Molecular and Experimental Mycobacteriology

2026

Diricks, M, Marschall, L, Biciusca, T, Zielbauer, A-S, Kevane-Campbell, M, Kuhns, M, Andres, S, Niemann, S, Wichelhaus, TA & Wetzstein, N 2026, 'Genomic population structure, antimicrobial susceptibility, and clinical features of Mycobacterium xenopi isolates, Frankfurt, Germany, 1995-2020', JOURNAL OF CLINICAL MICROBIOLOGY, S. e0151125. https://doi.org/10.1128/jcm.01511-25

Klingmüller, A, Zuber, S, Hoffmann, AM, Köhler, N, Suárez, I, Preßel, T, Niemann, S, Dreyer, V, Decosterd, LA, Choong, E, Schütz, B, Friesen, I & Rybniker, J 2026, 'Therapeutic drug monitoring-guided treatment of XDR TB with an RpoB I491F mutation-a case report', JAC-antimicrobial resistance, Jg. 8, Nr. 1, S. dlaf251. https://doi.org/10.1093/jacamr/dlaf251

2025

Belheouane, M, Kalsdorf, B, Niemann, S, Gaede, KI, Lange, C, Heyckendorf, J & Merker, M 2025, 'Serratia sp. traits distinguish the lung microbiome of patients with tuberculosis and non-tuberculous mycobacterial lung diseases', PLOS ONE, Jg. 20, Nr. 6, S. e0325362. https://doi.org/10.1371/journal.pone.0325362

Garcia-Prats, AJ, Garcia-Cremades, M, Cox, V, Kredo, T, Dunbar, R, Schaaf, HS, Seddon, JA, Furin, J, Achar, J, Radke, K, Sachs, T, Abubakirov, A, Ahmed, S, Akkerman, OW, Al Ani, NA, Amanullah, F, Ahmad, N, Anderson, LF, Asfaw, M, Bango, F, Bauer, T, Becerra, M, Boeree, M, Brinkmann, F, Brown, R, Brust, J, Campbell, JR, Carvalho, AC, Carvalho, I, Cegielski, JP, Centis, R, Chan, ED, Chauhan, S, Chiang, SS, Chan, P-C, D'Ambrosio, L, Dalcolmo, M, Daneilyan, N, de Vries, G, Draper, HR, endTB Study Group, Fairlie, L, Francis, JR, Franke, M, Gegia, M, Restrepo, CG, Guenther, A, Gureva, T, Haecker, B, Harausz, E, Hewison, C, Hicks, RM, Huerga, H, Hughes, J, Isaakidis, P, Syed M, K, Khan, MA, Kotrikadze, T, Kuksa, L, Lachenal, N, Lange, C, Lecca, L, Lopez-Varela, E, Lucena, S, Mariandyshev, A, Mattoo, S, Mendez-Echevarria, A, Migliori, GB, Mitnick, CD, Mohr-Holland, E, Mulanda, W, Murzabakova, T, Myrzalieve, B, Ndjeka, N, Niemann, S, Ozere, I, Padayatchi, N, Parmar, M, Parpieva, N, Manzur-Ul-Alam, M, Rybak, N, Sachdeva, KS, Salmon, K, Santiago-Garcia, B, Schaub, D, Shah, I, Shah, NS, Shah, V, Sharma, S, Shim, TS, Shin, SS, Sinha, A, Skrahina, A, Solanki, H, Solans, BP, Soriano-Arandes, A, Toktogonova, A, van der Werf , TS, Velásquez, GE, Williams, B, Yim, J-J, Savic, R & Hesseling, AC 2025, 'Characteristics of children and adolescents with multidrug-resistant and rifampicin-resistant tuberculosis and their association with treatment outcomes: a systematic review and individual participant data meta-analysis', Lancet child & adolescent health, Jg. 9, Nr. 2, S. 100-111. https://doi.org/10.1016/S2352-4642(24)00330-4

Deb, D, Heidari, ME, Kizito, B, Kesamang, M, Matila, T, Matsheka, M, Niemann, S, Shin, SS & Modongo, C 2025, 'HIV status is not associated with SARS-CoV-2 viral load and longer duration of infection among people with well-controlled HIV and high COVID-19 vaccine coverage', INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES , Jg. 161, S. 108142. https://doi.org/10.1016/j.ijid.2025.108142

Diricks, M, Frank, D, Friesen, I, Niemann, S, Wichelhaus, TA, Wetzstein, N & NTMscope-Eco study group 2025, 'Global lineages of non-tuberculous mycobacteria in residential water samples from Germany', BMC MICROBIOLOGY. https://doi.org/10.1186/s12866-025-04563-7

Diricks, M, Maurer, FP, Dreyer, V, Barilar, I, Utpatel, C, Merker, M, Wetzstein, N & Niemann, S 2025, 'Genomic insights into the plasmidome of non-tuberculous mycobacteria', Genome medicine, Jg. 17, Nr. 1, S. 19. https://doi.org/10.1186/s13073-025-01443-7

Dohál, M, Wetzstein, N, Hromádková, M, Mäsiarová, S, Rasmussen, EM, Kunč, P, Škereňová, M, Porvazník, I, Solovič, I, Niemann, S, Hnilicová, J, Mokrý, J, Dvořáková, V & Diricks, M 2025, 'Diagnostics, resistance and clinical relevance of non-tuberculous mycobacteria unidentified at the species level by line probe assays: a bi-national study', Annals of clinical microbiology and antimicrobials, Jg. 24, Nr. 1, S. 14. https://doi.org/10.1186/s12941-025-00781-z

Duque-Villegas, MA, Götz, MP, Rousseau, E, Homolka, S, Niemann, S, Garred, P, Hölscher, C, Walter, K & Rosbjerg, A 2025, 'C1q and mannose-binding lectin binding and complement activation across genetically diverse Mycobacterium tuberculosis complex strains', JOURNAL OF IMMUNOLOGY. https://doi.org/10.1093/jimmun/vkaf294

Harikumar Parvathy, G*, Hertz, D*, Bhandiwad, D, Eggers, L, von Borstel, L, Behrends, J, Hein, M, Dreyer, V, Marschner, J, Orinska, Z, Niemann, S, Kaufmann, SHE, Goldmann, T, Lotter, H, Flores-Valdez, MA & Schneider, BE 2025, 'Sex Differences in Vaccine-Induced Immunity and Protection Against Mycobacterium tuberculosis', JOURNAL OF INFECTIOUS DISEASES, S. jiaf277. https://doi.org/10.1093/infdis/jiaf277 *authors contributed equally

