CV

EDUCATION

• Bachelor of Applied Science (Biotechnology, Biochemistry), Queensland University of Technology, 2005

• Master of Biotechnology, The University of Queensland, 2013

  Dean’s commendation for academic excellence. Course GPA: 6.75/7.00 (96.4%)

• PhD (Microbial Genomics), The University of Queensland, 2019

  Thesis: Evolution and function of mobile genetic elements and DNA methyltransferases in extraintestinal pathogenic Escherichia coli.

RESEARCH EXPERIENCE

Freelance Researcher (Microbial Genomics) (Mar 2022 – continuing)

• Comparative genomics and phylogenomics of Gram-negative bacterial pathogens
• Scientific/academic writing and editing

Scientific Consultant (Biotechnology), Obsidian Ventures and Consulting (Mar 2022 – continuing)

• Facilitated meetings between researchers and biopharmaceutical manufacturing companies
• Data analysis - Designed a 3D risk matrix model for potential therapeutic development

Postdoctoral Research Officer in Bioinformatics (Oct 2019 – Feb 2022). Department of Microbiology and Immunology, The University of Melbourne, Australia.

Genomic epidemiology of Neisseria gonorrhoeae

• Genomics of within-host and within-sample population variation
• Phylogenomic and phylodynamic analysis of antimicrobial resistant lineages
• Longitudinal genomic epidemiology and transmission dynamics
• Comparative genomics and Nanopore sequencing of complete genomes

Research Associate (Feb 2019 – Sep 2019). School of Chemistry and Molecular Biosciences, The University of Queensland, Australia.

Genomics and epigenomics of extraintestinal pathogenic Escherichia coli

• Comparative genomics and phylogenomics of antimicrobial resistant lineages
• Characterising the function and evolution of DNA methylation

Graduate Researcher- PhD (2014-2019). School of Chemistry and Molecular Biosciences, The University of Queensland, Australia.

Genomics and epigenomics of extraintestinal pathogenic Escherichia coli

• Comparative genomics and PacBio sequencing of complete genomes
• Phylogenomic analysis of antimicrobial resistant lineages
• Characterising the function and evolution of DNA methylation
• Characterising the association between the methylome and transcriptome

Graduate Researcher – Master of Biotechnology (2013). School of Chemistry and Molecular Biosciences, The University of Queensland, Australia.

• Minor Thesis Project (2013): Potential IRF4 and MITF cooperative transcriptional regulation in melanoma and an evolutionary analysis of the intronic transcriptional enhancer region in IRF4
• Minor Thesis Project (2012): Determining a protocol for total RNA extraction and the measurement of RNA integrity for chemical irritant induced, skin inflammation gene expression studies
• Summer Research Project (2013): A bioinformatic analysis of the E. coli genome
• Summer Research Project (2012): Metabolic engineering for increased production of isoprenoids

TEACHING AND SUPERVISION EXPERIENCE

Guest lecturer – Department of Microbiology and Immunology, The University of Melbourne (2021).

MIIM30011 (Medical Microbiology: Bacteriology)

• Delivered 1-hour guest lecture on Niesseria gonorrhoeae pathogenesis, virulence, antimicrobial resistance, and genomics. Development of multiple-choice questions for examinations

Co-supervisor – Department of Microbiology and Immunology, The University of Melbourne (2020).

• Honours student (10% supervisor load). Student awarded first-class honours (88%), which led to first-author publication of thesis chapter in the Journal of Clinical Microbiology (2021)

Core practicals convenor and lecturer – School of Chemistry and Molecular and Molecular Biosciences, The University of Queensland (2019).

BIOL3004 – Genomics and Bioinformatics 3rd year undergraduate course

• Development of practical materials for 5 practicals and tutor training
• Development of and grading of assessment (5 quizzes and 1 assignment)
• Delivered two 1-hour lectures: i) Next Generation Sequencing and ii) Revision lecture on the core practicals module
• Class size was approximately 60-80 students per lecture and 30-40 students per practical. Received 4.7/5 average rating for teaching effectiveness from student evaluations

Teaching assistant – School of Chemistry and Molecular Biosciences, The University of Queensland (2015-2019).

