Genomic evolution of antimicrobial resistance in Escherichia coli

Pimlapas Leekitcharoenphon,Patrick Munk,Magdalena Zając,Ayla Hesp,Magdalena Skarżyńska,Burkhard Malorny,B Gonzales-Zorn ,Dick Heederik ,Pascal Sandérs ,Alex Bossers,Kees Veldman ,Markus Johansson ,Katharina Wadepohl,Jaap A Wagenaar,Dik Mevius,Michael S.m Brouwer ,Gabriel Moyano,Dariusz Wasyl,Frank Møller Aarestrup

doi:10.1038/s41598-021-93970-7

Abstract

The emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.

Highlights

In this study, we isolated E. coli from fecal samples in poultry flocks, swine, and veal calve herds from 6 European countries to investigate phylogenetic background and clustering of E. coli at country, animal source and farm levels
The Single nucleotide polymorphisms (SNPs) tree did not show any country and animal reservoir clusters of AMR genes nor chromosomal point mutation conferring to antimicrobial resistance
The 627 E. coli isolates comprised of 182 different sequence types (ST) types with 24 isolates being of unknown ST type, indicating high diversity in the E. coli isolates

Summary

Introduction

We isolated E. coli from fecal samples in poultry flocks, swine, and veal calve herds from 6 European countries to investigate phylogenetic background and clustering of E. coli at country, animal source and farm levels. This study provided an insight into the evolution of AMR in E. coli genomes including an association with virulence genes, plasmid and mobile genetic elements (MGEs). The correlation of AMR abundance between metagenomics and WGS analyses was determined

Methods

Results

Discussion

Conclusion