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Researcher
Matilda Berkell
- Research Expertise:My research is focused on studying human and animal pathogens and their commensal microbial flora in the context of infectious diseases by utilizing molecular microbiology and bioinformatics. My main effort is dedicated to study: (1) The impact of broad-spectrum antibiotic treatment on the human commensal flora and how antiseptics can be utilized to prevent colonization with antibiotic-resistant pathogenic bacteria. Specifically, by utilizing 16S rRNA gene and shotgun metagenomic sequencing technologies, the antibiotic impact on microbial composition, metabolic activity, and antibiotic resistance mechanisms harbored within the host microbial flora is studied in relation to development of adverse events like antibiotic-associated diarrhea (AAD) and Clostridioides difficile infection (CDI). Further, I study acquisition and transmission of resistant organisms within neonatal intensive care units in Europe and how decontaminating measures can be utilized for prevention. (2) Mechanisms of antibiotic resistance and virulence in pathogenic bacteria. Both clinical, patient-derived as well as in vitro-passaged bacterial strains, namely Clostridioides difficile and Pseudomonas aeruginosa, are studied using strain typing and whole genome sequencing to determine resistance stability and fitness cost to understand emergence of the resistance mechanisms as well as their fate in the community. (3) Markers within the respiratory microflora and genetic features of the SARS-CoV-2 virus predictive of disease severity and infection within the framework of a large pan-European COVID-19 cohort study including a large number of patient samples derived from health-care workers, fragile populations, severely ill COVID-19 patients, and healthy populations.
- Keywords:DNA SEQUENCING, RNA SEQUENCING, MICROBIAL GENETICS, MICROBIOME, Medicine
- Disciplines:Bioinformatics and computational biology, Diagnostics, Microbiology, Molecular and cell biology
- Research techniques:• Whole genome sequencing • Illumina sequencing • Pacbio sequencing • Nanopore sequencing • 16S rRNA gene profiling • Shotgun metagenomic sequencing • RNA sequencing • DNA extraction • PCR • Phylogenetic analysis • Bacterial genomics • Microbiome • Transcriptomic analysis
- Users of research expertise:NA