Benjamin P. Howden

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.

A synthetic MALDI-TOF MS atlas for microbial classification across hospitals

The paper creates a synthetic MALDI-TOF MS atlas to improve microbial classification across hospitals by addressing dataset fragmentation and variability.

Loss of GdpP function in Staphylococcus aureus confers β-lactam-specific antibiotic tolerance and promotes invasive infection

This study shows that loss of GdpP function in Staphylococcus aureus leads to β-lactam antibiotic tolerance and increases mortality in infections, highlighting its clinical relevance in treatment failure.

Antifungal resistance mechanisms and nosocomial transmission of Nakaseomyces glabratus: genomic investigation and observational study in Melbourne, Australia

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

Incremental AMR acquisition driving successive genotype replacements and the rise of extensively drug resistant (XDR) Shigella sonnei in Australia over 20 years.

This study tracks the rise of extensively drug-resistant Shigella sonnei in Australia over 20 years, linking genotype changes to antimicrobial resistance and public health threats.

Flex-It: A global standardised genotyping framework for Shigella flexneri

Flex-It is a genotyping framework for S. flexneri that rapidly characterizes genotypes and resistance determinants from sequencing data, enabling standardized surveillance of its population structure and antimicrobial resistance.

Integrated multi-omics reveals coordinated Staphylococcus aureus metabolic, iron transport and stress responses to human serum

This study integrates multi-omic data from Staphylococcus aureus exposed to human serum to identify genetic factors critical for survival, revealing interconnected metabolic, iron transport, and stress response mechanisms.

Extensive endemic transmission of multidrug resistant Mycobacterium tuberculosis in Bhutan: A retrospective genomic-epidemiological study

This study uses genomic data to show that most multidrug-resistant tuberculosis in Bhutan comes from local transmission, forming a large, recent endemic cluster.

A Practical Resource for Multi-Omics Data Integration in Microbial Systems

This paper introduces an R-based workflow for integrating microbial multi-omics data, enabling analysis of transcriptomic, proteomic, and metabolomic datasets and generating pathway-level insights.

Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi

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.

Comprehensive public health surveillance identifies novel human cryptosporidiosis subtypes and genetic diversity associated with swimming pool outbreaks in Australia, Victoria (2018-2024)

This study identifies novel Cryptosporidium subtypes and genetic diversity linked to swimming pool outbreaks in Victoria, Australia, using molecular surveillance and epidemiological data.

Exploring use of ozone nanobubbles for removal of cyanobacteria and co-occurring antimicrobial resistance genes in water supply and reuse systems

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.

Population structure and antimicrobial resistance of Corynebacterium diphtheriae in Victoria, Australia

This study analyzes the population structure and antimicrobial resistance of C. diphtheriae isolates from Victoria, Australia, revealing genetic diversity and multidrug resistance in contemporary isolates.

Stability and Processing Impacts on Faecal Microbiota Transplant Products: An Integrated Metagenomic-Culturomic Analysis

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.

Autocycler: long-read consensus assembly for bacterial genomes

Autocycler improves bacterial genome assembly accuracy by combining multiple long-read assemblies without user input, outperforming existing tools in error reduction and structural accuracy.

Regulation of airway fumarate by host and pathogen promotes S. aureus pneumonia

This study shows that fumarate, regulated by host and pathogen, limits S. aureus growth by blocking metabolic pathways, while FumC enables adaptation through fumarate degradation and utilization.

Uncovering bacterial pseudaminylation with pan-specific antibody tools

This study develops pan-specific monoclonal antibodies to detect pseudaminic acids in bacteria, enabling deeper glycoproteomic analysis and improved phagocytosis of multidrug-resistant strains.

Simple sequence repeats power Staphylococcus aureus adaptation

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.

Transposon-directed insertion-site sequencing (TraDIS) analysis of Enterococcus faecium using nanopore sequencing and a WebAssembly analysis platform

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

High-throughput method rapidly characterizes hundreds of novel antibiotic resistance mutations

This paper introduces QMS-Seq, a high-throughput method to identify antibiotic resistance mutations in E. coli, revealing distinct mutation patterns for multi-drug and antibiotic-specific resistance.

Genomic epidemiology and phenotypic characterisation of Salmonella entericaserovar Panama in Victoria, Australia

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.

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.

Distinct adaptation and epidemiological success of different genotypes within Salmonella enterica serovar Dublin

This study analyzes the genomic and epidemiological differences between two Salmonella Dublin lineages, revealing distinct adaptations that influence their success in different regions.

Bridging genomic gaps: A versatile SARS-CoV-2 benchmark dataset for adaptive laboratory workflows

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.

Global diversity and evolution of Salmonella Panama, an understudied serovar causing gastrointestinal and invasive disease worldwide: a genomic epidemiology study

This study analyzes 836 Salmonella Panama genomes to reveal population structure, antimicrobial resistance, and genetic markers of invasiveness across global regions.

High performance Legionella pneumophila source attribution using genomics-based machine learning classification

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

High performance enrichment-based genome sequencing to support the investigation of hepatitis A virus outbreaks

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

Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance

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

Bringing TB genomics to the clinic: A comprehensive pipeline to predict antimicrobial susceptibility from genomic data, validated and accredited to ISO standards.

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.

Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa

This study analyzes spatial-temporal and phylogenetic data from typhoid fever cases in Samoa to identify transmission patterns and the role of asymptomatic carriers.