Carlos Reding

OxBreaker is a species-agnostic pipeline for analyzing bacterial and plasmid outbreaks using nanopore sequencing, offering high accuracy and accessibility for real-time genomic surveillance.

The paper shows that fitness estimates based on growth rate are unreliable, revealing that plasmid carriage can be selectively advantageous even when it reduces growth rate.

The paper shows that gene cassettes in an integron, amplified by IS26, confer resistance to amikacin and piperacillin/tazobactam, often leaving meropenem as the last-resort antibiotic.

The paper identifies specific amino acid substitutions in NfsA and NfsB that reduce enzyme activity and cause nitrofurantoin resistance in E. coli, but finds that WGS alone cannot reliably predict resistance due to functional silent mutations and downregulated gene expression.

Hound maps genotype to phenotype in bacterial genomes by de novo assembly, gene detection, and mutation reporting, demonstrating its utility in predicting antibiotic resistance.