Priority Research Area Infections

2022

Akwani, WC, van Vliet, AHM, Joel, JO, Andres, S, Diricks, M, Maurer, FP, Chambers, MA & Hingley-Wilson, SM 2022, 'The Use of Comparative Genomic Analysis for the Development of Subspecies-Specific PCR Assays for Mycobacterium abscessus', Frontiers in Cellular and Infection Microbiology, Jg. 12, S. 816615. https://doi.org/10.3389/fcimb.2022.816615

Bateson, A, Ortiz Canseco, J, McHugh, TD, Witney, AA, Feuerriegel, S, Merker, M, Kohl, TA, Utpatel, C, Niemann, S, Andres, S, Kranzer, K, Maurer, FP, Ghodousi, A, Borroni, E, Cirillo, DM, Wijkander, M, Toro, JC, Groenheit, R, Werngren, J, Machado, D, Viveiros, M, Warren, RM, Sirgel, F, Dippenaar, A, Köser, CU, Sun, E & Timm, J 2022, 'Ancient and recent differences in the intrinsic susceptibility of Mycobacterium tuberculosis complex to pretomanid', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, Jg. 77, Nr. 6, S. 1685-1693. https://doi.org/10.1093/jac/dkac070

Chesov, E, Chesov, D, Maurer, FP, Andres, S, Utpatel, C, Barilar, I, Donica, A, Reimann, M, Niemann, S, Lange, C, Crudu, V, Heyckendorf, J & Merker, M 2022, 'Emergence of bedaquiline resistance in a high tuberculosis burden country', The European respiratory journal, Jg. 59, Nr. 3, 2100621. https://doi.org/10.1183/13993003.00621-2021

Diricks, M, Kohl, TA, Käding, N, Leshchinskiy, V, Hauswaldt, S, Jiménez Vázquez, O, Utpatel, C, Niemann, S, Rupp, J & Merker, M 2022, 'Whole genome sequencing-based classification of human-related Haemophilus species and detection of antimicrobial resistance genes', Genome medicine, Jg. 14, Nr. 1, S. 13. https://doi.org/10.1186/s13073-022-01017-x

Diricks, M, Kohl, TA, Käding, N, Leshchinskiy, V, Hauswaldt, S, Vázquez, OJ, Utpatel, C, Niemann, S, Rupp, J & Merker, M 2022, 'Correction to:Whole genome sequencing-based classifcation of human-related Haemophilus species and detection of antimicrobial resistance genes', Genome medicine, Jg. 14, Nr. 1, S. 22. https://doi.org/10.1186/s13073-022-01028-8

Gisch, N, Utpatel, C, Gronbach, LM, Kohl, TA, Schombel, U, Malm, S, Dobos, KM, Hesser, DC, Diel, R, Götsch, U, Gerdes, S, Shuaib, YA, Ntinginya, NE, Khosa, C, Viegas, S, Kerubo, G, Ali, S, Al-Hajoj, SA, Ndung’u, PW, Rachow, A, Hoelscher, M, Maurer, FP, Schwudke, D, Niemann, S, Reiling, N & Homolka, S 2022, 'Sub-Lineage Specific Phenolic Glycolipid Patterns in the Mycobacterium tuberculosis Complex Lineage 1', Frontiers in Microbiology, Jg. 13, S. 832054. https://www.frontiersin.org/article/10.3389/fmicb.2022.832054

Große, C, Kohl, TA, Niemann, S, Herzberg, M & Nies, DH 2022, 'Loss of mobile genomic islands in metal resistant, hydrogen-oxidizing Cupriavidus metallidurans', APPLIED AND ENVIRONMENTAL MICROBIOLOGY , Jg. 88, Nr. 4, S. e0204821. https://doi.org/10.1128/AEM.02048-21

Hansen, J, Kolbe, K, König, IR, Scherliess, R, Hellfritzsch, M, Malm, S, Zallet, J, Hillemann, D, Wiesmüller, K-H, Herzmann, C, Brandenburg, J & Reiling, N, Lipobiotin-capture magnetic bead assay for isolation, enrichment and detection of Mycobacterium tuberculosis from saliva, 2022, Veröffentlichungen auf Preprint Servern, Cold Spring Harbor Laboratory Press, biorxiv. https://doi.org/10.1101/2022.03.04.483051