• Subjects: Genomics and Bioinformatics (BIOL3004), Microbes and Human Health (MICR3001), Human Molecular Genetics and Disease (BIOC3003), Advanced Genome Informatics (BINF7001 – Masters level course)
• Class sizes ranged from 15 to 45 students per class. Taught an average of 3 classes per week. Received 4.84/5 average rating for tutoring effectiveness from student evaluations. Won three tutor awards
• Preparation and delivery of computer practicals and problem-based learning tutorials
• Creation and ongoing development of assessment and development of training materials as head tutor (BIOL3004) 2017-2019
• Grading assessments and examination invigilation (Also includes grading for the subjects: Genetics (BIOL2202), Emerging Biotechnologies (BIOT7009) and Issues in Biotechnology (BIOT2002/BIOT7033))

Tutoring – Indigenous Tutorial Assistance Scheme. Aboriginal and Torres Strait Islander Studies Unit, The University of Queensland (2017).

• One on one tutoring, 2 students each semester. Subjects: Genomics and Bioinformatics (BIOL3004), Genetics (BIOL2202) and Microbial Genomics (MICR3004) Tutoring – Disability services. Student services – The University of Queensland (2016).
• Helped to edit master and doctoral theses (Advanced Water Management, Biotechnology)

RESEARCH AND TEACHING INTERESTS

Microbial genomics, Computational Biology, Bioinformatics, Genomic epidemiology, Comparative genomics, Pathogen evolution, Phylogenomics, Antimicrobial resistance, Transmission dynamics, Virulence/Pathogenesis, Methylome/epigenomics, Phylodynamics, Data visualisation, Biostatistics

Publications

Primary Research Articles (Peer Reviewed)

Lee DYJ, Ashcroft MM, Chow EPF, Sait M, De Petra V, Tschape M, Lange S, Taiaroa G, Bradshaw CS, Whiley DM, Fairley CK, Howden BP, Chen MY, Pasricha S and Williamson DA. Reflex Detection of Ciprofloxacin Resistance in Neisseria gonorrhoeae by Use of the SpeeDx ResistancePlus GC Assay. J Clin Microbiol. 2021. 59(5): e00089-21. https://doi.org/10.1128/JCM.00089-21

Chow EPF, Vodstrcil LA, Williamson DA, Maddaford K, Hocking JS, Ashcroft M, De Petra V, Bradshaw CS and Fairley CK. Incidence and duration of incident oropharyngeal gonorrhoea and chlamydia infections among men who have sex with men: prospective cohort study. Sex Transm Infect. 2021. 97(6): 452-457. https://doi.org/ 10.1136/sextrans-2020-054764

Hicks AL, Kissler SM, Mortimer TD, Ma KC, Taiaroa G, Ashcroft M, Williamson DA, Lipstich M and Grad YH. Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants. eLife. 2020. 9: e56367. https://doi.org/10.7554/eLife.56367

Chhabra Y, Yong HXL, Fane ME, Soogrim A, Lim W, Mahiuddin DN, Kim RSQ, Ashcroft M, Beatson SA, Ainger SA, Smit DJ, Jagirdar K, Walker GJ, Sturm RA and Smith AG. Genetic variation in IRF4 expression modulates growth characteristics, tyrosinase expression and interferon-gamma response in melanocytic cells. Pigment Cell Melanoma Res. 2017. 31(1): 51-63. https://doi.org/10.1111/pcmr.12620

Ben Zakour NL, Alsheikh-Hussain AS, Ashcroft MM*, Khanh Nhu NT, Roberts LW, Stanton-Cook M, Schembri MA and Beatson SA. Sequential Acquisition of Virulence and Fluoroquinolone Resistance Has Shaped the Evolution of Escherichia coli ST131. mBio. 2016. 7(2): e00347-16. https://doi.org/10.1128/mBio.00347-16 *Authors contributed equally.

