A5086389449- Antibiotic Resistance in Bacteria
- Genomics and Phylogenetic Studies
- Bacterial Identification and Susceptibility Testing
- Mycobacterium research and diagnosis
- Oral microbiology and periodontitis research
- Enterobacteriaceae and Cronobacter Research
- Antimicrobial Resistance in Staphylococcus
- Legionella and Acanthamoeba research
- Microbial Community Ecology and Physiology
- Probiotics and Fermented Foods
- Infectious Diseases and Mycology
- Reproductive Health and Contraception
- Escherichia coli research studies
- Listeria monocytogenes in Food Safety
- Plant Pathogenic Bacteria Studies
- Neurogenesis and neuroplasticity mechanisms
- Bacterial biofilms and quorum sensing
- Salmonella and Campylobacter epidemiology
- Evolution and Paleontology Studies
- Cancer therapeutics and mechanisms
- Bacterial Genetics and Biotechnology
- Gut microbiota and health
- Animal Ecology and Behavior Studies
- Polymer Nanocomposite Synthesis and Irradiation
- Glioma Diagnosis and Treatment
Peter Doherty Institute
2015-2020
The University of Melbourne
2013-2020
Sumitomo Rubber Industries (Japan)
2016
Tokyo Medical University
2013
RMIT University
2007
Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use whole genome sequencing (WGS) these purposes poses significant challenges. Here we present SRST2, a read mapping-based tool fast accurate detection genes, alleles multi-locus sequence types (MLST) from WGS data. Using >900 genomes common pathogens, show SRST2 highly outperforms assembly-based methods in terms both gene allele assignment. We include...
ABSTRACT Whole-genome sequencing (WGS) has emerged as a powerful tool for comparing bacterial isolates in outbreak detection and investigation. Here we demonstrate that WGS performed prospectively national epidemiologic surveillance of Listeria monocytogenes the capacity to be superior our current approaches using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), variable-number tandem-repeat analysis (MLVA), binary typing, serotyping. Initially 423 L. underwent...
Until recently, Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae were rarely identified in Australia. Following an increase the number of incident cases across state Victoria, we undertook a real-time combined genomic and epidemiological investigation. The scope this study included identifying risk factors routes transmission, investigating utility genomics to enhance traditional field epidemiology for informing management established widespread outbreaks.All...
Mutations in the beta-subunit of bacterial RNA polymerase (RpoB) cause resistance to rifampin (Rifr), a critical antibiotic for treatment multidrug-resistant Staphylococcus aureus. In vitro studies have shown that RpoB mutations confer decreased susceptibility other antibiotics, but clinical relevance is unknown. Here, by analyzing 7,099 S. aureus genomes, we demonstrate most prevalent promote clinically relevant phenotypic plasticity resulting emergence stable lineages, associated with...
Enterococcus faecium is a major nosocomial pathogen causing significant morbidity and mortality worldwide. Assessment of E. using MLST to understand the spread this organism an important component hospital infection control measures. Recent studies, however, suggest that might be inadequate for surveillance. To use WGS characterize recently identified vancomycin-resistant (VREfm) isolates non-typeable by appear multi-jurisdictional outbreak in Australia. Illumina NextSeq Pacific Biosciences...
Since 2000, cases of the neglected tropical disease Buruli ulcer, caused by infection with Mycobacterium ulcerans, have increased 100-fold around Melbourne (population 4.4 million), capital Victoria, in temperate southeastern Australia. The reasons for this increase are unclear. Here, we used whole-genome sequence comparisons 178 M. ulcerans isolates obtained primarily from human clinical specimens, spanning 70 years, to model population dynamics pathogen region. Using phylogeographic and...
Multilocus sequence typing analysis of Streptococcus uberis has identified a cluster isolates associated with clinical and subclinical mastitis cows low somatic cell counts in their milk. Specific groups genotypes (global clonal complex [GCC] type 5s [ST5s] GCC ST143s) were highly (P = 0.006) may represent lineage virulent isolates, whereas belonging to ST86 low-cell-count cows. This study has, for the first time, demonstrated occurrence identical types (ST60 ST184) between different...
