Whole Genome Sequencing Reveals the Distribution of Resistance and Virulence Genes of an Enterohemorrhagic Escherichia coli O157∶H7 Strain from Swine
【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 bas...
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Guangdong Academy of Agricultural Sciences
2025-02-01
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| Series: | Guangdong nongye kexue |
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| author | Yan ZHOU Qiyang WAN Shujiao ZHU Hui ZHANG Hongduo BAO Ran WANG |
| author_facet | Yan ZHOU Qiyang WAN Shujiao ZHU Hui ZHANG Hongduo BAO Ran WANG |
| author_sort | Yan ZHOU |
| collection | DOAJ |
| description | 【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. |
| format | Article |
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| institution | OA Journals |
| issn | 1004-874X |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Guangdong Academy of Agricultural Sciences |
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| spelling | doaj-art-d678d14ee02f4edc916748728bc952c52025-08-20T01:51:41ZengGuangdong Academy of Agricultural SciencesGuangdong nongye kexue1004-874X2025-02-01522587010.16768/j.issn.1004-874X.2025.02.005202502005Whole Genome Sequencing Reveals the Distribution of Resistance and Virulence Genes of an Enterohemorrhagic Escherichia coli O157∶H7 Strain from SwineYan ZHOU0Qiyang WAN1Shujiao ZHU2Hui ZHANG3Hongduo BAO4Ran WANG5Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences / Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing 210014, ChinaInstitute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences / Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing 210014, ChinaInstitute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences / Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing 210014, ChinaInstitute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences / Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing 210014, ChinaInstitute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences / Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing 210014, ChinaInstitute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences / Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing 210014, China【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.http://gdnykx.cnjournals.org/gdnykx/ch/reader/view_abstract.aspx?file_no=202502005enterohemorrhagic escherichia coli o157: h7foodborne zoonoseswhole genome sequencinggenesfunctional annotation |
| spellingShingle | Yan ZHOU Qiyang WAN Shujiao ZHU Hui ZHANG Hongduo BAO Ran WANG Whole Genome Sequencing Reveals the Distribution of Resistance and Virulence Genes of an Enterohemorrhagic Escherichia coli O157∶H7 Strain from Swine Guangdong nongye kexue enterohemorrhagic escherichia coli o157: h7 foodborne zoonoses whole genome sequencing genes functional annotation |
| title | Whole Genome Sequencing Reveals the Distribution of Resistance and Virulence Genes of an Enterohemorrhagic Escherichia coli O157∶H7 Strain from Swine |
| title_full | Whole Genome Sequencing Reveals the Distribution of Resistance and Virulence Genes of an Enterohemorrhagic Escherichia coli O157∶H7 Strain from Swine |
| title_fullStr | Whole Genome Sequencing Reveals the Distribution of Resistance and Virulence Genes of an Enterohemorrhagic Escherichia coli O157∶H7 Strain from Swine |
| title_full_unstemmed | Whole Genome Sequencing Reveals the Distribution of Resistance and Virulence Genes of an Enterohemorrhagic Escherichia coli O157∶H7 Strain from Swine |
| title_short | Whole Genome Sequencing Reveals the Distribution of Resistance and Virulence Genes of an Enterohemorrhagic Escherichia coli O157∶H7 Strain from Swine |
| title_sort | whole genome sequencing reveals the distribution of resistance and virulence genes of an enterohemorrhagic escherichia coli o157∶h7 strain from swine |
| topic | enterohemorrhagic escherichia coli o157: h7 foodborne zoonoses whole genome sequencing genes functional annotation |
| url | http://gdnykx.cnjournals.org/gdnykx/ch/reader/view_abstract.aspx?file_no=202502005 |
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