Publications
2021
Nadarajan, D; Hillemann, D; Kamara, R; Foray, L; Conteh, OS; Merker, M; Niemann, S; Lau, J; Njoya, M; Kranzer, K; Somoskovi, A; Maurer, FP. 2021 Evaluation of the Roche cobas MTB and MTB-RIF/INH Assays in Samples from Germany and Sierra Leone. J Clin Microbiol. 2021 Apr 20;59(5):e02983-20. doi: 10.1128/JCM.02983-20. Print 2021 Apr 20.
(Article)
Kapitza, M; Tueffers, L; Schulenburg, H; Kremer, K. 2021. Tracking down resistances: a co-design approach for a biomedical educational program on antibiotic resistance. Science Activities Projects and Curriculum Ideas in STEM Classrooms Volume 58, 2021 - Issue 2
(Article)
Feuerriegel, S; Kohl, TA; Utpatel, C; Andres, S; Maurer, FP; Heyckendorf, J; Jouet, A; Badalato, N; Foray, L; Kamara, RF; Conteh, OS; Supply, P; Niemann, S. 2021. Rapid genomic first- and second-line drug resistance prediction from clinical Mycobacterium tuberculosis specimens using Deeplex-MycTB. Eur Respir J. 2021 Jan 5;57(1):2001796. doi: 10.1183/13993003.01796-2020. Print 2021 Jan
(Article)
Barbosa, C; Mahrt, N; Bunk, J; Grasser, M; Rosenstiel, P; Jansen, G; Schulenburg, H. 2021. The Genomic Basis of Rapid Adaptation to Antibiotic Combination Therapy in Pseudomonas aeruginosa. Mol Biol Evol. 2021 Jan 23;38(2):449-464. doi: 10.1093/molbev/msaa233.
(Article)
Sonnenkalb L, Strohe G, Dreyer V, Andres S, Hillemann D, Maurer FP, Niemann S, Merker M. 2021. Microevolution of Mycobacterium tuberculosis Subpopulations and Heteroresistance in a Patient Receiving 27 Years of Tuberculosis Treatment in Germany. Antimicrob Agents Chemother. 2021 Jun 17;65(7):e0252020.doi: 10.1128/AAC.02520-20. Epub 2021 Jun 1
(Article)
Batra A, Roemhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H (2021) High potency of sequential therapy with only beta-lactam antibiotics. eLife 10:e68876
(Article)
Mahrt N, Tietze A, Kuenzel S, Franzenburg S, Barbosa C, Jansen G, Schulenburg H. 2021. Bottleneck size and selection level reproducibly impact evolution of antibiotic resistance. Nature Ecology and Evolution 5, 1233–1242
(Article)
2020
Maxime Godfroid, Tal Dagan, Matthias Merker, Thomas A. Kohl, Roland Diel, P. Maurer, Stefan Niemann, Anne Kupczok 2020. Insertion and deletion evolution reflects antibiotics selection pressure in a Mycobacterium tuberculosis outbreak. bioRxiv doi.org/10.1101/2020.01.28.922765
(Article)
Matthias Merker, Elena Nikolaevskaya, Thomas A. Kohl, Barbara Molina-Moya, Olha Pavlovska, Patrik Brännberg, Andrii Dudnyk, Valentyna Stokich, Ivan Barilar, Iryna Marynova, Tetiana Filipova, Cristina Prat, Anders Sjöstedt, Jose Dominguez, Olena Rzhepishevska, and Stefan Niemann. 2020 M ultidrug- and Extensively Drug-Resistant Mycobacterium tuberculosis Beijing Clades, Ukraine, 2015 doi.org/10.3201/eid2603.190525.
