{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T20:32:06Z","timestamp":1790541126912,"version":"4.1.0"},"reference-count":81,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,8,12]],"date-time":"2019-08-12T00:00:00Z","timestamp":1565568000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2019,8,12]],"date-time":"2019-08-12T00:00:00Z","timestamp":1565568000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p><jats:italic>Mycobacterium bovis<\/jats:italic> is responsible for bovine tuberculosis in both animals and humans. Despite being one of the most important global zoonotic disease, data related to the ecology and pathogenicity of bovine tuberculosis is scarce, especially in developing countries. In this report, we examined the dynamics of <jats:italic>M. bovis<\/jats:italic> transmission among dairy cattle in the Nile Delta of Egypt. Animals belonging to 27 herds from 7 governorates were tested by the Single Intradermal Comparative Skin Tuberculin (SICST), as a preliminary screen for the presence of bovine tuberculosis. Positive SICST reactors were identified in 3% of the animals spread among 40% of the examined herds. Post-mortem examination of slaughtered reactors confirmed the presence of both pulmonary and\/or digestive forms of tuberculosis in\u2009&gt;\u200950% of the examined animals. Targeted and whole-genome analysis of <jats:italic>M. bovis<\/jats:italic> isolates indicated the emergences of a predominant spoligotype (SB0268) between 2013\u20132015, suggesting a recent clonal spread of this isolate within the Nile Delta. Surprisingly, 2 isolates belonged to <jats:italic>M. bovis<\/jats:italic> BCG group, which are not allowed for animal vaccination in Egypt, while the rest of isolates belonged to the virulent <jats:italic>M. bovis<\/jats:italic> clonal complex European 2 present in Latin America and several European countries. Analysis of strain virulence in the murine model of tuberculosis indicated the emergence of a more virulent strain (MBE4) with a specific genotype. More analysis is needed to understand the molecular basis for successful spread of virulent isolates of bovine tuberculosis among animals and to establish genotype\/phenotype association.<\/jats:p>","DOI":"10.1038\/s41598-019-48106-3","type":"journal-article","created":{"date-parts":[[2019,8,12]],"date-time":"2019-08-12T10:03:15Z","timestamp":1565604195000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Genomic Polymorphism Associated with the Emergence of Virulent Isolates of Mycobacterium bovis in the Nile Delta"],"prefix":"10.1038","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6559-5936","authenticated-orcid":false,"given":"Hazem F. M.","family":"Abdelaal","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Spalink","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ali","family":"Amer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Howard","family":"Steinberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emad A.","family":"Hashish","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Essam A.","family":"Nasr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adel M.","family":"Talaat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,8,12]]},"reference":[{"key":"48106_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/0378-1135(94)90041-8","volume":"40","author":"Proceedings of the International Conference on Mycobacterium bovis.","year":"1994","unstructured":"Proceedings of the International Conference on Mycobacterium bovis. Dublin, Ireland, 20\u201321 August 1991. Vet Microbiol 40, 1\u2013205 (1994).","journal-title":"Vet Microbiol"},{"key":"48106_CR2","first-page":"135","volume":"45","author":"CO Thoen","year":"2009","unstructured":"Thoen, C. O., Lobue, P. A., Enarson, D. A., Kaneene, J. B. & de Kantor, I. N. Tuberculosis: a re-emerging disease in