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

Author

Walker, A Sarah, Steyn, Adrie J C, Lalvani, Ajit, Baulard, Alain, Christoffels, Alan, Mendoza-Ticona, Alberto, Trovato, Alberto, Skrahina, Alena, Lachapelle, Alexander S, Brankin, Alice, Piatek, Amy, Gibertoni Cruz, Ana, Koch, Anastasia, Cabibbe, Andrea Maurizio, Spitaleri, Andrea, Brandao, Angela P, Chaiprasert, Angkana, Suresh, Anita, 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, Köser, Claudio U, Wilson, Daniel J, Cirillo, Daniela Maria, Matias, Daniela, Jorgensen, Danielle, Zimenkov, Danila, Chetty, Darren, Moore, David AJ, Clifton, David A, Crook, Derrick W, van Soolingen, Dick, Liu, Dongxin, Kohlerschmidt, Donna, Barreira, Draurio, Ngcamu, Dumisani, Santos Lazaro, Elias David, 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, Comas, Iñaki, Arandjelovic, Irena, Barilar, Ivan, Robledo, Jaime, Millard, James, Johnston, James, Posey, Jamie, Andrews, Jason R, Knaggs, Jeff, Gardy, Jennifer, Guthrie, Jennifer, Taylor, Jill, Werngren, Jim, Metcalfe, John, Coronel, Jorge, Shea, Joseph, Carter, Joshua, Pinhata, Juliana MW, Kus, Julianne V, Todt, Katharina, Holt, Kathryn, Nilgiriwala, Kayzad S, Ghisi, Kelen T, Malone, Kerri M, Faksri, Kiatichai, Musser, Kimberlee A, Joseph, Lavania, Rigouts, Leen, Chindelevitch, Leonid, Jarrett, Lisa, Grandjean, Louis, Ferrazoli, Lucilaine, Rodrigues, Mabel, Farhat, Maha, Schito, Marco, Fitzgibbon, Margaret M, Loembé, Marguerite Massinga, Wijkander, Maria, Ballif, Marie, Rabodoarivelo, Marie-Sylvianne, Mihalic, Marina, WILCOX, Mark, Hunt, Martin, ZIGNOL, Matteo, Merker, Matthias, Egger, Matthias, O'Donnell, Max, Caws, Maxine, Wu, Mei-Hua, Whitfield, Michael G, Inouye, Michael, Mansjö, Mikael, Dang Thi, Minh Ha, Joloba, Moses, Kamal, SM Mostofa, Okozi, Nana, ISMAIL, Nazir, Mistry, Nerges, Hoang, Nhung N, Rakotosamimanana, Niaina, Paton, Nicholas I, Rancoita, Paola M V, Miotto, Paolo, Lapierre, Pascal, Hall, Patricia J, Tang, Patrick, Claxton, Pauline, Wintringer, Penelope, Keller, Peter M, Thai, Phan Vuong Khac, Fowler, Philip W, Supply, Philip, Srilohasin, Prapaporn, Suriyaphol, Prapat, Rathod, Priti, Kambli, Priti, Groenheit, Ramona, Colman, Rebecca E, Ong, Rick Twee-Hee, Warren, Robin M, Wilkinson, Robert J, Diel, Roland, Oliveira, Rosangela S, Khot, Rukhsar, Jou, Ruwen, Tahseen, Sabira, Laurent, Sacha, Gharbia, Saheer, Kouchaki, Samaneh, Shah, Sanchi, Plesnik, Sara, Earle, Sarah G, Dunstan, Sarah, Hoosdally, Sarah J, Mitarai, Satoshi, Gagneux, Sebastien, Omar, Shaheed V, Yao, Shen-Yuan, Grandjean Lapierre, Simon, Battaglia, Simone, Niemann, Stefan, Pandey, Sushil, Uplekar, Swapna, Halse, Tanya A, Cohen, Ted, Cortes, Teresa, Prammananan, Therdsak, Kohl, Thomas A, Thuong, Nguyen T T, Teo, Tik Ying, Peto, Timothy E A, Rodwell, Timothy C, William, Timothy, Walker, Timothy M, Rogers, Thomas R, Surve, Utkarsha, Mathys, Vanessa, Furió, Victoria, Cook, Victoria, Vijay, Srinivasan, Escuyer, Vincent, Dreyer, Viola, Sintchenko, Vitali, Saphonn, Vonthanak, Solano, Walter, Lin, Wan-Hsuan, van Gemert, Wayne, He, Wencong, Yang, Yang, Zhao, Yanlin, Qin, Youwen, Xiao, Yu-Xin, Hasan, Zahra, Iqbal, Zamin, Puyen, Zully M, Farhat, Maha R, Posey, James, Peto, Timothy EA, Nathanson, Carl-Michael, Zignol, Matteo, Walker, Ann Sarah, and Ismail, Nazir

