Publications
2016
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K. Bjorn-Mortensen, B. Soborg, A. Koch, K. Ladefoged, M. Merker, T. Lillebaek, A. B. Andersen, S. Niemann & T. A. Kohl:
Tracing Mycobacterium tuberculosis transmission by whole genome sequencing in a high incidence setting: a retrospective population-based study in East Greenland
Scientific Reports 6, tbd, doi:10.1038/srep33180
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Bélard, S, Remppis, J, Bootsma, S, Janssen, S, Kombila, DU, Beyeme, JO, Rossatanga, EG, Kokou, C, Osbak, KK, Obiang Mba, RM, Kaba, HM, Traoré, AN, Ehrhardt, J, Bache, EB, Flamen, A, Rüsch-Gerdes, S, Frank, M, Adegnika, AA, Lell, B, Niemann, S, Kremsner, PG, Loembé, :
'Tuberculosis Treatment Outcome and Drug Resistance in Lambaréné, Gabon: A Prospective Cohort Study
The American journal of tropical medicine and hygiene, tbd, 10.4269/ajtmh.15-0668
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Taha M-K, Claus H, Lappann M, Veyrier FJ, Otto A, Becher D, Deghmane A-E, Frosch M, Hellenbrand W, Hong E., Parent du Châtelet I, Prior K, Harmsen D, Vogel U:
Evolutionary Events Associated with an Outbreak of Meningococcal Disease in Men Who Have Sex with Men
PLOS ONE, 11(5): e0154047, 10.1371/journal.pone.0154047
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Bruno Ribeiro-Gonçalves, Alexandre P. Francisco, Cátia Vaz, Mário Ramirez, and João André Carriço:
PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees.
Nucleic Acids Research 2016 July 8; 44(Web Server issue): W246–W251. , tbd, 10.1093/nar/gkw359
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Schena, E, Nedialkova, L, Borroni, E, Battaglia, S, Cabibbe, AM, Niemann, S, Utpatel, C, Merker, M, Trovato, A, Hofmann-Thiel, S, Hoffmann, H & Cirillo, DM :
Delamanid susceptibility testing of Mycobacterium tuberculosis using the resazurin microtitre assay and the BACTEC™ MGIT™ 960 system
Journal of Antimicrobial Chemotherapy Bd 71, Nr. 6, S. 1532-9, DOI: 10.1093/jac/dkw044
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Julia S. Sabirova, Basil Britto Xavier, Jasmine Coppens, Olympia Zarkotou, Christine Lammens, Lore Janssens, Ronald Burggrave, Trevor Wagner, Herman Goossens and Surbhi Malhotra-Kumar:
Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS.
Journal of Antimicrobial Chemotherapy 71 (6), 1501-1509, 10.1093/jac/dkw003
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Nikolayevskyy, V, Kranzer, K, Niemann, S & Drobniewski, F :
Whole genome sequencing of Mycobacterium tuberculosis for detection of recent transmission and tracing outbreaks: A systematic review
Tuberculosis Bd 98, S. 77-85, DOI: 10.1016/j.tube.2016.02.009
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Merker, M, Crudu, V, Noroc, E, Romancenco, E, Chesov, D, Günther, G, Niemann, S & Lange, C :
In reply
International journal of tuberculosis and lung disease Bd 20, Nr. 3, S. 424, DOI: 10.5588/ijtld.15.1024-2
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Philip Supply, Roisin S, Gaudin C, De Mendonça R, Bellon J, Van Vaerenbergh K, De Bruyne K, Byl B, Pouseele H, Denis O:
Pan-genome multilocus sequence typing and outbreak-specific reference-based single nucleotide polymorphism analysis to resolve two concurrent Staphylococcus aureus outbreaks in neonatal services
Clinical Microbiology and Infection 2016, 22(6):520-6, 10.1016/j.cmi.2016.01.024
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Hoffmann, H, Kohl, TA, Hofmann-Thiel, S, Merker, M, Beckert, P, Jaton, K, Nedialkova, L, Sahalchyk, E, Rothe, T, Keller, PM & Niemann:
Delamanid and Bedaquiline Resistance in Mycobacterium tuberculosis Ancestral Beijing Genotype Causing Extensively Drug-Resistant Tuberculosis in a Tibetan Refugee
American Journal of Respiratory and Critical Care Medicine 193(3), 337-40, 10.1164/rccm.201502-0372LE.
