Louise M. Judd

This study identifies a nosocomial transmission cluster of fluconazole-resistant Nakaseomyces glabratus and novel resistance-associated variants in a Melbourne hospital.

This study characterizes microbial communities in southeastern Australian montane fens, revealing high diversity and unique taxa not found in other environments.

The paper analyzes bacterial diversity and strain dynamics in the infant respiratory microbiome using whole genome sequencing and metagenomics, revealing age-dependent shifts in dominant taxa and expanding reference genomes for airway microbes.

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.

This study evaluates ozone nanobubbles for removing cyanobacteria and antimicrobial resistance genes in water systems, showing improved performance over conventional ozonation in drinking water but lower efficiency in treated wastewater.

This study evaluates the stability and viability of FMT products using metagenomic and culturomic analyses, showing high donor consistency and geographic specificity of gut microbiomes.

The paper isolates soil bacteria using diffusion chambers, screens for antibiotic activity, and combines mass spectrometry and genomics to identify known and novel antibiotics from Australian soil samples.

This study identifies simple sequence repeats (SSRs) as key drivers of genetic heterogeneity and rapid adaptation in Staphylococcus aureus through loss-of-function mutations and phase-variable evolution.

The paper develops a TraDIS platform for Enterococcus faecium using nanopore sequencing and a WebAssembly tool to study vancomycin resistance and persistence.

Amira detects AMR genes directly from long reads using gene-space de Bruijn graphs, achieving high recall and accuracy compared to assembly-based methods.

This study evaluates variant calling from bacterial genome assemblies versus read-based methods, finding that assembly-based approaches require error-free assemblies to achieve high accuracy.

This paper reports the complete genome of Candidatus Paracoxiella cheracis, revealing insights into its pathogenesis and phylogeny within the Coxiellaceae family.

The study tracks genomic changes in wMel Wolbachia over six years in three Aedes aegypti populations and finds minimal evolution, supporting its stability as a biocontrol agent.

This study identifies cyclic lipodepsipeptides as the molecular basis of haemolytic activity in Chromobacterium haemolyticum and shows their role in biofilm formation and swarming.

This paper demonstrates that CRISPR-Cas9 enrichment combined with Oxford Nanopore sequencing improves detection of AMR genes and MLST in patient samples compared to unenriched sequencing.

This study characterizes the genomic epidemiology and antimicrobial resistance of Salmonella enterica serovar Panama in Victoria, Australia, identifying two lineages and reporting the first case of plasmid-mediated colistin resistance.

This study benchmarks variant callers on bacterial nanopore data, finding deep learning tools outperform traditional methods and Illumina in accuracy and efficiency.

Roughly 25× short-read depth polishes nearly all residual errors in Nanopore-only bacterial assemblies; new '--careful' modes in Pypolca and Polypolish largely avoid introducing low-depth errors.

The paper analyzes the genetic diversity and functionality of rmpADC variants in Klebsiella pneumoniae to understand their role in virulence and antimicrobial resistance.

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

This paper develops a benchmark dataset for SARS-CoV-2 amplicon sequencing to improve genomic surveillance in resource-constrained labs, finding that basecaller choice has minimal impact on consensus quality.

This paper identifies a novel chlamydial species infecting photosynthetic dinoflagellates, expanding the known host range of chlamydiae and suggesting potential interactions with chloroplasts.

This paper introduces a hybrid capture enrichment assay for whole genome sequencing of HAV, improving sensitivity and enabling outbreak investigation.

This paper introduces RGStraP, a tool to infer genetic population structure from RNAseq data and shows it can control for population structure in gene expression analyses.

Bactabolize generates strain-specific bacterial metabolic models and growth predictions, outperforming existing tools for Klebsiella pneumoniae.

This study evaluates ONT-only assemblies for genomic surveillance of Klebsiella pneumoniae, showing reliable MLST, K type, and AMR detection but challenges in cluster detection.

The paper identifies a plasmid (Plasmid A) that transmitted four times into different Klebsiella lineages, causing 50% of ESBL episodes and persisting for 3-6 years, contributing to 21% of ESBL+ infections.

Kaptive 2.0 updates capsule and LPS locus typing for Klebsiella pneumoniae by adding novel sequences and improving O2 antigen prediction, enabling better surveillance and control strategies.

Trycycler improves bacterial genome assemblies by combining multiple long-read assemblies, reducing errors and improving accuracy when followed by polishing with Medaka and Pilon.

This study compares Oxford Nanopore ligation and rapid library preparation methods for bacterial genome sequencing, finding that rapid methods better recover small plasmids.