Cristin-resultat-ID: 1864211
Sist endret: 29. mars 2021, 11:51
NVI-rapporteringsår: 2020
Resultat
Vitenskapelig artikkel
2020

Plasmid Identification and Plasmid-Mediated Antimicrobial Gene Detection in Norwegian Isolates

Bidragsytere:
  • Abdolrahman Khezri
  • Ekaterina Avershina og
  • Rafi Ahmad

Tidsskrift

Microorganisms
ISSN 2076-2607
e-ISSN 2076-2607
NVI-nivå 1

Om resultatet

Vitenskapelig artikkel
Publiseringsår: 2020
Publisert online: 2021
Volum: 9
Hefte: 52
Open Access

Importkilder

Scopus-ID: 2-s2.0-85098888940

Beskrivelse Beskrivelse

Tittel

Plasmid Identification and Plasmid-Mediated Antimicrobial Gene Detection in Norwegian Isolates

Sammendrag

Norway is known for being one of the countries with the lowest levels of antimicrobial resistance (AMR). AMR, through acquired genes located on transposons or conjugative plasmids, is the horizontal transmission of genes required for a given bacteria to withstand antibiotics. In this work, bioinformatic analysis of whole-genome sequences and hybrid assembled data from Escherichia coli, and Klebsiella pneumoniae isolates from Norwegian patients was performed. For detection of putative plasmids in isolates, the plasmid assembly mode in SPAdes was used, followed by annotation of resulting contigs using PlasmidFinder and two curated plasmid databases (Brooks and PLSDB). Furthermore, ResFinder and Comprehensive Antibiotic Resistance Database (CARD) were used for the identification of antibiotic resistance genes (ARGs). The IncFIB plasmid was detected as the most prevalent plasmid in both E. coli, and K. pneumoniae isolates. Furthermore, ARGs such as aph(3″)-Ib, aph(6)-Id, sul1, sul2, tet(D), and qnrS1 were identified as the most abundant plasmid-mediated ARGs in Norwegian E. coli and K. pneumoniae isolates, respectively. Using hybrid assembly, we were able to locate plasmids and predict ARGs more confidently. In conclusion, plasmid identification and ARG detection using whole-genome sequencing data are heavily dependent on the database of choice; therefore, it is best to use several tools and/or hybrid assembly for obtaining reliable identification results. View Full-Text Keywords: Escherichia coli; Klebsiella pneumoniae; antimicrobial resistance; plasmid; plasmid-mediated genes; horizontal gene transfer

Bidragsytere

Abdolrahman Khezri

  • Tilknyttet:
    Forfatter
    ved Institutt for bioteknologi ved Høgskolen i Innlandet

Ekaterina Avershina

  • Tilknyttet:
    Forfatter
    ved Institutt for bioteknologi ved Høgskolen i Innlandet
  • Tilknyttet:
    Forfatter
    ved Russland

Rafi Ahmad

  • Tilknyttet:
    Forfatter
    ved Klinisk bioinformatikk ved UiT Norges arktiske universitet
  • Tilknyttet:
    Forfatter
    ved Institutt for bioteknologi ved Høgskolen i Innlandet
  • Tilknyttet:
    Forfatter
    ved Div Gjøvik/Lillehammer ved Sykehuset Innlandet HF
1 - 3 av 3