Dr Anna Sheppard

Lecturer

School of Biological Sciences

Faculty of Sciences, Engineering and Technology

Eligible to supervise Masters and PhD - email supervisor to discuss availability.


Dr Anna Sheppard is a Lecturer in Bioinformatics at the University of Adelaide. Her research uses bacterial whole-genome sequencing to investigate the molecular epidemiology and transmission of bacterial pathogens both within outbreaks, as well as across geographic and ecological barriers within a One Health framework. She has a particular focus on antimicrobial resistance dissemination driven by mobile genetic elements, and she has developed novel bioinformatic methods for resistance gene tracking. Her research has been published in leading journals including the New England Journal of Medicine, Nature Microbiology, and the Proceedings of the National Academy of Sciences.

Anna completed her PhD at the University of Adelaide in 2009, before undertaking postdoctoral training at Kiel University, Germany, and the University of Oxford, UK. She returned to the University of Adelaide as a Lecturer in the School of Biological Sciences in December 2021.

Modern medicine is heavily dependent on the availability of effective antibiotics. The increasing prevalence of antimicrobial resistance (AMR) in bacterial pathogens threatens to push medicine towards a ‘post-antibiotic’ era, where bacterial infections can no longer be reliably treated. Our research aims to improve understanding of bacterial genome evolution driving AMR dissemination, with the longer-term goal of using this information for designing interventions to reduce the spread of resistance.

Research in the Sheppard lab focuses particularly on ‘mobile AMR genes’ that can be transferred horizontally and confer resistance in different bacterial species. Mobility of these genes is driven by associations with different types of mobile genetic elements (MGEs), including:

  • Plasmids, which drive horizontal transfer between different bacteria
  • Transposons, which drive intracellular mobilisation from one genomic location to another (e.g. one plasmid to another, or from a plasmid to the chromosome)
  • Integrons, which can capture multiple AMR genes, generating multi-drug resistance regions

AMR genes can be contained within multiple nested MGEs, creating ‘Russian Doll-like’ hierarchies, where each MGE is capable of independent mobilisation (Fig. 1). Over time, activity of different MGEs drives AMR gene spread across different plasmids and to different host bacteria. Because many different MGEs can be involved, AMR gene spread is associated with varied, and often complex, genomic rearrangements.

Nested MGEs containing an AMR gene

Our research uses whole-genome sequencing of bacterial pathogens to investigate mobile AMR genes and their associated MGEs. We use both short-read and long-read sequencing technologies. Long-read sequencing is particularly important for determining the genetic contexts of AMR genes because many MGEs are repetitive and therefore assemble poorly using short-read data. With long-read whole-genome sequencing we can routinely assemble complete, fully closed bacterial genomes, with a single contig for the bacterial chromosome and one contig for each plasmid.

We are particularly interested in determining dissemination pathways of mobile AMR genes. This is important both for characterising short-term transmission pathways for guiding infection control, as well as broader dissemination across geographic, ecological and species barriers for guiding strategies to tackle resistance within a One Health framework. In addition, we are interested in developing approaches for AMR gene tracking in the context of AMR surveillance.

Our research aims to:

  • Determine how associations with different MGEs impact AMR spread
  • Determine how MGE activity impacts bacterial genome evolution
  • Improve biological understanding of MGEs driving AMR gene mobility
  • Inform optimal sequence-based surveillance strategies for tracking critical AMR genes
  • Develop software for AMR gene tracking using whole-genome sequencing data

Student Opportunities

Postgraduate and undergraduate student opportunities are available in the Sheppard lab, and we welcome students from both biological and computational backgrounds. While some previous bioinformatics experience is preferable, it is not necessary.

