Prevalence and genomic insights of carbapenem resistant and ESBL producing Multidrug resistant Escherichia coli in urinary tract infections
Abstract Urinary tract infections are a common condition affecting people globally, with multidrug-resistant (MDR) Escherichia coli (E. coli) being a major causative agent. Antimicrobial susceptibility profiling was performed using the VITEK 2 automated system for 1254 E. coli isolates, revealing th...
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Nature Portfolio
2025-01-01
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| Online Access: | https://doi.org/10.1038/s41598-024-84754-w |
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| author | Vidhyalakshmi Sivarajan Amirtha Varshini Ganesh Pavithra Subramani Priyanka Ganesapandi R. N. Sivanandan Sneha Prakash Nithyasri Manikandan Arunasalam Dharmarajan Frank Arfuso Sudha Warrier Marquess Raj Kumar Perumal |
| author_facet | Vidhyalakshmi Sivarajan Amirtha Varshini Ganesh Pavithra Subramani Priyanka Ganesapandi R. N. Sivanandan Sneha Prakash Nithyasri Manikandan Arunasalam Dharmarajan Frank Arfuso Sudha Warrier Marquess Raj Kumar Perumal |
| author_sort | Vidhyalakshmi Sivarajan |
| collection | DOAJ |
| description | Abstract Urinary tract infections are a common condition affecting people globally, with multidrug-resistant (MDR) Escherichia coli (E. coli) being a major causative agent. Antimicrobial susceptibility profiling was performed using the VITEK 2 automated system for 1254 E. coli isolates, revealing that 831(66.2%) isolates were determined as MDR E. coli. A significant resistance pattern was observed for nalidixic acid (86.04%), ampicillin (74.16%), ticarcillin (70.73%), cefalotin (65.23%), cefixime (62.68%), ciprofloxacin (55.18%), ceftriaxone (53.75%), amoxicillin-clavulanic acid (22.81%), ertapenem (7.18%), and fosfomycin (2.23%). Whole Genome Sequencing of Carbapenem-resistant E. coli (CREC)—CREC 3 (ST405), CREC 4 (ST448), and CREC 5 (ST167) was performed to determine genomic characteristics. CREC 3, CREC 4, and CREC 5 belong to the phylogroup D, B1, and A, respectively. The NDM-5 gene was common in all three isolates, with CTX-M-15 being present in CREC 3 and CREC 4. Virulence factors of CREC 3 (fliC, shuA), CREC 4 (spaS), CREC 5 (iucA, papH, papG, iucB, yigF), and plasmids (IncFIA, IncFIB) were identified to be significant. The use of pangenome analysis enhances our understanding of resistance traits of isolates ST167, ST405, and ST448, offering valuable insights into comparative genomics of uropathogenic MDR E. coli. |
| format | Article |
| id | doaj-art-9d7697b833b3400c80f14ef7b7028d19 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
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| spelling | doaj-art-9d7697b833b3400c80f14ef7b7028d192025-01-26T12:28:37ZengNature PortfolioScientific Reports2045-23222025-01-0115111310.1038/s41598-024-84754-wPrevalence and genomic insights of carbapenem resistant and ESBL producing Multidrug resistant Escherichia coli in urinary tract infectionsVidhyalakshmi Sivarajan0Amirtha Varshini Ganesh1Pavithra Subramani2Priyanka Ganesapandi3R. N. Sivanandan4Sneha Prakash5Nithyasri Manikandan6Arunasalam Dharmarajan7Frank Arfuso8Sudha Warrier9Marquess Raj10Kumar Perumal11Department of Biotechnology, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research (SRIHER)Department of Biotechnology, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research (SRIHER)Department of Biotechnology, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research (SRIHER)Department of Biotechnology, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research (SRIHER)Division of Infectious Disease, St. John’s Research InstituteDepartment of Biotechnology, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research (SRIHER)Department of Biotechnology, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research (SRIHER)Faculty of Clinical Research, Sri Ramachandra Institute of Higher Education and ResearchSchool of Human Sciences, The University of Western AustraliaDepartment of Biotechnology, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research (SRIHER)Regional Reference Laboratory, Apollo DiagnosticsDepartment of Biotechnology, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research (SRIHER)Abstract Urinary tract infections are a common condition affecting people globally, with multidrug-resistant (MDR) Escherichia coli (E. coli) being a major causative agent. Antimicrobial susceptibility profiling was performed using the VITEK 2 automated system for 1254 E. coli isolates, revealing that 831(66.2%) isolates were determined as MDR E. coli. A significant resistance pattern was observed for nalidixic acid (86.04%), ampicillin (74.16%), ticarcillin (70.73%), cefalotin (65.23%), cefixime (62.68%), ciprofloxacin (55.18%), ceftriaxone (53.75%), amoxicillin-clavulanic acid (22.81%), ertapenem (7.18%), and fosfomycin (2.23%). Whole Genome Sequencing of Carbapenem-resistant E. coli (CREC)—CREC 3 (ST405), CREC 4 (ST448), and CREC 5 (ST167) was performed to determine genomic characteristics. CREC 3, CREC 4, and CREC 5 belong to the phylogroup D, B1, and A, respectively. The NDM-5 gene was common in all three isolates, with CTX-M-15 being present in CREC 3 and CREC 4. Virulence factors of CREC 3 (fliC, shuA), CREC 4 (spaS), CREC 5 (iucA, papH, papG, iucB, yigF), and plasmids (IncFIA, IncFIB) were identified to be significant. The use of pangenome analysis enhances our understanding of resistance traits of isolates ST167, ST405, and ST448, offering valuable insights into comparative genomics of uropathogenic MDR E. coli.https://doi.org/10.1038/s41598-024-84754-wCarbapenem resistanceWhole genome sequenceUrinary tract infectionST405ST448ST167 |
| spellingShingle | Vidhyalakshmi Sivarajan Amirtha Varshini Ganesh Pavithra Subramani Priyanka Ganesapandi R. N. Sivanandan Sneha Prakash Nithyasri Manikandan Arunasalam Dharmarajan Frank Arfuso Sudha Warrier Marquess Raj Kumar Perumal Prevalence and genomic insights of carbapenem resistant and ESBL producing Multidrug resistant Escherichia coli in urinary tract infections Scientific Reports Carbapenem resistance Whole genome sequence Urinary tract infection ST405 ST448 ST167 |
| title | Prevalence and genomic insights of carbapenem resistant and ESBL producing Multidrug resistant Escherichia coli in urinary tract infections |
| title_full | Prevalence and genomic insights of carbapenem resistant and ESBL producing Multidrug resistant Escherichia coli in urinary tract infections |
| title_fullStr | Prevalence and genomic insights of carbapenem resistant and ESBL producing Multidrug resistant Escherichia coli in urinary tract infections |
| title_full_unstemmed | Prevalence and genomic insights of carbapenem resistant and ESBL producing Multidrug resistant Escherichia coli in urinary tract infections |
| title_short | Prevalence and genomic insights of carbapenem resistant and ESBL producing Multidrug resistant Escherichia coli in urinary tract infections |
| title_sort | prevalence and genomic insights of carbapenem resistant and esbl producing multidrug resistant escherichia coli in urinary tract infections |
| topic | Carbapenem resistance Whole genome sequence Urinary tract infection ST405 ST448 ST167 |
| url | https://doi.org/10.1038/s41598-024-84754-w |
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