Whole genome-based genetic insights of bla NDM producing clinical E. coli isolates in hospital settings of Pakistant
ABSTRACT Carbapenem resistance among Enterobacterales has become a global health concern. Clinical Escherichia coli isolates producing the metallo β-lactamase NDM have been isolated from two hospitals in Faisalabad, Pakistan. These E. coli strains were characterized by MALDI-TOF, PCR, antimicrobial...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2023-10-01
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| Series: | Microbiology Spectrum |
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| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.00584-23 |
| _version_ | 1827792053935800320 |
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| author | Sabahat Abdullah Abdulrahman Almusallam Mei Li Muhammad Shahid Mahmood Muhammad Ahmad Mushtaq Nahla O. Eltai Mark A. Toleman Mashkoor Mohsin |
| author_facet | Sabahat Abdullah Abdulrahman Almusallam Mei Li Muhammad Shahid Mahmood Muhammad Ahmad Mushtaq Nahla O. Eltai Mark A. Toleman Mashkoor Mohsin |
| author_sort | Sabahat Abdullah |
| collection | DOAJ |
| description | ABSTRACT Carbapenem resistance among Enterobacterales has become a global health concern. Clinical Escherichia coli isolates producing the metallo β-lactamase NDM have been isolated from two hospitals in Faisalabad, Pakistan. These E. coli strains were characterized by MALDI-TOF, PCR, antimicrobial susceptibility testing, XbaI and S1 nuclease pulsed-field gel electrophoresis (PFGE), conjugation assay, DNA hybridization, whole genome sequencing, bioinformatic analysis, and Galleria mellonella experiments. Thirty-four bla NDM producing E. coli strains were identified among 52 nonduplicate carbapenem-resistant strains. More than 90% of the isolates were found to be multidrug resistant by antimicrobial susceptibility testing. S1 PFGE confirmed the presence of bla NDM gene on plasmids ranging from 40 kbps to 250 kbps, and conjugation assays demonstrated transfer frequencies of bla NDM harboring plasmids ranging from 1.59 × 10−1 to 6.46 × 10−8 per donor. Whole genome sequencing analysis revealed bla NDM-5 as the prominent NDM subtype with the highest prevalence of bla OXA-1, bla CTX-M-15, aadA2, aac(6')-Ib-cr, and tet(A) associated resistant determinants. E. coli sequence types: ST405, ST361, and ST167 were prominent, and plasmid Inc types: FII, FIA, FIB, FIC, X3, R, and Y, were observed among all isolates. The genetic environment of bla NDM region on IncF plasmids included partial ISAba125, the bleomycin ble gene, and a class I integron. The virulence genes terC, traT, gad, fyuA, irp2, capU, and sitA were frequently observed, and G. mellonella experiments showed that virulence correlated with the number of virulence determinants. A strong infection control management in the hospital is necessary to check the emergence of carbapenem resistance in Gram-negative bacteria. IMPORTANCE We describe a detailed analysis of highly resistant clinical E. coli isolates from two tertiary care centers in Pakistan including carbapenem resistance as well as common co-resistance mechanisms. South Asia has a huge problem with highly resistant E. coli. However, we find that though these isolates are very difficult to treat they are of low virulence. Thus the Western world has an increasing problem with virulent E. coli that are mostly of low antibiotic resistance, whereas, South Asia has an increasing problem with highly resistant E. coli that are of low virulence potential. These observations allow us to start to devise methodologies to limit both virulence and resistance and combat problems in developing nations as well as the Western world. |
| first_indexed | 2024-03-11T17:55:22Z |
| format | Article |
| id | doaj.art-b67ffe5c187f4818baa6e5bb26b25060 |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-03-11T17:55:22Z |
