Priority Research Area Infections

Molecular and Experimental Mycobacteriology

Mission   Projects   Funding   Techniques   Publications    Staff

Publications

2020

Dreyer, V, Utpatel, C, Kohl, TA, Barilar, I, Gröschel, MI, Feuerriegel, S & Niemann, S 2020, 'Detection of low-frequency resistance-mediating SNPs in next-generation sequencing data of Mycobacterium tuberculosis complex strains with binoSNP', Scientific Reports, Jg. 10, Nr. 1, S. 7874. https://doi.org/10.1038/s41598-020-64708-8

Gröschel, MI, Meehan, CJ, Barilar, I, Diricks, M, Gonzaga, A, Steglich, M, Conchillo-Solé, O, Scherer, I-C, Mamat, U, Luz, CF, De Bruyne, K, Utpatel, C, Yero, D, Gibert, I, Daura, X, Kampmeier, S, Rahman, NA, Kresken, M, van der Werf, TS, Alio, I, Streit, WR, Zhou, K, Schwartz, T, Rossen, JWA, Farhat, MR, Schaible, UE, Nübel, U, Rupp, J, Steinmann, J, Niemann, S & Kohl, TA 2020, 'The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia', Nature communications, Jg. 11, Nr. 1, S. 2044. https://doi.org/10.1038/s41467-020-15123-0

Wetzstein, N, Kohl, TA, Andres, S, Schultze, TG, Geil, A, Kim, E, Biciusca, T, Hügel, C, Hogardt, M, Lehn, A, Vehreschild, MJGT, Wolf, T, Niemann, S, Maurer, FP & Wichelhaus, TA 2020, 'Comparative analysis of phenotypic and genotypic antibiotic susceptibility patterns in Mycobacterium avium complex', INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES , Jg. 93, S. 320-328. https://doi.org/10.1016/j.ijid.2020.02.059

Merker, M, Kohl, TA, Barilar, I, Andres, S, Fowler, PW, Chryssanthou, E, Ängeby, K, Jureen, P, Moradigaravand, D, Parkhill, J, Peacock, SJ, Schön, T, Maurer, FP, Walker, T, Köser, C & Niemann, S 2020, 'Phylogenetically informative mutations in genes implicated in antibiotic resistance in Mycobacterium tuberculosis complex', Genome medicine, Jg. 12, Nr. 1, S. 27. https://doi.org/10.1186/s13073-020-00726-5

Merker, M, Nikolaevskaya, E, Kohl, TA, Molina-Moya, B, Pavlovska, O, Brännberg, P, Dudnyk, A, Stokich, V, Barilar, I, Marynova, I, Filipova, T, Prat, C, Sjöstedt, A, Dominguez, J, Rzhepishevska, O & Niemann, S 2020, 'Multidrug- and Extensively Drug-Resistant Mycobacterium tuberculosis Beijing Clades, Ukraine, 2015', EMERGING INFECTIOUS DISEASES, Jg. 26, Nr. 3, S. 481-490. https://doi.org/10.3201/eid2603.190525

Klopper, M, Heupink, TH, Hill-Cawthorne, G, Streicher, EM, Dippenaar, A, de Vos, M, Abdallah, AM, Limberis, J, Merker, M, Burns, S, Niemann, S, Dheda, K, Posey, J, Pain, A & Warren, RM 2020, 'A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic', BMC Medicine, Jg. 18, Nr. 1, S. 24. https://doi.org/10.1186/s12916-019-1487-2

Shuaib, YA, Khalil, EAG, Wieler, LH, Schaible, UE, Bakheit, MA, Mohamed-Noor, SE, Abdalla, MA, Kerubo, G, Andres, S, Hillemann, D, Richter, E, Kranzer, K, Niemann, S & Merker, M 2020, 'Mycobacterium tuberculosis Complex Lineage 3 as Causative Agent of Pulmonary Tuberculosis, Eastern Sudan1', EMERGING INFECTIOUS DISEASES, Jg. 26, Nr. 3, S. 427-436. https://doi.org/10.3201/eid2603.191145

2019

Andres, S, Gröschel, MI, Hillemann, D, Merker, M, Niemann, S & Kranzer, K 2019, 'A Diagnostic Algorithm To Investigate Pyrazinamide and Ethambutol Resistance in Rifampin-Resistant Mycobacterium tuberculosis Isolates in a Low-Incidence Setting', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, Jg. 63, Nr. 2. https://doi.org/10.1128/AAC.01798-18

Arandjelović, I, Merker, M, Richter, E, Kohl, TA, Savić, B, Soldatović, I, Wirth, T, Vuković, D & Niemann, S 2019, 'Longitudinal Outbreak of Multidrug-Resistant Tuberculosis in a Hospital Setting, Serbia', EMERGING INFECTIOUS DISEASES, Jg. 25, Nr. 3, S. 555-558. https://doi.org/10.3201/eid2503.181220

Borrell, S, Trauner, A, Brites, D, Rigouts, L, Loiseau, C, Coscolla, M, Niemann, S, De Jong, B, Yeboah-Manu, D, Kato-Maeda, M, Feldmann, J, Reinhard, M, Beisel, C & Gagneux, S 2019, 'Reference set of Mycobacterium tuberculosis clinical strains: A tool for research and product development', PLOS ONE, Jg. 14, Nr. 3, S. e0214088. https://doi.org/10.1371/journal.pone.0214088

Diel, R, Kohl, TA, Maurer, FP, Merker, M, Meywald Walter, K, Hannemann, J, Nienhaus, A, Supply, P & Niemann, S 2019, 'Accuracy of whole genome sequencing to determine recent tuberculosis transmission: an 11-year population-based study in Hamburg, Germany', The European respiratory journal, Jg. 54, Nr. 5. https://doi.org/10.1183/13993003.01154-2019

Engström, A, Antonenka, U, Kadyrov, A, Kalmambetova, G, Kranzer, K, Merker, M, Kabirov, O, Parpieva, N, Rajabov, A, Sahalchyk, E, Sayfudtinov, Z, Niemann, S & Hoffmann, H 2019, 'Population structure of drug-resistant Mycobacterium tuberculosis in Central Asia', BMC INFECTIOUS DISEASES , Jg. 19, Nr. 1, S. 908. https://doi.org/10.1186/s12879-019-4480-7

Ghodousi, A, Tagliani, E, Karunaratne, E, Niemann, S, Perera, J, Köser, CU & Cirillo, DM 2019, 'Isoniazid Resistance in Mycobacterium tuberculosis Is a Heterogeneous Phenotype Composed of Overlapping MIC Distributions with Different Underlying Resistance Mechanisms', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, Jg. 63, Nr. 7. https://doi.org/10.1128/AAC.00092-19

Havlicek, J, Dachsel, B, Slickers, P, Andres, S, Beckert, P, Feuerriegel, S, Niemann, S, Merker, M & Labugger, I 2019, 'Rapid microarray-based assay for detection of pyrazinamide resistant Mycobacterium tuberculosis', Diagnostic microbiology and infectious disease, Jg. 94, Nr. 2, S. 147-154. https://doi.org/10.1016/j.diagmicrobio.2018.12.011

Homolka, S, Zallet, J, Albert, H, Witt, A-K & Kranzer, K 2019, 'Introduction of quality management in a National Reference Laboratory in Germany', PLOS ONE, Jg. 14, Nr. 10, S. e0222925. https://doi.org/10.1371/journal.pone.0222925

Hunt, M, Bradley, P, Lapierre, SG, Heys, S, Thomsit, M, Hall, MB, Malone, KM, Wintringer, P, Walker, TM, Cirillo, DM, Comas, I, Farhat, MR, Fowler, P, Gardy, J, Ismail, N, Kohl, TA, Mathys, V, Merker, M, Niemann, S, Omar, SV, Sintchenko, V, Smith, G, van Soolingen, D, Supply, P, Tahseen, S, Wilcox, M, Arandjelovic, I, Peto, TEA, Crook, DW & Iqbal, Z 2019, 'Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe', Wellcome open research, Jg. 4, S. 191. https://doi.org/10.12688/wellcomeopenres.15603.1

