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Romanis CS, Timms VJ, Crosbie ND, Neilan BA. 16S rRNA gene amplicon sequencing data from an Australian wastewater treatment plant. Microbiol Resour Announc 2024:e0123723. [PMID: 38700348 DOI: 10.1128/mra.01237-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/20/2024] [Indexed: 05/05/2024] Open
Abstract
Amplicon sequencing data of the 16S rRNA (V1-V3) gene from 56 effluent and sediment samples from an Australian wastewater treatment plant are reported. Proteobacteria (3.50%-90.09%), Actinobacteria (0.02%-45.71%), and Cyanobacteria (0.05%-63.73%) were dominant in the effluent. The sediment samples were dominated by Proteobacteria (13.14%-84.83%), Chloroflexi (0.84%-42.52%), and Firmicutes (1.54%-17.21%).
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Affiliation(s)
- C S Romanis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - V J Timms
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
- ARC Centre of Excellence for Synthetic Biology, Newcastle, Australia
| | - N D Crosbie
- Melbourne Water, Docklands, Victoria, Australia
| | - B A Neilan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
- ARC Centre of Excellence for Synthetic Biology, Newcastle, Australia
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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 2024; 19:e0294570. [PMID: 38349924 PMCID: PMC10863896 DOI: 10.1371/journal.pone.0294570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/04/2023] [Indexed: 02/15/2024] Open
Abstract
Johne's disease (JD), caused by Mycobacterium avium subspecies paratuberculosis (MAP) is a global burden for livestock producers and has an association with Crohn's disease in humans. Within MAP there are two major lineages, S/Type I/TypeIII and C/Type II, that vary in phenotype including culturability, host preference and virulence. These lineages have been identified using the IS1311 element, which contains a conserved, single nucleotide polymorphism. IS1311 and the closely related IS1245 element belong to the IS256 family of insertion sequences, are dispersed throughout M. avium taxa but remain poorly characterised. To investigate the distribution and diversity of IS1311 in MAP, 805 MAP genomes were collated from public databases. IS1245 was absent, while IS1311 sequence, copy number and insertion loci were conserved between MAP S lineages and varied within the MAP C lineage. One locus was specific to the S strains, which contained nine IS1311 copies. In contrast, C strains contained either seven or eight IS1311 loci. Most insertion loci were associated with the boundaries of homologous regions that had undergone genome rearrangement between the MAP lineages, suggesting that this sequence may be a driver of recombination. Phylogenomic geographic clustering of MAP subtypes was demonstrated for the first time, at continental scale, and indicated that there may have been recent MAP transmission between Europe and North America, in contrast to Australia where importation of live ruminants is generally prohibited. This investigation confirmed the utility of IS1311 typing in epidemiological studies and resolved anomalies in past studies. The results shed light on potential mechanisms of niche/host adaptation, virulence of MAP and global transmission dynamics.
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Affiliation(s)
- Rachel Mizzi
- School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Karren M. Plain
- School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Verlaine J. Timms
- Neilan Laboratory of Microbial and Molecular Diversity, College of Engineering, Science and Environment, The University of Newcastle, New South Wales, Australia
| | - Ian Marsh
- Microbiology and Parasitology Research, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
| | - Richard J. Whittington
- School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
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Timms VJ, Hassan KA, Pearson LA, Neilan BA. Cyanobacteria as a critical reservoir of the environmental antimicrobial resistome. Environ Microbiol 2023; 25:2266-2276. [PMID: 37365851 DOI: 10.1111/1462-2920.16453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/04/2023] [Indexed: 06/28/2023]
Abstract
Antimicrobial resistance (AMR) is predicted to cause a worldwide annual toll of 10 million deaths by 2050. This looming public health threat has been linked to antibiotic overuse and pollution, which places selective pressures on AMR maintenance and transfer in and between microbial populations. We examined the distribution, diversity and potential mobility of AMR genes in cyanobacteria. While cyanobacteria are not pathogenic, we hypothesised that they could be a major environmental reservoir for AMR genes. Genes encoding AMR to seven antimicrobial drug classes were found in 10% of cyanobacterial genomes. AMR genes were found in 13% of freshwater, 19% of terrestrial, 34% of symbiotic, 2% of thermal spring, and 3% of marine genomes. AMR genes were found in five cyanobacterial orders with 23% of Nostocales and 8% of Oscillatoriales strains containing AMR genes. The most frequently observed alleles were ansamycin resistance genes, which were present in 7% of strains. AMR genes responsible for resistance to broad-spectrum β-lactams, chloramphenicols, tetracyclines, macrolides, and aminoglycosides were associated with mobile genetic elements or plasmid replicons or both. These results suggest that cyanobacteria are an extensive reservoir, and potential vector, for AMR genes in diverse terrestrial and aquatic habitats.
