ORCID Profile
0000-0002-8331-275X
Current Organisation
Deakin University
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Analytical spectrometry | Analytical chemistry | Instrumental methods (excl. immunological and bioassay methods) | Separation science |
Publisher: Elsevier BV
Date: 12-2021
Publisher: Elsevier BV
Date: 2013
Publisher: Elsevier BV
Date: 12-2014
DOI: 10.1016/J.ANAEROBE.2014.09.007
Abstract: We compared the identification of Clostridium species using mass spectrometry by two different Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) platforms (Bruker MS and Vitek MS) against 16S rRNA sequencing as the reference standard. We then examined the impact of different s le preparations and (on one of those platforms) age of bacterial colonial growth on the performance of the MALDI-TOF MS systems. We identified 10 different species amongst the 52 isolates by 16S rRNA sequencing, with Clostridium perfringens the most prevalent (n=30). Spectrometric analysis using Vitek MS correctly speciated 47/52 (90.4%) isolates and was not affected by the s le preparation used. Performance of the Bruker MS was dependent on s le preparation with correct speciation obtained for 36 of 52 (69.2%) isolates tested using the Direct Transfer [DT] protocol, but all 52 (100%) isolates were correctly speciated using either an Extended Direct Transfer [EDT] or a Full Formic Extraction [EX] protocol. We then examined the effect of bacterial colonial growth age on the performance of Bruker MS and found substantial agreement in speciation using DT (Kappa=0.62, 95% CI: 0.46-0.75), almost perfect agreement for EDT (Kappa=0.94, 95% CI: 0.86-1.00) and exact agreement for EX (Kappa=1.00) between different days.
Publisher: Elsevier BV
Date: 06-2022
Publisher: Elsevier BV
Date: 10-2021
Publisher: MDPI AG
Date: 22-08-2021
Abstract: Rice is consumed as a staple food by more than half of the world’s population. Due to a higher fibre and micronutrient content, brown rice is more nutritious than white rice, but the consumption of brown rice is significantly lower than that of white rice, primarily due to sensory attributes. Therefore, the present research aimed to identify the sensory attributes which drive liking of Australian-grown brown and white rice varieties. Participants (n = 139) tasted and scored (9-point hedonic scale) their liking (i.e., overall liking, aroma, colour and texture) of brown and white rice types of Jasmine (Kyeema), Low GI (Doongara), and Medium grain rice (Amaroo). In addition, participants scored aroma, colour, hardness, fluffiness, stickiness, and chewiness, on Just About Right Scales. A within-subjects crossover design with randomised order (William’s Latin Square design) was used with six repeated s les for liking and Just About Right scales. Penalty analyses were applied to determine the relative influence of perception of sensory attributes on consumer liking of the rice varieties. Across all varieties, white rice was liked more than brown rice due to the texture and colour, and Jasmine rice was preferred over Low GI and Medium Grain. Rice texture (hardness and chewiness) was the most important sensory attribute among all rice varieties and aroma was important for driving of liking between white rice varieties.
Publisher: MDPI AG
Date: 29-03-2022
Abstract: The dual-sugar intestinal permeability test is a commonly used test to assess changes in gut barrier function. However, it does not identify functional changes and the exact mechanism of damage caused by the increased intestinal permeability. This study aims to explore the application of untargeted metabolomics and lipidomics to identify markers of increased intestinal permeability. Fifty fasting male participants (18–50 years) attended a single visit to conduct the following procedures: assessment of anthropometric measures, assessment of gastrointestinal symptoms, intestinal permeability test, and assessment of blood s les 90 min post-administration of the intestinal permeability test. Rhamnose and lactulose were analysed using gas chromatography-mass spectrometry (GC-MS). Untargeted polar metabolites and lipidomics were assessed by liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QToF MS). There was an elevated lactulose/rhamnose ratio in 27 subjects, indicating increased permeability compared to the remaining 23 control subjects. There were no significant differences between groups in characteristics such as age, body mass index (BMI), weight, height, and waist conference. Fourteen metabolites from the targeted metabolomics data were identified as statistically significant in the plasma s les from intestinal permeability subjects. The untargeted metabolomics and lipidomics analyses yielded fifteen and fifty-one statistically significant features, respectively. In iduals with slightly elevated intestinal permeability had altered energy, nucleotide, and amino acid metabolism, in addition to increased glutamine levels. Whether these biomarkers may be used to predict the early onset of leaky gut warrants further investigation.
