Emergent Escherichia coli of the highly virulent B2-ST1193 clone producing KPC-2 carbapenemase in ready-to-eat vegetable

Karine Dantas; Gregory Melocco; Fernanda Esposito; Herisson Fontana; Brenda Cardoso; Nilton Lincopan

doi:10.1016/j.jgar.2024.11.020

Emergent Escherichia coli of the highly virulent B2-ST1193 clone producing KPC-2 carbapenemase in ready-to-eat vegetable

J Glob Antimicrob Resist. 2024 Dec 12:S2213-7165(24)00461-2. doi: 10.1016/j.jgar.2024.11.020. Online ahead of print.

Authors

Karine Dantas¹, Gregory Melocco², Fernanda Esposito², Herisson Fontana², Brenda Cardoso³, Nilton Lincopan⁴

Affiliations

¹ Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil. Electronic address: karine.dantas@usp.br.
² Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.
³ Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.
⁴ Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil. Electronic address: lincopan@usp.br.

PMID: 39674367
DOI: 10.1016/j.jgar.2024.11.020

Abstract

Objectives: Critical priority carbapenem-resistant pathogens constitute a worldwide public health problem. Escherichia coli ST1193 is an emerging high-risk clone that demonstrates prolonged gut persistence, and association with community-onset urinary and bloodstream infections. The purpose of this study is to report microbiological and genomic data on the emergence of KPC-2-producing E. coli ST1193 in ready-to-eat (RTE) vegetable.

Methods: RTE vegetables were purchased from markets in southeastern Brazil. Epiphytic and endophytic Gram-negative bacteria displaying resistance to broad-spectrum beta-lactams were identified by MALDI-TOF. WGS was conducted using the Illumina NextSeq platform. Antimicrobial susceptibility, conjugation, and acid tolerance assays were performed. Virulence behavior was evaluated using the Galleria mellonella infection model.

Results: Epiphytic KPC-2-producing E. coli belonging to pandemic ST1193 was identified in RTE arugula. Genomic analysis predicted clinically relevant genes conferring resistance to β-lactams, fluoroquinolones, hazardous heavy metals, pesticides, disinfectants, and chlorine sanitizer. The bla_KPC-2 gene was carried by a conjugative IncF plasmid. Resistance of E. coli KPC-2/ST1193 at pH 2.0 was confirmed, being associated with gadWX and ibaG pH tolerance genes, supporting survival to stomach acid prior to reaching small intestine, and potential for a dietary mode of host colonization. Virulent behavior was supported by wide virulome of the highly virulent phylogroup B2, whereas cgSNP-based phylogenomics revealed clonal relationship with healthcare-associated lineages circulating in the United States, China, Mexico, France and Brazil.

Conclusions: We report the occurrence of KPC-2-producing E. coli of the highly virulent B2-ST1193 clone in RTE vegetable, highlighting a possible route of dissemination of WHO priority pathogens to humans.

Keywords: Acid tolerance; Carbapenem resistance; Enterobacterales; Genomic surveillance; WHO critical priority pathogens.