Adrian Egli

The paper evaluates antimicrobial peptide prediction tools and proposes a standardized evaluation framework to improve comparability and reproducibility.

The paper develops a rules-based classifier to predict ciprofloxacin resistance in Klebsiella pneumoniae from genotype data and demonstrates its global distribution association with quinolone consumption.

The paper creates a synthetic MALDI-TOF MS atlas to improve microbial classification across hospitals by addressing dataset fragmentation and variability.

The paper develops a machine learning model to detect pOXA-48-carrying Enterobacterales using MALDI-TOF MS spectra, achieving high accuracy across different cohorts.

This study identifies how the intestinal microbiota drives the evolution of pathoadaptive traits in ESBL E. coli through adhesion and biofilm formation.

The paper develops a machine learning pipeline using MALDI-TOF mass spectrometry data to predict antifungal resistance and identify biomarkers, achieving high performance across multiple yeast species and drug combinations.

This study evaluates cryopreservation methods for stool samples to maintain viable microbiota, finding that simple methods like glycerol preservation and snap-freezing are as effective as more complex protocols.

This study investigates how ecological interactions influence the growth of antibiotic-resistant E. coli strains in human gut microbiomes, finding that strain-specific factors and competitive interactions drive their success.

The paper maps E. coli capsule serotypes using genomic data, identifies novel K-types, and develops an in silico serotyping tool applicable to diverse E. coli genomes.

The paper identifies bacterial DNA remnants in blood immune cells of CRC and IBD patients, suggesting microbial translocation via intestinal barrier defects.

This study investigates resistance mechanisms to ceftazidime-avibactam and meropenem in Pseudomonas aeruginosa using multi-omics profiling and identifies strain-specific and common genetic factors associated with resistance.

This study tracks Legionella pneumophila in a building's water system over 25 years, finding all isolates belong to ST45 and show limited genetic diversity despite repeated decontamination efforts.

The paper completes the BASEL phage collection by overcoming host limitations to isolate new phages, revealing insights into viral host recognition and bacterial immunity.

This paper evaluates methods for sequencing bacterial STI genomes from clinical swabs, finding that target enrichment with a pan-genome panel is the most effective approach.

This paper reports whole genome sequences of Chlamydia trachomatis from Argentina and Finland, identifying a novel ompA-genotype L4 clade and a non-LGV strain associated with anorectal proctitis.

This paper reclassifies SHV β-lactamase alleles in K. pneumoniae genomes based on mutations, improving genotype-phenotype understanding and updating the Kleborate tool.

This paper evaluates a GPT-4-based agent for detecting antimicrobial resistance mechanisms in Gram-negative bacteria, finding it less accurate and specific than human experts.

This paper introduces a nanopore sequencing workflow for high-quality, full-length 16S rDNA amplicons to identify bacterial isolates and profile microbial communities, showing high agreement with MALDI-TOF and strong correlation with Illumina sequencing.

The paper compares sequencing and assembly methods' impact on plasmid and chromosomal phylogenies and horizontal gene transfer inference in E. coli.

The paper improves antimicrobial resistance prediction using MALDI-TOF MS by incorporating phylogenetic structure through hierarchical clustering, increasing average precision for specific resistance predictions.

The paper uses single molecule sequencing to analyze genomic diversity of carbapenemase-producing bacteria and identifies patterns of carbapenemase movement and recombination.