animals and humans. Veterinaria italiana 45, 135\u2013181 (2009).","journal-title":"Veterinaria italiana"},{"key":"48106_CR3","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/j.cimid.2007.07.003","volume":"31","author":"JC Hope","year":"2008","unstructured":"Hope, J. C. & Villarreal-Ramos, B. Bovine TB and the development of new vaccines. Comparative immunology, microbiology and infectious diseases 31, 77\u2013100, https:\/\/doi.org\/10.1016\/j.cimid.2007.07.003 (2008).","journal-title":"Comparative immunology, microbiology and infectious diseases"},{"key":"48106_CR4","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1017\/S0950268800067686","volume":"99","author":"JM Grange","year":"1987","unstructured":"Grange, J. M. & Collins, C. H. Bovine tubercle bacilli and disease in animals and man. Epidemiol Infect 99, 221\u2013234 (1987).","journal-title":"Epidemiol Infect"},{"key":"48106_CR5","doi-asserted-by":"publisher","first-page":"16076","DOI":"10.1038\/nrdp.2016.76","volume":"2","author":"M Pai","year":"2016","unstructured":"Pai, M. et al. Tuberculosis. Nat Rev Dis Primers 2, 16076, https:\/\/doi.org\/10.1038\/nrdp.2016.76 (2016).","journal-title":"Tuberculosis. Nat Rev Dis Primers"},{"key":"48106_CR6","doi-asserted-by":"publisher","first-page":"733","DOI":"10.20506\/rst.14.3.875","volume":"14","author":"O Cosivi","year":"1995","unstructured":"Cosivi, O., Meslin, F. X., Daborn, C. J. & Grange, J. M. Epidemiology of Mycobacterium bovis infection in animals and humans, with particular reference to Africa. Rev. Sci.Tech. 14, 733\u2013746 (1995).","journal-title":"Rev.Sci.Tech."},{"key":"48106_CR7","first-page":"924","volume":"8","author":"WY Ayele","year":"2004","unstructured":"Ayele, W. Y., Neill, S. D., Zinsstag, J., Weiss, M. G. & Pavlik, I. Bovine tuberculosis: an old disease but a new threat to Africa. International Journal of Tuberculosis & Lung Disease 8, 924\u2013937 (2004).","journal-title":"International Journal of Tuberculosis & Lung Disease"},{"key":"48106_CR8","doi-asserted-by":"publisher","first-page":"2389","DOI":"10.3389\/fmicb.2017.02389","volume":"8","author":"CK Zimpel","year":"2017","unstructured":"Zimpel, C. K. et al. Complete Genome Sequencing of Mycobacterium bovis SP38 and Comparative Genomics of Mycobacterium bovis and M. tuberculosis Strains. Front Microbiol 8, 2389, https:\/\/doi.org\/10.3389\/fmicb.2017.02389 (2017).","journal-title":"Front Microbiol"},{"key":"48106_CR9","doi-asserted-by":"publisher","first-page":"3361","DOI":"10.1128\/JCM.00301-11","volume":"49","author":"S Rodriguez-Campos","year":"2011","unstructured":"Rodriguez-Campos, S. et al. Limitations of spoligotyping and variable-number tandem-repeat typing for molecular tracing of Mycobacterium bovis in a high-diversity setting. J Clin Microbiol 49, 3361\u20133364, https:\/\/doi.org\/10.1128\/JCM.00301-11 (2011).","journal-title":"J Clin Microbiol"},{"key":"48106_CR10","doi-asserted-by":"publisher","first-page":"2126","DOI":"10.1128\/JCM.40.6.2126-2133.2002","volume":"40","author":"S Roring","year":"2002","unstructured":"Roring, S. et al. Development of variable-number tandem repeat typing of Mycobacterium bovis: comparison of results with those obtained by using existing exact tandem repeats and spoligotyping. J Clin Microbiol 40, 2126\u20132133 (2002).","journal-title":"J Clin Microbiol"},{"key":"48106_CR11","doi-asserted-by":"publisher","first-page":"e1003008","DOI":"10.1371\/journal.ppat.1003008","volume":"8","author":"R Biek","year":"2012","unstructured":"Biek, R. et al. Whole genome sequencing reveals local transmission patterns of Mycobacterium bovis in sympatric cattle and badger populations. PLoS Pathog 8, e1003008, https:\/\/doi.org\/10.1371\/journal.ppat.1003008 (2012).","journal-title":"PLoS Pathog"},{"key":"48106_CR12","doi-asserted-by":"publisher","first-page":"206","DOI":"10.2460\/javma.251.2.206","volume":"251","author":"CS