The DOI matches its Crossref record; 66 of the 66 references it cites were found in a registry or an index.
Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis
Open accessAbstract
Roland Brosch and colleagues report whole-genome sequencing of tubercle bacilli with smooth colony morphology, also known as Mycobacterium canetti and/or Mycobacterium prototuberculosis, obtained from humans with tuberculosis from geographically diverse regions. Their comparative genomic analysis with Mycobacterium tuberculosis and other M. tuberculosis complex members identifies extensive recombination and provides insights into the evolution of mycobacteria. The authors also report that tubercle bacilli with smooth colony morphology show reduced persistence and virulence compared to M. tuberculosis strains in infection experiments in mice. Global spread and limited genetic variation are hallmarks of M. tuberculosis, the agent of human tuberculosis. In contrast, Mycobacterium canettii and related tubercle bacilli that also cause human tuberculosis and exhibit unusual smooth colony morphology are restricted to East Africa. Here, we sequenced and analyzed the whole genomes of five representative strains of smooth tubercle bacilli (STB) using Sanger (4–5× coverage), 454/Roche (13–18× coverage) and/or Illumina DNA sequencing (45–105× coverage). We show that STB isolates are highly recombinogenic and evolutionarily early branching, with larger genome sizes, higher rates of genetic variation, fewer molecular scars and distinct CRISPR-Cas systems relative to M. tuberculosis. Despite the differences, all tuberculosis-causing mycobacteria share a highly conserved core genome. Mouse infection experiments showed that STB strains are less persistent and virulent than M. tuberculosis. We conclude that M. tuberculosis emerged from an ancestral STB-like pool of mycobacteria by gain of persistence and virulence mechanisms, and we provide insights into the molecular events involved.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“That concept was challenged when the comparative analysis of multiple genome sequences of Mycobacterium canettii (a smooth colony outlier of the MTBC) revealed thousands of SNPs: the striking similarity to the experimentally produced mosaic genomes of M. smegmatis provided the first indication that HGT had occurred in the MTBC (48–51).”
From Mycobacterium smegmatis: The Vanguard of Mycobacterial Research (2023) · cites this paper as [49]
Experimental — accuracy not yet measuredIn the citing paper
“representing a group of rare tubercle bacilli that are thought to resemble the ancestor of M. tuberculosis and have been isolated mainly from tuberculosis patients in the region of the Horn of Africa (East Africa) (56,57).”
From ESX/Type VII Secretion Systems—An Important Way Out for Mycobacterial Proteins (2019) · cites this paper as [56]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Saitou, N., & Nei, M. (1987) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040454 · Cited by 59,959
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
Velvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,587
Application of Phylogenetic Networks in Evolutionary Studies
Huson, D. H., & Bryant, D. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj030 · Cited by 8,895
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
Cole, S. T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S. V., Eiglmeier, K., Gas, S., Barry, C. E., et al. (1998) · Nature · doi:10.1038/31159 · Cited by 7,847
Self-citationShifting the genomic gold standard for the prokaryotic species definition
Richter, M., & Rossello-Mora, R. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906412106 · Cited by 6,343
DNA–DNA hybridization values and their relationship to whole-genome sequence similarities
Goris, J., Konstantinidis, K. T., Klappenbach, J. A., Coenye, T., Vandamme, P. A. R., & Tiedje, J. M. (2007) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.64483-0 · Cited by 4,733
Maiden, M. C. J., Bygraves, J. A., Feil, E. J., Morelli, G., Russell, J. E., Urwin, R., Zhang, Q., Zhou, J., Zurth, K., Caugant, D. A., et al. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.6.3140 · Cited by 3,891
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
Darling, A. E., Mau, B., & Perna, N. T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011147 · Cited by 3,848
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
Suyama, M., Torrents, D., & Bork, P. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl315 · Cited by 3,270
Cited by
Sorted by citations
Ecology and evolution of Mycobacterium tuberculosis
Gagneux, S. (2018) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2018.8 · Cited by 618
Consequences of genomic diversity in Mycobacterium tuberculosis
Coscollá, M., & Gagneux, S. (2014) · Seminars in Immunology · doi:10.1016/j.smim.2014.09.012 · Cited by 474
ESX secretion systems: mycobacterial evolution to counter host immunity
Gröschel, M. I., Sayes, F., Simeone, R., Majlessi, L., & Brosch, R. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.131 · Cited by 382
Self-citationCo‐evolution of M ycobacterium tuberculosis and H omo sapiens
Brites, D., & Gagneux, S. (2015) · Immunological Reviews · doi:10.1111/imr.12264 · Cited by 317
The Mycobacterial Cell Envelope--LipidsPreprint
Jackson, M. (2014) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a021105 · Cited by 282
Gene silencing by CRISPR interference in mycobacteria
Choudhary, E., Thakur, P., Pareek, M., & Agarwal, N. (2015) · Nature Communications · doi:10.1038/ncomms7267 · Cited by 253
THE BIOLOGY OF MYCOBACTERIUM TUBERCULOSIS INFECTION.
