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

Ekaterina Avershina,Abdolrahman Khezri,Rafi Ahmad

doi:10.3390/microorganisms9010052

Abstract

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.

Highlights

Antimicrobial resistance (AMR) is the ability of microorganisms to resist antimicrobial treatments, especially antibiotics
AMR can arise through various mechanisms, including mutations of chromosomal genes and the acquisition of antibiotic resistance genes (ARGs) from other strains in a process termed horizontal gene transfer (HGT)
It is the sharing of genes through HGT that has largely contributed to the global dissemination of ARGs [4]

Summary

Introduction

Antimicrobial resistance (AMR) is the ability of microorganisms to resist antimicrobial treatments, especially antibiotics. Infections due to AMR bacteria are a threat to modern health care and are responsible for an estimated 700,000 and 33,000 deaths/year globally and in Europe, respectively [1]. Extended spectrum β-lactamases (ESBL) producing and carbapenem-resistant Enterobacteriaceae are among the priority one critical section of the WHO pathogen list. Klebsiella pneumoniae and Escherichia coli [3]. AMR can arise through various mechanisms, including mutations of chromosomal genes and the acquisition of antibiotic resistance genes (ARGs) from other strains in a process termed horizontal gene transfer (HGT). It is the sharing of genes through HGT that has largely contributed to the global dissemination of ARGs [4].

Methods

Results

Discussion

Conclusion