Kerubo, G, Ndungu, P, Shuaib, YA, Amukoye, E, Revathi, G, Homolka, S, Kariuki, S, Merker, M & Niemann, S 2022, 'Molecular Epidemiology of Mycobacterium tuberculosis Complex Strains in Urban and Slum Settings of Nairobi, Kenya', Genes, Jg. 13, Nr. 3, 475. https://doi.org/10.3390/genes13030475

Klein, C, Borsche, M, Balck, A, Föh, B, Rahmöller, J, Peters, E, Knickmann, J, Lane, M, Vollstedt, E-J, Elsner, SA, Käding, N, Hauswaldt, S, Lange, T, Hundt, JE, Lehrian, S, Giese, J, Mischnik, A, Niemann, S, Maurer, F, Homolka, S, Paulowski, L, Kramer, J, Twesten, C, Sina, C, Gillessen-Kaesbach, G, Busch, H, Ehlers, M, Taube, S, Rupp, J & Katalinic, A 2022, 'One-year surveillance of SARS-CoV-2 transmission of the ELISA cohort: A model for population-based monitoring of infection risk', Science advances, Jg. 8, Nr. 15, S. eabm5016. https://doi.org/10.1126/sciadv.abm5016

Mbelele, PM, Utpatel, C, Sauli, E, Mpolya, EA, Mutayoba, BK, Barilar, I, Dreyer, V, Merker, M, Sariko, ML, Swema, BM, Mmbaga, BT, Gratz, J, Addo, KK, Pletschette, M, Niemann, S, Houpt, ER, Mpagama, SG & Heysell, SK 2022, 'Whole genome sequencing-based drug resistance predictions of multidrug-resistant Mycobacterium tuberculosis isolates from Tanzania', JAC-antimicrobial resistance, Jg. 4, Nr. 2, S. dlac042. https://doi.org/10.1093/jacamr/dlac042

Sibandze, DB, Kay, A, Dreyer, V, Sikhondze, W, Dlamini, Q, DiNardo, A, Mtetwa, G, Lukhele, B, Vambe, D, Lange, C, Glenn Dlamini, M, Ness, T, Mejia, R, Kalsdorf, B, Heyckendorf, J, Kuhns, M, Maurer, FP, Dlamini, S, Maphalala, G, Niemann, S & Mandalakas, A 2022, 'Rapid molecular diagnostics of tuberculosis resistance by targeted stool sequencing', Genome medicine, Jg. 14, Nr. 1, S. 52. https://doi.org/10.1186/s13073-022-01054-6

CRyPTIC Consortium & Niemann, S 2022, 'Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis', The European respiratory journal. https://doi.org/10.1183/13993003.00239-2022

CRyPTIC Consortium 2022, 'The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A genotypic analysis', The Lancet. Microbe, Jg. 3, Nr. 4, S. e265-e273. https://doi.org/10.1016/S2666-5247(21)00301-3

Antimycobacterial Susceptibility Testing Group 2022, 'Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment', The European respiratory journal, Jg. 59, Nr. 4, 2200166. https://doi.org/10.1183/13993003.00166-2022

 

2021

Alagna, R, Cabibbe, AM, Miotto, P, Saluzzo, F, Köser, CU, Niemann, S, Gagneux, S, Rodrigues, C, Rancoita, PVM & Cirillo, DM 2021, 'Is the new WHO definition of extensively drug-resistant tuberculosis easy to apply in practice?', The European respiratory journal, Jg. 58, Nr. 1. https://doi.org/10.1183/13993003.00959-2021

Ardizzoni, E, Ariza, E, Mulengwa, D, Mpala, Q, de La Tour, R, Maphalala, G, Varaine, F, Kerschberger, B, Graulus, P, Page, AL, Niemann, S, Dreyer, V, Van Deun, A, Decroo, T, Rigouts, L & de Jong, BC 2021, 'Thin-Layer-Agar-Based Direct Phenotypic Drug Susceptibility Testing on Sputum in Eswatini Rapidly Detects Mycobacterium tuberculosis Growth and Rifampicin Resistance Otherwise Missed by WHO-Endorsed Diagnostic Tests', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, Jg. 65, Nr. 6. https://doi.org/10.1128/AAC.02263-20