Ismail, NA, Said, HM, Rodrigues, C, Omar, SV, Ajbani, K, Sukhadiad, N, Kohl, TA, Niemann, S, Kranzer, K, Diels, M, Rigouts, L, Rüsch-Gerdes, S & Siddiqi, S 2019, 'Multicentre study to establish interpretive criteria for clofazimine drug susceptibility testing', INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE, Jg. 23, Nr. 5, S. 594-599. https://doi.org/10.5588/ijtld.18.0417

Jajou, R, Kohl, TA, Walker, T, Norman, A, Cirillo, DM, Tagliani, E, Niemann, S, de Neeling, A, Lillebaek, T, Anthony, RM & van Soolingen, D 2019, 'Towards standardisation: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases', Eurosurveillance, Jg. 24, Nr. 50. https://doi.org/10.2807/1560-7917.ES.2019.24.50.1900130

Lipworth, S, Jajou, R, de Neeling, A, Bradley, P, van der Hoek, W, Maphalala, G, Bonnet, M, Sanchez-Padilla, E, Diel, R, Niemann, S, Iqbal, Z, Smith, G, Peto, T, Crook, D, Walker, T & van Soolingen, D 2019, 'SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex', EMERGING INFECTIOUS DISEASES, Jg. 25, Nr. 3, S. 482-488. https://doi.org/10.3201/eid2503.180894

Loiseau, C, Brites, D, Moser, I, Coll, F, Pourcel, C, Robbe-Austerman, S, Escuyer, V, Musser, KA, Peacock, SJ, Feuerriegel, S, Kohl, TA, Niemann, S, Gagneux, S & Köser, CU 2019, 'Revised Interpretation of the Hain Lifescience GenoType MTBC To Differentiate Mycobacterium canettii and Members of the Mycobacterium tuberculosis Complex.', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, Jg. 63, Nr. 6. https://doi.org/10.1128/AAC.00159-19

Meehan, CJ, Goig, GA, Kohl, TA, Verboven, L, Dippenaar, A, Ezewudo, M, Farhat, MR, Guthrie, JL, Laukens, K, Miotto, P, Ofori-Anyinam, B, Dreyer, V, Supply, P, Suresh, A, Utpatel, C, van Soolingen, D, Zhou, Y, Ashton, PM, Brites, D, Cabibbe, AM, de Jong, BC, de Vos, M, Menardo, F, Gagneux, S, Gao, Q, Heupink, TH, Liu, Q, Loiseau, C, Rigouts, L, Rodwell, TC, Tagliani, E, Walker, TM, Warren, RM, Zhao, Y, Zignol, M, Schito, M, Gardy, J, Cirillo, DM, Niemann, S, Comas, I & Van Rie, A 2019, 'Whole genome sequencing of Mycobacterium tuberculosis:current standards and open issues', Nature reviews. Microbiology, Jg. 17, Nr. 9, S. 533-545. https://doi.org/10.1038/s41579-019-0214-5

Nikolayevskyy, V, Niemann, S, Anthony, R, van Soolingen, D, Tagliani, E, Ködmön, C, van der Werf, MJ & Cirillo, DM 2019, 'Role and value of whole genome sequencing in studying tuberculosis transmission', CLINICAL MICROBIOLOGY AND INFECTION , Jg. 25, Nr. 11, S. 1377-1382. https://doi.org/10.1016/j.cmi.2019.03.022

Obeng-Nkrumah, N, Labi, A-K, Blankson, H, Awuah-Mensah, G, Oduro-Mensah, D, Anum, J, Teye, J, Kwashie, SD, Bako, E, Ayeh-Kumi, PF & Asmah, R 2019, 'Household cockroaches carry CTX-M-15-, OXA-48- and NDM-1-producing enterobacteria, and share beta-lactam resistance determinants with humans', BMC MICROBIOLOGY, Jg. 19, Nr. 1, 272. https://doi.org/10.1186/s12866-019-1629-x

Polsfuss, S, Hofmann-Thiel, S, Merker, M, Krieger, D, Niemann, S, Rüssmann, H, Schönfeld, N, Hoffmann, H & Kranzer, K 2019, 'Emergence of Low-level Delamanid and Bedaquiline Resistance During Extremely Drug-resistant Tuberculosis Treatment', CLINICAL INFECTIOUS DISEASES , Jg. 69, S. 1229-1231. https://doi.org/10.1093/cid/ciz074

Shitikov, E, Guliaev, A, Bespyatykh, J, Malakhova, M, Kolchenko, S, Smirnov, G, Merker, M, Niemann, S, Mokrousov, I, Ilina, E & Govorun, V 2019, 'The role of IS6110 in micro- and macroevolution of Mycobacterium tuberculosis lineage 2', Molecular phylogenetics and evolution, Jg. 139, S. 106559. https://doi.org/10.1016/j.ympev.2019.106559

Vaziri, F, Kohl, TA, Ghajavand, H, Kargarpour Kamakoli, M, Merker, M, Hadifar, S, Khanipour, S, Fateh, A, Masoumi, M, Siadat, SD & Niemann, S 2019, 'Genetic Diversity of Multi- and Extensively Drug-Resistant Mycobacterium tuberculosis Isolates in the Capital of Iran, Revealed by Whole-Genome Sequencing', JOURNAL OF CLINICAL MICROBIOLOGY, Jg. 57, Nr. 1, S. e01477-18. https://doi.org/10.1128/JCM.01477-18

Wood, HN, Venken, T, Willems, H, Jacobs, A, Reis, AJ, Almeida da Silva, PE, Homolka, S, Niemann, S, Rohde, KH & Hooyberghs, J 2019, 'Molecular drug susceptibility testing and strain typing of tuberculosis by DNA hybridization', PLOS ONE, Jg. 14, Nr. 2, S. e0212064. https://doi.org/10.1371/journal.pone.0212064

Lancet Respiratory Medicine drug-resistant tuberculosis Commission group, Niemann, S & Lange, C 2019, 'The Lancet Respiratory Medicine Commission: 2019 update: epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant and incurable tuberculosis', Lancet Respiratory Medicine, Jg. 7, Nr. 9, S. 820-826. https://doi.org/10.1016/S2213-2600(19)30263-2

CRyPTIC Consortium, Niemann, S & Kohl, T 2019, 'DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis',  BIOINFORMATICS , Jg. 35, Nr. 18, S. 3240-3249. https://doi.org/10.1093/bioinformatics/btz067

CRyPTIC Consortium, Niemann, S, Merker, M & Kohl, T 2019, 'Application of machine learning techniques to tuberculosis drug resistance analysis',  BIOINFORMATICS , Jg. 35, Nr. 13, S. 2276-2282. https://doi.org/10.1093/bioinformatics/bty949

2018

Acosta, F, Pérez-Lago, L, Ruiz Serrano, MJ, Marín, M, Kohl, TA, Lozano, N, Niemann, S, Valerio, M, Olmedo, M, Pérez-Granda, MJ, Pérez Pérez, MR, Bouza, E, Muñoz, P & García de Viedma, D 2018, 'Fast update of undetected Mycobacterium chimaera infections to reveal unsuspected cases' The Journal of hospital infection, Jg. 100, Nr. 4, S. 451-455. https://doi.org/10.1016/j.jhin.2018.08.018

Al-Ghafli, H, Kohl, TA, Merker, M, Varghese, B, Halees, A, Niemann, S & Al-Hajoj, S 2018, 'Drug-resistance profiling and transmission dynamics of multidrug-resistant Mycobacterium tuberculosis in Saudi Arabia revealed by whole genome sequencing' Infection and drug resistance, Jg. 11, S. 2219-2229. https://doi.org/10.2147/IDR.S181124

