Comparative Genomics Revealed Fluoroquinolone Resistance Determinants and OmpF Deletion in Carbapenem-Resistant Escherichia coli
Escherichia coli (E. coli) is a major causative organism of complicated urinary tract infections, bloodstream infections, and pneumonia. With the widespread use of antimicrobial agents, the prevalence of carbapenem resistance in E. coli has been increasing with limited therapeutic options. Fluoroqui...
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Frontiers Media S.A.
2022-04-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.886428/full |
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| author | Wan-Ting Yang I-Ju Chiu Yao-Ting Huang Po-Yu Liu Po-Yu Liu Po-Yu Liu |
| author_facet | Wan-Ting Yang I-Ju Chiu Yao-Ting Huang Po-Yu Liu Po-Yu Liu Po-Yu Liu |
| author_sort | Wan-Ting Yang |
| collection | DOAJ |
| description | Escherichia coli (E. coli) is a major causative organism of complicated urinary tract infections, bloodstream infections, and pneumonia. With the widespread use of antimicrobial agents, the prevalence of carbapenem resistance in E. coli has been increasing with limited therapeutic options. Fluoroquinolone remains a choice in carbapenem-resistant E. coli (CREc) that were once susceptible to the drug. Despite robust studies on the fluoroquinolone-resistant mechanisms of E. coli, few studies focused specifically on the group of CREc. In this study, we used comparative genomics to identify the fluoroquinolone-resistant mechanisms of CREc and detected gyrA D87N mutation in all the fluoroquinolone-resistant and CREc. Moreover, to investigate the mechanism underlying non-carbapenemase-producing carbapenem-resistant E. coli, we targeted the complete genome sequences for in-depth analysis and found a deletion in OmpF (DEL264-269) that might contribute to carbapenem resistance, which has not been reported before. Further studies focusing on the impact of these mutations on the expression levels are warranted. We further investigate the MLST, serotype, fimH type, phylogroup, and clinical characteristics of the CREc. Combination analysis of clinical and genomic characteristics suggests the polyclonal and highly diverse nature of the CREc in Taiwan. This study provides an insight into the molecular epidemiology of CREc in Taiwan. |
| first_indexed | 2024-04-11T13:45:34Z |
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| id | doaj.art-8a7a7da5d8ea46a6bc684fbede42a735 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-11T13:45:34Z |
| publishDate | 2022-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-8a7a7da5d8ea46a6bc684fbede42a7352022-12-22T04:21:06ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-04-011310.3389/fmicb.2022.886428886428Comparative Genomics Revealed Fluoroquinolone Resistance Determinants and OmpF Deletion in Carbapenem-Resistant Escherichia coliWan-Ting Yang0I-Ju Chiu1Yao-Ting Huang2Po-Yu Liu3Po-Yu Liu4Po-Yu Liu5Division of Infection, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, TaiwanDepartment of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, TaiwanDepartment of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, TaiwanDivision of Infection, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, TaiwanPh.D. Program in Translational Medicine, National Chung Hsing University, Taichung, TaiwanRong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, TaiwanEscherichia coli (E. coli) is a major causative organism of complicated urinary tract infections, bloodstream infections, and pneumonia. With the widespread use of antimicrobial agents, the prevalence of carbapenem resistance in E. coli has been increasing with limited therapeutic options. Fluoroquinolone remains a choice in carbapenem-resistant E. coli (CREc) that were once susceptible to the drug. Despite robust studies on the fluoroquinolone-resistant mechanisms of E. coli, few studies focused specifically on the group of CREc. In this study, we used comparative genomics to identify the fluoroquinolone-resistant mechanisms of CREc and detected gyrA D87N mutation in all the fluoroquinolone-resistant and CREc. Moreover, to investigate the mechanism underlying non-carbapenemase-producing carbapenem-resistant E. coli, we targeted the complete genome sequences for in-depth analysis and found a deletion in OmpF (DEL264-269) that might contribute to carbapenem resistance, which has not been reported before. Further studies focusing on the impact of these mutations on the expression levels are warranted. We further investigate the MLST, serotype, fimH type, phylogroup, and clinical characteristics of the CREc. Combination analysis of clinical and genomic characteristics suggests the polyclonal and highly diverse nature of the CREc in Taiwan. This study provides an insight into the molecular epidemiology of CREc in Taiwan.https://www.frontiersin.org/articles/10.3389/fmicb.2022.886428/fullcarbapenem-resistantwhole-genome sequencingEscherichia colicarbapenemasevirulenceepidemiology |
| spellingShingle | Wan-Ting Yang I-Ju Chiu Yao-Ting Huang Po-Yu Liu Po-Yu Liu Po-Yu Liu Comparative Genomics Revealed Fluoroquinolone Resistance Determinants and OmpF Deletion in Carbapenem-Resistant Escherichia coli Frontiers in Microbiology carbapenem-resistant whole-genome sequencing Escherichia coli carbapenemase virulence epidemiology |
| title | Comparative Genomics Revealed Fluoroquinolone Resistance Determinants and OmpF Deletion in Carbapenem-Resistant Escherichia coli |
| title_full | Comparative Genomics Revealed Fluoroquinolone Resistance Determinants and OmpF Deletion in Carbapenem-Resistant Escherichia coli |
| title_fullStr | Comparative Genomics Revealed Fluoroquinolone Resistance Determinants and OmpF Deletion in Carbapenem-Resistant Escherichia coli |
| title_full_unstemmed | Comparative Genomics Revealed Fluoroquinolone Resistance Determinants and OmpF Deletion in Carbapenem-Resistant Escherichia coli |
| title_short | Comparative Genomics Revealed Fluoroquinolone Resistance Determinants and OmpF Deletion in Carbapenem-Resistant Escherichia coli |
| title_sort | comparative genomics revealed fluoroquinolone resistance determinants and ompf deletion in carbapenem resistant escherichia coli |
| topic | carbapenem-resistant whole-genome sequencing Escherichia coli carbapenemase virulence epidemiology |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.886428/full |
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