Batra, A, Roemhild, R, Rousseau, E, Franzenburg, S, Niemann, S & Schulenburg, H 2021, 'High potency of sequential therapy with only β-lactam antibiotics', eLife, Jg. 10, S. 68876. https://doi.org/10.7554/eLife.68876

Brandenburg, J, Marwitz, S, Tazoll, SC, Waldow, F, Kalsdorf, B, Vierbuchen, T, Scholzen, T, Gross, A, Goldenbaum, S, Hölscher, A, Hein, M, Linnemann, L, Reimann, M, Kispert, A, Leitges, M, Rupp, J, Lange, C, Niemann, S, Behrends, J, Goldmann, T, Heine, H, Schaible, UE, Hölscher, C, Schwudke, D & Reiling, N 2021, 'WNT6/ACC2-induced storage of triacylglycerols in macrophages is exploited by Mycobacterium tuberculosis', Journal of Clinical Investigation, Jg. 131, Nr. 16, e141833. https://doi.org/10.1172/JCI141833

Brill, FHH, Hambach, J, Utpatel, C, Mogrovejo, DC, Gabriel, H, Klock, J-H, Steinmann, J & Arndt, A 2021, 'Biofilm reduction potential of 0.02% polyhexanide irrigation solution in several types of urethral catheters', BMC urology, Jg. 21, Nr. 1, S. 58. https://doi.org/10.1186/s12894-021-00826-3

Chesov, E, Chesov, D, Maurer, FP, Andres, S, Utpatel, C, Barilar, I, Donica, A, Reimann, M, Niemann, S, Lange, C, Crudu, V, Heyckendorf, J & Merker, M 2021, 'Emergence of bedaquiline-resistance in a high-burden country of tuberculosis', The European respiratory journal. https://doi.org/10.1183/13993003.00621-2021

Cornejo-Granados, F, Kohl, TA, Sotomayor, FV, Andres, S, Hernández-Pando, R, Hurtado-Ramirez, JM, Utpatel, C, Niemann, S, Maurer, FP & Ochoa-Leyva, A 2021, 'Secretome characterization of clinical isolates from the Mycobacterium abscessus complex provides insight into antigenic differences', BMC GENOMICS , Jg. 22, Nr. 1, S. 385. https://doi.org/10.1186/s12864-021-07670-7

Coscolla, M, Gagneux, S, Menardo, F, Loiseau, C, Ruiz-Rodriguez, P, Borrell, S, Otchere, ID, Asante-Poku, A, Asare, P, Sánchez-Busó, L, Gehre, F, Sanoussi, CND, Antonio, M, Affolabi, D, Fyfe, J, Beckert, P, Niemann, S, Alabi, AS, Grobusch, MP, Kobbe, R, Parkhill, J, Beisel, C, Fenner, L, Böttger, EC, Meehan, CJ, Harris, SR, de Jong, BC, Yeboah-Manu, D & Brites, D 2021, 'Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history', Microbial genomics, Jg. 7, Nr. 2. https://doi.org/10.1099/mgen.0.000477

Distler, O, Ludwig, RJ, Niemann, S, Riemekasten, G & Schreiber, S 2021, 'Editorial: Precision Medicine in Chronic Inflammation', FRONTIERS IN IMMUNOLOGY, Jg. 12, S. 770462. https://doi.org/10.3389/fimmu.2021.770462

ECDC molecular surveillance project participants, Tagliani, E, Anthony, R, Kohl, TA, de Neeling, A, Nikolayevskyy, V, Ködmön, C, Maurer, FP, Niemann, S, van Soolingen, D, van der Werf, MJ & Cirillo, DM 2021, 'Use of a Whole Genome Sequencing-based approach for Mycobacterium tuberculosis surveillance in Europe in 2017-2019: an ECDC pilot study', The European respiratory journal, Jg. 57, Nr. 1. https://doi.org/10.1183/13993003.02272-2020

European Laboratory Initiative on TB, HIV and Viral Hepatitis, Maurer, FP, Shubladze, N, Kalmambetova, G, Felker, I, Kuchukhidze, G, Drobniewski, F, Yedilbayev, A & Ehsani, S 2021, 'Impact of the COVID-19 pandemic on tuberculosis national reference laboratory services in the WHO European Region, March to November 2020', Eurosurveillance, Jg. 26, Nr. 24. https://doi.org/10.2807/1560-7917.ES.2021.26.24.2100426

