A5020422477- SARS-CoV-2 and COVID-19 Research
- Antibiotic Resistance in Bacteria
- Salmonella and Campylobacter epidemiology
- Reproductive tract infections research
- Antimicrobial Resistance in Staphylococcus
- COVID-19 Clinical Research Studies
- Urinary Tract Infections Management
- Bacterial Identification and Susceptibility Testing
- Viral gastroenteritis research and epidemiology
- Bacterial biofilms and quorum sensing
- Zoonotic diseases and public health
- Vibrio bacteria research studies
- Bacteriophages and microbial interactions
- COVID-19 epidemiological studies
- SARS-CoV-2 detection and testing
- Syphilis Diagnosis and Treatment
- Respiratory viral infections research
- Infection Control and Ventilation
- Prostate Cancer Treatment and Research
- Mycobacterium research and diagnosis
- Genomics and Phylogenetic Studies
- Adolescent Sexual and Reproductive Health
- Escherichia coli research studies
- Dermatology and Skin Diseases
- Long-Term Effects of COVID-19
Peter Doherty Institute
2020-2025
The University of Melbourne
2020-2025
Charles Darwin University
2009-2022
Menzies School of Health Research
2009-2022
Australian National University
2018-2022
Department of Health and Aged Care
2017-2022
Australian Government
2022
ACT Government
2022
Northern Territory Health Services
2022
Royal Darwin Hospital
2022
Abstract Genomics is a cornerstone of modern pathogen epidemiology yet demonstrating transmission in One Health context challenging, as strains circulate and evolve within between diverse hosts environments. To identify phylogenetic linkages better define relevant measures genomic relatedness context, we collated 5471 Escherichia coli genome sequences from Australia originating humans ( n = 2996), wild animals 870), livestock 649), companion 375), environmental sources 292) food 289)...
The Bengal Bay clone (ST772) is a community-associated and multidrug-resistant Staphylococcus aureus lineage first isolated from Bangladesh India in 2004. In this study, we showed that the emerged virulent progenitor circulating on Indian subcontinent. Its subsequent global transmission was associated with travel or family contact region. ST772 progressively acquired specific resistance elements at limited cost to its fitness continues be exported globally, resulting small-scale community...
Chlamydia trachomatis is the world's most prevalent bacterial sexually transmitted infection and leading infectious cause of blindness, yet it one least understood human pathogens, in part due to difficulties vitro culturing lack available tools for genetic manipulation. Genome sequencing has reinvigorated this field, shedding light on contemporary history pathogen. Here, we analyze 563 full genomes, 455 which are novel, show that species comprises two phases, conclude currently circulating...
Salmonella Dublin is a host-adapted, invasive non-typhoidal (iNTS) serovar that causes bloodstream infections in humans and demonstrates increasing prevalence of antimicrobial resistance (AMR). Using global dataset 1,303 genomes, coupled with vitro assays, we examined the evolutionary, resistance, virulence characteristics S . Dublin. Our analysis revealed strong geographic associations between AMR profiles plasmid types, highly resistant isolates confined predominantly to North America,...
Pathogen whole genome sequencing (WGS) is being incorporated into public health surveillance and disease control systems worldwide has the potential to make significant contributions infectious surveillance, outbreak investigation infection prevention control. However, date, there are limited data regarding (i) optimal models for integration of genomic epidemiological investigations (ii) how quantify evaluate impacts resulting from investigations.We developed Genomics in Public HeAlth...
In Australia, cases of shigellosis usually occur in returned travelers from regions endemicity or men who have sex with men. Resistance to multiple antibiotics has significantly increased Shigella sonnei isolates and represents a significant public health concern. We investigate an outbreak multidrug-resistant S. Victoria, Australia. undertook whole-genome sequencing 54 extended-spectrum-beta-lactamase (ESBL)-producing received at the Microbiological Diagnostic Unit Public Health Laboratory...
Respiratory tract infection with SARS-CoV-2 results in varying immunopathology underlying COVID-19. We examine cellular, humoral and cytokine responses covering 382 immune components longitudinal blood respiratory samples from hospitalized COVID-19 patients. SARS-CoV-2-specific IgM, IgG, IgA are detected blood, however, receptor-binding domain (RBD)-specific IgM IgG seroconversion is enhanced specimens. neutralization activity correlates RBD-specific levels. Cytokines/chemokines vary between...