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Affiliation(s)
- V J Timms
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - K A Hassan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - L A Pearson
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - B A Neilan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
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Mizzi R, Plain KM, Whittington R, Timms VJ. Global Phylogeny of Mycobacterium avium and Identification of Mutation Hotspots During Niche Adaptation. Front Microbiol 2022; 13:892333. [PMID: 35602010 PMCID: PMC9121174 DOI: 10.3389/fmicb.2022.892333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/06/2022] [Indexed: 12/27/2022] Open
Abstract
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.
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Affiliation(s)
- Rachel Mizzi
- Farm Animal Health, School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Karren M Plain
- Farm Animal Health, School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia.,Microbiology and Parasitology Research, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Richard Whittington
- Farm Animal Health, School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Verlaine J Timms
- Neilan Laboratory of Microbial and Molecular Diversity, College of Engineering, Science and Environment, The University of Newcastle, Newcastle, NSW, Australia
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Cains T, Shalak H, Timms VJ, Kiss A, Smith A, Sintchenko V, Bateman-Steel C, Ferson MJ. Legionella pneumophila serogroup 1 infection associated with the use of an apartment building spa pool. Commun Dis Intell (2018) 2022; 46. [DOI: 10.33321/cdi.2022.46.82] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
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.
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Mizzi R, Timms VJ, Price-Carter ML, Gautam M, Whittington R, Heuer C, Biggs PJ, Plain KM. Comparative Genomics of Mycobacterium avium Subspecies Paratuberculosis Sheep Strains. Front Vet Sci 2021; 8:637637. [PMID: 33659287 PMCID: PMC7917049 DOI: 10.3389/fvets.2021.637637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
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.
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Affiliation(s)
- Rachel Mizzi
- Farm Animal Health Group, Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Verlaine J Timms
- Centre for Infectious Diseases and Microbiology, Public Health, Westmead Hospital, Westmead, NSW, Australia
| | | | - Milan Gautam
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Richard Whittington
- Farm Animal Health Group, Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Cord Heuer
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- School of Veterinary Science, Massey University, Palmerston North, New Zealand.,School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Karren M Plain
- Farm Animal Health Group, Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
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Baines SL, da Silva AG, Carter GP, Jennison A, Rathnayake I, Graham RM, Sintchenko V, Wang Q, Rockett RJ, Timms VJ, Martinez E, Ballard S, Tomita T, Isles N, Horan KA, Pitchers W, Stinear TP, Williamson DA, Howden BP, Seemann T. Complete microbial genomes for public health in Australia and the Southwest Pacific. Microb Genom 2020; 6:mgen000471. [PMID: 33180013 PMCID: PMC8116684 DOI: 10.1099/mgen.0.000471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
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 genomes chosen to represent a range of pathogenic bacteria with regional importance to Australia and the Southwest Pacific; enriching the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health microbiology laboratories. In this first step, we present 26 complete high-quality bacterial genomes. Additionally, we describe here a framework for reconstructing complete microbial genomes and highlight some of the challenges and considerations for accurate and reproducible genome reconstruction.
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Affiliation(s)
- Sarah L. Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Glen P. Carter
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
| | - Amy Jennison
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
| | - Irani Rathnayake
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
| | - Rikki M. Graham
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
| | - Rebecca J. Rockett
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Verlaine J. Timms
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
| | - Susan Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Takehiro Tomita
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Nicole Isles
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Kristy A. Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - William Pitchers
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
| | - Deborah A. Williamson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Communicable Diseases Genomics Network (CDGN)
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
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van Hal SJ, Beukers AG, Timms VJ, Ellem JA, Taylor P, Maley MW, Newton PJ, Ferguson JK, Lee A, Chen SCA, Sintchenko V. Relentless spread and adaptation of non-typeable vanA vancomycin-resistant Enterococcus faecium: a genome-wide investigation. J Antimicrob Chemother 2019; 73:1487-1491. [PMID: 29566173 DOI: 10.1093/jac/dky074] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/09/2018] [Indexed: 12/17/2022] Open
Abstract
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 hospital-based pathogen epidemiology, which in turn will continue to inform optimal infection control measures necessary to halt the spread of this important nosocomial organism.