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', The European respiratory journal, Jg. 57, Nr. 1. https://doi.org/10.1183/13993003.01796-2020

Freschi, L, Vargas, R, Husain, A, Kamal, SMM, Skrahina, A, Tahseen, S, Ismail, N, Barbova, A, Niemann, S, Cirillo, DM, Dean, AS, Zignol, M & Farhat, MR 2021, 'Population structure, biogeography and transmissibility of Mycobacterium tuberculosis', Nature communications, Jg. 12, Nr. 1, S. 6099. https://doi.org/10.1038/s41467-021-26248-1

Grobbel, H-P, Merker, M, Köhler, N, Andres, S, Hoffmann, H, Heyckendorf, J, Reimann, M, Barilar, I, Dreyer, V, Hillemann, D, Kalsdorf, B, Kohl, TA, Sanchez-Carballo, P, Schaub, D, Todt, K, Utpatel, C, Maurer, FP, Lange, C & Niemann, S 2021, 'Design of multidrug-resistant tuberculosis treatment regimens based on DNA sequencing', CLINICAL INFECTIOUS DISEASES , Jg. 73, Nr. 7, S. 1194-1202. https://doi.org/10.1093/cid/ciab359

Jouet, A, Gaudin, C, Badalato, N, Allix-Béguec, C, Duthoy, S, Ferré, A, Diels, M, Laurent, Y, Contreras, S, Feuerriegel, S, Niemann, S, André, E, Kaswa, MK, Tagliani, E, Cabibbe, A, Mathys, V, Cirillo, D, de Jong, BC, Rigouts, L & Supply, P 2021, 'Deep amplicon sequencing for culture-free prediction of susceptibility or resistance to 13 anti-tuberculous drugs', The European respiratory journal, Jg. 57, Nr. 3. https://doi.org/10.1183/13993003.02338-2020

Kontsevaya, I, Lange, C, Comella-Del-Barrio, P, Coarfa, C, DiNardo, AR, Gillespie, SH, Hauptmann, M, Leschczyk, C, Mandalakas, AM, Martinecz, A, Merker, M, Niemann, S, Reimann, M, Rzhepishevska, O, Schaible, UE, Scheu, KM, Schurr, E, Abel Zur Wiesch, P & Heyckendorf, J 2021, 'Perspectives for systems biology in the management of tuberculosis', European Respiratory Review, Jg. 30, Nr. 160. https://doi.org/10.1183/16000617.0377-2020

Merker, M, Egbe, NF, Ngangue, YR, Vuchas, C, Kohl, TA, Dreyer, V, Kuaban, C, Noeske, J, Niemann, S & Sander, MS 2021, 'Transmission patterns of rifampicin resistant Mycobacterium tuberculosis complex strains in Cameroon: a genomic epidemiological study', BMC INFECTIOUS DISEASES , Jg. 21, Nr. 1, S. 891. https://doi.org/10.1186/s12879-021-06593-8

Müller, SJ, Schurz, H, Tromp, G, van der Spuy, GD, Hoal, EG, van Helden, PD, Owusu-Dabo, E, Meyer, CG, Muntau, B, Thye, T, Niemann, S, Warren, RM, Streicher, E, Möller, M & Kinnear, C 2021, 'A multi-phenotype genome-wide association study of clades causing tuberculosis in a Ghanaian- and South African cohort', GENOMICS, Jg. 113, Nr. 4, S. 1802-1815. https://doi.org/10.1016/j.ygeno.2021.04.024

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', JOURNAL OF CLINICAL MICROBIOLOGY, Jg. 59, Nr. 5. https://doi.org/10.1128/JCM.02983-20

Peker, N, Schuele, L, Kok, N, Terrazos, M, Neuenschwander, SM, de Beer, J, Akkerman, O, Peter, S, Ramette, A, Merker, M, Niemann, S, Couto, N, Sinha, B & Rossen, JW 2021, 'Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis', Microbial genomics, Jg. 7, Nr. 11. https://doi.org/10.1099/mgen.0.000695

