Katie JM Jeffery

OxBreaker: species-agnostic pipeline for the analysis of outbreaks using nanopore sequencing

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.

Genomic epidemiology of Candida auris introduction and outbreaks in the United Kingdom

This study uses genomic data to trace the introduction and transmission of Candida auris in the UK between 2014 and 2019, identifying at least three introductions and multiple transmission events.

Targeting hepatitis B vaccine escape using immunogenetics in Bangladeshi infants

The paper identifies HLA variants associated with HBV vaccine response in Bangladeshi infants and links them to vaccine escape mechanisms.

Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission

Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies

This study optimizes Oxford Nanopore Flowcell usage for hybrid assemblies by reducing sequencing time and cost through washing steps, enabling more isolates per flowcell.

Multiuse patient monitoring equipment as a risk factor for acquisition of Candida auris

The paper identifies multiuse patient monitoring equipment as a risk factor for acquiring Candida auris in a neurological intensive care unit.