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Affiliation(s)
- Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Alicia G Beukers
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Verlaine J Timms
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, Australia
| | - Justin A Ellem
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, Australia
| | - Peter Taylor
- Department of Microbiology, NSW Health Pathology, St George Hospital, Kogarah, Australia.,School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Michael W Maley
- School of Medical Sciences, University of New South Wales, Sydney, Australia.,Department of Microbiology and Infectious Diseases, South Western Sydney LHD and NSW Health Pathology - Liverpool, Sydney, Australia
| | - Peter J Newton
- NSW Health Pathology, Microbiology, Wollongong Hospital, Wollongong, NSW, Australia
| | - John K Ferguson
- Department of Microbiology, NSW Health Pathology, John Hunter Hospital, University of Newcastle, Newcastle, Australia
| | - Andie Lee
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia
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Timms VJ, Fong W, Jeoffreys NJ, Sintchenko V. Evaluation of the BioGX BD-Max PCR assay for detection of pathogenic Bordetella. Pathology 2019; 51:323-324. [PMID: 30846228 DOI: 10.1016/j.pathol.2018.10.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/10/2018] [Accepted: 10/19/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Verlaine J Timms
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Australia; Sydney Medical School, The University of Sydney, NSW, Australia.
| | - Winkie Fong
- Sydney Medical School, The University of Sydney, NSW, Australia
| | - Neisha J Jeoffreys
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Australia; Sydney Medical School, The University of Sydney, NSW, Australia; Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Sydney, NSW, Australia
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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 2018; 19:869. [PMID: 30509172 PMCID: PMC6278121 DOI: 10.1186/s12864-018-5147-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 10/08/2018] [Indexed: 11/22/2022] Open
Abstract
Background Corynebacterium diphtheriae is the main etiological agent of diphtheria, a global disease causing life-threatening infections, particularly in infants and children. Vaccination with diphtheria toxoid protects against infection with potent toxin producing strains. However a growing number of apparently non-toxigenic but potentially invasive C. diphtheriae strains are identified in countries with low prevalence of diphtheria, raising key questions about genomic structures and population dynamics of the species. This study examined genomic diversity among 48 C. diphtheriae isolates collected in Australia over a 12-year period using whole genome sequencing. Phylogeny was determined using SNP-based mapping and genome wide analysis. Results C. diphtheriae sequence type (ST) 32, a non-toxigenic clone with evidence of enhanced virulence that has been also circulating in Europe, appears to be endemic in Australia. Isolates from temporospatially related patients displayed the same ST and similarity in their core genomes. The genome-wide analysis highlighted a role of pilins, adhesion factors and iron utilization in infections caused by non-toxigenic strains. Conclusions The genomic diversity of toxigenic and non-toxigenic strains of C. diphtheriae in Australia suggests multiple sources of infection and colonisation. Genomic surveillance of co-circulating toxigenic and non-toxigenic C. diphtheriae offer new insights into the evolution and virulence of pathogenic clones and can inform targeted public health actions and policy. The genomes presented in this investigation will contribute to the global surveillance of C. diphtheriae both for the monitoring of antibiotic resistance genes and virulent strains such as those belonging to ST32. Electronic supplementary material The online version of this article (10.1186/s12864-018-5147-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Verlaine J Timms
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, PO Box 533, Wentworthville, NSW, 2145, Australia.
| | - Trang Nguyen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR-Pathology West, Sydney, Australia
| | - Taryn Crighton
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR-Pathology West, Sydney, Australia
| | - Marion Yuen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR-Pathology West, Sydney, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, PO Box 533, Wentworthville, NSW, 2145, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR-Pathology West, Sydney, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
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Biswas C, Chen SCA, Halliday C, Martinez E, Rockett RJ, Wang Q, Timms VJ, Dhakal R, Sadsad R, Kennedy KJ, Playford G, Marriott DJ, Slavin MA, Sorrell TC, Sintchenko V. Whole Genome Sequencing of Candida glabrata for Detection of Markers of Antifungal Drug Resistance. J Vis Exp 2017. [PMID: 29364212 DOI: 10.3791/56714] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Candida glabrata can rapidly acquire mutations that result in drug resistance, especially to azoles and echinocandins. Identification of genetic mutations is essential, as resistance detected in vitro can often be correlated with clinical failure. We examined the feasibility of using whole genome sequencing (WGS) for genome-wide analysis of antifungal drug resistance in C. glabrata. The aim was torecognize enablers and barriers in the implementation WGS and measure its effectiveness. This paper outlines the key quality control checkpoints and essential components of WGS methodology to investigate genetic markers associated with reduced susceptibility to antifungal agents. It also estimates the accuracy of data analysis and turn-around-time of testing. Phenotypic susceptibility of 12 clinical, and one ATCC strain of C. glabrata was determined through antifungal susceptibility testing. These included three isolate pairs, from three patients, that developed rise in drug minimum inhibitory concentrations. In two pairs, the second isolate of each pair developed resistance to echinocandins. The second isolate of the third pair developed resistance to 5-flucytosine. The remaining comprised of susceptible and azole resistant isolates. Single nucleotide polymorphisms (SNPs) in genes linked to echinocandin, azole and 5-flucytosine resistance were confirmed in resistant isolates through WGS using the next generation sequencing. Non-synonymous SNPs in antifungal resistance genes such as FKS1, FKS2, CgPDR1, CgCDR1 and FCY2 were identified. Overall, an average of 98% of the WGS reads of C. glabrata isolates mapped to the reference genome with about 75-fold read depth coverage. The turnaround time and cost were comparable to Sanger sequencing. In conclusion, WGS of C. glabrata was feasible in revealing clinically significant gene mutations involved in resistance to different antifungal drug classes without the need for multiple PCR/DNA sequencing reactions. This represents a positive step towards establishing WGS capability in the clinical laboratory for simultaneous detection of antifungal resistance conferring substitutions.
