Derek R. MacFadden

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 evaluates the performance of short-read sequencing for detecting antimicrobial resistance genes in genomes and metagenomes, finding that assembly-based methods require 15X coverage for reliable detection.

This paper introduces a method to rapidly infer antibiotic resistance and susceptibility from bacterial genomes using genomic neighbor typing, achieving high sensitivity and specificity within minutes to hours.