Danielle J. Ingle

StrainSpy fits zero-inflated beta mixed models to containment ANI, reaching >98% simulated sensitivity versus ~79% for logistic regression and detecting colorectal-cancer E. coli strain shifts.

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.

The paper benchmarks six long-read simulators against Oxford Nanopore WGS data, finding PBSIM3 best reproduces read-level properties but none capture all error features.

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.

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.

The paper benchmarks 44 tools for plasmidome reconstruction from short-read assemblies in Klebsiella pneumoniae, finding PlaScope and MOB-suite as top performers.

The paper introduces TyphiNET, a dashboard for exploring Typhi genomics data to support public health decisions on antimicrobial resistance and vaccine implementation.

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

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

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

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

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.

GeneMates identifies horizontal gene co-transfer in bacteria using WGS data and controls for population structure to avoid spurious associations.