Dr Verlaine Timms

Dr Verlaine Timms

Senior Research Fellow

School of Environmental and Life Sciences

Career Summary

Biography

Combining Planetary and Public Health to tackle complex problems

I work (& teach) on environmental sustainability and antimicrobial resistance. My research helps to improve the management of both useful bacteria and those that are pathogenic to humans. By investigating how these microbes survive in the environment, we can draw valuable insights into how they infect humans and evade treatment.

Using cutting edge technologies such as Next Generation Sequencing (NGS) we can resolve the evolution of essential iron uptake systems and the evolution of antimicrobial resistance. Both are vital in learning about the microbes we are exposed to every day.

I am 6 years post-PhD and previously worked on pathogens with epidemic potential. I've used genomics to investigate antibiotic resistance and virulence evolution of multiple infectious disease outbreaks including Legionnaire's disease, pertussis, diphtheriae and VRE.

I was a founding member of the research team that established the pathogen sequencing facility at NSW Health Pathology, a facility that has been instrumental in NSW's Covid-19 response. I have promoted microbial genomics through the organizing of Bioinformatics Seminars and have advised at a National level on several working groups for the Communicable Disease Genomics Network.

I love teaching genomics and have established units in Pathogen Genomics, conducted summer schools and developed online courses with Prof. Vitali Sintchenko for the University of Sydney.


Qualifications

  • Doctor of Philosophy, University of New South Wales

Keywords

  • Bioinformatics
  • Genome sequencing
  • Microbial Genomics
  • Molecular Biology

Fields of Research

Code Description Percentage
310204 Genomics and transcriptomics 30
310206 Sequence analysis 50
320701 Medical bacteriology 20

Professional Experience

UON Appointment

Title Organisation / Department
Senior Research Fellow University of Newcastle
School of Environmental and Life Sciences
Australia

Academic appointment

Dates Title Organisation / Department
20/3/2015 - 25/3/2021 Postodoctoral Research Fellow in Molecular Microbiology Westmead Hospital (Sydney)
Australia
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Publications

For publications that are currently unpublished or in-press, details are shown in italics.


Journal article (23 outputs)

Year Citation Altmetrics Link
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)
DOI 10.3389/fmed.2021.641260
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)
DOI 10.3389/fvets.2021.637637
Citations Scopus - 1Web of Science - 1
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)
DOI 10.1038/s41591-020-1000-7
Citations Scopus - 76Web of Science - 73
2020 Fong W, Rockett R, Timms V, Sintchenko V, 'Optimization of sample preparation for culture-independent sequencing of Bordetella pertussis', MICROBIAL GENOMICS, 6 (2020)
DOI 10.1099/mgen.0.000332
Citations Scopus - 2Web of Science - 2
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)
DOI 10.1099/mgen.0.000471
Citations Scopus - 1Web of Science - 1
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)
DOI 10.1016/j.pathol.2018.10.018
2019 Xu Z, Octavia S, Luu LDW, Payne M, Timms V, Tay CY, et al., 'Pertactin-Negative and Filamentous Hemagglutinin-Negative Bordetella pertussis, Australia, 2013-2017', EMERGING INFECTIOUS DISEASES, 25 1196-1199 (2019)
DOI 10.3201/eid2506.180240
Citations Scopus - 10Web of Science - 10
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.

DOI 10.1093/jac/dky074
Citations Scopus - 11Web of Science - 11
Co-authors John Ferguson
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)
DOI 10.1016/j.pathol.2017.10.014
Citations Scopus - 6Web of Science - 4
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)
DOI 10.1128/AEM.02020-17
Citations Scopus - 6Web of Science - 5
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)
DOI 10.1186/s12864-018-5147-2
Citations Scopus - 7Web of Science - 8
2018 Rockett RJ, Oftadeh S, Bachmann NL, Timms VJ, Kong F, Gilbert GL, Sintchenko V, 'Genome-wide analysis of Streptococcus pneumoniae serogroup 19 in the decade after the introduction of pneumococcal conjugate vaccines in Australia', SCIENTIFIC REPORTS, 8 (2018)
DOI 10.1038/s41598-018-35270-1
Citations Scopus - 3Web of Science - 4
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)
DOI 10.3389/fpubh.2018.00363
Citations Scopus - 16Web of Science - 15
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)
DOI 10.3791/56714
Citations Scopus - 10Web of Science - 9
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)

On March 24 and 25, 2017 researchers and clinicians from around the world met at Temple University in Philadelphia to discuss the current knowledge of Mycobacterium avium ssp. par... [more]

On March 24 and 25, 2017 researchers and clinicians from around the world met at Temple University in Philadelphia to discuss the current knowledge of Mycobacterium avium ssp. paratuberculosis (MAP) and its relationship to human disease. The conference was held because of shared concern that MAP is a zoonotic bacterium that poses a threat not only to animal health but also human health. In order to further study this problem, the conferees discussed ways to improve MAP diagnostic tests and discussed potential future anti-MAP clinical trials. The conference proceedings may be viewed on the www.Humanpara.org website. A summary of the salient work in this field is followed by recommendations from a majority of the conferees.