Hillemann, D, Schweim, K, Boysen, F, Merker, M, Barilar, I, Niemann, S, Dolinger, DL, Friesen, I & Köser, CU 2025, 'Understanding systematic rifampicin resistance errors with the FluoroType MTBDR VER 2.0', INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE, Jg. 29, Nr. 10, S. 469-472. https://doi.org/10.5588/ijtld.25.0150

Hoffmann, H, Utpatel, C, Iskakova, A, Ahmedov, S, Antonenka, U, Dreyer, V, Sahalchyk, E, Kadyrov, A, Corbett, C, Niemann, S & Kalmambetova, G 2025, 'Systematic investigation of baseline nosocomial transmission of tuberculosis in the Kyrgyz Republic, Central Asia', CLINICAL MICROBIOLOGY AND INFECTION . https://doi.org/10.1016/j.cmi.2025.08.001

Kessel, J, Braner, A, Diricks, M, Walther, T, Holubec, T, Werner, R, Hogardt, M, Wichelhaus, TA, Niemann, S, Moter, A, Friesen, I & Wetzstein, N 2025, 'Mycobacterium chelonae infection of a cardiovascular bioprosthesis linked to a recent outbreak', Infection. https://doi.org/10.1007/s15010-025-02534-8

Khumalo, W, Maphalala, N, Mulengwa, D, Ziyane, M, Sibandze, DB, Niemann, S, Dreyer, V, Seeger, A, Madison, M, Ness, T, Jele, T, Garcia-Basteiro, AL, Maphalala, G, DiNardo, AR, Mandalakas, AM & Kay, A 2025, 'Drug susceptibility testing for TB using the Xpert MTB/XDR assay on stool specimens', INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE, Jg. 29, Nr. 4, S. 189-192. https://doi.org/10.5588/ijtld.24.0366

Költringer, F, Koreny, M, Werber, D, Heger, F, Chalupka, A, Schweiger, S, Brunner, G, Tuch, U, Karnthaler, U, Klintz, SR, Ködmön, C, Hoefer, A, Anthony, R, Kroeger, S, Domaszewska, T, Boes, L, Niemann, S, Walz, T, Kuhns, M, Jackson, S, Fitzgibbon, M, Mathys, V, Sizaire, V, Cirillo, DM, Sane Schepisi, M, Rønning, JO, Herrera-Leon, L, Cardona, P-J, Groenheit, R, Mansjö, M, Szél, V, Alm, E & Cabal, A 2025, 'Cross-border investigation of a tuberculosis outbreak in Vienna linked to a multi-country cluster among foreign-born individuals, Europe, 2021 to 2025', Eurosurveillance, Jg. 30, Nr. 33. https://doi.org/10.2807/1560-7917.ES.2025.30.33.2500565

Moyo, M, Ntshiqa, T, Hamada, Y, Copas, A, Sabi, I, Ntinginya, EN, Lalashowi, J, Matete, M, Kubeka, G, Tsope, L, Mukora, R, Mudzengi, D, Nielson, T, Lönnroth, K, Niemann, S, Rangaka, M, Velen, K, Charalambous, S, Stender, S & Minja, LT 2025, 'Community and Universal Testing for TB among close contacts of microbiologically confirmed pulmonary TB patients in two high TB burden countries: a protocol for a pragmatic cluster-randomised control trial', Trials, Jg. 26, Nr. 1, S. 285. https://doi.org/10.1186/s13063-025-08978-5

Ness, TE, Ziyane, M, Maphalala, N, Seeger, A, Vasiliu, A, Khumalo, W, Thunzini, M, Dlamini, S, Maphalala, G, Gascua, C, Lange, C, Meyer, S, Inman, B, Dreyer, V, Utpatel, C, Niemann, T, DiNardo, A, Kay, A, Niemann, S & Mandalakas, A 2025, 'Screening and targeted sequencing of stool for microbiologic confirmation and drug resistance determination in paucibacillary tuberculosis', PLOS global public health, Jg. 5, Nr. 11, S. e0005243. https://doi.org/10.1371/journal.pgph.0005243

Ntshiqa, T, Fasanmi, A, Nagudi, J, Tsope, L, Copas, A, Stender, S, Sabi, I, Ntinginya, EN, Lalashowi, J, Matete, M, Budiaki, L, Mahlalela, M, Kisinda, A, Mudzengi, D, Minja, LT, Chirwa, T, Lönnroth, K, Niemann, S, Dreyer, V, Charalambous, S, Velen, K, Hamada, Y & Rangaka, M 2025, 'Evaluation of QIAreach QuantiFERON-TB lateral-flow nanoparticle fluorescence assay for TB infection diagnosis among TB household contacts in three high-burden settings', PLOS ONE, Jg. 20, Nr. 9, S. e0332125. https://doi.org/10.1371/journal.pone.0332125

Ntshiqa, T, Nagudi, J, Hamada, Y, Copas, A, Stender, S, Sabi, I, Ntinginya, EN, Lalashowi, J, Matete, M, Ntshamane, K, Morojele, I, Ngobeni, M, Mudzengi, D, Minja, LT, Chirwa, T, Lönnroth, K, Dreyer, V, Niemann, S, Rangaka, M, Charalambous, S & Velen, K 2025, 'Risk factors associated with TB infection among household contacts of microbiologically confirmed pulmonary TB patients in three high TB burden countries', THE JOURNAL OF INFECTIOUS DISEASES. https://doi.org/10.1093/infdis/jiaf320

Nurjadi, D, Schulenburg, H, Niemann, S, Zinkernagel, AS & Rupp, J 2025, 'Are we overlooking the obvious? Bacterial evolution is at the heart of antimicrobial resistance', The Lancet. Microbe, S. 101069. https://doi.org/10.1016/j.lanmic.2024.101069

Palme, PR, Grover, S, Abdelaziz, R, Mann, L, Kany, AM, Ouologuem, L, Bartel, K, Sonnenkalb, L, Reiling, N, Hirsch, AKH, Schnappinger, D, Rubinstein, JL, Imming, P & Richter, A 2025, 'Design, Synthesis, and Biological Evaluation of Mono- and Diamino-Substituted Squaramide Derivatives as Potent Inhibitors of Mycobacterial Adenosine Triphosphate (ATP) Synthase', JOURNAL OF MEDICINAL CHEMISTRY. https://doi.org/10.1021/acs.jmedchem.5c02284

Petersen, S, Diricks, M, Utpatel, C, Schulenburg, H & Merker, M 2025, 'Evolution of beta-lactam resistance causes fitness reductions and several cases of collateral sensitivities in the human pathogen Haemophilus influenzae', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, S. e0057625. https://doi.org/10.1128/aac.00576-25

