Anna E. Sheppard

Lineage-Specific Evolution, Structural Diversity, and Activity of R2 Retrotransposons in Animals

This study expands the known distribution of R2 retrotransposons across animal taxa, identifies new avian candidates, and reveals lineage-specific structural and functional diversity.

Characterisation of vaginal Lactobacillus isolates from South African women towards the development of a biotherapeutic to optimise the vaginal microbiome

The paper characterizes vaginal Lactobacillus isolates from South African women to identify biotherapeutic candidates that can optimize the vaginal microbiome and reduce HIV risk.

Understanding the population structure of Moraxella catarrhalis using core genome multilocus sequence typing (cgMLST) and a life identification number (LIN) code classification system

The paper develops a cgMLST scheme and LIN code system to classify Moraxella catarrhalis lineages, revealing two divergent seroresistant and serosensitive lineages with distinct genetic and virulence characteristics.

Staphylococcus aureus adopts revertible intracellular viable-but-non-culturable phenotypes in chronic osteocyte infections

This study shows Staphylococcus aureus can enter a viable-but-non-culturable state within osteocytes, escape, and revert to active growth, explaining culture-negative but PCR-positive osteomyelitis.

Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies

Hybracter improves bacterial genome assembly accuracy and speed, outperforming existing tools in hybrid and long-read-only modes, especially for small plasmids.

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

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.

TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data

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

Severe infections emerge from the microbiome by adaptive evolution

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