Benjamin P. Howden

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

This study characterizes the genomic structure and evolutionary history of Salmonella Typhi in Samoa, revealing dominant rare genotypes with low antimicrobial resistance.

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

This study traces the global spread of Listeria monocytogenes clonal complex 1 (Lm-CC1) through historical data, identifying two waves of expansion linked to livestock trade and cattle farming.

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 uses genomic analysis to assess MDRO transmission within and across hospitals, finding high transmission rates for vanA VRE and linking genomic data with epidemiologic data to evaluate infection control.

The paper identifies extensive diversity in type I restriction modification systems in Staphylococcus epidermidis compared to Staphylococcus aureus, enabling efficient genetic manipulation of clinically relevant strains.

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.

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.

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.