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1. 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

Author

Fowler, Philip W, Wright, Carla, Spiers, Helen, Zhu, Tingting, Baeten, Elisabeth ML, Hoosdally, Sarah W, Cruz, Ana L Gibertoni, Roohi, Aysha, Kouchaki, Samaneh, Walker, Timothy M, Peto, Timothy EA, Miller, Grant, Lintott, Chris, Clifton, David, Crook, Derrick W, Walker, A Sarah, Barilar, Ivan, Battaglia, Simone, Borroni, Emanuele, Brandao, Angela Pires, Brankin, Alice, Cabibbe, Andrea Maurizio, Carter, Joshua, Cirillo, Daniela Maria, Claxton, Pauline, Clifton, David A, Cohen, Ted, Coronel, Jorge, Earle, Sarah G, Escuyer, Vincent, Ferrazoli, Lucilaine, Gao, George F, Gardy, Jennifer, Gharbia, Saheer, Ghisi, Kelen Teixeira, Ghodousi, Arash, Cruz, Ana Luıza Gibertoni, Grazian, Clara, Guthrie, Jennifer L, He, Wencong, Hoffmann, Harald, Hoosdally, Sarah J, Hunt, Martin, Iqbal, Zamin, Ismail, Nazir Ahmed, Jarrett, Lisa, Joseph, Lavania, Jou, Ruwen, Kambli, Priti, Knaggs, Jeff, Koch, Anastasia, Kohlerschmidt, Donna, Lachapelle, Alexander S, Lalvani, Ajit, Lapierre, Simon Grandjean, Laurenson, Ian F, Letcher, Brice, Lin, Wan-Hsuan, Liu, Chunfa, Liu, Dongxin, Malone, Kerri M, Mandal, Ayan, Matias, Daniela, Meintjes, Graeme, Mendes, Flavia Freitas, Merker, Matthias, Mihalic, Marina, Millard, James, Miotto, Paolo, Mistry, Nerges, Moore, David, Dreyer, Viola, Chetty, Darren, Musser, Kimberlee A, Ngcamu, Dumisani, Nhung, Hoang Ngoc, Grandjean, Louis, Nilgiriwala, Kayzad Soli, Nimmo, Camus, Okozi, Nana, Oliveira, Rosangela Siqueira, Omar, Shaheed Vally, Paton, Nicholas, Pinhata, Juliana Maira Watanabe, Plesnik, Sara, Puyen, Zully M, Rabodoarivelo, Marie Sylvianne, Rakotosamimanana, Niaina, Rancoita, Paola MV, Rathod, Priti, Robinson, Esther, Rodger, Gillian, Rodrigues, Camilla, Rodwell, Timothy C, and Santos-Lazaro, David

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Clinical Sciences, Emerging Infectious Diseases, Infectious Diseases, Prevention, Antimicrobial Resistance, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Infection, Good Health and Well Being, Antitubercular Agents, Humans, Microbial Sensitivity Tests, Mycobacterium tuberculosis, Tuberculosis, Volunteers, Zooniverse Volunteer Community, CRyPTIC Consortium, M. tuberculosis, antibiotics, citizen science, clinical microbiology, infectious disease, microbiology, tuberculosis, Biochemistry and Cell Biology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Tuberculosis is a respiratory disease that is treatable with antibiotics. An increasing prevalence of resistance means that to ensure a good treatment outcome it is desirable to test the susceptibility of each infection to different antibiotics. Conventionally, this is done by culturing a clinical sample and then exposing aliquots to a panel of antibiotics, each being present at a pre-determined concentration, thereby determining if the sample isresistant or susceptible to each sample. The minimum inhibitory concentration (MIC) of a drug is the lowestconcentration that inhibits growth and is a more useful quantity but requires each sample to be tested at a range ofconcentrations for each drug. Using 96-well broth micro dilution plates with each well containing a lyophilised pre-determined amount of an antibiotic is a convenient and cost-effective way to measure the MICs of several drugs at once for a clinical sample. Although accurate, this is still an expensive and slow process that requires highly-skilled and experienced laboratory scientists. Here we show that, through the BashTheBug project hosted on the Zooniverse citizen science platform, a crowd of volunteers can reproducibly and accurately determine the MICs for 13 drugs and that simply taking the median or mode of 11-17 independent classifications is sufficient. There is therefore a potential role for crowds to support (but not supplant) the role of experts in antibiotic susceptibility testing.