Mutation acquisition is a major mechanism of bacterial antibiotic resistance that remains insufficiently characterised. Here we present RM-seq, new amplicon-based deep sequencing workflow based on molecular barcoding technique adapted from Low Error Amplicon (LEA-seq). RM-seq allows detection and functional assessment mutational at high throughput mixed populations. The sensitive very low-frequency resistant sub-populations permits characterisation antibiotic-linked repertoires in vitro rare...
Abstract Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use whole genome sequencing (WGS) these purposes poses significant challenges. Here we present SRST2, a read mapping-based tool fast accurate detection genes, alleles multi-locus sequence types (MLST) from WGS data. Using >900 genomes common pathogens, show SRST2 highly outperforms assembly-based methods in terms both gene allele assignment....
Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health laboratory activities. Here, we announce a BioProject (PRJNA556438) dedicated to sharing complete chosen represent range pathogenic bacteria with regional importance Australia and Southwest Pacific; enriching catalogue globally available while providing valuable strains microbiology laboratories. In this first step, present 26 high-quality bacterial genomes....
ABSTRACT Public health agencies are increasingly relying on genomics during Legionnaires' disease investigations. However, the causative bacterium ( Legionella pneumophila ) has an unusual population structure, with extreme temporal and spatial genome sequence conservation. Furthermore, outbreaks can be caused by multiple L. genotypes in a single source. These factors confound cluster identification using standard phylogenomic methods. Here, we show that statistical learning approach based...
Plasmid vectors based on bacteriophage integrases are important tools in molecular microbiology for the introduction of foreign DNA, especially into bacterial species where other systems genetic manipulation limited. Site specific catalyze recombination between phage and attachment sites (attP attB, respectively) best studied actinomycetes serine from Streptomyces bacteriophages ΦC31 ΦBT1. As this reaction is unidirectional highly stable, containing integrase have been used a number...
ABSTRACT Acquired mutations are a major mechanism of bacterial antibiotic resistance generation and dissemination, can arise during treatment infections. Early detection sub-populations resistant bacteria harbouring defined could prevent inappropriate prescription. Here we present RM-seq, new amplicon-based DNA sequencing workflow based on single molecule barcoding coupled with deep-sequencing that enables the high-throughput characterisation sensitive from complex mixed populations...
Abstract Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete pathogen strains regional importance to Southwest Pacific and Australia. These enrich catalogue globally available while providing valuable labs. Announcement Whole-genome sequence (WGS) data is important in microbiology (1–4). The can be used replicate many basic bacterial sub-typing approaches, as well support...
ABSTRACT Background Until recently, KPC-producing Enterobacteriaceae were rarely identified in Australia. Following an increase the number of incident cases across state Victoria, we undertook a real-time combined genomic and epidemiological investigation. The scope this study included identifying risk factors routes transmission, investigating utility genomics to enhance traditional field epidemiology for informing management established widespread outbreaks. Methods Findings All isolates...
The strain dependence of the reaction rate rubbery materials with ozone was discussed on basis activation energy and energy. stretched molecular chains can acquire to be excited higher level than that unstretched chains, which results in temporary reduction degradation reaction. Our theory predicts spinodal-like transition will occur for evaluation behavior cracks at We observed such phenomena laminated rubber bearings. resistance material predicted by our experiment different conditions.
Abstract Public health agencies are increasingly relying on genomics during Legionnaires’ disease investigations. However, the causative bacterium ( Legionella pneumophila ) has an unusual population structure with extreme temporal and spatial genome sequence conservation. Furthermore, outbreaks can be caused by multiple L. genotypes in a single source. These factors confound cluster identification using standard phylogenomic methods. Here, we show that statistical learning approach based...