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3. Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment

Author

Georghiou, Sophia B, Rodwell, Timothy C, Korobitsyn, Alexei, Abbadi, Said H, Ajbani, Kanchan, Alffenaar, Jan-Willem, Alland, David, Alvarez, Nataly, Andres, Sönke, Ardizzoni, Elisa, Aubry, Alexandra, Baldan, Rossella, Ballif, Marie, Barilar, Ivan, Böttger, Erik C, Chakravorty, Soumitesh, Claxton, Pauline M, Cirillo, Daniela M, Comas, Iñaki, Coulter, Chris, Denkinger, Claudia M, Derendinger, Brigitta, Desmond, Edward P, de Steenwinkel, Jurriaan EM, Dheda, Keertan, Diacon, Andreas H, Dolinger, David L, Dooley, Kelly E, Egger, Matthias, Ehsani, Soudeh, Farhat, Maha R, Fattorini, Lanfranco, Finci, Iris, Le Ray, Laure Fournier, Furió, Victoria, Groenheit, Ramona, Gumbo, Tawanda, Heysell, Scott K, Hillemann, Doris, Hoffmann, Harald, Hsueh, Po-Ren, Hu, Yi, Huang, Hairong, Hussain, Alamdar, Ismail, Farzana, Izumi, Kiyohiko, Jagielski, Tomasz, Johnson, John L, Kambli, Priti, Kaniga, Koné, Karunaratne, GHR Eranga, Sharma, Meenu Kaushal, Keller, Peter M, Kelly, Ellis C, Kholina, Margarita, Kohli, Mikashmi, Kranzer, Katharina, Laurenson, Ian F, Limberis, Jason, Lin, S-Y Grace, Liu, Yongge, López-Gavín, Alexandre, Lyander, Anna, Machado, Diana, Martinez, Elena, Masood, Faisal, Mitarai, Satoshi, Mvelase, Nomonde R, Niemann, Stefan, Nikolayevskyy, Vladyslav, Maurer, Florian P, Merker, Matthias, Miotto, Paolo, Omar, Shaheed V, Otto-Knapp, Ralf, Palaci, Moisés, Gutiérrez, Juan José Palacios, Peacock, Sharon J, Peloquin, Charles A, Perera, Jennifer, Pierre-Audigier, Catherine, Pholwat, Suporn, Posey, James E, Prammananan, Therdsak, Rigouts, Leen, Robledo, Jaime, Rockwood, Neesha, Rodrigues, Camilla, Salfinger, Max, Schechter, Marcos C, Seifert, Marva, Sengstake, Sarah, Shinnick, Thomas, Shubladze, Natalia, Sintchenko, Vitali, Sirgel, Frederick, Somasundaram, Sulochana, Sterling, Timothy R, Spitaleri, Andrea, and Streicher, Elizabeth

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Clinical Sciences, Infectious Diseases, Biodefense, Antimicrobial Resistance, Prevention, Rare Diseases, Emerging Infectious Diseases, Tuberculosis, Clinical Research, Vaccine Related, Orphan Drug, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Infection, Good Health and Well Being, Antitubercular Agents, Drug Resistance, Bacterial, Drug Resistance, Multiple, Bacterial, Humans, Microbial Sensitivity Tests, Mycobacterium tuberculosis, Tuberculosis, Multidrug-Resistant, Antimycobacterial Susceptibility Testing Group, Medical and Health Sciences, Respiratory System, Cardiovascular medicine and haematology
Abstract

Inappropriately high breakpoints have resulted in systematic false-susceptible AST results to anti-TB drugs. MIC, PK/PD and clinical outcome data should be combined when setting breakpoints to minimise the emergence and spread of antimicrobial resistance. https://bit.ly/3i43wb6

Published
2022

5. Towards clinical breakpoints for non-tuberculous mycobacteria – Determination of epidemiological cut off values for the Mycobacterium avium complex and Mycobacterium abscessus using broth microdilution

Author

Fröberg, Gabrielle, Maurer, Florian P., Chryssanthou, Erja, Fernström, Louise, Benmansour, Hanaa, Boarbi, Samira, Mengshoel, Anne Torunn, Keller, Peter Michael, Viveiros, Miguel, Machado, Diana, Fitzgibbon, Margaret M., Mok, Simone, Werngren, Jim, Cirillo, Daniela Maria, Alcaide, Fernando, Hyyryläinen, Hanne-Leena, Aubry, Alexandra, Andres, Sönke, Nadarajan, Darshaalini, Svensson, Erik, Turnidge, John, Giske, Christian G., Kahlmeter, Gunnar, Cambau, Emmanuelle, van Ingen, Jakko, and Schön, Thomas

Published
2023
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6. Investigating resistance in clinical Mycobacterium tuberculosis complex isolates with genomic and phenotypic antimicrobial susceptibility testing: a multicentre observational study

Author

Finci, Iris, Albertini, Audrey, Merker, Matthias, Andres, Sönke, Bablishvili, Nino, Barilar, Ivan, Cáceres, Tatiana, Crudu, Valeriu, Gotuzzo, Eduardo, Hapeela, Nchimunya, Hoffmann, Harald, Hoogland, Christine, Kohl, Thomas A, Kranzer, Katharina, Mantsoki, Anna, Maurer, Florian P, Nicol, Mark P, Noroc, Ecaterina, Plesnik, Sara, Rodwell, Timothy, Ruhwald, Morten, Savidge, Theresa, Salfinger, Max, Streicher, Elizabeth, Tukvadze, Nestani, Warren, Robin, Zemanay, Widaad, Zurek, Anna, Niemann, Stefan, and Denkinger, Claudia M

Published
2022
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7. Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis

Author

Merker, Matthias, Rasigade, Jean-Philippe, Barbier, Maxime, Cox, Helen, Feuerriegel, Silke, Kohl, Thomas A., Shitikov, Egor, Klaos, Kadri, Gaudin, Cyril, Antoine, Rudy, Diel, Roland, Borrell, Sonia, Gagneux, Sebastien, Nikolayevskyy, Vladyslav, Andres, Sönke, Crudu, Valeriu, Supply, Philip, Niemann, Stefan, and Wirth, Thierry

Published
2022
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9. Genomic diversity and clinical relevance ofMycobacterium simiae

Author

Wetzstein, Nils, primary, Diricks, Margo, additional, Andres, Sönke, additional, Kuhns, Martin, additional, Marschall, Lisa, additional, Biciusca, Teodora, additional, Smaczny, Christina, additional, Friesen, Inna, additional, Niemann, Stefan, additional, and Wichelhaus, Thomas A., additional

Published
2024
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10. Molecular determinants of multidrug-resistant tuberculosis in Sierra Leone

Author

Blankson, Harriet N. A., primary, Kamara, Rashidatu Fouad, additional, Barilar, Ivan, additional, Andres, Sönke, additional, Conteh, Ousman S., additional, Dallenga, Tobias, additional, Foray, Lynda, additional, Maurer, Florian, additional, Kranzer, Katharina, additional, Utpatel, Christian, additional, and Niemann, Stefan, additional

Published
2024
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12. A Single-Run HPLC–MS Multiplex Assay for Therapeutic Drug Monitoring of Relevant First- and Second-Line Antibiotics in the Treatment of Drug-Resistant Tuberculosis

Author

Köhler, Niklas, primary, Karaköse, Hande, additional, Grobbel, Hans-Peter, additional, Hillemann, Doris, additional, Andres, Sönke, additional, König, Christina, additional, Kalsdorf, Barbara, additional, Brehm, Thomas Theo, additional, Böttcher, Laura, additional, Friesen, Inna, additional, Hoffmann, Harald, additional, Strelec, Dražen, additional, Schaub, Dagmar, additional, Peloquin, Charles A., additional, Schmiedel, Stefan, additional, Decosterd, Laurent A., additional, Choong, Eva, additional, Wicha, Sebastian G., additional, Aarnoutse, Rob E., additional, Lange, Christoph, additional, and Sánchez Carballo, Patricia M., additional

Published
2023
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17. Genetic sequencing for surveillance of drug resistance in tuberculosis in highly endemic countries: a multi-country population-based surveillance study

Author

Zignol, Matteo, Cabibbe, Andrea Maurizio, Dean, Anna S, Glaziou, Philippe, Alikhanova, Natavan, Ama, Cecilia, Andres, Sönke, Barbova, Anna, Borbe-Reyes, Angeli, Chin, Daniel P, Cirillo, Daniela Maria, Colvin, Charlotte, Dadu, Andrei, Dreyer, Andries, Driesen, Michèle, Gilpin, Christopher, Hasan, Rumina, Hasan, Zahra, Hoffner, Sven, Hussain, Alamdar, Ismail, Nazir, Kamal, S M Mostofa, Khanzada, Faisal Masood, Kimerling, Michael, Kohl, Thomas Andreas, Mansjö, Mikael, Miotto, Paolo, Mukadi, Ya Diul, Mvusi, Lindiwe, Niemann, Stefan, Omar, Shaheed V, Rigouts, Leen, Schito, Marco, Sela, Ivita, Seyfaddinova, Mehriban, Skenders, Girts, Skrahina, Alena, Tahseen, Sabira, Wells, William A, Zhurilo, Alexander, Weyer, Karin, Floyd, Katherine, and Raviglione, Mario C

Published
2018
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18. MDR M. tuberculosis outbreak clone in Eswatini missed by Xpert has elevated bedaquiline resistance dated to the pre-treatment era

Author

Beckert, Patrick, Sanchez-Padilla, Elisabeth, Merker, Matthias, Dreyer, Viola, Kohl, Thomas A., Utpatel, Christian, Köser, Claudio U., Barilar, Ivan, Ismail, Nazir, Omar, Shaheed Vally, Klopper, Marisa, Warren, Robin M., Hoffmann, Harald, Maphalala, Gugu, Ardizzoni, Elisa, de Jong, Bouke C., Kerschberger, Bernhard, Schramm, Birgit, Andres, Sönke, Kranzer, Katharina, Maurer, Florian P., Bonnet, Maryline, and Niemann, Stefan

Published
2020
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20. Population-based resistance of Mycobacterium tuberculosis isolates to pyrazinamide and fluoroquinolones: results from a multicountry surveillance project

Author

Zignol, Matteo, Dean, Anna S, Alikhanova, Natavan, Andres, Sönke, Cabibbe, Andrea Maurizio, Cirillo, Daniela Maria, Dadu, Andrei, Dreyer, Andries, Driesen, Michèle, Gilpin, Christopher, Hasan, Rumina, Hasan, Zahra, Hoffner, Sven, Husain, Ashaque, Hussain, Alamdar, Ismail, Nazir, Kamal, Mostofa, Mansjö, Mikael, Mvusi, Lindiwe, Niemann, Stefan, Omar, Shaheed V, Qadeer, Ejaz, Rigouts, Leen, Ruesch-Gerdes, Sabine, Schito, Marco, Seyfaddinova, Mehriban, Skrahina, Alena, Tahseen, Sabira, Wells, William A, Mukadi, Ya Diul, Kimerling, Michael, Floyd, Katherine, Weyer, Karin, and Raviglione, Mario C

Published
2016
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21. Pretomanid-resistant tuberculosis

