Sandra Reuter

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.

BaGPipe automates bacterial GWAS workflows, improving efficiency and reproducibility by integrating preprocessing, analysis, and visualization in a scalable pipeline.

This paper introduces a decontamination method for long-read metagenomic datasets, identifying and mitigating microbial contaminants in neonatal samples.

This paper evaluates RASE, a neighbor typing method using long-read sequencing, for predicting sequence types and antimicrobial susceptibility of Klebsiella pneumoniae in real time.

This study tracks clonal and plasmid transmission in colistin- and carbapenem-resistant K. pneumoniae using short and long read sequencing, revealing complex plasmid networks and highlighting the need for full-length sequencing to understand resistance spread.

This study evaluates three strain resolution tools on long-read metagenomes, finding TRACS excels in haplotype completeness and efficiency, while Strainy shows high haplotype accuracy.

The paper evaluates GWAS methods for detecting antibiotic resistance in Staphylococcus aureus genomes, finding they identify novel resistance mutations but are less accurate than literature-based approaches.

The paper identifies over 16,000 secreted proteins in Legionella species, revealing their ability to acquire eukaryotic-like genes for intracellular replication in human cells.

The paper compares bacterial genome assembly software for MinION data, finding Canu provides the most accurate assembly while Miniasm is fastest.

Roary builds large-scale prokaryote pan genomes efficiently, identifying core and dispensable accessory genes using a single CPU in under 5 hours.