V. Sintchenko

A dissection of the genomic antimicrobial resistance epidemiology of Salmonella Typhimurium

The paper analyzes antimicrobial resistance in Salmonella Typhimurium using genomic data to identify resistant strains and their geographic and host associations.

STECode: an automated virulence barcode generator to aid clinical and public health risk assessment of Shiga toxin-producing Escherichia coli

STECode automates virulence barcode generation for Shiga toxin-producing E. coli to assess pathogenic potential from sequencing data.

Genomic evolution of SARS-CoV-2 variants of concern under in vitro neutralising selection pressure following two doses of the Pfizer-BioNTech BNT162b2 COVID-19 vaccine

This study assesses the neutralizing antibody titres against SARS-CoV-2 variants Delta and Beta post-Pfizer-BioNTech vaccination, finding significant reductions compared to wild-type virus.

TMPRSS2 activation of Omicron lineage Spike glycoprotein is regulated by Collectrin-like domain of ACE2

The paper shows Omicron SARS-CoV-2 lineages rely on ACE2 without TMPRSS2 complexes for entry, due to changes in the ACE2 Collectrin-Like Domain affecting TMPRSS2 activation.

Genomic epidemiology and multilevel genome typing of Bordetella pertussis

This paper introduces a multilevel genome typing system for Bordetella pertussis to improve surveillance and understanding of circulating strains and their public health risks.

Genomic markers of drug resistance in Mycobacterium tuberculosis populations with minority variants

The paper identifies drug-resistant minority variants in Mycobacterium tuberculosis populations and shows their association with mixed strain populations and treatment outcomes.

Can genomics and meteorology predict outbreaks of legionellosis in urban settings?

This study investigates the role of genomics and meteorology in predicting Legionnaires disease outbreaks in urban areas, finding that cgMLST typing is effective for outbreak investigation but weather patterns are not strongly linked to the dominant outbreak clone.

Genomic dissection of the microevolution of Australian epidemic Bordetella pertussis

This study analyzes the genomic and phylogeographic dynamics of B. pertussis in Australia, revealing lineage expansion, selective sweeps, and spatial spread patterns linked to vaccination and transmission.

Improved neutralization of the SARS-CoV-2 Omicron variant after Pfizer-BioNTech BNT162b2 COVID-19 vaccine boosting

This study shows that Pfizer-BioNTech vaccine boosting increases neutralizing antibodies against Omicron, but they are still lower than against the A.2.2 lineage.

SARS-CoV-2 Genome Sequencing Methods Differ In Their Ability To Detect Variants From Low Viral Load Samples

This study compares three SARS-CoV-2 sequencing methods for their ability to detect variants from low viral load samples, finding that ARTIC v3 is most sensitive.

Genomic evaluation of Bordetella spp. originating from Australia

This study evaluates genomic changes in Bordetella spp. from Australia using long-read sequencing to close genomes and assess their relationship with global isolates.

Comparison of library preparation and sequencing depths for direct sequencing of Bordetella pertussis positive samples

This study evaluates WGS library preparation methods for direct sequencing of B. pertussis clinical samples, finding that the Illumina DNA prep kit with deep sequencing detects vaccine antigen variations and macrolide resistance.

REVEALING COVID-19 TRANSMISSION BY SARS-CoV-2 GENOME SEQUENCING AND AGENT BASED MODELLING

The paper uses SARS-CoV-2 genome sequencing and agent-based modeling to estimate local transmission rates during the early stages of the COVID-19 outbreak in New South Wales.

An emergent clade of SARS-CoV-2 linked to returned travellers from Iran

The paper identifies a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand through whole genome sequencing and phylogenetic analysis.

Genomic surveillance enables suitability assessment of Salmonella gene targets used for culture-independent diagnostic testing

The paper assesses the suitability of Salmonella gene targets for PCR-based diagnostic testing using genomic data from 3165 isolates, finding varying levels of nucleotide dissimilarity across targets.