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Affiliation(s)
- Chayanika Biswas
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital;
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital; Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney
| | - Catriona Halliday
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital; Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Rebecca J Rockett
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Verlaine J Timms
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Rajat Dhakal
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Rosemarie Sadsad
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Karina J Kennedy
- Department of Microbiology and Infectious Diseases, Canberra Hospital and Health Services, Australian National University Medical School
| | - Geoffrey Playford
- Department of Microbiology and Infectious Diseases, Canberra Hospital and Health Services, Australian National University Medical School; Infection Management Services, Australian National University Medical School
| | - Deborah J Marriott
- Department of Microbiology and Infectious Diseases, St. Vincent's Hospital
| | - Monica A Slavin
- Department of Infectious Diseases, Peter MacCallum Cancer Centre
| | - Tania C Sorrell
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital; Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney
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Timms VJ, Daskalopoulos G, Mitchell HM, Neilan BA. The Association of Mycobacterium avium subsp. paratuberculosis with Inflammatory Bowel Disease. PLoS One 2016; 11:e0148731. [PMID: 26849125 PMCID: PMC4746060 DOI: 10.1371/journal.pone.0148731] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 12/09/2015] [Indexed: 12/14/2022] Open
Abstract
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.
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Affiliation(s)
- Verlaine J. Timms
- School of Biotechnology and Biomolecular Sciences, Level 3, Biosciences Building, University of New South Wales, Sydney, Australia
| | - George Daskalopoulos
- Inner West Endoscopy Centre, Endoscopy Services Pty. Ltd., Marrickville, Sydney, Australia
| | - Hazel M. Mitchell
- School of Biotechnology and Biomolecular Sciences, Level 3, Biosciences Building, University of New South Wales, Sydney, Australia
| | - Brett A. Neilan
- School of Biotechnology and Biomolecular Sciences, Level 3, Biosciences Building, University of New South Wales, Sydney, Australia
- * E-mail:
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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 2015; 16:695. [PMID: 26370227 PMCID: PMC4570654 DOI: 10.1186/s12864-015-1889-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 09/01/2015] [Indexed: 12/25/2022] Open
Abstract
Background A human isolate of Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis 43525) was sequenced and compared genomically to other mycobacterial pathogens. M. paratuberculosis 43525 was recently isolated from a patient with ulcerative colitis and belongs to the M. avium complex, a group known to infect both humans and animals. While M. paratuberculosis is a known pathogen of livestock, there are only 20 human isolates from the last 20 years, therefore we took the opportunity to perform a whole genome comparison between human and animal mycobacterial pathogens. We also compared virulence determinants such as the mycobactin cluster, PE/PPE genes and mammalian cell entry (mce) operons between MAC subspecies that infect animals and those that infect humans. M. tuberculosis was also included in these analyses given its predominant role as a human pathogen. Results This genome comparison showed the PE/PPE profile of M. paratuberculosis 43525 to be largely the same as other M. paratuberculosis isolates, except that it had one PPE and one PE_PGRS protein that are only present in human MAC strains and M. tuberculosis. PE/PPE proteins that were unique to M. paratuberculosis 43525, M. avium subsp. hominissuis and a caprine M. paratuberculosis isolate, were also identified. In addition, the mycobactin cluster differed between human and animal isolates and a unique mce operon flanked by two mycobactin genes, mbtA and mbtJ, was identified in all available M. paratuberculosis genomes. Conclusions Despite the whole genome comparison placing M. paratuberculosis 43525 as closely related to bovine M. paratuberculosis, key virulence factors were similar to human mycobacterial pathogens. This study highlights key factors of mycobacterial pathogenesis in humans and forms the basis for future functional studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1889-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Verlaine J Timms
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia. .,Centre for Infectious Diseases and Microbiology, Institute of Clinical Microbiology and Medical Research, Westmead Hospital, Sydney, NSW, Australia.
