Data_Sheet_1_Deciphering Resistome and Virulome Diversity in a Porcine Slaughterhouse and Pork Products Through Its Production Chain.zip

We aimed to better understand resistome and virulome patterns on animal and process-area surfaces through a pig slaughterhouse to track possible contamination within the food production chain. Culture-dependent methods revealed high levels of microbial contamination, corresponding to mesophilic and pathogenic bacteria on both the animal and process-area surfaces mainly in the anesthesia (AA and AS) zone followed by “scorching and whip” (FA and FS) zone and also in the end products. To evaluate the potential risk of antibiotic resistance and virulence determinants, shotgun metagenomic DNA-sequencing of isolates from selected areas/products uncovered a high diversity and richness of antibiotic resistance genes (ARGs): 55–62 genes in the anesthesia area (AA and AS) and 35–40 in “animal-arrival zone” (MA and MS). The “scorching and whip” (FA and FS) area, however, exhibited lowered abundance of ARGs (1–6), indicating that the scalding and depilating process (an intermediate zone between “anesthesia” and “scorching and whip”) significantly decreased bacterial load by 1–3 log10 but also diminished the resistome. The high prevalence of antibiotic-inactivating enzyme genes in the “animal-arrival zone” (60–65%) and “anesthesia” area (56%) were mainly represented by those for aminoglycoside (46–51%) and lincosamide (14–19%) resistance, which did not reflect selective pressures by antibiotics most commonly used in pig therapy—tetracyclines and beta-lactams. Contrary to ARGs, greater number of virulence resistance genes were detected after evisceration in some products such as kidney, which reflected the poor hygienic practices. More than 19 general virulence features—mainly adherence, secretion system, chemotaxis and motility, invasion and motility were detected in some products. However, immune evasion determinants were detected in almost all samples analyzed from the beginning of the process, with highest amounts found from the anesthesia area. We conclude that there are two main sources of contamination in a pig slaughterhouse: the microorganisms carried on the animals’ hide, and those from the evisceration step. As such, focussing control measures, e.g., enhanced disinfection procedures, on these contamination-source areas may reduce risks to food safety and consumer health, since the antibiotic and virulence determinants may spread to end products and the environment; further, ARG and virulence traits can exacerbate pathogen treatments.

本研究旨在针对生猪屠宰场开展研究，解析动物体表及加工区域表面的耐药组（resistome）与毒力组（virulome）特征，追踪食品生产链中可能存在的污染风险。依赖培养的检测方法（culture-dependent methods）显示，动物体表与加工区域表面均存在高微生物污染水平，污染菌以嗜温菌（mesophilic）及病原菌（pathogenic bacteria）为主，主要集中于麻醉区（AA和AS），其次为“烫毛脱毛（scorching and whip）”区（FA和FS），终产品（end products）中亦检出此类污染。为评估抗生素抗性及毒力决定因子的潜在风险，本研究对选定区域/样本的分离株（isolates）进行鸟枪宏基因组DNA测序（shotgun metagenomic DNA-sequencing），结果显示抗生素抗性基因（antibiotic resistance genes, ARGs）的多样性与丰度均较高：麻醉区（AA和AS）检出55~62个ARGs，“动物抵达区”（MA和MS）检出35~40个ARGs。但“烫毛脱毛（scorching and whip）”区（FA和FS）的ARGs丰度显著降低（仅1~6个），提示烫毛脱毛工序（scalding and depilating process，即位于“麻醉区”与“烫毛脱毛区”之间的中间工序）可使细菌载量降低1~3 log10，同时也减少了耐药组的丰度。“动物抵达区”（60%~65%）与麻醉区（56%）中，抗生素灭活酶基因（antibiotic-inactivating enzyme genes）的高检出率主要由氨基糖苷类（aminoglycoside，46%~51%）与林可酰胺类（lincosamide，14%~19%）抗性基因构成，但这与生猪治疗中最常用的抗生素——四环素类（tetracyclines）与β-内酰胺类（beta-lactams）——的选择压力并不相符。与ARGs不同，部分产品（如肾脏）在开膛剔骨工序（evisceration）后检出的毒力基因数量更多，这反映出当前卫生操作存在不足。部分产品中检出了超过19种通用毒力特征，主要包括黏附、分泌系统、趋化与运动、侵袭及运动相关因子。但从屠宰流程初始阶段的几乎所有样本中，均检出了免疫逃逸决定因子（immune evasion determinants），其中麻醉区的检出量最高。本研究结论认为，生猪屠宰场的主要污染来源有两处：一是动物体表携带的微生物，二是开膛剔骨工序引入的微生物。因此，将防控措施（如强化消毒流程）聚焦于这两处污染来源区域，可降低食品安全与消费者健康风险——因为抗生素抗性与毒力决定因子可能会扩散至终产品与环境中；此外，ARGs与毒力性状还会加重病原菌的临床治疗难度。