Published
2022
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2. Genomic Epidemiology of Multidrug-Resistant Mycobacterium tuberculosis During Transcontinental Spread

Author

Coscolla, Mireia, Barry, Pennan M, Oeltmann, John E, Koshinsky, Heather, Shaw, Tambi, Cilnis, Martin, Posey, Jamie, Rose, Jordan, Weber, Terry, Fofanov, Viacheslav Y, Gagneux, Sebastien, Kato-Maeda, Midori, and Metcalfe, John Z

Subjects
Vaccine Related, Biodefense, Infectious Diseases, Genetics, Emerging Infectious Diseases, Prevention, Antimicrobial Resistance, Human Genome, Tuberculosis, Rare Diseases, 2.1 Biological and endogenous factors, Aetiology, Infection, Good Health and Well Being, California, Disease Outbreaks, Genome, Bacterial, Genotype, Humans, Molecular Epidemiology, Molecular Typing, Mycobacterium tuberculosis, Phylogeny, Polymorphism, Restriction Fragment Length, Polymorphism, Single Nucleotide, Prevalence, Thailand, Tuberculosis, Multidrug-Resistant, drug resistance, genomics, epidemiology, EmbR, Biological Sciences, Medical and Health Sciences, Microbiology
Abstract

The transcontinental spread of multidrug-resistant (MDR) tuberculosis is poorly characterized in molecular epidemiologic studies. We used genomic sequencing to understand the establishment and dispersion of MDR Mycobacterium tuberculosis within a group of immigrants to the United States. We used a genomic epidemiology approach to study a genotypically matched (by spoligotype, IS6110 restriction fragment length polymorphism, and mycobacterial interspersed repetitive units-variable number of tandem repeat signature) lineage 2/Beijing MDR strain implicated in an outbreak of tuberculosis among refugees in Thailand and consecutive cases within California. All 46 MDR M. tuberculosis genomes from both Thailand and California were highly related, with a median difference of 10 single-nucleotide polymorphisms (SNPs). The Wat Tham Krabok (WTK) strain is a new sequence type distinguished from all known Beijing strains by 55 SNPs and a genomic deletion (Rv1267c) associated with increased fitness. Sequence data revealed a highly prevalent MDR strain that included several closely related but distinct allelic variants within Thailand, rather than the occurrence of a single outbreak. In California, sequencing data supported multiple independent introductions of WTK with subsequent transmission and reactivation within the state, as well as a potential super spreader with a prolonged infectious period. Twenty-seven drug resistance-conferring mutations and 4 putative compensatory mutations were found within WTK strains. Genomic sequencing has substantial epidemiologic value in both low- and high-burden settings in understanding transmission chains of highly prevalent MDR strains.

Published
2015

3. Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance. Second Edition

Author

United States Agency for International Development, Comas, Iñaki [0000-0001-5504-9408], Ismail, Nazir Ahmed, Nathanson, Carl-Michael, Korobitsyn, Alexei, Zignol, Matteo, Kasaeva, Tereza, Rodwell, Timothy, Miotto, Paolo, Köser, Claudio, Walker, Timothy, Chindelevitch, Leonid, Laurent, Sacha, Farhat, Maha R., Cirillo, Daniela, Comas, Iñaki, Posey, Jamie, Omar, Shaheed V., Rigouts, Leen, Suresh, Anita, Colman, Rebecca, United States Agency for International Development, Comas, Iñaki [0000-0001-5504-9408], Ismail, Nazir Ahmed, Nathanson, Carl-Michael, Korobitsyn, Alexei, Zignol, Matteo, Kasaeva, Tereza, Rodwell, Timothy, Miotto, Paolo, Köser, Claudio, Walker, Timothy, Chindelevitch, Leonid, Laurent, Sacha, Farhat, Maha R., Cirillo, Daniela, Comas, Iñaki, Posey, Jamie, Omar, Shaheed V., Rigouts, Leen, Suresh, Anita, and Colman, Rebecca

