Ekaterina Avershina

• Istvan, Paula; Birkeland, Einar Elvbakken; Avershina, Ekaterina; Kværner, Ane Sørlie; Bemanian, Vahid & Pardini, Barbara [Show all 11 contributors for this article] (2024). Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study. Nature Communications. ISSN 2041-1723. 15(1), p. 1–12. doi: 10.1038/s41467-024-46033-0. Full text in Research Archive
• Avershina, Ekaterina; Khezri, Abdolrahman & Ahmad, Rafi (2023). Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics—Current State and Whole Genome Sequencing Implementation Perspectives. Antibiotics. ISSN 2079-6382. 12(4). doi: 10.3390/antibiotics12040781. Full text in Research Archive
• Avershina, Ekaterina; Frye, Stephan Alfons; Ali, Jawad; Taxt, Arne Michael & Ahmad, Rafi (2022). Ultrafast and Cost-Effective Pathogen Identification and Resistance Gene Detection in a Clinical Setting Using Nanopore Flongle Sequencing. Frontiers in Microbiology. ISSN 1664-302X. doi: 10.3389/fmicb.2022.822402.
• Hanrahan, Niall; Lister, Adam; Highmore, Callum; Rajith, Leena; Avershina, Ekaterina & Ali, Jawad [Show all 9 contributors for this article] (2022). Enhanced Raman techniques for infection diagnostics. Proceedings of SPIE, the International Society for Optical Engineering. ISSN 0277-786X. 12203, p. 6–17. doi: 10.1117/12.2635324. Full text in Research Archive
• Avershina, Ekaterina; Frye, Stephan Alfons; ali, jawad; Taxt, Arne Michael & Ahmad, Rafi (2022). Ultrafast and Cost-Effective Pathogen Identification and Resistance Gene Detection in a Clinical Setting Using Nanopore Flongle Sequencing. Frontiers in Microbiology. ISSN 1664-302X. 13. doi: 10.3389/fmicb.2022.822402. Show summary

  Rapid bacterial identification and antimicrobial resistance gene (ARG) detection are crucial for fast optimization of antibiotic treatment, especially for septic patients where each hour of delayed antibiotic prescription might have lethal consequences. This work investigates whether the Oxford Nanopore Technology’s (ONT) Flongle sequencing platform is suitable for real-time sequencing directly from blood cultures to identify bacteria and detect resistance-encoding genes. For the analysis, we used pure bacterial cultures of four clinical isolates of Escherichia coli and Klebsiella pneumoniae and two blood samples spiked with either E. coli or K. pneumoniae that had been cultured overnight. We sequenced both the whole genome and plasmids isolated from these bacteria using two different sequencing kits. Generally, Flongle data allow rapid bacterial ID and resistome detection based on the first 1,000–3,000 generated sequences (10 min to 3 h from the sequencing start), albeit ARG variant identification did not always correspond to ONT MinION and Illumina sequencing-based data. Flongle data are sufficient for 99.9% genome coverage within at most 20,000 (clinical isolates) or 50,000 (positive blood cultures) sequences generated. The SQK-LSK110 Ligation kit resulted in higher genome coverage and more accurate bacterial identification than the SQK-RBK004 Rapid Barcode kit.

• Khezri, Abdolrahman; Avershina, Ekaterina & Ahmad, Rafi (2021). Hybrid Assembly Provides Improved Resolution of Plasmids, Antimicrobial Resistance Genes, and Virulence Factors in Escherichia coli and Klebsiella pneumoniae Clinical Isolates. Microorganisms. ISSN 2076-2607. 9(12), p. 1–18. doi: 10.3390/microorganisms9122560. Full text in Research Archive Show summary

  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 coli and Klebsiella pneumoniae isolates from Norwegian clinical samples were sequenced using both MinION and Illumina platforms. Three out of nine samples were sequenced directly from blood culture, and one sample was sequenced from a mixed-blood culture. For genome assembly, several long-read, (Canu, Flye, Unicycler, and Miniasm), short-read (ABySS, Unicycler and SPAdes) and hybrid assemblers (Unicycler, hybridSPAdes, and MaSurCa) were tested. Assembled genomes from the best-performing assemblers (according to quality checks using QUAST and BUSCO) were subjected to downstream analyses. Flye and Unicycler assemblers performed best for the assembly of long and short reads, respectively. For hybrid assembly, Unicycler was the top-performing assembler and produced more circularized and complete genome assemblies. Hybrid assembled genomes performed substantially better in downstream analyses to predict putative plasmids, AMR genes and β-lactamase gene variants, compared to MinION and Illumina assemblies. Thus, hybrid assembly has the potential to reveal factors related to microbial pathogenicity in clinical and mixed samples.

• Avershina, Ekaterina; Shapovalova, Valeria & Shipulin, German (2021). Fighting Antibiotic Resistance in Hospital-Acquired Infections: Current State and Emerging Technologies in Disease Prevention, Diagnostics and Therapy. Frontiers in Microbiology. ISSN 1664-302X. 12. doi: 10.3389/fmicb.2021.707330. Full text in Research Archive

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• Avershina, Ekaterina; Birkeland, Einar Elvbakken; Berstad, Paula; Hoff, Geir Svein & Rounge, Trine Ballestad (2022). Total neoplastic polyp volume is correlated to several bacterial taxa in faecal immunochemical test-positive CRC-screening participants.
• Avershina, Ekaterina; Birkeland, Einar Elvbakken; Berstad, Paula; Hoff, Geir Svein & Rounge, Trine Ballestad (2022). Total neoplastic polyp volume is correlated to several bacterial taxa in faecal immunochemical test-positive CRC-screening participants.
• Birkeland, Einar Elvbakken; Kværner, Ane Sørlie; Istvan, Paula; Bermanian, Vahid; Bucher-Johannessen, Cecilie & Avershina, Ekaterina [Show all 9 contributors for this article] (2022). The microbiome in fecal immunochemical tests from colorectal cancer screening participants – can it be used as a screening biomarker?

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