一株猪源肠出血性大肠杆菌O157∶H7的全基因组测序及毒力和耐药基因分析

周艳; 万启旸; 朱树娇; 张辉; 包红朵; 王冉

doi:10.16768/j.issn.1004-874X.2025.02.005

一株猪源肠出血性大肠杆菌O157∶H7的全基因组测序及毒力和耐药基因分析

Whole Genome Sequencing Reveals the Distribution of Resistance and Virulence Genes of an Enterohemorrhagic Escherichia coli O157∶H7 Strain from Swine

摘要

摘要:
目的分析一株猪源肠出血性大肠杆菌O157∶H7菌株EO157-1的全基因组信息及其毒力和耐药基因。
方法基于Nanopore三代测序技术平台和Illumina二代测序技术平台对猪源肠出血性大肠杆菌O157∶H7菌株EO157-1进行全基因组测序，利用Prokka软件预测基因组序列信息，并通过UniProt、KEGG、KEGG Pathway、GO、Pfam、COG、TIGERfams、RefSeq和NR数据库进行基因预测和注释，再利用碳水化合物酶（CAZy）、病原与宿主互作（PHI）、毒力因子（VFDB）和耐药基因（CARD）数据库进行基因功能分析。
结果肠出血性大肠杆菌O157∶H7菌株EO157-1基因组大小为5 404 747 bp，GC含量为50.49%，该菌株含有3个质粒；共预测到5 674个蛋白质编码基因，包含22个rRNA（7个23S rRNA、7个16S rRNA、8个5S rRNA）、1个tmRNA、102个tRNA基因和282个小RNA分子；预测出9个CRISPR序列、273个重复序列；KEGG、KEGG Pathway、NR、UniProt、GO、COG、Pfam、RefSeq和TIGERfams数据库分别注释到1 712、1 693、5 265、5 264、4 029、4 294、4 688、5 252和2 741个基因；CAZy数据库注释筛选出100个基因，PHI数据库注释筛选出2 354个基因，VFDB数据库注释筛选出的毒力基因主要包括菌毛、鞭毛、II型分泌系统、III型分泌系统、VI型分泌系统、紧密黏附素、铁转运系统、脂多糖、荚膜、侵袭素和外毒素；CARD数据库注释筛选出的耐药基因与多重耐药外排泵、大环内酯类抗生素、四环素、多粘菌素、杆菌肽、氨基糖苷类抗生素、肽类抗生素及甲硝唑相关。
结论获得一株肠出血性大肠杆菌O157∶H7菌株EO157-1全基因组序列，序列分析表明该菌株携带大量毒力基因与耐药基因。

Abstract:
Objective In order to analyze the whole genome information of a porcine derived enterohemorrhagic Escherichia coli O157 ∶ H7 strain EO157-1 and its virulence and drug resistance genes.
Method This experiment conducted whole-genome sequencing of enterohemorrhagic E. coli O157 ∶ H7 strain EO157-1 based on the Nanopore third-generation sequencing technology platform and the Illumina second-generation sequencing technology platform. The Prokka software was used to predict the genome sequence information, and the genome sequence information was predicted through UniProt, KEGG and KEGG Pathway, GO, Pfam, COG, TIGERfams, RefSeq and NR databases were used for gene prediction and annotation, and then the carbohydrate enzyme (CAZy), pathogen and host interaction (PHI), virulence factor (VFDB) and drug resistance gene (CARD) databases were used Perform gene functional analysis.
Result The genome size of enterohemorrhagic E. coli O157 ∶ H7 strain EO157-1 is 5 404 747 bp, and the GC content is 50.49%. In addition, this strain also contains 3 plasmids. There are 5 674 predicted protein-coding genes, including 22 rRNA (7 23S rRNA, 7 16S rRNA, 8 5S rRNA), 1 tmRNA, 102 tRNA genes and 282 small RNA molecules; 9 are predicted CRISPR sequences, 273 repeat sequences; KEGG, KEGG Pathway, NR, UniProt, GO, COG, Pfam, RefSeq and TIGERfams databases annotated 1 712, 1 693, 5 265, 5 264, 4 029, 4 294, 4 688, 5 252 and 2 741 genes respectively. The CAZy database annotation screened out 100 genes, the PHI database annotation screened out 2 354 genes, and the VFDB database annotation screened out virulence genes mainly including pili, flagella, type II secretion system, type III secretion system, type VI secretion system, intimin, iron transport system, lipopolysaccharide, capsule, invasins and exotoxins; resistance genes and multidrug resistance efflux pumps, macrolide antibiotics, tetracyclines, polymyxins, bacitracin, and aminoglycoside antibiotics, peptide antibiotics and metronidazole related.
Conclusion The whole genome sequence of an enterohemorrhagic E. coli O157 ∶ H7 strain EO157-1 was obtained. Sequence analysis showed that this strain carries a large number of virulence genes and drug resistance genes.

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