摘要
为了阐释致病性多重耐药性鸡源大肠杆菌分离株的基因组信息及其耐药和致病机制,试验通过第二代测序技术,基于Illumina Nova Seq测序平台,对大肠杆菌JC78株进行基因组测序,利用CRISPRCasFinder软件预测基因序列信息,并通过GO(gene ontology)、KEGG(kyoto encyclopedia of genes and genomes)、COG(cluster of orthologous groups of proteins)、NR(non-redundant protein)、Pfam、TCDB(transporter classification database)、Swiss-Prot、碳水化合物活性酶(carbohydrate-active en ZYmes,CAZy)、病原与宿主互作(pathogen host interactions,PHI)、致病菌毒力因子综合性(virulence factors of pathogenic bacteria,VFDB)、抗生素耐药性综合(the comprehensive antibiotic resistance database,CARD)数据库进行基因功能分析。结果表明:大肠杆菌JC78株基因组大小为5316974 bp,GC含量为50.38%,预测到的蛋白质编码基因有5111个,包含4个rRNA(1个23S r RNA、1个16S rRNA、2个5S r RNA)、65个t RNA基因及80个其他RNA;预测出5个CRISPR序列,59个串联重复序列;NR、COG、Swiss-Prot、GO、KEGG、TCDB、PHI、CAZy数据库注释到5099,4577,4476,3894,3173,1260,1225,141个基因;VFDB数据库注释筛选出的毒力基因主要包括鞭毛、菌毛、K1荚膜、Ⅱ型分泌系统等;CARD数据库注释筛选出的耐药基因与链霉素、四环素、β-内酰胺类、氟喹诺酮类、大环内酯类及利福平等药物相关。说明大肠杆菌JC78株具有较强毒力且为多重耐药株,并携带大量毒力基因与耐药基因。
In order to elucidate the genomic information of pathogenic multidrug-resistant chicken-derived Escherichia coli strain and their mechanisms of resistance and pathogenicity,in the experiment,the genome of E.coli JC78 strain was sequenced by second-generation sequencing technology based on Illumina Nova Seq sequencing platform.The gene sequence information was predicted using CRISPRCasFinder;and the gene functions were analyzed by GO(gene ontology),KEGG(kyoto encyclopedia of genes and genomes),COG(cluster of orthologous groups of proteins),NR(non-redundant protein database),Pfam,TCDB(transporter classification database),Swiss-Prot,carbohydrate-active en ZYmes(CAZy),pathogen host interactions(PHI),virulence factors of pathogenic bacteria(VFDB),and the comprehensive antibiotic resistance database(CARD).The results showed that the genome size of E.coli JC78 strain was 5316974 bp;the content of GC content was 50.38%;there were 5111 predicted coding genes,which contained 4 r RNAs(one 23S r RNA,one 16S r RNA and two 5S r RNAs),65 t RNA genes and 80 other RNAs.Five CRISPR sequences with 59 tandem repeats were predicted;NR,COG,Swiss-Prot,GO,KEGG,TCDB,PHI,and CAZy databases were annotated to 5099,4577,4476,3894,3173,1260,and 1225,141 genes.The virulence genes screened by the VFDB database annotation mainly included flagella,fimbrium,K1 capsule,typeⅡsecretion system,etc.The resistance genes screened by the CARD database annotation were related to the drugs of streptomycin,tetracycline,β-lactams,fluoroquinolones,macrolides and rifampicin.The results suggested that E.coli JC78 strain was highly virulent and multi-drug resistant,and carried a large number of virulence genes and drug resistance genes.
作者
赵浪
孙嘉良
李佳丹扬
吴培福
ZHAO Lang;SUN Jialiang;LI Jiadanyang;WU Peifu(College of Life Science,Southwest Forest University,Kunming 650224,China)
出处
《黑龙江畜牧兽医》
CAS
北大核心
2024年第19期62-68,共7页
Heilongjiang Animal Science And veterinary Medicine
基金
国家自然科学基金项目(31902152)
生物学质量工程项目(503190106)
西南林业大学科技处科研预研基金项目(110823054)。
关键词
鸡
大肠杆菌
基因组测序
基因
功能注释
chickens
Escherichia coli
genome sequencing
gene
functional annotation
