A5020306115- Escherichia coli research studies
- Antibiotic Resistance in Bacteria
- Reproductive tract infections research
- Bacterial Identification and Susceptibility Testing
- Plant and fungal interactions
- Ruminant Nutrition and Digestive Physiology
- Antimicrobial Resistance in Staphylococcus
- Plant Virus Research Studies
- Mycobacterium research and diagnosis
- Urinary Tract Infections Management
- Forensic and Genetic Research
- Antibiotics Pharmacokinetics and Efficacy
- Genomics and Phylogenetic Studies
- Plant Pathogenic Bacteria Studies
- Gut microbiota and health
- Bacteriophages and microbial interactions
- Rabies epidemiology and control
- Plant-Microbe Interactions and Immunity
- Cell Image Analysis Techniques
- Bacterial biofilms and quorum sensing
- Neonatal and Maternal Infections
- Microbial infections and disease research
- Diet, Metabolism, and Disease
- Yersinia bacterium, plague, ectoparasites research
- Clostridium difficile and Clostridium perfringens research
Institute of Environmental Science and Research
2021-2025
The University of Queensland
2019-2024
University of the Sunshine Coast
2021-2023
AgriBio
2023
Peter Doherty Institute
2021
The University of Melbourne
2021
Cardiff University
2021
UNSW Sydney
2021
Escherichia coli sequence types 131 (ST131) and 1193 are multidrug-resistant extraintestinal pathogens that have recently spread epidemically among humans occasionally isolated from companion animals. This study characterized a nationwide collection of fluoroquinolone-resistant (FQ R ) E. isolates infections in Australian cats dogs. For this, 59 cat dog FQ clinical (representing 6.9% an 855-isolate collection) underwent PCR-based phylotyping whole-genome sequencing (WGS). Isolates...
Abstract Objective: To describe an outbreak of sequence type (ST)2 Clostridioides difficile infection (CDI) detected by a recently implemented multilocus (MLST)-based prospective genomic surveillance system using Oxford Nanopore Technologies (ONT) sequencing. Setting: Hemato-oncology ward public tertiary referral centre. Methods: From February 2022, we began prospectively sequencing all C. isolated from inpatients at our institution on the ONT MinION device, with output being MLST....
Chlamydia psittaci is a globally distributed veterinary pathogen with zoonotic potential. Although C. infections have been reported in various hosts, isolation and culture of challenging, hampering efforts to produce contemporary global genomes. This particularly evident the lack avian genomes from Australia New Zealand. In this study, we used culture-independent probe-based whole-genome sequencing expand genome catalogue. Here, provide new two pigeons, six psittacines, novel hosts such as...
Outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) are well described in the neonatal intensive care unit (NICU) setting. Genomics has revolutionized investigation such outbreaks; however, to date, this largely been completed retrospectively and typically relied on short-read platforms. In 2022, our laboratory established a prospective genomic surveillance system using Oxford Nanopore Technologies sequencing for rapid outbreak detection. Herein, system, we describe detection...
Abstract Background Klebsiella variicola has been implicated in neonatal intensive care unit (NICU) outbreaks previously and can be misidentified as pneumoniae . An increased incidence of K. bacteremia on the NICU our institution was notified to infection prevention control (IPC) team May 2024. The four isolates involved displayed wild-type susceptibility, so had not detected via multidrug-resistant organism surveillance. This triggered investigation with a nanopore-based decentralized...
Attaching and effacing pathogens overcome colonisation resistance by competing with metabolically similar organisms for limited resources. Enterohaemorrhagic E. coli (EHEC) utilises the pathogenicity island-encoded Accessory ʟ-arabinose Uptake (Aau) transporter to effectively colonise mouse gut, hypothesised be achieved via an enhanced capacity scavenge ʟ-arabinose. Aau is regulated exclusively in response ʟ-arabinose, but it unclear how this system specifically benefits EHEC vivo. Here, we...
Many hospital laboratories have technical capacity to perform whole-genome sequencing but lack bioinformatic expertise analyse sequence data. Sending isolates reference creates delays that can be highly detrimental outbreak responses. The Wellington Regional Hospital laboratory, which lacks on-site bioinformaticians, implemented real-time nanopore-based genomic surveillance has detected several outbreaks at an early stage. This required off-site analysis, often taking weeks. Solu Genomics, a...
Abstract Virulence and metabolism are often interlinked to control the expression of essential colonisation factors in response host-associated signals. Here, we identified an uncharacterised transporter dietary monosaccharide ʟ-arabinose that is widely encoded by zoonotic pathogen enterohaemorrhagic Escherichia coli (EHEC), required for full competitive fitness mouse gut highly expressed during human infection. Discovery this suggested EHEC strains have enhanced ability scavenge therefore...
Chlamydia psittaci is an avian pathogen with zoonotic potential. In Australia, C. has been well reported as a cause of reproductive loss in mares which subsequently have the source infection and illness some in-contact humans. To date, molecular typing studies describe predominant clonal sequence type (ST)24 strains horse, psittacine, human infections. We sought to assess clonality between ST24 emergence equine comprehensive genomics approach. used culture-independent probe-based metagenomic...
