This dataset supports a study investigating the prevalence and characteristics of antibiotic-resistant bacteria in ready-to-eat meat products from Switzerland. With antimicrobial resistance remaining a major global health concern—particularly in the context of intensive livestock production—this study examines ready-to-eat meat products as potential reservoirs for antibiotic resistant bacteria. A total of 804 ready-to-eat meat products were collected from butcheries across Switzerland. Selective culture methods were used to isolate presumptive antibiotic-resistant bacteria, specifically targeting vancomycin-resistant Enterococci (VRE), extended-spectrum beta-lactamase-producing Enterobacterales (ESBL), carbapenem-resistant Enterobacterales (CRE), and methicillin-resistant Staphylococcus aureus (MRSA). The "phenotypic resistance dataset" contains antibiotic susceptibility testing results for the isolates, performed using broth microdilution. It reports minimum inhibitory concentration (MIC) values for up to 31 antibiotics (Enterobacterales) or 24 antibiotics (Enterococci). Colistin resistance was assessed separately using the drop test. The dataset also includes multidrug resistance classifications (e.g., MDR index). The "resistance gene and mobile genetic element annotations" include resistance genes identified via AMRFinder Plus, classified by antibiotic class (e.g., beta-lactams, cephalosporins, carbapenems, metals). Mobile genetic elements were identified using MobileElementFinder, and plasmid typing was performed using MOB-suite. The "ARG localization dataset" categorizes resistance genes based on their genomic location—plasmid, chromosome, or phage—using SourceFinder. Key findings from the dataset include the recovery of 177 antibiotic-resistant bacterial isolates, of which 148 were multidrug-resistant (resistant to ≥3 antibiotic classes). These included third-generation cephalosporin-resistant Enterobacterales, vancomycin-resistant Enterococci, and one methicillin-resistant Staphylococcus aureus (MRSA). All isolates remained susceptible to critical last-resort antibiotics such as carbapenems and colistin. Whole genome sequencing of 31 representative isolates revealed 164 unique resistance genes across 25 resistance classes, including those conferring resistance to beta-lactams, cephalosporins, tetracyclines, and macrolides. Co-selection factors such as metal resistance genes were also identified. Most ARGs were chromosomally encoded, though several were plasmid-borne, indicating potential for horizontal gene transfer. The dataset includes isolate metadata, phenotypic resistance profiles, and annotated resistance gene information. Sequencing data (both short- and long-read) are available via the National Center for Biotechnology Information (NCBI).