Matthias Merker, Thomas A. Kohl, Ivan Barilar, Sönke Andres, Philip W. Fowler, Erja Chryssanthou, Kristian Ängeby, Pontus Jureen, Danesh Moradigaravand, Julian Parkhill, Sharon J. Peacock, Thomas Schön, Florian P. Maurer, Timothy Walker, Claudio Köser , Stefan Niemann 2020. Phylogenetically informative mutations in genes implicated in antibiotic resistance in Mycobacterium tuberculosis complex. doi.org/10.1186/s13073-020-00726-5
(Article)
Matthias I. Gröschel, Conor J. Meehan, Ivan Barilar, Margo Diricks, Aitor Gonzaga, Matthias Steglich, Oscar Conchillo-Solé, Isabell-Christin Scherer, Uwe Mamat, Christian F. Luz, Katrien De Bruyne, Christian Utpatel, Daniel Yero, Isidre Gibert, Xavier Daura, Stefanie Kampmeier, Nurdyana Abdul Rahman, Michael Kresken, Tjip S. van der Werf, Ifey Alio, Wolfgang R. Streit, Kai Zhou, Thomas Schwartz, John W. A. Rossen, Maha R. Farhat, Ulrich E. Schaible, Ulrich Nübel, Jan Rupp, Joerg Steinmann, Stefan Niemann & Thomas A. Kohl 2020. The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. doi.org/10.1038/s41467-020-15123-0
(Article)
2019
Lüersen K, Roeder T, Rimbach G,. 2019. Drosophila melanogaster in nutrition research - the importance of standardizing experimental diets. Genes and Nutrition, 14(3) doi.org/10.1186/s12263-019-0627-9.
(Article)
Polsfuss S*, Hofmann-Thiel S*, Merker M*, Krieger D, Niemann S, Rüssmann H, Schönfeld N, Hoffmann H, Kranzer K. Emergence of Low-level Delamanid and Bedaquiline Resistance During Extremely Drug-resistant Tuberculosis Treatment. Clin Infect Dis. 2019. *equal contribution.
(Article)
Roemhild R, Schulenburg H (2019) Evolutionary Ecology meets the Antibiotic Crisis: Can we control Pathogen Adaptation through Sequential Therapy? Evol Med Public Health 2019:37-45
(Article)
Ilhan J, Kupczok A, Woehle C, Wein T, Hülter NF, Rosenstiel P, Landan G, Mizrahi I, Dagan T. Segregational Drift and the Interplay between Plasmid Copy Number and Evolvability. Mol Biol Evol. 2019 Mar 1;36(3):472-486. doi: 10.1093/molbev/msy225.
(Article)
Arandjelović I*, Merker M*, Richter E, Kohl TA, Savić B, Soldatović I, Wirth T, Vuković D, Niemann S. Longitudinal Outbreak of Multidrug-Resistant Tuberculosis in a Hospital Setting, Serbia. Emerg Infect Dis. 2019 Mar;25(3):555-558. *equal contribution.
(Article)
Bossen J, Uliczka K, Steen L, Pfefferkorn R, Mai MM, Burkhardt L, Spohn M, Bruchhaus I, Fink C, Heine H, Roeder T. An EGFR-induced Drosophila lung tumor model identifies alternative combination treatments. Mol Cancer Ther. 2019 Jun 19.
(Article)
Bartel S, La Grutta S, Cilluffo G, Perconti G, Bongiovanni A, Giallongo A, Behrends J, Kruppa J, Hermann S, Chiang D, Pfaffl MW, Krauss-Etschmann S. Human airway epithelial extracellular vesicle miRNA signature is altered upon asthma development. Allergy. 2019 Aug 6. doi: 10.1111/all.14008. [Epub ahead of print]PMID:31386204
(Article)
Kupczok A, Dagan T. Rates of Molecular Evolution in a Marine Synechococcus Phage Lineage. Viruses. 2019 Aug 6;11(8). pii: E720. doi: 10.3390/v11080720.