Author

Koehler, Niklas, primary, Andres, Sönke, additional, Merker, Matthias, additional, Dreyer, Viola, additional, John, Agnieszka, additional, Kuhns, Martin, additional, Krieger, David, additional, Choong, Eva, additional, Verougstraete, Nick, additional, zur Wiesch, Pia Abel, additional, Wicha, Sebastian G., additional, König, Christina, additional, Kalsdorf, Barbara, additional, Sanchez Carballo, Patricia M., additional, Schaub, Dagmar, additional, Werngren, Jim, additional, Schön, Thomas, additional, Peloquin, Charles A., additional, Schönfeld, Nicolas, additional, Verstraete, Alain G., additional, Decosterd, Laurent A., additional, Aarnoutse, Rob, additional, Niemann, Stefan, additional, Maurer, Florian P., additional, and Lange, Christoph, additional

Published
2023
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22. Molecular Epidemiology of Mycobacterium abscessus Isolates Recovered from German Cystic Fibrosis Patients

Author

Wetzstein, Nils, primary, Diricks, Margo, additional, Kohl, Thomas A., additional, Wichelhaus, Thomas A., additional, Andres, Sönke, additional, Paulowski, Laura, additional, Schwarz, Carsten, additional, Lewin, Astrid, additional, Kehrmann, Jan, additional, Kahl, Barbara C., additional, Dichtl, Karl, additional, Hügel, Christian, additional, Eickmeier, Olaf, additional, Smaczny, Christina, additional, Schmidt, Annika, additional, Zimmermann, Stefan, additional, Nährlich, Lutz, additional, Hafkemeyer, Sylvia, additional, Niemann, Stefan, additional, Maurer, Florian P., additional, and Hogardt, Michael, additional

Published
2022
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23. Prevalence and Molecular Characterization of Mycobacterium bovis in Slaughtered Cattle Carcasses in Burkina Faso; West Africa

Author

Kanyala, Estelle, primary, Shuaib, Yassir Adam, additional, Schwarz, Norbert Georg, additional, Andres, Sönke, additional, Richter, Elvira, additional, Sawadogo, Bernard, additional, Sawadogo, Mamadou, additional, Germaine, Minoungou, additional, Lassina, Ouattara, additional, Poppert, Sven, additional, and Frickmann, Hagen, additional

Published
2022
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24. Molecular Epidemiology of Mycobacterium abscessus Isolates Recovered from German Cystic Fibrosis Patients

Author

Wetzstein, Nils, Diricks, Margo, Kohl, Thomas A., Wichelhaus, Thomas A., Andres, Sönke, Paulowski, Laura, Schwarz, Carsten, Lewin, Astrid, Kehrmann, Jan, Kahl, Barbara C., Dichtl, Karl, Hügel, Christian, Eickmeier, Olaf, Smaczny, Christina, Schmidt, Annika, Zimmermann, Stefan, Nährlich, Lutz, Hafkemeyer, Sylvia, Niemann, Stefan, Maurer, Florian P., Hogardt, Michael, and Doucet-Populaire, Florence Claude

Subjects
Medizin
Abstract

Infections due to Mycobacterium abscessus are a major cause of mortality and morbidity in cystic fibrosis (CF) patients. Furthermore, M. abscessus has been suspected to be involved in person-to-person transmissions. In 2016, dominant global clonal complexes (DCCs) that occur worldwide among CF patients have been described. To elucidate the epidemiological situation of M. abscessus among CF patients in Germany and to put these data into a global context, we performed whole-genome sequencing of a set of 154 M. abscessus isolates from 123 German patients treated in 14 CF centers. We used MTBseq pipeline to identify clusters of closely related isolates and correlate those with global findings. Genotypic drug susceptibility for macrolides and aminoglycosides was assessed by characterization of the erm(41), rrl, and rrs genes. By this approach, we could identify representatives of all major DCCs (Absc 1, Absc 2, and Mass 1) in our cohort. Intrapersonal isolates showed higher genetic relatedness than interpersonal isolates (median 3 SNPs versus 16 SNPs; P < 0.001). We further identified four clusters with German patients from same centers clustering with less than 25 SNPs distance (range 3 to 18 SNPs) but did not find any hint for in-hospital person-to-person transmission. This is the largest study investigating phylogenetic relations of M. abscessus isolates in Germany. We identified representatives of all reported DCCs but evidence for nosocomial transmission remained inconclusive. Thus, the occurrence of genetically closely related isolates of M. abscessus has to be interpreted with care, as a direct interhuman transmission cannot be directly deduced. IMPORTANCE Mycobacterium abscessus is a major respiratory pathogen in cystic fibrosis (CF) patients. Recently it has been shown that dominant global clonal complexes (DCCs) have spread worldwide among CF patients. This study investigated the epidemiological situation of M. abscessus among CF patients in Germany by performing whole-genome sequencing (WGS) of a set of 154 M. abscessus from 123 German patients treated in 14 CF centers. This is the largest study investigating the phylogenetic relationship of M. abscessus CF isolates in Germany. CA extern

Published
2022

25. Prevalence and Molecular Characterization of Mycobacterium bovis in Slaughtered Cattle Carcasses in Burkina Faso; West Africa

Author

Kanyala, Estelle, Shuaib, Yassir Adam, Schwarz, Norbert G., Andres, Sönke, Richter, Elvira, Sawadogo, Bernard, Sawadogo, Mamadou, Germaine, Minoungou, Lassina, Ouattara, Poppert, Sven, and Frickmann, Hagen