Delogu, G., Sali, M., & Fadda, G. (2013) · Mediterranean Journal of Hematology and Infectious Diseases · doi:10.4084/mjhid.2013.070 · Cited by 279
Genomic insights into tuberculosis
Galagan, J. E. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3664 · Cited by 251
GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands
Lassalle, F., Perian, S., Bataillon, T. M., Nesme, X., Duret, L., & Daubin, V. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1004941 · Cited by 218
Ngabonziza, J. C. S., Loiseau, C., Marceau, M., Jouet, A., Menardo, F., Tzfadia, O., Antoine, R., Niyigena, E. B., Mulders, W., Fissette, K., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16626-6 · Cited by 229
Self-citationSafi, H., Lingaraju, S., Amin, A. G., Kim, S., Jones, M. B., Holmes, M. H., McNeil, M., Peterson, S. N., Chatterjee, D., Fleischmann, R., et al. (2013) · Nature Genetics · doi:10.1038/ng.2743 · Cited by 209
Vallenet, D., Calteau, A., Cruveiller, S., Gachet, M., Lajus, A., Josso, A., Mercier, J., Renaux, A., Rollin, J., Rouy, Z., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1101 · Cited by 212
Self-citationA New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex
Brites, D., Loiseau, C., Menardo, F., Borrell, S., Boniotti, M. B., Warren, R. M., Dippenaar, A., Parsons, S. D. C., Beisel, C., Behr, M. A., et al. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02820 · Cited by 207
Simeone, R., Sayes, F., Song, O., Gröschel, M. I., Brodin, P., Brosch, R., & Majlessi, L. (2015) · PLOS Pathogens · doi:10.1371/journal.ppat.1004650 · Cited by 198
Self-citationPhylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history
Coscollá, M., Gagneux, S., Menardo, F., Loiseau, C., Ruiz-Rodríguez, P., Borrell, S., Otchere, I. D., Asante-Poku, A., Asare, P. P. A., Sánchez-Busó, L., et al. (2021) · Microbial Genomics · doi:10.1099/mgen.0.000477 · Cited by 208
Self-citationPawlik, A., Garnier, G., Orgeur, M., Tong, P., Lohan, A. J., Chevalier, F. L., Sapriel, G., Roux, A., Conlon, K. M., Honoré, N., et al. (2013) · Molecular Microbiology · doi:10.1111/mmi.12387 · Cited by 194
Self-citationEvolutionary history of tuberculosis shaped by conserved mutations in the PhoPR virulence regulator
Gonzalo‐Asensio, J., Malaga, W., Pawlik, A., Astarie‐Dequeker, C., Passemar, C., Moreau, F., Laval, F., Daffé, M., Martı́n, C., Brosch, R., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1406693111 · Cited by 195
Self-citationMycobacterium tuberculosis: ecology and evolution of a human bacterium
Bañuls, A., Sanou, A., Anh, N. T. V., & Godreuil, S. (2015) · Journal of Medical Microbiology · doi:10.1099/jmm.0.000171 · Cited by 184
The cell envelope glycoconjugates ofMycobacterium tuberculosis
Angala, S. K., Belardinelli, J. M., Huc‐Claustre, E., Wheat, W. H., & Jackson, M. (2014) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409238.2014.925420 · Cited by 168
Jagielski, T., Minias, A. E., van Ingen, J., Rastogi, N., Brzostek, A. M., Żaczek, A., & Dziadek, J. (2016) · Clinical Microbiology Reviews · doi:10.1128/cmr.00055-15 · Cited by 169
Rodríguez, S., Smith, N. H., Boniotti, M. B., & Aranaz, A. (2014) · Research in Veterinary Science · doi:10.1016/j.rvsc.2014.02.009 · Cited by 177
Kanabalan, R. D., Lee, L. J., Lee, T. Y., Chong, P. P., Hassan, L., Ismail, R., & Chin, V. K. (2021) · Microbiological Research · doi:10.1016/j.micres.2020.126674 · Cited by 188