Pohl, J, Gröschel, MI, Neumann, N, Tillmann, A, Waldeck, S, Schneider, T, Overhoff, D, Lange, SG, Bucksch, T, Peuker, R, Rauschning, D, Scheumann, G, Scheit, L, Schreiner, M, Wenzel, W, Kehe, K, Friesen, I, Dreyer, V, Niemann, S, Sander, L-E, Witzenrath, M, Nouailles, G, Zobel, CM & Retro-TB-Bw-Study Group 2025, 'Active case finding for tuberculosis among Ukrainian soldiers at the German Armed Forces', The European respiratory journal. https://doi.org/10.1183/13993003.00728-2025

Protic, D, Bascarevic, D, Dimitrijevic, S, Pesovic, J, Nikolic, V, Nikolic, S, Novicevic, V, Markovic, J, Arandjelovic, I, Savic-Pavicevic, D, Diricks, M, Belheouane, M & Merker, M 2025, 'Microbiome modulation and behavioural improvements in children with fragile X syndrome following probiotic intake: A pilot study', Scientific Reports. https://doi.org/10.1038/s41598-025-29896-1

Quansah, N, Arriaga, MB, Calderon, RI, Shin, S, Molldrem, S, Niemann, S & Ugarte-Gil, C 2025, 'Flying blind: urgency for drug-resistant testing for new tuberculosis drugs', The Lancet. Microbe, S. 101106. https://doi.org/10.1016/j.lanmic.2025.101106

Skouvig Pedersen, O, Butova, T, Miasoiedov, V, Feshchenko, Y, Kuzhko, M, Niemann, S, Rosenthal, A, Grinev, A, Rosenfeld, G, Hoppes, MD, Kilmnick, J, Crudu, V, Ciobanu, N, Codreanu, A, Toxanbayeva, B, Chingissova, L, Yurko, K, Kucheriavchenko, V, Vekshyn, V, Vashakidze, S, Shubladze, N, Avaliani, Z, Kadyrov, A, Kalmambetova, G, Sydykova, M, Ghita, E, Grecu, VI, Miulescu, AM, Wejse, CM, Fløe, A, Dahl, VN & Butov, D 2025, 'Sex differences in risk factors for unsuccessful tuberculosis treatment outcomes in Eastern Europe from 2020 to 2022: a multi-country retrospective cohort study', The Lancet regional health. Europe, Jg. 55, S. 101354. https://doi.org/10.1016/j.lanepe.2025.101354

Sonnenkalb, L, Trubenová, B, Regoes, RR, Merker, M & Niemann, S 2025, 'The mutant selection window of moxifloxacin and bedaquiline resistant Mycobacterium tuberculosis', Journal of infection, S. 106523. https://doi.org/10.1016/j.jinf.2025.106523

Szél, V, Phelan, JE, Georghiou, SB, Dolinger, DL, Clark, TG, Niemann, S, Lőrinczi, LK & Köser, CU 2025, 'The ahpC c-54t compensatory mutation is not always a valid surrogate for isoniazid resistance in Mycobacterium tuberculosis', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, S. e0026525. https://doi.org/10.1128/aac.00265-25

Trauth, J, Laspoulas, A, Dakischew, O, Gentil, K, Dreyer, V, Kuhns, M, Friesen, I & Herold, S 2025, 'Bedaquiline-Pretomanid-Linezolid as a Bridging Therapy for Adverse Events in Drug-Sensitive Tuberculosis', American journal of respiratory and critical care medicine. https://doi.org/10.1164/rccm.202501-0150RL

Tukvadze, N, Mashatole, S, Jacobs, A, Ngwanto, T, Heinrich, N, Van Rie, A, Crudu, V, Tudor, E, Goginashvili, L, Ibraim, E, Khosa, C, Howell, P, Rajaram, S, Naidoo, K, Niemann, S, Reither, K & Wallis, RS 2025, 'Drtb-hdt: a randomized controlled trial of two adjunctive host-directed therapies in rifampin-resistant tuberculosis', BMC INFECTIOUS DISEASES , Jg. 25, Nr. 1, S. 768. https://doi.org/10.1186/s12879-025-11072-5

Wang, Q, Barilar, I, Minin, VM, Modongo, C, Moonan, PK, Finlay, A, Boyd, R, Oeltmann, JE, Molefi, TL, Zetola, NM, Brewer, TF, Niemann, S & Shin, SS 2025, 'Phylodynamic analysis reveals disparate transmission dynamics of Mycobacterium tuberculosis complex lineages in Botswana', Scientific Reports. https://doi.org/10.1038/s41598-025-31425-z

Wei, KC, Purushothaman, S, Azzato, F, Baker, KS, Birkeland, KW, Brunet, S, Campos, J, Connor, TR, Giske, CG, Greub, G, Hallbäck, ET, Harmsen, D, Hodcroft, EB, Holden, MTG, Jacob, J, Kahles, A, Lagos, AC, Lipworth, S, Loo, E, Miotto, P, Neher, RA, Neves, A, Ready, D, Roloff, T, Rooney, A, Rousseau, E, Schrenzel, J, Sundqvist, M, Viegas, S, Wegner, F, Aamot, HV, Niemann, S, Williamson, DA, Mölling, P & Egli, A 2025, 'Conference report: The second Bacterial Genome Sequencing Pan-European Network conference', Microbes and Infection, S. 105557. https://doi.org/10.1016/j.micinf.2025.105557

2024

Adegbite, BR, Dreyer, V, Agbo, JBPAA, Mevyann, RC, Mfoumbi, GARI, Ndanga, MED, Biyogho, CM, Edoa, JR, M'Baidiguim, FB, Ndong, AROO, Alabi, AS, Kremsner, PG, Adegnika, AA, Niemann, S & Grobusch, MP 2025, 'Clinical epidemiology, genetic diversity, and drug susceptibility patterns by whole genome sequencing of Mycobacterium tuberculosis complex isolates in Gabon from 2012 to 2022', IJID regions, Jg. 14, S. 100501. https://doi.org/10.1016/j.ijregi.2024.100501

Barilar, I, Fernando, T, Utpatel, C, Abujate, C, Madeira, CM, José, B, Mutaquiha, C, Kranzer, K, Niemann, T & Ismael, N et al. 2024, 'Emergence of bedaquiline-resistant tuberculosis and of multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis strains with rpoB Ile491Phe mutation not detected by Xpert MTB/RIF in Mozambique: a retrospective observational study', Lancet Infectious Diseases, Jg. 24, Nr. 3, S. 297-307. https://doi.org/10.1016/S1473-3099(23)00498-X

Blankson, HNA, Kamara, RF, Barilar, I, Andres, S, Conteh, OS, Dallenga, T, Foray, L, Maurer, F, Kranzer, K & Utpatel, C et al. 2024, 'Molecular determinants of multidrug-resistant tuberculosis in Sierra Leone', Microbiology spectrum, Jg. 12, Nr. 3, S. e0240523. https://doi.org/10.1128/spectrum.02405-23

