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

Abstract

BackgroundAntibiotic 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.MethodsWe 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.ResultsNearly 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.ConclusionsOur 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.

Prevalence and Epidemiology of Multidrug-Resistant Pathogens in the Food Chain and the Urban Environment in Northwestern Germany

“…In other European countries, the prevalence of mcr - 1 in the community or among patients in hospitals was also low (0–0.4%) [ 22 , 23 , 24 ]. The travel-associated acquisition of mcr - E. coli is in agreement with findings of mcr - 1 carriage rates of 5–88% in China, Bolivia, and Vietnam [ 25 , 26 ]. In these countries, reports indicate a livestock- or food-associated exchange of mcr - E. coli .…”

Investigating potential transmission of antimicrobial resistance in an open-plan hospital ward: a cross-sectional metagenomic study of resistome dispersion in a lower middle-income setting

“…AMR determinants can move between bacterial populations through horizontal gene transfer. As a result, microbiota and resistome traits are not always strongly aligned, and indeed, intestinal microbiota depletion can result in increased acquisition of resistant bacteria from the environment [30]. However, in our study population, microbiota diversity was not significantly correlated with the number of AMR genes carried and was unrelated to patient location.…”

Cross-sectional analysis of the microbiota of human gut and their direct environment (exposome) in a household cohort in northern Vietnam

“…Recent studies suggest that through feces, humans and domestic animals disseminate antibiotic resistant bacteria into the environment (41). Our previous report showed that antibiotic resistance genes were detected in water at low proportion as compared to humans and animals (42). Along with the antibiotic pollution in water resources, antibiotic resistant microbes might become a part of water microbiota (43).…”

“…The demographics of this complete cohort have been described in our previous study, which was designed to explore the circulation of ARGs in humans, animals and their environment (42) (see supplementary-Table S1).…”

“…Metagenomic DNA has been isolated as described previously (42). In brief, Repeated Bead-Beating (RBB) combined with column-based purification was used to extract DNA from human and animal fecal samples according to protocol Q of the International Human Microbiome Standards consortium [20].…”