(Article)
Romero Picazo D, Dagan T, Ansorge R, Petersen JM, Dubilier N, Kupczok A. Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated. ISME J. 2019 Aug 8. doi: 10.1038/s41396-019-0475-z. [Epub ahead of print]
(Article)
Tueffers L, Barbosa C, Bobis I, Schubert S, Höppner M, Rühlemann M, Franke A, Rosenstel P, Friedrichs A, Krenz-Weinreich A, Fickenscher H, Bewig B, Schreiber S, Schulenburg H. Pseudomonas aeruginosa populations in the cystic fibrosis lung lose susceptibility to newly applied β-lactams within 3 days. J Antimicrob Chemother. 2019 Oct 1;74(10):2916-2925. doi: 10.1093/jac/dkz297
(Article)
Camilo Barbosa, Roderich Römhild, Philip Rosenstiel, Hinrich Schulenburg. Evolutionary stability of collateral sensitivity to antibiotics in the model pathogen Pseudomonas aeruginosa. eLife 2019;8:e51481 doi: 10.7554/eLife.51481
(Article)
Roland Diel, Thomas A. Kohl, Florian P. Maurer, Matthias Merker, Karen Meywald Walter , Jörg Hannemann, Albert Nienhaus, Philip Supply and Stefan Niemann. 2019 Accuracy of whole-genome sequencing to determine recent tuberculosis transmission: an 11-year population-based study in Hamburg, Germany. Eur Respir J. 2019 Nov; 54(5): 1901154. doi: 10.1183/13993003.01154-2019
(Article)
Silke Polsfuss, Sabine Hofmann-Thiel, Matthias Merker, David Krieger, Stefan Niemann, Holger Rüssmann, Nicolas Schönfeld, Harald Hoffmann, Katharina Kranzer. 2019. Emergence of Low-level Delamanid and Bedaquiline Resistance During Extremely Drug-resistant Tuberculosis Treatment. Clinical Infectious Diseases, Volume 69, Issue 7, 1 October 2019, Pages 1229–1231.doi.org/10.1093
(Article)
von Frieling J, Fink C, Hamm J, Klischies K, Forster M, Bosch TC, Roeder T, Rosenstiel P, Sommer F. 2018. Grow with the challenge - microbial effects on epithelial proliferation, carcinogenesis and cancer therapy. Frontiers in Microbiology, doi: 10.3389/fmicb.2018.02020.
(Article)
2018
Merker M, Barbier M, Cox H, Rasigade JP, Feuerriegel S, Kohl TA, Diel R, Borrell S, Gagneux S, Nikolayevskyy V, Andres S, Nübel U, Supply P, Wirth T, Niemann S. Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia. Elife. 2018 Oct 30;7. pii: e38200.
Roemhild R, Gokhale CS, Dirksen P, Blake C, Rosenstiel P, Traulsen A, Andersson, DI, Schulenburg H (2018) Cellular hysteresis as a principle to maximize the efficacy of antibiotic therapy. PNAS September 25, 2018 115 (39) 9767-9772
(Article)
Dallenga T, Repnik U, Corleis B, Eich J, Reimer R, Griffiths GW, Schaible UE. M. tuberculosis-Induced Necrosis of Infected Neutrophils Promotes Bacterial Growth Following Phagocytosis by Macrophages. Cell Host Microbe. 2017 Oct 11;22(4):519-530.e3. doi: 10.1016/j.chom.2017.09.003.
Peuker, K., Muff, S., Wang, J., Künzel, S., Bosse, E., Zeissig, Y., Luzzi, G., Basic, M., Strigli, A., Ulbricht, A., Kasser, A., Arlt, A., Chavakis, T., van den Brink, G.R., Schafmayer, C., Egberts, J.H., Becker, T., Bianchi, M.E., Bleich, A., Röcken, C., Hampe, J., Schreiber, S., Baines, J. F., Blumberg, R.S. & Zeissig, S. Epithelial calcineurin controls microbiota-dependent intestinal tumor development. Nature Medicine 2016; 22, 506-515
Wang, J., Thingholm, L.B., Skiecevičienė, J., Rausch, P., Kummen, M., Hov, J.R., Degenhardt, F., Heinsen, F.-A., Rühlemann, M.C., Szymczak, S., Holm, K., Esko, T., Sun, J., Pricop-Jeckstadt, M., Al-Dury, S., Bohov, P., Bethune, J., Sommer, F., Ellinghaus, D., Berge, R.K., Hübenthal, M., Koch, M., Schwarz, K., Rimbach, G., Hübbe, P., Pan, W.-H., Sheibani-Tezerji, R., Häsler, R., Rosenstiel, P., D'Amato, M., Cloppenborg-Schmidt, K., Künzel, S., Laudes, M., Marschall, H.-U., Lieb, W., Nöthlings, U., Karlsen, T.H.*, Baines, J.F.* & Franke, A.* Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota. Nature Genetics 2016; 48, 1396-1406
Belheouane, M., Gupta, Y., Künzel, S., Ibrahim, S. & Baines, J.F. Improved detection of gene-microbe interactions in the mouse skin microbiota using high-resolution QTL mapping of 16S rRNA transcripts. Microbiome 2017; 5, 59
M. Kostric, K. Milger, S. Krauss-Etschmann, M. Engel, G.Vestergaarda, M. Schloter, A. Schöler. Development of a stable lung microbiome in healthy neonatal mice.