CRyPTIC Consortium 2024, 'Quantitative drug susceptibility testing for Mycobacterium tuberculosis using unassembled sequencing data and machine learning', PLoS Computational Biology , Jg. 20, Nr. 8, S. e1012260. https://doi.org/10.1371/journal.pcbi.1012260

CRyPTIC Consortium 2024, 'Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach', Nature communications, Jg. 15, Nr. 1, S. 488. https://doi.org/10.1038/s41467-023-44325-5

Danchuk, SN, Solomon, OE, Kohl, TA, Dreyer, V, Barilar, I, Utpatel, C, Niemann, S, Soolingen, DV, Anthony, R & van Ingen, J et al. 2024, 'Challenging the gold standard: the limitations of molecular assays for detection of Mycobacterium tuberculosis heteroresistance', Thorax, Jg. 79, Nr. 7, S. 670-675. https://doi.org/10.1136/thorax-2023-220202

Diricks, M, Petersen, S, Bartels, L, Lâm, T-T, Claus, H, Bajanca-Lavado, MP, Hauswaldt, S, Stolze, R, Vázquez, OJ, Utpatel, C, Niemann, S, Rupp, J, Wohlers, I & Merker, M 2024, 'Revisiting mutational resistance to ampicillin and cefotaxime in Haemophilus influenzae', Genome medicine, Jg. 16, Nr. 1, S. 140. https://doi.org/10.1186/s13073-024-01406-4

Dreyer, V, Sonnenkalb, L, Diricks, M, Utpatel, C, Barilar, I, Mohr, V, Niemann, S, Kohl, TA & Merker, M 2024, 'Use of Whole Genome Sequencing for Mycobacterium tuberculosis Complex Antimicrobial Susceptibility Testing: From Sequence Data to Resistance Profiles', Methods in Molecular Biology, Jg. 2833, S. 195-210. https://doi.org/10.1007/978-1-0716-3981-8_18

Dyer, NP, Päuker, B, Baxter, L, Gupta, A, Bunk, B, Overmann, J, Diricks, M, Dreyer, V, Niemann, S, Holt, KE, Rahman, M, Brown, PE, Stark, R, Zhou, Z, Ott, S & Nübel, U 2024, 'EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens', NUCLEIC ACIDS RESEARCH. https://doi.org/10.1093/nar/gkae902

Friesen, I, Dreyer, V, Klingmüller, A, Zuber, S, Hoffmann, AM, Suárez, I, Schütz, B, Preßel, T, Andres, S & Niemann, S et al. 2024, 'First detection of a Mycobacterium tuberculosis XDR clinical isolate harbouring an RpoB I491F mutation in a Ukrainian patient treated in Germany, October 2023', Eurosurveillance, Jg. 29, Nr. 28. https://doi.org/10.2807/1560-7917.ES.2024.29.28.2400420

Friesen, I, Saluzzo, F, Groenheit, R, Aubry, A, Anthony, R, Niemann, S, Mathys, V, Cirillo, DM & TB European Reference Laboratory Network (ERLTB-Net-3) 2024, 'Re: 'Availability of drugs and resistance testing for BPaLM regimen for rifampicin-resistant tuberculosis in Europe' by Lange et al', CLINICAL MICROBIOLOGY AND INFECTION , Jg. 30, Nr. 9, S. 1204-1206. https://doi.org/10.1016/j.cmi.2024.06.001

Germuskova, Z, Sosa, E, Lagos, AC, Aamot, HV, Beale, MA, Bertelli, C, Björkmann, J, Couto, N, Feige, L & Greub, G et al. 2024, 'Conference report: The first Bacterial Genome Sequencing Pan-European Network Conference', Microbes and Infection, S. 105410. https://doi.org/10.1016/j.micinf.2024.105410

Götz, MP, Duque Villegas, MA, Fageräng, B, Kerfin, A, Skjoedt, M-O, Garred, P & Rosbjerg, A 2024, 'Transient Binding Dynamics of Complement System Pattern Recognition Molecules on Pathogens', JOURNAL OF IMMUNOLOGY, Jg. 212, Nr. 9, S. 1493-1503. https://doi.org/10.4049/jimmunol.2300768

Gröschel, MI, Pérez-Llanos, FJ, Diel, R, Vargas, R, Escuyer, V, Musser, K, Trieu, L, Meissner, JS, Knorr, J & Klinkenberg, D et al. 2024, 'Differential rates of Mycobacterium tuberculosis transmission associate with host-pathogen sympatry', Nature Microbiology, Jg. 9, Nr. 8, S. 2113-2127. https://doi.org/10.1038/s41564-024-01758-y

Günther, G, Mhuulu, L, Diergaardt, A, Dreyer, V, Moses, M, Anyolo, K, Ruswa, N, Claassens, M, Niemann, S & Nepolo, E 2024, 'Bedaquiline Resistance after Effective Treatment of Multidrug-Resistant Tuberculosis, Namibia', EMERGING INFECTIOUS DISEASES, Jg. 30, Nr. 3, S. 568-571. https://doi.org/10.3201/eid3003.240134

Hansen, J, Kolbe, K, König, IR, Scherließ, R, Hellfritzsch, M, Malm, S, Müller-Loennies, S, Zallet, J, Hillemann, D, Wiesmüller, K-H, Herzmann, C, Brandenburg, J & Reiling, N 2022, 'Lipobiotin-capture magnetic bead assay for isolation, enrichment and detection of Mycobacterium tuberculosis from saliva', PLOS ONE, Jg. 17, Nr. 7, S. e0265554. https://doi.org/10.1371/journal.pone.0265554

Idris, R, Zielbauer, A-S, Koepsell, J, Kloka, J & Wetzstein, N 2024, 'Extracorporeal membrane oxygenation (ECMO) in patients with tuberculosis: systematic review and meta-analysis of 43 cases', BMC PULMONARY MEDICINE, Jg. 24, Nr. 1, S. 47. https://doi.org/10.1186/s12890-023-02715-x

Köser, CU, Miotto, P, Ismail, N, Anthony, RM, Utpatel, C, Merker, M, Niemann, S, Tahseen, S, Rigouts, L & Rodrigues, C et al. 2024, 'A composite reference standard is needed for bedaquiline antimicrobial susceptibility testing for Mycobacterium tuberculosis complex', The European respiratory journal, Jg. 64, Nr. 1. https://doi.org/10.1183/13993003.00391-2024

Larsson, L, Corbett, C, Kalmambetova, G, Utpatel, C, Ahmedov, S, Antonenka, U, Iskakova, A, Kadyrov, A, Kohl, TA & Barilar, V et al. 2024, 'Whole-genome sequencing drug susceptibility testing is associated with positive MDR-TB treatment response', INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE, Jg. 28, Nr. 10, S. 494-499. https://doi.org/10.5588/ijtld.24.0052

