Draft genome of the multidrug-resistant Citrobacter freundii strain CAPA023 isolated from Arapaima gigas in Peru: Is it a reservoir of resistance and virulence genes?

Abstract

Objectives: The purpose of this study was to analyze the genome of the multidrug-resistant Citrobacter freundii strain CAPA023, which was obtained from diseased Arapaima gigas fry. The study focused on determining mobile genetic elements and genetic factors that contribute to antibiotic resistance and pathogenicity. Methods: Genomic DNA was sequenced using Illumina NovaSeq (2 × 150 bp) and assembled de novo using Shovill v1.1.0. Resistance genes, virulence factors, plasmids, and mobile elements were identified using ResFinder, CARD, PlasmidFinder, MobileFinder, PathogenFinder, and VFDB. Results: The 5,059,550 bp draft genome (60 contigs, 51.5% GC) revealed resistance genes for various antibiotic classes, efflux pumps, IncFIB(K) and Col440I plasmids, insertion sequences, and multiple virulence genes. Conclusion: Considering that this bacterium was found in diseased fish, it is possible that C. freundii plays an important role in the spread of virulence factors and antibiotic resistance in aquaculture environments. This highlights the importance of genomic surveillance in Amazonian aquaculture. © 2025 Elsevier B.V., All rights reserved.