Bruning-Fann","year":"2017","unstructured":"Bruning-Fann, C. S. et al. Use of whole-genome sequencing and evaluation of the apparent sensitivity and specificity of antemortem tuberculosis tests in the investigation of an unusual outbreak of Mycobacterium bovis infection in a Michigan dairy herd. J Am Vet Med Assoc 251, 206\u2013216, https:\/\/doi.org\/10.2460\/javma.251.2.206 (2017).","journal-title":"J Am Vet Med Assoc"},{"key":"48106_CR13","doi-asserted-by":"publisher","first-page":"e0201981","DOI":"10.1371\/journal.pone.0201981","volume":"13","author":"CA Perea Razo","year":"2018","unstructured":"Perea Razo, C. A. et al. Molecular epidemiology of cattle tuberculosis in Mexico through whole-genome sequencing and spoligotyping. PLoS One 13, e0201981, https:\/\/doi.org\/10.1371\/journal.pone.0201981 (2018).","journal-title":"PLoS One"},{"key":"48106_CR14","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-017-4249-6","volume":"19","author":"M Lasserre","year":"2018","unstructured":"Lasserre, M. et al. Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates. BMC Genomics 19, 2, https:\/\/doi.org\/10.1186\/s12864-017-4249-6 (2018).","journal-title":"BMC Genomics"},{"key":"48106_CR15","doi-asserted-by":"publisher","first-page":"272","DOI":"10.3389\/fvets.2018.00272","volume":"5","author":"M Price-Carter","year":"2018","unstructured":"Price-Carter, M. et al. Whole Genome Sequencing for Determining the Source of Mycobacterium bovis Infections in Livestock Herds and Wildlife in New Zealand. Front Vet Sci 5, 272, https:\/\/doi.org\/10.3389\/fvets.2018.00272 (2018).","journal-title":"Front Vet Sci"},{"key":"48106_CR16","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evx022","author":"JS Patane","year":"2017","unstructured":"Patane, J. S. et al. Patterns and processes of Mycobacterium bovis evolution revealed by phylogenomic analyses. Genome Biol Evol. https:\/\/doi.org\/10.1093\/gbe\/evx022 (2017).","journal-title":"Genome Biol Evol"},{"key":"48106_CR17","doi-asserted-by":"publisher","first-page":"253","DOI":"10.3389\/fvets.2018.00253","volume":"5","author":"K Orloski","year":"2018","unstructured":"Orloski, K., Robbe-Austerman, S., Stuber, T., Hench, B. & Schoenbaum, M. Whole Genome Sequencing of Mycobacterium bovis Isolated From Livestock in the United States, 1989\u20132018. Front Vet Sci 5, 253, https:\/\/doi.org\/10.3389\/fvets.2018.00253 (2018).","journal-title":"Front Vet Sci"},{"key":"48106_CR18","doi-asserted-by":"publisher","unstructured":"Barbier, M. & Wirth, T. The Evolutionary History, Demography, and Spread of the Mycobacterium tuberculosis Complex. Microbiol Spectr 4, https:\/\/doi.org\/10.1128\/microbiolspec.TBTB2-0008-2016 (2016).","DOI":"10.1128\/microbiolspec.TBTB2-0008-2016"},{"key":"48106_CR19","doi-asserted-by":"publisher","first-page":"1274","DOI":"10.1128\/jb.178.5.1274-1282.1996","volume":"178","author":"GG Mahairas","year":"1996","unstructured":"Mahairas, G. G., Sabo, P. J., Hickey, M. J., Singh, D. C. & Stover, C. K. Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M-bovis. Journal of Bacteriology 178, 1274\u20131282 (1996).","journal-title":"Journal of Bacteriology"},{"key":"48106_CR20","doi-asserted-by":"publisher","first-page":"643","DOI":"10.1046\/j.1365-2958.1999.01383.x","volume":"32","author":"SV Gordon","year":"1999","unstructured":"Gordon, S. V. et al. Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays. Molecular.Microbiology. 32, 643\u2013655 (1999).","journal-title":"Molecular.Microbiology."