TY - JOUR
T1 - Phylogenetic diversity and mutational analysis of New Delhi Metallo-β-lactamase (NDM) producing E. coli strains from pediatric patients in Pakistan
AU - Nosheen, Sumbal
AU - Bukhari, Nadeem Irfan
AU - Junaid, Kashaf
AU - Anwar, Naeem
AU - Ahmad, Fahad
AU - Younas, Sonia
AU - Ejaz, Hasan
N1 - Funding Information:
Authors are thankful to The Children's Hospital and The Institute of Child Health, Lahore, and the University of the Punjab, Lahore, Pakistan, for the facilitation.
Publisher Copyright:
© 2021 The Author(s)
PY - 2021/10/1
Y1 - 2021/10/1
N2 - 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.
AB - 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.
KW - Carbapenemases
KW - E. coli
KW - Multidrug resistance
KW - NDM
KW - Phylogeny
KW - Resistant genes
UR - http://www.scopus.com/inward/record.url?scp=85108848763&partnerID=8YFLogxK
U2 - 10.1016/j.sjbs.2021.06.037
DO - 10.1016/j.sjbs.2021.06.037
M3 - Article
SN - 1319-562X
VL - 28
SP - 5875
EP - 5883
JO - Saudi Journal of Biological Sciences
JF - Saudi Journal of Biological Sciences
IS - 10
ER -