Andres, S, Gröschel, MI, Hillemann, D, Merker, M, Niemann, S & Kranzer, K 2018, 'A diagnostic algorithm to investigate pyrazinamide and ethambutol resistance in rifampicin resistant Mycobacterium tuberculosis isolates in a low incidence setting' ANTIMICROBIAL AGENTS AND CHEMOTHERAPY. https://doi.org/10.1128/AAC.01798-18

Cabibbe, AM, Walker, TM, Niemann, S & Cirillo, DM 2018, 'Whole Genome Sequencing of Mycobacterium tuberculosis' The European respiratory journal, Jg. 52, Nr. 5, S. 1801163. https://doi.org/10.1183/13993003.01163-2018

Caño-Muñiz, S, Anthony, R, Niemann, S & Alffenaar, J-WC 2018, 'New Approaches and Therapeutic Options for Mycobacterium tuberculosis in a Dormant State' Clinical microbiology reviews, Jg. 31, Nr. 1. https://doi.org/10.1128/CMR.00060-17

CRyPTIC Consortium and the 100,000 Genomes Project 2018, 'Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing' New England Journal of Medicine, Jg. 379, Nr. 15, S. 1403-1415. https://doi.org/10.1056/NEJMoa1800474

CRyPTIC Consortiumfor the CRyPTIC Consortiumfor the CRyPTIC Consortium & Niemann, S 2018, 'Validating a 14-Drug Microtiter Plate Containing Bedaquiline and Delamanid for Large-Scale Research Susceptibility Testing of Mycobacterium tuberculosis' ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, Jg. 62, Nr. 9. https://doi.org/10.1128/AAC.00344-18

EUSeqMyTB Consortium & Niemann, S 2018, 'EUSeqMyTB to set standards and build capacity for whole genome sequencing for tuberculosis in the EU' Lancet Infectious Diseases, Jg. 18, Nr. 4, S. 377. https://doi.org/10.1016/S1473-3099(18)30132-4

Global Tuberculosis Network (GTN) & Niemann, S 2018, 'Evolution of programmatic definitions used in tuberculosis prevention and care' CLINICAL INFECTIOUS DISEASES . https://doi.org/10.1093/cid/ciy990

Gröschel, MI, Walker, TM, van der Werf, TS, Lange, C, Niemann, S & Merker, M 2018, 'Pathogen-based precision medicine for drug-resistant tuberculosis' PLOS PATHOGENS, Jg. 14, Nr. 10, S. e1007297. https://doi.org/10.1371/journal.ppat.1007297

Havlicek, J, Dachsel, B, Slickers, P, Andres, S, Beckert, P, Feuerriegel, S, Niemann, S, Merker, M & Labugger, I 2018, 'Rapid Microarray-Based Detection of Rifampin, Isoniazid, and Fluoroquinolone Resistance in Mycobacterium tuberculosis by Use of a Single Cartridge' JOURNAL OF CLINICAL MICROBIOLOGY, Jg. 56, Nr. 2. https://doi.org/10.1128/JCM.01249-17

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, Lange, C & Merker, M 2018, 'What is resistance? Impact of phenotypic versus molecular drug resistance testing on multi- and extensively drug-resistant tuberculosis therapy: Impact of Phenotypic versus Molecular Drug Resistance Testing on Therapy for Multi- and Extensively Drug-Resistant Tuberculosis' ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, Jg. 62, Nr. 2, S. e01550-17. https://doi.org/10.1128/AAC.01550-17

Kohl, TA, Harmsen, D, Rothgänger, J, Walker, T, Diel, R & Niemann, S 2018, 'Harmonized Genome Wide Typing of Tubercle Bacilli Using a Web-Based Gene-By-Gene Nomenclature System' EBioMedicine, Jg. 34, S. 131-138. https://doi.org/10.1016/j.ebiom.2018.07.030

Kohl, TA, Utpatel, C, Niemann, S & Moser, I 2018, 'Mycobacterium bovis Persistence in Two Different Captive Wild Animal Populations in Germany: a Longitudinal Molecular Epidemiological Study Revealing Pathogen Transmission by Whole-Genome Sequencing' JOURNAL OF CLINICAL MICROBIOLOGY, Jg. 56, Nr. 9. https://doi.org/10.1128/JCM.00302-18

Kohl, TA, Utpatel, C, Schleusener, V, De Filippo, MR, Beckert, P, Cirillo, DM & Niemann, S 2018, 'MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates' PeerJ, Jg. 6, S. e5895. https://doi.org/10.7717/peerj.5895

Köser, CU, Heyckendorf, J, Andres, S, Olaru, ID, Schön, T, Sturegård, E, Beckert, P, Schleusener, V, Kohl, TA, Hillemann, D, Moradigaravand, D, Parkhill, J, Peacock, SJ, Niemann, S, Lange, C & Merker, M 2018, 'Reply to Dookie et al., "Whole-Genome Sequencing To Guide the Selection of Treatment for Drug-Resistant Tuberculosis"' ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, Jg. 62, Nr. 8. https://doi.org/10.1128/AAC.00616-18

Lange, C, Alghamdi, WA, Al-Shaer, MH, Brighenti, S, Diacon, AH, DiNardo, AR, Grobbel, HP, Gröschel, MI, von Groote-Bidlingmaier, F, Hauptmann, M, Heyckendorf, J, Köhler, N, Kohl, TA, Merker, M, Niemann, S, Peloquin, CA, Reimann, M, Schaible, UE, Schaub, D, Schleusener, V, Thye, T & Schön, T 2018, 'Perspectives for personalized therapy for patients with multidrug-resistant tuberculosis' JOURNAL OF INTERNAL MEDICINE . https://doi.org/10.1111/joim.12780

Makhado, NA, Matabane, E, Faccin, M, Pinçon, C, Jouet, A, Boutachkourt, F, Goeminne, L, Gaudin, C, Maphalala, G, Beckert, P, Niemann, S, Delvenne, J-C, Delmée, M, Razwiedani, L, Nchabeleng, M, Supply, P, de Jong, BC & André, E 2018, 'Outbreak of multidrug-resistant tuberculosis in South Africa undetected by WHO-endorsed commercial tests: an observational study' Lancet Infectious Diseases, Jg. 18, Nr. 12, S. 1350-1359. https://doi.org/10.1016/S1473-3099(18)30496-1

Malm, S, Maaß, S, Schaible, UE, Ehlers, S & Niemann, S 2018, 'In vivo virulence of Mycobacterium tuberculosis depends on a single homologue of the LytR-CpsA-Psr proteins' Scientific Reports, Jg. 8, Nr. 1, S. 3936. https://doi.org/10.1038/s41598-018-22012-6

Meehan, CJ, Moris, P, Kohl, TA, Pečerska, J, Akter, S, Merker, M, Utpatel, C, Beckert, P, Gehre, F, Lempens, P, Stadler, T, Kaswa, MK, Kühnert, D, Niemann, S & de Jong, BC 2018, 'The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology' EBioMedicine, Jg. 37, S. 410-416. https://doi.org/10.1016/j.ebiom.2018.10.013

Mekonnen, A, Merker, M, Collins, JM, Addise, D, Aseffa, A, Petros, B, Ameni, G & Niemann, S 2018, 'Molecular epidemiology and drug resistance patterns of Mycobacterium tuberculosis complex isolates from university students and the local community in Eastern Ethiopia' PLOS ONE, Jg. 13, Nr. 9, S. e0198054. https://doi.org/10.1371/journal.pone.0198054

Plate, A, Kohl, TA, Keller, PM, Majer, S, Fulchini, R, Strahm, C, Medugno, C, Rancic, Z, Husmann, L, Sax, H, Niemann, S & Hasse, B 2018, 'Aortic Endograft Infection with Mycobacterium chimaera and Granulicatella adiacens, Switzerland, 2014' EMERGING INFECTIOUS DISEASES, Jg. 24, Nr. 9, S. 1700-1704. https://doi.org/10.3201/eid2409.180247

Reiling, N, Homolka, S, Kohl, TA, Steinhäuser, C, Kolbe, K, Schütze, S & Brandenburg, J 2018, 'Shaping the niche in macrophages: Genetic diversity of the M. tuberculosis complex and its consequences for the infected host' INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY, Jg. 308, Nr. 1, S. 118-128. https://doi.org/10.1016/j.ijmm.2017.09.009

Schleusener, V, Merker, M, Kohl, T & Niemann, S 2018, 'Tuberkulose: Neue Herausforderungen durch zunehmende Resistenzen' Der Pneumologe, Jg. 2018, Nr. 1, S. 35-41.