},{"key":"48106_CR21","first-page":"818","volume":"10","author":"RM Warren","year":"2006","unstructured":"Warren, R. M. et al. Differentiation of Mycobacterium tuberculosis complex by PCR amplification of genomic regions of difference. Int J Tuberc Lung Dis 10, 818\u2013822 (2006).","journal-title":"Int J Tuberc Lung Dis"},{"key":"48106_CR22","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.tube.2017.05.003","volume":"106","author":"LD Teeter","year":"2017","unstructured":"Teeter, L. D. et al. Evaluation of 24-locus MIRU-VNTR genotyping in Mycobacterium tuberculosis cluster investigations in four jurisdictions in the United States, 2006\u20132010. Tuberculosis (Edinb) 106, 9\u201315, https:\/\/doi.org\/10.1016\/j.tube.2017.05.003 (2017).","journal-title":"Tuberculosis (Edinb)"},{"key":"48106_CR23","doi-asserted-by":"publisher","first-page":"2692","DOI":"10.1128\/JCM.00540-08","volume":"46","author":"C Allix-Beguec","year":"2008","unstructured":"Allix-Beguec, C., Harmsen, D., Weniger, T., Supply, P. & Niemann, S. Evaluation and strategy for use of MIRU-VNTRplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates. J Clin Microbiol 46, 2692\u20132699, https:\/\/doi.org\/10.1128\/JCM.00540-08 (2008).","journal-title":"J Clin Microbiol"},{"key":"48106_CR24","doi-asserted-by":"publisher","first-page":"e11147","DOI":"10.1371\/journal.pone.0011147","volume":"5","author":"AE Darling","year":"2010","unstructured":"Darling, A. E., Mau, B. & Perna, N. T. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5, e11147, https:\/\/doi.org\/10.1371\/journal.pone.0011147 (2010).","journal-title":"PLoS One"},{"key":"48106_CR25","doi-asserted-by":"publisher","DOI":"10.1186\/s12967-017-1172-1","volume":"15","author":"S Roperto","year":"2017","unstructured":"Roperto, S. et al. Proteomic analysis of protein purified derivative of Mycobacterium bovis. J Transl Med 15, 68, https:\/\/doi.org\/10.1186\/s12967-017-1172-1 (2017).","journal-title":"J Transl Med"},{"key":"48106_CR26","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1016\/j.vetmic.2008.07.004","volume":"133","author":"MC Garcia Pelayo","year":"2009","unstructured":"Garcia Pelayo, M. C. et al. Gene expression profiling and antigen mining of the tuberculin production strain Mycobacterium bovis AN5. Vet Microbiol 133, 272\u2013277, https:\/\/doi.org\/10.1016\/j.vetmic.2008.07.004 (2009).","journal-title":"Vet Microbiol"},{"key":"48106_CR27","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-016-0270-7","volume":"8","author":"E Xia","year":"2016","unstructured":"Xia, E., Teo, Y. Y. & Ong, R. T. SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Genome Med 8, 19, https:\/\/doi.org\/10.1186\/s13073-016-0270-7 (2016).","journal-title":"Genome Med"},{"key":"48106_CR28","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1016\/j.ijid.2017.07.012","volume":"63","author":"SE Sandoval-Azuara","year":"2017","unstructured":"Sandoval-Azuara, S. E. et al. Whole genome sequencing of Mycobacterium bovis to obtain molecular fingerprints in human and cattle isolates from Baja California, Mexico. Int J Infect Dis 63, 48\u201356, https:\/\/doi.org\/10.1016\/j.ijid.2017.07.012 (2017).","journal-title":"Int J Infect Dis"},{"key":"48106_CR29","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1016\/j.meegid.2010.09.004","volume":"11","author":"N Lari","year":"2011","unstructured":"Lari, N., Bimbi, N., Rindi, L., Tortoli, E. & Garzelli, C. Genetic diversity of human isolates of Mycobacterium bovis assessed by spoligotyping and Variable Number Tandem Repeat genotyping. Infect Genet Evol 11, 175\u2013180, https:\/\/doi.org\/10.1016\/j.meegid.2010.09.004 (2011).","journal-title":"Infect Genet Evol"},{"key":"48106_CR30","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1007\/s11250-013-0488-y","volume":"46","author":"H Lamine-Khemiri","year":"2014","unstructured":"Lamine-Khemiri, H. et al. Genotypic characterization by spoligotyping and VNTR typing of Mycobacterium bovis and Mycobacterium caprae isolates from cattle of Tunisia. Trop Anim Health Prod 46, 305\u2013311, https:\/\/doi.org\/10.1007\/s11250-013-0488-y (2014).","journal-title":"Trop