2024 |
Mizzi R, Plain KM, Timms VJ, Marsh I, Whittington RJ, 'Characterisation of IS1311 in Mycobacterium avium subspecies paratuberculosis genomes: Typing, continental clustering, microbial evolution and host adaptation.', PLoS One, 19 e0294570 (2024) [C1]
|
|
Nova |
2024 |
Foysal MJ, Timms V, Neilan BA, 'Dynamics of the benthic and planktic microbiomes in a Planktothrix-dominated toxic cyanobacterial bloom in Australia', Water Research, 249 (2024) [C1]
Cyanobacterial blooms are a concerning issue that threaten ecosystems, ecology and animal health. Bloom frequency has increased tremendously in recent times due to pollution, eutr... [more]
Cyanobacterial blooms are a concerning issue that threaten ecosystems, ecology and animal health. Bloom frequency has increased tremendously in recent times due to pollution, eutrophication of waterways, climate change, and changes in microbial community dynamics within the aquatic environment. Information about the spatiotemporal variation in microbial communities that drive a cyanobacterial bloom is very limited. Here, we analysed the spatiotemporal diversity and composition of bacterial communities, with a focus on cyanobacteria, during the bloom phase in a natural reservoir in Eastern Australia using high throughput amplicon sequencing. Sampling points and season had no influence on the richness and evenness of microbial communities during the bloom period, however some compositional differences were apparent across the seasons. Cyanobacteria were highly abundant during summer and autumn compared to winter and spring. The dominant cyanobacterial taxa were Planktothrix, Cyanobium and Microcystis and were found to be significantly abundant during summer and autumn. While cyanobacterial abundance soared in summer (25.4 %), dominated by Planktothrix (12.2 %) and Cyanobium (8.0 %), the diversity was highest in autumn (24.9 %) and consisted of Planktothrix (7.8 %), Nodularia (5.3 %), Planktothricoides (4.6 %), Microcystis (3.5 %), and Cyanobium (2.3 %). The strongly correlated non-photosynthetic Gastranaerophilales found in the sediment and water, suggested vertical transmission from the animal gut through faeces. To our knowledge, this is the first report of Planktothrix-driven toxic cyanobacterial bloom in Australia. Our study expands current understanding of the spatiotemporal variation in bacterial communities during a cyanobacterial bloom and sheds light on setting future management strategies for its control.
|
|
Nova |
2024 |
Romanis CS, Timms VJ, Nebauer DJ, Crosbie ND, Neilan BA, 'Microbiome analysis reveals Microcystis blooms endogenously seeded from benthos within wastewater maturation ponds.', Appl Environ Microbiol, 90 e0158523 (2024) [C1]
|
|
Nova |
2023 |
Timms VJ, Hassan KA, Pearson LA, Neilan BA, 'Cyanobacteria as a critical reservoir of the environmental antimicrobial resistome.', Environmental microbiology, 25 2266-2276 (2023) [C1]
|
|
Nova |
2023 |
AL-Tameemi AI, Masarudin MJ, Rahim RA, Timms V, Neilan B, Isa NM, 'ANTIBACTERIAL PROPERTIES OF ZINC OXIDE NANOPARTICLES SYNTHESIZED BY THE SUPERNATANT OF WEISSELLA CONFUSA UPM22MT04', Iraqi Journal of Agricultural Sciences, 54 1209-1222 (2023) [C1]
This study was aimed to produce zinc oxide nanoparticles (ZnO-NPs) using the supernatant of Weissella confusa UPM22MT04 and assess their effectiveness in inhibiting methicillinres... [more]
This study was aimed to produce zinc oxide nanoparticles (ZnO-NPs) using the supernatant of Weissella confusa UPM22MT04 and assess their effectiveness in inhibiting methicillinresistant Staphylococcus aureus (MRSA). An isolate of Weissella confusa UPM22MT04 was isolated from a wastewater treatment plant in Johor, Malaysia, and was utilized to synthesize ZnO-NPs. The synthesized ZnO-NPs were characterized through several techniques, including UV-visible spectroscopy, Fourier-transform infrared spectroscopy, transmission electron microscopy, energy-dispersive X-ray spectroscopy, and dynamic light scattering. Monodisperse spherical ZnO-NPs of 1.7-7.9 nm were obtained with 0.1 M zinc nitrate at 80°C. The biosynthesized ZnO-NPs exhibited vigorous inhibitory activity against MRSA. Results found that ZnO-NPs inhibited MRSA at a minimum concentration of 0.625 mg/mL and were bactericidal at a minimum concentration of 1.25 mg/mL. In MTT assays, ZnO-NPs showed no toxicity to HS-27 fibroblasts. The supernatant of Weissella confusa UPM22MT04 could be used to synthesize ZnO-NPs, which are an antibacterial agent, eco-friendly and nontoxic.