Machado, E, Vasconcellos, S, Gomes, L, Catanho, M, Ramos, J, de Carvalho, L, Goldenberg, T, Redner, P, Caldas, P & Campos, C et al. 2024, 'Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species', Microbial genomics, Jg. 10, Nr. 7. https://doi.org/10.1099/mgen.0.001266

Meiwes, L, Kontsevaya, I, Chesov, D, Kulciţkaia, S, Dreyer, V, Hillemann, D, Dlamini, Q, Williams, C, Barer, M & Brinkmann, F et al. 2024, 'Whispers in the wind: Face mask sampling for Mycobacterium tuberculosis detection in children with pulmonary tuberculosis', JOURNAL OF INFECTIOUS DISEASES. https://doi.org/10.1093/infdis/jiae282

Mohr, V, Sonnenkalb, L, Utpatel, C, Barilar, I, Diricks, M, Dreyer, V, Niemann, S, Kohl, TA & Merker, M 2024, 'Use of Whole Genome Sequencing for Mycobacterium tuberculosis Complex Antimicrobial Susceptibility Testing', Methods in Molecular Biology, Jg. 2833, S. 185-193. https://doi.org/10.1007/978-1-0716-3981-8_17

Olbrich, L, Franckling-Smith, Z, Larsson, L, Sabi, I, Ntinginya, NE, Khosa, C, Banze, D, Nliwasa, M, Corbett, EL, Semphere, R, Verghese, VP, Michael, JS, Ninan, MM, Saathoff, E, McHugh, TD, Razid, A, Graham, SM, Song, R, Nabeta, P, Trollip, A, Nicol, MP, Hoelscher, M, Geldmacher, C, Heinrich, N, Zar, HJ & RaPaed-AIDA-TB consortium 2024, 'Sequential and parallel testing for microbiological confirmation of tuberculosis disease in children in five low-income and middle-income countries: a secondary analysis of the RaPaed-TB study', Lancet Infectious Diseases. https://doi.org/10.1016/S1473-3099(24)00494-8

Phelan, JE, Utpatel, C, Ismail, N, Cortes, T, Niemann, S, Cirillo, DM, Schön, T, Miotto, P & Köser, CU 2024, 'Careful classification of potential bedaquiline resistance mutations is critical when analysing their clinical impact', INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE, Jg. 28, Nr. 6, S. 312-313. https://doi.org/10.5588/ijtld.24.0083

Rachwal, N, Idris, R, Dreyer, V, Richter, E, Wichelhaus, TA, Niemann, S, Wetzstein, N & Götsch, U 2024, 'Pathogen and host determinants of extrapulmonary tuberculosis among 1035 patients in Frankfurt am Main, Germany, 2008-2023', CLINICAL MICROBIOLOGY AND INFECTION . https://doi.org/10.1016/j.cmi.2024.11.009

Rupasinghe, P, Reenaers, R, Vereecken, J, Mulders, W, Cogneau, S, Merker, M, Niemann, S, Vally Omar, S, Rigouts, L & Köser, CU et al. 2024, 'Refined understanding of the impact of the Mycobacterium tuberculosis complex diversity on the intrinsic susceptibility to pretomanid', Microbiology spectrum, Jg. 12, Nr. 3, S. e0007024. https://doi.org/10.1128/spectrum.00070-24

Shavuka, O, Iipumbu, E, Boois, L, Günther, G, Hoddinott, G, Lin, H-H, Nepolo, E, Niemann, S, Ruswa, N & Seddon, J et al. 2024, 'Enhanced active case finding of drug-resistant tuberculosis in Namibia: a protocol for the hotspots, hospitals, and households (H3TB) study', BMJ open, Jg. 14, Nr. 2, S. e082665. https://doi.org/10.1136/bmjopen-2023-082665

Svensson, E, Ketelsen, H, Andres, S, Folkvardsen, DB, Hillemann, D, Conteh, O, Norman, A, Niemann, S, Lillebaek, T & Kuhns, M 2024, 'Dual-centre evaluation of the FluoroType MTBDR version 2 assay for detection of Mycobacterium tuberculosis complex and resistance-conferring mutations in pulmonary and extrapulmonary samples from Denmark, Germany and Sierra Leone', CLINICAL MICROBIOLOGY AND INFECTION , Jg. 30, Nr. 8, S. 1055-1060. https://doi.org/10.1016/j.cmi.2024.04.006

Utpatel, C, Zavaleta, M, Rojas-Bolivar, D, Mühlbach, A, Picoy, J, Portugal, W, Esteve-Solé, A, Alsina, L, Miotto, P & Bartholomeu, DC et al. 2024, 'Prison as a driver of recent transmissions of multidrug-resistant tuberculosis in Callao, Peru: a cross-sectional study', Lancet regional health. Americas, Jg. 31, S. 100674. https://doi.org/10.1016/j.lana.2024.100674

Wetzstein, N, Diricks, M, Andres, S, Kuhns, M, Marschall, L, Biciusca, T, Smaczny, C, Friesen, I, Niemann, S & Wichelhaus, TA 2024, 'Genomic diversity and clinical relevance of Mycobacterium simiae', ERJ Open Research, Jg. 10, Nr. 2, 00773-2023. https://doi.org/10.1183/23120541.00773-2023

Wetzstein, N, Diricks, M, Anton, TB, Andres, S, Kuhns, M, Kohl, TA, Schwarz, C, Lewin, A, Kehrmann, J & Kahl, BC et al. 2024, 'Clinical and genomic features of Mycobacterium avium complex: a multi-national European study', Genome medicine, Jg. 16, Nr. 1, S. 86. https://doi.org/10.1186/s13073-024-01359-8

2023

Baker, CR, Barilar, I, de Araujo, LS, Rimoin, AW, Parker, DM, Boyd, R, Tobias, JL, Moonan, PK, Click, ES, Finlay, A, Oeltmann, JE, Minin, VN, Modongo, C, Zetola, NM, Niemann, S & Shin, SS 2023, 'Use of High-Resolution Geospatial and Genomic Data to Characterize Recent Tuberculosis Transmission, Botswana', EMERGING INFECTIOUS DISEASES, Jg. 29, Nr. 5, S. 977-987. https://doi.org/10.3201/eid2905.220796

Botelho, J, Tüffers, L, Fuss, J, Buchholz, F, Utpatel, C, Klockgether, J, Niemann, S, Tümmler, B & Schulenburg, H 2023, 'Phylogroup-specific variation shapes the clustering of antimicrobial resistance genes and defence systems across regions of genome plasticity in Pseudomonas aeruginosa', EBioMedicine, Jg. 90, S. 104532. https://doi.org/10.1016/j.ebiom.2023.104532

