mcr) 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 CTX-M-9 (23.7% [72/304]), CTX-M-1 (18.8% [57/304]). Quinolone resistance genes (qnrS) were detected in all human and 91% (41/45) of animal stool samples. Mcr-1 and mcr-3 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. Mcr-2, mrc-4 and mcr-5 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.

中文翻译：

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在越南北部一个社区中，与抗生素使用有关的肠道和环境抵抗物组的探索。

背景技术抗生素耐药性是全球主要的公共卫生威胁。抗生素的使用可以直接影响人体肠道微生物组的抗生素抗性基因（ARG）概况，进而通过脱落影响环境。方法我们在一个社区队列中的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，井水和灌溉用水）的样本（n = 304），并将其与抗生素的使用相关联。分离出超基因组DNA，并使用qPCR确定可移动的粘菌素抗性（mcr）基因，编码超广谱β-内酰胺酶（ESBL）的基因，碳青霉烯酶和喹诺酮抗性基因的存在。结果近40％（39.5％，120/304）的样本包含ESBL基因（最常见的是CTX-M-9（23.7％[72/304]），CTX-M-1（18.8％[57/304]） 。在所有人类和91％（41/45）的动物粪便样本中检测到喹诺酮抗性基因（qnrS）。主要在人类粪便中检出的Mcr-1和mcr-3分别为88％（82/93）和55％（51/93）和动物粪便中的检出率分别为93％（42/45）和51％（23/45） 。在人类粪便中未检测到Mcr-2，mrc-4和mcr-5，而在其他样本中仅偶发（<6％）。碳青霉烯酶编码基因最常见于水（15％[14/91]）和熟食（13％[10/75]）样品中，而它们在人和动物粪便中的患病率均较低，在两个人中均为4％（4 / 93）和动物（2/45）样本。我们没有发现最近的抗生素消费与人类粪便中的ARG之间存在关联。主成分分析表明，不同的生态系统之间的抵抗力有所不同，一方面人类和动物粪便的ARGs轮廓与另一方面与煮熟的食物和水样的ARGs轮廓强烈分离。结论我们的研究表明，越南农村社区的人和动物粪便中含有大量的ARG，其中包括针对后生抗生素的ARG。动物和人类粪便的抵抗力与水和食物来源的抵抗力相似。在高AMR背景发生率的情况下，未发现抗生素使用与ARG配置文件之间存在关联。动物和人类粪便的抵抗力与水和食物来源的抵抗力相似。在高AMR背景发生率的情况下，未发现抗生素使用与ARG配置文件之间存在关联。动物和人类粪便的抵抗力与水和食物来源的抵抗力相似。在高AMR背景发生率的情况下，未发现抗生素使用与ARG配置文件之间存在关联。