Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues von Meehan, Conor J., Goig, Galo A., Kohl, Thomas A., Verboven, Lennert, Dippenaar, Anzaan, Ezewudo, Matthew, Farhat, Maha R., Guthrie, Jennifer L., Laukens, Kris, Miotto, Paolo, Ofori-Anyinam, Boatema, Dreyer, Viola, Supply, Philip, Suresh, Anita, Utpatel, Christian, van Soolingen, Dick, Zhou, Yang, Ashton, Philip M., Brites, Daniela, Cabibbe, Andrea M., de Jong, Bouke C., de Vos, Margaretha, Menardo, Fabrizio, Gagneux, Sebastien, Gao, Qian, Heupink, Tim H., Liu, Qingyun, Loiseau, Chloé, Rigouts, Leen, Rodwell, Timothy C., Tagliani, Elisa, Walker, Timothy M., Warren, Robin M., Zhao, Yanlin, Zignol, Matteo, Schito, Marco, Gardy, Jennifer, Cirillo, Daniela M., Niemann, Stefan, Comas, Inaki, Van Rie, Annelies

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MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates von Kohl, Thomas Andreas, Utpatel, Christian, Schleusener, Viola, De Filippo, Maria Rosaria, Beckert, Patrick, Cirillo, Daniela Maria, Niemann, Stefan

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The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia von Gröschel, Matthias I., Meehan, Conor J., Barilar, Ivan, Diricks, Margo, Gonzaga, Aitor, Steglich, Matthias, Conchillo-Solé, Oscar, Scherer, Isabell-Christin, Mamat, Uwe, Luz, Christian F., De Bruyne, Katrien, Utpatel, Christian, Yero, Daniel, Gibert, Isidre, Daura, Xavier, Kampmeier, Stefanie, Rahman, Nurdyana Abdul, Kresken, Michael, van der Werf, Tjip S., Alio, Ifey, Streit, Wolfgang R., Zhou, Kai, Schwartz, Thomas, Rossen, John W. A., Farhat, Maha R., Schaible, Ulrich E., Nübel, Ulrich, Rupp, Jan, Steinmann, Joerg, Niemann, Stefan, Kohl, Thomas A.

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Rapid genomic first- and second-line drug resistance prediction from clinical Mycobacterium tuberculosis specimens using Deeplex-MycTB von Feuerriegel, Silke, Kohl, Thomas A., Utpatel, Christian, Andres, Soenke, Maurer, Florian P., Heyckendorf, Jan, Jouet, Agathe, Badalato, Nelly, Foray, Lynda, Kamara, Rashidatu Fouad, Conteh, Osman S., Supply, Philip, Niemann, Stefan

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Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country von Vogel, Monica, Utpatel, Christian, Corbett, Caroline, Kohl, Thomas A., Iskakova, Altyn, Ahmedov, Sevim, Antonenka, Uladzimir, Dreyer, Viola, Ibrahimova, Ainura, Kamarli, Chynara, Kosimova, Dilorom, Mohr, Vanessa, Sahalchyk, Evgeni, Sydykova, Meerim, Umetalieva, Nagira, Kadyrov, Abdylat, Kalmambetova, Gulmira, Niemann, Stefan, Hoffmann, Harald

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Survival of hypoxia-induced dormancy is not a common feature of all strains of the Mycobacterium tuberculosis complex von Tizzano, Barbara, Dallenga, Tobias K., Utpatel, Christian, Behrends, Jochen, Homolka, Susanne, Kohl, Thomas A., Niemann, Stefan

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Detection of low-frequency resistance-mediating SNPs in next-generation sequencing data of Mycobacterium tuberculosis complex strains with binoSNP von Dreyer, Viola, Utpatel, Christian, Kohl, Thomas A., Barilar, Ivan, Gröschel, Matthias I., Feuerriegel, Silke, Niemann, Stefan

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A novel metagenomic short-chain dehydrogenase/reductase attenuates Pseudomonas aeruginosa biofilm formation and virulence on Caenorhabditis elegans von Bijtenhoorn, Patrick, Mayerhofer, Hubert, Müller-Dieckmann, Jochen, Utpatel, Christian, Schipper, Christina, Hornung, Claudia, Szesny, Matthias, Grond, Stephanie, Thürmer, Andrea, Brzuszkiewicz, Elzbieta, Daniel, Rolf, Dierking, Katja, Schulenburg, Hinrich, Streit, Wolfgang R

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Secretome characterization of clinical isolates from the Mycobacterium abscessus complex provides insight into antigenic differences von Cornejo-Granados, Fernanda, Kohl, Thomas A., Sotomayor, Flor Vasquez, Andres, Sonke, Hernandez-Pando, Rogelio, Hurtado-Ramirez, Juan Manuel, Utpatel, Christian, Niemann, Stefan, Maurer, Florian P., Ochoa-Leyva, Adrian

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Whole genome sequencing-based classification of human-related Haemophilus species and detection of antimicrobial resistance genes von Diricks, Margo, Kohl, Thomas A, Käding, Nadja, Leshchinskiy, Vladislav, Hauswaldt, Susanne, Jiménez Vázquez, Omar, Utpatel, Christian, Niemann, Stefan, Rupp, Jan, Merker, Matthias