Chesov, E, Chesov, D, Reimann, M, Dreyer, V, Utpatel, C, Gröschel, MI, Ciobanu, N, Crudu, V, Lange, C, Heyckendorf, J & Merker, M 2023, 'Impact of Mycobacterium tuberculosis strain type on multidrug-resistant tuberculosis severity, Republic of Moldova', Journal of infection, Jg. 87, Nr. 6, S. 588-591. https://doi.org/10.1016/j.jinf.2023.10.001

Comprehensive Resistance Prediction for Tuberculosis: an International Consortium, Sonnenkalb, L, Carter, JJ, Spitaleri, A, Iqbal, Z, Hunt, M, Malone, KM, Utpatel, C, Cirillo, DM, Rodrigues, C, Nilgiriwala, KS, Fowler, PW, Merker, M & Niemann, S 2023, 'Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis', The Lancet. Microbe, Jg. 4, Nr. 5, S. e358-e368. https://doi.org/10.1016/S2666-5247(23)00002-2

de Araujo, L, Cabibbe, AM, Mhuulu, L, Ruswa, N, Dreyer, V, Diergaardt, A, Günther, G, Claassens, M, Gerlach, C, Utpatel, C, Cirillo, DM, Nepolo, E & Niemann, S 2023, 'Implementation of targeted next-generation sequencing for the diagnosis of drug-resistant tuberculosis in low-resource settings: a programmatic model, challenges, and initial outcomes', Frontiers in public health, Jg. 11, S. 1204064. https://doi.org/10.3389/fpubh.2023.1204064

Diel, R, Meywald-Walther, K, Schwarzbach, C, Voss, K, Dreyer, V & Niemann, S 2023, 'Risk of tuberculosis transmission by children in Hamburg, Germany', RESPIRATORY MEDICINE , Jg. 209, S. 107152. https://doi.org/10.1016/j.rmed.2023.107152

Economou Lundeberg, E, Andersson, V, Wijkander, M, Groenheit, R, Mansjö, M, Werngren, J, Cortes, T, Barilar, I, Niemann, S, Merker, M, Köser, CU & Davies Forsman, L 2023, 'In vitro activity of new combinations of β-lactam and β-lactamase inhibitors against the Mycobacterium tuberculosis complex', Microbiology spectrum, Jg. 11, Nr. 5, S. e0178123. https://doi.org/10.1128/spectrum.01781-23

ERA4TB consortium, van Wijk, RC, Lucía, A, Sudhakar, PK, Sonnenkalb, L, Gaudin, C, Hoffmann, E, Dremierre, B, Aguilar-Ayala, DA, Molin, MD, Rybniker, J, de Giorgi, S, Cioetto-Mazzabò, L, Segafreddo, G, Manganelli, R, Degiacomi, G, Recchia, D, Pasca, MR, Simonsson, USH & Ramón-García, S 2023, 'Implementing best practices on data generation and reporting of Mycobacterium tuberculosis in vitro assays within the ERA4TB consortium', iScience, Jg. 26, Nr. 4, S. 106411. https://doi.org/10.1016/j.isci.2023.106411

Gries, R, Dal Molin, M, Chhen, J, van Gumpel, E, Dreyer, V, Niemann, S & Rybniker, J 2023, 'Characterization of Two Novel Inhibitors of the Mycobacterium tuberculosis Cytochrome bc1 Complex', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, Jg. 67, Nr. 7, S. e0025123. https://doi.org/10.1128/aac.00251-23

Ismael, N, van Wyk, S, Tegally, H, Giandhari, J, San, JE, Moir, M, Pillay, S, Utpatel, C, Singh, L, Naidoo, Y, Ramphal, U, Mabunda, N, Abílio, N, Arnaldo, P, Xavier, J, Amoako, DG, Everatt, J, Ramphal, Y, Maharaj, A, de Araujo, L, Anyaneji, UJ, Tshiabuila, D, Viegas, S, Lessells, R, Engelbrecht, S, Gudo, E, Jani, I, Niemann, S, Wilkinson, E & de Oliveira, T 2023, 'Genomic epidemiology of SARS-CoV-2 during the first four waves in Mozambique', PLOS global public health, Jg. 3, Nr. 3, S. e0001593. https://doi.org/10.1371/journal.pgph.0001593

Koehler, N, Andres, S, Merker, M, Dreyer, V, John, A, Kuhns, M, Krieger, D, Choong, E, Verougstraete, N, Zur Wiesch, PA, Wicha, SG, König, C, Kalsdorf, B, Sanchez Carballo, PM, Schaub, D, Werngren, J, Schön, T, Peloquin, CA, Schönfeld, N, Verstraete, AG, Decosterd, LA, Aarnoutse, R, Niemann, S, Maurer, FP & Lange, C 2023, 'Pretomanid-Resistant Tuberculosis', Journal of infection, Jg. 86, Nr. 5, S. 520-524. https://doi.org/10.1016/j.jinf.2023.01.039

Noroc, E, Chesov, D, Merker, M, Gröschel, MI, Barilar, I, Dreyer, V, Ciobanu, N, Reimann, M, Crudu, V & Lange, C 2023, 'Limited Nosocomial Transmission of Drug-Resistant Tuberculosis, Moldova', EMERGING INFECTIOUS DISEASES, Jg. 29, Nr. 5, S. 1046-1050. https://doi.org/10.3201/eid2905.230035

Pérez-Llanos, FJ, Dreyer, V, Barilar, I, Utpatel, C, Kohl, TA, Murcia, MI, Homolka, S, Merker, M & Niemann, S 2023, 'Transmission Dynamics of a Mycobacterium tuberculosis Complex Outbreak in an Indigenous Population in the Colombian Amazon Region', Microbiology spectrum, S. e0501322. https://doi.org/10.1128/spectrum.05013-22

Rollo, RF, Mori, G, Hill, TA, Hillemann, D, Niemann, S, Homolka, S, Fairlie, DP & Blumenthal, A 2023, 'Wollamide Cyclic Hexapeptides Synergize with Established and New Tuberculosis Antibiotics in Targeting Mycobacterium tuberculosis', Microbiology spectrum, Jg. 11, Nr. 4, S. e0046523. https://doi.org/10.1128/spectrum.00465-23

Schlanderer, J, Hoffmann, H, Lüddecke, J, Golubov, A, Grasse, W, Kindler, EV, Kohl, TA, Merker, M, Metzger, C, Mohr, V, Niemann, S, Pilloni, C, Plesnik, S, Raya, B, Shresta, B, Utpatel, C, Zengerle, R, Beutler, M & Paust, N 2023, 'Two-stage tuberculosis diagnostics: combining centrifugal microfluidics to detect TB infection and Inh and Rif resistance at the point of care with subsequent antibiotic resistance profiling by targeted NGS', Lab on a chip, Jg. 24, Nr. 1, S. 74-84. https://doi.org/10.1039/d3lc00783a

