Blar i forfatter "Avershina, Ekaterina"

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    • AMR-Diag: Neural network based genotype-to-phenotype prediction of resistance towards β-lactams in Escherichia coli and Klebsiella pneumoniae 

      Avershina, Ekaterina; Sharma, Priyanka; Taxt, Arne Michael; Singh, Harpreet; Frye, Stephan Alfons; Paul, Kolin; Kapil, Arti; Naseer, Mohammed Umaer; Kaur, Punit; Ahmad, Rafi (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-03-29)
      Antibiotic resistance poses a major threat to public health. More effective ways of the antibiotic prescription are needed to delay the spread of antibiotic resistance. Employment of sequencing technologies coupled with the use of trained neural network algorithms for genotype-to-phenotype prediction will reduce the time needed for antibiotic susceptibility profile identification from days to ...

    • Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics—Current State and Whole Genome Sequencing Implementation Perspectives 

      Avershina, Ekaterina; Khezri, Abdolrahman; Ahmad, Rafi (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-04-19)
      Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of AMR across continents warrants systematic changes in healthcare routines and protocols. One of the fundamental issues with AMR spread is the lack of rapid diagnostic tools for pathogen identification and AMR detection. ...

    • Hybrid Assembly Provides Improved Resolution of Plasmids, Antimicrobial Resistance Genes, and Virulence Factors in Escherichia coli and Klebsiella pneumoniae Clinical Isolates 

      Khezri, Abdolrahman; Avershina, Ekaterina; Ahmad, Rafi (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-12-10)
      Emerging new sequencing technologies have provided researchers with a unique opportunity to study factors related to microbial pathogenicity, such as antimicrobial resistance (AMR) genes and virulence factors. However, the use of whole-genome sequence (WGS) data requires good knowledge of the bioinformatics involved, as well as the necessary techniques. In this study, a total of nine Escherichia ...

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

      Khezri, Abdolrahman; Avershina, Ekaterina; Ahmad, Rafi (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-12-27)
      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 ...

    • Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing 

      Taxt, Arne Michael; Avershina, Ekaterina; Frye, Stephan Alfons; Naseer, Mohammed Umaer; Ahmad, Rafi (Journal article; Tidsskriftartikkel; Peer reviewed, 2020-05-06)
      Bloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide. Blood culture-based diagnostics usually requires 1–2 days for identification of bacterial agent and an additional 2–3 days for phenotypic determination of antibiotic susceptibility pattern. With the escalating burden of antimicrobial resistance (AMR) rapid diagnostics becomes increasingly important to ...