Shima, K, Wanker, M, Skilton, RJ, Cutcliffe, LT, Schnee, C, Kohl, TA, Niemann, S, Geijo, J, Klinger, M, Timms, P, Rattei, T, Sachse, K, Clarke, IN & Rupp, J 2018, 'The Genetic Transformation of Chlamydia pneumoniae' mSphere, Jg. 3, Nr. 5, e00412-18. https://doi.org/10.1128/mSphere.00412-18

Shuaib, YA, Khalil, EAG, Schaible, UE, Wieler, LH, Bakheit, MAM, Mohamed-Noor, SE, Abdalla, MA, Homolka, S, Andres, S, Hillemann, D, Lonnroth, K, Richter, E, Niemann, S & Kranzer, K 2018, 'Smear Microscopy for Diagnosis of Pulmonary Tuberculosis in Eastern Sudan' Tuberculosis research and treatment, Jg. 2018, S. 8038137. https://doi.org/10.1155/2018/8038137

Steinmann, J, Mamat, U, Abda, EM, Kirchhoff, L, Streit, WR, Schaible, UE, Niemann, S & Kohl, TA 2018, 'Analysis of Phylogenetic Variation of Reveals Human-Specific Branches' Frontiers in Microbiology, Jg. 9, S. 806. https://doi.org/10.3389/fmicb.2018.00806

Tortoli, E, Kohl, TA, Brown-Elliott, BA, Trovato, A, Cardoso-Leão, S, Garcia, MJ, Vasireddy, S, Turenne, CY, Griffith, DE, Philley, JV, Niemann, S, Wallace, RJ & Cirillo, DM 2018, 'Mycobacterium abscessus, a taxonomic puzzle' INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Jg. 68, Nr. 1, S. 467-469. https://doi.org/10.1099/ijsem.0.002457

Vaziri, F, Kohl, TA, Ghajavand, H, Kargarpour Kamakoli, M, Merker, M, Hadifar, S, Khanipour, S, Fateh, A, Masoumi, M, Siadat, SD & Niemann, S 2018, 'The genetic diversity of multi and extensively drug resistant Mycobacterium tuberculosis in the capital of Iran revealed by whole genome sequencing' JOURNAL OF CLINICAL MICROBIOLOGY. https://doi.org/10.1128/JCM.01477-18

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, Böttger, EC, Keller, PM, MDR-TB Cluster Consortium & Lange, C 2018, 'A cluster of multidrug-resistant Mycobacterium tuberculosis among patients arriving in Europe from the Horn of Africa: a molecular epidemiological study' Lancet Infectious Diseases, Jg. 18, Nr. 4, S. 431-440. https://doi.org/10.1016/S1473-3099(18)30004-5

Zignol, M, Cabibbe, AM, Dean, AS, Glaziou, P, Alikhanova, N, Ama, C, Andres, S, Barbova, A, Borbe-Reyes, A, Chin, DP, Cirillo, DM, Colvin, C, Dadu, A, Dreyer, A, Driesen, M, Gilpin, C, Hasan, R, Hasan, Z, Hoffner, S, Hussain, A, Ismail, N, Kamal, SMM, Khanzada, FM, Kimerling, M, Kohl, TA, Mansjö, M, Miotto, P, Mukadi, YD, Mvusi, L, Niemann, S, Omar, SV, Rigouts, L, Schito, M, Sela, I, Seyfaddinova, M, Skenders, G, Skrahina, A, Tahseen, S, Wells, WA, Zhurilo, A, Weyer, K, Floyd, K & Raviglione, MC 2018, 'Genetic sequencing for surveillance of drug resistance in tuberculosis in highly endemic countries: a multi-country population-based surveillance study' Lancet Infectious Diseases, Jg. 18, Nr. 6, S. 675-683. https://doi.org/10.1016/S1473-3099(18)30073-2

2017

Marais, BJ, Walker, TM, Cirillo, DM, Raviglione, M, Abubakar, I, van der Werf, MJ, Boehme, C, Niemann, S, Castro, KG, Zumla, A, Sintchenko, V & Crook, DW 2017, 'Aiming for zero tuberculosis transmission in low-burden countries' Lancet Respiratory Medicine, Bd 5, Nr. 11, S. 846-848. DOI: 10.1016/S2213-2600(17)30382-X

Fiebig, L, Kohl, TA, Popovici, O, Mühlenfeld, M, Indra, A, Homorodean, D, Chiotan, D, Richter, E, Rüsch-Gerdes, S, Schmidgruber, B, Beckert, P, Hauer, B, Niemann, S, Allerberger, F & Haas, W 2017, 'A joint cross-border investigation of a cluster of multidrug-resistant tuberculosis in Austria, Romania and Germany in 2014 using classic, genotyping and whole genome sequencing methods: lessons learned' Euro Surveillance, Bd 22, Nr. 2. DOI: 10.2807/1560-7917.ES.2017.22.2.30439

Havlicek, J, Rivera-Milla, E, Slickers, P, Andres, S, Feuerriegel, S, Niemann, S, Merker, M & Labugger, I 2017, 'An application of competitive reporter monitored amplification (CMA) for rapid detection of single nucleotide polymorphisms (SNPs)' PLOS ONE, Bd 12, Nr. 8, S. e0183561. DOI: 10.1371/journal.pone.0183561

Miotto, P, Tessema, B, Tagliani, E, Chindelevitch, L, Starks, AM, Emerson, C, Hanna, D, Kim, PS, Liwski, R, Zignol, M, Gilpin, C, Niemann, S, Denkinger, CM, Fleming, J, Warren, RM, Crook, D, Posey, J, Gagneux, S, Hoffner, S, Rodrigues, C, Comas, I, Engelthaler, DM, Murray, M, Alland, D, Rigouts, L, Lange, C, Dheda, K, Hasan, R, Ranganathan, UDK, McNerney, R, Ezewudo, M, Cirillo, DM, Schito, M, Köser, CU & Rodwell, TC 2017, 'A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis' The European respiratory journal, Bd 50, Nr. 6. DOI: 10.1183/13993003.01354-2017

Kolbe, K, Möckl, L, Sohst, V, Brandenburg, J, Engel, R, Malm, S, Bräuchle, C, Holst, O, Lindhorst, TK & Reiling, N 2017, 'Azido pentoses: A New Tool to Efficiently Label Mycobacterium tuberculosis Clinical Isolates' Chembiochem : a European journal of chemical biology, Bd 18, Nr. 13, S. 1172-1176. DOI: 10.1002/cbic.201600706

Andre, E, Goeminne, L, Cabibbe, A, Beckert, P, Kabamba Mukadi, B, Mathys, V, Gagneux, S, Niemann, S, Van Ingen, J & Cambau, E 2017, 'Consensus numbering system for the rifampicin resistance-associated rpoB gene mutations in pathogenic mycobacteria' CLINICAL MICROBIOLOGY AND INFECTION , Bd 23, Nr. 3, S. 167-172. DOI: 10.1016/j.cmi.2016.09.006

Labugger, I, Heyckendorf, J, Dees, S, Häussinger, E, Herzmann, C, Kohl, TA, Richter, E, Rivera-Milla, E & Lange, C 2017, 'Detection of transrenal DNA for the diagnosis of pulmonary tuberculosis and treatment monitoring' INFECTION, Bd 45, Nr. 3, S. 269-276. DOI: 10.1007/s15010-016-0955-2