Anim Health Prod"},{"key":"48106_CR31","doi-asserted-by":"publisher","first-page":"866","DOI":"10.1016\/j.meegid.2011.09.004","volume":"12","author":"S Rodriguez-Campos","year":"2012","unstructured":"Rodriguez-Campos, S. et al. European 2\u2013a clonal complex of Mycobacterium bovis dominant in the Iberian Peninsula. Infect Genet Evol 12, 866\u2013872, https:\/\/doi.org\/10.1016\/j.meegid.2011.09.004 (2012).","journal-title":"Infect Genet Evol"},{"key":"48106_CR32","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1159\/000329489","volume":"21","author":"K Mohareer","year":"2011","unstructured":"Mohareer, K., Tundup, S. & Hasnain, S. E. Transcriptional regulation of Mycobacterium tuberculosis PE\/PPE genes: a molecular switch to virulence? J Mol Microbiol Biotechnol 21, 97\u2013109, https:\/\/doi.org\/10.1159\/000329489 (2011).","journal-title":"J Mol Microbiol Biotechnol"},{"key":"48106_CR33","doi-asserted-by":"publisher","first-page":"2787","DOI":"10.1128\/IAI.70.6.2787-2795.2002","volume":"70","author":"E Dubnau","year":"2002","unstructured":"Dubnau, E., Fontan, P., Manganelli, R., Soares-Appel, S. & Smith, I. Mycobacterium tuberculosis genes induced during infection of human macrophages. Infect Immun 70, 2787\u20132795 (2002).","journal-title":"Infect Immun"},{"key":"48106_CR34","doi-asserted-by":"publisher","first-page":"1233","DOI":"10.1128\/IAI.74.2.1233-1242.2006","volume":"74","author":"H Rachman","year":"2006","unstructured":"Rachman, H. et al. Unique transcriptome signature of Mycobacterium tuberculosis in pulmonary tuberculosis. Infect Immun 74, 1233\u20131242, https:\/\/doi.org\/10.1128\/IAI.74.2.1233-1242.2006 (2006).","journal-title":"Infect Immun"},{"key":"48106_CR35","doi-asserted-by":"crossref","unstructured":"MacGurn, J. A. & Cox, J. S. A Genetic Screen for M. tuberculosis Mutants Defective for Phagosome Maturation Arrest Identifies Components of the ESX-1 Secretion System. Infection and Immunity, IAI (2007).","DOI":"10.1128\/IAI.01872-06"},{"key":"48106_CR36","doi-asserted-by":"publisher","first-page":"899","DOI":"10.3201\/eid1906.120543","volume":"19","author":"B Muller","year":"2013","unstructured":"Muller, B. et al. Zoonotic Mycobacterium bovis-induced tuberculosis in humans. Emerg Infect Dis 19, 899\u2013908, https:\/\/doi.org\/10.3201\/eid1906.120543 (2013).","journal-title":"Emerg Infect Dis"},{"key":"48106_CR37","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/0962-8479(95)90591-X","volume":"76","author":"LM O\u2019Reilly","year":"1995","unstructured":"O\u2019Reilly, L. M. & Daborn, C. J. The epidemiology of Mycobacterium bovis infections in animals and man: a review. Tuber Lung Dis 76, 1\u201346 (1995).","journal-title":"Tuber Lung Dis"},{"key":"48106_CR38","doi-asserted-by":"publisher","first-page":"59","DOI":"10.3201\/eid0401.980108","volume":"4","author":"O Cosivi","year":"1998","unstructured":"Cosivi, O. et al. Zoonotic tuberculosis due to Mycobacterium bovis in developing countries. Emerging infectious diseases 4, 59\u201370, https:\/\/doi.org\/10.3201\/eid0401.980108 (1998).","journal-title":"Emerging infectious diseases"},{"key":"48106_CR39","unstructured":"GOVS. Annual Report of the General Organization of Veterinary Services (GOVS). Report about TB eradication, (1989)."