Chlamydia trachomatis causes sexually transmitted infections and the blinding disease trachoma. Current data on C. phylogeny show that there is only a single trachoma-causing clade, which distinct from lineages causing urogenital tract (UGT) lymphogranuloma venerum diseases. Here we report whole-genome sequences of ocular isolates obtained young children with clinical signs trachoma in endemic region northern Australia. The form two fall outside classical lineage, instead being placed within...
Background. In Australia, community-associated methicillin-resistant Staphylococcus aureus (MRSA) lineage sequence type (ST) 93 has rapidly risen to dominance since being described in the early 1990s. We examined 459 ST93 genome sequences from New Zealand, Samoa and Europe investigate evolutionary history of ST93, its emergence Australia subsequent spread overseas. Results. Comparisons with other S. genomes indicate that is an diverging recombinant lineage, comprising segments ST59/ST121 a...
Mutation is one of the most important drivers viral evolution and genome variability, allowing viruses to potentially evade host immune responses develop drug resistance. In context COVID-19, local genomic surveillance circulating virus populations therefore critical. The goals this study were describe distribution different SARS-CoV-2 lineages, assess their differences, infer importation events in Bangladesh. We individually aligned 1965 sequences obtained between April 2020 June 2021...
Salmonella Dublin is a host-adapted, invasive non-typhoidal (iNTS) serovar that causes bloodstream infections in humans and demonstrates increasing prevalence of antimicrobial resistance (AMR). Using global dataset 1,303 genomes, coupled with vitro assays, we examined the evolutionary, resistance, virulence characteristics S . Dublin. Our analysis revealed strong geographic associations between AMR profiles plasmid types, highly resistant isolates confined predominantly to North America,...
We assessed turnaround times in the national Listeria monocytogenes genomic surveillance system Australia before and after decentralized sequencing. Using 1,204 samples collected during 2016-2023, we observed statistically significant reductions median time from sample collection to issuance of report 26 days, despite numbers doubling 2022 2023. During 2016-2018, all jurisdictions referred National Reference Laboratory for sequencing analysis, but as jurisdictional capacity increased, 4...
The knowledge of somatic mutations that arise in penile cancer is limited. We examined the dysregulation components phosphatidylinositol 3-kinase and Ras pathways.Using single stranded conformational analysis direct sequencing we performed mutational PIK3CA, PTEN, HRAS, KRAS, NRAS BRAF genes 28 tumors.We identified missense 11 samples (39%). In PIK3CA gene 8 (29%) were E542K or E545K. HRAS a G12S Q61L mutation found (7%). KRAS contained 1 (3%), change. all grades stages, whereas larger more...
Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of hospital-associated infection, but there growing awareness the emergence multidrug-resistant lineages in community settings around world. One such lineage ST772-MRSA-V, which has disseminated globally and increasingly prevalent India. Here, we present complete genome sequence DAR4145, strain ST772-MRSA-V from India, investigate its genomic characteristics regards to antibiotic resistance virulence factors.Sequencing using...
Typhoid fever is an invasive bacterial disease of humans that disproportionately affects low- and middle-income countries. Antimicrobial resistance (AMR) has been increasingly prevalent in recent decades Salmonella enterica serovar Typhi (S. Typhi), the causative agent typhoid fever, limiting treatment options. In Australia, most cases are imported due to travel regions where endemic. Here, all 116 isolates S. isolated Victoria, between 1 July 2018 30 June 2020, underwent whole-genome...
During the COVID-19 pandemic, phylodynamics and phylogeography have been launched into spotlight as tools to model spread of SARS-CoV-2 virus.In Australia, we relied on genomic epidemiology (and associated derived parameters such viral growth rate, reproductive number, estimated sampling proportion) inform public health policy changes [1].This was possible due high proportion cases sequenced in Australia throughout 2020 2021, where maintained low burdens both deaths.The recent Omicron...
Here we report a single nucleotide polymorphism (SNP) based genotyping method for Klebsiella pneumoniae utilising high-resolution melting (HRM) analysis of fragments within the multilocus sequence typing (MLST) loci. The approach is termed mini-MLST or Minim and it has previously been applied to Streptococcus pyogenes, Staphylococcus aureus Enterococcus faecium. Six SNPs were derived from concatenated MLST sequences on basis maximisation Simpsons Index Diversity (D). DNA incorporating these...
Objectives The objective was to determine the frequency of trachoma genotypes Chlamydia trachomatis- positive urogenital tract (UGT) specimens from remote areas Australian Northern Territory (NT). Setting setting analysis remnants C. trachomatis primarily UGT obtained in course clinical practice. were two pathology service providers. Participants From 3356 collected during May 2012–April 2013, 439 selected for genotyping, with a focus on postpubescent patients, Aboriginal communities where...