Publisher: Hindawi Limited
Date: 06-02-2022
DOI: 10.1111/JFPP.16409
Publisher: Elsevier BV
Date: 10-2014
DOI: 10.1016/J.IJFOODMICRO.2014.07.023
Abstract: Psychrotrophic bacteria in raw milk produce heat-resistant extracellular proteases, resulting in spoilage and shelf-life reduction of ultrahigh temperature treated milk and milk products. Controlling of these spoilage microbes requires rapid and reliable identification systems for screening of raw milk. This study aimed to compare commercial bacterial identification systems with a genetic method (considered as the 'gold standard' method) for the identification of heat-resistant protease producing bacteria in raw milk. Five bacterial identification systems were compared based on typability, discrimination power (i.e. Simpson's Index of Diversity), reproducibility and speed of analysis. The accuracy of 16S rRNA gene sequencing, Biolog, MALDI-TOF MS, API, and Microbact for the identification of Gram negative bacilli at the species level was 100.0%, 86.8%, 63.2%, 60.5% and 57.9%, respectively. The Gram positive bacilli were identified by 16S rRNA gene sequencing, Biolog, MALDI-TOF MS, and API with accuracies at the species level of 100.0%, 85.0%, 95.0% and 90.0%, respectively. The 16S rRNA gene sequencing and phylogenetic analysis discriminated Pseudomonas fluorescens, Pseudomonas syringae, Hafnia alvei, Bacillus cereus, Bacillus pumilus and Bacillus licheniformis to the subspecies level. The Simpson's Index of Diversity scores were 0.966, 0.711, 0.496, 0.472, and 0.140, for 16S rRNA gene sequencing, Biolog, MALDI-TOF MS, API and Microbact, respectively. Limited reference profiles in the databases of Biolog, MALDI-TOF MS, API and Microbact systems reduced their accuracy in bacterial identification, compared to 16S rRNA gene sequencing. The rapidity of each assay is in the following order MALDI-TOF MS>16S rRNA gene sequencing>Biolog>Microbact>API. The reproducibility of the assays is in the order of 16S rRNA gene sequencing>API>Microbact>MALDI-TOF MS>Biolog. Thus, 16S rRNA gene sequencing appears to be the most reliable and robust system for the identification of dairy spoilage bacteria. The Biolog system is suitable for the identification of Gram negative spoilage bacteria, while MALDI-TOF MS and API systems are suitable for the identification of Gram positive spoilage bacteria isolated from raw milk. The commercial systems used in this study have been developed and extensively used for the identification of clinical microbes but only a limited number of studies used those systems to identify the environmental microorganisms that often contaminate raw milk. Therefore, comparison of those systems for the identification of spoilage microbes in raw milk would provide better understanding of their suitability for routine dairy microbiology and more extensive dairy research.
