Data Sheet 1_Phenotypic and genotypic characterization of antibiotic-resistant bacteria from Swiss ready-to-eat meat products.zip

Antimicrobial resistance is a global health concern, which is partly driven by rising meat consumption, which has led to the intensive farming of livestock that relies on antibiotics. ready-to-eat animal products can carry antibiotic-resistant bacteria, posing risks to humans since they are often consumed without further cooking. While countries such as Switzerland limit antibiotic use in agriculture, contamination of meat with antibiotic-resistant bacteria can still occur during meat processing, and non-antibiotic agents such as heavy metals may contribute to the co-selection of resistance. This study aimed to characterize antibiotic-resistant bacteria in ready-to-eat meat products from various Swiss butcheries. Presumptive resistant bacteria were isolated using selective plating and analyzed phenotypically and genotypically. A total of 53 bacteria-antibiotic resistance combinations were identified, including Enterobacterales resistant to third-generation cephalosporins, vancomycin-resistant Enterococci, and one strain of methicillin-resistant Staphylococcus aureus. Of the 804 products sampled, 177 antibiotic-resistant bacteria were isolated, 148 of which showed multidrug resistance. Notably, these strains remained susceptible to last-resort antibiotics such as carbapenems and colistin. Whole-genome sequencing of 31 selected isolates revealed 164 antibiotic resistance genes spanning 25 classes, confirming resistance to beta-lactams, cephalosporins, and tetracyclines. We also detected genes conferring resistance to metals, suggesting co-selection pressures. Long-read sequencing revealed that the majority of the antibiotic resistance genes were chromosomal, while others were plasmid-encoded, indicating the potential for horizontal gene transfer. This study demonstrates that ready-to-eat meat products are reservoirs of antibiotic and metal resistance genes, as well as antibiotic-resistant bacteria, even at low levels. From a One Health perspective, our results highlight the importance of extending AMR surveillance across the food chain and underscore the need to include non-traditional bacterial indicators.

抗菌素耐药性（Antimicrobial Resistance, AMR）是一项全球性公共卫生问题，其部分诱因源于肉类消费的持续增长，进而催生了依赖抗生素的集约化畜禽养殖模式。即食动物源产品可能携带抗生素耐药菌（antibiotic-resistant bacteria, ARB），此类产品通常无需进一步烹煮即可食用，因此会对人类健康构成威胁。尽管瑞士等国家已对农业抗生素使用加以限制，但在肉类加工过程中仍可能出现抗生素耐药菌污染肉类的情况；此外，重金属等非抗生素类物质也可能推动耐药性的共选择。
本研究旨在对瑞士多家肉铺售卖的即食肉类产品中的抗生素耐药菌进行特征分析。研究人员通过选择性平板培养法分离得到疑似耐药菌，并从表型与基因型两个维度开展分析。本次研究共鉴定出53组细菌-抗生素耐药组合，包括对第三代头孢菌素耐药的肠杆菌目（Enterobacterales）、万古霉素耐药肠球菌（vancomycin-resistant Enterococci, VRE），以及1株耐甲氧西林金黄色葡萄球菌（methicillin-resistant Staphylococcus aureus, MRSA）。在抽检的804份产品中，共计分离得到177株抗生素耐药菌，其中148株呈现多重耐药表型。值得关注的是，上述菌株对碳青霉烯类、粘菌素等最后一线抗生素仍保持敏感性。
对31株筛选分离株开展全基因组测序后，共检出164个抗生素耐药基因，涵盖25个耐药类别，证实菌株对β-内酰胺类、头孢菌素类及四环素类药物存在耐药性。研究同时检出金属耐药基因，提示存在耐药性共选择压力。长读长测序结果显示，大部分抗生素耐药基因定位于染色体上，其余则由质粒编码，这表明耐药基因存在水平转移的潜在风险。
本研究证实，即便处于低污染水平，即食肉类产品仍可作为抗生素耐药基因、金属耐药基因及抗生素耐药菌的储存库。从同一健康（One Health）视角出发，本研究结果凸显了在全食品链拓展抗菌素耐药性监测工作的必要性，同时强调需纳入非传统细菌指标以完善监测体系。