Comparative genomics of multidrug resistant Acinetobacter baumannii clinical isolates reveals genome plasticity and polyclonal dissemination in Recife-Brazil

Acinetobacter baumannii is an opportunistic bacterial pathogen infecting immunocompromised patients in hospital settings, particularly in intensive care units (ICUs). Acinetobacter species have gained attention worldwide due its increasing resistance to antibiotics, and adaptation to hospital environments. Here, we performed whole-genome sequencing of 46 isolates originated from five different hospitals located in the tropical city of Recife, Brazil. We applied a bioinformatic workflow for the assembly, gene prediction, annotation, and identification of genomic elements which can confer differences in antibiotic resistance, virulence and pathogenicity profiles. Moreover, we carried out Multilocus Sequence Typing (MLST) and an alignment-free approach for phylogenetic analysis of the sequenced isolates including published reference genomes. The phylogenetic analysis recovered distinct monophyletic groups, corresponding to their MLST sequence types. Our comparative analysis reveals the spread of multiple STs and the genomic plasticity of A. baumannii of different hospitals in Recife, setting a starting point for monitoring and rational treatment of A. baumannii in the ongoing and future outbreaks.