  • Journals

    Year Citation
    2021 Matlock, W., Chau, K. K., AbuOun, M., Stubberfield, E., Barker, L., Kavanagh, J., . . . Woodford, N. (2021). Genomic network analysis of environmental and livestock F-type plasmid populations. The ISME Journal, 15(8), 2322-2335.
    DOI Scopus6 Europe PMC4
    2021 AbuOun, M., Jones, H., Stubberfield, E., Gilson, D., Shaw, L. P., Hubbard, A. T. M., . . . Anjum, M. F. (2021). A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage. Microbial Genomics, 7(10).
    DOI
    2021 Shaw, L. P., Chau, K. K., Kavanagh, J., AbuOun, M., Stubberfield, E., Gweon, H. S., . . . Sheppard, A. (2021). Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae. Science Advances, 7(15).
    DOI
    2020 Mathers, A. J., Vegesana, K., German-Mesner, I., Ainsworth, J., Pannone, A., Crook, D. W., . . . Eyre, D. W. (2020). Risk factors for Klebsiella pneumoniae carbapenemase (KPC) gene acquisition and clinical outcomes across multiple bacterial species. Journal of Hospital Infection, 104(4), 456-468.
    DOI Scopus13 Europe PMC4
    2020 Davies, T. J., Stoesser, N., Sheppard, A. E., Abuoun, M., Fowler, P., Swann, J., . . . Walker, A. S. (2020). Reconciling the Potentially Irreconcilable? Genotypic and Phenotypic Amoxicillin-Clavulanate Resistance in Escherichia coli. Antimicrobial Agents and Chemotherapy, 64(6), 1-16.
    DOI Scopus12 Europe PMC7
    2020 David, S., Cohen, V., Reuter, S., Sheppard, A. E., Giani, T., Parkhill, J., . . . Aanensen, D. M. (2020). Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among Klebsiella pneumoniae. Proceedings of the National Academy of Sciences, 117(40), 25043-25054.
    DOI Scopus38 Europe PMC32
    2019 Elliott, Z. S., Barry, K. E., Cox, H. L., Stoesser, N., Carroll, J., Vegesana, K., . . . Mathers, A. J. (2019). The Role of fosA in Challenges with Fosfomycin Susceptibility Testing of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Clinical Isolates. Journal of Clinical Microbiology, 57(10), 1-8.
    DOI Scopus14 WoS18 Europe PMC10
    2019 De Maio, N., Shaw, L. P., Hubbard, A., George, S., Sanderson, N. D., Swann, J., . . . Woodford, N. (2019). Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes. MICROBIAL GENOMICS, 5(9), 12 pages.
    DOI Scopus94 WoS90 Europe PMC65
    2019 Rooney, C. M., Sheppard, A. E., Clark, E., Davies, K., Hubbard, A. T. M., Sebra, R., . . . Chilton, C. H. (2019). Dissemination of multiple carbapenem resistance genes in an in vitro gut model simulating the human colon. Journal of Antimicrobial Chemotherapy, 74(7), 1876-1883.
    DOI Scopus14 WoS13 Europe PMC3
    2019 Mathers, A. J., Crook, D., Vaughan, A., Barry, K. E., Vegesana, K., Stoesser, N., . . . Sheppard, A. E. (2019). Klebsiella quasipneumoniae Provides a Window into Carbapenemase Gene Transfer, Plasmid Rearrangements, and Patient Interactions with the Hospital Environment. Antimicrobial Agents and Chemotherapy, 63(6), 1-12.
    DOI Scopus30 WoS30 Europe PMC13
    2019 Barry, K. E., Wailan, A. M., Sheppard, A. E., Crook, D., Vegesana, K., Stoesser, N., . . . Mathers, A. J. (2019). Don't overlook the little guy: An evaluation of the frequency of small plasmids co-conjugating with larger carbapenemase gene containing plasmids. Plasmid, 103, 1-8.
    DOI Scopus19 WoS18 Europe PMC11
    2019 van Aartsen, J. J., Moore, C. E., Parry, C. M., Turner, P., Phot, N., Mao, S., . . . Stoesser, N. (2019). Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia. BMC Microbiology, 19(1), 1-14.
    DOI Scopus9 WoS9 Europe PMC7
    2019 Gweon, H. S., Shaw, L. P., Swann, J., De Maio, N., AbuOun, M., Niehus, R., . . . Stoesser, N. (2019). The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples. Environmental Microbiome, 14(1).
