Justin O’Grady

The paper investigates how antibiotic resistance affects the MexT regulatory switch in Pseudomonas aeruginosa, leading to phenotypic plasticity in virulence and antibiotic resistance.

This study uses nanopore metagenomic sequencing to analyze the microbiomes of HAP patients, revealing high fungal prevalence and multi-drug-resistant microbes.

This study uses long-read metagenomics to detect Paracoccus yeei in SBP patients, revealing its pathogenicity and antimicrobial resistance profile.

This study characterizes the genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in rural Gambia, identifying novel sequence types and antimicrobial resistance genes.

This study analyzes genomic diversity and antimicrobial resistance in Escherichia coli isolates from non-human primates in the Gambia, identifying novel sequence types and potential human pathogen exchange.

CoronaHiT is a method for high-throughput SARS-CoV-2 genome sequencing that improves coverage and throughput compared to existing protocols.

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.

This study develops a nanopore-based metagenomics pipeline for rapid and accurate diagnosis of bacterial lower respiratory infections, achieving high concordance with culture and fast turnaround time.

Nanopore-only sequencing of GM12878 across 39 MinION flowcells (91.2 Gb) yielded an assembly with NG50 ∼3 Mb; adding 5× ultra-long reads raised NG50 to 6.4 Mbp.