Leah Wendy Roberts

Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype prediction from genotype and global distribution of resistance determinants

The paper develops a rules-based classifier to predict ciprofloxacin resistance in Klebsiella pneumoniae from genotype data and demonstrates its global distribution association with quinolone consumption.

Evaluating Nanopore read trimming and quality filtering in bacterial genomics

The paper benchmarks preprocessing pipelines for Oxford Nanopore reads in bacterial genomics, finding that no single approach optimally balances variant calling and assembly performance across all metrics.

OXA-181 transmission confounded by a stable IncX3 plasmid

This study analyzes the spread of blaOXA-181-producing bacteria in Australia, finding that the IncX3 plasmid is highly stable with minimal genetic variation, suggesting that genomic similarity does not necessarily indicate recent transmission.

Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae

This paper reclassifies SHV β-lactamase alleles in K. pneumoniae genomes based on mutations, improving genotype-phenotype understanding and updating the Kleborate tool.

Applying rearrangement distances to enable plasmid epidemiology with pling

This paper introduces pling, a tool that uses rearrangement distances to cluster plasmids more accurately by accounting for structural changes and avoiding over-clustering caused by transposable elements.

CELEBRIMBOR: Pangenomes from metagenomes

CELEBRIMBOR improves core gene identification in metagenome-assembled genomes by adjusting frequency thresholds based on genome completeness.

Nucleotide-resolution bacterial pan-genomics with reference graphs

This paper introduces a pan-genome graph structure and software tool, pandora, to analyze bacterial genomic variation across multiple isolates with higher SNP recovery and lower error rates than existing methods.

MicroPIPE: An end-to-end solution for high-quality complete bacterial genome construction

MicroPIPE constructs high-quality bacterial genomes using ONT and Illumina sequencing with an automated pipeline.

Strain and lineage-level methylome heterogeneity in the multi-drug resistant pathogenic Escherichia coli ST101 clone

The paper analyzes DNA methylation patterns in seven Escherichia coli ST101 strains to identify methylome diversity linked to mobile genetic elements and their impact on functional differences between nearly identical isolates.

Genomic characterisation and context of the blaNDM-1 carbapenemase in Escherichia coli ST101.

This study characterizes the genomic context of blaNDM-1 in E. coli ST101 isolates using long-read sequencing, revealing two clades with distinct resistance profiles and plasmid-mediated blaNDM-1 carriage mechanisms.

Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei

The paper uses three whole genome sequencing technologies to analyze a carbapenemase-producing Enterobacter hormaechei outbreak, identifying transmission dynamics and plasmid context.