Transcriptomic Responses and Antimicrobial Resistance Gene Profiles of Outbreak-Associated Aeromonas salmonicida subsp. salmonicida Isolates from Salmonid Fish

Aeromonas salmonicida subsp. salmonicida (A.s.s.s) is a major bacterial pathogen associated with furunculosis and disease outbreaks in salmonid aquaculture. This study investigated eight outbreak-associated A.s.s.s from clinically diseased salmonid fish in Bavaria, Germany, by integrating transcriptomic profiling with antimicrobial resistance gene screening. For transcriptomic analysis, isolates were cultured under four conditions: Tryptic Soy Broth, Mueller–Hinton Broth, and both media supplemented with 1% fetal bovine serum. Oxford Nanopore sequencing was performed on cDNA and DNA samples to assess culture-dependent transcriptional responses and resistance-associated genetic features. Transcript-level analysis focused on virulence-associated genes involved in motility, secretion systems, and toxin-related functions, including fliP, aerA, rtxA, exeC, flpH, exeN, tssB, exeL, exeG, flpI, exeB, and exeH. Culture medium composition clearly influenced transcriptional activity, with TSB-based conditions generally showing higher expression of several virulence-associated loci than Mueller–Hinton-based conditions. In particular, TSB supplemented with 1% fetal bovine serum showed a more stable expression pattern, with fewer broadly down regulated genes, suggesting that nutrient availability and host-like supplementation may affect bacterial physiological activity and virulence-related transcription. Antimicrobial resistance gene screening further showed that the same isolates carried multiple resistance-associated genes. In total, 16 genes related to beta-lactam, aminoglycoside, phenicol, sulfonamide, trimethoprim, tetracycline, and colistin resistance were detected, with blaOXA-956, cphA-5, and mcr-3 present in all isolates. Together, these results indicate that outbreak-associated A.s.s.s isolates combine environment-responsive virulence-associated transcriptional patterns with a broad antimicrobial resistance gene repertoire, highlighting the importance of evaluating both functional gene expression and resistance potential in aquaculture pathogens.