草鱼肠道微生物抗生素抗性基因研究

水产养殖过程中抗生素的过度使用导致耐药菌株不断出现，细菌耐药性成了威胁公共安全的一个全球性问题。抗性基因是细菌产生耐药性的根本原因，动物肠道微生物是抗性基因的储存库，然而目前我国对水产养殖动物消化道微生物抗生素抗性基因的研究匮乏。为探究草鱼（Ctenopharyngodon idellus）肠道微生物中抗性基因的类型和丰度，通过提取草鱼肠道内容物的基因组DNA，采用shotgun宏基因组技术进行测序和序列注释，分析草鱼肠道内容物微生物数据，对比抗性基因数据库ARDB筛选出微生物序列中的抗性基因。结果表明，草鱼肠道内容物共有61554个可注释微生物的基因序列，包括409个真核生物序列、88个古细菌序列和61057个真细菌序列；共得到1011个抗性基因，归为123种基因型，包括78种单抗性基因型（679个单抗性基因），45种多抗性基因型（304个多抗性基因），多抗性基因数量占抗性基因总数的30.1%，说明草鱼肠道中可能存在大量的多重耐药性微生物；检出草鱼肠道中数量最多的抗性基因是抗大环内酯类抗生素基因MacB，其在国内水环境中研究甚少，可能是因为其单独存在时无法使微生物表现出抗性。本研究统计了草鱼肠道中微生物抗生素抗性基因的种类及数量，为水产养殖中抗生素的使用监管提供基础数据，验证了宏基因组测序技术检测抗性基因的可行性。

Antibiotic Resistance Genes in the Intestinal Microorganisms of Grass Carp

Abuse of antibiotics in the aquaculture industry has resulted in antibiotic-resistant bacteria, which pose a global threat to human and animal health. The resistance gene is the underlying cause of resistance to antibiotics, and intestinal microbes are a repository of resistance genes. However, little research has been carried out on bacterial antibiotic resistance genes in the digestive tract of aquaculture animals in China. In this study, we explored the type and abundance of resistance genes in the intestinal microbiome of grass carp (Ctenopharyngodon idellus). Genomic DNA from the intestinal contents of grass carp was extracted and sequenced, and the sequences were then annotated using shotgun metagenomic sequencing technology. The resistance gene database (ARDB) was then screened for antibiotic resistance genes. We obtained a total of 61,554 annotated microbial gene sequences, including 409 eukaryotic sequences, 88 archaeal sequences and 61,057 eubacterial sequences. A total of 1,011 antibiotic resistance genes from 123 genotypes were obtained, including 78 single-resistance genotypes (679 single resistance genes) and 45 multi-resistance genotypes (304 multi-resistance genes). The multi-resistance genes accounted for 30.1% of the total resistance genes, indicating the possibility of a large number of multi-drug resistant microorganisms in the intestinal tract of grass carp. Further, the anti-macrolide antibiotic gene, MacB, was the most abundant resistance gene in the grass carp gut. This gene is rarely reported in studies on the domestic water environment, probably because microorganisms are not resistant when MacB exists alone. This study documented the types and quantities of microbial antibiotic resistance genes in the gut of grass carp, providing basic data for the regulation of antibiotic use in aquaculture and verifying the feasibility of detecting resistance genes by metagenomic sequencing technology.