Torsten Seemann

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

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 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.

This paper compares strict and soft core SNP filtering strategies for bacterial phylogenetics, showing soft cores retain more informative sites and improve phylogenetic accuracy.

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

This paper describes the discovery of a marine sponge-associated mycobacterium closely related to M. tuberculosis, which shares virulence factors but lacks virulence in mice.

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.

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.

This paper develops a machine learning method to accurately attribute Legionella pneumophila outbreaks to environmental sources using genomic data, outperforming traditional phylogenetic approaches.

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

This study investigates discordant sequence data in SARS-CoV-2 whole genome sequencing to improve bioinformatic quality standards and surveillance practices.

This paper develops and validates tbtAMR, a bioinformatics tool for predicting antimicrobial susceptibility from Mycobacterium tuberculosis genomic data, accredited to ISO standards for clinical use.

This study identifies genome degradation and convergent mutations in Staphylococcus aureus during severe infections, linking them to adaptation and clinical outcomes.

The paper systematically evaluates key parameters affecting SNP-based transmission inference of MDROs, finding that using a closely-related reference genome and sliding-window analysis improves accuracy.

The paper presents complete microbial genomes for public health in Australia and the Southwest Pacific to enhance global genomic resources and support regional surveillance.

The paper analyzes genomic evolution in persistent Staphylococcus aureus bacteraemia, identifying a molecular signature with low mutation frequency and high non-silent mutations.

RM-seq detects and quantifies antibiotic resistance mutations in bacterial populations with high sensitivity and accuracy.

The paper analyzes the genomic epidemiology of VREfm in Victoria, Australia, finding that vanA-VREfm is associated with multiple STs and clonal transmission within hospitals, while vanB-VREfm is widespread and disseminated across institutions.

This study combines real-time genomic and epidemiological analysis to identify and manage KPC-producing Enterobacteriaceae outbreaks, revealing transmission networks and informing infection control.

The paper provides best practice data life cycle approaches for life sciences researchers focusing on omics datasets and computational data analysis.

This study reconstructs genomes of drug-resistant bacteria from human faeces using metagenomic sequencing and self-organising maps, demonstrating the potential for culture-independent pathogen analysis.

This study compares six MLST software tools using real and simulated data, evaluating their accuracy, performance on outbreak datasets, contamination impact, and computational requirements.

The paper develops a TaqMan qPCR assay for specific and rapid detection of M. chimaera DNA in clinical and environmental samples, showing higher sensitivity than culture methods.

The paper refutes claims about the essentiality of specific amino acid residues in the WalK sensor kinase of Staphylococcus aureus by showing that observed phenotypes may arise from secondary mutations rather than the intended single amino acid substitutions.

NGMASTER enables in silico NG-MAST analysis of Neisseria gonorrhoeae genomes, comparing results with prior epidemiological studies.

SNP-sites efficiently extracts SNPs from large multi-FASTA alignments using minimal resources, enabling scalable analysis on modest hardware.