Exploring the resistome, virulome, mobilome and microbiome along pork production chain using metagenomics

Lili Li; Yawen Xiao; Chong Wang; Rikke Heidemann Olsen; Hecheng Meng; Lei Shi

doi:10.1016/j.ijfoodmicro.2022.109674

Exploring the resistome, virulome, mobilome and microbiome along pork production chain using metagenomics

Int J Food Microbiol. 2022 Jun 16:371:109674. doi: 10.1016/j.ijfoodmicro.2022.109674. Epub 2022 Apr 6.

Authors

Lili Li¹, Yawen Xiao², Chong Wang³, Rikke Heidemann Olsen⁴, Hecheng Meng⁵, Lei Shi⁶

Affiliations

¹ Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China; School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China.
² Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China.
³ Shandong New Hope Liuhe Group Ltd., Qingdao, China.
⁴ Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark.
⁵ School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China. Electronic address: femenghc@scut.edu.cn.
⁶ Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China; State Key Laboratory of Food Safety Technology for Meat Products, Xiamen, China.

PMID: 35413521
DOI: 10.1016/j.ijfoodmicro.2022.109674

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. bla_OXA, bla_VIM, bla_IMP, bla_GES, bla_NDM, bla_KPC and bla_SME) 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.

Keywords: Metagenomic; Microbiome; Pork production; Resistome; Virulome.

MeSH terms

Animals
Anti-Bacterial Agents / pharmacology
Bacteria / genetics
Genes, Bacterial
Metagenomics
Microbiota*
Pork Meat*
Red Meat*
Swine
beta-Lactamases / genetics

Substances

Anti-Bacterial Agents
beta-Lactamases