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Dr Catherine Burke

Biography

I obtained my PhD in microbiology from the University of New South Wales in 2010. My research focused on the ecology of host associated bacterial communities from the marine environment, and on the search for novel bioactive compounds produced by these communities, employing both sequence based and functional metagneomic techniques.

Since moving to the ithree institute, my research has focused on the discovery of novel genes and molecules that regulate cell division in bacteria to cause filamentation, through the use of expression libraries and flow cytometry screening.  Filamentation is a survival strategy employed by both environmental and pathogenic bacteria, and proteins which regulate this process make attractive drug targets.

My other area of research involves the microbial ecology of diabetic skin and wounds.  Skin microbes (the skin microbiome) play a vital role in the protection of our skin from pathogenic infection, and chronic conditions such as diabetes are likely to influence the microbes living on skin, and their interactions with us.  Using 16S and metagneomic sequencing, I am characterising the skin microbiome of diabetic skin and chronic wounds, to understand how skin microbes affect wound infections in diabetes.

Professional

  • Member of ISME (International Society for Microbial Ecology)
  • Member of ASM (Australian Society for Microbiology)

Image of Catherine Burke
Lecturer, School of Life Sciences
Core Member, ithree - Institute of Infection, Immunity and Innovation
B Sc (Hons - First Class), Ph D Microbiology & Immunology
 
Phone
+61 2 9514 8203

Research Interests

I am interested in understanding the ecology of microbial communities, and how those communities interact with living hosts.  In the case of microbial communities that live on humans (the human microbiome), these microbes are thought to play important roles in our immune development, and to protect us from pathogenic microbes.  Many diseases have been linked to shifts in our microbial communities, and these shifts are implicated in disease development.  My ultimate aim is to understand how our native microbial communities interact with us to keep us healthy, and how these communities can be manipulated in the case of disease to achieve better health outcomes.