Bjorn-Mortensen, K, Lillebaek, T, Koch, A, Soborg, B, Ladefoged, K, Sørensen, HCF, Kohl, TA, Niemann, S & Andersen, AB 2017, 'Extent of transmission captured by contact tracing in a tuberculosis high endemic setting' The European respiratory journal, Bd 49, Nr. 3. DOI: 10.1183/13993003.01851-2016

van Ingen, J, Kohl, TA, Kranzer, K, Hasse, B, Keller, PM, Katarzyna Szafrańska, A, Hillemann, D, Chand, M, Schreiber, PW, Sommerstein, R, Berger, C, Genoni, M, Rüegg, C, Troillet, N, Widmer, AF, Becker, SL, Herrmann, M, Eckmanns, T, Haller, S, Höller, C, Debast, SB, Wolfhagen, MJ, Hopman, J, Kluytmans, J, Langelaar, M, Notermans, DW, Ten Oever, J, van den Barselaar, P, Vonk, ABA, Vos, MC, Ahmed, N, Brown, T, Crook, DW, Lamagni, T, Phin, N, Smith, EG, Zambon, M, Serr, A, Götting, T, Ebner, W, Thürmer, A, Utpatel, C, Spröer, C, Bunk, B, Nübel, U, Bloemberg, GV, Böttger, EC, Niemann, S, Wagner, D & Sax, H 2017, 'Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study' Lancet Infectious Diseases, Bd 17, Nr. 10, S. 1033-1041. DOI: 10.1016/S1473-3099(17)30324-9

Mellmann, A, Andersen, PS, Bletz, S, Friedrich, AW, Kohl, TA, Lilje, B, Niemann, S, Prior, K, Rossen, JW & Harmsen, D 2017, 'High Interlaboratory Reproducibility and Accuracy of Next-Generation-Sequencing-Based Bacterial Genotyping in a Ring Trial' JOURNAL OF CLINICAL MICROBIOLOGY, Bd 55, Nr. 3, S. 908-913. DOI: 10.1128/JCM.02242-16

Bengtson, HN, Homolka, S, Niemann, S, Reis, AJ, da Silva, PE, Gerasimova, YV, Kolpashchikov, DM & Rohde, KH 2017, 'Multiplex detection of extensively drug resistant tuberculosis using binary deoxyribozyme sensors' Biosensors & Bioelectronics, Bd 94, S. 176-183. DOI: 10.1016/j.bios.2017.02.051

Tortoli, E, Kohl, TA, Trovato, A, Baldan, R, Campana, S, Cariani, L, Colombo, C, Costa, D, Cristadoro, S, Di Serio, MC, Manca, A, Pizzamiglio, G, Rancoita, PMV, Rossolini, GM, Taccetti, G, Teri, A, Niemann, S & Cirillo, DM 2017, 'Mycobacterium abscessus in patients with cystic fibrosis: low impact of inter-human transmission in Italy' The European respiratory journal, Bd 50, Nr. 1. DOI: 10.1183/13993003.02525-2016

Birmes, FS, Wolf, T, Kohl, TA, Rüger, K, Bange, F-C, Kalinowski, J & Fetzner, S 2017, 'Mycobacterium abscessus subsp. abscessus Is Capable of Degrading Pseudomonas aeruginosa Quinolone Signals' Frontiers in Microbiology, Bd 8, S. 339. DOI: 10.3389/fmicb.2017.00339

Schleusener, V, Köser, CU, Beckert, P, Niemann, S & Feuerriegel, S 2017, 'Mycobacterium tuberculosis resistance prediction and lineage classification from genome sequencing: comparison of automated analysis tools' Scientific Reports, Bd 7, S. 46327. DOI: 10.1038/srep46327

Malm, S, Linguissi, LSG, Tekwu, EM, Vouvoungui, JC, Kohl, TA, Beckert, P, Sidibe, A, Rüsch-Gerdes, S, Madzou-Laboum, IK, Kwedi, S, Penlap Beng, V, Frank, M, Ntoumi, F & Niemann, S 2017, 'New Mycobacterium tuberculosis Complex Sublineage, Brazzaville, Congo' EMERGING INFECTIOUS DISEASES, Bd 23, Nr. 3, S. 423-429. DOI: 10.3201/eid2303.160679

André, E, Goeminne, L, Colmant, A, Beckert, P, Niemann, S & Delmee, M 2017, 'Novel rapid PCR for the detection of Ile491Phe rpoB mutation of Mycobacterium tuberculosis, a rifampicin-resistance-conferring mutation undetected by commercial assays' CLINICAL MICROBIOLOGY AND INFECTION , Bd 23, Nr. 4, S. 267.e5-267.e7. DOI: 10.1016/j.cmi.2016.12.009

Wagner, NM, Van Aken, C, Butschkau, A, Bierhansl, L, Kellner, P, Schleusener, V, Seggewiss, J, Vollmar, B, Nöldge-Schomburg, G & Roesner, JP 2017, 'Procalcitonin impairs endothelial cell function and viability' ANESTHESIA AND ANALGESIA , Bd 124, Nr. 3, S. 836-845.

Stöckel, S, Meisel, S, Lorenz, B, Kloß, S, Henk, S, Dees, S, Richter, E, Andres, S, Merker, M, Labugger, I, Rösch, P & Popp, J 2017, 'Raman spectroscopic identification of Mycobacterium tuberculosis' Journal of Biophotonics, Bd 10, Nr. 5, S. 727-734. DOI: 10.1002/jbio.201600174

Nakatani, Y, Opel-Reading, HK, Merker, M, Machado, D, Andres, S, Kumar, SS, Moradigaravand, D, Coll, F, Perdigão, J, Portugal, I, Schön, T, Nair, D, Devi, KRU, Kohl, TA, Beckert, P, Clark, TG, Maphalala, G, Khumalo, D, Diel, R, Klaos, K, Aung, HL, Cook, GM, Parkhill, J, Peacock, SJ, Swaminathan, S, Viveiros, M, Niemann, S, Krause, KL & Köser, CU 2017, 'Role of alanine racemase mutations in Mycobacterium tuberculosis D-cycloserine resistance' ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, Bd 61, Nr. 12, e01575-14. DOI: 10.1128/AAC.01575-17

Ajileye, A, Alvarez, N, Merker, M, Walker, TM, Akter, S, Brown, K, Moradigaravand, D, Schön, T, Andres, S, Schleusener, V, Omar, SV, Coll, F, Huang, H, Diel, R, Ismail, NA, Parkhill, J, de Jong, BC, Peto, TEA, Crook, DW, Niemann, S, Robledo, J, Smith, EG, Peacock, SJ & Köser, CU 2017, 'Some Synonymous and Nonsynonymous gyrA Mutations in Mycobacterium tuberculosis Lead to Systematic False-Positive Fluoroquinolone Resistance Results with the Hain GenoType MTBDRsl Assays' ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, Bd 61, Nr. 4, S. e02169-16. DOI: 10.1128/AAC.02169-16

Dheda, K, Gumbo, T, Maartens, G, Dooley, KE, McNerney, R, Murray, M, Furin, J, Nardell, EA, London, L, Lessem, E, Theron, G, van Helden, PD, Niemann, S, Merker, M, Dowdy, D, Van Rie, A, Siu, GKH, Pasipanodya, JG, Rodrigues, C, Clark, TG, Sirgel, FA, Esmail, A, Lin, H-H, Atre, SR, Schaaf, HS, Chang, K-C, Lange, C, Nahid, P, Udwadia, ZF, Horsburgh, CR, Churchyard, GJ, Menzies, D, Hesseling, AC, Nuermberger, E, McIlleron, H, Fennelly, KP, Goemaere, E, Jaramillo, E, Low, M, Jara, CM, Padayatchi, N & Warren, RM 2017, 'The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis' Lancet Respiratory Medicine. DOI: 10.1016/S2213-2600(17)30079-6

Merker, M, Kohl, TA, Niemann, S & Supply, P 2017, 'The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex'  Advances in Experimental Medicine and Biology , Bd 1019, S. 43-78. DOI: 10.1007/978-3-319-64371-7_3