| | - Karl A Hassan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia.
| | - Hazel M Mitchell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
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14
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Timms VJ, Mitchell HM, Neilan BA. Optimisation of DNA extraction and validation of PCR assays to detect Mycobacterium avium subsp. paratuberculosis. J Microbiol Methods 2015; 112:99-103. [PMID: 25797305 DOI: 10.1016/j.mimet.2015.03.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/10/2015] [Accepted: 03/17/2015] [Indexed: 11/27/2022]
Abstract
The aim of this study was to investigate DNA extraction methods and PCR assays suitable for the detection of Mycobacterium paratuberculosis in bovine tissue. The majority of methods currently used to detect M. paratuberculosis have been developed using bovine samples, such as faeces, blood or tissue and, in many cases, have been based on detection from pooled samples from a herd. However most studies have not compared PCR results to culture results. In order to address this problem, four DNA extraction protocols and three PCR assays were employed to detect M. paratuberculosis in bovine tissue. Given that culture is reliable from cows, the results were then compared with the known M. paratuberculosis culture status. The following DNA extractions were included, two commercial kits, a boiling method, an in house extraction based on a published method and enrichment by sonication. The three PCR assays used included single round IS900 and f57 assays and a nested IS900 assay. In addition, another PCR assay was validated for the detection of any Mycobacterial species and a universal bacterial 16S rRNA gene assay was used to detect sample inhibition. The in-house DNA extraction was the most consistent in extracting good quality DNA compared to all other methods. The use of two PCR markers, IS900 and f57, and a universal PCR enabled the correct samples to be identified as M. paratuberculosis positive. In addition, when compared to the culture result, false-positives did not occur and PCR inhibition was readily identified. Using an in house DNA extraction coupled with the IS900 and f57 PCR markers, this study provides a reliable and simple method to detect M. paratuberculosis in both veterinary and spill over infections.
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Affiliation(s)
- Verlaine J Timms
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia.
| | - Hazel M Mitchell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia.
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia.
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Timms VJ, Gehringer MM, Mitchell HM, Daskalopoulos G, Neilan BA. How accurately can we detect Mycobacterium avium subsp. paratuberculosis infection? J Microbiol Methods 2011; 85:1-8. [PMID: 21281678 DOI: 10.1016/j.mimet.2011.01.026] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 01/20/2011] [Accepted: 01/24/2011] [Indexed: 01/03/2023]
Abstract
Mycobacteria have thwarted detection by scientists for centuries. Mycobacterium paratuberculosis is one of the most fastidious of the Mycobacteriaceae, and has been implicated in both animal and human diseases. In domestic livestock, M. paratuberculosis has been associated with Johne's disease, which given its increasing incidence, is currently a cause for concern, due to the potential for M. paratuberculosis to enter our food chain. In addition, a tenuous link has been reported between M. paratuberculosis and Crohn's disease, however evidence to support this link is hampered by the lack of accurate methodologies for detection of M. paratuberculosis in humans. This review compares the sensitivity and specificity of traditional and more recent techniques to the culture and molecular detection of M. paratuberculosis. While serology and culture are popular choices for the livestock industry they have not produced useful data for human infection. Although the advent of molecular biology has enabled faster diagnosis of M. paratuberculosis in human infection, there is currently no gold standard such as culture on which to validate these findings. Even with DNA/RNA detection methods, there is the ever present issue of the genetic relatedness of M. paratuberculosis to other mycobacteria of the Mycobacterium avium complex, some of which also infect humans with very different pathological outcomes. Recent developments in this field include more rapid methods of M. paratuberculosis culture as well as the development of more accurate and sensitive PCR assays. The application of these techniques should offer a greater insight as to the role of M. paratuberculosis in human gastrointestinal diseases.
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Affiliation(s)
- Verlaine J Timms
- School of Biotechnology and Biomolecular Science, University of NSW, Sydney, NSW 2052, Australia.
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