Abstract
BackgroundAntibiotics administered to farm animals have led to increasing prevalence of resistance genes in different microbiomes and environments. While antibiotic treatments help cure infectious diseases in farm animals, the possibility of spreading antibiotic resistance genes into the environment and human microbiomes raises significant concerns. Through long-term evolution, antibiotic resistance genes have mutated, thereby complicating the resistance problems.ResultsIn this study, we performed deep sequencing of the gut microbiomes of 36 swine and 41 cattle in Korean farms, and metagenomic analysis to understand the diversity and prevalence of antibiotic resistance genes. We found that aminoglycoside, β-lactam, lincosamide, streptogramin, and tetracycline were the prevalent resistance determinants in both swine and cattle. Tetracycline resistance was abundant and prevalent in cattle and swine. Specifically, tetQ, tetW, tetO, tet32, and tet44 were the 5 most abundant and prevalent tetracycline resistance genes. Their prevalence was almost 100% in swine and cattle. While tetQ was similarly abundant in both swine and cattle, tetW was more abundant in swine than in cattle. Aminoglycoside was the second highest abundant resistance determinant in swine, but not in cattle. In particular, ANT(6) and APH(3′′) were the dominant resistance gene families in swine. β-lactam was also an abundant resistance determinant in both swine and cattle. Cfx was the major contributing gene family conferring resistance against β-lactams.ConclusionsAntibiotic resistome was more pervasive in swine than in cattle. Specifically, prevalent antibiotic resistance genes (prevalence >50%) were found more in swine than in cattle. Genomic investigation of specific resistance genes from the gut microbiomes of swine and cattle in this study should provide opportunities to better understand the exchange of antibiotic resistance genes in farm animals.
Highlights
Antibiotics administered to farm animals have led to increasing prevalence of resistance genes in different microbiomes and environments
A large-scale study on the prevalence and diversity of antibiotic resistance genes in farm animals should help better elucidate the current situation of antibiotic resistance prevalence, and guide the development of public health policies
The sales rates for β-lactams, tetracyclines, aminoglycosides, sulfonamides, macrolides, and phenicols were high, which is consistent with the abundance of resistance gene determinants that we identified in the swine and cattle gut microbiomes
Summary
Antibiotics have been widely used to cure infectious diseases. In farms, antibiotics have been used to treat and prevent diseases or to promote the growth of animals. For the gut microbiomes of farm animals, several studies have explored the prevalence of antibiotic resistance genes [5, 9]. Consistent with previous studies [13,14,15,16], the major phyla in swine and cattle were Bacteroidetes and Firmicutes, which were commonly observed in human gut microbiomes [17] Their proportions, were quite different in the 2 animals: 21.65% and 67.16%, respectively, in swine; 4.15% and 58.63%, respectively, for cattle (Fig. 1C and D). The abundance of aminoglycoside resistance genes in swine was higher than that in cattle: 427.22 vs 18.40 median RPKM in swine and cattle, respectively (Fig. 3). They need to be validated by antibiotic susceptibility testing
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