Genomic evolution of antimicrobial resistance in Escherichia coli.
Animals
Anti-Bacterial Agents
/ pharmacology
Cattle
Drug Resistance, Bacterial
/ genetics
Escherichia coli
/ drug effects
Escherichia coli Infections
/ drug therapy
Europe
Evolution, Molecular
Feces
/ microbiology
Genome, Bacterial
/ genetics
Genomics
/ methods
Microbial Sensitivity Tests
/ methods
Phylogeny
Poultry
/ microbiology
Red Meat
/ microbiology
Swine
/ microbiology
Virulence
/ genetics
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
23 07 2021
23 07 2021
Historique:
received:
11
01
2021
accepted:
05
07
2021
entrez:
24
7
2021
pubmed:
25
7
2021
medline:
3
11
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 34301966
doi: 10.1038/s41598-021-93970-7
pii: 10.1038/s41598-021-93970-7
pmc: PMC8302606
doi:
Substances chimiques
Anti-Bacterial Agents
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
15108Investigateurs
Haitske Graveland
(H)
Alieda van Essen
(A)
Antonio Battisti
(A)
Andrea Caprioli
(A)
Thomas Blaha
(T)
Tine Hald
(T)
Hristo Daskalov
(H)
Helmut W Saatkamp
(HW)
Katharina D C Stärk
(KDC)
Roosmarijn E C Luiken
(REC)
Liese Van Gompel
(L)
Rasmus Borup Hansen
(RB)
Jeroen Dewulf
(J)
Ana Sofia Ribeiro Duarte
(ASR)
Informations de copyright
© 2021. The Author(s).
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