|
|
Nova |
2023 |
Al-Tameemi AI, Masarudin MJ, Abdul Rahim R, Mills T, Timms VJ, Neilan BA, Mat Isa N, 'Biosynthesis of zinc oxide nanoparticles using the supernatant of
|
|
Nova |
2022 |
Garby TJ, Jordan M, Timms V, Walter MR, Neilan BA, '2-Methylhopanoids in geographically distinct, arid biological soil crusts are primarily cyanobacterial in origin', ENVIRONMENTAL MICROBIOLOGY REPORTS, 14 164-169 (2022) [C1]
|
|
Nova |
2022 |
Fong W, Timms V, Sim E, Pey K, Nguyen T, Sintchenko V, 'Genomic and transcriptomic variation in Bordetella spp. following induction of erythromycin resistance', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 77 3016-3025 (2022) [C1]
|
|
Nova |
2022 |
Mizzi R, Plain KM, Whittington R, Timms VJ, 'Global Phylogeny of Mycobacterium avium and Identification of Mutation Hotspots During Niche Adaptation', Frontiers in Microbiology, 13 (2022) [C1]
Mycobacterium avium is separated into four subspecies: M. avium subspecies avium (MAA), M. avium subspecies silvaticum (MAS), M. avium subspecies hominissuis (MAH), and M. avium s... [more]
Mycobacterium avium is separated into four subspecies: M. avium subspecies avium (MAA), M. avium subspecies silvaticum (MAS), M. avium subspecies hominissuis (MAH), and M. avium subspecies paratuberculosis (MAP). Understanding the mechanisms of host and tissue adaptation leading to their clinical significance is vital to reduce the economic, welfare, and public health concerns associated with diseases they may cause in humans and animals. Despite substantial phenotypic diversity, the subspecies nomenclature is controversial due to high genetic similarity. Consequently, a set of 1,230 M. avium genomes was used to generate a phylogeny, investigate SNP hotspots, and identify subspecies-specific genes. Phylogeny reiterated the findings from previous work and established that Mycobacterium avium is a species made up of one highly diverse subspecies, known as MAH, and at least two clonal pathogens, named MAA and MAP. Pan-genomes identified coding sequences unique to each subspecies, and in conjunction with a mapping approach, mutation hotspot regions were revealed compared to the reference genomes for MAA, MAH, and MAP. These subspecies-specific genes may serve as valuable biomarkers, providing a deeper understanding of genetic differences between M. avium subspecies and the virulence mechanisms of mycobacteria. Furthermore, SNP analysis demonstrated common regions between subspecies that have undergone extensive mutations during niche adaptation. The findings provide insights into host and tissue specificity of this genetically conserved but phenotypically diverse species, with the potential to provide new diagnostic targets and epidemiological and therapeutic advances.