},{"key":"48106_CR40","doi-asserted-by":"publisher","first-page":"2899","DOI":"10.1017\/S095026881600131X","volume":"144","author":"JM Broughan","year":"2016","unstructured":"Broughan, J. M. et al. A review of risk factors for bovine tuberculosis infection in cattle in the UK and Ireland. Epidemiol Infect 144, 2899\u20132926, https:\/\/doi.org\/10.1017\/S095026881600131X (2016).","journal-title":"Epidemiol Infect"},{"key":"48106_CR41","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1016\/j.prevetmed.2015.04.005","volume":"120","author":"MJ O\u2019Hagan","year":"2015","unstructured":"O\u2019Hagan, M. J. et al. Risk factors for visible lesions or positive laboratory tests in bovine tuberculosis reactor cattle in Northern Ireland. Prev Vet Med 120, 283\u2013290, https:\/\/doi.org\/10.1016\/j.prevetmed.2015.04.005 (2015).","journal-title":"Prev Vet Med"},{"key":"48106_CR42","doi-asserted-by":"publisher","first-page":"e53884","DOI":"10.1371\/journal.pone.0053884","volume":"8","author":"A Menin","year":"2013","unstructured":"Menin, A. et al. Asymptomatic cattle naturally infected with Mycobacterium bovis present exacerbated tissue pathology and bacterial dissemination. PLoS ONE 8, e53884 (2013).","journal-title":"PLoS ONE"},{"key":"48106_CR43","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1016\/0378-1135(94)90046-9","volume":"40","author":"LA Corner","year":"1994","unstructured":"Corner, L. A. Post mortem diagnosis of Mycobacterium bovis infection in cattle. Vet Microbiol 40, 53\u201363 (1994).","journal-title":"Vet Microbiol"},{"key":"48106_CR44","doi-asserted-by":"publisher","first-page":"3623","DOI":"10.1128\/JCM.39.10.3623-3632.2001","volume":"39","author":"N Haddad","year":"2001","unstructured":"Haddad, N. et al. Spoligotype diversity of Mycobacterium bovis strains isolated in France from 1979 to 2000. J Clin Microbiol 39, 3623\u20133632, https:\/\/doi.org\/10.1128\/JCM.39.10.3623-3632.2001 (2001).","journal-title":"J Clin Microbiol"},{"key":"48106_CR45","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1016\/s0966-842x(02)02335-1","volume":"10","author":"MJ Brennan","year":"2002","unstructured":"Brennan, M. J. & Delogu, G. The PE multigene family: a \u2018molecular mantra\u2019 for mycobacteria. Trends in Microbiology 10, 246\u2013249, https:\/\/doi.org\/10.1016\/s0966-842x(02)02335-1 (2002).","journal-title":"Trends in Microbiology"},{"key":"48106_CR46","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1016\/j.micpath.2010.07.004","volume":"49","author":"C Tian","year":"2010","unstructured":"Tian, C. & Jian-Ping, X. Roles of PE_PGRS family in Mycobacterium tuberculosis pathogenesis and novel measures against tuberculosis. Microb Pathog 49, 311\u2013314, https:\/\/doi.org\/10.1016\/j.micpath.2010.07.004 (2010).","journal-title":"Microb Pathog"},{"key":"48106_CR47","doi-asserted-by":"publisher","unstructured":"Brennan, M. J. The Enigmatic PE\/PPE Multigene Family of Mycobacteria and Tuberculosis Vaccination. Infect Immun 85, https:\/\/doi.org\/10.1128\/IAI.00969-16 (2017).","DOI":"10.1128\/IAI.00969-16"},{"key":"48106_CR48","doi-asserted-by":"publisher","first-page":"4501","DOI":"10.1128\/IAI.70.8.4501-4509.2002","volume":"70","author":"AA Chackerian","year":"2002","unstructured":"Chackerian, A. A., Alt, J. M., Perera, T. V., Dascher, C. C. & Behar, S. M. Dissemination of Mycobacterium tuberculosis is influenced by host factors and precedes the initiation of T-cell immunity. Infect Immun 70, 4501\u20134509, https:\/\/doi.org\/10.1128\/IAI.70.8.4501-4509.2002 (2002).","journal-title":"Infect Immun"},{"key":"48106_CR49","doi-asserted-by":"publisher","first-page":"670","DOI":"10.1128\/JB.00750-10","volume":"193","author":"S Berg","year":"2011","unstructured":"Berg, S. et al. African 2, a clonal complex of Mycobacterium bovis epidemiologically important in East Africa. J Bacteriol 193, 670\u2013678, https:\/\/doi.org\/10.1128\/JB.00750-10 (2011).","journal-title":"J Bacteriol"},{"key":"48106_CR50","doi-asserted-by":"publisher","first-page":"e76891","DOI":"10.1371\/journal.pone.0076891","volume":"8","author":"G Ameni","year":"2013","unstructured":"Ameni, G. et al. Transmission of Mycobacterium tuberculosis between farmers and cattle in central Ethiopia. PLoS One 8, e76891, https:\/\/doi.org\/10.1371\/journal.pone.0076891 (2013).","journal-title":"PLoS One"},{"key":"48106_CR51","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1016\/j.rvsc.2005.11.005","volume":"81","author":"R