Forde BM, Phan MD, Gawthorne JA, Ashcroft MM, Stanton-Cook M, Sarkar S, Peters KM, Chan KG, Chong TM, Yin WF, Upton M, Schembri MA and Beatson SA. Lineage-Specific Methyltransferases Define the Methylome of the Globally Disseminated Escherichia coli ST131 Clone. mBio. 2015. 6(6): e01602-15. https://doi.org/10.1128/mBio.01602-15

Primary Research Articles (Not Peer Reviewed)

White RT, Bull MJ, Barker CR, Arnott JM, Wootton M, Jones LS, Howe RA, Morgan M, Ashcroft MM, Forde BM, Connor TR and Beatson SA. Genomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli sequence type (ST)131 associated with bacteraemia in Wales, United Kingdom. medRxiv. 2021. https://doi.org/10.1101/2021.05.21.21257487

Ashcroft MM, Chow EPF, Lee DYJ, De Petra V, Soumilas M, Tschaepe M, Zhang L, Ingle DJ, Taiaroa G, Hicks AL, Grad YH, Howeden BP, Fairley CK and Williamson DA. Genomic assessment of within-host population variation in Neisseria gonorrhoeae: Implications for gonorrhoea transmission. medRxiv. 2020. https://doi.org/10.1101/2020.08.24.20181230

Ashcroft MM, Forde BM, Phan MD, Peters KM, Henderson A, Hancock SJ, Roberts LW, White RT, Chan KG, Chong TM, Yin WF, Walsh TR, Paterson DL, Schembri MA and Beatson SA. Genomic characterisation and context of the blaNDM-1 carbapenemase in Escherichia coli ST101. bioRxiv. 2020. https://doi.org/10.1101/860726

Ashcroft MM, Forde BM, Peters KM, Phan MD, Chan KG, Chong TM, Yin WF, Walsh TR, Paterson DL, Schembri MA and Beatson SA. Strain and lineage-level methylome heterogeneity in the multi-drug resistant pathogenic Escherichia coli ST101 clone. bioRxiv. 2020. https://doi.org/10.1101/2020.06.07.138552

Conferences, symposiums and invited seminars

Invited talks/seminars

• Phylogenomic analysis of Neisseria gonorrhoeae lineages associated with reduced susceptibility to extended spectrum cephalosporins and mosaic penA alleles in Australia. Joint Australasian Sexual Health and HIV&AIDS Conferences: Virtual. Sep 2021
• Defining within-host genetic variation for understanding gonorrhoea transmission between individuals. Department Seminar: Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia: Virtual. Jul 2021
• Genomic assessment of within-host population variation in Neisseria gonorrhoeae: Implications for gonorrhoea transmission. Australian Society of Microbiology meeting: Virtual. Jun 2021
• A minimum bioinformatics framework for Neisseria gonorrhoeae transmission studies: Defining within-host and within-site genetic diversity. Department Seminar: Murdoch Children’s Research Institute, Melbourne, VIC, Australia. Feb 2020
• The benefits of long-read sequencing technology in the genomics of Escherichia coli ST101. Genomics in clinical and public health microbiology workshop. Australian Society of Microbiology meeting, Adelaide, SA, Australia. Jul 2019
• Mobile Genetic Elements drive the evolution of Escherichia coli lineages. Brisbane Joint Academic Microbiology Seminars, Brisbane, QLD, Australia. May 2019
• The evolutionary implications of mobile genetic element acquisition in multidrug resistant Escherichia coli ST101. The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia. May 2019
• Genomic characterisation of mobile genetic elements and their association with antimicrobial resistance and DNA methylation in an atypical ExPEC clone. Microbiology in Moreton Bay, QLD, Australia. Nov 2017
• Genomic characterisation of carbapenem resistance conferred by the plasmid-encoded blaNDM-1 gene in the extraintestinal pathogenic lineage Escherichia coli ST101. Australian Society of Microbiology meeting – Planetary Health Conference, Hobart, TAS, Australia. Jul 2017

Oral presentations

• Genomic characterisation of the Neisseria gonorrhoeae population structure in Victoria, Australia from 2017-2020. Plus On Demand Content: Genomic assessment of within-host population variation in Neisseria gonorrhoeae: Implications for gonorrhoea transmission. Joint Australasian Sexual Health and HIV&AIDS Conferences: Virtual. Nov 2020. ECR award: best presentation
• Whole genome sequencing reveals limited within-host variability in Neisseria gonorrhoeae from multiple anatomical sites. MicroBinfie Virtual Conference International. Apr 2020
• Clonal replacement rather than persistence of lineages drives the gonorrhoea epidemic in Victoria, Australia. Antimicrobials 2020, Australian Society for Antimicrobials. Feb 2020
• The evolutionary implications of mobile genetic element acquisition in the multidrug resistant Escherichia coli ST101 clone. Australian Society of Microbiology meeting, Adelaide, SA, Australia. Jul 2019
• Genomic characterisation of carbapenem resistance conferred by the plasmid-encoded blaNDM-1 gene in the extraintestinal pathogenic lineage Escherichia coli ST101. Mobile Genetic Elements Conference, Sydney, NSW, Australia. Apr 2017