Stepwise pathogenic evolution of Mycobacterium abscessus
Bryant, J. M., Brown, K., Burbaud, S., Everall, I., Belardinelli, J. M., Rodriguez-Rincon, D., Grogono, D., Peterson, C. M., Verma, D., Evans, I., et al. (2021) · Science · doi:10.1126/science.abb8699 · Cited by 159
Self-citationMycobacterium smegmatis: The Vanguard of Mycobacterial Research
Sparks, I. L., Derbyshire, K. M., Jacobs, W. R., & Morita, Y. S. (2023) · Journal of Bacteriology · doi:10.1128/jb.00337-22 · Cited by 149
Mycobacterium:General Characteristics, Laboratory Detection, and Staining Procedures
Pfyffer, G. E. (2015) · ASM Press eBooks · doi:10.1128/9781555817381.ch30 · Cited by 153
Coscollá, M., Copin, R., Sutherland, J. S., Gehre, F., de Jong, B. C., Owolabi, O., Mbayo, G., Giardina, F., Ernst, J., & Gagneux, S. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.10.008 · Cited by 141
The Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations
Pepperell, C. S., Casto, A. M., Kitchen, A., Granka, J. M., Cornejo, O. E., Holmes, E. C., Birren, B. W., Galagan, J. E., & Feldman, M. W. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003543 · Cited by 133
Aguiló, N., Gonzalo‐Asensio, J., Álvarez-Arguedas, S., Marinova, D., Gómez, A. B., Uranga, S., Spallek, R., Singh, M., Audran, R., Spertini, F., et al. (2017) · Nature Communications · doi:10.1038/ncomms16085 · Cited by 129
Wang, X., Cai, Z., Wang, Q., Wu, C., Sun, Y., Wang, Z., Xu, X., Xue, W., Cao, Z., Zhang, M., et al. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.11.005 · Cited by 128
Boritsch, E. C., Khanna, V., Pawlik, A., Honoré, N., Navas, V. H., Ma, L., Bouchier, C., Seemann, T., Supply, P., Stinear, T. P., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1604921113 · Cited by 111
Self-citationDumas, E., Christina Boritsch, E., Vandenbogaert, M., Rodríguez de la Vega, R. C., Thiberge, J.-M., Caro, V., Gaillard, J.-L., Heym, B., Girard-Misguich, F., Brosch, R., et al. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw001 · Cited by 112
Self-citationJouet, A., Gaudin, C., Badalato, N., Allix‐Béguec, C., Duthoy, S., Ferré, A., Diels, M., Laurent, Y., Contreras, S., Feuerriegel, S., et al. (2020) · European Respiratory Journal · doi:10.1183/13993003.02338-2020 · Cited by 114
Self-citationBottai, D., Frigui, W., Sayes, F., Luca, M. D., Spadoni, D., Pawlik, A., Zoppo, M., Orgeur, M., Khanna, V., Hardy, D., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14508-5 · Cited by 112
Self-citationEvolution of virulence in the Mycobacterium tuberculosis complex
Orgeur, M., & Brosch, R. (2018) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.11.021 · Cited by 107
Self-citationThe Enigmatic PE/PPE Multigene Family of Mycobacteria and Tuberculosis Vaccination
Brennan, M. J. (2017) · Infection and Immunity · doi:10.1128/iai.00969-16 · Cited by 107
Cao, Y., Parmar, H., Gaur, R. L., Lieu, D., Raghunath, S., Via, N., Battaglia, S., Cirillo, D. M., Denkinger, C. M., Georghiou, S. B., et al. (2020) · Journal of Clinical Microbiology · doi:10.1128/jcm.02314-20 · Cited by 108
Mycobacterium tuberculosis MetabolismPreprint
Warner, D. F. (2014) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a021121 · Cited by 108
