Dr Torsten Seemann - Researcher Profile

We do not have a photograph of this person yet.

Address

Department of Microbiology
Faculty of Medicine, Nursing & Health Sciences, Clayton

Biography

The rise and rise of genome sequencing

Genome sequencing has come a long way in a short time. As recently as seven years ago, it took many years to sequence, assemble and annotate a genome. Now, that process takes four weeks and is much cheaper. Dr Torsten Seemann says the DNA sequencing machine at Micromon (the commercial services unit of the Monash Department of Microbiology) has revolutionised biology, with bioinformatics being vital to improved efficiencies. Torsten is using his expertise in this area to research some of our most challenging bacteria.

 

A genome is a long string of DNA. The human genome consists of about three billion DNA letters, and chunks of those letters are what we know as genes. Torsten says the process of understanding genomes has improved significantly.

“People used to pick a gene and analyse it without knowing what the rest of the genome looked like. It was blind,” Torsten explains. “When you have the whole genome it’s a lot easier. 

“Genome assembly is the process of determining the letters and the order they sit within the genome, while annotating involves figuring out where all the interesting bits are and what they do. You can’t enter a three million-long bit of DNA and read it like a ticker tape. You have to chop it into little bits and sequence those, and then it becomes a complicated jigsaw puzzle where some pieces are missing, some are broken, and others look identical to each other. A lot of what I do is that jigsaw puzzle step.”

Bioinformatics is the application of information technology to biology and medicine, with an aim of creating more efficient ways to analyse and understand the science. Torsten’s knowledge of bioinformatics has been vitally important to his research.

“We’re the first stage of the scientific discovery process. You have this thing with so many possibilities, and we try and use as much existing knowledge in public databases to narrow down what the next steps should be. You want to minimise how many ‘wet lab’ experiments you need to do because they’re expensive and time consuming. 

“We have developed a software ‘pipeline’ to streamline the annotation, assembly and analysis of genomes. Within days we can have a bit of DNA, send it to Micromon and get it back within a week, so we can assemble and annotate it,” he says.

Torsten was part of the team that sequenced and assembled the bacterium Leptospira which causes disease in humans and can cause dairy cows to abort their foetuses. He says this was an important breakthrough.

“Leptospira was the first bacterial genome to be wholly sequenced, assembled and annotated in Australia. There is a vaccine for Leptospira, but it’s not 100 per cent protective. We’ve also collaborated on the first big eukaryotic organism wholly produced in Australia, the coral Acropora millepora, important for the Great Barrier Reef”, Torsten says.

Multi-drug resistant hospital infections like Golden Staph also present Torsten with an interesting basis from which to research bacterial genomes.

“We work on a lot of antibiotic-resistant bacteria that are found in hospitals and the community,” Torsten says. “Because people often don’t finish their course of antibiotics, a small number of bacteria survive. The ones that survive actually change their genome in response to the antibiotic. We’re trying to figure out what genes have made these bacteria resistant. If you understand that, you can begin to design drugs to target them.”

“When I first started, there were only a handful of bacterial genomes to look at, whereas now we can look at hundreds of new ones every week. Understanding the variation and commonality between these is very interesting.”

 

Qualifications

DOCTOR OF PHILOSOPHY
Institution: Monash University
Year awarded: 2003
SCIENCE (HONOURS I)
Institution: Monash University
Year awarded: 1995

Publications

Books

Seemann, T., Tischer, P.E., 1997, Generalized locally adaptive DPCM, Dept Computer Science, Monash University, Melbourne Vic Australia.

Book Chapters

Zuerner, R., Bulach, D.M., Seemann, T., Coppel, R.L., Adler, B., 2006, Comparative analysis of pathogenic leptospira genomes, in Molecular Biology of Spirochetes, eds FC Cabello, D Hulinska and HP Godgrey, IOS Press, Amsterdam Netherlands, pp. 101-114.

Bulach, D.M., Seemann, T., Zuerner, R., Adler, B., 2006, The organization of Leptospira at a genomic level, in Bacterial Genomes and Infectious Diseases, eds Voon L Chan, Philip M. Sherman, Billy Bourke, Humana Press, USA, pp. 109-123.

Journal Articles

Murray, G.L., Lo, M., Bulach, D.M., Srikram, A., Seemann, T., Quinsey, N.S., Sermswan, R., Allen, A., Adler, B., 2013, Evaluation of 238 antigens of Leptospira borgpetersenii serovar Hardjo for protection against kidney colonisation, Vaccine [P], vol 31, issue 3, Elsevier Ltd, UK, pp. 495-499.