Published
2023

4. Clinical Research and Development of Tuberculosis Diagnostics: Moving From Silos to Synergy

Author

Nahid, Payam, Kim, Peter S., Evans, Carlton A., Alland, David, Barer, Michael, Diefenbach, Jane, Ellner, Jerrold, Hafner, Richard, Hamilton, Carol Dukes, Iademarco, Michael F., Ireton, Gregory, Kimerling, Michael E., Lienhardt, Christian, MacKenzie, William R., Murray, Megan, Perkins, Mark D., Posey, Jamie E., Roberts, Teri, Sizemore, Christine, Stevens, Wendy S., Via, Laura, Williams, Sharon D., Yew, Wing W., and Swindells, Susan

Published
2012
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5. Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance

Author

Ismail, Nazir Ahmed, Nathanson, Carl-Michael, Korobitsyn, Alexei, Zignol, Matteo, Kasaeva, Tereza, Rodwell, Timothy, Miotto, Paolo, Walker, Timothy, Fowler, Philip, Knaggs, Jeff, Iqbal, Zamin, Hunt, Martin, Chindelevitch, Leonid, Farhat, Maha, Cirillo, Daniela, Crook, Derrick, Comas, Iñaki, Posey, Jamie, Omar, Shaheed Vally, Peto, Tim, Walker, Sarah, Suresh, Anita, Uplekar, Swapna, Laurent, Sacha, Colman, Rebecca, United States Agency for International Development, Comas, Iñaki, and Comas, Iñaki [0000-0001-5504-9408]

Abstract

96 páginas, figuras y tablas, This work was funded by grants provided by Unitaid and the United States Agency for International Development

Published
2021

7. Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance

Author

United States Agency for International Development, Comas, Iñaki [0000-0001-5504-9408], Ismail, Nazir Ahmed, Nathanson, Carl-Michael, Korobitsyn, Alexei, Zignol, Matteo, Kasaeva, Tereza, Rodwell, Timothy, Miotto, Paolo, Walker, Timothy, Fowler, Philip, Knaggs, Jeff, Iqbal, Zamin, Hunt, Martin, Chindelevitch, Leonid, Farhat, Maha R., Cirillo, Daniela, Crook, Derrick, Comas, Iñaki, Posey, Jamie, Omar, Shaheed V., Peto, Tim, Walker, Sarah, Suresh, Anita, Uplekar, Swapna, Laurent, Sacha, Colman, Rebecca, United States Agency for International Development, Comas, Iñaki [0000-0001-5504-9408], Ismail, Nazir Ahmed, Nathanson, Carl-Michael, Korobitsyn, Alexei, Zignol, Matteo, Kasaeva, Tereza, Rodwell, Timothy, Miotto, Paolo, Walker, Timothy, Fowler, Philip, Knaggs, Jeff, Iqbal, Zamin, Hunt, Martin, Chindelevitch, Leonid, Farhat, Maha R., Cirillo, Daniela, Crook, Derrick, Comas, Iñaki, Posey, Jamie, Omar, Shaheed V., Peto, Tim, Walker, Sarah, Suresh, Anita, Uplekar, Swapna, Laurent, Sacha, and Colman, Rebecca

Published
2021

8. Genomic Epidemiology of Multidrug-Resistant Mycobacterium tuberculosis During Transcontinental Spread

Author

Coscolla, Mireia, Barry, Pennan M., Oeltmann, John E., Koshinsky, Heather, Shaw, Tambi, Cilnis, Martin, Posey, Jamie, Rose, Jordan, Weber, Terry, Fofanov, Viacheslav Y., Gagneux, Sebastien, Kato-Maeda, Midori, Metcalfe, John Z., Coscolla, Mireia, Barry, Pennan M., Oeltmann, John E., Koshinsky, Heather, Shaw, Tambi, Cilnis, Martin, Posey, Jamie, Rose, Jordan, Weber, Terry, Fofanov, Viacheslav Y., Gagneux, Sebastien, Kato-Maeda, Midori, and Metcalfe, John Z.