    DOI Scopus29
    2018 Sheppard, A. E., Stoesser, N., German-Mesner, I., Vegesana, K., Walker, A. S., Crook, D. W., & Mathers, A. J. (2018). TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data. Microbial Genomics, 4(12), 1-9.
    DOI Scopus18 WoS17 Europe PMC12
    2018 Eyre, D. W., Sheppard, A. E., Madder, H., Moir, I., Moroney, R., Quan, T. P., . . . Jeffery, K. J. M. (2018). A Candida auris Outbreak and Its Control in an Intensive Care Setting. NEW ENGLAND JOURNAL OF MEDICINE, 379(14), 1322-1331.
    DOI Scopus233 WoS224 Europe PMC139
    2018 Barkham, T., Sheppard, A., Jones, N., & Chen, S. L. (2018). Streptococcus agalactiae that caused meningitis in healthy adults in 1998 are ST283, the same type that caused a food-borne outbreak of invasive sepsis in 2015: an observational molecular epidemiology study. Clinical Microbiology and Infection, 24(8), 923-925.
    DOI Scopus4 WoS3 Europe PMC2
    2018 George, S., Pankhurst, L., Hubbard, A., Votintseva, A., Stoesser, N., Sheppard, A. E., . . . Phan, H. T. T. (2018). Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches (vol 3, 2017). MICROBIAL GENOMICS, 4(3), 1 page.
    DOI Scopus1 WoS1
    2018 Zhong, L. -L., Phan, H. T. T., Shen, C., Vihta, K. -D., Sheppard, A. E., Huang, X., . . . Tian, G. -B. (2018). High Rates of Human Fecal Carriage of mcr-1-Positive Multidrug-Resistant Enterobacteriaceae Emerge in China in Association With Successful Plasmid Families. CLINICAL INFECTIOUS DISEASES, 66(5), 676-685.
    DOI Scopus45 WoS42 Europe PMC29
    2017 Hollensteiner, J., Poehlein, A., Sproeer, C., Bunk, B., Sheppard, A. E., Rosentstiel, P., . . . Liesegang, H. (2017). Complete Genome sequence of the nematicidal Bacillus thuringiensis MYBT18246. Standards in Genomic Sciences, 12(1), 1-10.
    DOI Scopus6 WoS6 Europe PMC3
    2017 Hollensteiner, J., Poehlein, A., Sproeer, C., Bunk, B., Sheppard, A. E., Rosenstiel, P., . . . Liesegang, H. (2017). Complete genome sequence of the nematicidal Bacillus thuringiensis MYBT18247. JOURNAL OF BIOTECHNOLOGY, 260, 48-52.
    DOI Scopus7 WoS7 Europe PMC3
    2017 Stoesser, N., Sheppard, A. E., Peirano, G., Anson, L. W., Pankhurst, L., Sebra, R., . . . Pitout, J. D. (2017). Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli. SCIENTIFIC REPORTS, 7(1), 11 pages.
    DOI Scopus73 WoS72 Europe PMC44
    2017 Orlek, A., Phan, H., Sheppard, A. E., Doumith, M., Ellington, M., Peto, T., . . . Stoesser, N. (2017). A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database. Data in Brief, 12, 423-426.
    DOI Scopus27 Europe PMC16
    2017 Cheruvanky, A., Stoesser, N., Sheppard, A. E., Crook, D. W., Hoffman, P. S., Weddle, E., . . . Mathers, A. J. (2017). Enhanced Klebsiella pneumoniae Carbapenemase Expression from a Novel Tn4401 Deletion. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 61(6), 10 pages.
    DOI Scopus36 WoS35 Europe PMC23
    2017 Orlek, A., Phan, H., Sheppard, A. E., Doumith, M., Ellington, M., Peto, T., . . . Stoesser, N. (2017). Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids. Plasmid, 91, 42-52.
    DOI Scopus40 WoS36 Europe PMC23
    2017 Mathers, A. J., Stoesser, N., Chai, W., Carroll, J., Barry, K., Cherunvanky, A., . . . Sheppard, A. E. (2017). Chromosomal Integration of the Klebsiella pneumoniae Carbapenemase Gene, bla(KPC), in Klebsiella Species Is Elusive but Not Rare. Antimicrobial Agents and Chemotherapy, 61(3), 1-12.
    DOI Scopus33 WoS33 Europe PMC22
    2017 Orlek, A., Stoesser, N., Anjum, M. F., Doumith, M., Ellington, M. J., Peto, T., . . . Sheppard, A. E. (2017). Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology. FRONTIERS IN MICROBIOLOGY, 8(FEB), 10 pages.