Chandry, P.S., Gladman, S.L., Moore, S.C., Seemann, T., Crandall, K.A., Fegan, N., 2012, A Genomic Island in Salmonella enterica ssp. salamae provides new insights on the genealogy of the locus of enterocyte effacement, PLoS ONE [P], vol 7, issue 7, Public Library of Science, USA, pp. 1-15.

Henry, R.M., Vithanage (Sulthanagoda), N.R., Harrison, P., Seemann, T., Coutts, S.A., Moffatt, J.H., Nation, R.L., Li, J., Harper, M., Adler, B., Boyce, J.D., 2012, Colistin-resistant, lipopolysaccharide-deficient Acinetobacter baumannii responds to lipopolysaccharide loss through increased expression of genes involved in the synthesis and transport of lipoproteins, phospholipids, and poly-, Antimicrobial Agents And Chemotherapy [P], vol 56, issue 1, American Society for Microbiology, USA, pp. 59-69.

Lam, M.M., Seemann, T., Bulach, D.M., Gladman, S.L., Chen, H., Haring, V., Moore, R., Ballard, S.A., Grayson, M.L., Johnson, P., Howden, B.P., Stinear, T.P., 2012, Comparative analysis of the first complete Enterococcus faecium genome, Journal Of Bacteriology [P], vol 194, issue 9, American Society for Microbiology, USA, pp. 2334-2341.

Shepard, S.M., Danzeisen, J.L., Isaacsohn, R.E., Seemann, T., Achtman, M., Johnson, T.J., 2012, Genome sequences and phylogenetic analysis of K88- and F18-positive porcine enterotoxigenic Escherichia coli, Journal Of Bacteriology [P], vol 194, issue 2-4, American Society for Microbiology, USA, pp. 395-405.

Doig, K.D., Holt, K.E., Fyfe, J.A.M., Lavender, C.J., Eddyani, M., Portaels, F., Yeboah-Manu, D., Pluschke, G., Seemann, T., Stinear, T.P., 2012, On the origin of Mycobacterium ulcerans, the causative agent of Buruli ulcer, BMC Genomics [P], vol 13, issue 258, BioMed Central Ltd, UK, pp. 0-19.

Boyce, J.D., Seemann, T., Adler, B., Harper, M., 2012, Pathogenomics of pasteurella multocida, Current Topics In Microbiology And Immunology [P], vol 361, Springer New York LLC, USA, pp. 23-38.

Castro-Nallar, E., Chen, H., Gladman, S.L., Moore, S.C., Seemann, T., Powell, I., Hillier, A., Crandall, K.A., Chandry, P.S., 2012, Population genomics and phylogeography of an Australian dairy factory derived lytic bacteriophage, Genome Biology and Evolution [E], vol 4, issue 3, Oxford University Press, UK, pp. 382-393.

Rainczuk, A.K., Yamaryo-Botte, Y., Brammananth, R., Stinear, T.P., Seemann, T., Coppel, R.L., McConville, M.J., Crellin, P.K., 2012, The lipoprotein LpqW is essential for the mannosylation of periplasmic glycolipids in Corynebacteria, Journal Of Biological Chemistry [P], vol 287, issue 51, American Society for Biochemistry and Molecular Biology Inc., USA, pp. 42726-42738.

Traven, A., Janicke, A., Harrison, P., Swaminathan, A., Seemann, T., Beilharz, T.H., 2012, Transcriptional profiling of a yeast colony provides new insight into the heterogeneity of multicellular fungal communities, PLoS ONE [P], vol 7, issue 9, Public Library of Science, USA, pp. e46243.1-e46243.11.

Johnson, T., Fernandez-Alarcon, C., Bojesen, A., Nolan, L., Trampel, D., Seemann, T., 2011, Complete genome sequence of Gallibacterium anatis strain UMN179, isolated from a laying hen with peritonitis, Journal Of Bacteriology [P], vol 193, issue 14, Amercian Society for Microbiology, USA, pp. 3676-3677.

Howden, B.P., McEvoy, C.R., Allen, D.L., Chua, K., Gao, W., Harrison, P.F., Bell, J., Coombs, G., Bennett-Wood, V., Porter, J.L., Robins-Browne, R.M., Davies, J.K., Seemann, T., Stinear, T.P., 2011, Evolution of multidrug resistance during Staphylococcus aureus infection involves mutation of the essential two component regulator walKR, Plos Pathogens [P], vol 7, issue 11 (Art. No: e1002359), Public Library of Science, USA, pp. 1-15.