|
|
Nova |
2022 |
Cains T, Shalak H, Timms VJ, Kiss A, Smith A, Sintchenko V, et al., 'Legionella pneumophila serogroup 1 infection associated with the use of an apartment building spa pool', Communicable diseases intelligence (2018), 46 (2022) [C1]
Background: Legionnaires' disease is a notifiable condition in New South Wales (NSW), Australia; clinicians and laboratories are required to report the disease to NSW Health.... [more]
Background: Legionnaires' disease is a notifiable condition in New South Wales (NSW), Australia; clinicians and laboratories are required to report the disease to NSW Health. We describe the investigation of a sporadic case associated with the use of a communal spa pool in the case's apartment building complex and the use of whole genome sequencing to examine relatedness between clinical and environmental Legionella pneumophila serogroup 1 (Lp1) strains. Methods: In February 2018, a confirmed case of Lp1 infection was notified in a man in his 60s hospitalised with pneumonia. We asked the clinical team to obtain sputum in the event we found a potential source. The case described the use of the communal spa pool in his apartment building on two occasions during the putative exposure period. Environmental Health Officers from the Public Health Unit inspected the spa pool and found that the free chlorine level was well below the recommended concentration; a water sample was submitted for microbial analysis. Results: Lp1 was grown from the case's sputum and microbial analysis of the spa water sample found Lp1 at a concentration of 20 CFU/mL. The human and environmental isolates were subjected to whole genome sequencing and found to be highly genomically related. There was no other plausible environmental source of legionella. Conclusions: Whole genome sequencing of the clinical and environmental Lp1 isolates implicated a contaminated spa pool as the source of the case's exposure. This strongly supports the application of whole genome sequencing to the investigation of single cases of legionellosis. Communal spa pools in apartment buildings are not regulated in most Australian jurisdictions but must be considered to pose a potential legionella risk if improperly maintained.
|
|
|
2021 |
Mizzi R, Timms VJ, Price-Carter ML, Gautam M, Whittington R, Heuer C, et al., 'Comparative Genomics of Mycobacterium avium Subspecies Paratuberculosis Sheep Strains', Frontiers in Veterinary Science, 8 (2021) [C1]
Mycobacterium avium subspecies paratuberculosis (MAP) is the aetiological agent of Johne's disease (JD), a chronic enteritis that causes major losses to the global livestock ... [more]
Mycobacterium avium subspecies paratuberculosis (MAP) is the aetiological agent of Johne's disease (JD), a chronic enteritis that causes major losses to the global livestock industry. Further, it has been associated with human Crohn's disease. Several strains of MAP have been identified, the two major groups being sheep strain MAP, which includes the Type I and Type III sub-lineages, and the cattle strain or Type II MAP lineage, of which bison strains are a sub-grouping. Major genotypic, phenotypic and pathogenic variations have been identified in prior comparisons, but the research has predominately focused on cattle strains of MAP. In countries where the sheep industries are more prevalent, however, such as Australia and New Zealand, ovine JD is a substantial burden. An information gap exists regarding the genomic differences between sheep strain sub-lineages and the relevance of Type I and Type III MAP in terms of epidemiology and/or pathogenicity. We therefore investigated sheep MAP isolates from Australia and New Zealand using whole genome sequencing. For additional context, sheep MAP genome datasets were downloaded from the Sequence Read Archive and GenBank. The final dataset contained 18 Type III and 16 Type I isolates and the K10 cattle strain MAP reference genome. Using a pan-genome approach, an updated global phylogeny for sheep MAP from de novo assemblies was produced. When rooted with the K10 cattle reference strain, two distinct clades representing the lineages were apparent. The Australian and New Zealand isolates formed a distinct sub-clade within the type I lineage, while the European type I isolates formed another less closely related group. Within the type III lineage, isolates appeared more genetically diverse and were from a greater number of continents. Querying of the pan-genome and verification using BLAST analysis revealed lineage-specific variations (n = 13) including genes responsible for metabolism and stress responses. The genetic differences identified may represent important epidemiological and virulence traits specific to sheep MAP. This knowledge will potentially contribute to improved vaccine development and control measures for these strains.
