鸭源马尿气球菌的鉴定及全基因组测序分析  

Identification and whole genome sequencing of a duck-derived Aerococcus urinaequi strain

作　　者：张菡 舒静超 张晓静 董青[1,4] 彭志锋 边传周[1,4] 乔宏兴 ZHANG Han;SHU Jing-chao;ZHANG Xiao-jing;DONG Qing;PENG Zhi-feng;BIAN Chuan-zhou;QIAO Hong-xing(Henan International Joint Laboratory for Prevention and Control of Animal Enteric Diseases,Zhengzhou 450046,China;Henan Yanhuang Biological Engineering Co.,Ltd.,Zhengzhou 453822,China;Zhengzhou Antu Biological Engineering Co.,Ltd.,Zhengzhou 450016,China;College of Veterinary Medicine,Henan University of Animal Husbandry and Economy,Zhengzhou 450046,China)

机构地区：[1]河南省动物肠道疫病防控国际联合实验室,河南郑州450046 [2]河南炎黄生物工程有限公司,河南郑州453822 [3]郑州安图生物工程股份有限公司,河南郑州450016 [4]河南牧业经济学院动物医药学院,河南郑州450046

出　　处：《中国预防兽医学报》2024年第2期128-139,共12页Chinese Journal of Preventive Veterinary Medicine

基　　金：河南重点研发专项项目(221111111300);河南省现代农业体系岗位专家项目(HARS-22-12-G2);河南牧业经济学院校重点学科项目(XJXK202202);河南牧业经济学院博士科研启动资金资助项目(2021HNUAHEDF004)。

摘　　要：为鉴定一株鸭源分离菌,并探究其生物信息学特性,本研究分别通过Pacbio Sequel三代测序技术和Illumina NovaSeq二代测序技术对该株鸭源分离菌进行全基因组测序;基于该分离菌16S rRNA基因序列构建进化树;通过GTDB基于基因组之间的平均核苷酸相似性及采用infer软件构建120个单拷贝基因序列进化树并对其分类;利用NR数据库比对分离菌全基因组蛋白编码基因序列;采用VFDB数据库分析该分离菌相关毒力基因;采用K-B纸片法测定分离菌对21种药物的药敏性试验;采用CARD数据库分析分离菌的耐药基因;利用GO、KEGG、COG数据库对分离菌进行基因功能、信号通路及基因的注释。测序结果显示分离菌由一个环形染色体和一个环形质粒组成,大小分别为2 133 811 bp和37 505 bp,GC含量分别为39.04%和35.03%;通过GTDB分类及NR数据库比对分析显示,该菌为马尿气球菌亚种;VFDB数据库比对发现6种致病毒力基因;药敏试验结果显示分离菌对红霉素、多西环素、庆大霉素、卡那霉素等多种药物耐药,CARD数据库比对发现6种耐药基因;基因功能分析显示,1 277个基因参与25类代谢通路,1 767个基因编码蛋白质,3 304个基因与分子功能相关,1 977个基因与细胞组分相关,4 421个基因与生物学过程相关。本研究对鸭源分离菌进行全基因组测序及基因组结构、功能分析,丰富了鸭源马尿气球菌全基因组数据库资料,完善了该菌的系统进化信息,分析了其毒力因子和相关耐药基因,为后续对该菌株分子生物学特征、致病性和耐药基因筛选提供了基因组信息和基因资源。To identify a duck derived isolate and explore its bioinformatics function,the whole genome of the isolate was sequenced by Pacbio Sequel and Illumina NovaSeq,one phylogenetic tree was constructed using 16S rRNA gene sequence,and another tree was constructed by GTDB based on the average nucleotide similarity between genomes and 120 single-copy gene sequences to classify them,and the NR database was employed to compare the protein-coding gene sequences of whole genome of the isolate,and the VFDB database was used to analyze the virulence genes.The antimicrobial susceptibility test was carried out with 21 kinds of antibiotics,the drug resistance genes were analyzed using CARD database,and the GO KEGG and COG databases were used to annotate the gene function of the isolate.The sequencing results showed that the isolate consisted of one chromosome and one plasmid,with the size of 2133811bp and 37505bp,respectively,and the GC content was 39.04% and 35.03%,respectively.GTDB classification and NR database comparison showed that the isolate was a subspecies of Aerococcus urinaeequi(A.urinaeequi),six virulence genes were found in VFDB database.Antimicrobial susceptibility test results showed that the isolate was resistant to erythromycin,doxycycline,gentamicin,kanamycin and other drugs.Six drug resistance genes were found in CARD database.Gene function analysis showed that 1277 genes were involved in 25 types of metabolic pathways,1767 genes encoded proteins,3304 genes were related to molecular function,1977 genes were related to cell components,and 4421genes were associated with biological processes.In this study,whole genome sequencing identification and genome structure and function analysis of a duck-derived A.urinaeequi isolate were carried out,which enriched the whole genome data and improved the phylogenetic information,and the analysis of its virulence factors and effective target drug resistance genes provided genomic information and gene resources for the subsequent screening of molecular biological characterist

关 键 词：马尿气球菌 全基因组序列 耐药性 致病性 

分 类 号：S852.61[农业科学—基础兽医学]