Vitali Sintchenko

COSMOS: integrated vector-pathogen metagenomics for mosquito-borne disease

COSMOS integrates vector-pathogen metagenomics to monitor mosquito-borne diseases, detecting pathogens and mosquito communities in field samples with high accuracy.

Proteolytic control of the SARS-CoV-2 furin cleavage site defines the phenotypic evolution from the pandemic to endemic state

The paper shows how SARS-CoV-2 variants, particularly Omicron, evolved proteolytic controls at the Spike furin cleavage site to enhance transmission while reducing lower respiratory tract pathogenicity.

A mobile ESX type VII secretion system enhances intracellular persistence in globally distributed Mycobacterium abscessus

This study identifies a novel plasmid-borne ESX type VII secretion system in M. abscessus that enhances intracellular survival in macrophages.

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.

A laboratory framework for ongoing optimisation of amplification based genomic surveillance programs

This study develops a framework to optimize sequencing efficiency for genomic surveillance by adjusting primer pooling and sets based on evolving viral populations.

Genomic epidemiology and multilevel genome typing of Australian Salmonella enterica serovar Enteritidis

This study uses multilevel genome typing to analyze Australian Salmonella Enteritidis isolates, finding strong epidemiological links to Asian strains and a local outbreak linked to European isolates.

MGTdb: A web service and database for studying the global and local genomic epidemiology of bacterial pathogens

MGTdb provides a web service for assigning and analyzing multilevel genome types of bacterial isolates, supporting epidemiological studies of Salmonella and Vibrio species.

Elucidation of global and local genomic epidemiology of Salmonella enterica Enteritidis through multilevel genome typing

This study develops a multilevel genome typing method for Salmonella Enteritidis and analyzes 26,670 genomes to reveal global and local genomic epidemiology, including multidrug resistance and outbreak patterns.

Whole genome sequencing based differentiation between re-infection and relapse in Indian patients with tuberculosis recurrence, with and without HIV co-infection

This study uses whole genome sequencing to differentiate between TB relapse and re-infection in HIV-positive and negative patients, finding 95% relapse in HIV-negative and 75% re-infection in HIV-positive cases.

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.

GenomegaMap: within-species genome-wide dN/dS estimation from over 10,000 genomes

GenomegaMap estimates genome-wide dN/dS ratios across 10,209 tuberculosis genomes to identify selection pressures shaping the pathogen's evolution.

Genome Sequencing Links Persistent Outbreak Of Legionellosis In Sydney To An Emerging Clone Of Legionella pneumophila ST211

Genome sequencing of Legionella pneumophila isolates from a Sydney outbreak identified an emerging ST211 clone linked to environmental sources and a unique T4ASS element.