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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.

An exploration of the gut and environmental resistome in a community in northern Vietnam in relation to antibiotic use