为了了解并尽量减少微生物污染物从动物传播到生猪肉产品,我们探索了抗生素抗性基因(ARGs)的多样性,毒力因子(VFs),猪粪便中的移动遗传元件(MGEs)和细菌群落组成,加工区域以及使用宏基因组学在中国大型生猪屠宰场的最终猪肉产品。微生物群落的丰度和多样性在到达和屠宰场面积上较高,在最终猪肉产品中急剧下降。此外,某些临床相关病原体和机会病原体的相对丰度在最终猪肉产品和切块样本中更高。我们确定了与30种抗生素相关的1412种ARGs亚型,其中与多药耐药和β-内酰胺酶相关的ARGs占优势。对临床至关重要的重要抗生素的耐药性决定因素,包括与MCR相关的序列,optrA,poxtA,tetX和β-内酰胺酶基因(即blaOXA,BlaVIM,blaIMP,blages,blaNDM,检测到blaKPC和blaSME)。超过42个一般毒力特征,主要是坚持,分泌系统,铁吸收,毒素,抗吞噬作用和免疫逃避,已确定。共有1922种类型的MGE,主要观察到质粒。预测大多数ARG与MGE相关联。ARGs的患病率,VF和MGE在后续处理步骤中减少。剩下的大部分ARG,最终猪肉产品中的VF和MGE也存在于其他样品中,表明这些基因在生产线上的流动。这些结果拓宽了我们对全球ARGs的理解,VF和MGE在猪肉生产链上的多样性,建议实施改进的控制措施,以降低病原菌及其相关耐药性传播的风险,从动物到食物链和周围环境的病毒组和动员体。
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.