Sanchini, A, Jandrasits, C, Tembrockhaus, J, Kohl, TA, Utpatel, C, Maurer, FP, Niemann, S, Haas, W, Renard, BY & Kröger, S 2021, 'Improving tuberculosis surveillance by detecting international transmission using publicly available whole genome sequencing data', Eurosurveillance, Jg. 26, Nr. 2. https://doi.org/10.2807/1560-7917.ES.2021.26.2.1900677

Sanoussi, CND, Coscolla, M, Ofori-Anyinam, B, Otchere, ID, Antonio, M, Niemann, S, Parkhill, J, Harris, S, Yeboah-Manu, D, Gagneux, S, Rigouts, L, Affolabi, D, de Jong, BC & Meehan, CJ 2021, 'Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv', Microbial genomics, Jg. 7, Nr. 7. https://doi.org/10.1099/mgen.0.000437

Schreiber, PW, Kohl, TA, Kuster, SP, Niemann, S & Sax, H 2021, 'The global outbreak of Mycobacterium chimaera infections in cardiac surgery - A systematic review of whole genome sequencing studies and joint analysis', CLINICAL MICROBIOLOGY AND INFECTION , Jg. 27, Nr. 11, S. 1613-1620. https://doi.org/10.1016/j.cmi.2021.07.017

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', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, Jg. 65, Nr. 7, S. e0252020. https://doi.org/10.1128/AAC.02520-20

Steindor, M, Stehling, F, Olivier, M, Kehrmann, J, Diricks, M, Maurer, FP, Horn, PA, Straßburg, S, Welsner, M, Sutharsan, S & Lindemann, M 2021, 'Species-Specific Interferon-Gamma Release Assay for the Diagnosis of Mycobacterium abscessus Complex Infection', Frontiers in Microbiology, S. 692395. https://doi.org/10.3389/fmicb.2021.692395

Tizzano, B, Dallenga, T, Utpatel, C, Behrends, J, Homolka, S, Kohl, T & Niemann, S 2021, 'Survival of hypoxia-induced dormancy is not a common feature of all strains of the Mycobacterium tuberculosis complex', Scientific Reports, Jg. 11, Nr. 1, S. 2628. https://doi.org/10.1038/s41598-021-81223-6

Vargas, R, Freschi, L, Spitaleri, A, Tahseen, S, Barilar, I, Niemann, S, Miotto, P, Cirillo, DM, Köser, CU & Farhat, MR 2021, 'Role of Epistasis in Amikacin, Kanamycin, Bedaquiline, and Clofazimine Resistance in Mycobacterium tuberculosis Complex', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, Jg. 65, Nr. 11, S. e0116421. https://doi.org/10.1128/AAC.01164-21

Vogel, M, Utpatel, C, Corbett, C, Kohl, TA, Iskakova, A, Ahmedov, S, Antonenka, U, Dreyer, V, Ibrahimova, A, Kamarli, C, Kosimova, D, Mohr, V, Sahalchyk, E, Sydykova, M, Umetalieva, N, Kadyrov, A, Kalmambetova, G, Niemann, S & Hoffmann, H 2021, 'Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country', Scientific Reports, Jg. 11, Nr. 1, S. 15333. https://doi.org/10.1038/s41598-021-94297-z

 

2020

Alio, I, Gudzuhn, M, Pérez García, P, Danso, D, Schoelmerich, M, Mamat, U, Schaible, UE, Steinmann, J, Yero, D, Gibert, I, Kohl, TA, Niemann, S, Gröschel, MI, Haerdter, J, Hackl, T, Vollstedt, C, Bömeke, M, Egelkamp, R, Daniel, R, Poehlein, A & Streit, WR 2020, 'Phenotypic and Transcriptomic Analyses of Seven Clinical Stenotrophomonas maltophilia Isolates Identify a Small Set of Shared and Commonly Regulated Genes Involved in the Biofilm Lifestyle', APPLIED AND ENVIRONMENTAL MICROBIOLOGY , Jg. 86, Nr. 24. https://doi.org/10.1128/AEM.02038-20

