Prof. Dr. med. Dr. phil. Adrian Egli

Area of Research

Description of Research Interest

Since 2022 I am the director of the Institute of Medical Microbiology and chair of Medical Microbiology at UZH.
My research focus is to study host–pathogen interactions with a interest on pathogen assessment in acute infection and AMR. Scientifically, I build interoperable clinical-genomic data spaces through SPHN (Driver “Sepsis”, National Data Stream IICU) and the national Swiss Pathogen Surveillance Platform (SPSP) to enable large-scale, FAIR analyses. We apply AI/ML to complex diagnostic streams e.g., MALDI-TOF MS, whole-genome sequencing, metagenomics, and contextual EHR data to extract stable features that predict resistance, severity, and treatment response. We then translate these findings into novel diagnostics and embedded analytics that run inside a 24/7 clinical laboratory, shortening time-to-decision and enabling targeted therapy. This bench-to-bedside loop—platforms (SPHN/SPSP) → AI on real-world data → validated assays—drives measurable gains in patient care and national surveillance.

Special Expertise

• Medical microbiology & AMR: EUCAST AST, intrinsic/acquired resistance, sepsis workflows; leadership of 24/7 clinical lab with highest diagnostic responsibility.
  
• Translational diagnostics: From discovery to novel assays and workflow-embedded decision support (MALDI-TOF MS, rapid PCR/panels, WGS/long-read, metagenomics).
  
• Outbreak & pathogen genomics: cgMLST/SNP phylogenies, plasmid/porin analysis, genotype–phenotype mapping for pathogen assessment.
  
• Host–pathogen interaction: Biomarker discovery/validation (sepsis, AMR); linking pathogen features and host signals to clinical severity and therapy response.
  
• Bioinformatics & data platforms: WGS/MALDI/metagenomic pipelines; FAIR governance; multi-institutional data spaces via SPHN (Driver “Sepsis”, NDS) and SPSP.
  
• AI/ML for diagnostics: Learning from large, heterogeneous datasets (MALDI, WGS, EHR) for AMR prediction, risk stratification, triage; external validation, MLOps, human-in-the-loop.
  
• Bridge-building & delivery: USZ–UZH–ETH collaboration, multicenter governance, KPI/SLA-driven implementation to shorten time-to-decision and improve patient outcomes.
  

Shareable Platforms, Services, Equipment & Infrastructure

• Clinical microbiology diagnostic platform (24/7, ISO):
  Phenotyping—culture, MALDI-TOF MS, EUCAST AST (MIC/gradient), synergy/kill-curves; Genotyping—WGS (short/long-read, hybrid for plasmids/SVs), cgMLST/SNP phylogenomics, targeted panels, mNGS; sample-to-report pipelines.
  
• Bacterial biobanks / repositories:
  Curated clinical isolate collections with linked AST/MIC, WGS, and metadata; AMR-mechanism panels for benchmarking and validation; standardized −80 °C storage and tracking. We store more than 200k isolates (bacteria and fungi).
  
• Bioinformatics & data analysis:
  Validated pipelines for assembly/variant calling, AMR/porin detection, plasmid reconstruction; MALDI spectra analytics; metagenomic taxonomic/functional profiling; reproducible workflows (containers, Nextflow/Snakemake); FAIR/SPHN-compliant data models.
  
• AI/ML on diagnostic datasets:
  Supervised/deep learning across MALDI, WGS, metagenomics, EHR for AMR prediction, severity/risk stratification, and pathogen assessment; explainability, external validation; translation into novel diagnostics and embedded decision support.
  

Member of Collaborative/interdisciplinary Research Consortia

• NCCR AntiResist — Co-PI
  
• NCCR Microbiomes — Partner
  
• Swiss Pathogen Surveillance Platform (SPSP) — Executive Board Chair
  
• SPHN National Data Stream IICU — Executive Chair
  
• Swiss Biobanking Platform (SBP) — Co-President
  
• Swiss Society of Microbiology (SSM) — Section Head (Clinical Microbiology)