A. Egli

A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities

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.

Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans

This study shows type IV-A3 CRISPR-Cas systems use host adaptation machinery to update their CRISPR arrays and interfere with plasmid and phage transfer, supporting their role in plasmid competition.

Ancient methicillin-resistant Staphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection

The paper characterizes ancient MRSA isolates from 1965-1987 and compares them to modern isolates, identifying novel sequence types and lineage dynamics.

Phage Paride hijacks bacterial stress responses to kill dormant, antibiotic-tolerant cells

This paper identifies a phage, Paride, that kills dormant, antibiotic-tolerant bacterial cells by hijacking stress responses that also confer antibiotic tolerance.

Automatic discrimination of species within the Enterobacter cloacae complex using MALDI-TOF Mass Spectrometry and supervised algorithms

This paper develops machine learning models using MALDI-TOF MS data to accurately differentiate species within the Enterobacter cloacae complex.

A rationally designed oral vaccine induces Immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants

This paper shows that an oral vaccine inducing IgA in mice can direct Salmonella to evolve into less virulent variants with shorter O-antigens.

Real-time respiration changes as a viability indicator for rapid antibiotic susceptibility testing in a microfluidic chamber array

This paper develops a microfluidic platform that measures antibiotic susceptibility by tracking real-time respiration changes in bacterial cultures within 2-3 hours.

Evolution of Antibiotic Tolerance Shapes Resistance Development in Chronic Pseudomonas aeruginosa Infections

This study shows that antibiotic tolerance evolves before resistance in Pseudomonas aeruginosa, promoting resistance development in chronic infections.

Model-based inference of neutralizing antibody avidities against influenza virus

This paper develops a biophysical model to infer neutralizing antibody avidities from hemagglutination inhibition (HI) assay data and validates it in vaccinated immunocompromised patients.

Direct Antimicrobial Resistance Prediction from clinical MALDI-TOF mass spectra using Machine Learning

This study uses machine learning to predict antimicrobial resistance from MALDI-TOF mass spectra, achieving high AUROC values and showing potential to improve clinical treatment decisions.

Characterising the epidemic spread of Influenza A/H3N2 within a city through phylogenetics

The paper uses genetic sequence data and patient metadata to analyze local influenza transmission dynamics in Basel, Switzerland, finding that temperature trends correlate with transmission and that elderly and school children drive different transmission networks.

High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters

This study maps influenza transmission in a city at high resolution, finding socioeconomic factors like income influence infection patterns and vaccination rates, independent of population density.

Clinical extended-spectrum beta-lactamase antibiotic resistance plasmids have diverse transfer rates and can spread in the absence of antibiotic selection

This study quantifies the conjugative transfer dynamics of ESBL plasmids in vitro and in vivo, showing variation in transfer efficiency and potential for predicting plasmid spread.

Evolution, geographic spreading, and demographic distribution of Enterovirus D68

This study analyzes the evolution and geographic spread of EV-D68 using genomic data from 2018, revealing distinct subclades and age-related patterns in infection.

Impact of different amino acid substitutions in penicillin-binding protein 3 on beta-lactam susceptibility in Haemophilus influenzae

The paper examines how amino acid substitutions in PBP3 affect beta-lactam resistance in H. influenzae by analyzing clinical isolates and their binding site interactions.