Codon Usage Insights into the Functional Organization of Acinetobacter baumannii Virulence and Resistance Genes

Abstract

The increasing prevalence of Acinetobacter baumannii as a multidrug-resistant pathogen poses significant challenges in treatment and patient care. In response to this growing threat, we investigated the genomic, functional and evolutionary characteristics of antibiotic resistance genes and virulence genes in A. baumannii 1425. Our analysis revealed that β-lactamase genes such as blaADC-25 (36%) and blaOXA-98 (39%) have lower GC contents, whereas biofilm-associated gene clusters, such as pga (39% to 43%) gene cluster, exhibit higher GC contents. Codon usage bias across specific gene cluster was found to be consistent, with minimal effect of mutational pressure (6%-28%) and significant effect of translational selection (0.31 to 0.50). Overall, the codon usage signatures across specific genes cluster and across functionally related genes were found to be very similar. Leucine and alanine predominated in the genes while amino acids like tryptophan and cysteine were significantly avoided. Phylogenetic analysis showed that gene clustering correlates with codon usage patterns. Protein interaction network analysis supported the results of codon usage analysis with similar codon usage trends across interconnected genes. These findings underscore the importance of ongoing surveillance and research to develop more effective treatment strategies and mitigate the impact of A. baumannii infections.