2015
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Bradley, P, Gordon NC, Walker TM, Dunn L, Heys S, Huang B, Earle S, Pankhurst LJ, Anson L, de Cesare M, Piazza P, Votintseva AA, Golubchik T, Wilson DJ, Wyllie DH, Diel R, Niemann S, Feuerriegel S, Kohl TA, Ismail N, Omar SV, Smith EG, Buck D, McVean G, Walker AS, Pe:
Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
Nature Communications 6:10063, tbd, doi: 10.1038/ncomms10063
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Pankhurst, LJ, Del Ojo Elias C, Votintseva AA, Walker TM, Cole K, Davies J, Fermont JM, Gascoyne-Binzi DM, Kohl TA, Kong C, Lemaitre N, Niemann S, Paul J, Rogers TR, Roycroft E, Smith EG, Supply P, Tang P, Wilcox MH, Wordsworth S, Wyllie D, Xu L, Crook DW; COMPASS-TB St:
Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study
The Lancet Respiratory Medicine 4(1), Jan;4(1):49-58, 10.1016/S2213-2600(15)00466-X
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Ebrahim M. Abda, Dagmar Krysciak, Ines Krohn-Molt, Uwe Mamat, Christel Schmeisser, Konrad U. Förstner, Ulrich E. Schaible, Thomas A. Kohl, Stefan Nieman, Wolfgang R. Streit:
Phenotypic Heterogeneity Affects Stenotrophomonas maltophilia K279a Colony Morphotypes and β-Lactamase Expression
Frontiers in Microbiology 2015; 6: 1373, tbd, 10.3389/fmicb.2015.01373
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de Been M, Pinholt M, Top J, Bletz S, Mellmann A, van Schaik W, Brouwer E, Rogers M, Kraat Y, Bonten M, Corander J, Westh H, Harmsen D, Willems RJ:
Core Genome Multilocus Sequence Typing Scheme for High- Resolution Typing of Enterococcus faecium
J Clin Microbiol. 53(12), 53(12):3788-97
Additional link
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Crudu, V, Merker, M, Lange, C, Noroc, E, Romancenco, E, Chesov, D, Günther, G & Niemann, S :
Nosocomial transmission of multidrug-resistant tuberculosis
International Journal of Tubercolosis and Lung Disease Bd 19, Nr. 12, S. 1520-3, DOI: 10.5588/ijtld.15.0327
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Ruppitsch W, Pietzka A, Prior K, Bletz S, Fernandez HL, Allerberger F, Harmsen D, Mellmann A:
Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Listeria monocytogenes
J Clin Microbiol. 53(9), 53(9):2869-76, 10.1128/JCM.01193-15
Additional link
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Moran-Gilad J, Prior K, Yakunin E, Harrison TG, Underwood A, Lazarovitch T, Valinsky L, Luck C, Krux F, Agmon V, Grotto I, Harmsen D:
Design and application of a core genome multilocus sequence typing scheme for investigation of Legionnaires' disease incidents
Euro Surveill. 20(28), 20(28). pii: 21186
Additional link
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Philip Supply, Hannes Pouseele:
Accurate whole genome sequencing-based epidemiological surveillance of Mycobacterium tuberculosis
Current and Emerging Technologies for the Diagnosis of Microbial Infections, Methods in Microbiology Vol 42, June 2015, 359–394, doi:10.1016/bs.mim.2015.04.001
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Walker, TM, Kohl, TA, Omar, SV, Hedge, J, Elias, CDO, Bradley, P, Iqbal, Z, Feuerriegel, S, Niehaus, KE, Wilson, DJ, Clifton, DA, Kapatai, G, Ip, C, Bowden, R, Drobniewski, FA, Allix-Béguec, C, Gaudin, C, Parkhill, J, Diel, R, Supply, P, Crook, DW, Smith, EG, Walker,:
Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study.
The Lancet Infectious Diseases, 10.1016/S1473-3099(15)00062-6
Additional link
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Bjorn-Mortensen, K,, Zallete, J, Lillebaek,T, Andersen, A B, Niemann, S, Rasmussen, E M, and Kohl, T A:
Direct DNA extraction from Mycobacterium tuberculosis frozen stocks as a re-culture independent approach to whole genome sequencing
Journal of Clinical Microbiology vol. 53 no. 8, 2716-2719, doi: 10.1128/JCM.00662-15
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Alexander Mellmann, Stefan Bletz, Jörg Rothgänger, Dag Harmsen:
Ensuring backwards compatibility: traditional genotyping efforts in the era of whole genome sequencing
Clinical Microbiology and Infection 21(4), 347.e1-4, http://dx.doi.org/10.1016/j.cmi.2014.11.005
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Antwerpen MH, Prior K, Mellmann A, Höppner S, Splettstoesser WD, Harmsen D:
Rapid High Resolution Genotyping of Francisella tularensis by Whole Genome Sequence Comparison of Annotated Genes (“MLST+”)
Plos One 10(4): e0123298, 0.1371/journal.pone.0123298
Additional link
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Feuerriegel, S, Schleusener, V, Beckert, P, Kohl, TA, Miotto, P, Cirillo, DM, Cabibbe, AM, Niemann, S & Fellenberg, K :
PhyResSE a Web Tool Delineating Mycobacterium tuberculosis Antibiotic Resistance and Lineage from Whole-Genome Sequencing Data
Journal of Clinical Microbiology Bd 53, Nr. 6, S. 1908-14, DOI: 10.1128/JCM.00025-15
