Integrative phenotypic and functional genomic characterization of virulence and antimicrobial resistance in Salmonella enterica isolates from reptiles.

The popularity of reptiles as exotic pets has increased over the years. Reptiles can harbor zoonotic pathogens, including Salmonella, posing a significant public health risk. This study evaluated the diversity of hosts affected by non-typhoidal Salmonella infections in reptiles, as well as the antimicrobial resistance (AMR), multidrug resistance (MDR), and virulence factor (VF) genes in whole-genome, plasmid DNA, and RNA in Salmonella isolated from reptiles in Florida, United States. Data on Salmonella culture testing from 2018 to 2025, available at the Bronson Animal Disease Diagnostic Laboratory, were analyzed for host diversity in Salmonella infections. Functional genomic analysis was conducted using whole-genome sequences (WGS), plasmid DNA, and RNA obtained from selected Salmonella isolates, targeting AMR and VF genes. The Salmonella culture case positivity rate in reptiles was 16.41% during the study period. The highest positivity percentage was observed in the order Squamata (35%), which includes lizards, dragons, iguanas, and snakes, followed by the orders Testudines and Crocodilia (12.2%). The antibiotic susceptibility testing of 24 Salmonella enterica isolates revealed that 58.3% were MDR and specifically resistant to beta-lactams (62.5%), aminoglycosides (62.5%), and tetracyclines (8.3%). Genomic analysis confirmed phenotypic AMR and revealed the presence of 55 AMR genes, with the majority showing resistance to fluoroquinolones (18.2%), carbapenems and quinolones (16.4%), tetracyclines and rifamycins (14.5%), amphenicols (12.7%), and other classes. The presence of the tetA gene in both the genomic and plasmid DNA of a tetracycline-resistant isolate highlighted reptiles' role as stable zoonotic reservoirs for highly mobile genetic elements that can facilitate rapid horizontal gene transfer among pathogens. Transcriptomic analysis of isolates with MDR revealed differential expression patterns largely consistent with WGS analysis and identified additional AMR-related genes associated with MDR, efflux pumps, and membrane transport systems. A total of 239 VF genes were identified in isolates. Despite the health status of reptiles, the largest number of genes was associated with the Type III secretory system, invasion, motility, iron uptake, siderophore, fimbrial adherence, endotoxin, and lipopolysaccharides. Findings from this study underscore the importance of ongoing surveillance and improved hygiene practices when handling reptiles to reduce the risk of reptile-associated salmonellosis in humans.