Phylogenetic diversity and mutational analysis of New Delhi Metallo-β-lactamase (NDM) producing E. coli strains from pediatric patients in Pakistan

Sumbal Nosheen, Nadeem Irfan Bukhari, Kashaf Junaid, Naeem Anwar, Fahad Ahmad, Sonia Younas, Hasan Ejaz

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Abstract

The evolution of NDM genes (blaNDM) in E. coli is accounted for expansive multidrug resistance (MDR), causing severe infections and morbidities in the pediatric population. This study aimed to analyze the phylogeny and mutations in NDM variants of E. coli recovered from the pediatric population. Carbapenem-resistant clinical strains of E. coli were identified using microbiological phenotypic techniques. PCR technique used to amplify the blaNDM genes, identified on agarose gel, and analyzed by DNA sequencing. The amino acid substitutions were examined for mutations after aligning with wild types. Mutational and phylogenetic analysis was performed using Lasergene, NCBI blastn, Clustal Omega, and MEGA software, whereas PHYRE2 software was used for the protein structure predictions. PCR amplification of the blaNDM genes detected 113 clinical strains of E. coli with the contribution of blaNDM-1 (46%), blaNDM-4 (3.5%), and blaNDM-5 (50%) variants. DNA sequencing of blaNDM variants showed homology to the previously described blaNDM-1, blaNDM-4, and blaNDM-5 genes available at GenBank and NCBI database. In addition, the mutational analysis revealed in frame substitutions of Pro60Ala and Pro59Ala in blaNDM-4 and blaNDM-5 respectively. The blaNDM-1 was ortholog with related sequences of E. coli available at GenBank. The phylogenetic analysis indicated that the NDM gene variants resemble other microbes reported globally with some new mutational sites.

Original languageEnglish
Pages (from-to)5875-5883
Number of pages9
JournalSaudi Journal of Biological Sciences
Volume28
Issue number10
Early online date18 Sept 2021
DOIs
Publication statusPublished - 1 Oct 2021

Keywords

  • Carbapenemases
  • E. coli
  • Multidrug resistance
  • NDM
  • Phylogeny
  • Resistant genes

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