Abstract

The transcontinental spread of multidrug-resistant (MDR) tuberculosis is poorly characterized in molecular epidemiologic studies. We used genomic sequencing to understand the establishment and dispersion of MDR Mycobacterium tuberculosis within a group of immigrants to the United States. We used a genomic epidemiology approach to study a genotypically matched (by spoligotype, IS6110 restriction fragment length polymorphism, and mycobacterial interspersed repetitive units-variable number of tandem repeat signature) lineage 2/Beijing MDR strain implicated in an outbreak of tuberculosis among refugees in Thailand and consecutive cases within California. All 46 MDR M. tuberculosis genomes from both Thailand and California were highly related, with a median difference of 10 single-nucleotide polymorphisms (SNPs). The Wat Tham Krabok (WTK) strain is a new sequence type distinguished from all known Beijing strains by 55 SNPs and a genomic deletion (Rv1267c) associated with increased fitness. Sequence data revealed a highly prevalent MDR strain that included several closely related but distinct allelic variants within Thailand, rather than the occurrence of a single outbreak. In California, sequencing data supported multiple independent introductions of WTK with subsequent transmission and reactivation within the state, as well as a potential super spreader with a prolonged infectious period. Twenty-seven drug resistance-conferring mutations and 4 putative compensatory mutations were found within WTK strains. Genomic sequencing has substantial epidemiologic value in both low- and high-burden settings in understanding transmission chains of highly prevalent MDR strains

Published
2017

9. Genomic Epidemiology of Multidrug-ResistantMycobacterium tuberculosisDuring Transcontinental Spread

Author

Coscolla, Mireia, primary, Barry, Pennan M., additional, Oeltmann, John E., additional, Koshinsky, Heather, additional, Shaw, Tambi, additional, Cilnis, Martin, additional, Posey, Jamie, additional, Rose, Jordan, additional, Weber, Terry, additional, Fofanov, Viacheslav Y., additional, Gagneux, Sebastien, additional, Kato-Maeda, Midori, additional, and Metcalfe, John Z., additional

Published
2015
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10. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

Author

Massachusetts Institute of Technology. Department of Biology, Lander, Eric S., Farhat, Maha R., Shapiro, B. Jesse, Kieser, Karen J., Sultana, Razvan, Jacobson, Karen R., Victor, Thomas C., Warren, Robin M., Streicher, Elizabeth M., Calver, Alistair, Sloutsky, Alex, Kaur, Devinder, Posey, Jamie E., Plikaytis, Bonnie, Oggioni, Marco R., Gardy, Jennifer L., Johnston, James C., Rodrigues, Mabel, Tang, Patrick K. C., Kato-Maeda, Midori, Borowsky, Mark L., Muddukrishna, Bhavana, Kreiswirth, Barry N., Kurepina, Natalia, Galagan, James E., Gagneux, Sebastien, Birren, Bruce W., Rubin, Eric J., Sabeti, Pardis C., Murray, Megan B., Lander, Eric Steven, Massachusetts Institute of Technology. Department of Biology, Lander, Eric S., Farhat, Maha R., Shapiro, B. Jesse, Kieser, Karen J., Sultana, Razvan, Jacobson, Karen R., Victor, Thomas C., Warren, Robin M., Streicher, Elizabeth M., Calver, Alistair, Sloutsky, Alex, Kaur, Devinder, Posey, Jamie E., Plikaytis, Bonnie, Oggioni, Marco R., Gardy, Jennifer L., Johnston, James C., Rodrigues, Mabel, Tang, Patrick K. C., Kato-Maeda, Midori, Borowsky, Mark L., Muddukrishna, Bhavana, Kreiswirth, Barry N., Kurepina, Natalia, Galagan, James E., Gagneux, Sebastien, Birren, Bruce W., Rubin, Eric J., Sabeti, Pardis C., Murray, Megan B., and Lander, Eric Steven

