Susan A. Ballard

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.

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.

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.

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.

Persistence of rare Salmonella Typhi genotypes susceptible to first-line antibiotics in the remote islands of Samoa

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

Proficiency Testing for bacterial whole genome sequencing in assuring the quality of microbiology diagnostics in clinical and public health laboratories

This study evaluates a pilot proficiency testing program for bacterial whole genome sequencing in clinical and public health labs, showing labs can generate and analyze high-quality data using diverse bioinformatics tools.

Complete microbial genomes for public health in Australia and Southwest Pacific

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 changing landscape of VREfm in Victoria, Australia: a state-wide genomic snapshot

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.

Real-time genomic and epidemiological investigation of a multi-institution outbreak of KPC-producing Enterobacteriaceae: a translational study

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

Genome reconstruction and characterisation of extensively drug-resistant bacterial pathogens through direct metagenomic sequencing of human faeces

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.