Aeromonas salmonicida isolated from pigs: Genomic and phenotypic antimicrobial resistance characterization

The emergence of Aeromonas salmonicida in swine respiratory disease represents a significant animal health concern with potential public health implications due to the risk of zoonotic antimicrobial resistance transmission.

This study aimed to characterize the phenotypic and genotypic antimicrobial resistance profiles of A. salmonicida isolated from pigs with respiratory disease in Jilin Province, China, to assess its potential threat to animal and public health.

Between January 2023 and December 2023, 786 pigs with mild respiratory disease were randomly sampled from 19 conveniently selected farms in Jilin Province, China. The presence of one or more mild clinical signs, such as nasal discharge, coughing, labored breathing, lethargy, or anorexia, defines this condition. From these pigs, 13 A. salmonicida strains were isolated from the upper respiratory tracts. The isolates' taxonomic identification was systematically determined through a polyphasic approach. This included 16S rRNA gene sequencing, phylogenetic analyses based on the gyrB and rpoB housekeeping genes, and Average Nucleotide Identity analysis. Antimicrobial susceptibility testing against 21 agents was performed using the CLSI-standardized agar dilution minimum inhibitory concentration assay, with Escherichia coli ATCC 25922 as the quality control. Second-generation sequencing analysis was conducted, followed by a comprehensive screening of antibiotic resistance genes using the Comprehensive Antibiotic Resistance Database database (Resistance Gene Identifier module).

Antimicrobial susceptibility was interpreted according to the Clinical and Laboratory Standards Institute guidelines. All 13 isolates demonstrated complete resistance (13/13, 100.00%) to β-lactams (meropenem, aztreonam, cefazolin, and ampicillin) and sulfonamides (sulfamethoxazole and trimethoprim). In contrast, all isolates were susceptible to fosfomycin and rifampicin (13/13, 100%). Variable susceptibility to florfenicol was observed (9/13, 69.23%). Genomic analysis revealed the spread of resistance genes (mcr-3.16, cphA5, bla _OXA-956) in A. salmonicida. The key mechanisms include enzymatic inactivation and efflux pumps. Biocide resistance genes (qacEdelta1) indicate disinfectant co-selection. No explicitly novel genes were reported; however, emerging variants (e.g., bla _OXA-956) were identified.

This study provides the first comprehensive antimicrobial resistance profile of porcine-associated A. salmonicida. Our results demonstrated that these bacteria were resistant to almost all commonly used antibiotics. The genes conferring this extensive resistance were located on mobile genetic elements, meaning they can spread to other bacteria, which poses a significant threat to both animal and public health. To address this, we recommend the following: (1) implementing antibiotic susceptibility testing in veterinary practice to guide treatment choices and avoid ineffective drugs; (2) prioritizing prevention through improved farm hygiene and biosecurity to reduce infection rates; and (3) establishing coordinated surveillance across human, animal, and environmental sectors to monitor the spread of these resistant bacteria.