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Updated: Jul 24, 2025
Rapid and Specific Detection of Acinetobacter baumannii Infections Using a Recombinase Polymerase Amplification/Cas12a-based System
Published on: April 25, 2025
Outbreak of high-risk XDR CRAB of international clone 2 (IC2) in Rio Janeiro, Brazil
Sérgio M Morgado1, Érica L Fonseca1, Fernanda S Freitas1
1Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.
Objectives:
Among the high-risk clones of Acinetobacter baumannii, called international clones (ICs), IC2 represents the main lineage causing outbreaks worldwide. Despite the successful global spread of IC2, the occurrence of IC2 is rarely reported in Latin America. Here, we aimed to evaluate the susceptibility and genetic relatedness of isolates from a nosocomial outbreak in Rio de Janeiro/Brazil (2022) and perform genomic epidemiology analyses of the available genomes of A. baumannii.
Methods:
Sixteen strains of A. baumannii were subjected to antimicrobial susceptibility tests and genome sequencing. These genomes were compared phylogenetically with other IC2 genomes from the NCBI database, and virulence and antibiotic resistance genes were searched.
Results:
The 16 strains represented carbapenem-resistant A. baumannii (CRAB) with an extensively drug-resistant profile. In silico analysis established the relationship between the Brazilian CRAB genomes and IC2/ST2 genomes in the world. The Brazilian strains belonged to three sub-lineages, associated with genomes from countries in Europe, North America, and Asia. These sub-lineages presented three distinct capsules, KL7, KL9, and KL56. The Brazilian strains were characterised by the co-presence of blaOXA-23 and blaOXA-66, in addition to the genes APH(6), APH(3"), ANT(3"), AAC(6'), armA, and the efflux pumps adeABC and adeIJK. A large set of virulence genes was also identified: adeFGH/efflux pump; the siderophores barAB, basABCDFGHIJ, and bauBCDEF; lpxABCDLM/capsule; tssABCDEFGIKLM/T6SS; and pgaABCD/biofilm.
Conclusion:
Widespread extensively drug-resistant CRAB IC2/ST2 is currently causing outbreaks in clinical settings in southeastern Brazil. This is due to at least three sub-lineages characterised by an enormous apparatus of virulence and resistance to antibiotics, both intrinsic and mobile.
Insights
Extensively drug-resistant Acinetobacter baumannii International Clone 2 (IC2/ST2) is causing outbreaks in Brazil. Genomic analysis revealed three sub-lineages with significant antibiotic resistance and virulence genes, highlighting a global health threat.
Area of Science:
- Microbiology
- Genomics
- Epidemiology
Background:
- Acinetobacter baumannii International Clone 2 (IC2) is a high-risk lineage causing global outbreaks.
- The prevalence of IC2 in Latin America, particularly Brazil, is underreported.
- Understanding the genetic makeup and spread of A. baumannii is crucial for infection control.
Purpose of the Study:
- To investigate the antimicrobial susceptibility and genetic relatedness of A. baumannii isolates from a nosocomial outbreak in Rio de Janeiro, Brazil.
- To perform genomic epidemiology analyses of Brazilian A. baumannii strains and compare them with global IC2 genomes.
- To identify key resistance and virulence factors contributing to the spread of carbapenem-resistant A. baumannii (CRAB).
Main Methods:
- Antimicrobial susceptibility testing of 16 A. baumannii strains.
- Whole-genome sequencing of the isolates.
- Phylogenetic analysis and comparative genomics against NCBI database.
- In silico identification of antibiotic resistance and virulence genes.
Main Results:
- All 16 strains were carbapenem-resistant A. baumannii (CRAB) with extensively drug-resistant profiles.
- Brazilian CRAB strains belonged to three sub-lineages within IC2/ST2, linked to global strains from Europe, North America, and Asia.
- These sub-lineages harbored specific capsules (KL7, KL9, KL56) and a combination of resistance genes (blaOXA-23, blaOXA-66, armA) and virulence factors (efflux pumps, siderophores, T6SS, biofilm genes).
Conclusions:
- Extensively drug-resistant CRAB IC2/ST2 strains are causing clinical outbreaks in southeastern Brazil.
- At least three distinct sub-lineages contribute to these outbreaks, characterized by extensive antibiotic resistance and virulence.
- The findings underscore the global threat posed by multidrug-resistant A. baumannii and the need for enhanced surveillance and control measures.
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