Smith, JP, Modongo, C, Oeltmann, JE, Dima, M, Matsiri, O, Fane, O, Molefi, T, Shin, SS, Barilar, I, Niemann, S, Zetola, NM & Moonan, PK 2023, 'High-Resolution Characterization of Nosocomial Mycobacterium tuberculosis Transmission Events in Botswana', American journal of epidemiology, Jg. 192, Nr. 3, S. 503-506. https://doi.org/10.1093/aje/kwac214

Tagliani, E, Kohl, TA, Ghodousi, A, Groenheit, R, Holicka, Y, Niemann, S, Maurer, FP, Cirillo, DM & Cambau, E 2023, 'Appeal from the European reference laboratory network for tuberculosis for improving the diagnosis of infections caused by non-tuberculous mycobacteria', CLINICAL MICROBIOLOGY AND INFECTION . https://doi.org/10.1016/j.cmi.2023.06.005

TBNET and RESIST-TB networks, Domínguez, J, Boeree, MJ, Cambau, E, Chesov, D, Conradie, F, Cox, V, Dheda, K, Dudnyk, A, Farhat, MR, Gagneux, S, Grobusch, MP, Gröschel, MI, Guglielmetti, L, Kontsevaya, I, Lange, B, van Leth, F, Lienhardt, C, Mandalakas, AM, Maurer, FP, Merker, M, Miotto, P, Molina-Moya, B, Morel, F, Niemann, S, Veziris, N, Whitelaw, A, Horsburgh, CR & Lange, C 2023, 'Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis: a 2023 TBnet/RESIST-TB consensus statement', Lancet Infectious Diseases, Jg. 23, Nr. 4, S. e122-e137. https://doi.org/10.1016/S1473-3099(22)00875-1

Trauth, J, Matt, U, Kohl, TA, Niemann, S & Herold, S 2023, 'Blind spot in endocarditis guidelines: Mycobacterium chimaera prosthetic valve endocarditis after cardiac surgery-a case series', European heart journal. Case reports, Jg. 7, Nr. 8, S. ytad400. https://doi.org/10.1093/ehjcr/ytad400

Wetzstein, N, Kohl, TA, Diricks, M, Mas-Peiro, S, Holubec, T, Kessel, J, Graf, C, Koch, B, Herrmann, E, Vehreschild, MJGT, Hogardt, M, Niemann, S, Stephan, C & Wichelhaus, TA 2023, 'Clinical characteristics and outcome of Mycobacterium chimaera infections after cardiac surgery: systematic review and meta-analysis of 180 heater-cooler unit associated cases', CLINICAL MICROBIOLOGY AND INFECTION , Jg. 29, Nr. 8, S. 1008-1014. https://doi.org/10.1016/j.cmi.2023.03.005

Zwyer, M, Rutaihwa, LK, Windels, E, Hella, J, Menardo, F, Sasamalo, M, Sommer, G, Schmülling, L, Borrell, S, Reinhard, M, Dötsch, A, Hiza, H, Stritt, C, Sikalengo, G, Fenner, L, De Jong, BC, Kato-Maeda, M, Jugheli, L, Ernst, JD, Niemann, S, Jeljeli, L, Ballif, M, Egger, M, Rakotosamimanana, N, Yeboah-Manu, D, Asare, P, Malla, B, Dou, HY, Zetola, N, Wilkinson, RJ, Cox, H, Carter, EJ, Gnokoro, J, Yotebieng, M, Gotuzzo, E, Abimiku, A, Avihingsanon, A, Xu, ZM, Fellay, J, Portevin, D, Reither, K, Stadler, T, Gagneux, S & Brites, D 2023, 'Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania', PLOS PATHOGENS, Jg. 19, Nr. 4, S. e1010893. https://doi.org/10.1371/journal.ppat.1010893

2022

Abdul, JBPAA, Adegbite, BR, Ndanga, MED, Edoa, JR, Mevyann, RC, Mfoumbi, GRAI, de Dieu, TJ, Mahoumbou, J, Biyogho, CM, Jeyaraj, S, Niemann, S, Lell, B, Kremsner, PG, Alabi, AS, Adegnika, AA & Grobusch, MP 2022, 'Resistance patterns among drug-resistant tuberculosis patients and trends-over-time analysis of national surveillance data in Gabon, Central Africa', Infection, S. 1-8. https://doi.org/10.1007/s15010-022-01941-5

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

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

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

Brandenburg, J, Heyckendorf, J, Marwitz, F, Zehethofer, N, Linnemann, L, Gisch, N, Karaköse, H, Reimann, M, Kranzer, K, Kalsdorf, B, Sanchez-Carballo, P, Weinkauf, M, Scholz, V, Malm, S, Homolka, S, Gaede, KI, Herzmann, C, Schaible, UE, Hölscher, C, Reiling, N & Schwudke, D 2022, 'Tuberculostearic Acid-Containing Phosphatidylinositols as Markers of Bacterial Burden in Tuberculosis', ACS infectious diseases, Jg. 8, Nr. 7, S. 1303-1315. https://doi.org/10.1021/acsinfecdis.2c00075

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

Claassens, M, Dreyer, V, Nepolo, E, Mokomele, Q, van Rooyen, G, Ruswa, N, Günther, G & Niemann, S 2022, 'Whole-Genome Sequencing for Resistance Prediction and Transmission Analysis of Mycobacterium tuberculosis Complex Strains from Namibia', Microbiology spectrum, Jg. 10, Nr. 5, S. e0158622. https://doi.org/10.1128/spectrum.01586-22

CRyPTIC Consortium 2022, 'A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics', PLOS BIOLOGY , Jg. 20, Nr. 8, S. e3001721. https://doi.org/10.1371/journal.pbio.3001721

CRyPTIC Consortium 2022, 'High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region', Genome medicine, Jg. 14, Nr. 1, S. 95. https://doi.org/10.1186/s13073-022-01076-0

CRyPTIC Consortium, Barilar, I, Dreyer, V, Kohl, T, Merker, M, Niemann, S & Utpatel, C 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

CRyPTIC Consortium, Niemann, S, Barilar, I, Dreyer, V, Merker, M, Kohl, T & Utpatel, C 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, Jg. 60, Nr. 4, 2200239. https://doi.org/10.1183/13993003.00239-2022

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, Merker, M, Wetzstein, N, Kohl, TA, Niemann, S & Maurer, FP 2022, 'Delineating Mycobacterium abscessus population structure and transmission employing high-resolution core genome multilocus sequence typing', Nature communications, Jg. 13, Nr. 1, S. 4936. https://doi.org/10.1038/s41467-022-32122-5

