Antimicrobial resistance and population genomics of multidrug-resistant Escherichia coli in pig farms in mainland China

Zhong Peng,Bin Wu,Huanchun Chen,Xiangru Wang,Zhuofei Xu,Chaoying Jia,Zizhe Hu,Chen Tan,Xiaoxue Zhang,Menghong Dai,Tianzhi Li,Zugang Li

doi:10.1038/s41467-022-28750-6

Abstract

The expanding use of antimicrobials in livestock is an important contributor to the worldwide rapid increase in antimicrobial resistance (AMR). However, large-scale studies on AMR in livestock remain scarce. Here, we report findings from surveillance of E. coli AMR in pig farms in China in 2018–2019. We isolated E. coli in 1,871 samples from pigs and their breeding environments, and found AMR in E. coli in all provinces in mainland China. We detected multidrug-resistance in 91% isolates and found resistance to last-resort drugs including colistin, carbapenems and tigecycline. We also identified a heterogeneous group of O-serogroups and sequence types among the multidrug-resistant isolates. These isolates harbored multiple resistance genes, virulence factor-encoding genes, and putative plasmids. Our data will help to understand the current AMR profiles of pigs and provide a reference for AMR control policy formulation for livestock in China.

Highlights

The expanding use of antimicrobials in livestock is an important contributor to the worldwide rapid increase in antimicrobial resistance (AMR)
E. coli has been found to play important roles in the dissemination of blaNDM-1, mcr, and/or tet(X3)/(X4); these antimicrobial resistance genes (ARGs) mediate resistance to lastresort drugs in gramnegative bacteria, which may lead to unavailability of antimicrobials in both human and veterinary medicine[3,4,9]
The widespread and expanding use of antimicrobials can lead to the development of drug-resistant bacteria in animal guts, and these resistant bacteria can spread to humans[1]

Summary

Introduction

The expanding use of antimicrobials in livestock is an important contributor to the worldwide rapid increase in antimicrobial resistance (AMR). Several drug-resistant bacteria are of great concern worldwide, among which Escherichia coli is notable[1,5,6] This bacterial species is a leading cause of foodborne infections and represents a major reservoir of antimicrobial resistance genes (ARGs) due to its high capacity to accumulate ARGs, mostly through horizontal gene transfer[7]. In the past two decades, meat production has plateaued in high-income countries but has greatly increased in low- and middle-income countries, in Asia[14] Against this background, antimicrobials are widely used in livestock for growth promotion and/or health maintenance. The analysis of E. coli isolates from pigs and other animals by antimicrobial susceptibility testing (AST) in combination with whole-genome sequencing (WGS) has facilitated a better understanding of AMR development and dissemination[17–20]

Methods

Results

Conclusion