Exploring the resistome, virulome, mobilome and microbiome along pork production chain using metagenomics
Exploring the resistome, virulome, mobilome and microbiome along pork production chain using metagenomics
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利用宏基因组学探索猪肉生产链中的抗性组、病毒组、移动组和微生物组
DOI：
10.1016/j.ijfoodmicro.2022.109674
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发表时间：
2022
影响因子：
5.4
通讯作者：
Lei Shi
中科院分区：
文献类型：
--
作者：
Lili Li;Yawen Xiao;Chong Wang;Rikke Heidemann Olsen;Hecheng Meng;Lei Shi
为了了解和减少微生物污染从动物传播到生猪肉产品，利用元基因组学方法对中国某大型生猪屠宰场生猪粪便、加工区和成品猪肉中的抗生素耐药基因(ARGs)、毒力因子(VFS)、移动遗传元件(MGES)的多样性和细菌群落组成进行了研究。进货区和屠宰区微生物群落丰富度和多样性较高，成品猪肉微生物群落丰富度和多样性急剧下降。此外，一些临床相关病原菌和机会致病菌在成品猪肉和切肉样品中的相对丰度较高。共鉴定出30个抗生素类共1412个ARGs亚型，其中与多重耐药和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决定因素，包括与tomcr、optrA、poxtA、tlX和β-内酰胺酶基因相关的序列(即blaOXA、blaVIM、blaIMP、blages、blaNDM、blaKPC和blaSME)。鉴定出42种一般毒力特征，主要是粘附性、分泌系统、铁摄取、毒素、抗吞噬和免疫逃避。共观察到1922种类型的MGES，主要是质粒。大多数ARG被预测与MGES有关。在随后的处理步骤中，ARGs、VFS和MGES的患病率有所下降。最终猪肉产品中剩余的大部分ARGs、VFS和MGES也存在于其他样品中，表明这些基因在生产线上流动。这些结果扩大了我们对猪肉生产链上全球ARGs、VFS和MGES多样性的理解，并建议实施改进的控制措施，以降低病原菌及其相关耐药组、病毒组和移动组从动物向食物链和周围环境传播的风险。
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 tomcr,optrA,poxtA,tetXand β-lactamase genes (i.e.blaOXA,blaVIM,blaIMP,blaGES,blaNDM,blaKPCandblaSME) 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.