|
|
Nova |
2021 |
Sintchenko V, Timms V, Sim E, Rockett R, Bachmann N, O'Sullivan M, Marais B, 'Microbial Genomics as a Catalyst for Targeted Antivirulence Therapeutics', FRONTIERS IN MEDICINE, 8 (2021)
|
|
|
2020 |
Rockett RJ, Arnott A, Lam C, Sadsad R, Timms V, Gray K-A, et al., 'Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling', NATURE MEDICINE, 26 (2020) [C1]
|
|
|
2020 |
Fong W, Rockett R, Timms V, Sintchenko V, 'Optimization of sample preparation for culture-independent sequencing of Bordetella pertussis', MICROBIAL GENOMICS, 6 (2020) [C1]
|
|
|
2020 |
Baines SL, da Silva AG, Carter GP, Jennison A, Rathnayake I, Graham RM, et al., 'Complete microbial genomes for public health in Australia and the Southwest Pacific', MICROBIAL GENOMICS, 6 (2020) [C1]
|
|
|
2019 |
Timms VJ, Fong W, Jeoffreys NJ, Sintchenko V, 'Evaluation of the BioGX BD-Max PCR assay for detection of pathogenic Bordetella', PATHOLOGY, 51 323-324 (2019)
|
|
|
2019 |
Xu Z, Octavia S, Luu LDW, Payne M, Timms V, Tay CY, et al., 'Pertactin-Negative and Filamentous Hemagglutinin-Negative
|
|
|
2018 |
van Hal SJ, Beukers AG, Timms VJ, Ellem JA, Taylor P, Maley MW, et al., 'Relentless spread and adaptation of non-typeable vanA vancomycinresistant Enterococcus faecium: A genome-wide investigation', Journal of Antimicrobial Chemotherapy, 73 1487-1491 (2018) [C1]
Background: VRE are prevalent among patients in ICUs. Non-typeable vanA VRE, due to loss of one of the genes used for MLST (pstS), have increased in Australia, suggestive of a new... [more]
Background: VRE are prevalent among patients in ICUs. Non-typeable vanA VRE, due to loss of one of the genes used for MLST (pstS), have increased in Australia, suggestive of a new, hospital-acquired lineage. Objectives: To understand the significance of this lineage and its transmission using WGS of strains isolated from patients in ICUs across New South Wales, Australia. Methods: A total of 240 Enterococcus faecium isolates collected between February and May 2016, and identified by conventional PCR as vanA positive, were sequenced. Isolates originated from 12 ICUs in New South Wales, grouped according to six local health districts, and represented both rectal screening swab (n=229) and clinical (n=11) isolates. Results: ST analysis revealed the absence of the pstS gene in 84.2% (202 of 240) of vanA isolates. Two different non-typeable STs were present based on different allelic backbone patterns. Loss of the pstS gene appeared to be the result of multiple recombination events across this region. Evidence for pstS-negative lineage spread across all six local health districts was observed suggestive of inter-hospital transmission. In addition, multiple outbreaks were detected, some of which were protracted and lasted for the duration of the study. Conclusions: These findings confirmed the evolution, emergence and dissemination of non-typeable vanA E. faecium. This study has highlighted the utility of WGS when attempting to describe accurately the hospitalbased pathogen epidemiology, which in turn will continue to inform optimal infection control measures necessary to halt the spread of this important nosocomial organism.
|
|
Nova |
2018 |
Fong W, Timms V, Holmes N, Sintchenko V, 'Detection and incidence of Bordetella holmesii in respiratory specimens from patients with pertussis-like symptoms in New South Wales, Australia', PATHOLOGY, 50 322-326 (2018) [C1]
|
|
|
2018 |
Timms VJ, Rockett R, Bachmann NL, Martinez E, Wang Q, Chen SC-A, et al., 'Genome Sequencing Links Persistent Outbreak of Legionellosis in Sydney (New South Wales, Australia) to an Emerging Clone of Legionella pneumophila Sequence Type 211', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 84 (2018) [C1]
|
|
|
2018 |
Timms VJ, Nguyen T, Crighton T, Yuen M, Sintchenko V, 'Genome-wide comparison of Corynebacterium diphtheriae isolates from Australia identifies differences in the Pan-genomes between respiratory and cutaneous strains', BMC GENOMICS, 19 (2018) [C1]
|
|
|
2018 |
Rockett RJ, Oftadeh S, Bachmann NL, Timms VJ, Kong F, Gilbert GL, Sintchenko V, 'Genome-wide analysis of