Can supervise: Yes

Journal articles

Joss, T.V., Burke, C.M., Hudson, B.J., Darling, A.E., Forer, M., Alber, D.G., Charles, I.G. & Stow, N.W. 2016, 'Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients.', Frontiers in microbiology, vol. 6, pp. 1532-1532.
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Chronic rhinosinusitis (CRS) is a common and potentially debilitating disease characterized by inflammation of the sinus mucosa for longer than 12 weeks. Bacterial colonization of the sinuses and its role in the pathogenesis of this disease is an ongoing area of research. Recent advances in culture-independent molecular techniques for bacterial identification have the potential to provide a more accurate and complete assessment of the sinus microbiome, however there is little concordance in results between studies, possibly due to differences in the sampling location and techniques. This study aimed to determine whether the microbial communities from one sinus could be considered representative of all sinuses, and examine differences between two commonly used methods for sample collection, swabs, and tissue biopsies. High-throughput DNA sequencing of the bacterial 16S rRNA gene was applied to both swab and tissue samples from multiple sinuses of 19 patients undergoing surgery for treatment of CRS. Results from swabs and tissue biopsies showed a high degree of similarity, indicating that swabbing is sufficient to recover the microbial community from the sinuses. Microbial communities from different sinuses within individual patients differed to varying degrees, demonstrating that it is possible for distinct microbiomes to exist simultaneously in different sinuses of the same patient. The sequencing results correlated well with culture-based pathogen identification conducted in parallel, although the culturing missed many species detected by sequencing. This finding has implications for future research into the sinus microbiome, which should take this heterogeneity into account by sampling patients from more than one sinus.
Liu, M., Lu, J., Muller, P., Turnbull, L., Burke, C.M., Schlothauer, R.C., Carter, D.A., Whitchurch, C.B. & Harry, E.J. 2015, 'Antibiotic-specific differences in the response of Staphylococcus aureus to treatment with antimicrobials combined with manuka honey', Frontiers in Microbiology, vol. 6, no. JAN.
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Skin infections caused by antibiotic resistant Staphylococcus aureus are a significant health problem worldwide; often associated with high treatment cost and mortality rate. Complex natural products like New Zealand (NZ) manuka honey have been revisited and studied extensively as an alternative to antibiotics due to their potent broad-spectrum antimicrobial activity, and the inability to isolate honey-resistant S. aureus. Previous studies showing synergistic effects between manuka-type honeys and antibiotics have been demonstrated against the growth of one methicillin-resistant S. aureus (MRSA) strain. We have previously demonstrated strong synergistic activity between NZ manuka-type honey and rifampicin against growth and biofilm formation of multiple S. arueus strains. Here, we have expanded our investigation using multiple S. aureus strains and four different antibiotics commonly used to treat S. aureus-related skin infections: rifampicin, oxacillin, gentamicin, and clindamycin. Using checkerboard microdilution and agar diffusion assays with S. aureus strains including clinical isolates and MRSA we demonstrate that manuka-type honey combined with these four antibiotics frequently produces a synergistic effect. In some cases when synergism was not observed, there was a significant enhancement in antibiotic susceptibility. Some strains that were highly resistant to an antibiotic when present alone become sensitive to clinically achievable concentrations when combined with honey. However, not all of the S. aureus strains tested responded in the same way to these combinational treatments. Our findings support the use of NZ manuka-type honeys in clinical treatment against S. aureus-related infections and extend their potential use as an antibiotic adjuvant in combinational therapy. Our data also suggest that manuka-type honeys may not work as antibiotic adjuvants for all strains of S. aureus, and this may help determine the mechanistic processes behind honey syner...
Liu, M., Lu, J., Muller, P., Turnbull, L., Burke, C.M., Schlothauer, R.C., Carter, D.A., Whitchurch, C.B. & Harry, E.J. 2015, 'Antibiotic-specific differences in the response of Staphylococcus aureus to treatment with antimicrobials combined with manuka honey', Frontiers in Microbiology, vol. 6, no. JAN.
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Skin infections caused by antibiotic resistant Staphylococcus aureus are a significant health problem worldwide; often associated with high treatment cost and mortality rate. Complex natural products like New Zealand (NZ) manuka honey have been revisited and studied extensively as an alternative to antibiotics due to their potent broad-spectrum antimicrobial activity, and the inability to isolate honey-resistant S. aureus. Previous studies showing synergistic effects between manuka-type honeys and antibiotics have been demonstrated against the growth of one methicillin-resistant S. aureus (MRSA) strain. We have previously demonstrated strong synergistic activity between NZ manuka-type honey and rifampicin against growth and biofilm formation of multiple S. arueus strains. Here, we have expanded our investigation using multiple S. aureus strains and four different antibiotics commonly used to treat S. aureus-related skin infections: rifampicin, oxacillin, gentamicin, and clindamycin. Using checkerboard microdilution and agar diffusion assays with S. aureus strains including clinical isolates and MRSA we demonstrate that manuka-type honey combined with these four antibiotics frequently produces a synergistic effect. In some cases when synergism was not observed, there was a significant enhancement in antibiotic susceptibility. Some strains that were highly resistant to an antibiotic when present alone become sensitive to clinically achievable concentrations when combined with honey. However, not all of the S. aureus strains tested responded in the same way to these combinational treatments. Our findings support the use of NZ manuka-type honeys in clinical treatment against S. aureus-related infections and extend their potential use as an antibiotic adjuvant in combinational therapy. Our data also suggest that manuka-type honeys may not work as antibiotic adjuvants for all strains of S. aureus, and this may help determine the mechanistic processes behind honey syner...
