Annika Sobkowiak

PhD Student

 

© Annika Sobkowiak

Hospital and Environmental Hygiene
Institute of Hygiene
Robert-Koch-Str. 41
D-48149 Münster, Germany
annika.sobkowiak@ukmuenster.de

Nationality: German De

Education

  • Since 2023:
    PhD studies in the Hospital and Environmental Hygiene Group, Institute of Hygiene, University Hostipal Münster, Germany

2019 - 2022:

  • Master of Science (M.Sc.) in Interdisciplinary Biomedicine and Bioinformatics, Bielefeld University, Germany
  • 2016 - 2019:
    Bachelor of Science (B.Sc.) in Biochemistry, Bielefeld University, Germany

Work experience

  • 2021:
    Supervisor of biological laboratory training for medical students, Bielefeld University, Germany
  • 2019:
    Supervisor of chemical laboratory training, Bielefeld University, Germany
  • 2018 - 2019:
    Tutor in statistics, Bielefeld University, Germany
  • 2013 - 2015:
    Supervisor of elementary school students, Teutolab Marienschule, Lippstadt, Germany

Supervisors

  • PD Dr. Vera Schwierzeck, Hospital and Environmental Hygiene Group, Institute of Hygiene, University Hospital Münster, Germany
  • Prof. Dr. Joachim Kurtz, Animal Evolutionary Ecology Group, Institute for Evolution and Biodiversity, University of Münster, Germany
  • Prof. Dr. Stephan Ludwig, Institute of Molecular Virology, Center for Molecular Biology of Inflammation, University of Münster, Germany

Research interests

  • Microbiology

  • Genomics

  • Microbiome research

  • Antibiotic resistances

PhD project description

Surveillance and characterisation of antimicrobial resistance harbouring plasmids

Gram-negative multidrug resistant bacteria (MDRB) are a global health problem and economic burden. Until recently research has focussed on antimicrobial resistance (AMR) spread through whole bacteria transmission while the role of AMR plasmids has rarely been addressed yet.

The aim of this study is to analyse clinical relevant AMR genes on plasmids and monitor AMR transmission via horizontal gene transfer (HGT). We will monitor stability and movement activity of AMR genes in clinical isolates with follow-up samples using long-read whole genome sequencing (lrWGS). In addition, in vitro experiments will be performed with clinical isolates to test stability of selected AMR harbouring plasmids under different culture conditions. These include sub inhibitory antibiotic concentrations and different pH, for example, to mimic
gastro-intestinal conditions and to induce stress. In another in vitro experiment, it is planned to recover the AMR of a MDRB with a CRISPR-Cas based approach and perform co-cultivation experiments afterwards to monitor possible HGT of AMR genes. The evaluation of in vitro experiments will primarily be done using lrWGS.

The project results will enhance the knowledge about AMR transmission and should generate new ideas for strategies to prevent spread of AMR in the hospital setting.

Publications

  • van Almsick, V.F., Sobkowiak, A., Scherff, N. et al.  (2023).  Characterization of blaOXA-48-carrying plasmids and small non-AMR-coding plasmids collected from Ukrainian patients. Infection. 10.1007/s15010-023-02136-2 [doi]
  • Sobkowiak, A., Scherff, N., Schuler, F., Bletz, S., Mellmannn, A., Schwierzeck, V., & van Almsick, V. F. (2024) Plasmid encoded gene duplications of extended-spectrum β-lactamases in clinical bacterial isolates. Frontiers in Cellular and Infection Microbiology, 14, 1343858. 10.3389/fcimb.2024.1343858 [doi]