Jacqueline A. Keane

This study shows that colistin resistance in K. pneumoniae modifies LPS, leading to different inflammatory responses in host cells.

Mykrobe k-mer panel genotypes Salmonella Typhi lineages, antimicrobial resistance (AMR) markers and plasmids from Illumina or nanopore reads, matching mapping-based lineage calls for 99.8% of genomes.

The paper introduces TyphiNET, a dashboard for exploring Typhi genomics data to support public health decisions on antimicrobial resistance and vaccine implementation.

The paper tests PCR enzymes for NGS library amplification, finding three that perform well for short reads and one that is best for long fragments.

The paper introduces Pathogenwatch, a tool for genomic surveillance of Salmonella Typhi, enabling AMR prediction and population-level risk assessment through global data sharing.

Krocus predicts bacterial sequence types directly from uncorrected long reads, providing results in minutes with high accuracy.

SeroBA predicts Streptococcus pneumoniae serotypes from whole genome sequencing data with high concordance and scalability.

PlasmidTron identifies mobile genetic elements linked to phenotypes by analyzing short read WGS data and phenotypic metadata from bacterial populations.

ARIBA rapidly identifies antimicrobial resistance genes and SNPs from sequencing reads, outperforming existing tools on bacterial datasets.

This study compares six MLST software tools using real and simulated data, evaluating their accuracy, performance on outbreak datasets, contamination impact, and computational requirements.

This paper introduces a high-throughput pipeline for bacterial genome assembly and improvement, demonstrating robust performance across diverse datasets and achieving high gene completeness.

SNP-sites efficiently extracts SNPs from large multi-FASTA alignments using minimal resources, enabling scalable analysis on modest hardware.