Published
2022

2. The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis

Author

Walker, Timothy M, Miotto, Paolo, Köser, Claudio U, Fowler, Philip W, Knaggs, Jeff, Iqbal, Zamin, Hunt, Martin, Chindelevitch, Leonid, Farhat, Maha R, Cirillo, Daniela Maria, Comas, Iñaki, Posey, James, Omar, Shaheed V, Peto, Timothy EA, Suresh, Anita, Uplekar, Swapna, Laurent, Sacha, Colman, Rebecca E, Nathanson, Carl-Michael, Zignol, Matteo, Walker, Ann Sarah, Crook, Derrick W, Ismail, Nazir, Rodwell, Timothy C, Consortium, the SeqTreat Consortium CRyPTIC, Walker, A Sarah, Steyn, Adrie JC, Lalvani, Ajit, Baulard, Alain, Christoffels, Alan, Mendoza-Ticona, Alberto, Trovato, Alberto, Skrahina, Alena, Lachapelle, Alexander S, Brankin, Alice, Piatek, Amy, Cruz, Ana Gibertoni, Koch, Anastasia, Cabibbe, Andrea Maurizio, Spitaleri, Andrea, Brandao, Angela P, Chaiprasert, Angkana, Barbova, Anna, Van Rie, Annelies, Ghodousi, Arash, Bainomugisa, Arnold, Mandal, Ayan, Roohi, Aysha, Javid, Babak, Zhu, Baoli, Letcher, Brice, Rodrigues, Camilla, Nimmo, Camus, NATHANSON, Carl-Michael, Duncan, Carla, Coulter, Christopher, Utpatel, Christian, Liu, Chunfa, Grazian, Clara, Kong, Clare, Wilson, Daniel J, Matias, Daniela, Jorgensen, Danielle, Zimenkov, Danila, Chetty, Darren, Moore, David AJ, Clifton, David A, van Soolingen, Dick, Liu, Dongxin, Kohlerschmidt, Donna, Barreira, Draurio, Ngcamu, Dumisani, Lazaro, Elias David Santos, Kelly, Ellis, Borroni, Emanuele, Roycroft, Emma, Andre, Emmanuel, Böttger, Erik C, Robinson, Esther, Menardo, Fabrizio, Mendes, Flavia F, Jamieson, Frances B, Coll, Francesc, Gao, George Fu, Kasule, George W, Rossolini, Gian Maria, Rodger, Gillian, Smith, E Grace, Meintjes, Graeme, Thwaites, Guy, Hoffmann, Harald, Albert, Heidi, Cox, Helen, Laurenson, Ian F, and Arandjelovic, Irena

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Microbiology, Clinical Sciences, Tuberculosis, Infectious Diseases, Rare Diseases, Antimicrobial Resistance, Orphan Drug, Development of treatments and therapeutic interventions, 5.1 Pharmaceuticals, Infection, Good Health and Well Being, Antitubercular Agents, Drug Resistance, Ethambutol, Microbial Sensitivity Tests, Mutation, Mycobacterium tuberculosis, World Health Organization, CRyPTIC Consortium, Seq&Treat Consortium, Immunology, Medical microbiology
Abstract

BackgroundMolecular diagnostics are considered the most promising route to achieving rapid, universal drug susceptibility testing for Mycobacterium tuberculosiscomplex (MTBC). We aimed to generate a WHO endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction.MethodsA candidate gene approach was used to identify mutations as associated with resistance, or consistent with susceptibility, for 13 WHO endorsed anti-tuberculosis drugs. 38,215 MTBC isolates with paired whole-genome sequencing and phenotypic drug susceptibility testing data were amassed from 45 countries. For each mutation, a contingency table of binary phenotypes and presence or absence of the mutation computed positive predictive value, and Fisher's exact tests generated odds ratios and Benjamini-Hochberg corrected p-values. Mutations were graded as Associated with Resistance if present in at least 5 isolates, if the odds ratio was >1 with a statistically significant corrected p-value, and if the lower bound of the 95% confidence interval on the positive predictive value for phenotypic resistance was >25%. A series of expert rules were applied for final confidence grading of each mutation.Findings15,667 associations were computed for 13,211 unique mutations linked to one or more drugs. 1,149/15,667 (7·3%) mutations were classified as associated with phenotypic resistance and 107/15,667 (0·7%) were deemed consistent with susceptibility. For rifampicin, isoniazid, ethambutol, fluoroquinolones, and streptomycin, the mutations' pooled sensitivity was >80%. Specificity was over 95% for all drugs except ethionamide (91·4%), moxifloxacin (91·6%) and ethambutol (93·3%). Only two resistance mutations were classified for bedaquiline, delamanid, clofazimine, and linezolid as prevalence of phenotypic resistance was low for these drugs.InterpretationThis first WHO endorsed catalogue of molecular targets for MTBC drug susceptibility testing provides a global standard for resistance interpretation. Its existence should encourage the implementation of molecular diagnostics by National Tuberculosis Programmes.FundingUNITAID, Wellcome, MRC, BMGF.

Published
2022

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, Orphan Drug, Emerging Infectious Diseases, Tuberculosis, Biodefense, Antimicrobial Resistance, Infectious Diseases, Rare Diseases, 5.1 Pharmaceuticals, 6.1 Pharmaceuticals, 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

4. Challenges and Pitfalls in Generating Representative ICS Datasets in Cyber Security Research

Author

Mitseva, Asya, Thierse, Paul, Hoffmann, Harald, Er, Devran, Panchenko, Andriy, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Katsikas, Sokratis, editor, Cuppens, Frédéric, editor, Kalloniatis, Christos, editor, Mylopoulos, John, editor, Pallas, Frank, editor, Pohle, Jörg, editor, Sasse, M. Angela, editor, Abie, Habtamu, editor, Ranise, Silvio, editor, Verderame, Luca, editor, Cambiaso, Enrico, editor, Maestre Vidal, Jorge, editor, Sotelo Monge, Marco Antonio, editor, Albanese, Massimiliano, editor, Katt, Basel, editor, Pirbhulal, Sandeep, editor, and Shukla, Ankur, editor

Published
2023
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6. Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis

Author

Barilar, Ivan, Battaglia, Simone, Borroni, Emanuele, Brandao, Angela Pires, Brankin, Alice, Cabibbe, Andrea Maurizio, Carter, Joshua, Cirillo, Daniela Maria, Claxton, Pauline, Clifton, David A, Cohen, Ted, Coronel, Jorge, Crook, Derrick W, Dreyer, Viola, Earle, Sarah G, Escuyer, Vincent, Ferrazoli, Lucilaine, Fowler, Philip W, Fu Gao, George, Gardy, Jennifer, Gharbia, Saheer, Ghisi, Kelen Teixeira, Ghodousi, Arash, Gibertoni Cruz, Ana Luíza, Grandjean, Louis, Grazian, Clara, Groenheit, Ramona, Guthrie, Jennifer L, He, Wencong, Hoffmann, Harald, Hoosdally, Sarah J, Hunt, Martin, Iqbal, Zamin, Ismail, Nazir Ahmed, Jarrett, Lisa, Joseph, Lavania, Jou, Ruwen, Kambli, Priti, Khot, Rukhsar, Knaggs, Jeff, Koch, Anastasia, Kohlerschmidt, Donna, Kouchaki, Samaneh, Lachapelle, Alexander S, Lalvani, Ajit, Grandjean Lapierre, Simon, Laurenson, Ian F, Letcher, Brice, Lin, Wan-Hsuan, Liu, Chunfa, Liu, Dongxin, Malone, Kerri M, Mandal, Ayan, Mansjö, Mikael, Matias, Daniela, Meintjes, Graeme, de Freitas Mendes, Flávia, Merker, Matthias, Mihalic, Marina, Millard, James, Miotto, Paolo, Mistry, Nerges, Moore, David, Musser, Kimberlee A, Ngcamu, Dumisani, Hoang, Ngoc Nhung, Niemann, Stefan, Nilgiriwala, Kayzad Soli, Nimmo, Camus, Okozi, Nana, Oliveira, Rosangela Siqueira, Omar, Shaheed Vally, Paton, Nicholas, Peto, Timothy EA, Watanabe Pinhata, Juliana Maira, Plesnik, Sara, Puyen, Zully M, Rabodoarivelo, Marie Sylvianne, Rakotosamimanana, Niaina, Rancoita, Paola MV, Rathod, Priti, Rodger, Gillian, Rodrigues, Camilla, Rodwell, Timothy C, Roohi, Eaysha, Santos-Lazaro, David, Shah, Sanchi, Kohl, Thomas Andreas, Smith, Grace, Solano, Walter, Spitaleri, Andrea, Supply, Philip, Surve, Utkarsha, Tahseen, Sabira, Thuong, Nguyen Thuy Thuong, Thwaites, Guy, Todt, Katharina, Trovato, Alberto, Utpatel, Christian, Van Rie, Annelies, Vijay, Srinivasan, Walker, Timothy M, Walker, Sarah A, Warren, Robin, Werngren, Jim, Wijkander, Maria, Wilkinson, Robert J, Wilson, Daniel J, Wintringer, Penelope, Yu, Xin Xiao, Yang, Yang, Zhao, Yanlin, Yao, Shen-Yuan, Zhu, Baoli, Sonnenkalb, Lindsay, Carter, Joshua James, Malone, Kerri Marie, and Fowler, Philip William

Published
2023
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8. 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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9. Space Weathering

Author

Hoffmann, Harald, Gargaud, Muriel, editor, Irvine, William M., editor, Amils, Ricardo, editor, Claeys, Philippe, editor, Cleaves, Henderson James, editor, Gerin, Maryvonne, editor, Rouan, Daniel, editor, Spohn, Tilman, editor, Tirard, Stéphane, editor, and Viso, Michel, editor

Published
2023
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10. Regolith, Planetary

Author

Hoffmann, Harald, Gargaud, Muriel, editor, Irvine, William M., editor, Amils, Ricardo, editor, Claeys, Philippe, editor, Cleaves, Henderson James, editor, Gerin, Maryvonne, editor, Rouan, Daniel, editor, Spohn, Tilman, editor, Tirard, Stéphane, editor, and Viso, Michel, editor

Published
2023
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12. Deimos

Author

Hoffmann, Harald, Gargaud, Muriel, editor, Irvine, William M., editor, Amils, Ricardo, editor, Claeys, Philippe, editor, Cleaves, Henderson James, editor, Gerin, Maryvonne, editor, Rouan, Daniel, editor, Spohn, Tilman, editor, Tirard, Stéphane, editor, and Viso, Michel, editor

Published
2023
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13. Phobos

Author

Hoffmann, Harald, Gargaud, Muriel, editor, Irvine, William M., editor, Amils, Ricardo, editor, Claeys, Philippe, editor, Cleaves, Henderson James, editor, Gerin, Maryvonne, editor, Rouan, Daniel, editor, Spohn, Tilman, editor, Tirard, Stéphane, editor, and Viso, Michel, editor

Published
2023
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14. Rapid Tuberculosis Diagnostics Including Molecular First- and Second-Line Resistance Testing Based on a Novel Microfluidic DNA Extraction Cartridge

Author

Beutler, Markus, Homann, Ana R., Mihalic, Marina, Plesnik, Sara, Niebling, Laura, Eckart, Martin, Allerheiligen, Vera, Czurratis, Daniel, Maharjan, Bhagwan, Shrestha, Bhabana, Parpieva, Nargiza, Turaev, Laziz, Sayfutdinov, Zayniddin, Hofmann-Thiel, Sabine, Grasse, Wolfgang, Metzger-Boddien, Christoph, Paust, Nils, and Hoffmann, Harald

Published
2021
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19. 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

Author

Schlanderer, Judith, primary, Hoffmann, Harald, additional, Lüddecke, Jan, additional, Golubov, Andrey, additional, Grasse, Wolfgang, additional, Kindler, Elisabeth V., additional, Kohl, Thomas A., additional, Merker, Matthias, additional, Metzger, Christoph, additional, Mohr, Vanessa, additional, Niemann, Stefan, additional, Pilloni, Claudia, additional, Plesnik, Sara, additional, Raya, Bijendra, additional, Shresta, Bhawana, additional, Utpatel, Christian, additional, Zengerle, Roland, additional, Beutler, Markus, additional, and Paust, Nils, additional

Published
2024
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20. A cluster of multidrug-resistant Mycobacterium tuberculosis among patients arriving in Europe from the Horn of Africa: a molecular epidemiological study

Author

Avsar, Korkut, Bauer, Christoph, Bernasconi, Enos, Borroni, Emanuele, Brusin, Sergio, Coscollá Dévis, Mireia, Crook, Derrick W., Dedicoat, Martin, Fitzgibbon, Margaret, Gagneux, Sébastien, Geiger, Francisca, Guthmann, Jean-Paul, Hendrickx, David, Hoffmann-Thiel, Sabine, van Ingen, Jakko, Jackson, Sarah, Jaton, Katia, Lange, Christoph, Mazza Stalder, Jessica, O'Donnell, Joan, Opota, Onya, Peto, Tim E.A., Preiswerk, Benjamin, Roycroft, Emma, Sato, Mariko, Schacher, Regina, Schulthess, Bettina, Smith, E. Grace, Soini, Hanna, Sougakoff, Wladimir, Tagliani, Elisa, Utpatel, Christian, Veziris, Nicolas, Wagner-Wiening, Christiane, Witschi, Mark, Walker, Timothy M, Merker, Matthias, Knoblauch, Astrid M, Helbling, Peter, Schoch, Otto D, van der Werf, Marieke J, Kranzer, Katharina, Fiebig, Lena, Kröger, Stefan, Haas, Walter, Hoffmann, Harald, Indra, Alexander, Egli, Adrian, Cirillo, Daniela M, Robert, Jérôme, Rogers, Thomas R, Groenheit, Ramona, Mengshoel, Anne T, Mathys, Vanessa, Haanperä, Marjo, Soolingen, Dick van, Niemann, Stefan, Böttger, Erik C, and Keller, Peter M

Published
2018
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22. 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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23. Development of prevalence and incidence of non-tuberculous Mycobacteria in German laboratories from 2016 to 2020

Author

Corbett, Caroline, primary, Finger, Philipp, additional, Heiß-Neumann, Marion, additional, Bohnert, Juergen, additional, Eder, Ines B., additional, Eisele, Melanie, additional, Friesen, Inna, additional, Kaasch, Achim J., additional, Kehrmann, Jan, additional, Lang, Roland, additional, Roedel, Juergen, additional, Roessler, Susann, additional, Schmidt, Annika, additional, Schneitler, Sophie, additional, Schui, Daniela, additional, Schuler, Franziska, additional, Sedlacek, Ludwig, additional, Serr, Annerose, additional, Sitaru, Ana-Gabriela, additional, Steinmann, Joerg, additional, Wagner, Dirk, additional, Wichelhaus, Thomas A., additional, Hofmann-Thiel, Sabine, additional, and Hoffmann, Harald, additional

Published
2023
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24. 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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27. Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis

Author

Sonnenkalb, Lindsay, primary, Carter, Joshua James, additional, Spitaleri, Andrea, additional, Iqbal, Zamin, additional, Hunt, Martin, additional, Malone, Kerri Marie, additional, Utpatel, Christian, additional, Cirillo, Daniela Maria, additional, Rodrigues, Camilla, additional, Nilgiriwala, Kayzad Soli, additional, Fowler, Philip William, additional, Merker, Matthias, additional, Niemann, Stefan, additional, Barilar, Ivan, additional, Battaglia, Simone, additional, Borroni, Emanuele, additional, Brandao, Angela Pires, additional, Brankin, Alice, additional, Cabibbe, Andrea Maurizio, additional, Carter, Joshua, additional, Claxton, Pauline, additional, Clifton, David A, additional, Cohen, Ted, additional, Coronel, Jorge, additional, Crook, Derrick W, additional, Dreyer, Viola, additional, Earle, Sarah G, additional, Escuyer, Vincent, additional, Ferrazoli, Lucilaine, additional, Fowler, Philip W, additional, Fu Gao, George, additional, Gardy, Jennifer, additional, Gharbia, Saheer, additional, Ghisi, Kelen Teixeira, additional, Ghodousi, Arash, additional, Gibertoni Cruz, Ana Luíza, additional, Grandjean, Louis, additional, Grazian, Clara, additional, Groenheit, Ramona, additional, Guthrie, Jennifer L, additional, He, Wencong, additional, Hoffmann, Harald, additional, Hoosdally, Sarah J, additional, Ismail, Nazir Ahmed, additional, Jarrett, Lisa, additional, Joseph, Lavania, additional, Jou, Ruwen, additional, Kambli, Priti, additional, Khot, Rukhsar, additional, Knaggs, Jeff, additional, Koch, Anastasia, additional, Kohlerschmidt, Donna, additional, Kouchaki, Samaneh, additional, Lachapelle, Alexander S, additional, Lalvani, Ajit, additional, Grandjean Lapierre, Simon, additional, Laurenson, Ian F, additional, Letcher, Brice, additional, Lin, Wan-Hsuan, additional, Liu, Chunfa, additional, Liu, Dongxin, additional, Malone, Kerri M, additional, Mandal, Ayan, additional, Mansjö, Mikael, additional, Matias, Daniela, additional, Meintjes, Graeme, additional, de Freitas Mendes, Flávia, additional, Mihalic, Marina, additional, Millard, James, additional, Miotto, Paolo, additional, Mistry, Nerges, additional, Moore, David, additional, Musser, Kimberlee A, additional, Ngcamu, Dumisani, additional, Hoang, Ngoc Nhung, additional, Nimmo, Camus, additional, Okozi, Nana, additional, Oliveira, Rosangela Siqueira, additional, Omar, Shaheed Vally, additional, Paton, Nicholas, additional, Peto, Timothy EA, additional, Watanabe Pinhata, Juliana Maira, additional, Plesnik, Sara, additional, Puyen, Zully M, additional, Rabodoarivelo, Marie Sylvianne, additional, Rakotosamimanana, Niaina, additional, Rancoita, Paola MV, additional, Rathod, Priti, additional, Rodger, Gillian, additional, Rodwell, Timothy C, additional, Roohi, Eaysha, additional, Santos-Lazaro, David, additional, Shah, Sanchi, additional, Kohl, Thomas Andreas, additional, Smith, Grace, additional, Solano, Walter, additional, Supply, Philip, additional, Surve, Utkarsha, additional, Tahseen, Sabira, additional, Thuong, Nguyen Thuy Thuong, additional, Thwaites, Guy, additional, Todt, Katharina, additional, Trovato, Alberto, additional, Van Rie, Annelies, additional, Vijay, Srinivasan, additional, Walker, Timothy M, additional, Walker, Sarah A, additional, Warren, Robin, additional, Werngren, Jim, additional, Wijkander, Maria, additional, Wilkinson, Robert J, additional, Wilson, Daniel J, additional, Wintringer, Penelope, additional, Yu, Xin Xiao, additional, Yang, Yang, additional, Zhao, Yanlin, additional, Yao, Shen-Yuan, additional, and Zhu, Baoli, additional

Published
2023
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29. Sample Preparation and qPCR Detection of Tuberculosis on a Centrifugal Microfluidic Cartridge Enabling Molecular Downstream Resistance Profiling †.

Author

Schlanderer, Judith, Beutler, Markus, Lüddecke, Jan, Hoffmann, Harald, and Paust, Nils

Subjects
RAPID diagnostic tests, GENETIC markers, POINT-of-care testing, TUBERCULOSIS, DETECTION limit
Abstract

Tuberculosis (TB) is still one of the world's deadliest infections. Fast detection of the pathogen M. tuberculosis (MTB) and its genetic resistance markers substantially improves treatment success and outcome. A key element for rapid genetic diagnostics is the efficient extraction of DNA from sputum for qPCR detection at the point of care. We present the fully automated sample preparation of MTB DNA from 3 mL of liquefied sputum and qPCR detection of MTB on a centrifugal microfluidic cartridge. Our method achieves a limit of detection (LoD) between 17 and 57 CFU/mL and provides a purified DNA solution for molecular downstream testing, such as targeted NGS. [ABSTRACT FROM AUTHOR]

Published
2024
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36. Origin and Global Expansion of Complex Lineage 3

Author

Shuaib, Yassir A, Utpatel, Christian, Kohl, Thomas A, Barilar, Ivan, Diricks, Margo, Ashraf, Nadia, Wieler, Lothar H, Kerubo, Glennah, Mesfin, Eyob A, Diallo, Awa Ba, Al-Hajoj, Sahal, Ndung'u, Perpetua, Fitzgibbon, Margaret M, Vaziri, Farzam, Sintchenko, Vitali, Martinez, Elena, Viegas, Sofia O, Zhou, Yang, Azmy, Aya, Al-Amry, Khaled, Godreuil, Sylvain, Varma-Basil, Mandira, Narang, Anshika, Ali, Solomon, Beckert, Patrick, Dreyer, Viola, Kabwe, Mwila, Bates, Matthew, Hoelscher, Michael, Rachow, Andrea, Gori, Andrea, Tekwu, Emmanuel M, Sidze, Larissa K, Jean-Paul, Assam A, Beng, Veronique P, Ntoumi, Francine, Frank, Matthias, Diallo, Aissatou Gaye, Mboup, Souleymane, Tessema, Belay, Beyene, Dereje, Khan, Sadiq N, Diel, Roland, Supply, Philip, Maurer, Florian P, Hoffmann, Harald, Niemann, Stefan, and Merker, Matthias

Subjects
C500 Microbiology
Abstract

complex (MTBC) Lineage 3 (L3) strains are abundant in world regions with the highest tuberculosis burden. To investigate the population structure and the global diversity of this major lineage, we analyzed a dataset comprising 2682 L3 strains from 38 countries over 5 continents, by employing 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats genotyping (MIRU-VNTR) and drug susceptibility testing. We further combined whole-genome sequencing (WGS) and phylogeographic analysis for 373 strains representing the global L3 genetic diversity. Ancestral state reconstruction confirmed that the origin of L3 strains is located in Southern Asia and further revealed multiple independent introduction events into North-East and East Africa. This study provides a systematic understanding of the global diversity of L3 strains and reports phylogenetic variations that could inform clinical trials which evaluate the effectivity of new drugs/regimens or vaccine candidates.

Published
2022

37. A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics

Author

Brankin, Alice, Malone, Kerri, Barilar, Ivan, Battaglia, Simone, Borroni, Emanuele, Pires Brandao, Angela, Cabibbe, Andrea Maurizio, Carter, Joshua, Chetty, Darren, Cirillo, Daniela María, Claxton, Pauline, Clifton, David, Cohen, Ted, Coronel, Jorge, Crook, Derrick, Dreyer, Viola, Earle, Sarah, Escuyer, Vincent, Ferrazoli, Lucilaine, Gāo, George Fú, Gardy, Jennifer, Gharbia, Saheer, Teixeira Ghisi, Kelen, Ghodousi, Arash, Gibertoni Cruz, Ana Lúıza, Grandjean, Louis, Grazian, Clara, Groenheit, Ramona, Guthrie, Jennifer, He, Wencong, Hoffmann, Harald, J., Sarah, Hunt, Martin, Ismail, Nazir Ahmed, Jarrett, Lisa, Joseph, Lavania, Jou, Ruwen, Kambli, Priti, Khot, Rukhsar, Knaggs, Jeff, Koch, Anastasia, Kohlerschmidt, Donna, Kouchaki, Samaneh, Lachapelle, Alexander, Lalvani, Ajit, Grandjean Lapierre, Simon, Laurenson, Ian, Letcher, Brice, Lin, Wan-Hsuan, Liu, Chunfa, Liu, Dongxin, Mandal, Ayan, Mansjö, Mikael, Matias, Daniela, Meintjes, Graeme, de Freitas Mendes, Flávia, Merker, Matthias, Mihalic, Marina, Millard, James, Miotto, Paolo, Mistry, Nerges, Moore, David, Musser, Kimberlee A., Ngcamu, Dumisani, Ngoc Nhung, Hoang, Niemann, Stefan, Soli Nilgiriwala, Kayzad, Nimmo, Camus, O'Donnell, Max, Okozi, Nana, Siqueira Oliveira, Rosangela, Omar, Shaheed Vally, Paton, Nicholas, Peto, Timothy Ea, Watanabe Pinhata, Juliana Maira, Plesnik, Sara, Puyen, Zully, Rabodoarivelo, Marie, Rakotosamimanana, Niaina, Rancoita, Paola, Rathod, Priti, Robinson, Esther, Rodger, Gillian, Rodrigues, Camilla, Rodwell, Timothy, Roohi, Aysha, Santos-Lazaro, David, Shah, Sanchi, Kohl, Thomas Andreas, Smith, Grace, Solano, Walter, Spitaleri, Andrea, Supply, Philip, Steyn, Adrie, Surve, Utkarsha, Tahseen, Sabira, Thuong, Nguyen, Thwaites, Guy, Todt, Katharina, Trovato, Alberto, Utpatel, Christian, van Rie, Annelies, Vijay, Srinivasan, Walker, Timothy, Walker, A. Sarah, Warren, Robin M., Werngren, Jim, Wijkander, Maria, Wilkinson, Robert, Wilson, Daniel, Wintringer, Penelope, Xiao, Yu-Xin, Yang, Yang, Zhao, Yanlin, Yao, Shen-Yuan, Zhu, Baoli, Fowler, Philip, Iqbal, Zamin, Consortium, The CRyPTIC, University of Oxford, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Forschungszentrum Borstel - Research Center Borstel, IRCCS San Raffaele Scientific Institute [Milan, Italie], Casa de Oswaldo Cruz [Rio de Janeiro] (COC), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Instituto Adolfo Lutz [São Paulo, Brazil], Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Africa Health Research Institute [Durban/Mtubatuba] (AHRI), University of Edinburgh, Yale School of Public Health (YSPH), Universidad Peruana de Ciencias Aplicadas (Lima) (UPC), Wadsworth Center, New York State Department of Health [Albany], Chinese Center for Disease Control and Prevention, Bill & Melinda Gates Foundation [Seattle], UK Health Security Agency [London] (UKHSA), Universita Vita Salute San Raffaele = Vita-Salute San Raffaele University [Milan, Italie] (UniSR), University College of London [London] (UCL), University of New South Wales [Sydney] (UNSW), Public Health Agency of Sweden, University of British Columbia [Vancouver], Public Health Ontario - Santé publique Ontario, Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim, National Institute for Communicable Diseases [Johannesburg] (NICD), Taipei Medical University, PD Hinduja Hospital & Research Institute, Mumbai, University of Cape Town, University of Surrey (UNIS), Imperial College London, Université de Montréal (UdeM), PRA Health sciences [Mumbai], London School of Hygiene and Tropical Medicine (LSHTM), Oxford University Clinical Research Unit [Ho Chi Minh City] (OUCRU), German Centre for Infection Research - partner site Hamburg-Lübeck-Borstel-Riems (DZIF), Columbia University Irving Medical Center (CUIMC), National University of Singapore (NUS), Socios En Salud [Lima, Peru], Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), Foundation for Innovative New Diagnostics (FIND), University of California [San Diego] (UC San Diego), University of California (UC), Universidad Peruana Cayetano Heredia (UPCH), 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), National TB control Program [Islamabad, Pakistan], University of Antwerp (UA), Stellenbosch University, Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, Department of Medicine, University of Cape Town, The Francis Crick Institute [London], Shanghai Jiao Tong University School of Medicine, Chinese Academy of Sciences [Beijing] (CAS), and Wellcome Trust (200205/Z/15/Z)Bill and Melinda Gates Foundation (OPP1133541)National Institute for Health Research Oxford Biomedical Research CentreNational Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial ResistanceWellcome Trust (203919/Z/16/Z)National Mega Project on Major Infectious Disease Prevention (2018ZX10103001)H2020 Marie Skłodowska-Curie Actions (EIPOD3)Unitaid (2019-32-FIND MDR)FAPESP (17/16082-7)FAPESP (2012/51756-5)National Natural Science Foundation of China (81991534)Beijing Municipal Science and Technology Commission (Z201100005520041)Wellcome Trust International Intermediate Fellowship (206724/Z/17/Z)Wellcome TrustSouth African Medical Research Councilthe Rhodes Trust and Stanford Medical Scientist Training Program (T32 GM007365)National Institute for Health Research (NIHR) Health Protection Research Unit in Respiratory Infections at Imperial College LondonFonds de Recherche en Santé du QuébecWellcome Trust (203583/Z/16/Z)Research Foundation Flanders (G0F8316N)Wellcome Trust (98316)Wellcome Trust (214321/Z/18/Z)Wellcome Trust (203135/Z/16/Z)National Research Foundation South Africa (64787)Wellcome Trust (201470/Z/16/Z)National Institute of Allergy and Infectious Diseases (1R01AI146338)GOSH (1R01AI146338)GOSH/ICH Biomedical Research CentreOxford Medical Research Council Doctoral Training Partnership (NDM Prize Studentship)Nuffield Department of Clinical MedicineSir Henry Dale Fellowship (101237/Z/13/B)The Robertson FoundationNIHRWellcome Trust (214560/Z/18/Z)Rhodes TrustWellcome Trust (FC0010218)UK Research and Innovation (FC0010218)Cancer Research UK (FC0010218)National Institutes of HealthCenters for Disease Control and PreventionUSAIDBill and Melinda Gates FoundationWellcome Trust (203141/Z/16/Z)NIHR Oxford Biomedical Research Centre (BRC BRC-1215-20008)Deutsches Zentrum für InfektionsforschungPublic Health ScotlandCenters for Disease Control and Prevention (U60OE000103)Division of Intramural Research, National Institute of Allergy and Infectious Diseases (AI-117312)

Subjects
General Immunology and Microbiology, General Neuroscience, Extensively Drug-Resistant Tuberculosis, Antitubercular Agents, Microbial Sensitivity Tests, Mycobacterium tuberculosis, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, General Biochemistry, Genetics and Molecular Biology, Phenotype, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Drug Resistance, Multiple, Bacterial, Mutation, Tuberculosis, Multidrug-Resistant, Humans, Rifampin, General Agricultural and Biological Sciences
Abstract

The Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC) presents here a data compendium of 12,289 Mycobacterium tuberculosis global clinical isolates, all of which have undergone whole-genome sequencing and have had their minimum inhibitory concentrations to 13 antitubercular drugs measured in a single assay. It is the largest matched phenotypic and genotypic dataset for M. tuberculosis to date. Here, we provide a summary detailing the breadth of data collected, along with a description of how the isolates were selected, collected, and uniformly processed in CRyPTIC partner laboratories across 23 countries. The compendium contains 6,814 isolates resistant to at least 1 drug, including 2,129 samples that fully satisfy the clinical definitions of rifampicin resistant (RR), multidrug resistant (MDR), pre-extensively drug resistant (pre-XDR), or extensively drug resistant (XDR). The data are enriched for rare resistance-associated variants, and the current limits of genotypic prediction of resistance status (sensitive/resistant) are presented by using a genetic mutation catalogue, along with the presence of suspected resistance-conferring mutations for isolates resistant to the newly introduced drugs bedaquiline, clofazimine, delamanid, and linezolid. Finally, a case study of rifampicin monoresistance demonstrates how this compendium could be used to advance our genetic understanding of rare resistance phenotypes. The data compendium is fully open source and it is hoped that it will facilitate and inspire future research for years to come.

Published
2022
Full Text
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39. Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment

Author

Ministerio de Ciencia e Innovación (España), European Research Council, Comas, Iñaki [0000-0001-5504-9408], 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, Ministerio de Ciencia e Innovación (España), European Research Council, Comas, Iñaki [0000-0001-5504-9408], 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., and Schön, Thomas

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.

Published
2022

40. Origin and Global Expansion of Mycobacterium tuberculosis Complex Lineage 3

Author

Shuaib, Yassir A., primary, Utpatel, Christian, additional, Kohl, Thomas A., additional, Barilar, Ivan, additional, Diricks, Margo, additional, Ashraf, Nadia, additional, Wieler, Lothar H., additional, Kerubo, Glennah, additional, Mesfin, Eyob A., additional, Diallo, Awa Ba, additional, Al-Hajoj, Sahal, additional, Ndung’u, Perpetua, additional, Fitzgibbon, Margaret M., additional, Vaziri, Farzam, additional, Sintchenko, Vitali, additional, Martinez, Elena, additional, Viegas, Sofia O., additional, Zhou, Yang, additional, Azmy, Aya, additional, Al-Amry, Khaled, additional, Godreuil, Sylvain, additional, Varma-Basil, Mandira, additional, Narang, Anshika, additional, Ali, Solomon, additional, Beckert, Patrick, additional, Dreyer, Viola, additional, Kabwe, Mwila, additional, Bates, Matthew, additional, Hoelscher, Michael, additional, Rachow, Andrea, additional, Gori, Andrea, additional, Tekwu, Emmanuel M., additional, Sidze, Larissa K., additional, Jean-Paul, Assam A., additional, Beng, Veronique P., additional, Ntoumi, Francine, additional, Frank, Matthias, additional, Diallo, Aissatou Gaye, additional, Mboup, Souleymane, additional, Tessema, Belay, additional, Beyene, Dereje, additional, Khan, Sadiq N., additional, Diel, Roland, additional, Supply, Philip, additional, Maurer, Florian P., additional, Hoffmann, Harald, additional, Niemann, Stefan, additional, and Merker, Matthias, additional

Published
2022
Full Text
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41. 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
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42. Space Weathering

Author

Hoffmann, Harald, Gargaud, Muriel, editor, Irvine, William M., editor, Amils, Ricardo, editor, Cleaves, Henderson James (Jim), II, editor, Pinti, Daniele L., editor, Quintanilla, José Cernicharo, editor, Rouan, Daniel, editor, Spohn, Tilman, editor, Tirard, Stéphane, editor, and Viso, Michel, editor

Published
2015
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43. Regolith, Planetary

Author

Hoffmann, Harald, Gargaud, Muriel, editor, Irvine, William M., editor, Amils, Ricardo, editor, Cleaves, Henderson James (Jim), II, editor, Pinti, Daniele L., editor, Quintanilla, José Cernicharo, editor, Rouan, Daniel, editor, Spohn, Tilman, editor, Tirard, Stéphane, editor, and Viso, Michel, editor

Published
2015
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46. Dione’s spectral and geological properties

Author

Stephan, Katrin, Jaumann, Ralf, Wagner, Roland, Clark, Roger N., Cruikshank, Dale P., Hibbitts, Charles A., Roatsch, Thomas, Hoffmann, Harald, Brown, Robert H., Filiacchione, G., Buratti, Bonnie J., Hansen, Gary B., McCord, Tom B., Nicholson, Phil D., and Baines, Kevin H.

Published
2010
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