European Laboratory Initiative on TB, HIV and Viral Hepatitis(3) & Niemann, S 2022, 'Diagnostic Capacities for Multidrug-Resistant Tuberculosis in the World Health Organization European Region: Action is Needed by all Member States', Journal of Molecular Diagnostics, Jg. 24, Nr. 11, S. 1189-1194. https://doi.org/10.1016/j.jmoldx.2022.07.005

Finci, I, Albertini, A, Merker, M, Andres, S, Bablishvili, N, Barilar, I, Cáceres, T, Crudu, V, Gotuzzo, E, Hapeela, N, Hoffmann, H, Hoogland, C, Kohl, TA, Kranzer, K, Mantsoki, A, Maurer, FP, Nicol, MP, Noroc, E, Plesnik, S, Rodwell, T, Ruhwald, M, Savidge, T, Salfinger, M, Streicher, E, Tukvadze, N, Warren, R, Zemanay, W, Zurek, A, Niemann, S & Denkinger, CM 2022, 'Investigating resistance in clinical Mycobacterium tuberculosis complex isolates with genomic and phenotypic antimicrobial susceptibility testing: a multicentre observational study', The Lancet. Microbe, Jg. 3, Nr. 9, S. e672-e682. https://doi.org/10.1016/S2666-5247(22)00116-1

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

Goldstein, IH, Bayer, D, Barilar, I, Kizito, B, Matsiri, O, Modongo, C, Zetola, NM, Niemann, S, Minin, VM & Shin, SS 2022, 'Using genetic data to identify transmission risk factors: Statistical assessment and application to tuberculosis transmission', PLoS Computational Biology , Jg. 18, Nr. 12, S. e1010696. https://doi.org/10.1371/journal.pcbi.1010696

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, Müller-Loennies, S, Zallet, J, Hillemann, D, Wiesmüller, K-H, Herzmann, C, Brandenburg, J & Reiling, N 2022, 'Lipobiotin-capture magnetic bead assay for isolation, enrichment and detection of Mycobacterium tuberculosis from saliva', PLOS ONE, Jg. 17, Nr. 7, S. e0265554. https://doi.org/10.1371/journal.pone.0265554

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

Merker, M, Rasigade, J-P, Barbier, M, Cox, H, Feuerriegel, S, Kohl, TA, Shitikov, E, Klaos, K, Gaudin, C, Antoine, R, Diel, R, Borrell, S, Gagneux, S, Nikolayevskyy, V, Andres, S, Crudu, V, Supply, P, Niemann, S & Wirth, T 2022, 'Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis', Nature communications, Jg. 13, Nr. 1, S. 5105. https://doi.org/10.1038/s41467-022-32455-1

Mesfin, EA, Merker, M, Beyene, D, Tesfaye, A, Shuaib, YA, Addise, D, Tessema, B & Niemann, S 2022, 'Prediction of drug resistance by Sanger sequencing of Mycobacterium tuberculosis complex strains isolated from multidrug resistant tuberculosis suspect patients in Ethiopia', PLOS ONE, Jg. 17, Nr. 8, S. e0271508. https://doi.org/10.1371/journal.pone.0271508

Rachow, A, Saathoff, E, Mindru, R, Popescu, O, Lugoji, D, Mahler, B, Merker, M, Niemann, S, Olaru, ID, Kastner, S, Hoelscher, M, Lange, C & Ibraim, E 2022, 'Diagnostic performance of the AID line probe assay in the detection of Mycobacterium tuberculosis and drug resistance in Romanian patients with presumed TB', PLOS ONE, Jg. 17, Nr. 8, S. e0271297. https://doi.org/10.1371/journal.pone.0271297

Shuaib, YA, Utpatel, C, Kohl, TA, Barilar, I, Diricks, M, Ashraf, N, Wieler, LH, Kerubo, G, Mesfin, EA, Diallo, AB, Al-Hajoj, S, Ndung'u, P, Fitzgibbon, MM, Vaziri, F, Sintchenko, V, Martinez, E, Viegas, SO, Zhou, Y, Azmy, A, Al-Amry, K, Godreuil, S, Varma-Basil, M, Narang, A, Ali, S, Beckert, P, Dreyer, V, Kabwe, M, Bates, M, Hoelscher, M, Rachow, A, Gori, A, Tekwu, EM, Sidze, LK, Jean-Paul, AA, Beng, VP, Ntoumi, F, Frank, M, Diallo, AG, Mboup, S, Tessema, B, Beyene, D, Khan, SN, Diel, R, Supply, P, Maurer, FP, Hoffmann, H, Niemann, S & Merker, M 2022, 'Origin and Global Expansion of Mycobacterium tuberculosis Complex Lineage 3', Genes, Jg. 13, Nr. 6, 990. https://doi.org/10.3390/genes13060990

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

The CRyPTIC Consortium & Niemann, S 2022, 'Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms', PLOS BIOLOGY , Jg. 20, Nr. 8, S. e3001755. https://doi.org/10.1371/journal.pbio.3001755

Wetzstein, N, Diricks, M, Kohl, TA, Wichelhaus, TA, Andres, S, Paulowski, L, Schwarz, C, Lewin, A, Kehrmann, J, Kahl, BC, Dichtl, K, Hügel, C, Eickmeier, O, Smaczny, C, Schmidt, A, Zimmermann, S, Nährlich, L, Hafkemeyer, S, Niemann, S, Maurer, FP & Hogardt, M 2022, 'Molecular Epidemiology of Mycobacterium abscessus Isolates Recovered from German Cystic Fibrosis Patients', Microbiology spectrum, Jg. 10, Nr. 4, S. e0171422. https://doi.org/10.1128/spectrum.01714-22

Zooniverse Volunteer Community & Niemann, S 2022, 'A crowd of BashTheBug volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates', eLife, Jg. 11, e75046. https://doi.org/10.7554/eLife.75046

2025

Geng, X, Barilar, I, Kesamang, M, Tumedi, KA, Matsheka, M, Modongo, C, Minin, V, Niemann, S & Shin, SS, SARS-CoV-2 Evolution in an HIV-Endemic Setting: A Genomic Epidemiology Study from Botswana, 2025, medRxiv. https://doi.org/10.1101/2025.11.21.25340589

2024

Baker, CR, Barilar, I, de Araujo, LS, Parker, DM, Fornace, K, Moonan, PK, Oeltmann, JE, Tobias, JL, Minin, VM, Modongo, C, Zetola, NM, Niemann, S & Shin, SS, Using genomic epidemiology and geographic activity spaces to investigate tuberculosis outbreaks in Botswana, 2024, bioRxiv. https://doi.org/10.1101/2024.12.04.24318520