Microb Ecol. 2018 75(2):529-542;doi: 10.1007/s00248-017-1068
S. Bartel, G. Carraro, F. Alessandrini, S. Krauss-Etschmann, FLM. Ricciardolo, S. Bellusci . miR-142-3p is associated with aberrant WNT signaling during airway remodeling in asthma. Am J Physiol Lung Cell Mol Physiol. 2018 Aug 1;315(2):L328-L333. doi: 10.1152/ajplung.00113.2018
Stucki D, Brites D, Jeljeli L (equal contribution), Coscolla M, Liu Q, Trauner A, Fenner L, Rutaihwa L, Borrell S, Luo T, Gao Q, Kato-Maeda M, Ballif M, Egger M, Macedo R, Mardassi H, Moreno M, Vilanova GT, Fyfe J, Globan M, Thomas J, Jamieson F, Guthrie JL, Asante-Poku A, Yeboah-Manu D, Wampande E, Ssengooba W, Joloba M, Boom WH, Basu I, Bower J, Saraiva M, Vasconcellos SE, Suffys P, Koch A, Wilkinson R, Gail-Bekker L, Malla B, Ley SD, Beck HP, de Jong BC, Toit K, Sanchez-Padilla E, Bonnet M, Gil-Brusola A, Frank M, Penlap Beng VN, Eisenach K, Alani I, Ndung'u PW, Revathi G, Gehre F, Akter S, Ntoumi F, Stewart-Isherwood L, Ntinginya NE, Rachow A, Hoelscher M, Cirillo DM, Skenders G, Hoffner S, Bakonyte D, Stakenas P, Diel R, Crudu V, Moldovan O, Al-Hajoj S, Otero L, Barletta F, Carter EJ, Diero L, Supply P, Comas I, Niemann S, Gagneux S. Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nat Genet 2016 48(12):1535-1543
Fehrenbach H, Wagner C, Wegmann M. Airway remodeling in asthma: what really matters. Cell Tissue Res. 2017 Mar;367(3):551-569.
Reiling N, Homolka S, Kohl TA, Steinhäuser C, Kolbe K, Schütze S, Brandenburg J. Shaping the niche in macrophages: Genetic diversity of the M. tuberculosis complex and its consequences for the infected host. Int J Med Microbiol. 2017 Sep 14. pii: S1438-4221(17)30294-1
Romey-Glüsing R*, Li Y*, Hoffmann J, von Frieling J, Knop M, Pfefferkorn R, Bruchhaus I, Fink C, Roeder T Nutritional regimens with periodically recurring phases of dietary restriction extend lifespan in Drosophila. FASEB, 2018; J 32: 1993-2003. doi: 10.1096/fj.201700934R
Prange R*, Thiedmann M*, Bhandari A, Mishra N, Sinha A, Häsler R, Rosenstiel P, Uliczka K, Wagner C, Yldirim AÖ, Fink C, Roeder T A Drosophila model of cigarette smoke induced COPD identifies Nrf2 signaling as an expendient target for intervention Aging 2018; 10: 2122-2135. doi: 10.18632/aging.101536.
Barbosa C, Beardmore R, Schulenburg H*, Jansen G* (2018) Antibiotic combination efficacy (ACE) networks for a Pseudomonas aeruginosa model. PLoS Biol. 16: e2004356. * Shared senior authorship.
Barbosa C, Trebosc V, Kemmer C, Rosenstiel P, Beardmore R, Schulenburg H*, Jansen G* Alternative evolutionary paths to bacterial antibiotic resistance cause distinct collateral effects. Mol. Biol. Evol. 2017; 34:2229-2244. * Shared senior authorship.
Heyckendorf J, Andres S, Köser CU, Olaru ID, Schön T, Sturegård E, Beckert P, Schleusener V, Kohl TA, Hillemann D, Moradigaravand D, Parkhill J, Peacock SJ, Niemann S (equal contribution), Lange C, Merker M. What is resistance? Impact of phenotypic versus molecular drug resistance testing on multi- and extensively drug-resistant tuberculosis therapy. Antimicrob Agents Chemother 2017 pii: AAC.01550-17
Walker TM, Merker M, Knoblauch AM, Helbling P, Schoch OD, van der Werf MJ, Kranzer K, Fiebig L, Kröger S, Haas W, Hoffmann H, Indra A, Egli A, Cirillo DM, Robert J, Rogers TR, Groenheit R, Mengshoel AT, Mathys V, Haanperä M, Soolingen DV, Niemann S (equal contribution), Böttger EC, Keller PM; MDR-TB Cluster Consortium. A cluster of multidrug-resistant Mycobacterium tuberculosis among patients arriving in Europe from the Horn of Africa: a molecular epidemiological study. Lancet Infect Dis 2018 18(4):431-440. doi: 10.1016/S1473-3099(18)30004-5.