    DOI Scopus97 WoS96 Europe PMC56
    2017 George, S., Pankhurst, L., Hubbard, A., Votintseva, A., Stoesser, N., Sheppard, A. E., . . . Phan, H. T. T. (2017). Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches. MICROBIAL GENOMICS, 3(8), 8 pages.
    DOI Scopus50 WoS47 Europe PMC29
    2017 Young, B. C., Wu, C. -H., Gordon, N. C., Cole, K., Price, J. R., Liu, E., . . . Wilson, D. J. (2017). Severe infections emerge from commensal bacteria by adaptive evolution. ELIFE, 6, 25 pages.
    DOI Scopus50 WoS48 Europe PMC20
    2016 Seale, A. C., Koech, A. C., Sheppard, A. E., Barsosio, H. C., Langat, J., Anyango, E., . . . Berkley, J. A. (2016). Maternal colonization with Streptococcus agalactiae and associated stillbirth and neonatal disease in coastal Kenya. NATURE MICROBIOLOGY, 1(7), 10 pages.
    DOI Scopus66 WoS64 Europe PMC56
    2016 Sheppard, A. E., Stoesser, N., Wilson, D. J., Sebra, R., Kasarskis, A., Anson, L. W., . . . Mathers, A. J. (2016). Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene bla(KPC). ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 60(6), 3767-3778.
    DOI Scopus165 WoS161 Europe PMC116
    2016 Stoesser, N., Sheppard, A. E., Pankhurst, L., De Maio, N., Moore, C. E., Sebra, R., . . . Crook, D. W. (2016). Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131. MBIO, 7(2), 15 pages.
    DOI Scopus202 WoS199 Europe PMC147
    2016 Sheppard, A. E., Vaughan, A., Jones, N., Turner, P., Turner, C., Efstratiou, A., . . . Seale, A. C. (2016). Capsular Typing Method for Streptococcus agalactiae Using Whole-Genome Sequence Data. JOURNAL OF CLINICAL MICROBIOLOGY, 54(5), 1388-1390.
    DOI Scopus25 WoS20 Europe PMC18
    2016 Senn, L., Clerc, O., Zanetti, G., Basset, P., Prod'hom, G., Gordon, N. C., . . . Blanc, D. S. (2016). The Stealthy Superbug: the Role of Asymptomatic Enteric Carriage in Maintaining a Long-Term Hospital Outbreak of ST228 Methicillin-Resistant Staphylococcus aureus. MBIO, 7(1), 9 pages.
    DOI Scopus57 WoS56 Europe PMC43
    2016 Stoesser, N., Sheppard, A. E., Peirano, G., Sebra, R., Lynch, T., Anson, L., . . . Pitout, J. D. (2016). Complete Sequencing of Plasmids Containing bla(OXA-163) and bla(OXA-48) in Escherichia coli Sequence Type 131. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 60(11), 6948-6951.
    DOI Scopus14 WoS15 Europe PMC7
    2016 Stoesser, N., Sheppard, A. E., Peirano, G., Sebra, R. P., Lynch, T., Anson, L. W., . . . Pitout, J. D. (2016). First Report of bla(IMP-14) on a Plasmid Harboring Multiple Drug Resistance Genes in Escherichia coli Sequence Type 131. Antimicrobial Agents and Chemotherapy, 60(8), 5068-5071.
    DOI Scopus13 WoS13 Europe PMC7
    2016 Hardiman, C. A., Weingarten, R. A., Conlan, S., Khil, P., Dekker, J. P., Mathers, A. J., . . . Frank, K. M. (2016). Horizontal transfer of carbapenemase-encoding plasmids and comparison with hospital epidemiology data. Antimicrobial Agents and Chemotherapy, 60(8), 4910-4919.
    DOI Scopus49 WoS44 Europe PMC32
    2016 Sheppard, A. E., Stoesser, N., Sebra, R., Kasarskis, A., Deikus, G., Anson, L., . . . Mathers, A. J. (2016). Complete Genome Sequence of KPC-Producing Klebsiella pneumoniae Strain CAV1193.. Genome announcements, 4(1), e01649-e01615.
    DOI Scopus15 Europe PMC10
    2016 Sheppard, A. E., Nakad, R., Saebelfeld, M., Masche, A. C., Dierking, K., & Schulenburg, H. (2016). High instability of a nematicidal Cry toxin plasmid in Bacillus thuringiensis. Journal of Invertebrate Pathology, 133, 34-40.
    DOI Scopus4 WoS4 Europe PMC2
    2015 Masri, L., Branca, A., Sheppard, A. E., Papkou, A., Laehnemann, D., Guenther, P. S., . . . Schulenburg, H. (2015). Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology, 13(6), 1-30.