Subjects
Burkina Faso, cattle, tuberculosis, Mycobacterium bovis
Abstract

This cross-sectional study was conducted at the slaughterhouses/slabs of Oudalan and Ouagadougou in Burkina Faso, between August and September 2013. It aimed at determining the prevalence of bovine tuberculosis (bTB) suggestive lesions in slaughtered cattle carcasses and to identify and characterize the mycobacteria isolated from these lesions. A thorough postmortem examination was conducted on carcasses of a total of 2165 randomly selected cattle. The overall prevalence of bTB suggestive lesions was 2.7% (58/2165; 95% CI 2.1–3.5%). Due to the low number of positive samples, data were descriptively presented. The lesions were either observed localized in one or a few organs or generalized (i.e., miliary bTB) in 96.6% (n = 57) and 3.4% (n = 2), respectively. The identified mycobacteria were M. bovis (44.4%, n = 20), M. fortuitum (8.9%, n = 4), M. elephantis (6.7%, n = 3), M. brumae (4.4%, n = 2), M. avium (2.2%, n = 1), M. asiaticum (2.2%, n = 1), M. terrae (2.2%, n = 1), and unknown non-tuberculous mycobacteria (NTM) (11.1%, n = 5). Moreover, eight mixed cultures with more than one Mycobacterium species growing were also observed, of which three were M. bovis and M. fortuitum and three were M. bovis and M. elephantis. In conclusion, M. bovis is the predominant causative agent of mycobacterial infections in the study area. Our study has identified a base to broaden the epidemiological knowledge on zoonotic transmission of mycobacteria in Burkina Faso by future studies investigating further samples from humans and animals, including wild animals employing molecular techniques.

Published
2022

26. Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment

Author

Antimycobacterial Susceptibility Testing Group, Georghiou, Sophia B., Rodwell, Timothy C., Korobitsyn, Alexei, Abbadi, Said H., Ajbani, Kanchan, Alffenaar, Jan-Willem, Alland, David, Alvarez, Nataly, Andres, Sönke, Ardizzoni, Elisa, Aubry, Alexandra, Baldan, Rossella, Ballif, Marie, Barilar, Ivan, Böttger, Erik C., Chakravorty, Soumitesh, Claxton, Pauline M., Cirillo, Daniela M., Comas, Iñaki, Coulter, Chris, Denkinger, Claudia M., Derendinger, Brigitta, Desmond, Edward P., Steenwinkel, Jurriaan E. M. de, Dheda, Keertan, Diacon, Andreas H., Dolinger, David L., Dooley, Kelly E., Egger, Matthias, Ehsani, Soudeh, Farhat, Maha R., Fattorini, Lanfranco, Finci, Iris, Fournier Le Ray, Laure, Furió, Victoria, Groenheit, Ramona, Gumbo, Tawanda, Heysell, Scott K., Hillemann, Doris, Hoffmann, Harald, Hsueh, Po-Ren, Hu, Yi, Huang, Hairong, Hussain, Alamdar, Ismail, Farzana, Izumi, Kiyohiko, Jagielski, Tomasz, Johnson, John L., Kambli, Priti, Kaniga, Koné, Karunaratne, G. H. R. Eranga, Sharma, Meenu Kaushal, Keller, Peter M., Kelly, Ellis C., Kholina, Margarita, Kohli, Mikashmi, Kranzer, Katharina, Laurenson, Ian F., Limberis, Jason, Lin, S-Y. Grace, Liu, Yongge, López-Gavín, Alexandre, Lyander, Anna, Machado, Diana, Martínez, Elena, Masood, Faisal, Mitarai, Satoshi, Mvelase, Nomonde R., Niemann, Stefan, Nikolayevskyy, Vladyslav, Maurer, Florian P., Merker, Matthias, Miotto, Paolo, Omar, Shaheed V., Otto-Knapp, Ralf, Palaci, Moisés, Palacios Gutiérrez, Juan José, Peacock, Sharon J., Peloquin, Charles A., Perera, Jennifer, Pierre-Audigier, Catherine, Pholwat, Suporn, Posey, James E., Prammananan, Therdsak, Rigouts, Leen, Robledo, Jaime, Rockwood, Neesha, Rodrigues, Camilla, Salfinger, Max, Schechter, Marcos C., Seifert, Marva, Sengstake, Sarah, Shinnick, Thomas, Shubladze, Natalia, Sintchenko, Vitali, Sirgel, Frederick, Somasundaram, Sulochana, Sterling, Timothy R., Spitaleri, Andrea, Streicher, Elizabeth, Supply, Philip, Svensson, Erik, Tagliani, Elisa, Tahseen, Sabira, Takaki, Akiko, Theron, Grant, Torrea, Gabriela, Van Deun, Armand, van Ingen, Jakko, Van Rie, Annelies, van Soolingen, Dick, Vargas Jr, Roger, Venter, Amour, Veziris, Nicolas, Villellas, Cristina, Viveiros, Miguel, Warren, Robin, Wen, Shu'an, Werngren, Jim, Wilkinson, Robert J., Yang, Caie, Yılmaz, F. Ferda, Zhang, Tingting, Zimenkov, Danila, Ismail, Nazir, Köser, Claudio U., Schön, Thomas, University of Zurich, Antimycobacterial Susceptibility Testing Group, Department of Genetics [Cambridge], University of Cambridge [UK] (CAM), Centre d'Immunologie et des Maladies Infectieuses (CIMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre Médical de l'Institut Pasteur (CMIP), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Institut de médecine et d'épidémiologie appliquée [AP-HP Hôpital Bichat-Claude Bernard] (IMEA), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), As current or former employees or consultants for FIND, the work of R.B. Baldan, I. Comas, C.M. Denkinger, D.L. Dolinger, S.B. Georghiou, C.U. Köser and T.C. Rodwell on the systematic reviews, including this viewpoint, was supported by Unitaid (grant 2019-32-FIND MDR), BMGF (grant OPP1105925), the German Federal Ministry of Education and Research through KfW, the Dutch Ministry of Foreign Affairs, the Australian Department of Foreign Affairs and Trade, and UK aid from the British people. N. Alvarez and J. Robledo are funded by MinCiencias, Colombia (number 221389666216 CT-783-2018). A. Aubry and N. Veziris work at the Centre National de Reference des Mycobactéries, which receives an annual grant from Santé Publique France and have received research grants from Janssen for studies on bedaquiline. P. Claxton and I.F. Laurenson are funded through National Services Scotland. I. Comas was supported by PID2019-104477RB-I00 from the Spanish Science Ministry and by ERC (CoG 101001038). M. Egger is supported by the Swiss National Science Foundation (grant number 320030_153442 and 189498) and the US National Institutes of Health, National Institute of Allergy and Infectious Diseases, the Eunice Kennedy Shriver National Institute of Child Health and Human Development, the National Cancer Institute, the National Institute of Mental Health, the National Institute on Drug Abuse, the National Heart, Lung, and Blood Institute, the National Institute on Alcohol Abuse and Alcoholism, the National Institute of Diabetes and Digestive and Kidney Diseases, the Fogarty International Center, and the National Library of Medicine: Asia-Pacific, U01AI069907, CCASAnet, U01AI069923, Central Africa, U01AI096299, East Africa, U01AI069911, NA-ACCORD, U01AI069918, Southern Africa, U01AI069924, West Africa, U01AI069919. M.R. Farhat is supported by NIH NIAID R01AI155765. S.K. Heysell was funded by NIH NIAID grants R01 AI137080 and U01 AI150508. T. Jagielski was supported by a DAINA grant (number 2017/27/L/NZ6/03279) from the National Science Centre, Poland. J.L. Johnson was supported by contracts NO1-AI95383 and NO1-AI-70022 of the US National Institutes of Health. P.M. Keller was supported by Innosuisse 36198.1 IP-LS. C.U. Köser is a research associate at Wolfson College and visiting scientist at the Department of Genetics, University of Cambridge. The Federal Government of Germany supported C.U. Köser as part of his work for the European Laboratory Initiative, WHO Regional Office for Europe. C.U. Köser was further supported by the Royal Society of Tropical Medicine and Hygiene and the National Institute for Health Research Cambridge Biomedical Research Centre and received an observership by the European Society of Clinical Microbiology and Infectious Diseases to the EUCAST Development Laboratory for Bacteria (Växjö, Sweden), hosted by Gunnar Kahlmeter and Erika Matuschek. D. Machado and M. Viveiros are funded in part by Fundação para a Ciência e a Tecnologia, Portugal (PTDC/BIA-MIC/30692/2017, UID/Multi/04413/2020 and DL57/ CEECIND/0256/2017). S. Niemann is supported by the German Center for Infection Research, Excellenz Cluster Precision Medicine in Chronic Inflammation EXC 2167, Leibniz Science Campus Evolutionary Medicine of the LUNG (EvoLUNG). S.V. Omar has received funding to prepare and provide training for Janssen Pharmaceutica activities. L. Rigouts is supported by the Belgian Directorate General for Development. T.C. Rodwell was additionally funded in part by FIND and NIH NIAD, grants: P30 AI036214 and R21 AI135756. T. Schön is funded by the Swedish Heart and Lung Foundation and the Swedish Research Council. T.R. Sterling has received funding from the US National Institutes of Health and the Centers for Disease Control and Prevention. G. Theron and R. Warren are supported by baseline funding from the South African Medical Research Council. R.J. Wilkinson receives funding from the Wellcome Trust (203135) and from the Francis Crick Institute, which is supported by Cancer Research UK (FC0010218), UKRI (FC0010218) and the Wellcome Trust (FC0010218), Ministerio de Ciencia e Innovación (España), European Research Council, Comas, Iñaki, Comas, Iñaki [0000-0001-5504-9408], Antimycobacterial Susceptibility T, and Wellcome Trust

Subjects
[SDV]Life Sciences [q-bio], Respiratory System, Drug Resistance, Antitubercular Agents, Infektionsmedicin, Medical and Health Sciences, Drug Resistance, Multiple, Bacterial, Tuberculosis, Multidrug-Resistant, 11 Medical and Health Sciences, Human Biology & Physiology, MESH: Microbial Sensitivity Tests, 10179 Institute of Medical Microbiology, Bacterial, Multidrug-Resistant, Infectious Diseases, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Infection, Life Sciences & Biomedicine, Multiple, Model organisms, Pulmonary and Respiratory Medicine, Infectious Medicine, Immunology, Infectious Disease, 610 Medicine & health, Microbial Sensitivity Tests, Vaccine Related, Rare Diseases, Clinical Research, Biodefense, MESH: Drug Resistance, Bacterial, Drug Resistance, Bacterial, Tuberculosis, Humans, Science & Technology, MESH: Humans, Antimycobacterial Susceptibility Testing Group, FOS: Clinical medicine, Prevention, MESH: Drug Resistance, Multiple, Bacterial, Mycobacterium tuberculosis, Eucast, MESH: Antitubercular Agents, lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4], Orphan Drug, Emerging Infectious Diseases, Good Health and Well Being, 2740 Pulmonary and Respiratory Medicine, 570 Life sciences, biology, Human medicine, Antimicrobial Resistance, Model
Abstract

11 páginas, 2 figuras, 1 tabla, Inappropriately high breakpoints have resulted in systematic false-susceptible AST results to anti-TB drugs. MIC, PK/PD and clinical outcome data should be combined when setting breakpoints to minimise the emergence and spread of antimicrobial resistance., I. Comas was supported by PID2019-104477RB-I00 from the Spanish Science Ministry and by ERC (CoG 101001038)

Published
2022

28. Ancient and recent differences in the intrinsic susceptibility of Mycobacterium tuberculosis complex to pretomanid

Author

Bateson, Anna, primary, Ortiz Canseco, Julio, additional, McHugh, Timothy D., additional, Witney, Adam A., additional, Feuerriegel, Silke, additional, Merker, Matthias, additional, Kohl, Thomas A., additional, Utpatel, Christian, additional, Niemann, Stefan, additional, Andres, Sönke, additional, Kranzer, Katharina, additional, Maurer, Florian P, additional, Ghodousi, Arash, additional, Borroni, Emanuele, additional, Cirillo, Daniela Maria, additional, Wijkander, Maria, additional, Toro, Juan C., additional, Groenheit, Ramona, additional, Werngren, Jim, additional, Machado, Diana, additional, Viveiros, Miguel, additional, Warren, Robin M., additional, Sirgel, Frederick, additional, Dippenaar, Anzaan, additional, Köser, Claudio U., additional, Sun, Eugene, additional, and Timm, Juliano, additional

Published
2022
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29. Emergence of bedaquiline resistance in a high tuberculosis burden country

Author

Chesov, Elena, primary, Chesov, Dumitru, additional, Maurer, Florian P., additional, Andres, Sönke, additional, Utpatel, Christian, additional, Barilar, Ivan, additional, Donica, Ana, additional, Reimann, Maja, additional, Niemann, Stefan, additional, Lange, Christoph, additional, Crudu, Valeriu, additional, Heyckendorf, Jan, additional, and Merker, Matthias, additional

Published
2021
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30. Late Breaking Abstract - Therapeutic drug monitoring in a patient with very advanced XDR-TB

Author

Köhler, Niklas, primary, Aarnoutse, Rob, additional, Abel Zur Wiesch, Pia, additional, Andres, Sönke, additional, Bonomo, Robert A., additional, Choong, Eva, additional, Clarelli, Fabrizio, additional, Decosterd, Laurent, additional, Dinardo, Andrew, additional, Grobbel, Hans-Peter, additional, Heyckendorf, Jan, additional, Hillemann, Doris, additional, Hoffmann, Harald, additional, Kalsdorf, Barbara, additional, Karaköse, Hande, additional, Knaack, Wiebke, additional, König, Christina, additional, Martinecz, Antal, additional, Maurer, Florian, additional, Merker, Matthias, additional, Niemann, Stefan, additional, Nowak, Markus, additional, Peloquin, Charles A., additional, Sanchez Carballo, Patricia, additional, Schaub, Dagmar, additional, Schön, Thomas, additional, Schwudke, Dominik, additional, Teulen, Marga, additional, Verougstraete, Nick, additional, Verstraete, Alain, additional, Waldow, Franziska, additional, Werngren, Jim, additional, Wicha, Sebastian Georg, additional, and Lange, Christoph, additional

Published
2021
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31. Schnelle Resistenzvorhersage gegenüber TB-Medikamenten der Standard- und Nicht-Standardtherapie: Methodenevaluation zur gezielten Genomsequenzierung aus klinischem Primärmaterial

Author

Feuerriegel, Silke, Dreyer, Viola, Andres, Sönke, Kohl, Thomas A., Utpate, Christian, Heyckendorf, Jan, Maurer, Florian P., and Niemann, Stefan

Subjects
Resistenz, ddc:610, Genomsequenzierung, 610 Medizin und Gesundheit, TB-Resistenztypen, Antituberkulotika, Tuberkulose
Abstract

Multi- und extensiv-resistente Mycobacterium tuberculosis Komplex-Stämme stellen weltweit eine zunehmende Herausforderung für die Kontrolle der Tuberkulose dar. Eine umfangreiche Empfindlichkeitstestung ist essenziell für den schnellen Beginn einer effektiven Therapie. Eine phänotypische, kul¬turbasierte Empfindlichkeitstestung benötigt aller¬dings mehrere Wochen und ist nicht ausreichend standardisiert. Wie das Epidemiologische Bulletin in der Ausgabe 11/2021 ausführt, wurde nun mit einer neuen Methode der sequenzbasierten Mutationsanalyse, dem sogenannten targeted Next Generation Sequencing (tNGS) ein robustes Verfahren zur schnellen Resis¬tenztestung in der TB-Diagnostik entwickelt.

Published
2021

32. Additional file 6 of Secretome characterization of clinical isolates from the Mycobacterium abscessus complex provides insight into antigenic differences

Author

Cornejo-Granados, Fernanda, Kohl, Thomas A., Sotomayor, Flor Vásquez, Andres, Sönke, Hernández-Pando, Rogelio, Hurtado-Ramirez, Juan Manuel, Utpatel, Christian, Niemann, Stefan, Maurer, Florian P., and Ochoa-Leyva, Adrian

Abstract

Additional file 6: Figure S2. GO enrichment analysis of enzymes for M. abscessus ATCC19977. Percentage of sequences annotated with each GO term for the secreted proteins (blue) and the complete proteins in the genome (red).

Published
2021
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33. Additional file 4 of Secretome characterization of clinical isolates from the Mycobacterium abscessus complex provides insight into antigenic differences

Author

Cornejo-Granados, Fernanda, Kohl, Thomas A., Sotomayor, Flor Vásquez, Andres, Sönke, Hernández-Pando, Rogelio, Hurtado-Ramirez, Juan Manuel, Utpatel, Christian, Niemann, Stefan, Maurer, Florian P., and Ochoa-Leyva, Adrian

Abstract

Additional file 4: Table S3. Comparison of the core secretome of each subspecies vs NCBI genomes.

Published
2021
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34. Additional file 3 of Secretome characterization of clinical isolates from the Mycobacterium abscessus complex provides insight into antigenic differences

Author

Cornejo-Granados, Fernanda, Kohl, Thomas A., Sotomayor, Flor Vásquez, Andres, Sönke, Hernández-Pando, Rogelio, Hurtado-Ramirez, Juan Manuel, Utpatel, Christian, Niemann, Stefan, Maurer, Florian P., and Ochoa-Leyva, Adrian

Abstract

Additional file 3: Table S2. Statistic data of the de novo assemblies for the sequenced isolates.

Published
2021
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35. Additional file 5 of Secretome characterization of clinical isolates from the Mycobacterium abscessus complex provides insight into antigenic differences

Author

Cornejo-Granados, Fernanda, Kohl, Thomas A., Sotomayor, Flor Vásquez, Andres, Sönke, Hernández-Pando, Rogelio, Hurtado-Ramirez, Juan Manuel, Utpatel, Christian, Niemann, Stefan, Maurer, Florian P., and Ochoa-Leyva, Adrian

Abstract

Additional file 5: Table S4. AAR values for random constructed secretomes of the rough and smooth phenotypes.

Published
2021
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36. Additional file 2 of Secretome characterization of clinical isolates from the Mycobacterium abscessus complex provides insight into antigenic differences

Author

Cornejo-Granados, Fernanda, Kohl, Thomas A., Sotomayor, Flor Vásquez, Andres, Sönke, Hernández-Pando, Rogelio, Hurtado-Ramirez, Juan Manuel, Utpatel, Christian, Niemann, Stefan, Maurer, Florian P., and Ochoa-Leyva, Adrian

Abstract

Additional file 2: Figure S1. Bioinformatics pipeline to indentify and analyze the secreted proteins of M. abscessus.

Published
2021
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37. Additional file 1 of Secretome characterization of clinical isolates from the Mycobacterium abscessus complex provides insight into antigenic differences

Author

Cornejo-Granados, Fernanda, Kohl, Thomas A., Sotomayor, Flor Vásquez, Andres, Sönke, Hernández-Pando, Rogelio, Hurtado-Ramirez, Juan Manuel, Utpatel, Christian, Niemann, Stefan, Maurer, Florian P., and Ochoa-Leyva, Adrian

Subjects
bacteria, bacterial infections and mycoses
Abstract

Additional file 1: Table S1. Complete metadata of the 15 clinical isolates of M. abscessus genomes sequenced.

Published
2021
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38. Additional file 7 of Secretome characterization of clinical isolates from the Mycobacterium abscessus complex provides insight into antigenic differences

Author

Cornejo-Granados, Fernanda, Kohl, Thomas A., Sotomayor, Flor Vásquez, Andres, Sönke, Hernández-Pando, Rogelio, Hurtado-Ramirez, Juan Manuel, Utpatel, Christian, Niemann, Stefan, Maurer, Florian P., and Ochoa-Leyva, Adrian

Subjects
bacteria, bacterial infections and mycoses
Abstract

Additional file 7: Table S5. List of 222 M. abscessus proteins with homologues in M. tuberculosis H37Rv and with previous experimental support for secretion according to Cornejo-Granados et al. [19].

Published
2021
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40. Design of Multidrug-Resistant Tuberculosis Treatment Regimens Based on DNA Sequencing

Author

Grobbel, Hans-Peter, primary, Merker, Matthias, additional, Köhler, Niklas, additional, Andres, Sönke, additional, Hoffmann, Harald, additional, Heyckendorf, Jan, additional, Reimann, Maja, additional, Barilar, Ivan, additional, Dreyer, Viola, additional, Hillemann, Doris, additional, Kalsdorf, Barbara, additional, Kohl, Thomas A, additional, Sanchez Carballo, Patricia, additional, Schaub, Dagmar, additional, Todt, Katharina, additional, Utpatel, Christian, additional, Maurer, Florian P, additional, Lange, Christoph, additional, and Niemann, Stefan, additional

Published
2021
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41. Mycobacterium tuberculosis Complex Lineage 3 as Causative Agent of Pulmonary Tuberculosis, Eastern Sudan1

Author

Shuaib, Yassir A, Khalil, Eltahir AG, Wieler, Lothar H, Schaible, Ulrich E, Bakheit, Mohammed A, Mohamed-Noor, Saad E, Abdalla, Mohamed A, Kerubo, Glennah, Andres, Sönke, Hillemann, Doris, Richter, Elvira, Kranzer, Katharina, Niemann, Stefan, and Merker, Matthias

Abstract

Pathogen-based factors associated with tuberculosis (TB) in eastern Sudan are not well defined. We investigated genetic diversity, drug resistance, and possible transmission clusters of Mycobacterium tuberculosis complex (MTBC) strains by using a genomic epidemiology approach. We collected 383 sputum specimens at 3 hospitals in 2014 and 2016 from patients with symptoms suggestive of TB; of these, 171 grew MTBC strains. Whole-genome sequencing could be performed on 166 MTBC strains; phylogenetic classification revealed that most (73.4%; n = 122) belonged to lineage 3 (L3). Genome-based cluster analysis showed that 76 strains (45.9%) were grouped into 29 molecular clusters, comprising 2-8 strains/patients. Of the strains investigated, 9.0% (15/166) were multidrug resistant (MDR); 10 MDR MTBC strains were linked to 1 large MDR transmission network. Our findings indicate that L3 strains are the main causative agent of TB in eastern Sudan; MDR TB is caused mainly by transmission of MDR L3 strains.

Published
2020

42. Mycobacterium tuberculosis Complex Lineage 3 as Causative Agent of Pulmonary Tuberculosis, Eastern Sudan

Author

Shuaib, Yassir A., Khalil, Eltahir A.G., Wieler, Lothar H., Schaible, Ulrich E., Bakheit, Mohammed A., Mohamed-Noor, Saad E., Abdalla, Mohamed A., Kerubo, Glennah, Andres, Sönke, Hillemann, Doris, Richter, Elvira, Kranzer, Katharina, and Merker, Matthias

Subjects
Sudan, whole-genome sequencing, MDR, Mycobacterium tuberculosis complex, transmission, ddc:610, antimicrobial resistance, MDR TB, bacteria, 610 Medizin und Gesundheit, lineage 3, tuberculosis and other mycobacteria
Abstract

Pathogen-based factors associated with tuberculosis (TB) in eastern Sudan are not well defined. We investigated genetic diversity, drug resistance, and possible transmission clusters of Mycobacterium tuberculosis complex (MTBC) strains by using a genomic epidemiology approach. We collected 383 sputum specimens at 3 hospitals in 2014 and 2016 from patients with symptoms suggestive of TB; of these, 171 grew MTBC strains. Whole-genome sequencing could be performed on 166 MTBC strains; phylogenetic classification revealed that most (73.4%; n = 122) belonged to lineage 3 (L3). Genome-based cluster analysis showed that 76 strains (45.9%) were grouped into 29 molecular clusters, comprising 2–8 strains/patients. Of the strains investigated, 9.0% (15/166) were multidrug resistant (MDR); 10 MDR MTBC strains were linked to 1 large MDR transmission network. Our findings indicate that L3 strains are the main causative agent of TB in eastern Sudan; MDR TB is caused mainly by transmission of MDR L3 strains.

Published
2020

43. Additional file 2 of MDR M. tuberculosis outbreak clone in Eswatini missed by Xpert has elevated bedaquiline resistance dated to the pre-treatment era

Author

Beckert, Patrick, Sanchez-Padilla, Elisabeth, Merker, Matthias, Dreyer, Viola, Kohl, Thomas A., Utpatel, Christian, Köser, Claudio U., Barilar, Ivan, Ismail, Nazir, Shaheed Vally Omar, Klopper, Marisa, Warren, Robin M., Hoffmann, Harald, Gugu Maphalala, Ardizzoni, Elisa, Jong, Bouke C. De, Kerschberger, Bernhard, Schramm, Birgit, Andres, Sönke, Kranzer, Katharina, Maurer, Florian P., Bonnet, Maryline, and Niemann, Stefan

Abstract

Additional file 2. Supplemental methods and description of resistance mutations.

Published
2020
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44. Additional file 3 of MDR M. tuberculosis outbreak clone in Eswatini missed by Xpert has elevated bedaquiline resistance dated to the pre-treatment era

Author

Beckert, Patrick, Sanchez-Padilla, Elisabeth, Merker, Matthias, Dreyer, Viola, Kohl, Thomas A., Utpatel, Christian, Köser, Claudio U., Barilar, Ivan, Ismail, Nazir, Shaheed Vally Omar, Klopper, Marisa, Warren, Robin M., Hoffmann, Harald, Gugu Maphalala, Ardizzoni, Elisa, Jong, Bouke C. De, Kerschberger, Bernhard, Schramm, Birgit, Andres, Sönke, Kranzer, Katharina, Maurer, Florian P., Bonnet, Maryline, and Niemann, Stefan

Abstract

Additional file 3: Fig. S1. Phylogenetic diversity and drug susceptibility of the 412 M. tuberculosis complex isolates from Eswatini. Fig. S2. Lineage distribution across Eswatini. Fig. S3. Isolates selected for further whole-genome sequencing analysis.

Published
2020
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45. Antimicrobial Susceptibility and Phylogenetic Relations in a German Cohort Infected with Mycobacterium abscessus

Author

Wetzstein, Nils, primary, Kohl, Thomas A., additional, Schultze, Tilman G., additional, Andres, Sönke, additional, Bellinghausen, Carla, additional, Hügel, Christian, additional, Kempf, Volkhard A. J., additional, Lehn, Annette, additional, Hogardt, Michael, additional, Serve, Hubert, additional, Vehreschild, Maria J. G. T., additional, Wolf, Timo, additional, Niemann, Stefan, additional, Maurer, Florian P., additional, and Wichelhaus, Thomas A., additional

Published
2020
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47. In silico secretome characterization of clinical Mycobacterium abscessus isolates provides insights into antigenic differences

Author

Cornejo-Granados, Fernanda, primary, Kohl, Thomas A., additional, Sotomayor, Flor Vásquez, additional, Andres, Sönke, additional, Hernández-Pando, Rogelio, additional, Hurtado-Ramírez, Juan Manuel, additional, Utpatel, Christian, additional, Niemann, Stefan, additional, Maurer, Florian P., additional, and Ochoa-Leyva, Adrian, additional

Published
2020
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49. Rapid genomic first- and second-line drug resistance prediction from clinical Mycobacterium tuberculosis specimens using Deeplex-MycTB

Author

Feuerriegel, Silke, primary, Kohl, Thomas A., additional, Utpatel, Christian, additional, Andres, Sönke, additional, Maurer, Florian P., additional, Heyckendorf, Jan, additional, Jouet, Agathe, additional, Badalato, Nelly, additional, Foray, Lynda, additional, Fouad Kamara, Rashidatu, additional, Conteh, Osman S., additional, Supply, Philip, additional, and Niemann, Stefan, additional

Published
2020
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50. Bedaquiline-Resistant Tuberculosis: Dark Clouds on the Horizon

Author

Andres, Sönke, primary, Merker, Matthias, additional, Heyckendorf, Jan, additional, Kalsdorf, Barbara, additional, Rumetshofer, Rudolf, additional, Indra, Alexander, additional, Hofmann-Thiel, Sabine, additional, Hoffmann, Harald, additional, Lange, Christoph, additional, Niemann, Stefan, additional, and Maurer, Florian P., additional

Published
2020
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