Robert A. Petit

This study uses ANI to group S. aureus strains and identifies strain-specific genes in the pangenome by analyzing gene distribution patterns.

The paper develops a coevolution score method to detect coevolving genes in bacterial genomes, finding coordinated gene gain/loss patterns in S. aureus related to antibiotic resistance.

The paper analyzes the agr operon across S. aureus genomes to identify frameshift mutations and their evolutionary patterns, finding over 5% of strains have non-functional agr systems.

This study benchmarks nine bioinformatics tools for detecting AMR genes in shotgun metagenomic data using simulated samples and a custom pipeline.

Bactopia provides a flexible pipeline for analyzing bacterial genomes, including quality control, assembly, and post-processing tools for comparative genomics.

This study tracks USA300 MRSA persistence on multiple body sites post-infection, finding clonal lineages persist up to a year with genetic changes.