Wynne, J., Bull, T., Seemann, T., Bulach, D., Wagner, J., Kirkwood, C., Michalski, W., 2011, Exploring the zoonotic potential of Mycobacterium avium subspecies paratuberculosis through comparative genomics, PLoS ONE [P], vol 6, issue 7 (Art. No: 22171), Public Library of Science, USA, pp. 1-15.

Bannam, T.L., Yan, X., Harrison, P.F., Seemann, T., Keyburn, A.L., Stubenrauch, C., Weeramantri, L.H., Cheung, J.K., McClane, B.A., Boyce, J.D., Moore, R.J., Rood, J.I., 2011, Necrotic enteritis-derived Clostridium perfringens strain with three closely related independently conjugative toxin and antibiotic resistance plasmids, mBio [E], vol 2, issue 5 (Art. No: e00190), American Society for Microbiology, USA, pp. 1-9.

Adler, B., Lo, M., Seemann, T., Murray, G.L., 2011, Pathogenesis of leptospirosis: The influence of genomics, Veterinary Microbiology [P], vol 153, issue 1-2, Elsevier BV, The Netherlands, pp. 73-81.

Naughton, S., Parker, D., Seemann, T., Thomas, T., Turnbull, L., Rose, B., Bye, P., Cordwell, S., Whitchurch, C.B., Manos, J., 2011, Pseudomonas aeruginosa AES-1 exhibits increased virulence gene expression during chronic infection of cystic fibrosis lung, PLoS ONE [P], vol 6, issue 9 (Art. No: e24526), Public Library of Science, USA, pp. 1-8.

Carter, G.P., Awad, M.M., Hao, Y., Thelen, T., Bergin, I.L., Howarth, P.M., Seemann, T., Rood, J.I., Aronoff, D.M., Lyras, D., 2011, TcsL Is an Essential Virulence Factor in Clostridium sordellii ATCC 9714, Infection And Immunity [P], vol 79, issue 3, American Society for Microbiology, USA, pp. 1025-1032.

Chua, K., Seemann, T., Harrison, P.F., Monagle, S., Korman, T.M., Johnson, P.D.R., Coombs, G.W., Howden, B.O., Davies, J.K., Howden, B.P., Stinear, T.P., 2011, The dominant Australian community-acquired methicillin-resistant Staphylococcus aureus clone ST93-IV [2B] is highly virulent and genetically distinct, PLoS ONE [P], vol 6, issue 10 (Art. No: e25887), Public Library of Science, USA, pp. 1-10.

Johnson, P.D., Ballard, S.A., Grabsch, E.A., Stinear, T.P., Seemann, T., Young, H.L., Grayson, M.L., Howden, B.P., 2010, A Sustained hospital outbreak of Vancomycin-Resistant Enterococcus faecium Bacteremia due to emergence of vanB E. faecium sequence type 203, Journal Of Infectious Diseases [P], vol 202, issue 8, University of Chicago Press, USA, pp. 1278-1286.

Fyfe, J.A., Lavender, C.J., Handasyde, K.A., Legione, A.R., O'Brien, C.R., Stinear, T.P., Pidot, S.J., Seemann, T., Benbow, M.E., Wallace, J.R., McCowan, C., Johnson, P.D.R., 2010, A major role for mammals in the ecology of Mycobacterium ulcerans, Public Library of science: Neglected Tropical Diseases [P], vol 4, issue 8 (e791), Public Library of Science, USA, pp. 1-12.

Moffatt, J.H., Harper, M., Harrison, P.F., Hale, J.D., Vinogradov, E., Seemann, T., Henry, R.M., Crane, B.A., St Michael, F., Cox, A.D., Adler, B., Nation, R.L., Li, J., Boyce, J.D., 2010, Colistin resistance in Acinetobacter baumannii is mediated by complete loss of lipopolysaccharide production, Antimicrobial Agents And Chemotherapy [P], vol 54, issue 12, American Society for Microbiology, USA, pp. 4971-4977.

Howden, B.P., Seemann, T., Harrison, P.F., McEvoy, C.R., Stanton, J.L., Rand, C., Mason, C.W., Jensen, S.O., Firth, N., Davies, J.K., Johnson, P.D., Stinear, T., 2010, Complete genome sequence of Staphylococcus aureus strain JKD6008, an ST239 clone of methicillin-resistant Staphylococcus aureus with intermediate-level vancomycin resistance, Journal Of Bacteriology [P], vol 192, issue 21, American Society for Microbiology, USA, pp. 5848-5849.

