TY - JOUR
T1 - Genomic evolution of antimicrobial resistance in Escherichia coli
AU - Leekitcharoenphon, Pimlapas
AU - Johansson, Markus Hans Kristofer
AU - Munk, Patrick
AU - Malorny, Burkhard
AU - Skarżyńska, Magdalena
AU - Wadepohl, Katharina
AU - Moyano, Gabriel
AU - Hesp, Ayla
AU - Veldman, Kees T.
AU - Bossers, Alex
AU - Zając, Magdalena
AU - Wasyl, Dariusz
AU - Sanders, Pascal
AU - Gonzalez-Zorn, Bruno
AU - Brouwer, Michael S.M.
AU - Wagenaar, Jaap A.
AU - Heederik, Dick J.J.
AU - Mevius, Dik
AU - Aarestrup, Frank M.
AU - consortium, EFFORT
A2 - Graveland, Haitske
A2 - van Essen, Alieda
A2 - Battisti, Antonio
A2 - Caprioli, Andrea
A2 - Blaha, Thomas
A2 - Hald, Tine
A2 - Daskalov, Hristo
A2 - Saatkamp, Helmut W.
A2 - Stärk, Katharina D.C.
A2 - Luiken, Roosmarijn E.C.
A2 - Van Gompel, Liese
A2 - Hansen, Rasmus Borup
A2 - Dewulf, Jeroen
A2 - Duarte, Ana Sofia Ribeiro
PY - 2021
Y1 - 2021
N2 - 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.
AB - 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.
U2 - 10.1038/s41598-021-93970-7
DO - 10.1038/s41598-021-93970-7
M3 - Journal article
C2 - 34301966
VL - 11
JO - Scientific Reports
JF - Scientific Reports
SN - 2045-2322
M1 - 15108
ER -