PolyTB: A genomic variation map for Mycobacterium tuberculosis
Coll, F., Preston, M. D., Guerra‐Assunção, J. A., Hill-Cawthorne, G. A., Harris, D. E., Perdigão, J., Viveiros, M., Portugal, I., Drobniewski, F. A., Gagneux, S., et al. (2014) · Tuberculosis · doi:10.1016/j.tube.2014.02.005 · Cited by 109
Self-citationpks5-recombination-mediated surface remodelling in Mycobacterium tuberculosis emergence
Boritsch, E. C., Frigui, W., Cascioferro, A., Malaga, W., Etienne, G., Laval, F., Pawlik, A., Le Chevalier, F., Orgeur, M., Ma, L., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2015.19 · Cited by 104
Self-citationAntimicrobial Resistance in Mycobacterium tuberculosis : The Odd One Out
Eldholm, V., & Balloux, F. (2016) · Trends in Microbiology · doi:10.1016/j.tim.2016.03.007 · Cited by 104
Comas, I., Hailu, E., Kiros, T., Bekele, S., Mekonnen, W., Gumi, B., Tschopp, R., Ameni, G., Hewinson, R. G., Robertson, B. D., et al. (2015) · Current Biology · doi:10.1016/j.cub.2015.10.061 · Cited by 102
Gray, T. A., Krywy, J. A., Harold, J., Palumbo, M. J., & Derbyshire, K. M. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001602 · Cited by 100
Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex
Chiner‐Oms, Á., Sánchez-Busó, L., Corander, J., Gagneux, S., Harris, S. R., Young, D. B., Gónzález‐Candelas, F., & Comas, I. (2019) · Science Advances · doi:10.1126/sciadv.aaw3307 · Cited by 102
Molecular Genetics of Mycobacteriophages
Hatfull, G. F. (2014) · Microbiology Spectrum · doi:10.1128/microbiolspec.mgm2-0032-2013 · Cited by 100
Clinical value of whole-genome sequencing of Mycobacterium tuberculosis
Takiff, H. E., & Feo, O. (2015) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(15)00071-7 · Cited by 96
Abdallah, A. M., Hill-Cawthorne, G. A., Otto, T. D., Coll, F., Guerra‐Assunção, J. A., Gao, G., Naeem, R., Ansari, H. R., Malas, T. B., Adroub, S. A., et al. (2015) · Scientific Reports · doi:10.1038/srep15443 · Cited by 102
Self-citationThe role of hydrophobicity in tuberculosis evolution and pathogenicity
Jankute, M., Nataraj, V., Lee, O. Y.-C., Wu, H. H. T., Ridell, M., Garton, N. J., Barer, M. R., Minnikin, D. E., Bhatt, A., & Besra, G. S. (2017) · Scientific Reports · doi:10.1038/s41598-017-01501-0 · Cited by 96
Solans, L., Aguiló, N., Samper, S., Pawlik, A., Frigui, W., Martı́n, C., Brosch, R., & Gonzalo‐Asensio, J. (2014) · Infection and Immunity · doi:10.1128/iai.01824-14 · Cited by 107
Self-citationRelease of mycobacterial antigens
Majlessi, L., Prados‐Rosales, R., Casadevall, A., & Brosch, R. (2015) · Immunological Reviews · doi:10.1111/imr.12251 · Cited by 93
Self-citationLipid transport in Mycobacterium tuberculosis and its implications in virulence and drug development
Bailo, R., Bhatt, A., & Aínsa, J. A. (2015) · Biochemical Pharmacology · doi:10.1016/j.bcp.2015.05.001 · Cited by 93
Insights on the Emergence of Mycobacterium tuberculosis from the Analysis of Mycobacterium kansasii
Wang, J., McIntosh, F. A., Radomski, N., Dewar, K., Siméone, R., Enninga, J., Brosch, R., Rocha, E. P. C., Veyrier, F. J., & Behr, M. A. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv035 · Cited by 98
Self-citationBoritsch, E. C., Supply, P., Honoré, N., Seeman, T., Stinear, T. P., & Brosch, R. (2014) · Molecular Microbiology · doi:10.1111/mmi.12720 · Cited by 92