DOI 10.3389/fpubh.2017.00208
Citations Scopus - 47Web of Science - 47
Co-authors Brett Neilan
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]
DOI 10.1371/journal.pone.0148731
Citations Scopus - 24Web of Science - 24
Co-authors Brett Neilan
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]
DOI 10.1016/j.mimet.2015.03.016
Citations Scopus - 11Web of Science - 11
Co-authors Brett Neilan
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]
DOI 10.1186/s12864-015-1889-2
Citations Scopus - 15Web of Science - 14
Co-authors Karl Hassan, Brett Neilan
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)
DOI 10.1016/j.mimet.2011.01.026
Citations Scopus - 43Web of Science - 41
Co-authors Brett Neilan
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)
DOI 10.1136/gut.49.3.341
Citations Scopus - 70Web of Science - 53
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)
DOI 10.1136/jcp.54.5.408
Citations Scopus - 7Web of Science - 7
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)
DOI 10.1136/jcp.51.1.55
Citations Scopus - 106Web of Science - 91
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)
DOI 10.1093/infdis/174.3.631
Citations Scopus - 116Web of Science - 126
Show 20 more journal articles

Conference (3 outputs)

Year Citation Altmetrics Link
1999 Warburton-Timms VJ, Nair S, Uff JS, McNulty CAM, 'CagA is important for the persistence of Helicobacter pylori infection', GUT (1999)
1999 Basynat PS, Evans G, Warburton VJ, McNulty CAM, Stock D, Woodward A, Foster ME, 'Is there an association between Helicobacter pylori and colorectal cancer?', GUT (1999)
Citations Web of Science - 1
1998 Warburton VJ, McNulty CAM, Shepherd N, Valori R, Barr H, Uff JS, 'The importance of cagA(+) Helicobacter pylori to the development of oesophageal disease', GUT (1998)
Citations Web of Science - 2

Other (6 outputs)

Year Citation Altmetrics Link
2021 Fong W, Pey K, Rockett R, Sadsad R, Sintchenko V, Timms V, 'Comparison of library preparation and sequencing depths for direct sequencing of Bordetella pertussis positive samples', bioRxiv (2021) [O1]
DOI 10.1101/2021.02.14.430694
2020 Rockett R, Arnott A, Lam C, Sadsad R, Timms V, Gray K-A, et al., 'Revealing COVID-19 Transmission by SARS-CoV-2 Genome Sequencing and Agent Based Modelling', bioRxiv (2020) [O1]
DOI 10.1101/2020.04.19.048751
2019 Baines S, Gonçalves da Silva A, Carter G, Jennison A, Rathnayake I, Graham R, et al., 'Complete microbial genomes for public health in Australia and Southwest Pacific', bioRxiv (2019) [O1]
DOI 10.1101/829663
2017 Timms VJ, Rockett R, Bachmann NL, Martinez E, Wang Q, Chen SC-A, et al., 'Genome sequencing links persistent outbreak of legionellosis in Sydney to an emerging clone of Legionella pneumophila ST211', bioRxiv (2017) [O1]
DOI 10.1101/144790
2017 Timms V, Nguyen T, Crighton T, Yuen M, Sintchenko V, 'Genome-wide comparison of toxigenic and non-toxigenicCorynebacterium diphtheriaeisolates identifies differences in the pan genomes between respiratory and cutaneous strains', bioRxiv (2017) [O1]
DOI 10.1101/143800
Fong W, Timms V, Sim E, Sintchenko V, 'Genomic evaluation of Bordetella spp. originating from Australia', Cold Spring Harbor Laboratory [O1]
DOI 10.1101/2021.03.02.433639
Show 3 more others
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Dr Verlaine Timms

Position

Senior Research Fellow
School of Environmental and Life Sciences
College of Engineering, Science and Environment

Contact Details

Email verlaine.timms@newcastle.edu.au
Link Twitter

Office

Room 216b
Building Chemistry Building
Location Callaghan
University Drive
Callaghan, NSW 2308
Australia
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