title: Computational gene network study on antibiotic resistance genes of Acinetobacter baumannii.
abstract: Multi Drug Resistance (MDR) in Acinetobacter baumannii is one of the major threats for emerging nosocomial infections in hospital environment. Multidrug-resistance in A. baumannii may be due to the implementation of multi-combination resistance mechanisms such as β-lactamase synthesis, Penicillin-Binding Proteins (PBPs) changes, alteration in porin proteins and in efflux pumps against various existing classes of antibiotics. Multiple antibiotic resistance genes are involved in MDR. These resistance genes are transferred through plasmids, which are responsible for the dissemination of antibiotic resistance among Acinetobacter spp. In addition, these resistance genes may also have a tendency to interact with each other or with their gene products. Therefore, it becomes necessary to understand the impact of these interactions in antibiotic resistance mechanism. Hence, our study focuses on protein and gene network analysis on various resistance genes, to elucidate the role of the interacting proteins and to study their functional contribution towards antibiotic resistance. From the search tool for the retrieval of interacting gene/protein (STRING), a total of 168 functional partners for 15 resistance genes were extracted based on the confidence scoring system. The network study was then followed up with functional clustering of associated partners using molecular complex detection (MCODE). Later, we selected eight efficient clusters based on score. Interestingly, the associated protein we identified from the network possessed greater functional similarity with known resistance genes. This network-based approach on resistance genes of A. baumannii could help in identifying new genes/proteins and provide clues on their association in antibiotic resistance.
authors.affiliation: Bioinformatics Division, School of Biosciences & Technology (SBST), VIT University, Vellore 632014, India.
authors.forename: P
authors.initials: P
authors.lastname: Anitha
authors.affiliation: Bioinformatics Division, School of Biosciences & Technology (SBST), VIT University, Vellore 632014, India.
authors.forename: Anand
authors.initials: A
authors.lastname: Anbarasu
authors.affiliation: Bioinformatics Division, School of Biosciences & Technology (SBST), VIT University, Vellore 632014, India. Electronic address: sudhaanand@vit.ac.in.
authors.forename: Sudha
authors.initials: S
authors.lastname: Ramaiah
mesh_terms: D040981:Acinetobacter baumannii / Q000187:drug effects / Q000235:genetics; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001426:Bacterial Proteins / Q000235:genetics; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics*; D060066:Protein Interaction Maps / Q000235:genetics*
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins
keywords: A. baumannii; Clustering analysis; Gene expression data; Protein network; Resistance genes