    DOI Scopus55 WoS54 Europe PMC40
    2015 Mathers, A. J., Stoesser, N., Sheppard, A. E., Pankhurst, L., Giess, A., Yeh, A. J., . . . Sifri, C. D. (2015). Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: Insights into endemicity from Whole-genome sequencing. Antimicrobial Agents and Chemotherapy, 59(3), 1656-1663.
    DOI Scopus102 WoS99 Europe PMC75
    2015 Stoesser, N., Sheppard, A. E., Moore, C. E., Golubchik, T., Parry, C. M., Nget, P., . . . Walker, A. S. (2015). Extensive within-host diversity in fecally carried extended-spectrum-beta-lactamase-producing Escherichia coli Isolates: Implications for transmission analyses. Journal of Clinical Microbiology, 53(7), 2122-2131.
    DOI Scopus53 WoS51 Europe PMC39
    2014 Stoesser, N., Giess, A., Batty, E. M., Sheppard, A. E., Walker, A. S., Wilson, D. J., . . . Joshi, S. (2014). Genome sequencing of an extended series of NDM-producing Klebsiella pneumoniae isolates from neonatal infections in a Nepali hospital characterizes the extent of community- Versus hospital- associated transmission in an endemic setting. Antimicrobial Agents and Chemotherapy, 58(12), 7347-7357.
    DOI Scopus93 WoS91 Europe PMC77
    2014 Stoesser, N., Sheppard, A. E., Shakya, M., Sthapit, B., Thorson, S., Giess, A., . . . Crook, D. W. (2014). Dynamics of MDR Enterobacter cloacae outbreaks in a neonatal unit in Nepal: Insights using wider sampling frames and next-generation sequencing. Journal of Antimicrobial Chemotherapy, 70(4), 1008-1015.
    DOI Scopus40 WoS37 Europe PMC22
    2013 Sheppard, A. E., Poehlein, A., Rosenstiel, P., Liesegang, H., & Schulenburg, H. (2013). Complete genome sequence of Bacillus thuringiensis strain 407 Cry-. Genome Announcements, 1(1), e00158-e00112.
    DOI Scopus33 Europe PMC20
    2011 Sheppard, A., Madesis, P., Lloyd, A., Day, A., Ayliffe, M., & Timmis, J. (2011). Introducing an RNA editing requirement into a plastid-localised transgene reduces but does not eliminate functional gene transfer to the nucleus. Plant Molecular Biology, 76(3-5), 299-309.
    DOI Scopus12 WoS11 Europe PMC9
    2009 Sheppard, A., & Timmis, J. (2009). Instability of Plastid DNA in the Nuclear Genome. PLoS Genetics, 5(1), 323.
    DOI Scopus50 WoS48 Europe PMC42
    2008 Sheppard, A., Ayliffe, M., Blatch, L., Day, A., Delaney, S., Khairul-Fahmy, N., . . . Timmis, J. (2008). Transfer of plastid DNA to the nucleus is elevated during male gametogenesis in tobacco. Plant Physiology, 148(1), 328-336.
    DOI Scopus49 WoS48 Europe PMC35
  • Book Chapters

  • Current Higher Degree by Research Supervision (University of Adelaide)

    Date Role Research Topic Program Degree Type Student Load Student Name
    2022 Co-Supervisor The Evolution, Distribution, and Activity of R2 Elements Doctor of Philosophy Doctorate Full Time Ms Nozhat Tabassum Hassan
    2022 Co-Supervisor Machine-learning guided evolution of heme enzymes to optimise catalytic activity Doctor of Philosophy Doctorate Full Time Miss Alecia Rachel Gee
    2022 Principal Supervisor Characterisation of Mobile Genetic Elements Driving the Global Dissemination of Key Antimicrobial Resistance Genes Master of Philosophy Master Full Time Miss Bethany Jane Cross
    2022 Co-Supervisor Investigating pangenome graphs in plants Doctor of Philosophy Doctorate Full Time Miss Chelsea Anne Matthews
  • Position: Lecturer
  • Phone: 83130232
  • Email: anna.sheppard@adelaide.edu.au
  • Campus: North Terrace
  • Building: Molecular Life Sciences, floor 4
  • Org Unit: School of Biological Sciences

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