摘要
      为了了解并最大限度地减少微生物污染物从动物传播到生猪肉产品，我们利用宏基因组学研究了中国大型生猪屠宰场猪粪便、加工区和最终猪肉产品中抗生素抗性基因（ARGs）、毒力因子（VFs）、可移动遗传元件（MGE）的多样性和细菌群落组成。微生物群落的丰度和多样性在到达和屠宰室区域较高，而在最终猪肉产品中急剧下降。此外，一些临床相关病原体和机会病原体在最终猪肉产品和切割样品中的相对丰度更高。我们鉴定了与30种抗生素类别相关的1412种ARGs亚型，其中与多药耐药性和β-内酰胺酶相关的ARGs占主导地位。检测临床关键抗生素的耐药性决定因素，包括与mcr、optrA、poxtA、tetX和β-内酰胺酶基因（即blaOXA、blaVIM、blaIMP、blaGES、blaNDM、blaKPC和blaSME）相关的序列。鉴定出42种以上的一般毒力特征，主要是粘附性、分泌系统、铁摄取、毒素、抗吞噬细胞和免疫逃避。共观察到1922种MGE，主要是质粒。大多数ARG被预测为与MGE相关联。ARGs、VFs和MGE的患病率在随后的处理步骤中降低。最终猪肉产品中剩余的大多数ARGs、VFs和MGE也存在于其他样品中，表明这些基因通过生产线流动。这些结果拓宽了我们对猪肉生产链中全球ARGs、VFs和MGE多样性的理解，并建议实施改进的控制措施，以降低致病菌及其相关耐药性、病毒群和移动性从动物传播到食物链和周围环境的风险。
Abstract
In order to understand and minimize microbial contaminants spread from animal to raw pork products, we explored the diversity of antibiotic resistance genes (ARGs), virulence factors (VFs), mobile genetic elements (MGEs) and the bacterial community composition in feces of pigs, processing areas as well as the end pork products in a large-scale pig slaughterhouse in China using metagenomics. The abundance and diversity of microbial community was higher in arrival and slaughtering room area and decreased sharply in the end pork products. Furthermore, the relative abundance of some clinically relevant pathogens and opportunity pathogens were greater in the end pork products and cutter samples. We identified 1412 subtypes of ARGs related to 30 antibiotic classes, in which ARGs related to multidrug resistance and β-lactamase were dominant. Resistance determinants to clinically critical important antibiotics, including sequences related to mcr, optrA, poxtA, tetX and β-lactamase genes (i.e. blaOXA, blaVIM, blaIMP, blaGES, blaNDM, blaKPC and blaSME) were detected. More than 42 general virulence features, mainly adherence, secretion system, iron uptake, toxin, antiphagocytosis and immune evasion, were identified. A total of 1922 types of MGEs, mainly plasmids were observed. Most of the ARGs are predicted to be associated with MGEs. The prevalence of ARGs, VFs and MGEs decreased over subsequential processing steps. Most of the remaining ARGs, VFs and MGEs in end pork products were also present on other samples, indicating the flow of these genes through the production line. These results broaden our understanding of the global ARGs, VFs and MGEs diversity along the pork production chain, with the suggestion of implementing improved control measures to reduce the risk of spread of pathogenic bacteria and their associated resistome, virulome and mobilome from animal to the food chain and the surrounding environment.

https://www.sciencedirect.com/science/article/abs/pii/S0168160522001453