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Molecular determinants of multidrug-resistant tuberculosis in Sierra Leone von Blankson, Harriet N A, Kamara, Rashidatu Fouad, Barilar, Ivan, Andres, Sönke, Conteh, Ousman S, Dallenga, Tobias, Foray, Lynda, Maurer, Florian, Kranzer, Katharina, Utpatel, Christian, Niemann, Stefan

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Implementation of targeted next-generation sequencing for the diagnosis of drug-resistant tuberculosis in low-resource settings: a programmatic model, challenges, and initial outco... von de Araujo, Leonardo, Cabibbe, Andrea Maurizio, Mhuulu, Lusia, Ruswa, Nunurai, Dreyer, Viola, Diergaardt, Azaria, Günther, Gunar, Claassens, Mareli, Gerlach, Christiane, Utpatel, Christian, Cirillo, Daniela Maria, Nepolo, Emmanuel, Niemann, Stefan

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Correction to: Whole genome sequencing-based classifcation of human-related Haemophilus species and detection of antimicrobial resistance genes von Diricks, Margo, Kohl, Thomas A, Käding, Nadja, Leshchinskiy, Vladislav, Hauswaldt, Susanne, Vázquez, Omar Jiménez, Utpatel, Christian, Niemann, Stefan, Rupp, Jan, Merker, Matthias

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The Janthinobacterium sp. HH01 genome encodes a homologue of the V. cholerae CqsA and L. pneumophila LqsA autoinducer synthases von Hornung, Claudia, Poehlein, Anja, Haack, Frederike S, Schmidt, Martina, Dierking, Katja, Pohlen, Andrea, Schulenburg, Hinrich, Blokesch, Melanie, Plener, Laure, Jung, Kirsten, Bonge, Andreas, Krohn-Molt, Ines, Utpatel, Christian, Timmermann, Gabriele, Spieck, Eva, Pommerening-Röser, Andreas, Bode, Edna, Bode, Helge B, Daniel, Rolf, Schmeisser, Christel, Streit, Wolfgang R

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Sub-Lineage Specific Phenolic Glycolipid Patterns in the Mycobacterium tuberculosis Complex Lineage 1 von Gisch, Nicolas, Utpatel, Christian, Gronbach, Lisa M, Kohl, Thomas A, Schombel, Ursula, Malm, Sven, Dobos, Karen M, Hesser, Danny C, Diel, Roland, Götsch, Udo, Gerdes, Silke, Shuaib, Yassir A, Ntinginya, Nyanda E, Khosa, Celso, Viegas, Sofia, Kerubo, Glennah, Ali, Solomon, Al-Hajoj, Sahal A, Ndung'u, Perpetual W, Rachow, Andrea, Hoelscher, Michael, Maurer, Florian P, Schwudke, Dominik, Niemann, Stefan, Reiling, Norbert, Homolka, Susanne

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Transmission Dynamics of a Mycobacterium tuberculosis Complex Outbreak in an Indigenous Population in the Colombian Amazon Region von Pérez-Llanos, Francy J, Dreyer, Viola, Barilar, Ivan, Utpatel, Christian, Kohl, Thomas A, Murcia, Martha Isabel, Homolka, Susanne, Merker, Matthias, Niemann, Stefan

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Biofilm reduction potential of 0.02% polyhexanide irrigation solution in several types of urethral catheters von Brill, Florian H. H., Hambach, Julia, Utpatel, Christian, Mogrovejo, Diana C., Gabriel, Henrik, Klock, Jan-Hendrik, Steinmann, Joerg, Arndt, Andreas

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Genomic epidemiology of SARS-CoV-2 during the first four waves in Mozambique von Ismael, Nalia, van Wyk, Stephanie, Tegally, Houriiyah, Giandhari, Jennifer, San, James Emmanuel, Moir, Monika, Pillay, Sureshnee, Utpatel, Christian, Singh, Lavanya, Naidoo, Yeshnee, Ramphal, Upasana, Mabunda, Nédio, Abílio, Nuro, Arnaldo, Paulo, Xavier, Joicymara, Amoako, Daniel Gyamfi, Everatt, Josie, Ramphal, Yajna, Maharaj, Arisha, de Araujo, Leonardo, Anyaneji, Ugochukwu J, Tshiabuila, Derek, Viegas, Sofia, Lessells, Richard, Engelbrecht, Susan, Gudo, Eduardo, Jani, Ilesh, Niemann, Stefan, Wilkinson, Eduan, de Oliveira, Túlio

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Emergence of bedaquiline resistance in a high tuberculosis burden country von Chesov, Elena, Chesov, Dumitru, Maurer, Florian P, Andres, Sönke, Utpatel, Christian, Barilar, Ivan, Donica, Ana, Reimann, Maja, Niemann, Stefan, Lange, Christoph, Crudu, Valeriu, Heyckendorf, Jan, Merker, Matthias

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Delamanid susceptibility testing of Mycobacterium tuberculosis using the resazurin microtitre assay and the BACTEC™ MGIT™ 960 system von Schena, Elisa, Nedialkova, Lubov, Borroni, Emanuele, Battaglia, Simone, Cabibbe, Andrea Maurizio, Niemann, Stefan, Utpatel, Christian, Merker, Matthias, Trovato, Alberto, Hofmann-Thiel, Sabine, Hoffmann, Harald, Cirillo, Daniela Maria

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