Lu, J., Turnbull, L., Burke, C.M., Liu, M.Y., Carter, D.A., Schlothauer, R.C., Whitchurch, C.B. & Harry, L. 2014, 'Manuka-type honeys can eradicate biofilms produced by Staphylococcus aureus strains with different biofilm-forming abilities', PeerJ, vol. 2.
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Chronic wounds are a major global health problem. Their management is difficult and costly, and the development of antibiotic resistance by both planktonic and biofilm-associated bacteria necessitates the use of alternative wound treatments. Honey is now being revisited as an alternative treatment due to its broad-spectrum antibacterial activity and the inability of bacteria to develop resistance to it. Many previous antibacterial studies have used honeys that are not well characterized, even in terms of quantifying the levels of the major antibacterial components present, making it difficult to build an evidence base for the efficacy of honey as an antibiofilm agent in chronic wound treatment. Here we show that a range of well-characterized New Zealand manuka-type honeys, in which two principle antibacterial components, methylglyoxal and hydrogen peroxide, were quantified, can eradicate biofilms of a range of Staphylococcus aureus strains that differ widely in their biofilm-forming abilities. Using crystal violet and viability assays, along with confocal laser scanning imaging, we demonstrate that in all S. aureus strains, including methicillin-resistant strains, the manuka-type honeys showed significantly higher anti-biofilm activity than clover honey and an isotonic sugar solution. We observed higher anti-biofilm activity as the proportion of manuka-derived honey, and thus methylglyoxal, in a honey blend increased. However, methylglyoxal on its own, or with sugar, was not able to effectively eradicate S. aureus biofilms. We also demonstrate that honey was able to penetrate through the biofilm matrix and kill the embedded cells in some cases. As has been reported for antibiotics, sub-inhibitory concentrations of honey improved biofilm formation by some S. aureus strains, however, biofilm cell suspensions recovered after honey treatment did not develop resistance towards manuka-type honeys. New Zealand manuka-type honeys, at the concentrations they can be applie...
Egan, S., Harder, T., Burke, C.M., Steinberg, P., Kjelleberg, S.L. & Thomas, T. 2013, 'The Seaweed Holobiont: Understanding Seaweed-bacteria Interactions', FEMS Microbiology Reviews, vol. 37, no. 3, pp. 462-476.
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Seaweeds (macroalgae) form a diverse and ubiquitous group of photosynthetic organisms that play an essential role in aquatic ecosystems. These ecosystem engineers contribute significantly to global primary production and are the major habitat formers on
Burke, C.M., Liu, M.Y., Britton, W.J., Triccas, J.A., Thomas, T., Smith, A., Allen, S., Salomon, R. & Harry, L. 2013, 'Harnessing Single Cell Sorting To Identify Cell Division Genes And Regulators In Bacteria', Plos One, vol. 8, no. 4, pp. 1-13.
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Cell division is an essential cellular process that requires an array of known and unknown proteins for its spatial and temporal regulation. Here we develop a novel, high-throughput screening method for the identification of bacterial cell division genes and regulators. The method combines the over-expression of a shotgun genomic expression library to perturb the cell division process with high-throughput flow cytometry sorting to screen many thousands of clones. Using this approach, we recovered clones with a filamentous morphology for the model bacterium, Escherichia coli. Genetic analysis revealed that our screen identified both known cell division genes, and genes that have not previously been identified to be involved in cell division. This novel screening strategy is applicable to a wide range of organisms, including pathogenic bacteria, where cell division genes and regulators are attractive drug targets for antibiotic development.
Burke, C.M., Steinberg, P., Rusch, D.B., Kjelleberg, S.L. & Thomas, T. 2011, 'Bacterial community assembly based on functional genes rather than species', Proceedings of The National Academy of Sciences of the United States of America, vol. 108, no. 34, pp. 14288-14293.
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The principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. We previously analyzed the community membership of bacterial communities associated with the green macroalga Ulva australis, and proposed a competitive lottery model for colonization of the algal surface in an attempt to explain the surprising lack of similarity in species composition across different algal samples. Here we extend the previous study by investigating the link between community structure and function in these communities, using metagenomic sequence analysis. Despite the high phylogenetic variability in microbial species composition on different U. australis (only 15% similarity between samples), similarity in functional composition was high (70%), and a core of functional genes present across all algal-associated communities was identified that were consistent with the ecology of surface- and host-associated bacteria. These functions were distributed widely across a variety of taxa or phylogenetic groups. This observation of similarity in habitat (niche) use with respect to functional genes, but not species, together with the relative ease with which bacteria share genetic material, suggests that the key level at which to address the assembly and structure of bacterial communities may not be ½species½ (by means of rRNA taxonomy), but rather the more functional level of genes.