| publishDate | 2023-10-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-b67ffe5c187f4818baa6e5bb26b250602023-10-17T13:04:36ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972023-10-0111510.1128/spectrum.00584-23Whole genome-based genetic insights of bla NDM producing clinical E. coli isolates in hospital settings of PakistantSabahat Abdullah0Abdulrahman Almusallam1Mei Li2Muhammad Shahid Mahmood3Muhammad Ahmad Mushtaq4Nahla O. Eltai5Mark A. Toleman6Mashkoor Mohsin7Institute of Microbiology, University of Agriculture , Faisalabad, PakistanDepartment of Medical Microbiology, School of Medicine, Institute of Infection and Immunity, Cardiff University , Cardiff, United KingdomDepartment of Medical Microbiology, School of Medicine, Institute of Infection and Immunity, Cardiff University , Cardiff, United KingdomInstitute of Microbiology, University of Agriculture , Faisalabad, PakistanInstitute of Microbiology, University of Agriculture , Faisalabad, PakistanBiomedical Research Center, Qatar University , Doha, QatarDepartment of Medical Microbiology, School of Medicine, Institute of Infection and Immunity, Cardiff University , Cardiff, United KingdomInstitute of Microbiology, University of Agriculture , Faisalabad, PakistanABSTRACT Carbapenem resistance among Enterobacterales has become a global health concern. Clinical Escherichia coli isolates producing the metallo β-lactamase NDM have been isolated from two hospitals in Faisalabad, Pakistan. These E. coli strains were characterized by MALDI-TOF, PCR, antimicrobial susceptibility testing, XbaI and S1 nuclease pulsed-field gel electrophoresis (PFGE), conjugation assay, DNA hybridization, whole genome sequencing, bioinformatic analysis, and Galleria mellonella experiments. Thirty-four bla NDM producing E. coli strains were identified among 52 nonduplicate carbapenem-resistant strains. More than 90% of the isolates were found to be multidrug resistant by antimicrobial susceptibility testing. S1 PFGE confirmed the presence of bla NDM gene on plasmids ranging from 40 kbps to 250 kbps, and conjugation assays demonstrated transfer frequencies of bla NDM harboring plasmids ranging from 1.59 × 10−1 to 6.46 × 10−8 per donor. Whole genome sequencing analysis revealed bla NDM-5 as the prominent NDM subtype with the highest prevalence of bla OXA-1, bla CTX-M-15, aadA2, aac(6')-Ib-cr, and tet(A) associated resistant determinants. E. coli sequence types: ST405, ST361, and ST167 were prominent, and plasmid Inc types: FII, FIA, FIB, FIC, X3, R, and Y, were observed among all isolates. The genetic environment of bla NDM region on IncF plasmids included partial ISAba125, the bleomycin ble gene, and a class I integron. The virulence genes terC, traT, gad, fyuA, irp2, capU, and sitA were frequently observed, and G. mellonella experiments showed that virulence correlated with the number of virulence determinants. A strong infection control management in the hospital is necessary to check the emergence of carbapenem resistance in Gram-negative bacteria. IMPORTANCE We describe a detailed analysis of highly resistant clinical E. coli isolates from two tertiary care centers in Pakistan including carbapenem resistance as well as common co-resistance mechanisms. South Asia has a huge problem with highly resistant E. coli. However, we find that though these isolates are very difficult to treat they are of low virulence. Thus the Western world has an increasing problem with virulent E. coli that are mostly of low antibiotic resistance, whereas, South Asia has an increasing problem with highly resistant E. coli that are of low virulence potential. These observations allow us to start to devise methodologies to limit both virulence and resistance and combat problems in developing nations as well as the Western world.https://journals.asm.org/doi/10.1128/spectrum.00584-23E. coliGalleria mellonellabla NDMST167carbapenemase |
| spellingShingle | Sabahat Abdullah Abdulrahman Almusallam Mei Li Muhammad Shahid Mahmood Muhammad Ahmad Mushtaq Nahla O. Eltai Mark A. Toleman Mashkoor Mohsin Whole genome-based genetic insights of bla NDM producing clinical E. coli isolates in hospital settings of Pakistant Microbiology Spectrum E. coli Galleria mellonella bla NDM ST167 carbapenemase |
| title | Whole genome-based genetic insights of bla NDM producing clinical E. coli isolates in hospital settings of Pakistant |
| title_full | Whole genome-based genetic insights of bla NDM producing clinical E. coli isolates in hospital settings of Pakistant |
| title_fullStr | Whole genome-based genetic insights of bla NDM producing clinical E. coli isolates in hospital settings of Pakistant |
| title_full_unstemmed | Whole genome-based genetic insights of bla NDM producing clinical E. coli isolates in hospital settings of Pakistant |
| title_short | Whole genome-based genetic insights of bla NDM producing clinical E. coli isolates in hospital settings of Pakistant |
| title_sort | whole genome based genetic insights of bla ndm producing clinical e coli isolates in hospital settings of pakistant |
| topic | E. coli Galleria mellonella bla NDM ST167 carbapenemase |
| url | https://journals.asm.org/doi/10.1128/spectrum.00584-23 |
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