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, Lange, C & Merker, M 2017, 'What is resistance?: Impact of phenotypic versus molecular drug resistance testing on multi- and extensively drug-resistant tuberculosis therapy' ANTIMICROBIAL AGENTS AND CHEMOTHERAPY. DOI: 10.1128/AAC.01550-17

2016

Ali, S, Beckert, P, Haileamlak, A, Wieser, A, Pritsch, M, Heinrich, N, Löscher, T, Hoelscher, M, Niemann, S & Rachow, A 2016, 'Drug resistance and population structure of M.tuberculosis isolates from prisons and communities in Ethiopia' BMC INFECTIOUS DISEASES , Bd 16, Nr. 1, S. 687. DOI: 10.1186/s12879-016-2041-x

Niemann, S, Merker, M, Kohl, T & Supply, P 2016, 'Impact of Genetic Diversity on the Biology of Mycobacterium tuberculosis Complex Strains' Microbiology spectrum, Bd 4, Nr. 6. DOI: 10.1128/microbiolspec.TBTB2-0022-2016

Zignol, M, Dean, AS, Alikhanova, N, Andres, S, Cabibbe, AM, Cirillo, DM, Dadu, A, Dreyer, A, Driesen, M, Gilpin, C, Hasan, R, Hasan, Z, Hoffner, S, Husain, A, Hussain, A, Ismail, N, Kamal, M, Mansjö, M, Mvusi, L, Niemann, S, Omar, SV, Qadeer, E, Rigouts, L, Rüsch-Gerdes, S, Schito, M, Seyfaddinova, M, Skrahina, A, Tahseen, S, Wells, WA, Mukadi, YD, Kimerling, M, Floyd, K, Weyer, K & Raviglione, MC 2016, 'Population-based resistance of Mycobacterium tuberculosis isolates to pyrazinamide and fluoroquinolones results from a multicountry surveillance project' Lancet Infectious Diseases, Bd 16, Nr. 10, S. 1185-92. DOI: 10.1016/S1473-3099(16)30190-6

Varma-Basil, M, Narang, A, Chakravorty, S, Garima, K, Gupta, S, Kumar Sharma, N, Giri, A, Zozio, T, Couvin, D, Hanif, M, Bhatnagar, A, Menon, B, Niemann, S, Rastogi, N, Alland, D & Bose, M 2016, 'A snapshot of the predominant single nucleotide polymorphism cluster groups of Mycobacterium tuberculosis clinical isolates in Delhi, India' Tuberculosis, Bd 100, S. 72-81. DOI: 10.1016/j.tube.2016.07.007

Mühlig, A, Bocklitz, T, Labugger, I, Dees, S, Henk, S, Richter, E, Andres, S, Merker, M, Stöckel, S, Weber, K, Cialla-May, D & Popp, J 2016, 'LOC-SERS: A Promising Closed System for the Identification of Mycobacteria' ANALYTICAL CHEMISTRY , Bd 88, Nr. 16, S. 7998-8004. DOI: 10.1021/acs.analchem.6b01152

Tortoli, E, Kohl, TA, Brown-Elliott, BA, Trovato, A, Cardoso Leao, S, Garcia, MJ, Vasireddy, S, Turenne, CY, Griffith, DE, Philley, JV, Baldan, R, Campana, S, Cariani, L, Colombo, C, Taccetti, G, Teri, A, Niemann, S, Wallace, RJ & Cirillo, DM 2016, 'Emended description of Mycobacterium abscessus, Mycobacterium abscessus subs. abscessus, Mycobacterium abscessus subsp. bolletii and designation of Mycobacterium abscessus subsp. massiliense comb. nov' INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY. DOI: 10.1099/ijsem.0.001376

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 2016, '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

Nikolayevskyy, V, Kranzer, K, Niemann, S & Drobniewski, F 2016, '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

Kaufmann, E, Spohr, C, Battenfeld, S, De Paepe, D, Holzhauser, T, Balks, E, Homolka, S, Reiling, N, Gilleron, M & Bastian, M 2016, 'BCG Vaccination Induces Robust CD4+ T Cell Responses to Mycobacterium tuberculosis Complex-Specific Lipopeptides in Guinea Pigs' JOURNAL OF IMMUNOLOGY, Bd 196, Nr. 6, S. 2723-2732. DOI: 10.4049/jimmunol.1502307

Merker, M, Crudu, V, Noroc, E, Romancenco, E, Chesov, D, Günther, G, Niemann, S & Lange, C 2016, 'In reply: The impact of mixed infections on the interpretation of molecular epidemiology studies of tuberculosis' INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE, Bd 20, Nr. 3, S. 424. DOI: 10.5588/ijtld.15.1024-2

Hoffmann, H, Kohl, TA, Hofmann-Thiel, S, Merker, M, Beckert, P, Jaton, K, Nedialkova, L, Sahalchyk, E, Rothe, T, Keller, PM & Niemann, S 2016, '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, Bd 193, Nr. 3, S. 337-340. DOI: 10.1164/rccm.201502-0372LE

Domínguez, J, Boettger, EC, Cirillo, D, Cobelens, F, Eisenach, KD, Gagneux, S, Hillemann, D, Horsburgh, R, Molina-Moya, B, Niemann, S, Tortoli, E, Whitelaw, A, Lange, C & TBNET and RESIST-TB networks 2016, 'Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis: a TBNET/RESIST-TB consensus statement' INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE, Bd 20, Nr. 1, S. 24-42. DOI: 10.5588/ijtld.15.0221

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 Study Group 2016, 'Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study' Lancet Respiratory Medicine, Bd 4, Nr. 1, S. 49-58. DOI: 10.1016/S2213-2600(15)00466-X

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, Peto, TEA, Crook, DW & Iqbal, Z 2016, 'Corrigendum: Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis' Nature communications, Bd 7, S. 11465. DOI: 10.1038/ncomms11465

Kerubo, G, Amukoye, E, Niemann, S & Kariuki, S 2016, 'Drug susceptibility profiles of pulmonary Mycobacterium tuberculosis isolates from patients in informal urban settlements in Nairobi, Kenya' BMC INFECTIOUS DISEASES , Bd 16, Nr. 1, S. 583. DOI: 10.1186/s12879-016-1920-5

Homolka, S, Ubben, T & Niemann, S 2016, 'High Sequence Variability of the ppE18 Gene of Clinical Mycobacterium tuberculosis Complex Strains Potentially Impacts Effectivity of Vaccine Candidate M72/AS01E' PLOS ONE, Bd 11, Nr. 3, S. e0152200. DOI: 10.1371/journal.pone.0152200

Stucki, D, Brites, D, Jeljeli, L, 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, SEG, Suffys, P, Koch, A, Wilkinson, R, Gail-Bekker, L, Malla, B, Ley, SD, Beck, H-P, 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 2016, 'Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages' NATURE GENETICS, Bd 48, Nr. 12, S. 1535-1543. DOI: 10.1038/ng.3704

2015

Crudu V, Merker M, Lange C, Noroc E, Romancenco E, Chesov D, Günther G, Niemann S. Nosocomial transmission of multidrug-resistant tuberculosis. Int J Tuberc Lung Dis. 2015 Dec;19(12):1520-3. doi: 10.5588/ijtld.15.0327.

Steglich M, Nitsche A, von Müller L, Herrmann M, Kohl TA, Niemann S, Nübel U. Tracing the Spread of Clostridium difficile Ribotype 027 in Germany Based on Bacterial Genome Sequences. PLoS One. 2015 Oct 7;10(10):e0139811. doi:10.1371/journal.pone.0139811. eCollection 2015.

Biadglegne F, Merker M, Sack U, Rodloff AC, Niemann S. Tuberculous Lymphadenitis in Ethiopia Predominantly Caused by Strains Belonging to the Delhi/CAS Lineage and Newly Identified Ethiopian Clades of the Mycobacterium tuberculosis Complex. PLoS One. 2015 Sep 16;10(9):e0137865. doi: 10.1371/journal.pone.0137865. eCollection 2015.

