Aeromonas caviae, an emerging aquaculture pathogen, causes significant economic losses. This study characterized the genomic profile of A. caviae strain CAPA007, isolated from diseased Arapaima gigas exhibiting hemorrhagic disease signs in a recirculating aquaculture system in San Martín, Peru. The study focused on antimicrobial resistance (AMR) genes, virulence factors, and mobile genetic elements. Phenotypic testing showed resistance to oxytetracycline, sulfa trimethoprim, enrofloxacin, and oxolinic acid. The strain exhibited beta-hemolytic activity on blood agar, consistent with its virulence potential.
Whole genome sequencing used Illumina NovaSeq 6000. The draft genome was assembled with Unicycler v0.5.0 and annotated with PGAP v6.0. The assembly (GenBank: GCA_026309435.1) yielded 45 contigs totaling 4,522,767 bp with 61.7% G+C content. Annotation identified 4,237 genes, including 4,089 protein-coding sequences. PubMLST confirmed the strain as A. caviae ST220372. AMR gene analysis using CARD v3.2.7 and ResFinder v4.5 revealed β-lactam resistance genes (blaOXA-10, blaMOX-6), aminoglycoside resistance genes (aph(3’)-Ia, aadA1, aac(6’)-Ib3), tetracycline resistance gene (tet(A)), and quinolone resistance gene (qnrVC1). Additional genes conferred resistance to sulfonamides (sul1), trimethoprim (dfrA14, dfrA12), and quaternary ammonium compounds (qacE). Virulence Factors Database (VFDB) analysis identified genes related to adherence (tap type IV pili, msh pilus cluster), secretion systems (T2SS, T6SS), and notably, several hemolysins (hemolysin III, hlyA, thermostable hemolysin). These hemolysins likely contribute to the observed beta-hemolytic phenotype and may be associated with the hemorrhagic disease signs in the infected A. gigas. Additional virulence factors included genes for iron acquisition and flagellar systems, which may enhance the pathogen’s ability to colonize and cause tissue damage. MobileElementFinder v1.0.3 and mobileOG-db (beatrix v1.6) revealed various transposases, integrases, and conjugative transfer proteins. Notable elements include IS6100, ISPpu12, plasmid replication genes (repA, repB), conjugation genes (traA, traB, traC, traD), and recombinases (intI, xerC/xerD). AMR and virulence genes were found near these mobile elements, suggesting potential for horizontal transfer.
This comprehensive analysis provides insights into the genetic basis of antimicrobial resistance and virulence in A. caviae from aquaculture. The correlation between phenotypic characteristics (antibiotic resistance and beta-hemolysis) and specific genes underscores the clinical relevance of these findings. The co-occurrence of multiple resistance genes, virulence factors - particularly hemolysins, and mobile genetic elements highlights the pathogenic potential of this strain in aquaculture settings, emphasizing the need for prudent antimicrobial use and enhanced biosecurity measures.