applied microbiology research lab

At ESCMID Global 2026, many members of our group had the opportunity to share their ongoing projects with the gigantic clinical microbiology and infectious diseases community 🧫🌍. It was a great chance to present our work, exchange ideas with colleagues from different institutions, and discuss new approaches to understanding, detecting, and tackling challenges in applied microbiology. Also a nice time to have some fun in Munich!

Our contributions covered a broad range of topics: from antibiotic resistance mechanisms and bacterial interactions to rapid diagnostics, MALDI-TOF MS quality control, microbiome methods, diagnostic AI, and digital tools for susceptibility testing 💊🤖.

Zoey Germuskova — PhD candidate

Project: Antibiotic resistance in Capnocytophaga canimorsus

Zoey’s project investigates antibiotic resistance in Capnocytophaga canimorsus, a bacterium that can be transmitted from dogs and cats to humans and cause severe infections. The study identified β-lactamase enzymes OXA-347 and a novel variant, OXA-1422, in human clinical isolates, showing that they can reduce susceptibility to commonly used antibiotics such as penicillins and cephalosporins.

Mariella Greutmann — PhD candidate

Project: Bacterial interactions and antibiotic responses in multidrug-resistant E. coli

Mariella’s project uses pairwise co-culture experiments to study how bacterial interactions reshape antibiotic responses in multidrug-resistant E. coli. The results show that both bacterial growth and AMR gene expression vary depending on the antibiotic context and the neighbouring bacterial partner.

Janis Rogenmoser — PhD candidate

Project: Rapid LAMP-based detection of invasive-risk uropathogenic E. coli

Janis’s project developed and validated a rapid Loop-Mediated Isothermal Amplification (LAMP) assay to detect E. coli and the urosepsis-associated virulence marker papGII directly from urine samples. The assay delivered results within 40 minutes and showed strong diagnostic performance in routine clinical samples, highlighting its potential for early UPEC identification and invasiveness risk assessment.

Dr. Alejandro Guerrero-López — Postdoc

Project 1 : Knowledge distillation for MALDI-TOF antimicrobial resistance prediction

Alejandro’s knowledge distillation study shows that large AI models for MALDI-TOF antimicrobial resistance prediction can be compressed into much smaller neural networks without major loss of accuracy. Using a pretrained transformer as teacher and a lightweight student model, the project achieved near-teacher performance while substantially reducing model size, training time, and energy consumption, supporting more accessible and sustainable deployment of AI in microbiology.

Project 2: ASTAnnotator: digital measurement of disc diffusion inhibition zones

Alejandro also presented ASTAnnotator, an app supporting the digital measurement of antibiotic inhibition zones from disc diffusion images in a human-in-the-loop workflow. The application enables standardized, traceable, and offline annotation of routine AST plates, combining automatic disc detection with manual correction to improve reproducibility and facilitate retrospective analyses and future AI-assisted susceptibility testing workflows.

Eline Meijer — PhD candidate

Project: Batch effects and quality control in AI-driven MALDI-TOF MS analysis

Eline’s project investigates batch effects and quality control strategies in AI-driven MALDI-TOF MS analysis. The results demonstrate that machine-related batch effects can compromise identification beyond species level, while targeted quality control, particularly filtering spectra based on peak reproducibility, improves model performance across machines and supports more accurate downstream analyses.

Dr. Ashley Rooney — Postdoc

Project: DNA extraction methods for microbiome profiling in tissue biopsy samples
 

Ashley’s project compares DNA extraction methods for microbiome profiling in tissue biopsy samples. The study found that biopsy samples had low bacterial DNA yield, but that the extraction method did not significantly affect DNA yield, sequencing depth, pathogen detection, or microbiome richness.

A warm welcome to our two new team members!

Wannisa joins us as a new PhD student and will be working on the sepsis project under Ashley’s supervision. We are very much looking forward to her contributions and to having her in the group.

Ruan joins us as a visiting scientist. We are excited about the insights and perspectives he brings to the team and look forward to working with him.

Grants are in the house! 🎊
Multiple lab members secured substantial funding for ongoing and future projects:

Dr. Alejandro Guerrero López received the highly competitive Marie Skłodowska-Curie Actions Postdoctoral Fellowships (only 9.6% acceptance rate) for the OUTBRAID project. The project aims to transform hospital outbreak detection by developing machine learning models that analyse MALDI-TOF mass spectra, complemented by WGS-derived relatedness metrics. Cheers to 2 years funding! 

PhD candidate Zoey Germuskova was awarded the ESCMID Individual Research Grant for her ongoing project on the rare zoonotic pathogen Capnocytophaga and the Global Capnocytophaga Consortium. Go team Capno!

PhD candidate Elisa Sosa secured a SNF mobility grant (formerly Doc.Mobility) for a 6-months research stay with Dr. Gerry Tonkin-Hill at the University of Melbourne, Australia. Yeah mate!

Congratulations to all grantees, well done! 

This month, we are delighted to welcome several new members to the AMR group. It is always exciting to see our team grow, and we look forward to the energy and ideas each of them brings to our research.

Niloofar joins us as a visiting PhD student from Milan. She will be working on the Acinetobacter project, with a focus on Nanopore sequencing and plasmid analysis. We are very much looking forward to her contributions to our genomic investigations.

Luis, a visiting PhD student from Madrid, will be contributing his expertise in Artificial Intelligence and MALDI-TOF–based analyses. We are excited about the new perspectives he brings to the group.

We also welcome Dilaksa and Brenden, who are starting their BSc thesis projects on an AMR app. We look forward to supporting them as they develop and expand this important tool.

Finally, Laurent joins us for his BSc thesis project in collaboration with Ashley, working on a 16S-related research project. We are pleased to have him in the team and look forward to the progress of his work.

A very warm welcome to all of you, we wish you a great start and an inspiring and productive time in the AMR group!