Abstract
BackgroundAntimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in animal feces. We used metagenome-wide analysis to investigate the changes in bacterial community, variations in antibiotic resistance genes (ARGs), and their bacterial hosts in the feces of broiler chickens over a full-treatment course of chlortetracycline at low and therapeutic dose levels.ResultsThe effects of chlortetracycline on resistome were dependent on the specific ARG subtypes and not simply the overall community-level ARGs. Therapeutic dose of chlortetracycline promoted the abundance of tetracycline resistance genes (tetA and tetW) and inhibited multidrug resistance genes (mdtA, mdtC, mdtK, ompR, and TolC). The therapeutic dose of chlortetracycline led to loss of Proteobacteria mainly due to the decrease of Escherichia/Shigella (from 72 to 58%). Inhibition of Escherichia by chlortetracycline was the primary reason for the decrease of genes resistant to multiple drugs in the therapeutic dose group. The ARG host Bifidobacterium were enriched due to tetW harbored by Bifidobacterium under chlortetracycline treatment. Escherichia was always the major host for multidrug resistance genes, whereas the primary host was changed from Escherichia to Klebsiella for aminoglycoside resistance genes with the treatment of therapeutic dose of chlortetracycline.ConclusionsWe provided the first metagenomic insights into antibiotic-mediated alteration of ARG-harboring bacterial hosts at community-wide level in chicken feces. These results indicated that the changes in the structure of antibiotic-induced feces microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the feces microbiota. These findings will help to optimize therapeutic schemes for the effective treatment of antibiotic resistant pathogens in poultry farms.Graphical abstractResistome variations in faecal microbiome of chickens exposed to chlortetracycline
Highlights
Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth
antibiotic resistance genes (ARGs) variations On average, we found 5.1 ARG copies per 16S rRNA gene calculated from all fecal metagenomes of broiler chickens (Additional file 2: Table S3)
Metagenomic analysis showed that the ARGs were diverse and abundant in feces of broiler chickens, even when chlortetracycline was not administered in control animals
Summary
Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in animal feces. We used metagenome-wide analysis to investigate the changes in bacterial community, variations in antibiotic resistance genes (ARGs), and their bacterial hosts in the feces of broiler chickens over a full-treatment course of chlortetracycline at low and therapeutic dose levels. Antibiotic resistance is one of the most serious global threats to human health, as strongly evidenced by the serious implications of the recent worldwide emergence of KPC-2 (Klebsiella pneumoniae carbapenemase-2), NDM-1 (New Delhi metallo-β-lactamase-1), and MCR-1. Animal fecal microflora harbors a vast reservoir of antibiotic resistance genes (ARGs) that could be acquired by human commensals and pathogens [5]. Large-scale intensive farming systems depend on antimicrobials to prevent and treat animal disease and to enhance growth performance. It is estimated that the global consumption of antimicrobials used for chickens, pigs, and cattle will increase by 67%, from 63,151 tons in 2010 to 105,596 tons in 2030 [11]
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