Andres, S, Merker, M, Heyckendorf, J, Kalsdorf, B, Rumetshofer, R, Indra, A, Hofmann-Thiel, S, Hoffmann, H, Lange, C, Niemann, S & Maurer, FP 2020, 'Bedaquiline-resistant Tuberculosis:Dark Clouds on the Horizon', American journal of respiratory and critical care medicine, Jg. 201, Nr. 12, S. 1564-1568. https://doi.org/10.1164/rccm.201909-1819LE

Battaglia, S, Spitaleri, A, Cabibbe, AM, Meehan, CJ, Utpatel, C, Ismail, N, Tahseen, S, Skrahina, A, Alikhanova, N, Mostofa Kamal, SM, Barbova, A, Niemann, S, Groenheit, R, Dean, AS, Zignol, M, Rigouts, L & Cirillo, DM 2020, 'Characterization of genomic variants associated with resistance to bedaquiline and delamanid in naïve Mycobacterium tuberculosis clinical strains', JOURNAL OF CLINICAL MICROBIOLOGY. https://doi.org/10.1128/JCM.01304-20

Beckert, P, Sanchez-Padilla, E, Merker, M, Dreyer, V, Kohl, TA, Utpatel, C, Köser, CU, Barilar, I, Ismail, N, Omar, SV, Klopper, M, Warren, RM, Hoffmann, H, Maphalala, G, Ardizzoni, E, de Jong, BC, Kerschberger, B, Schramm, B, Andres, S, Kranzer, K, Maurer, FP, Bonnet, M & Niemann, S 2020, 'MDR M. tuberculosis outbreak clone in Eswatini missed by Xpert has elevated bedaquiline resistance dated to the pre-treatment era', Genome medicine, Jg. 12, Nr. 1, S. 104. https://doi.org/10.1186/s13073-020-00793-8

Conceição, MLD, Conceição, EC, Furlaneto, IP, Silva, SPD, Guimarães, AEDS, Gomes, P, Boschiroli, ML, Michelet, L, Kohl, TA, Kranzer, K, Francez, LDC, Lima, LNGC, Portugal, I, Perdigão, J & Lima, KVB 2020, 'Phylogenomic Perspective on a Unique Mycobacterium bovis Clade Dominating Bovine Tuberculosis Infections among Cattle and Buffalos in Northern Brazil', Scientific Reports, Jg. 10, Nr. 1, S. 1747. https://doi.org/10.1038/s41598-020-58398-5

CRyPTIC Consortium & Niemann, S 2020, 'GenomegaMap: Within-Species Genome-Wide dN/dS Estimation from over 10,000 Genomes', Molecular biology and evolution, Jg. 37, Nr. 8, S. 2450-2460. https://doi.org/10.1093/molbev/msaa069

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

ECDC molecular surveillance project participants, Tagliani, E, Anthony, R, Kohl, TA, de Neeling, A, Nikolayevskyy, V, Ködmön, C, Maurer, FP, Niemann, S, van Soolingen, D, van der Werf, MJ & Cirillo, DM 2020, 'Use of a Whole Genome Sequencing-based approach for Mycobacterium tuberculosis surveillance in Europe in 2017-2019: an ECDC pilot study', The European respiratory journal. https://doi.org/10.1183/13993003.02272-2020

Ezewudo, M, Borens, A, Chiner-Oms, Á, Miotto, P, Chindelevitch, L, Starks, AM, Hanna, D, Liwski, R, Zignol, M, Gilpin, C, Niemann, S, Kohl, TA, Warren, RM, Crook, D, Gagneux, S, Hoffner, S, Rodrigues, C, Comas, I, Engelthaler, DM, Alland, D, Rigouts, L, Lange, C, Dheda, K, Hasan, R, McNerney, R, Cirillo, DM, Schito, M, Rodwell, TC & Posey, J 2020, 'Author Correction: Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase', Scientific Reports, Jg. 10, Nr. 1, S. 3531. https://doi.org/10.1038/s41598-020-58955-y

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 2020, 'Rapid genomic first- and second-line drug resistance prediction from clinical Mycobacterium tuberculosis specimens using Deeplex®-MycTB', The European respiratory journal. https://doi.org/10.1183/13993003.01796-2020

