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

Abstract

The evolution of NDM genes ( bla NDM ) 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 bla NDM 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 bla NDM genes detected 113 clinical strains of E. coli with the contribution of bla NDM-1 (46%), bla NDM-4 (3.5%), and bla NDM-5 (50%) variants. DNA sequencing of bla NDM variants showed homology to the previously described bla NDM-1 , bla NDM-4, and bla NDM-5 genes available at GenBank and NCBI database. In addition, the mutational analysis revealed in frame substitutions of Pro60Ala and Pro59Ala in bla NDM-4 and bla NDM-5, respectively. The bla NDM-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.

Molecular detection of carbanemase in gram negative bacteria Isolated from intensive care unit patients Molecular detection of carbanemase in gram negative bacteria Isolated from intensive care unit patients in wasit province, Iraqin wasit province, Iraq

“…whereas the result of bacteria Pseudomonas aeruginosa for this gene was 4( 33.3%) The results of our study are similar to those from previous studies in Diyala, Iraq [45][46][47] in Iran, It is similar to the result of this study because it contains this gene NDM (25%) ; (4%) ; (35%) respectively. The result of this gene among bacteria Escherichia coli was 1(10%),this result agreed with the results in Pakistan [48][49][50] who observed in these studies that its isolates carry this gene NDM (3.5%) ; (12.9% ) ; (13.5% ) respectively. While it does not agree with this study in Wasit [17] because its results do not contain this gene NDM.…”

Efficacy of Ceftazidime-Avibactam Versus Polymyxin B and Risk Factors Affecting Clinical Outcomes in Patients With Carbapenem-Resistant Klebsiella pneumoniae Infections a Retrospective Study

“…Molecular analysis of NDM-1gene in clinical isolates of Enterobacteriaceae form two tertiary hospital in Sakaka, Saudi Arabia found that bla NDM-1 and bla NDM harbored isolates were respectively accounted for 63.2 and 36.8% (Ejaz et al, 2020). In asian padiatric patients, carbapenem resistance were accounted for 24% of total E. coli and the NDM producing E. coli strains harbored more NDM-5 (50%) than NDM-1 (46%) and NDM-4 (3.5%)variants (Nosheen et al, 2020;Nosheen et al, 2021). Until now, multiple NMD-1 inhibitors have been designed and tested, but there is still no inhibitor on market.…”

A systematic review and meta-analysis of carbapenem resistance and its possible treatment options with focus on clinical Enterobacteriaceae: Thirty years of development in Pakistan

“…In K. pneumoniae studies reported variable carbapenem resistance levels i.e., 37.5% (75/200) [ 113 ], 32.5% (39/120) [ 114 ], the isolates were clinical and human-animal-environment origin, respectively. Similarly in E. coli variable levels of resistance was observed 3.7% (12/324) from blood and cerebrospinal cultures [ 115 ], 7.4% (113/1522) from paediatric patients [ 116 ], 28.3% (184/650) from diagnostic samples [ 117 ], and 49.5% (98/198) from tertiary care outpatients [ 118 ]. These studies reported bla NDM to be the most prevalent genetic determinant for carbapenem resistance.…”