bc2378b8-e8d4-4ee8-a28a-fd4d5552b4f3
Cross-sectional analysis of the microbiota of human gut and their direct environment in a household cohort with high background of antibiotic use.
Abstract Comprehensive insight into the microbiota of the gut of humans and animals as well as their living environment in communities with a high background of antibiotic use and antibiotic resistance genes is scarce. Here, we used 16S rRNA gene sequencing to describe the (dis)similarities in the microbiota of feces from humans (n = 107), domestic animals (n = 36), water (n = 89) and processed food (n = 74) in a cohort with individual's history of antibiotic use in northern Vietnam. A significantly lower microbial diversity was observed among individuals who used antibiotics in the past four months (n = 44) compared to those who did not (n = 63). Fecal microbiota of humans was more diverse than non-human samples, and shared a small part of its amplicon sequence variants (ASVs) with feces from animals (7.4% [3.2-9.9]), water (2.2% [1.2-2.8]) and food (3.1% [1.5-3.1]). Sharing of ASVs between humans and companion animals was not associated with household. However, we did observe a correlation between an Enterobacteriaceae ASV and the presence of extended-spectrum beta-lactamase CTX-M-group-2 encoding genes in feces from humans and animals (p = 0.0016 and p = 0.026, respectively), hinting towards an exchange of antimicrobial-resistant strains between reservoirs.
Abstract Comprehensive insight into the microbiota of the gut of humans and animals as well as their living environment in communities with a high background of antibiotic use and antibiotic resistance genes is scarce. Here, we used 16S rRNA gene sequencing to describe the (dis)similarities in the microbiota of feces from humans (n = 107), domestic animals (n = 36), water (n = 89) and processed food (n = 74) in a cohort with individual's history of antibiotic use in northern Vietnam. A significantly lower microbial diversity was observed among individuals who used antibiotics in the past four months (n = 44) compared to those who did not (n = 63). Fecal microbiota of humans was more diverse than non-human samples, and shared a small part of its amplicon sequence variants (ASVs) with feces from animals (7.4% [3.2-9.9]), water (2.2% [1.2-2.8]) and food (3.1% [1.5-3.1]). Sharing of ASVs between humans and companion animals was not associated with household. However, we did observe a correlation between an Enterobacteriaceae ASV and the presence of extended-spectrum beta-lactamase CTX-M-group-2 encoding genes in feces from humans and animals (p = 0.0016 and p = 0.026, respectively), hinting towards an exchange of antimicrobial-resistant strains between reservoirs.