Cabibbe AM, Miotto P, Moure R, Alcaide F, Feuerriegel S, Pozzi G, Nikolayevskyy V, Drobniewski F, Niemann S, Reither K, Cirillo DM. Lab-on-Chip-Based Platform for Fast Molecular Diagnosis of Multidrug-Resistant Tuberculosis. J Clin Microbiol. 2015 Dec;53(12):3876-80. doi:
10.1128/JCM.01824-15.

Walker TM, Kohl TA, Omar SV, Hedge J, Del Ojo Elias C, Bradley P, Iqbal Z, Feuerriegel S, Niehaus KE, Wilson DJ, Clifton DA, Kapatai G, Ip CL, Bowden R, Drobniewski FA, Allix-Béguec C, Gaudin C, Parkhill J, Diel R, Supply P, Crook DW, Smith EG, Walker AS, Ismail N, Niemann S, Peto TE; Modernizing Medical Microbiology (MMM) Informatics Group. Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. Lancet Infect Dis. 2015 Oct;15(10):1193-202. doi: 10.1016/S1473-3099(15)00062-6. Epub 2015 Jun 23.

Bjorn-Mortensen K, Zallet J, Lillebaek T, Andersen AB, Niemann S, Rasmussen EM, Kohl TA. Direct DNA Extraction from Mycobacterium tuberculosis Frozen Stocks  as a Reculture-Independent Approach to Whole-Genome Sequencing. J Clin Microbiol. 2015 Aug;53(8):2716-9. doi: 10.1128/JCM.00662-15.

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. J Clin Microbiol. 2015 Jun;53(6):1908-14. doi:10.1128/JCM.00025-15. Epub 2015 Apr 8.

Barletta F, Otero L, de Jong BC, Iwamoto T, Arikawa K, Van der Stuyft P, Niemann S, Merker M, Uwizeye C, Seas C, Rigouts L. Predominant Mycobacterium tuberculosis Families and High Rates of Recent Transmission among New Cases Are Not Associated with Primary Multidrug Resistance in Lima, Peru. J Clin Microbiol. 2015 Jun;53(6):1854-63. doi: 10.1128/JCM.03585-14. Epub 2015 Mar 25.

Sanchez-Padilla E, Merker M, Beckert P, Jochims F, Dlamini T, Kahn P, Bonnet M, Niemann S. Detection of drug-resistant tuberculosis by Xpert MTB/RIF in Swaziland. N Engl J Med. 2015 Mar 19;372(12):1181-2. doi: 10.1056/NEJMc1413930.

Salamon H, Yamaguchi KD, Cirillo DM, Miotto P, Schito M, Posey J, Starks AM,  Niemann S, Alland D, Hanna D, Aviles E, Perkins MD, Dolinger DL. Integration of published information into a resistance-associated mutation database for Mycobacterium tuberculosis. J Infect Dis. 2015 Apr 1;211 Suppl 2:S50-7. doi: 10.1093/infdis/jiu816. Review.

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. 2015 Jan 24;385(9965):305-7. doi: 10.1016/S0140-6736(14)62450-8.

Merker M, Blin C, Mona S, Duforet-Frebourg N, Lecher S, Willery E, Blum MG, Rüsch-Gerdes S, Mokrousov I, Aleksic E, Allix-Béguec C, Antierens A, Augustynowicz-Kopeć E, Ballif M, Barletta F, Beck HP, Barry CE 3rd, Bonnet M, Borroni E, Campos-Herrero I, Cirillo D, Cox H, Crowe S, Crudu V, Diel R, Drobniewski F, Fauville-Dufaux M, Gagneux S, Ghebremichael S, Hanekom M, Hoffner  S, Jiao WW, Kalon S, Kohl TA, Kontsevaya I, Lillebæk T, Maeda S, Nikolayevskyy V, Rasmussen M, Rastogi N, Samper S, Sanchez-Padilla E, Savic B, Shamputa IC, Shen A, Sng LH, Stakenas P, Toit K, Varaine F, Vukovic D, Wahl C, Warren R, Supply P,  Niemann S, Wirth T. Evolutionary history and global spread of the Mycobacterium
tuberculosis Beijing lineage. Nat Genet. 2015 Mar;47(3):242-9. doi: 10.1038/ng.3195.

Olaru ID, Rachow A, Lange C, Ntinginya NE, Reither K, Hoelscher M, Vollrath O, Niemann S. Ascertaining in vivo virulence of Mycobacterium tuberculosis lineages in patients in Mbeya, Tanzania. Int J Tuberc Lung Dis. 2015 Jan;19(1):70-3. doi: 10.5588/ijtld.14.0403.

2014

Knobloch, JK-M, Niemann, S, Kohl, TA, Lindner, U, Nitschke, M, Sayk, F & Solbach, W 2014, 'Whole-genome sequencing for risk assessment of long-term Shiga toxin-producing Escherichia coli' EMERGING INFECTIOUS DISEASES, Bd 20, Nr. 4, S. 732-3., 10.3201/eid2004.131782

Kohl, TA, Diel, R, Harmsen, D, Rothgänger, J, Walter, KM, Merker, M, Weniger, T & Niemann, S 2014, 'Whole-Genome-Based Mycobacterium tuberculosis Surveillance: a Standardized, Portable, and Expandable Approach' JOURNAL OF CLINICAL MICROBIOLOGY, Bd 52, Nr. 7, S. 2479-86.

de Beer, JL, Ködmön, C, van Ingen, J, Supply, P, van Soolingen, D, Global Network for Molecular Surveillance of Tuberculosis 2010 & Niemann, S 2014, 'Second worldwide proficiency study on variable number of tandem repeats typing of Mycobacterium tuberculosis complex' THE INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE, Bd 18, Nr. 5, S. 594-600.

Allix-Béguec, C, Wahl, C, Hanekom, M, Nikolayevskyy, V, Drobniewski, F, Maeda, S, Campos-Herrero, I, Mokrousov, I, Niemann, S, Kontsevaya, I, Rastogi, N, Samper, S, Sng, L-H, Warren, RM & Supply, P, 'Proposal of a Consensus Set of Hypervariable Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat loci for Subtyping of Mycobacterium tuberculosis Beijing Isolates' JOURNAL OF CLINICAL MICROBIOLOGY. 2014 Jan;52(1):164-72

Bos, KI, Harkins, KM, Herbig, A, Coscolla, M, Weber, N, Comas, I, Forrest, SA, Bryant, JM, Harris, SR, Schuenemann, VJ, Campbell, TJ, Majander, K, Wilbur, AK, Guichon, RA, Wolfe Steadman, DL, Cook, DC, Niemann, S, Behr, MA, Zumarraga, M, Bastida, R, Huson, D, Nieselt, K, Young, D, Parkhill, J, Buikstra, JE, Gagneux, S, Stone, AC & Krause, J 2014, 'Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis' Nature, Bd 514, Nr. 7523, S. 494-507.

Feuerriegel, S, Köser, CU & Niemann, S 2014, 'Phylogenetic polymorphisms in antibiotic resistance genes of the Mycobacterium tuberculosis complex' JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, Bd 69, Nr. 5, S. 1205-10.

Miotto, P, Cabibbe, AM, Feuerriegel, S, Casali, N, Drobniewski, F, Rodionova, Y, Bakonyte, D, Stakenas, P, Pimkina, E, Augustynowicz-Kopeć, E, Degano, M, Ambrosi, A, Hoffner, S, Mansjö, M, Werngren, J, Rüsch-Gerdes, S, Niemann, S & Cirillo, DM 2014, 'Mycobacterium tuberculosis Pyrazinamide Resistance Determinants: a Multicenter Study' mBio, Bd 5, Nr. 5., 10.1128/mBio.01819-14

De Beer, JL, Kodmon, C, van der Werf, MJ, van Ingen, J, van Soolingen, D, ECDC MDR-TB Molecular Surveillance Project Participants & Niemann, S 2014, 'Molecular surveillance of multi- and extensively drug-resistant tuberculosis transmission in the European Union from 2003 to 2011' Euro surveillance : bulletin Européen sur les maladies transmissibles = European communicable disease bulletin, Bd 19, Nr. 11.

