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Mark Achtman

Job Title
Professor
Department
WMS - Biomedical Sciences
Phone
024 7657 5592
Web Link
Research Interests

Epidemiological and sequence data are used to evaluate the evolution and population structure of pathogenic bacteria, including Helicobacter pylori , Salmonella enterica , Escherichia coli and Yersinia pestis . Sequences of housekeeping genes from global collections have been used to define multi-locus sequence types for epidemiological purposes. Sequence relationships have also been used to determine population genetic structures. We are currently developing fine typing for species such as Y. pestis whose housekeeping genes are highly uniform. Novel mathemical approaches are being developed to extract information content from extensive sequence-based datasets. Bayesian approaches have been applied to the population structure of H. pylori and are being extended to other organisms in order to provide algorithms that can be used in general. A major goal is to deduce the phylogenetic structure and ancestry of bacterial species that experience frequent recombination. Molecular epidemiology has been performed on a variety of organisms in an attempt to reveal the microevolution of these bacteria over periods of decades to centuries. Formerly, epidemic Neisseria meningitides were investigated extensively but a large proportion of current efforts are addressed to the global population structure of H. pylori.

Title Funder Award start Award end
Deep evolutionary history of bacterial pathogens: Supplement for 48452 due to Covid-19. Wellcome Trust 01 Sept 2021 28 Feb 2022
Wellcome Trust Investigator Award - Deep evolutionary history of bacterial pathogens Wellcome Trust 01 Sept 2016 31 Aug 2021
THE MRC CONSORTIUM FOR MEDICAL MICROBIAL BIOINFORMATICS MRC 01 Apr 2014 01 Oct 2020
Pettenkofer Prize Max von Pettenkofer-Institute for Hygiene and Medical Microbiology 07 Dec 2018 06 Dec 2019
BBSRC / Achten / EnteroBase: A Powerful, User-Friendly Online Resource for Analyzing and Visualizing Genomic Variation within Escherichia coli and Salmonella enterica BBSRC 01 Apr 2014 15 Oct 2019

All authors for A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics

Frentrup, Martinique, Zhou, Zhemin, Steglich, Matthias, Meier-Kolthoff, Jan P., Göker, Markus, Riedel, Thomas, Bunk, Boyke, Spröer, Cathrin, Overmann, Jörg, Blaschitz, Marion, Indra, Alexander, von Müller, Lutz, Kohl, Thomas A., Niemann, Stefan, Seyboldt, Christian, Klawonn, Frank, Kumar, Nitin, Lawley, Trevor D., García-Fernández, Sergio, Cantón, Rafael, del Campo, Rosa, Zimmermann, Ortrud, Groß, Uwe, Achtman, Mark, Nübel, Ulrich

All authors for What's in a name? Species-wide whole-genome sequencing resolves invasive and noninvasive lineages of salmonella enterica serotype paratyphi B

Connor, Thomas R., Owen, Sian V., Langridge, Gemma, Connell, Steve, Nair, Satheesh, Reuter, Sandra, Dallman, Timothy J., Corander, Jukka, Tabing, Kristine C., Le Hello, Simon, Fookes, Maria, Doublet, Benoît, Zhou, Zhemin, Feltwell, Theresa, Ellington, Matthew J., Herrera, Silvia, Gilmour, Matthew, Cloeckaert, Axel, Achtman, Mark, Parkhill, Julian, Wain, John, De Pinna, Elizabeth, Weill, François-Xavier, Peters, Tansy, Thomson, Nick

All authors for Parallel independent evolution of pathogenicity within the genus Yersinia

Reuter, S., Connor, T. R., Barquist, L., Walker, D., Feltwell, T., Harris, S. R., Fookes, M., Hall, M. E., Petty, N. K., Fuchs, T. M., Corander, J., Dufour, M., Ringwood, T., Savin, C., Bouchier, C., Martin, L., Miettinen, M., Shubin, M., Riehm, J. M., Laukkanen-Ninios, R., Sihvonen, L. M., Siitonen, A., Skurnik, M., Falcao, J. P., Fukushima, H., Scholz, H. C., Prentice, M. B., Wren, B. W., Parkhill, J., Carniel, E., Achtman, Mark, McNally, A., Thomson, N. R.

All authors for A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

Holden, M. T. G., Hsu, L.-Y., Kurt, K., Weinert, L. A., Mather, A. E., Harris, S. R., Strommenger, B., Layer, F., Witte, W., de Lencastre, H., Skov, R., Westh, H., Zemlickova, H., Coombs, G., Kearns, A. M., Hill, R. L. R., Edgeworth, J., Gould, I., Gant, V., Cooke, J., Edwards, G. F., McAdam, P. R., Templeton, K. E., McCann, A., Zhou, Z., Castillo-Ramirez, S., Feil, E. J., Hudson, L. O., Enright, M. C., Balloux, F., Aanensen, D. M., Spratt, B. G., Fitzgerald, J. R., Parkhill, J., Achtman, Mark, Bentley, S. D., Nubel, U.

All authors for Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis

Cui, Y., Yu, C., Yan, Y., Li, D., Li, Y., Jombart, T., Weinert, L. A., Wang, Z., Guo, Z., Xu, L., Zhang, Y., Zheng, H., Qin, N., Xiao, X., Wu, M., Wang, X., Zhou, D., Qi, Z., Du, Z., Wu, H., Yang, X., Cao, H., Wang, H., Wang, J., Yao, S., Rakin, A., Li, Y., Falush, D., Balloux, F., Achtman, Mark, Song, Y., Wang, J., Yang, R.

All authors for Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

Morelli, Giovanna, Song, Yajun, Mazzoni, Camila J., Eppinger, Mark, Roumagnac, Philippe, Wagner, David M., Feldkamp, Mirjam, Kusecek, Barica, Vogler, Amy J., Li, Yanjun, Cui, Yujun, Thomson, Nicholas R., Jombart, Thibaut, Leblois, Raphael, Lichtner, Peter, Rahalison, Lila, Petersen, Jeannine M., Balloux, Francois, Keim, Paul, Wirth, Thierry, Ravel, Jacques, Yang, Ruifu, Carniel, Elisabeth, Achtman, Mark

All authors for Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica

Zhou, Zhemin, Lundstrøm, Inge, Dien, Alicia Tran, Duchêne, Sebastián, Alikhan, Nabil-Fareed, Sergeant, Martin J., Langridge, Gemma, Fotakis, Anna K., Nair, Satheesh, Stenøien, Hans K., Hamre, Stian S., Casjens, Sherwood, Green, Monica H., Christophersen, Axel, Quince, Christopher, Thomson, Nicholas R., Weill, François-Xavier, Ho, Simon, Thomas, M., Gilbert, P., Achtman, Mark

All authors for Supplementary information to support : 'Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity'

Morelli, Giovanna, Song, Yajun, Mazzoni, Camila J., Eppinger, Mark, Roumagnac, Philippe, Wagner, David M., Feldkamp, Mirjam, Kusecek, Barica, Vogler, Amy J., Li, Yanjun, Cui, Yujun, Thomson, Nicholas R., Jombart, Thibaut, Leblois, Raphael, Lichtner, Peter, Rahalison, Lila, Petersen, Jeannine M., Balloux, Francois, Keim, Paul, Wirth, Thierry, Ravel, Jacques, Yang, Ruifu, Carniel, Elisabeth, Achtman, Mark