Genomic characterization of Escherichia coli with a polyketide synthase (pks) island isolated from ulcerative colitis patients
Abstract The E. coli strains harboring the polyketide synthase (pks) island encode the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involves whole-genome-wide comparison and phylogen...
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2025-01-01
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| Online Access: | https://doi.org/10.1186/s12864-024-11198-x |
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| author | Chao Lv Mohd Abdullah Chun-Li Su Weiye Chen Nan Zhou Zile Cheng Yiwen Chen Min Li Kenneth W. Simpson Ahmed Elsaadi Yongzhang Zhu Steven M. Lipkin Yung-Fu Chang |
| author_facet | Chao Lv Mohd Abdullah Chun-Li Su Weiye Chen Nan Zhou Zile Cheng Yiwen Chen Min Li Kenneth W. Simpson Ahmed Elsaadi Yongzhang Zhu Steven M. Lipkin Yung-Fu Chang |
| author_sort | Chao Lv |
| collection | DOAJ |
| description | Abstract The E. coli strains harboring the polyketide synthase (pks) island encode the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involves whole-genome-wide comparison and phylogenetic analysis of pks harboring E. coli isolates to gain insight into the distribution and evolution of these organisms. Fifteen E. coli strains isolated from patients with ulcerative colitis (UC) were sequenced, 13 of which harbored pks islands. In addition, 2,654 genomes from the public database were also screened for pks harboring E. coli genomes, 158 of which were pks-positive (pks + ) isolates. Whole-genome-wide comparison and phylogenetic analysis revealed that 171 (158 + 13) pks + isolates belonged to phylogroup B2, and most of the isolates belong to sequence types ST73 and ST95. One isolate from a UC patient was of the sequence type ST8303. The maximum likelihood tree based on the core genome of pks + isolates revealed horizontal gene transfer across sequence types and serotypes. Virulome and resistome analyses revealed the0020preponderance of virulence genes and a reduced number of antimicrobial genes in pks + isolates. This study significantly contributes to understanding the evolution of pks islands in E. coli. |
| format | Article |
| id | doaj-art-ed08c00c3e4243c7abd549268147cc07 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj-art-ed08c00c3e4243c7abd549268147cc072025-02-02T12:10:17ZengBMCBMC Genomics1471-21642025-01-0126111310.1186/s12864-024-11198-xGenomic characterization of Escherichia coli with a polyketide synthase (pks) island isolated from ulcerative colitis patientsChao Lv0Mohd Abdullah1Chun-Li Su2Weiye Chen3Nan Zhou4Zile Cheng5Yiwen Chen6Min Li7Kenneth W. Simpson8Ahmed Elsaadi9Yongzhang Zhu10Steven M. Lipkin11Yung-Fu Chang12School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of MedicineDepartment of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell UniversityGraduate Program of Nutrition Science, School of Life Science, National Taiwan Normal UniversitySchool of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of MedicineSchool of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of MedicineSchool of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of MedicineSchool of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of MedicineSchool of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of MedicineGraduate Program of Nutrition Science, School of Life Science, National Taiwan Normal UniversityDepartment of Clinical Sciences, College of Veterinary Medicine, Cornell UniversitySchool of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of MedicineDepartment of Clinical Sciences, College of Veterinary Medicine, Cornell UniversityDepartment of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell UniversityAbstract The E. coli strains harboring the polyketide synthase (pks) island encode the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involves whole-genome-wide comparison and phylogenetic analysis of pks harboring E. coli isolates to gain insight into the distribution and evolution of these organisms. Fifteen E. coli strains isolated from patients with ulcerative colitis (UC) were sequenced, 13 of which harbored pks islands. In addition, 2,654 genomes from the public database were also screened for pks harboring E. coli genomes, 158 of which were pks-positive (pks + ) isolates. Whole-genome-wide comparison and phylogenetic analysis revealed that 171 (158 + 13) pks + isolates belonged to phylogroup B2, and most of the isolates belong to sequence types ST73 and ST95. One isolate from a UC patient was of the sequence type ST8303. The maximum likelihood tree based on the core genome of pks + isolates revealed horizontal gene transfer across sequence types and serotypes. Virulome and resistome analyses revealed the0020preponderance of virulence genes and a reduced number of antimicrobial genes in pks + isolates. This study significantly contributes to understanding the evolution of pks islands in E. coli.https://doi.org/10.1186/s12864-024-11198-xColibactinColorectal cancerGenome sequencingPhylogenetics |
| spellingShingle | Chao Lv Mohd Abdullah Chun-Li Su Weiye Chen Nan Zhou Zile Cheng Yiwen Chen Min Li Kenneth W. Simpson Ahmed Elsaadi Yongzhang Zhu Steven M. Lipkin Yung-Fu Chang Genomic characterization of Escherichia coli with a polyketide synthase (pks) island isolated from ulcerative colitis patients BMC Genomics Colibactin Colorectal cancer Genome sequencing Phylogenetics |
| title | Genomic characterization of Escherichia coli with a polyketide synthase (pks) island isolated from ulcerative colitis patients |
| title_full | Genomic characterization of Escherichia coli with a polyketide synthase (pks) island isolated from ulcerative colitis patients |
| title_fullStr | Genomic characterization of Escherichia coli with a polyketide synthase (pks) island isolated from ulcerative colitis patients |
| title_full_unstemmed | Genomic characterization of Escherichia coli with a polyketide synthase (pks) island isolated from ulcerative colitis patients |
| title_short | Genomic characterization of Escherichia coli with a polyketide synthase (pks) island isolated from ulcerative colitis patients |
| title_sort | genomic characterization of escherichia coli with a polyketide synthase pks island isolated from ulcerative colitis patients |
| topic | Colibactin Colorectal cancer Genome sequencing Phylogenetics |
| url | https://doi.org/10.1186/s12864-024-11198-x |
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