Antibiotic resistomes discovered in the gut microbiomes of Korean swine and cattle
Antibiotic resistomes discovered in the gut microbiomes of Korean swine and cattle
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DOI：
10.1093/gigascience/giaa043
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发表时间：
2020-05-01
期刊：
影响因子：
9.2
通讯作者：
Rho, Mina
中科院分区：
文献类型：
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作者：
Lim, Suk-Kyung;Kim, Dongjun;Rho, Mina
背景：给予农场动物的抗生素导致耐药基因在不同微生物组和环境中的流行率增加。虽然抗生素治疗有助于治愈农场动物的传染病，但将抗生素耐药基因传播到环境和人类微生物组中的可能性引起了人们的严重关注。经过长期的进化，抗生素耐药基因发生了突变，从而使耐药问题复杂化。结果如下：在这项研究中，我们对韩国农场的36头猪和41头牛的肠道微生物组进行了深度测序，并进行了宏基因组分析，以了解抗生素耐药基因的多样性和流行率。我们发现氨基糖苷类、β-内酰胺类、林可酰胺类、链阳性菌素和四环素类是猪和牛中普遍存在的耐药决定因素。四环素耐药在牛和猪中广泛存在。具体而言，tetQ、tetW、tetO、tet 32和tet 44是5个最丰富和最普遍的四环素耐药基因。它们在猪和牛中的患病率几乎为100%。虽然tetQ在猪和牛中同样丰富，但tetW在猪中比在牛中更丰富。氨基糖苷类抗生素在猪中是第二高丰度的耐药决定簇，但在牛中不是。其中ANT（6）和APH（3“）是猪的显性抗病基因家族。β-内酰胺也是猪和牛中丰富的抗性决定因子。Cfx基因家族是产生β-内酰胺类抗生素抗性的主要贡献基因。结论：抗生素耐药组在猪中比在牛中更普遍。具体而言，猪中普遍存在的抗生素耐药基因（流行率>50%）多于牛。本研究中猪和牛肠道微生物组特异性耐药基因的基因组学研究为更好地了解农场动物中抗生素耐药基因的交换提供了机会。
Background: Antibiotics 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. Results: In 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, beta-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. beta-lactam was also an abundant resistance determinant in both swine and cattle. Cfx was the major contributing gene family conferring resistance against beta-lactams. Conclusions: Antibiotic 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.