Godfroid M, Dagan T, Kupczok A. Recombination Signal in Mycobacterium tuberculosis Stems from Reference-guided Assemblies and Alignment Artefacts. Genome Biol Evol. 2018 Aug 1;10(8):1920-1926.
(Article)
2017
The potential for targeted rewriting of epigenetic marks in COPD as a new therapeutic approach.
Wu DD, Song J, Bartel S, Krauss-Etschmann S, Rots MG, Hylkema MN.
(Article)
Pulmonary microRNA profiles identify involvement of Creb1 and Sec14l3 in bronchial epithelial changes in allergic asthma.
Bartel S, Schulz N, Alessandrini F, Schamberger AC, Pagel P, Theis FJ, Milger K, Noessner E, Stick SM, Kicic A, Eickelberg O, Freishtat RJ, Krauss-Etschmann S.
Sci Rep. 2017 Apr 6;7:46026. doi: 10.1038/srep46026.
(Article)
D-tryptophan from probiotic bacteria influences the gut microbiome and allergic airway disease.
Kepert I, Fonseca J, Müller C, Milger K, Hochwind K, Kostric M, Fedoseeva M, Ohnmacht C, Dehmel S, Nathan P, Bartel S, Eickelberg O, Schloter M, Hartmann A, Schmitt-Kopplin P, Krauss-Etschmann S.
J Allergy Clin Immunol. 2017 May;139(5):1525-1535. doi: 10.1016/j.jaci.2016.09.003. Epub 2016 Sep 23.
(Article)
Identification of a plasma miRNA biomarker-signature for allergic asthma: a translational approach.
K. Milger, J.Götschke, L. Krause, P. Nathan, F. Alessandrini, A. Tufman, R. Fischer, S. Bartel, F. J. Theis, J. Behr, S. Dehmel, N.S. Mueller, N. Kneidinger, S. Krauss-Etschmann.
Allergy 2017 Dec;72(12):1962-1971. doi: 10.1111/all.13205
(Article)
Development of a Stable Lung Microbiome in Healthy Neonatal Mice.
Kostric M, Milger K, Krauss-Etschmann S, Engel M, Vestergaard G, Schloter M, Schöler A.
Microb Ecol. 2017 Sep 13. doi: 10.1007/s00248-017-1068-x. [Epub ahead of print]
(Article)
Influences of environmental bacteria and their metabolites on allergies, asthma, and host microbiota.
Jatzlauk G, Bartel S, Heine H, Schloter M, Krauss-Etschmann S.
Allergy. 2017 Dec;72(12):1859-1867. doi: 10.1111/all.13220. Epub 2017 Jun 28. Review.
(Article)
Airway remodeling in asthma: what really matters
Fehrenbach H, Wagner C, Wegmann M [2017] Cell Tissue Res 2017: 551-569
(Article)
Alternative evolutionary paths to bacterial antibiotic resistance cause distinct collateral effects. Barbosa C, Trebosc V, Kemmer C, Rosenstiel P, Beardmore R, Schulenburg H*, Jansen G* (2017) Mol. Biol. Evol. 34:2229-2244 (Article). *Shared senior authorship
(Article)
2016
Jansen G, Mahrt N, Tueffers L, Barbosa C, Harjes M, Adolph G, Friedrichs A, Krenz-Weinreich A, Rosenstiel P, Schulenburg H (2016) Association between clinical antibiotic resistance and susceptibility of Pseudomonas in the cystic fibrosis lung. Evol Med Publ Health 2016:182-194
(Article)
Prenatal exposure to tobacco smoke sex dependently influences methylation and mRNA levels of the Igf axis in lungs of mouse offspring.
K. Meyer, S. Krauss-Etschmann, W. Kooistra, M. Reinders-Luinge, W. Timens, L. Kobzik, T. Plösch, M. Hylkema..
AJP Lung Apr 1;312(4):L542-L555. doi: 10.1152/ajplung.00271.2016
(Article)