Chua, K., Seemann, T., Harrison, P.F., Davies, J.K., Coutts, S.J., Chen, H., Haring, V., Moore, R., Howden, B.P., Stinear, T.P., 2010, Complete genome sequence of Staphylococcus aureus strain JKD6159, a unique Australian clone of ST93-IV community methicillin-resistant Staphylococcus aureus, Journal Of Bacteriology [P], vol 192, issue 20, American Society for Microbiology, USA, pp. 5556-5557.

Steen, J.A., Steen, J.A., Harrison, P.F., Seemann, T., Wilkie, I.W., Harper, M., Adler, B., Boyce, J.D., 2010, Fis is essential for capsule production in Pasteurella multocida and regulates expression of other important virulence factors, Plos Pathogens [P], vol 6, issue 2, Public Library of Science, USA, pp. e1000750-1-e1000750-14.

Pidot, S.J., Porter, J.L., Tobias, N.J., Anderson, J., Catmull, D., Seemann, T., Kidd, S., Davies, J.K., Reynolds, E.C., Dashper, S.G., Stinear, T.P., 2010, Regulation of the 18-kDa heat shock protein in Mycobacterium ulcerans: An alpha-crystallin orthologue that promotes biofilm formation, Molecular Microbiology [P], vol 78, issue 5, Wiley-Blackwell Publishing Ltd, UK, pp. 1216-1231.

Wynne, J.W., Seemann, T., Bulach, D., Coutts, S.A., Talaat, A.M., Michalski, W.P., 2010, Resequencing the Mycobacterium avium subsp. paratuberculosis K10 genome: Improved annotation and revised genome sequence, Journal Of Bacteriology [P], vol 192, issue 23, American Society for Microbiology, USA, pp. 6319-6320.

Pidot, S., Porter, J., Marsollier, L., Chauty, A., Migot-Nabias, F., Badaut, C., Benard, A., Ruf, M., Seemann, T., Johnson, P., Davies, J., Jenkin, G., Pluschke, G., Stinear, T., 2010, Serological evaluation of Mycobacterium ulcerans antigens identified by comparative genomics, Public Library of science: Neglected Tropical Diseases [P], vol 4, issue 11 (e872), Public Library of Science, USA, pp. 1-10.

Roltgen, K., Qi, W., Ruf, M., Mensah-Quainoo, E., Pidot, S.J., Seemann, T., Stinear, T.P., Kaser, M., Yeboah-Manu, D., Pluschke, G., 2010, Single nucleotide polymorphism typing of Mycobacterium ulcerans reveals focal transmission of buruli ulcer in a highly endemic region of Ghana, Public Library of science: Neglected Tropical Diseases [P], vol 4, issue 7 (e751), Public Library of Science, USA, pp. 1-9.

Gao, W., Chua, K., Davies, J.K., Newton, H.J., Seemann, T., Harrison, P.F., Holmes, N.E., Rhee, H., Hong, J., Hartland, E.L., Stinear, T.P., Howden, B.P., 2010, Two novel point mutations in clinical Staphylococcus aureus reduce linezolid susceptibility and switch on the stringent response to promote persistent infection, Plos Pathogens [P], vol 6, issue 6 (e1000944), Public Library of Science, USA, pp. 1-15.

Tobias, N.J., Seemann, T., Pidot, S.J., Porter, J.L., Marsollier, L., Marion, E., Letournel, F., Zakir, T.S., Azuolas, J., Wallace, J.R., Hong, H., Davies, J.K., Howden, B.P., Johnson, P.D., Jenkin, G.A., Stinear, T.P., 2009, Mycolactone gene expression is controlled by strong SigA-like promoters with utility in studies of Mycobacterium ulcerans and Buruli Ulcer, Public Library of science: Neglected Tropical Diseas..., vol 3, issue 11, Public Library of Science, USA, pp. e553-1-e553-10.

Newton, H.J., Sloan, J., Bulach, D.M., Seemann, T., Allison, C.C., Tauschek, M., Robins-Browne, R.M., Paton, J.C., Whittam, T.S., Paton, A.W., Hartland, E.L., 2009, Shiga toxin-producing Escherichia coli strains negative for locus of enterocyte effacement, Emerging Infectious Diseases (Print), vol 15, issue 3, US Department of Health and Human Services, USA, pp. 372-380.

