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Whole genome-based genetic insights of blaNDM producing clinical E. coli isolates in hospitals settings of Pakistan

Abdullah, Sabahat, Almusallam, Abdul Rahman, Li, Mei, Mahmood, Muhammad Shahid, Mushtaq, Muhammad Ahmad, Eltai, Nahla O., Toleman, Mark A. ORCID: and Mohsin, Mashkoor 2023. Whole genome-based genetic insights of blaNDM producing clinical E. coli isolates in hospitals settings of Pakistan. Microbiology Spectrum 11 (5) , e00584-23. 10.1128/spectrum.00584-23

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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.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Medicine
Publisher: American Society for Microbiology
ISSN: 2165-0497
Date of First Compliant Deposit: 20 July 2023
Date of Acceptance: 2 July 2023
Last Modified: 12 Jan 2024 13:25

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