|
|
|
2018 |
Bachmann NL, Rockett RJ, Timms VJ, Sintchenko V, 'Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics', FRONTIERS IN PUBLIC HEALTH, 6 (2018) [C1]
|
|
|
2017 |
Kuenstner JT, Naser S, Chamberlin W, Borody T, Graham DY, McNees A, et al., 'The Consensus from the Mycobacterium avium ssp. paratuberculosis (MAP) Conference 2017', FRONTIERS IN PUBLIC HEALTH, 5 (2017)
|
|
|
2017 |
Biswas C, Chen SC-A, Halliday C, Martinez E, Rockett RJ, Wang Q, et al., 'Whole Genome Sequencing of Candida glabrata for Detection of Markers of Antifungal Drug Resistance', JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, (2017) [C1]
|
|
|
2016 |
Timms VJ, Daskalopoulos G, Mitchell HM, Neilan BA, 'The association of mycobacterium avium subsp. paratuberculosis with inflammatory bowel disease', PLoS ONE, 11 (2016) [C1]
The association of Mycobacterium avium subspecies paratuberculosis (M. paratuberculosis) with Crohn's disease is a controversial issue. M. paratuberculosis is detected by amp... [more]
The association of Mycobacterium avium subspecies paratuberculosis (M. paratuberculosis) with Crohn's disease is a controversial issue. M. paratuberculosis is detected by amplifying the IS900 gene, as microbial culture is unreliable from humans. We determined the presence of M. paratuberculosis in patients with Crohn's disease (CD) (n = 22), ulcerative colitis (UC) (n = 20), aphthous ulcers (n = 21) and controls (n = 42) using PCR assays validated on bovine tissue. Culture from human tissue was also performed. M. paratuberculosis prevalence in the CD and UC groups was compared to the prevalence in age and sex matched non-inflammatory bowel disease controls. Patients and controls were determined to be M. paratuberculosis positive if all three PCR assays were positive. A significant association was found between M. paratuberculosis and Crohn's disease (p = 0.02) that was not related to age, gender, place of birth, smoking or alcohol intake. No significant association was detected between M. paratuberculosis and UC or aphthous ulcers; however, one M. paratuberculosis isolate was successfully cultured from a patient with UC.We report the resistance of this isolate to ethambutol, rifampin, clofazamine and streptomycin. Interestingly this isolate could not only survive but could grow slowly at 5°C. We demonstrate a significant association between M. paratuberculosis and CD using multiple pre-validated PCR assays and that M. paratuberculosis can be isolated from patients with UC.
|
|
|
2015 |
Timms VJ, Mitchell HM, Neilan BA, 'Optimisation of DNA extraction and validation of PCR assays to detect Mycobacterium avium subsp paratuberculosis', JOURNAL OF MICROBIOLOGICAL METHODS, 112 99-103 (2015) [C1]
|
|
|
2015 |
Timms VJ, Hassan KA, Mitchell HM, Neilan BA, 'Comparative genomics between human and animal associated subspecies of the Mycobacterium avium complex: a basis for pathogenicity', BMC GENOMICS, 16 (2015) [C1]
|
|
|
2011 |
Timms VJ, Gehringer MM, Mitchell HM, Daskalopoulos G, Neilan BA, 'How accurately can we detect Mycobacterium avium subsp paratuberculosis infection?', JOURNAL OF MICROBIOLOGICAL METHODS, 85 1-8 (2011)
|
|
|
2001 |
Warburton-Timms VJ, Charlett A, Valori RM, Uff JS, Shepherd NA, Barr H, McNulty CAM, 'The significance of cagA(+) Helicobacter pylori in reflux oesophagitis', GUT, 49 341-346 (2001)
|
|
|
2001 |
Warburton-Timms VJ, McNulty CAM, 'Role of screening agar plates for in vitro susceptibility testing of Helicobacter pylori in a routine laboratory setting', JOURNAL OF CLINICAL PATHOLOGY, 54 408-411 (2001)
|
|
|
1998 |
Warburton VJ, Everett S, Mapstone NP, Axon ATR, Hawkey P, Dixon MF, 'Clinical and histological associations of cagA and vacA genotypes in Helicobacter pylori gastritis', JOURNAL OF CLINICAL PATHOLOGY, 51 55-61 (1998)
|
|
|
1996 |
Jorgensen M, Daskalopoulos G, Warburton V, Mitchell HM, Hazell SL, 'Multiple strain colonization and metronidazole resistance in Helicobacter pylori-infected patients: Identification from sequential and multiple biopsy specimens', JOURNAL OF INFECTIOUS DISEASES, 174 631-635 (1996)
|
|
|