Publisher: MDPI AG
Date: 06-03-2020
Abstract: Our understanding of the human gut microbiome has grown exponentially. Advances in genome sequencing technologies and metagenomics analysis have enabled researchers to study microbial communities and their potential function within the context of a range of human gut related diseases and disorders. However, up until recently, much of this research has focused on characterizing the gut microbiological community structure and understanding its potential through system wide (meta) genomic and transcriptomic-based studies. Thus far, the functional output of these microbiomes, in terms of protein and metabolite expression, and within the broader context of host-gut microbiome interactions, has been limited. Furthermore, these studies highlight our need to address the issues of in idual variation, and of s les as proxies. Here we provide a perspective review of the recent literature that focuses on the challenges of exploring the human gut microbiome, with a strong focus on an integrated perspective applied to these themes. In doing so, we contextualize the experimental and technical challenges of undertaking such studies and provide a framework for capitalizing on the breadth of insight such approaches afford. An integrated perspective of the human gut microbiome and the linkages to human health will pave the way forward for delivering against the objectives of precision medicine, which is targeted to specific in iduals and addresses the issues and mechanisms in situ.
Publisher: Springer Science and Business Media LLC
Date: 18-03-2023
DOI: 10.1038/S41467-023-37200-W
Abstract: Even in the setting of optimal resuscitation in high-income countries severe sepsis and septic shock have a mortality of 20–40%, with antibiotic resistance dramatically increasing this mortality risk. To develop a reference dataset enabling the identification of common bacterial targets for therapeutic intervention, we applied a standardized genomic, transcriptomic, proteomic and metabolomic technological framework to multiple clinical isolates of four sepsis-causing pathogens: Escherichia coli , Klebsiella pneumoniae species complex, Staphylococcus aureus and Streptococcus pyogenes . Exposure to human serum generated a sepsis molecular signature containing global increases in fatty acid and lipid biosynthesis and metabolism, consistent with cell envelope remodelling and nutrient adaptation for osmoprotection. In addition, acquisition of cholesterol was identified across the bacterial species. This detailed reference dataset has been established as an open resource to support discovery and translational research.
Publisher: American Chemical Society (ACS)
Date: 09-01-2018
Abstract: The ability of bacteria to form biofilms and the emergence of antibiotic-resistant strains have prompted the need to develop the next generation of antibacterial coatings. Antimicrobial peptides (AMPs) are showing promise as molecules that can address these issues, especially if used when immobilized as a surface coating. We present a method that explores how surface patterns together with the selective immobilization of an AMP called PuroA (FPVTWRWWKWWKG-NH
Publisher: American Society for Microbiology
Date: 11-2014
DOI: 10.1128/JCM.02121-14
Abstract: We compared the diagnostic accuracy of the Carba NP test with that of a straightforward matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) method for detecting carbapenemase-producing Enterobacteriaceae (CPE). Using PCR as the reference method, both tests demonstrated a sensitivity of 87% and a specificity of 100%. MALDI-TOF MS offers a potential alternative for the rapid detection of CPE in the clinical laboratory setting.
Publisher: Elsevier BV
Date: 03-2012
DOI: 10.1016/J.MIMET.2012.01.002
Abstract: Listeria monocytogenes is an important foodborne pathogen responsible for non-invasive and invasive diseases in the elderly, pregnant women, neonates and immunocompromised populations. This bacterium has many similarities with other non-pathogenic Listeria species which makes its detection from food and environmental s les challenging. Subtyping of L. monocytogenes strains can prove to be crucial in epidemiological investigations, source tracking contamination from food processing plants and determining evolutionary relationships between different strains. In recent years there has been a shift towards the use of molecular subtyping. This has led to the development of new subtyping techniques such as multi-locus variable number tandem repeat analysis (MLVA) and multi-locus sequence based typing (MLST). This review focuses on the available methods for Listeria detection including immuno-based techniques and the more recently developed molecular methods and analytical techniques such as matrix-assisted laser desorption/ionisation time-of-flight based mass spectrometry (MALDI-TOF MS). It also includes a comparison and critical analysis of the available phenotypic and genotypic subtyping techniques that have been investigated for L. monocytogenes.