Self-citationMaio, F. D., Berisio, R., Manganelli, R., & Delogu, G. (2020) · Virulence · doi:10.1080/21505594.2020.1785815 · Cited by 89
Evolution and emergence ofMycobacterium tuberculosis
Orgeur, M., Sous, C., Madacki, J., & Brosch, R. (2024) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuae006 · Cited by 97
Self-citationToxin–antitoxin systems and regulatory mechanisms in Mycobacterium tuberculosis
Slayden, R. A., Dawson, C. C., & Cummings, J. E. (2018) · Pathogens and Disease · doi:10.1093/femspd/fty039 · Cited by 82
Blending genomes: distributive conjugal transfer in mycobacteria, a sexier form of HGT
Gray, T. A., & Derbyshire, K. M. (2018) · Molecular Microbiology · doi:10.1111/mmi.13971 · Cited by 70
Krasnov, G. S., Dmitriev, A. A., Kudryavtseva, A. V., Shargunov, A., Karpov, D. S., Урошлев, Л. А., Melnikova, N. V., Blinov, V. M., Poverennaya, E. V., Archakov, A. I., et al. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00490 · Cited by 81
Diversity and Evolution of Mycobacterium tuberculosis: Moving to Whole-Genome-Based ApproachesPreprint
Niemann, S., & Supply, P. (2014) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a021188 · Cited by 83
Self-citationThe Nature and Evolution of Genomic Diversity in the Mycobacterium tuberculosis Complex
Brites, D., & Gagneux, S. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-64371-7_1 · Cited by 88
Siméone, R., Bottai, D., Frigui, W., Majlessi, L., & Brosch, R. (2015) · Tuberculosis · doi:10.1016/j.tube.2015.02.019 · Cited by 79
Self-citationGonzalo‐Asensio, J., Pérez, I., Aguiló, N., Uranga, S., Picó, A., Lampreave, C., Cebollada, A., Otal, I., Samper, S., & Martı́n, C. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007282 · Cited by 79
Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications
Sapriel, G., Konjek, J., Orgeur, M., Bouri, L., Frézal, L., Roux, A., Dumas, É., Brosch, R., Bouchier, C., Brisse, S., et al. (2016) · BMC Genomics · doi:10.1186/s12864-016-2448-1 · Cited by 82
Self-citationDerbyshire, K. M., & Gray, T. A. (2014) · Microbiology Spectrum · doi:10.1128/microbiolspec.mgm2-0022-2013 · Cited by 75
Palucci, I., Camassa, S., Cascioferro, A., Sali, M., Anoosheh, S., Zumbo, A., Minerva, M., Iantomasi, R., Maio, F. D., Sante, G. D., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0150800 · Cited by 74
Self-citationProgenitor “Mycobacterium canettii” Clone Responsible for Lymph Node Tuberculosis Epidemic, Djibouti
Blouin, Y., Cazajous, G., Dehan, C., Soler, C., Vong, R., Hassan, M. O., Hauck, Y., Boulais, C., Andriamanantena, D., Martinaud, C., et al. (2014) · Emerging infectious diseases · doi:10.3201/eid2001.130652 · Cited by 79
Global Distribution and Evolution of Mycobacterium bovis Lineages
Zimpel, C. K., Patané, J. S. L., Guedes, A. C. P., de Souza, R. F., Silva‐Pereira, T. T., Camargo, N., Filho, A. F. D. S., Ikuta, C. Y., Neto, J. S. F., Setúbal, J. C., et al. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00843 · Cited by 72
Population genomics of Mycobacterium tuberculosis in the Inuit
Lee, R. S., Radomski, N., Proulx, J., Levade, I., Shapiro, B. J., McIntosh, F. A., Soualhine, H., Menzies, D., & Behr, M. A. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1507071112 · Cited by 72
The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex
Merker, M., Kohl, T. A., Niemann, S., & Supply, P. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-64371-7_3 · Cited by 73
Self-citationDiversity and disease pathogenesis in Mycobacterium tuberculosis
Warner, D. F., Koch, A. S., & Mizrahi, V. (2014) · Trends in Microbiology · doi:10.1016/j.tim.2014.10.005 · Cited by 71
Ecology, global diversity and evolutionary mechanisms in the Mycobacterium tuberculosis complex
Goig, G. A., Windels, E. M., Loiseau, C., Stritt, C., Biru, L., Borrell, S., Brites, D., & Gagneux, S. (2025) · Nature Reviews Microbiology · doi:10.1038/s41579-025-01159-w · Cited by 75
Vitamin B 12 Metabolism in Mycobacterium Tuberculosis
Gopinath, K., Moosa, A., Mizrahi, V., & Warner, D. F. (2013) · Future Microbiology · doi:10.2217/fmb.13.113 · Cited by 68
Types and functions of heterogeneity in mycobacteria
Chung, E. S., Johnson, W. C., & Aldridge, B. B. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00721-0 · Cited by 61
Copin, R., Coscollá, M., Efstathiadis, E., Gagneux, S., & Ernst, J. (2014) · Vaccine · doi:10.1016/j.vaccine.2014.07.113 · Cited by 65
Panas, M. W., Jain, P., Yang, H., Mitra, S., Biswas, D., Wattam, A. R., Letvin, N. L., & Jacobs, W. R. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1414207111 · Cited by 62
An ancestral mycobacterial effector promotes dissemination of infection
Saelens, J. W., Sweeney, M. I., Viswanathan, G., Xet-Mull, A. M., Smith, K. L. J., Sisk, D. M., Hu, D. D., Cronin, R. M., Hughes, E. J., Brewer, W. J., et al. (2022) · Cell · doi:10.1016/j.cell.2022.10.019 · Cited by 58
Multilocus sequence typing scheme for the Mycobacterium abscessus complex
Macheras, E., Konjek, J., Roux, A., Thiberge, J.-M., Bastian, S., Leão, S. C., Palaci, M., Sivadon‐Tardy, V., Gutierrez, C., Richter, E., et al. (2014) · Research in Microbiology · doi:10.1016/j.resmic.2013.12.003 · Cited by 66
Self-citationType VII Secretion Systems in Gram-Positive Bacteria
Bottai, D., Gröschel, M. I., & Brosch, R. (2015) · Current topics in microbiology and immunology · doi:10.1007/82_2015_5015 · Cited by 60
Self-citationYano, H., Iwamoto, T., Nishiuchi, Y., Nakajima, C., Starkova, D. A., Владиславович, М. И., Narvskaya, O. V., Yoshida, S., Arikawa, K., Nakanishi, N., et al. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx183 · Cited by 57
Mycobacterium tuberculosis Metabolism
Mashabela, G. T., de Wet, T. J., & Warner, D. F. (2019) · Microbiology Spectrum · doi:10.1128/microbiolspec.gpp3-0067-2019 · Cited by 57
ESX/Type VII Secretion Systems—An Important Way Out for Mycobacterial Proteins
Vaziri, F., & Brosch, R. (2019) · Microbiology Spectrum · doi:10.1128/microbiolspec.psib-0029-2019 · Cited by 50
Self-citationThe Evolutionary History, Demography, and Spread of the Mycobacterium tuberculosis Complex
Barbier, M., & Wirth, T. (2016) · Microbiology Spectrum · doi:10.1128/microbiolspec.tbtb2-0008-2016 · Cited by 58
Ancient mycobacterial lipids: Key reference biomarkers in charting the evolution of tuberculosis
Minnikin, D. E., Lee, O. Y.-C., Wu, H. H. T., Besra, G. S., Bhatt, A., Nataraj, V., Rothschild, B. M., Spigelman, M., & Donoghue, H. D. (2015) · Tuberculosis · doi:10.1016/j.tube.2015.02.009 · Cited by 53
Mycobacterial Pathogenomics and Evolution
Bottai, D., Stinear, T. P., Supply, P., & Brosch, R. (2014) · Microbiology Spectrum · doi:10.1128/microbiolspec.mgm2-0025-2013 · Cited by 55
