Phylogenomic analysis of aquatic and clinical OXA-23-positive Acinetobacter baumannii belonging to the international clone 5 (ST79) from Southeast Brazil

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Martins-Goncalves, Thais ; Sano, Elder ; Melocco, Gregory ; Dantas, Karine ; Esposito, Fernanda ; Becerra, Johana ; Fontana, Herrison ; Queiroga, Gustavo ; Pariona, Jesus G. M. ; Cayo, Rodrigo ; Gales, Ana C. ; Sato, Maria I. Z. ; Lincopan, Nilton

• Document type: Journal article
• Source: ONE HEALTH; v. 21, p. 7-pg., 2025-12-01.

Abstract

Categorized as a critical priority pathogen by the World Health Organization (WHO), carbapenem-resistant Acinetobacter baumannii (CRAB) is a leading cause of healthcare-associated infections (HAIs) worldwide. Although the environmental spread of healthcare-acquired A. baumannii strains through hospital wastewater and urban sewage has been suggested, evidence from genomic studies is still lacking. In this study, as part of the Grand Challenges Explorations: New Approaches to Characterize the Global Burden of Antimicrobial Resistance Program, we present genomic data supporting the expansion of international clone IC5/ST79 (Pasteur) to an anthropogenically impacted urban river in Brazil. The environmental OXA-23-producing A. baumannii Ab120 strain conserved a broad resistome to clinically important antimicrobials and carried efflux pump genes associated with tolerance to disinfectants. On the other hand, a wide virulome associated with colonization, evasion of the immune system, as well as survival and persistence in distinct environments was predicted. Noteworthy, a comparative phylogenomic analysis of the environmental Ab120 strain provided evidence that indicates its nosocomial origin and genomic relationship with human-derived OXA-23-positive clinical strains isolated between 2010 and 2017 in Brazil. Our genomic findings suggest adaptation of OXA-23-producing CRAB ST79 beyond hospital settings into non-clinical environments, which is a critical issue deserving active surveillance, particularly in Pan-American countries with a currently endemic clinical status. (AU)

• FAPESP's process: 19/15578-4 - Virulome and pathogenicity of carbapenem- and polymyxin-resistant priority pathogens
• Grantee: Fernanda Ribeiro dos Santos Esposito
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 20/08224-9 - OneBR (One Health Brazilian Resistance): integrated genomic database for surveillance, diagnosis, management and treatment of antimicrobial resistance in the human-animal-environment interface, in Brazil
• Grantee: Nilton Erbet Lincopan Huenuman
• Support Opportunities: Regular Research Grants
• FAPESP's process: 24/20180-8 - WildBR: platform for epidemiological and genomic surveillance of bacterial and fungal resistance in Brazilian wildlife
• Grantee: Thais Martins Gonçalves
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 23/18292-0 - BiocinBR: Bacteriocin research platform to combat pathogens resistant to critical priority antimicrobials in Brazil
• Grantee: Zuleyma Johana Becerra Tellez
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 24/07885-2 - EccBR: Genomic surveillance of Enterobacter cloacae complex in One Health for the control, diagnostic and management of antimicrobial resistance in Brazil
• Grantee: Karine Sousa Dantas
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 21/10599-3 - The Antimicrobial Resistance Institute of São Paulo (The Aries Project)
• Grantee: Arnaldo Lopes Colombo
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC