Comparative genomic analysis reveals the evolution and environmental adaptation of Acinetobacter johnsonii

• Comparative genomic analysis was conducted to reveal the evolution of A. johnsonii . • A. johnsonii has an open pan-genome and could well adapt to different environments. • Seletive pressure drives the accumulation of relevant ARGs. • The characteristic of genome is a result of adaptation to the environment. Genome plasticity is a key determinant that Acinetobacter johnsonii could widely distribute in natural and clinical environments. However, little attention has been paid to figure out the changes in the genome during A. johnsonii ’s evolution. Here, a comparative genomic analysis of A. johnsonii isolated from clinical and environmental sources was conducted. In this study, we found A. johnsonii has an open pan-genome and has great adaptability to different environments. Based on the results of the phylogenetic tree, ANI value and the distribution of accessory genes, we found that strains from the same habitat had a high degree of similarity. Though genes associated with the fundamental process were mostly conserved in evolution, clinical-derived isolates accumulate more genes associated with translational modification, β-lactamase and defense mechanisms, whereas environmental-derived isolates enriched more genes related to substances degradation. In addition, clinical-derived strains harbored some “strong” virulence islands and resistance islands. This study highlights the evolutionary relationship of A. johnsonii isolates from clinical and environmental sources.