Self-citationRevisiting the role of phospholipases C in virulence and the lifecycle of Mycobacterium tuberculosis
Chevalier, F. L., Cascioferro, A., Frigui, W., Pawlik, A., Boritsch, E. C., Bottai, D., Majlessi, L., Herrmann, J., & Brosch, R. (2015) · Scientific Reports · doi:10.1038/srep16918 · Cited by 51
Self-citationMycobacterial Evolution Intersects With Host Tolerance
Saelens, J. W., Viswanathan, G., & Tobin, D. M. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.00528 · Cited by 52
Ates, L. S., Sayes, F., Frigui, W., Ummels, R., Damen, M. P. M., Bottai, D., Behr, M. A., van Heijst, J. W. J., Bitter, W., Majlessi, L., et al. (2018) · PLoS Pathogens · doi:10.1371/journal.ppat.1007139 · Cited by 44
Self-citationLevillain, F., Poquet, Y., Mallet, L., Mazères, S., Marceau, M., Brosch, R., Bange, F., Supply, P., Magalon, A., & Neyrolles, O. (2017) · PLoS Pathogens · doi:10.1371/journal.ppat.1006752 · Cited by 46
Self-citationMinnikin, D. E., Lee, O. Y.-C., Wu, H. H. T., Nataraj, V., Donoghue, H. D., Ridell, M., Watanabe, M., Alderwick, L., Bhatt, A., & Besra, G. S. (2015) · Tuberculosis - Expanding Knowledge · doi:10.5772/59585 · Cited by 43
Peters, J. S., Ismail, N. A., Dippenaar, A., Ma, S., Sherman, D. R., Warren, R. M., & Kana, B. D. (2020) · Annual Review of Genetics · doi:10.1146/annurev-genet-022820-085940 · Cited by 43
Wlodarska, M., Johnston, J. C., Gardy, J. L., & Tang, P. (2015) · Clinical Microbiology Reviews · doi:10.1128/cmr.00124-14 · Cited by 42
Slama, N., Jamet, S., Frigui, W., Pawlik, A., Bottai, D., Laval, F., Constant, P., Lemassu, A., Cam, K., Daffé, M., et al. (2015) · Molecular Microbiology · doi:10.1111/mmi.13266 · Cited by 41
Self-citationPaleomicrobiology of Human Tuberculosis
Donoghue, H. D. (2016) · Microbiology Spectrum · doi:10.1128/microbiolspec.poh-0003-2014 · Cited by 45
Donoghue, H. D., Spigelman, M., O’Grady, J., Szikossy, I., Pap, I., Lee, O. Y.-C., Wu, H. H. T., Besra, G. S., & Minnikin, D. E. (2015) · Tuberculosis · doi:10.1016/j.tube.2015.02.020 · Cited by 43
Sapriel, G., & Brosch, R. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz162 · Cited by 42
Self-citationGenomic Signatures of Distributive Conjugal Transfer among Mycobacteria
Mortimer, T. D., & Pepperell, C. S. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu175 · Cited by 40
Zumbo, A., Palucci, I., Cascioferro, A., Sali, M., Ventura, M., D’Alfonso, P., Iantomasi, R., Sante, G. D., Ria, F., Sanguinetti, M., et al. (2013) · Pathogens and Disease · doi:10.1111/2049-632x.12096 · Cited by 40
Self-citationIncreased Phagocytosis of Mycobacterium marinum Mutants Defective in Lipooligosaccharide Production
Alibaud, L., Pawełczyk, J., Gannoun-Zaki, L., Singh, V. K., Rombouts, Y., Drancourt, M., Dziadek, J., Guérardel, Y., & Kremer, L. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.525550 · Cited by 46
Winglee, K., Manson, A. L., Maïga, M., Abeel, T., Shea, T., Desjardins, C. A., Diarra, B., Baya, B., Sanogo, M., Diallo, S., et al. (2016) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0004332 · Cited by 39
Houghton, J., Cortes, T., Schubert, O. T., Rose, G., Rodgers, A., Croix, M. D. S., Aebersold, R. H., Young, D. B., & Arnvig, K. B. (2013) · PLoS ONE · doi:10.1371/journal.pone.0080047 · Cited by 40