Poster presentations

• Genomic surveillance of Neisseria gonorrhoeae population structure and antimicrobial resistance in Victoria, Australia. Wellcome Trust: Antimicrobial Resistance - Genomes, Big Data and Emerging Technologies (Virtual Conference). Nov 2020
• Whole genome sequencing reveals limited intra-patient variability in Neisseria gonorrhoeae from multiple anatomical sites within individuals. Australian Society of Antimicrobials 2020 conference, Melbourne, VIC, Australia. Feb 2020. Winner of best poster: Travel award
• New insights into the functional roles of DNA methylation in extraintestinal pathogenic Escherichia coli. Australian Society of Microbiology meeting, Brisbane, QLD, Australia. Jul 2018
• Understanding the genomic context of DNA methyltransferases in the extraintestinal pathogenic Escherichia coli ST101 clone. BacPath 14: The Molecular Biology of Bacterial Pathogens, Adelaide, SA, Australia. Sep 2017. Winner of best student poster
• Genomic characterisation of E. coli ST101; an extraintestinal pathogenic clonal lineage. COMBINE 2016 and The Australian Bioinformatics and Computational Biology Society Inc. Conference. Brisbane, QLD, Australia. Nov 2016
• Mapping the methylome: Distribution of methyltransferase target sites in the uropathogen Escherichia coli EC958. 11th Annual SCMB Student Research Symposium. The University of Queensland, QLD, Australia. Nov 2015. Poster presentation award: Third Prize
• Mapping the methylome: Distribution of methyltransferase target sites in the uropathogen Escherichia coli EC958. BacPath 13: Molecular Analysis of Bacterial Pathogens. Phillip Island, VIC, Australia. Sep 2015

SERVICE, DEVELOPMENT AND OUTREACH

Academic Service

• Education and professional development Committee member – Microbiology at the Royal Melbourne Hospital (2020-2022)
• Student representative on the selection panel for the new Level D/E (Program director) position in Biotechnology at the School of Chemistry and Molecular Biosciences (2018)
• Elected chair of the School of Chemistry and Molecular Biosciences Research Students Advisory Group (2015). Elected deputy chair (2016). Active member of the committee involved in communication between the school and students.
• Organising committee member of the School of Chemistry and Molecular Biosciences Research Students Symposium (2015 and 2016)
• Student representative at the School of Chemistry and Molecular Biosciences Strategic Retreat (2016) – With a focus on teaching, learning, research, and engagement

Professional Service

• Australian Society of Microbiology Communications Ambassador (2017-2022)
• Journal reviewer: Microbial Genomics (2021 outstanding reviewer award, 2020 top reviewer award), mSystems and Journal of Global Antimicrobial Resistance
• Session chair: Omics. Australian Society of Microbiology meeting. Adelaide, SA, Australia. July 2019
• Online science communication outreach activities. Twitter: @biominnie (2016-2022)
• COMBINE Media and Communications Ambassador (2018)
• Helped to organise social networking events as a member of the COMBINE Brisbane Branch (2015-2017)
• Vice President of the UQ Molecular Biotechnology Student Club (Facebook) (2014-2019)
• Graduate mentor and program supervisor – Pairing new masters students in biotechnology and molecular biology with more experienced students to help with cultural differences, provide study advice and help with finding a research supervisor. Organised through the UQ Molecular Biotechnology Student Club (2013-2015)