Frentrup, M, Zhou, Z, Steglich, M, Meier-Kolthoff, JP, Göker, M, Riedel, T, Bunk, B, Spröer, C, Overmann, J, Blaschitz, M, Indra, A, von Müller, L, Kohl, TA, Niemann, S, Seyboldt, C, Klawonn, F, Kumar, N, Lawley, TD, García-Fernández, S, Cantón, R, Del Campo, R, Zimmermann, O, Groß, U, Achtman, M & Nübel, U 2020, 'A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics', Microbial genomics, Jg. 6, Nr. 8. https://doi.org/10.1099/mgen.0.000410

Godfroid, M, Dagan, T, Merker, M, Kohl, TA, Diel, R, Maurer, FP, Niemann, S & Kupczok, A 2020, 'Insertion and deletion evolution reflects antibiotics selection pressure in a Mycobacterium tuberculosis outbreak', PLOS PATHOGENS, Jg. 16, Nr. 9, S. e1008357. https://doi.org/10.1371/journal.ppat.1008357

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

Hess, JF, Kohl, TA, Kotrová, M, Roensch, K, Paprotka, T, Mohr, V, Hutzenlaub, T, Brüggemann, M, Zengerle, R, Niemann, S & Paust, N 2020, 'Library preparation for next generation sequencing: A review of automation strategies', Biotechnology advances, Jg. 41, S. 107537. https://doi.org/10.1016/j.biotechadv.2020.107537

Homolka, S, Paulowski, L, Andres, S, Hillemann, D, Jou, R, Günther, G, Claassens, M, Kuhns, M, Niemann, S & Maurer, FP 2020, 'Two Pandemics, One Challenge-Leveraging Molecular Test Capacity of Tuberculosis Laboratories for Rapid COVID-19 Case-Finding', EMERGING INFECTIOUS DISEASES, Jg. 26, Nr. 11. https://doi.org/10.3201/eid2611.202602

Lange, C, Aarnoutse, R, Chesov, D, van Crevel, R, Gillespie, SH, Grobbel, H-P, Kalsdorf, B, Kontsevaya, I, van Laarhoven, A, Nishiguchi, T, Mandalakas, A, Merker, M, Niemann, S, Köhler, N, Heyckendorf, J, Reimann, M, Ruhwald, M, Sanchez-Carballo, P, Schwudke, D, Waldow, F & DiNardo, AR 2020, 'Perspective for Precision Medicine for Tuberculosis', FRONTIERS IN IMMUNOLOGY, Jg. 11, S. 566608. https://doi.org/10.3389/fimmu.2020.566608

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

Kohl, TA, Kranzer, K, Andres, S, Wirth, T, Niemann, S & Moser, I 2020, 'Population structure of Mycobacterium bovis in Germany: A long-term study using Whole Genome Sequencing combined with conventional molecular typing methods', JOURNAL OF CLINICAL MICROBIOLOGY. https://doi.org/10.1128/JCM.01573-20

M. chimaera ISCVID investigators 2020, 'International Society of Cardiovascular Infectious Diseases Guidelines for the Diagnosis, Treatment and Prevention of Disseminated Mycobacterium chimaera Infection Following Cardiac Surgery with Cardiopulmonary Bypass', Journal of hospital infection, Jg. 104, Nr. 2, S. 214-235. https://doi.org/10.1016/j.jhin.2019.10.009

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

Merker, M, Tueffers, L, Vallier, M, Groth, EE, Sonnenkalb, L, Unterweger, D, Baines, JF, Niemann, S & Schulenburg, H 2020, 'Evolutionary Approaches to Combat Antibiotic Resistance:Opportunities and Challenges for Precision Medicine', FRONTIERS IN IMMUNOLOGY, Jg. 11, S. 1938. https://doi.org/10.3389/fimmu.2020.01938

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

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

Wetzstein, N, Kohl, TA, Schultze, TG, Andres, S, Bellinghausen, C, Hügel, C, Kempf, VAJ, Lehn, A, Hogardt, M, Serve, H, Vehreschild, MJGT, Wolf, T, Niemann, S, Maurer, FP & Wichelhaus, TA 2020, 'Antimicrobial susceptibility and phylogenetic relations in a German cohort infected with Mycobacterium abscessus', JOURNAL OF CLINICAL MICROBIOLOGY. https://doi.org/10.1128/JCM.01813-20

 

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