苗睿, 刘垒成, 姜玉莎, 等. 绿孔雀肠道菌群基因组特征和耐药性的宏基因组测序分析[J]. 西南林业大学学报(自然科学), 2024, 44(5): 1–8 . DOI: 10.11929/j.swfu.202311058
引用本文: 苗睿, 刘垒成, 姜玉莎, 等. 绿孔雀肠道菌群基因组特征和耐药性的宏基因组测序分析[J]. 西南林业大学学报(自然科学), 2024, 44(5): 1–8 . DOI: 10.11929/j.swfu.202311058
Miao Rui, Liu Leicheng, Jiang Yusha, Zhao Lang, Sun Jialiang, Wu Peifu. Genomic Characteristics and Drug Resistance of Intestinal Flora of Pavo muticus were Analyzed by Metagenomic Sequencing[J]. Journal of Southwest Forestry University. DOI: 10.11929/j.swfu.202311058
Citation: Miao Rui, Liu Leicheng, Jiang Yusha, Zhao Lang, Sun Jialiang, Wu Peifu. Genomic Characteristics and Drug Resistance of Intestinal Flora of Pavo muticus were Analyzed by Metagenomic Sequencing[J]. Journal of Southwest Forestry University. DOI: 10.11929/j.swfu.202311058

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绿孔雀肠道菌群基因组特征和耐药性的宏基因组测序分析

Genomic Characteristics and Drug Resistance of Intestinal Flora of Pavo muticus were Analyzed by Metagenomic Sequencing

  • 摘要: 为明确绿孔雀肠道菌群耐药基因及可移动元件的分布特征,对云南野生动物园,开放式饲养的健康绿孔雀粪便采样,提取DNA后进行宏基因组测序。使用NCBI-nr数据库进行物种注释及相对丰度计算,得出绿孔雀肠道菌群物种分布特征;通过功能注释及聚类分析,得出耐药基因的类型及分布特征。使用BLAST程序搜寻样本中的可移动耐药基因,并与不同的地域、宿主和体位的细菌基因组进行对比,分析其差异及近期水平转移频率;同时,对每个可移动抗生素耐药基因(ARGs)的侧翼区进行搜索分析,以便找出关联ARGs的可移动元件(MGEs)。结果表明:绿孔雀肠道菌群物种具有较强的偏向性,以普雷沃氏菌为优势菌种,拟杆菌门为优势菌门。菌群携带的可移动耐药基因以ant(6)-Iaerm(B)tet(W/32/O)为主,样本中aph(3'')-Ib基因丰度较低,但水平转移频率较高,因其侧翼区富集大量MGEs。样本中耐药基因的获得主要依靠IS5转座子的协助,耐药基因分布具有偏向性,主要集中在变形菌门和厚壁菌门,种水平上为猪链球菌和大肠杆菌,其携带较多耐药基因且可移动性较强;耐药基因的水平转移易受抗生素使用策略、耐药基因种类、生态环境和宿主系统发育遗传因素的影响。针对云南野生动物园绿孔雀,临床中需加强对氨基糖苷类耐药基因监测,避免使用该类抗生素,同时警惕猪链球菌和大肠杆菌感染。

     

    Abstract: Through this study, the distribution characteristics of drug resistance genes and mobile elements in intestinal flora of Pavo muticus were clarified, which laid a theoretical foundation for preventing the spread of animal-derived drug resistance reservoir and provided theoretical reference for clinical drug use of Pavo muticus diseases. In this study, the feces of healthy Pavo muticus raised in Yunnan Wildlife Park were sampled, and the DNA was extracted for metagenomic sequencing. Species annotation and relative abundance calculation were carried out using NCBI-nr database to obtain the species distribution characteristics of intestinal flora of Pavo muticus. Through functional annotation and cluster analysis, the types and distribution characteristics of drug resistance genes were obtained. The BLAST program was used to search for mobile resistance genes in samples, and the bacterial genomes in different regions, different hosts and different body positions were compared to analyze their differences and the frequency of recent horizontal transfer. At the same time, flanking regions of each Mobile Antibiotic resistance gene (ARGs) were searched for analysis in order to identify Mobile genetic elements (MGEs) associated with ARGs. The results showed that the intestinal flora species of Pavo muticus have strong bias, Prevotella is the dominant species, bacteroidetes is the dominant bacteria. The mobile resistance genes carried by bacteria were mainly ant(6)-Ia, erm(B) and tet(W/32/O).The abundance of aph(3")-Ib genes in the samples was low, but the horizontal transfer frequency was high, because the flanking region was rich in a large number of MGEs. The acquisition of drug resistance genes in the samples mainly depended on the assistance of IS5 transposons. The distribution of drug resistance genes is biased, mainly concentrated in Proteobacteria and Firmicutes, and at the species level, Streptococcus suis and Escherichia coli carry more drug resistance genes and are highly mobile. The horizontal transfer of drug resistance genes is easily affected by antibiotic use strategy, drug resistance gene species, ecological environment and genetic factors of host phylogeny. For Pavo muticus in Yunnan Wildlife Park, aminoglycoside resistance gene monitoring should be strengthened in clinic, such antibiotics should be avoided, and the infection of Streptococcus suis and Escherichia coli should be vigilant.. This study laid a foundation for rational and personalized antibiotic use in the intestinal flora of Pavo muticus.

     

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