TY - JOUR

T1 - Exploring the resistome, virulome, mobilome and microbiome along pork production chain using metagenomics

AU - Li, Lili

AU - Xiao, Yawen

AU - Wang, Chong

AU - Olsen, Rikke Heidemann

AU - Meng, Hecheng

AU - Shi, Lei

N1 - Publisher Copyright: © 2022

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

KW - Metagenomic

KW - Microbiome

KW - Pork production

KW - Resistome

KW - Virulome

U2 - 10.1016/j.ijfoodmicro.2022.109674

DO - 10.1016/j.ijfoodmicro.2022.109674

M3 - Journal article

C2 - 35413521

AN - SCOPUS:85127810847

VL - 371

JO - International Journal of Food Microbiology

JF - International Journal of Food Microbiology

SN - 0168-1605

M1 - 109674

ER -