Fiona S. L. Brinkman

Atypical BlaIR Two-Component System in Pseudomonas aeruginosa Regulates Virulence but not β-Lactam Resistance

This study identifies an atypical BlaIR system, pvmSR, in Pseudomonas aeruginosa that regulates virulence but not β-lactam resistance, using C. elegans as a model.

Analysing antimicrobial resistance mobility patterns using a diverse dataset of over 8000 bacterial species

The paper analyzes antimicrobial resistance gene mobility across 8000 bacterial species, finding that certain resistance mechanisms are more associated with mobile elements than others.

VIRUS-MVP: A framework for comprehensive surveillance of viral mutations and their functional impacts

VIRUS-MVP tracks viral mutations and their functional impacts across multiple viruses, providing tools for analysis and visualization.

AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics

A uniformly processed set of 2,440,377 bacterial and archaeal genomes with search tools and annotations, plus an AI-mined peptide set yielding ATB20, active in a mouse skin infection model.

Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents

This study profiles resistance determinants, virulence factors, and mobile genetic elements in 1273 Enterococcus faecium genomes from UK and Canada, showing habitat-associated gene and MGE patterns and a workflow for AMR surveillance.

Similarities Between Bacterial GAD and Human GAD65: Implications in Gut Mediated Autoimmune Type 1 Diabetes

The paper identifies sequence and motif similarities between bacterial and human GAD65, suggesting a potential link between gut microbiome dysbiosis and T1D via immune cross-reactivity.

Metagenome-Assembled Genome Binning Methods with Short Reads Disproportionately Fail for Plasmids and Genomic Islands

This study shows that short-read MAG binning methods poorly recover plasmids and genomic islands, missing key AMR and VF genes, and recommends using unassembled reads or long-read approaches instead.

The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform

A decentralized open-source web platform lets public health labs run outbreak sequencing pipelines on local compute, keeping data under their own governance while still exchanging results between instances.

Spatiotemporal dynamics of river viruses, bacteria and microeukaryotes

This study examines the spatiotemporal dynamics of riverine microbial communities, including viruses, bacteria, and microeukaryotes, revealing distinct patterns and highlighting the need for holistic analysis.

SNVPhyl: A Single Nucleotide Variant Phylogenomics pipeline for microbial genomic epidemiology

SNVPhyl is a phylogenomics pipeline that identifies SNVs and constructs whole-genome phylogenies from WGS data, showing high sensitivity and specificity in outbreak detection.