Professional Development

• Sydney Phylogenetics Workshop: Bayesian phylogenetics, molecular dating and phylogenomics (2021)
• PUBH7630: Introduction to Biostatistics. GPA: 7/7 (High Distinction) – The University of Queensland, Australia (2019)
• Communications Training Workshop – The Social Science. Australian Society of Microbiology meeting, Brisbane, QLD, Australia (2018)
• Nature Microbiology Writing Workshop, The University of Queensland, Australia – Hosted by the Australian Society of Microbiology (2017)
• 3 Minute Thesis – School of Chemistry and Molecular Biosciences, The University of Queensland, Australia (2017)
• MixOmics – exploration and integration of ‘omics data’ 2-day statistics workshop. QLD Australia (2015)
• Winter School in Mathematical and Computational Biology, hosted at the Institute for Molecular Biosciences, The University of Queensland, Australia (2014 & 2015)
• Australian Microbial Genomics Symposium – Sydney Institute of Marine Science, NSW Australia (2015)
• Software Carpentry Workshop. Introduction to Bash, Python, GitHub and Databases – The University of Queensland, Australia (2014)
• Statistics for Frightened Bio-Researchers workshop – Hosted at the Institute of Molecular Biosciences, The University of Queensland, Australia (2014)
• The Data Scientists Toolbox – Johns Hopkins University, USA (delivered through Coursera) (2014). High Distinction
• Audited STAT7174: Applications of Computational Statistics

FUNDING, HONOURS AND AWARDS

• Early Career Researcher Grant – The University of Melbourne (2021). $31,886 for Project: Applying genomic epidemiology to understand gonorrhoea transmission
• Early Career Award Winner. Best presentation in the Discovery and Translational Science Theme. Awarded complimentary registration to attend the 2021 ASHM conference. Joint Australasian Sexual Health and HIV&AIDS Conferences (2020)
• Best Poster Prize. Travel Award with flights, accommodation, and conference registration (up to a value of $2500). Australian Society of Antimicrobials conference (2020)
• Conference registration bursary (2018 & 2019). $200 – Australian Society of Microbiology meeting
• Top tutor award (semester 2, 2017, semester 1, 2018 and semester 1, 2019) – The University of Queensland
• Best Student Poster Prize. $300. BacPath14: The Molecular Biology of Bacterial Pathogens Conference (2017)
• Becton Dickinson (now Nancy Millis) Student Travel Award. Flights, accommodation, and conference registration (Approx. $1200). Australian Society of Microbiology meeting – Planetary Health Conference (2017)
• Poster Presentation, Third prize. $50. School of Chemistry and Molecular Biosciences Research Students Symposium (2015)
• Australian Postgraduate Award (APA) – Australian Government scholarship. $25,000 annually (2014-2017)
• Dean’s commendation for Academic Excellence – Master of Biotechnology (2013)
• The University of Queensland Future Leader (Class of 2013)
• Summer research scholarship (2013). $3000. School of Chemistry and Molecular Biosciences, The University of Queensland
• Summer research scholarship (2012). $3000. Australian Institute of Bioengineering and Nanotechnology, The University of Queensland

AREAS OF EXPERTISE

Computers:

Unix and Linux systems. Competent using terminal. High Performance Computing Clusters. Microsoft Office Suite and Adobe Creative Suite

Programming:

Intermediate scripting proficiency in Bash, R (inc. Bioconductor) and Python (inc. Biopython, Numpy, Pandas)

Genomics/Bioinformatics:

Next-Generation Sequence analysis – Oxford Nanopore, Pacific Biosciences and Illumina sequencing; genome assembly, genome annotation; comparative genomics; read mapping and variant calling; genome alignments; phylogenetic trees; recombination detection; in silico typing; data visualisation; statistical inference and probability; demonstrated ability to manage, interpret and analyse large and complex datasets

Research:

Effective project management; demonstrated interpersonal and teamwork skills; strong organisational and critical-thinking skills; ability to work autonomously; accurate record keeping skills for version control and reproducibility; excellent verbal and written communication skills; endorsed and capable supervisor; proficient science communicator

PROFESSIONAL MEMBERSHIPS

• Australian Society for Microbiology. 2014-2022
• The Australian Bioinformatics and Computational Biology Society. 2015-2022
• American Society of Microbiology. 2016-2022
• Australian Society of Antimicrobials. 2019-2022
• Society for Molecular Biology and Evolution. 2015-2020
• COMBINE - a student-run Australian organisation for students in computational biology, bioinformatics, and related fields (2016-2018)