Köser, CU, Comas, I, Feuerriegel, S, Niemann, S, Gagneux, S & Peacock, SJ 2014, 'Genetic diversity within Mycobacterium tuberculosis complex impacts on the accuracy of genotypic pyrazinamide drug-susceptibility assay' Tuberculosis (Edinburgh, Scotland), Bd 94, Nr. 4, S. 451-3.

Niemann, S & Supply, P, 'Diversity and Evolution of Mycobacterium tuberculosis: Moving to Whole-Genome-Based Approaches' Cold Spring Harbor perspectives in medicine. 2014 Sep 4;4(12)

Köser, CU, Bryant, JM, Comas, I, Feuerriegel, S, Niemann, S, Gagneux, S, Parkhill, J & Peacock, SJ 2014, 'Comment on: Characterization of the embB gene in Mycobacterium tuberculosis isolates from Barcelona and rapid detection of main mutations related to ethambutol resistance using a low-density DNA array' JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, Bd 69, Nr. 8, S. 2298-9.

2013

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. 2013 Dec 6;8(12):e82551.

Comas I, Coscolla M, Luo T, Borrell S, Holt KE, Kato-Maeda M, Parkhill J, Malla B, Berg S, Thwaites G, Yeboah-Manu D, Bothamley G, Mei J, Wei L, Bentley S, Harris SR, Niemann S, Diel R, Aseffa A, Gao Q, Young D, Gagneux S. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet. 2013 Sep 1;45:1176–1182.

Reiling N, Homolka S, Walter K, Brandenburg J, Niwinski L, Ernst M, Herzmann C, Lange C, Diel R, Ehlers S, Niemann S. Clade-specific virulence patterns of Mycobacterium tuberculosis complex strains in human primary macrophages and aerogenically infected mice. MBio. 2013 Jul 30;4(4).

Coscolla M, Lewin A, Metzger S, Maetz-Rennsing K, Calvignac-Spencer S, Nitsche A, Dabrowski PW, Radonic A, Niemann S, Parkhill J, Couacy-Hymann E, Feldman J, Comas I, Boesch C, Gagneux S, Leendertz FH. Novel Mycobacterium tuberculosis complex isolate from a wild chimpanzee. Emerg Infect Dis. 2013 Jun;19(6):969-76.

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 2013 10(2): e1001387. Open Access

Tessema B, Beer J, Merker M, Emmrich F, Sack U, Rodloff AC, et al. Molecular epidemiology and transmission dynamics of Mycobacterium tuberculosis in Northwest Ethiopia: new phylogenetic lineages found in Northwest Ethiopia. BMC Infectious Diseases. 2013;13(1):131. Open Access

Aleksic E, Merker M, Cox H, Reiher B, Sekawi Z, Hearps AC, et al. First Molecular Epidemiology Study of Mycobacterium tuberculosis in Kiribati. Mokrousov I, editor. PLoS ONE. 2013 Jan;8(1):e55423. Open Access

Feuerriegel S, Köser CU, Richter E, Niemann S. Mycobacterium canettii is intrinsically resistant to both pyrazinamide and pyrazinoic acid. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY. 2013 Jun 1;68(6):1439-40

Khan SN, Niemann S, Gulfraz M, Qayyum M, Siddiqi S, Mirza ZS, et al. Molecular Characterization of Multidrug-Resistant Isolates of Mycobacterium tuberculosis from Patients in Punjab, Pakistan. PAKISTAN JOURNAL OF ZOOLOGY. 2013 Feb;45(1):93–100.

2012

Köser CU, Feuerriegel S, Summers DK, Archer JAC, Niemann S. Importance of the Genetic Diversity within the Mycobacterium tuberculosis Complex for the Development of Novel Antibiotics and Diagnostic Tests of Drug Resistance. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY 2012 Dec;56(12):6080–6087.

Ballif M, Harino P, Ley S, Coscolla M, Niemann S, Carter R, Coulter C, Borrell S, Siba P, Phuanukoonnon S, Gagneux S, Beck H-P. Drug resistance-conferring mutations in Mycobacterium tuberculosis from Madang, Papua New Guinea. BMC Microbiology 2012;12:191. Open Access
Agarwal V, Hammerschmidt S, Malm S, Bergmann S, Riesbeck K, Blom AM. Enolase of Streptococcus pneumoniae binds human complement inhibitor C4b-binding protein and contributes to complement evasion. JOURNAL OF IMMUNOLOGY 2012 Oct;189(7):3575–3584.

Ballif M, Harino P, Ley S, Carter R, Coulter C, Niemann S, Borrell S, Fenner L, Siba P, Phuanukoonnon S, Gagneux S, Beck H-P. Genetic diversity of Mycobacterium tuberculosis in Madang, Papua New Guinea. INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE 2012 Aug;16(8):1100–1107.

Homolka S, Projahn M, Feuerriegel S, Ubben T, Diel R, Nübel U, Niemann S. High Resolution Discrimination of Clinical Mycobacterium tuberculosis Complex Strains Based on Single Nucleotide Polymorphisms. PLoS ONE 2012;7(7):e39855. Open Access

Reddington K, Zumla A, Bates M, Van Soolingen D, Niemann S, Barry T, O’Grady J. SeekTB, a Two-Stage Multiplex Real-Time-PCR-Based Method for Differentiation of the Mycobacterium tuberculosis Complex. JOURNAL OF CLINICAL MICROBIOLOGY 2012 Jul;50(7):2203–2206.

Weniger T, Krawczyk J, Supply P, Harmsen D, Niemann S. Online tools for polyphasic analysis of Mycobacterium tuberculosis complex genotyping data: Now and next. INFECTION GENETICS AND EVOLUTION 2012 Jun;12(4):748–754.

Köser CU, Niemann S, Summers DK, Archer JAC. Overview of errors in the reference sequence and annotation of Mycobacterium tuberculosis H37Rv, and variation amongst its isolates. INFECTION GENETICS AND EVOLUTION 2012 Jun;12(4):807–810.

Feuerriegel S, Oberhauser B, George AG, Dafae F, Richter E, Rüsch-Gerdes S, Niemann S. Sequence analysis for detection of first-line drug resistance in Mycobacterium tuberculosis strains from a high-incidence setting. BMC Microbiology 2012 May;12(1):90. Open Access

Maertzdorf J, Weiner J 3rd, Mollenkopf H-J, TBornotTB Network, Bauer T, Prasse A, Müller-Quernheim J, Kaufmann SHE. Common patterns and disease-related signatures in tuberculosis and sarcoidosis. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES 2012 May;109(20):7853-8.

Malm S, Jusko M, Eick S, Potempa J, Riesbeck K, Blom AM. Acquisition of Complement Inhibitor Serine Protease Factor I and Its Cofactors C4b-Binding Protein and Factor H by Prevotella intermedia. PLoS ONE 2012 Apr;7(4):e34852. Open Access

De Beer JL, Kremer K, Ködmön C, Supply P, Van Soolingen D, Global Network for the Molecular Surveillance of Tuberculosis 2009. First worldwide proficiency study on variable-number tandem-repeat typing of Mycobacterium tuberculosis complex strains. JOURNAL OF CLINICAL MICROBIOLOGY 2012 Mar;50(3):662–669.

Beckert P, Hillemann D, Kohl TA, Kalinowski J, Richter E, Niemann S, Feuerriegel S. rplC T460C Identified as a Dominant Mutation in Linezolid-Resistant Mycobacterium tuberculosis Strains. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY 2012 Feb;56(5):2743–2745.

Comas I, Borrell S, Roetzer A, Rose G, Malla B, Kato-Maeda M, Galagan J, Niemann S, Gagneux S. Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. NATURE GENETICS 2012 Jan;44(1):106-10.