Pidot, S.J., Hong, H., Seemann, T., Porter, J.L., Yip, M., Men, A., Johnson, M., Wilson, P., Davies, J.K., Leadlay, P.F., Stinear, T.P., 2008, Deciphering the genetic basis for polyketide variation among mycobacteria producing mycolactones, BMC Genomics, vol 9, issue 462, BioMed Central Ltd, UK, pp. 1-15.

Picardeau, M., Bulach, D.M., Bouchier, C., Zuerner, R.L., Zidane, N., Wilson, P., Creno, S., Kuczek, E., Bommezzadri, S., Davis, J., McGrath, A., Johnson, M., Boursaux-Eude, C., Seemann, T., Rouy, Z., Coppel, R.L., Rood, J.I., Lajus, A., Davies, J.K., Medigue, C., Adler, B., 2008, Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis, PL o S One, vol 3, issue 2 (e1607), Public Library of Science, USA, pp. 1-9.

Stinear, T.P., Seemann, T., Harrison, P.F., Jenkin, G.A., Davies, J.K., Johnson, P.D.R., Abdellah, Z., Arrowsmith, C., Chillingworth, T., Churcher, C., Clarke, K., Cronin, A., Davis, P., Goodhead, I., Holroyd, N., Jagels, K., Lord, A., Moule, S., Mungall, K., Norbertczak, H., Quail, M.A., Rabbinowitsch, E., Walker, D., White, B., Whitehead, S., Small, P.L.C., Brosch, R., Ramakrishnan, L., Fischbach, M.A., Parkhill, J., Cole, S.T., 2008, Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis, Genome Research, vol 18, issue 5, Cold Spring Harbor Laboratory Press, USA, pp. 729-741.

Myers, G.S., Parker, D., Al-Hasani, K., Kennan, R.M., Seemann, T., Ren, Q., Badger, J.H., Selengut, J.D., DeBoy, R.T., Tettelin, H., Boyce, J.D., McCarl, V., Han, X.Y., Nelson, W.C., Madupu, R., Mohamoud, Y., Holley, T., Fedorova, N., Bottomley, S.P., Whittington, R.J., Adler, B., Songer, J., Rood, J.I., Paulsen, I.T., 2007, Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus, Nature Biotechnology, vol 25, issue 5, Nature Publishing Group, New York NY USA, pp. 569-575.

Stinear, T.P., Seemann, T., Pidot, S.J., Frigui, W., Reysset, G., Garnier, T., Meurice, G., Simon, D., Bouchier, C., Ma, L., Tichit, M., Porter, J.L., Ryan, J., Johnson, P.D.R., Davies, J.K., Jenkin, G.A., Small, P.L.C., Jones, L.M., Tekaia, F., Laval, F., Daffe, M., Parkhill, J., Cole, S.T., 2007, Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer, Genome Research, vol 17, issue 2, Cold Spring Harbor Lab Press, Publications Dept, Woodbury NY USA, pp. 192-200.

Bulach, D.M., Zuerner, R.L., Wilson, P., Seemann, T., McGrath, A., Cullen, P.A., Davis, J., Johnson, M., Kuczek, E., Alt, D.P., Peterson-Burch, B., Coppel, R.L., Rood, J.I., Davies, J.K., Adler, B., 2006, Genome reduction in Leptospira borgpetersenii reflects limited transmission potential, Proceedings of The National Academy of Sciences of The United States of America, vol 103, issue 39, Natl Acad Scicences, Washington DC USA, pp. 14560-14565.

Conference Proceedings

Seemann, T., Tischer, P.E., 1997, Generalised locally adaptive DPCM, Proceedings DCC'97 Data Compression Conference, Snowbird USA, 25-27 March 1997, IEEE Computer Society Press, Los Alamitos USA, p. 473.

Seemann, T., Tischer, P.E., Meyer, B., 1997, History-based blending of image sub-predictors, PCS97 1997 Picture Coding Symposium, Berlin Germany, 10-12 September 1997, VDE-Verlag GMBH, Berlin Germany, pp. 147-151.

Seemann, T., Tischer, P.E., 1997, MML based noise cleaning of images, PCS97 1997 Picture Coding Symposium, Berlin Germany, 10-12 September 1997, VDE-Verlag GMBH, Berlin Germany, pp. 39-43.

Other

Dowe, D.L., Seemann, T., 1999, Flaming Ostrich Eyes 1999 Footy Title, Monash University News, Public Affairs, Clayton Vic Australia.

Seemann, T., Dowe, D.L., Rosenberg, J., 1999, Safe Footy Bet on the Internet, Monash Post, Monash University, Clayton Vic Australia.