Comparative genomics of Acinetobacter baumannii clinical strains from Brazil reveals polyclonal dissemination and selective exchange of mobile genetic elements associated with resistance genes. A.baumannii-Recife-2020

Acinetobacter baumannii is an opportunistic bacterial pathogen infecting immunocompromised patients in hospital settings that has gained attention worldwide due to its increased resistance to antibiotics. Here, we report a comparative whole-genome sequencing and analysis coupled with an assessment of antibiotic resistance of 46 Acinetobacter strains (45 A. baumannii plus one A. nosocomialis) originated from five different hospitals from the city of Recife, Brazil, between 2010 and 2014. An average of 3,809 genes were identified per genome, although only 2,006 genes were single copy orthologs or core genes conserved across all sequenced strains, with an average of 42 new genes found per strain. We evaluated genetic distance through a phylogenetic analysis and MLST as well as the presence of antibiotic resistance genes, virulence markers and mobile genetic elements. The phylogenetic analysis recovered distinct monophyletic A. baumannii groups corresponding to five known (ST1P, ST15P, ST25P, ST79P and ST113P) and one novel ST (ST881P, related to ST1P). A large number of ST specific genes were found, with the ST79P strains having the largest number of genes in common that were missing from the other STs. Multiple genes associated with resistance to beta-lactamases, aminoglycosides and other antibiotics were also found. Some of those were clearly mapped to defined mobile genetic elements and an analysis of those revealed known elements as well as a novel Tn7-Tn3 transposon with a clear ST specific distribution. An association of selected resistance/virulence markers to specific STs was indeed clearly seen, as well as the more recent spread of the gene encoding the OXA-253 β-lactamase. Virulence genes associated with the synthesis of the capsular antigens were noticeably more variable in the ST133P and ST79P strains. Indeed, several resistance and virulence genes were common to the ST79P and ST133P strains only, despite a greater genetic distance between them, suggesting common means of genetic exchange. Our comparative analysis reveals the spread of multiple STs and the genomic plasticity of A. baumannii from different hospitals in a single metropolitan area. It also highlights a differential ability for the spread of resistance markers and other mobile elements between distinct STs, impacting on the monitoring and treatment of A. baumannii in the ongoing and future outbreaks.