Abstract

M. tuberculosis is evolving antibiotic resistance, threatening attempts at tuberculosis epidemic control. Mechanisms of resistance, including genetic changes favored by selection in resistant isolates, are incompletely understood. Using 116 newly sequenced and 7 previously sequenced M. tuberculosis whole genomes, we identified genome-wide signatures of positive selection specific to the 47 drug-resistant strains. By searching for convergent evolution—the independent fixation of mutations in the same nucleotide position or gene—we recovered 100% of a set of known resistance markers. We also found evidence of positive selection in an additional 39 genomic regions in resistant isolates. These regions encode components in cell wall biosynthesis, transcriptional regulation and DNA repair pathways. Mutations in these regions could directly confer resistance or compensate for fitness costs associated with resistance. Functional genetic analysis of mutations in one gene, ponA1, demonstrated an in vitro growth advantage in the presence of the drug rifampicin.

Published
2014

11. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

Author

Farhat, Maha R, primary, Shapiro, B Jesse, additional, Kieser, Karen J, additional, Sultana, Razvan, additional, Jacobson, Karen R, additional, Victor, Thomas C, additional, Warren, Robin M, additional, Streicher, Elizabeth M, additional, Calver, Alistair, additional, Sloutsky, Alex, additional, Kaur, Devinder, additional, Posey, Jamie E, additional, Plikaytis, Bonnie, additional, Oggioni, Marco R, additional, Gardy, Jennifer L, additional, Johnston, James C, additional, Rodrigues, Mabel, additional, Tang, Patrick K C, additional, Kato-Maeda, Midori, additional, Borowsky, Mark L, additional, Muddukrishna, Bhavana, additional, Kreiswirth, Barry N, additional, Kurepina, Natalia, additional, Galagan, James, additional, Gagneux, Sebastien, additional, Birren, Bruce, additional, Rubin, Eric J, additional, Lander, Eric S, additional, Sabeti, Pardis C, additional, and Murray, Megan, additional

Published
2013
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12. Genomic Epidemiology of Multidrug-Resistant Mycobacterium tuberculosis During Transcontinental Spread

Author

Coscolla, Mireia, Barry, Pennan M., Oeltmann, John E., Koshinsky, Heather, Shaw, Tambi, Cilnis, Martin, Posey, Jamie, Rose, Jordan, Weber, Terry, Fofanov, Viacheslav Y., Gagneux, Sebastien, Kato-Maeda, Midori, Metcalfe, John Z., Coscolla, Mireia, Barry, Pennan M., Oeltmann, John E., Koshinsky, Heather, Shaw, Tambi, Cilnis, Martin, Posey, Jamie, Rose, Jordan, Weber, Terry, Fofanov, Viacheslav Y., Gagneux, Sebastien, Kato-Maeda, Midori, and Metcalfe, John Z.

Abstract

The transcontinental spread of multidrug-resistant (MDR) tuberculosis is poorly characterized in molecular epidemiologic studies. We used genomic sequencing to understand the establishment and dispersion of MDR Mycobacterium tuberculosis within a group of immigrants to the United States. We used a genomic epidemiology approach to study a genotypically matched (by spoligotype, IS6110 restriction fragment length polymorphism, and mycobacterial interspersed repetitive units-variable number of tandem repeat signature) lineage 2/Beijing MDR strain implicated in an outbreak of tuberculosis among refugees in Thailand and consecutive cases within California. All 46 MDR M. tuberculosis genomes from both Thailand and California were highly related, with a median difference of 10 single-nucleotide polymorphisms (SNPs). The Wat Tham Krabok (WTK) strain is a new sequence type distinguished from all known Beijing strains by 55 SNPs and a genomic deletion (Rv1267c) associated with increased fitness. Sequence data revealed a highly prevalent MDR strain that included several closely related but distinct allelic variants within Thailand, rather than the occurrence of a single outbreak. In California, sequencing data supported multiple independent introductions of WTK with subsequent transmission and reactivation within the state, as well as a potential super spreader with a prolonged infectious period. Twenty-seven drug resistance-conferring mutations and 4 putative compensatory mutations were found within WTK strains. Genomic sequencing has substantial epidemiologic value in both low- and high-burden settings in understanding transmission chains of highly prevalent MDR strains

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