An integrated gene network analysis to decode the multi-drug resistance mechanism in Klebsiella pneumoniae

Antimicrobial resistance (AMR) among microorganisms has become one of the worldwide concerns of this century and continues to challenge us. To properly understand this problem, it is essential to know the genes that cause AMR and their resistance mechanisms. Our present study focused on Klebsiella pneumoniae, which possesses AMR genes conferring resistance against multiple antibiotics. A gene interaction network of 42 functional partners was constructed and analyzed to broaden our understanding. Three closely related clusters (C1–C3) having an association with multi-drug resistance mechanisms were identified by clustering analysis. The enrichment analysis illustrated 30 genes in biological processes, 24 genes in molecular function, and 25 genes in cellular components having a significant role. The analysis of the gene interaction network revealed genes birA2, folP, pabC, folA, gyrB, glmM, gyrA, thyA_2 had maximum no. of interactions with their functional partners viz. 26, 25, 25, 24, 23, 23, 23, 23 respectively and can be considered as hub genes. Analyzing the enriched pathways and Gene Ontologies provides insight into AMR's molecular basis. In addition, the proposed study could aid the researchers in developing new treatment options to combat multi-drug resistant K. pneumoniae. •AMR is a leading cause of death around the world, with the highest burdens in low-resource settings.•Klebsiella pneumoniae is the most common pathogenic bacteria in clinical settings owing to its resistant mechanism pattern.•We have used gene interaction network to analyze the AMR genes in the bacteria to find potential hub genes in the network.•The gene network analysis revealed birA2, folP, pabC, folA, gyrB,etc. as hub genes making them a potential drug target.•The hub genes were also associated with various enriched pathways, which gave us a broader understanding on the topic..