Antibiotic resistance is a significant global public health concern. Uropathogenic Escherichia coli sequence type (ST)131, widely prevalent multidrug-resistant clone, frequently associated with bacteraemia. This study investigates third-generation cephalosporin in bloodstream infections caused by E. ST131. From 2013-2014 blood culture surveillance Wales, 142 ST131 genomes were studied alongside data. All three major clades represented across clade C/H30 predominant (n = 102/142, 71.8%)....
Pantoea stewartii , a plant pathogen, is primarily transmitted through contaminated seeds and insect vectors, with the corn flea beetle ( Chaetocnema pulicaria ) being primary carrier. P. bacterium belonging to order Enterobacterales can lead crop diseases that have significant economic impact worldwide. Due its high potential for spread, classified as quarantine organism in numerous countries. Despite on agriculture, limited genome sequences of hamper understanding pathogenicity host...
Chlamydia pecorum, an obligate intracellular pathogen, causes significant morbidity and mortality in livestock the koala (Phascolarctos cinereus). A variety of C. pecorum gene-centric molecular studies have revealed important observations about infection dynamics genetic diversity both hosts. In contrast to a studies, date, only four complete 16 draft genomes been published. Of those, five are from koalas. Here, using whole-genome sequencing comparative genomics approach, we describe first...
Abstract Objectives Our laboratory began prospective genomic surveillance for healthcare-associated organisms in 2022 using Oxford Nanopore Technologies (ONT) sequencing as a standalone platform. This has permitted the early detection of outbreaks but been insufficient single-nucleotide variant (SNV)-level analysis due to lower read accuracy than Illumina sequencing. study aimed determine whether Haplotype-aware ERRor cOrrection (HERRO) ONT data could permit high-resolution comparison...
Fowl cholera caused by Pasteurella multocida has re-emerged in Australian poultry production since the increasing adoption of free-range systems. Currently, autogenous killed whole-cell vaccines prepared from isolates previously obtained each farm are main preventative measures used. In this study, we use whole-genome sequencing and phylogenomic analysis to investigate outbreak dynamics, as well monitoring comparing variations lipopolysaccharide (LPS) outer core biosynthesis loci vaccine...
At least 300 million urinary tract infections (UTIs) occur annually worldwide. Uropathogenic Escherichia coli (UPEC) are the leading cause of UTIs. The discovery antibiotics has revolutionised modern medicine. Yet, overusing accelerated emergence antimicrobial resistance (AMR), with UPEC driving dissemination AMR globally. Resistance to broad-spectrum like third-generation cephalosporins (3GCs) and fluoroquinolones threatens public health. Extended-spectrum β-lactamase (ESBL)-producing E....
Fluoroquinolone-resistant Escherichia coli sequence type (ST)1193 is a profound, emerging lineage associated with systemic, urinary tract, and neonatal infections. Humans, companion animals, the environment are reservoirs for ST1193, which has been disseminated globally. Following its detection in 2007, ST1193 identified repeatedly amongst fluoroquinolone-resistant clones Australia. However, despite growing importance of only three complete genomes published literature, none from Here we...
Fluoroquinolone-resistant Escherichia coli sequence type (ST)1193 is a profound, emerging lineage associated with systemic, urinary tract and neonatal infections. Humans, companion animals the environment are reservoirs for ST1193, which has been disseminated globally. Following its detection in 2007, ST1193 identified repeatedly amongst fluoroquinolone-resistant clones Australia. However, despite growing importance of only three complete genomes published literature, none from Here we...
Fluoroquinolone-resistant Escherichia coli sequence type (ST)1193 is a profound, emerging lineage associated with systemic, urinary tract, and neonatal infections. Humans, companion animals, the environment are reservoirs for ST1193, which has been disseminated globally. Following its detection in 2007, ST1193 identified repeatedly amongst fluoroquinolone-resistant clones Australia. However, despite growing importance of only three complete genomes published literature, none from Here we...
<title>Abstract</title> Background <italic>Klebsiella variicola</italic> has been implicated in neonatal intensive care unit (NICU) outbreaks previously and can be misidentified as pneumoniae</italic>. An increased incidence of <italic>K. pneumoniae</italic> bacteremia on the NICU our institution was notified to infection prevention control (IPC) team May 2024. The four isolates involved displayed wild-type susceptibility, so had not detected via multi-drug resistant organism surveillance....
Abstract Carbapenems are last-resort antibiotics; however, the spread of plasmid-encoded carbapenemases such as New Delhi metallo-β-lactamase 1 (NDM-1) challenges their effectiveness. The rise NDM-1 has coincided with emergence extensively multidrug resistant (MDR) lineages Escherichia coli ST101. Here we present a comprehensive genomic analysis seven E. ST101 isolates that carry bla gene. We determined complete genomes two and draft five isolates, enabling resolution plasmid context ....
Chlamydia abortus, an obligate intracellular bacterium, is a major causative agent of reproductive loss in ruminants, with zoonotic potential. Though this pathogen primarily known to infect livestock, recent studies have detected and isolated genetically distinct avian strains C. abortus from wild birds globally. Before study, only five genomes were publicly available. Therefore, we performed culture-independent probe-based whole-genome sequencing on clinical swabs positive for obtained...