Ann Sarah Walker

The paper identifies and masks artefactual variants in SARS-CoV-2 sequencing data to improve the accuracy of within-host diversity and transmission analysis.

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.

This study evaluates Nanopore long-read only genome assembly for clinical Enterobacterales isolates, finding Autocycler with Medaka polishing achieves accuracy comparable to hybrid assemblies.

The paper shows that E. coli phylogeny influences blaTEM-1 expression and co-amoxiclav resistance through lineage-specific regulatory differences.

The paper validates a workflow for detecting antibiotic residues and measuring water chemistry in hospital sink samples, and confirms boric acid preserves microbial and resistome composition for metagenomic sequencing.

This study compares taxonomic and resistome variability between single-timepoint grab and 24H-composite wastewater samples, finding that composites better capture AMR genes and reduce temporal variability.

The paper evaluates metagenomic, 16S rRNA gene, and ultra-plexed PCR-based sequencing methods for taxonomic and AMR gene profiling in polymicrobial samples, finding that AmpliSeq and shotgun metagenomics perform best for resistome profiling.

This paper uses MinHash to rapidly approximate genomic distances and predict ribotypes in Clostridioides difficile genomes, reducing computational demands for transmission analysis.

Flanker clusters gene flanking sequences to identify mobile genetic element patterns associated with antimicrobial resistance genes.

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

The paper analyzes IncF plasmid diversity across environmental and livestock settings using network community analysis, revealing niche-driven partitioning and core gene-defined communities.

GenomegaMap estimates genome-wide dN/dS ratios across 10,209 tuberculosis genomes to identify selection pressures shaping the pathogen's evolution.

The paper develops a metagenomic metric to predict antibiotic resistance in Enterobacterales infections using pooled human faecal samples from LMICs and high-income settings.

This study evaluates SNP calling pipelines' performance on bacterial data, finding that reference genome selection strongly impacts accuracy, with Snippy performing consistently well across diverse genomes.

The paper evaluates methods for detecting human contamination in microbial sequencing data and finds that classification-based methods are most effective, though combining methods improves accuracy for short reads.

This study analyzes the genomic epidemiology of a blaKPC carbapenemase outbreak in Enterobacterales in the UK, revealing genetic plasticity and plasmid dynamics across multiple species and lineages.

This study compares hybrid assemblies of bacterial genomes using Illumina and long-read sequencing technologies, finding that combining ONT and Illumina reads provides high-quality, low-cost genome reconstruction.

This study develops a hybrid protocol combining culture enrichment and plasmid extraction to improve detection of antimicrobial resistance genes in faecal samples.

This paper predicts pyrazinamide resistance in Mycobacterium tuberculosis using machine learning models trained on pncA mutations and structural features, achieving 80.2% sensitivity and 76.9% specificity.

TETyper classifies transposable element variation and genetic contexts from whole-genome sequencing data, revealing high transposition diversity in KPC-associated Tn4401.

Severe S. aureus infections arise from the nasal microbiome through adaptive evolution, with specific mutations enriched in infecting bacteria compared to colonizing ones.

This study traces the evolutionary history of the ST131 E. coli lineage, showing its clonal expansion linked to antibiotic use and plasmid acquisition, with implications for antimicrobial resistance control.