Publisher: Springer US
Date: 26-09-2020
Publisher: American Chemical Society (ACS)
Date: 03-05-2017
DOI: 10.1021/ACS.JPROTEOME.6B01046
Abstract: Identification of psychrotrophic pathogenic and spoilage Gram-negative bacteria using rapid and reliable techniques is important in commercial milk processing, as these bacteria can produce heat-resistant proteases and act as postprocessing contaminants in pasteurized milk. Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is a proven technology for identification of bacteria in food, however, may require optimization for identification of pathogenic and spoilage bacteria in milk and dairy products. The current study evaluated the effects of various culture conditions and s le preparation methods on assigning of raw milk isolates to the species level by MALDI-TOF MS. The results indicated that culture media, incubation conditions (temperature and time), and s le preparation significantly affected the identification rates of bacteria to the species level. Nevertheless, the development of spectral libraries of isolates grown on different media using a web tool for hierarchical clustering of peptide mass spectra (SPECLUST) followed by a ribosomal protein based bioinformatics approach significantly enhanced the assigning of bacteria, with at least one unique candidate biomarker peak identified for each species. Phyloproteomic relationships based on spectral profiles were compared to phylogenetic analysis using 16S rRNA gene sequences and demonstrated similar clustering patterns with significant discriminatory power. Thus, with appropriate optimization, MALDI-TOF MS is a valuable tool for species-level discrimination of pathogenic and milk spoilage bacteria.
Publisher: Elsevier BV
Date: 2014
DOI: 10.1016/J.JPROT.2013.09.014
Abstract: Conventional methods used for primary detection of Listeria monocytogenes from foods and subsequent confirmation of presumptive positive s les involve prolonged incubation and biochemical testing which generally require four to five days to obtain a result. In the current study, a simple and rapid proteomics-based MALDI-TOF MS approach was developed to detect L. monocytogenes directly from selective enrichment broths. Milk s les spiked with single species and multiple species cultures were incubated in a selective enrichment broth for 24h, followed by an additional 6h secondary enrichment. As few as 1 colony-forming unit (cfu) of L. monocytogenes per mL of initial selective broth culture could be detected within 30h. On applying the same approach to solid foods previously implicated in listeriosis, namely chicken pâté, cantaloupe and Camembert cheese, detection was achieved within the same time interval at inoculation levels of 10cfu/mL. Unlike the routine application of MALDI-TOF MS for identification of bacteria from solid media, this study proposes a cost-effective and time-saving detection scheme for direct identification of L. monocytogenes from broth cultures.This article is part of a Special Issue entitled: Trends in Microbial Proteomics. Globally, foodborne diseases are major causes of illness and fatalities in humans. Hence, there is a continual need for reliable and rapid means for pathogen detection from food s les. Recent applications of MALDI-TOF MS for diagnostic microbiology focused on detection of microbes from clinical specimens. However, the current study has emphasized its use as a tool for detecting the major foodborne pathogen, Listeria monocytogenes, directly from selective enrichment broths. This proof-of-concept study proposes a detection scheme that is more rapid and simple compared to conventional methods of Listeria detection. Very low levels of the pathogen could be identified from different food s les post-enrichment in selective enrichment broths. Use of this scheme will facilitate rapid and cost-effective testing for this important foodborne pathogen.
Publisher: MDPI AG
Date: 25-01-2021
Abstract: Shiga toxigenic E. coli (STEC) are an important cause of foodborne disease globally with many outbreaks linked to the consumption of contaminated foods such as leafy greens. Existing methods for STEC detection and isolation are time-consuming. Rapid methods may assist in preventing contaminated products from reaching consumers. This proof-of-concept study aimed to determine if a metabolomics approach could be used to detect STEC contamination in spinach. Using untargeted metabolic profiling, the bacterial pellets and supernatants arising from bacterial and inoculated spinach enrichments were investigated for the presence of unique metabolites that enabled categorization of three E. coli risk groups. A total of 109 and 471 metabolite features were identified in bacterial and inoculated spinach enrichments, respectively. Supervised OPLS-DA analysis demonstrated clear discrimination between bacterial enrichments containing different risk groups. Further analysis of the spinach enrichments determined that pathogen risk groups 1 and 2 could be easily discriminated from the other groups, though some clustering of risk groups 1 and 2 was observed, likely representing their genomic similarity. Biomarker discovery identified metabolites that were significantly associated with risk groups and may be appropriate targets for potential biosensor development. This study has confirmed that metabolomics can be used to identify the presence of pathogenic E. coli likely to be implicated in human disease.
