Outbreak of High-risk XDR CRAB of International Clone 2 (IC2) in Rio Janeiro, Brazil

Abstract

AbstractThe high-risk clones ofAcinetobacter baumannii, called international clones (ICs), span several ICs, IC1 to IC7 being the most reported. Among them, IC2 represents the main lineage causing outbreaks worldwide. IC2 presents a great diversity of sub-lineages with different sequence types (ST). Despite successful global spread, the occurrence of IC2 is rarely reported in Latin America, including Brazil. Here, through genomic analysis, we investigated 16 IC2/ST2 strains obtained from a clinical setting in Brazil (2022). These strains represented carbapenem-resistantA. baumannii(CRAB) with an extensively drug-resistant (XDR) profile, with most showing some resistance to tigecycline. Overall, these strains showed susceptibility only to polymyxins, thus leading to restricted therapeutic choices. Based onin silicoanalysis, the relationship between Brazilian CRAB genomes and IC2/ST2 genomes circulating in the world, particularly in South America, was established. The Brazilian IC2 strains belonged to three discrete and distinct sub-lineages, being more associated with IC2/ST2 genomes from countries in Europe, North America and Asia, suggesting their epidemiological link. These Brazilian strains were characterized by the co-presence ofblaOXA-23 andblaOXA-66, in addition to the genes APH(6), APH(3”), ANT(3”), AAC(6’),armA, and the efflux pumpsadeABC andadeIJK, associated with the XDR/CRAB phenotype. Furthermore, the three sub-lineages presented three distinct capsules, KL7, KL9 and KL56, the latter not yet associated with IC2 genomes. A large set of virulence genes was also identified in the genomes:adeFGH/efflux pump, the siderophoresbarAB,basABCDFGHIJ andbauBCDEF,lpxABCDLM/capsule,tssABCDEFGIKLM/T6SS,pgaABCD/biofilm.