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Sanchez-Padilla, M. et al. :
Common Multidrug-Resistant TB Strain in Swaziland Not Detectable by Most Advanced Rapid Diagnostic Tests
N Engl J Med., 10.1056/NEJMc1413930
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Köser, CU, Javid, B, Liddell, K, Ellington, MJ, Feuerriegel, S, Niemann, S, Brown, NM, Burman, WJ, Abubakar, I, Ismail, NA, Moore, D, Peacock, SJ & Török, ME :
Drug-resistance mechanisms and tuberculosis drugs
Lancet Bd 385, Nr. 9965, S. 305-7, DOI: 10.1016/S0140-6736(14)62450-8
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Matthias Merker, Camille Blin, Stefano Mona, Nicolas Duforet-Frebourg, Sophie Lecher, Eve Willery, Michael Blum, Sabine Rüsch-Gerdes, Igor Mokrousov, Eman Aleksic, Caroline Allix-Béguec, Annick Antierens,Ewa Augustynowicz-Kopeć, Marie Ballif, Francesca Barletta:
Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage
Nature Genetics 2015 Jan 19, doi: 10.1038/ng.3195
2014
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Cátia Vaz, Alexandre P. Francisco, Mickael Silva, Keith A. Jolley, James Bray, Hannes Pouseele, Joerg Rothganger, Mario Ramirez, Joao A. Carrico:
TypOn: The Microbial Typing Ontology
BMC Journal of Biomedical Semantics, doi:10.1186/2041-1480-5-43
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Sebastian Jünemann, Karola Prior, Andreas Albersmeier, Stefan Albaum, Jörn Kalinowski, Alexander Goesmann, Jens Stoye, Dag Harmsen:
GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers
PLoS ONE 9(9), e107014, 10.1371/journal.pone.0107014
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Niemann S, Supply P:
Diversity and Evolution of Mycobacterium tuberculosis: Moving to Whole-Genome-Based Approaches.
Cold Spring Harb Perspect Med 2014 Sep 4, 10.1101/cshperspect.a021188
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S.A. Boers, R. Burggrave, M. vanWestreenen,W.H.F. Goessens, J.P. Hays:
Whole-genome mapping for high-resolution genotyping of Pseudomonas aeruginosa.
Journal of Microbiological Methods 106C, 19-22, doi: 10.1016/j.mimet.2014.07.020
Additional link
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Thomas A. Kohl, Roland Diel, Dag Harmsen, Jörg Rothgänger, Karen Meywald Walter, Matthias Merker, Thomas Weniger, Stefan Niemann:
Whole genome based Mycobacterium tuberculosis surveillance: A standardized, portable and expandable approach
J. Clin. Microbiol. 52(7), 2479-86, doi:10.1128/JCM.00567-14
Additional link
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Shana R. Leopold, Richard V. Goering, Anika Witten, Dag Harmsen, Alexander Mellmann:
Bacterial whole-genome sequencing revisited: portable, scalable, and standardized analysis for typing and detection of virulence and antibiotic resistance genes
Journal of Clinical Microbiology 52(7), 2365-2370, 10.1128/JCM.00262-14
2013
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Merker M, Kohl TA, Roetzer A, Truebe L, Richter E, Rüsch-Gerdes S, Fattorini L, Oggioni MR, Cox H, Varaine F, Niemann S.:
Whole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug-Resistant Mycobacterium tuberculosis Beijing Strains in Patients
Plos One 8(12):e82551., 10.1371/journal.pone.0082551.
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Maiden MC, van Rensburg MJ, Bray JE, Earle SG, Ford SA, Jolley KA, McCarthy ND.:
MLST revisited: the gene-by-gene approach to bacterial genomics.
Nature Reviews Microbiology 2013 Oct;11, 728-36, doi: 10.1038/nrmicro3093
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Thijs Bosch, Erwin Verkade, Martijn van Luit, Bruno Pot, Paul Vauterin, Ronald Burggrave, Paul Savelkoul, Jan Kluytmans, Leo Schouls:
High Resolution Typing by Whole Genome Mapping Enables Discrimination of LA-MRSA (CC398) Strains and Identification of Transmission Events
PLoS ONE 8(6): e66493. , doi:10.1371/journal.pone.0066493
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Martin Maiden, Cody, A. J. McCarthy, N. D. Jansen van Rensburg, M. Isinkaye, T. Bentley, S. Parkhill, J. Dingle, K. E. Bowler, I. C. Jolley, K. A.:
Real-time genomic epidemiology of human Campylobacter isolates using whole genome multilocus sequence typing
Journal of Clinical Microbiology 2013 Aug;51(8):2526-34. doi: 10.1128/JCM.00066-13. Epub 2013 May 22., 10.1128/JCM.00066-13
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Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D:
Updating benchtop sequencing performance comparison.
Nature Biotechnology 31(4): 294–296, doi:10.1038/nbt.2522
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Stefan Niemann, Roetzer A, Diel R, Kohl TA, Rückert C, Nübel U, Blom J, Wirth T, Jaenicke S, Schuback S, Rüsch-Gerdes S, Supply P, Kalinowski J, Niemann S.:
Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study.
Plos Medicine PLoS Med. 2013 Feb;10(2):e1001387., doi: 10.1371/journal.pmed.1001387.