The global tuberculosis situation and the inexorable rise of drug-resistant disease
Marais, B. J. (2016) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2016.01.021 · Cited by 39
Metadata
- Authors
- Supply, P., Marceau, M., Mangenot, S., Roche, D., Rouanet, C., Khanna, V., Majlessi, L., Criscuolo, A., Tap, J., Pawlik, A., Fiette, L., Orgeur, M., Fabre, M., Parmentier, C., Frigui, W., Simeone, R., Boritsch, E. C., Debrie, A.-S., Willery, E., Walker, D., Quail, M. A., Ma, L., Bouchier, C., Salvignol, G., Sayes, F., Cascioferro, A., Seemann, T., Barbe, V., Locht, C., Gutierrez, M.-C., Leclerc, C., Bentley, S. D., Stinear, T. P., Brisse, S., Médigue, C., Parkhill, J., Cruveiller, S., & Brosch, R.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
- Institut Pasteur (FR)
- Inserm (FR)
- Hôpital d'instruction des Armées Percy (FR)
- Wellcome Sanger Institute (GB)
- Monash University (AU)
- The University of Melbourne (AU)
- Corresponding author
- Supply, Philip
- Brosch, Roland
- ORCID
- Supply, Philip
- Mangenot, Sophie
- Roche, David
- Rouanet, Carine
- Khanna, Varun
- Majlessi, Laleh
- Criscuolo, Alexis
- Tap, Julien
- Pawlik, Alexandre
- Frigui, Wafa
- Debrie, Anne-Sophie
- Quail, Michael A
- Ma, Laurence
- Bouchier, Christiane
- Salvignol, Grégory
- Sayes, Fadel
- Cascioferro, Alessandro
- Seemann, Torsten
- Barbe, Valérie
- Locht, Camille
- Gutierrez, Maria-Cristina
- Leclerc, Claude
- Bentley, Stephen D
- Stinear, Timothy P
- Brisse, Sylvain
- Médigue, Claudine
- Parkhill, Julian
- Cruveiller, Stéphane
- Brosch, Roland
- Venue
- Nature Genetics
- Published
- 2013-01-06
- Volume
- 45
- Issue
- 2
- Pages
- 172-179
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC3856870
- OpenAlex
- W2005360702
- Cited by
- 305
- References
- 66
- Citations by year
- 2026: 11 · 2025: 14 · 2024: 11 · 2023: 18 · 2022: 12 · 2021: 24 · 2020: 25 · 2019: 21 · 2018: 12 · 2017: 27 · 2016: 30 · 2015: 39 · 2014: 44 · 2013: 15
- FWCI
- 31.13
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc-sa
- www.springer.com/tdm (unspecified)
- Locations
- Nature Genetics (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion, other-oa)
- Minerva Access (University of Melbourne) (submittedVersion)
- LillOA (Université de Lille (University Of Lille)) (submittedVersion, other-oa)
- Funders
- Wellcome Trust (098051)
- European Commission (260872)
- Agence Nationale de la Recherche (ANR-10-INBS-0009)
- Topics
- Health Sciences › Medicine › Infectious Diseases › Tuberculosis Research and Epidemiology
- Health Sciences › Medicine › Epidemiology › Mycobacterium research and diagnosis
- Health Sciences › Medicine › Infectious Diseases › Infectious Diseases and Tuberculosis
- Keywords
- Mycobacterium tuberculosis, Mycobacterium tuberculosis complex, recombination, bacterial evolution, pathoadaptation, virulence, persistence, CRISPR-Cas, core genome, East Africa
- MeSH terms
- Adaptation, Biological, Animals, Base Sequence, Lung, Mice, Inbred BALB C, Molecular Sequence Data, Mycobacterium tuberculosis, Phylogeny, Species Specificity, Spleen, Genetic Variation, Virulence, Cluster Analysis, Genome, Bacterial, Sequence Analysis, DNA, Evolution, Molecular, Polymorphism, Single Nucleotide, Genomics, Mice, Inverted Repeat Sequences
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