Publisher: Walter de Gruyter GmbH
Date: 03-2016
DOI: 10.1515/CORRREV-2015-0046
Abstract: Microbial-influenced corrosion (MIC) has been known to have economic, environmental, and social implications to offshore oil and gas pipelines, concrete structures, and piped water assets. While corrosion itself is a relatively simple process, the localised manner of corrosion makes in situ assessments difficult. Furthermore, corrosion assessments tend to be measured as part of a forensic investigation. Compounding the issue further is the impact of microbiological/biofilm processes, where corrosion is influenced by the complex processes of different microorganisms performing different electrochemical reactions and secreting proteins and metabolites that can have secondary effects. While traditional microbiological culture-dependent techniques and electrochemical hysical assessments provide some insight into corrosion activity, the identity and role of microbial communities that are related to corrosion and corrosion inhibition in different materials and in different environments are scarce. One avenue to explore MIC and MIC inhibition is through the application of omics-based techniques, where insight into the bacterial population in terms of ersification and their metabolism can be further understood. As such, this paper discusses the recent progresses made in a number of fields that have used omics-based applications to improve the fundamental understanding of biofilms and MIC processes.
Publisher: Elsevier BV
Date: 06-2015
DOI: 10.1016/J.IJFOODMICRO.2015.01.023
Abstract: Listeria monocytogenes is an important foodborne pathogen responsible for the sometimes fatal disease listeriosis. Public health concerns and stringent regulations associated with the presence of this pathogen in food and food processing environments underline the need for rapid and reliable detection and subtyping techniques. In the current study, the application of matrix assisted laser desorption/ionisation-time-of-flight mass spectrometry (MALDI-TOF MS) as a single identification and source-tracking tool for a collection of L. monocytogenes isolates, obtained predominantly from dairy sources within Australia, was explored. The isolates were cultured on different growth media and analysed using MALDI-TOF MS at two incubation times (24 and 48 h). Whilst reliable genus-level identification was achieved from most media, identification at the species level was found to be dependent on culture conditions. Successful speciation was highest for isolates cultured on the chromogenic Agar Listeria Ottaviani Agosti agar (ALOA, 91% of isolates) and non-selective horse blood agar (HBA, 89%) for 24h. Chemometric statistical analysis of the MALDI-TOF MS data enabled source-tracking of L. monocytogenes isolates obtained from four different dairy sources. Strain-level discrimination was also observed to be influenced by culture conditions. In addition, t-test/analysis of variance (ANOVA) was used to identify potential biomarker peaks that differentiated the isolates according to their source of isolation. Source-tracking using MALDI-TOF MS was compared and correlated with the gold standard pulsed-field gel electrophoresis (PFGE) technique. The discriminatory index and the congruence between both techniques were compared using the Simpsons Diversity Index and adjusted Rand and Wallace coefficients. Overall, MALDI-TOF MS based source-tracking (using data obtained by culturing the isolates on HBA) and PFGE demonstrated good congruence with a Wallace coefficient of 0.71 and comparable discriminatory indices of 0.89 and 0.86, respectively. MALDI-TOF MS thus represents a rapid and cost-effective source-tracking technique for L. monocytogenes.
Publisher: Wiley
Date: 22-11-2019
Publisher: Springer Science and Business Media LLC
Date: 21-12-2022
Location: Australia
Start Date: 08-2023
End Date: 08-2028
Amount: $4,958,927.00
Funder: Australian Research Council
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