Yung, P., Burke, C.M., Kjelleberg, S.L., Thomas, T. & Lewis, M. 2011, 'Novel Antibacterial Proteins From The Microbial Communities Associated With The Sponge Cymbastela Concentrica And The Green Alga Ulva Australis', Applied and Environmental Microbiology, vol. 77, no. 4, pp. 1512-1515.
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The functional metagenomic screening of the microbial communities associated with a temperate marine sponge and a green alga identified three novel hydrolytic enzymes with antibacterial activities. The results suggest that uncultured alpha- and gammaprot
Burke, C.M., Thomas, T., Lewis, M., Steinberg, P. & Kjelleberg, S. 2011, 'Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis', ISME Journal, vol. 5, no. 4, pp. 590-600.
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Green Ulvacean marine macroalgae are distributed worldwide in coastal tidal and subtidal ecosystems. As for many living surfaces in the marine environment, little is known concerning the epiphytic bacterial biofilm communities that inhabit algal surfaces. This study reports on the largest published libraries of near full-length 16S rRNA genes from a marine algal surface (5293 sequences from six samples) allowing for an in-depth assessment of the diversity and phylogenetic profile of the bacterial community on a green Ulvacean alga. Large 16S rRNA gene libraries of surrounding seawater were also used to determine the uniqueness of this bacterial community. The surface of Ulva australis is dominated by sequences of Alphaproteobacteria and the Bacteroidetes, especially within the Rhodobacteriaceae, Sphingomonadaceae, Flavobacteriaceae and Sapropiraceae families. Seawater libraries were also dominated by Alphaproteobacteria and Bacteroidetes sequences, but were shown to be clearly distinct from U. australis libraries through the clustering of sequences into operational taxonomic units and BrayCurtis similarity analysis. Almost no similarity was observed between these two environments at the species level, and only minor similarity was observed at levels of sequence clustering representing clades of bacteria within family and genus taxonomic groups. Variability between libraries of U. australis was relatively high, and a consistent sub-population of bacterial species was not detected. The competitive lottery model, originally derived to explain diversity in coral reef fishes, may explain the pattern of colonization of this algal surface.
Ballestriero, F., Thomas, T., Burke, C., Egan, S. & Kjelleberg, S. 2010, 'Identification of Compounds with Bioactivity against the Nematode Caenorhabditis elegans by a Screen Based on the Functional Genomics of the Marine Bacterium Pseudoalteromonas tunicata D2', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 76, no. 17, pp. 5710-5717.
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Tujula, N.A., Crocetti, G.R., Burke, C., Thomas, T., Holmstrom, C. & Kjelleberg, S. 2010, 'Variability and abundance of the epiphytic bacterial community associated with a green marine Ulvacean alga', ISME JOURNAL, vol. 4, no. 2, pp. 301-311.
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Yung, P.Y., Burke, C., Lewis, M., Egan, S., Kjelleberg, S. & Thomas, T. 2009, 'Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion', NUCLEIC ACIDS RESEARCH, vol. 37, no. 21.
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Burke, C., Kjelleberg, S. & Thomas, T. 2009, 'Selective Extraction of Bacterial DNA from the Surfaces of Macroalgae', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 75, no. 1, pp. 252-256.
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Yung, P.Y., Burke, C., Lewis, M., Egan, S., Kjelleberg, S. & Thomas, T. 2009, 'Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion.', Nucleic acids research, vol. 37, no. 21.
Metagenomics provides access to the uncultured majority of the microbial world. The approaches employed in this field have, however, had limited success in linking functional genes to the taxonomic or phylogenetic origin of the organism they belong to. Here we present an efficient strategy to recover environmental DNA fragments that contain phylogenetic marker genes from metagenomic libraries. Our method involves the cleavage of 23S ribsosmal RNA (rRNA) genes within pooled library clones by the homing endonuclease I-CeuI followed by the insertion and selection of an antibiotic resistance cassette. This approach was applied to screen a library of 6500 fosmid clones derived from the microbial community associated with the sponge Cymbastela concentrica. Several fosmid clones were recovered after the screen and detailed phylogenetic and taxonomic assignment based on the rRNA gene showed that they belong to previously unknown organisms. In addition, compositional features of these fosmid clones were used to classify and taxonomically assign a dataset of environmental shotgun sequences. Our approach represents a valuable tool for the analysis of rapidly increasing, environmental DNA sequencing information.
Thomas, T., Evans, F.F., Schleheck, D., Mai-Prochnow, A., Burke, C., Penesyan, A., Dalisay, D.S., Stelzer-Braid, S., Saunders, N., Johnson, J., Ferriera, S., Kjelleberg, S. & Egan, S. 2008, 'Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment', PLOS ONE, vol. 3, no. 9.
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Burke, C., Thomas, T., Egan, S. & Kjelleberg, S. 2007, 'The use of functional genomics for the identification of a gene cluster encoding for the biosynthesis of an antifungal tambjamine in the marine bacterium Pseudoalteromonas tunicata', ENVIRONMENTAL MICROBIOLOGY, vol. 9, no. 3, pp. 814-818.
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