de la Rua-Domenech","year":"2006","unstructured":"de la Rua-Domenech, R. et al. Ante mortem diagnosis of tuberculosis in cattle: a review of the tuberculin tests, gamma-interferon assay and other ancillary diagnostic techniques. Res Vet Sci 81, 190\u2013210, https:\/\/doi.org\/10.1016\/j.rvsc.2005.11.005 (2006).","journal-title":"Res Vet Sci"},{"key":"48106_CR52","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1016\/j.vetmic.2005.11.047","volume":"112","author":"C Thoen","year":"2006","unstructured":"Thoen, C., LoBue, P. & de, K. I. The importance of Mycobacterium bovis as a zoonosis. Vet.Microbiol. 112, 339\u2013345 (2006).","journal-title":"Vet.Microbiol."},{"key":"48106_CR53","doi-asserted-by":"publisher","first-page":"e5068","DOI":"10.1371\/journal.pone.0005068","volume":"4","author":"S Berg","year":"2009","unstructured":"Berg, S. et al. The burden of mycobacterial disease in ethiopian cattle: implications for public health. PLoS ONE. 4, e5068 (2009).","journal-title":"PLoS ONE."},{"key":"48106_CR54","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1590\/S1517-83822008000200008","volume":"39","author":"SR Ambrosio","year":"2008","unstructured":"Ambrosio, S. R., de Deus Oliveira, E. M., Rodriguez, C. A., Ferreira Neto, J. S. & Amaku, M. Comparison of three decontamination methods for Mycobacterium bovis isolation. Braz J Microbiol 39, 241\u2013244, https:\/\/doi.org\/10.1590\/S1517-83822008000200008 (2008).","journal-title":"Braz J Microbiol"},{"key":"48106_CR55","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1111\/j.1472-765X.2011.03185.x","volume":"54","author":"L Medeiros","year":"2012","unstructured":"Medeiros, L., Marassi, C. D., Duarte, R. S., da Silva, M. G. & Lilenbaum, W. Comparison of decontamination methods for primary isolation of Mycobacterium bovis in paucibacillary bovine tissues. Lett Appl Microbiol 54, 182\u2013186, https:\/\/doi.org\/10.1111\/j.1472-765X.2011.03185.x (2012).","journal-title":"Lett Appl Microbiol"},{"key":"48106_CR56","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1128\/JCM.38.1.152-157.2000","volume":"38","author":"S Niemann","year":"2000","unstructured":"Niemann, S., Richter, E. & R\u00fcsch-Gerdes, S. Differentiation among members of the Mycobacterium tuberculosis complex by molecular and biochemical features: evidence for two pyrazinamide-susceptible subtypes of M. bovis. J Clin Microbiol 38, 152\u2013157 (2000).","journal-title":"J Clin Microbiol"},{"key":"48106_CR57","doi-asserted-by":"publisher","first-page":"e31947","DOI":"10.1371\/journal.pone.0031947","volume":"7","author":"P Ghosh","year":"2012","unstructured":"Ghosh, P. et al. Genome-wide analysis of the emerging infection with Mycobacterium avium subspecies paratuberculosis in the Arabian camels (Camelus dromedarius). PLoS One 7, e31947, https:\/\/doi.org\/10.1371\/journal.pone.0031947 (2012).","journal-title":"PLoS One"},{"key":"48106_CR58","unstructured":"CLSI. (CLSI document M24-A2. Wayne: Clinical and Laboratory Standards Institute, 2011)."},{"key":"48106_CR59","doi-asserted-by":"crossref","unstructured":"Chimara, E., Ferrazoli, L. & Le\u00e3o, S. C. Mycobacterium tuberculosis complex differentiation using gyrB-restriction fragment length polymorphism analysis. Mem Inst Oswaldo Cruz 99, 745\u2013748, doi:\/S0074-02762004000700014 (2004).","DOI":"10.1590\/S0074-02762004000700014"},{"key":"48106_CR60","doi-asserted-by":"crossref","first-page":"3231","DOI":"10.1128\/JCM.38.9.3231-3234.2000","volume":"38","author":"S Niemann","year":"2000","unstructured":"Niemann, S., Harmsen, D., R++sch-Gerdes, S. & Richter, E. Differentiation of Clinical Mycobacterium tuberculosis Complex Isolates by gyrB DNA Sequence Polymorphism Analysis. Journal of Clinical Microbiology 38, 3231\u20133234 (2000).","journal-title":"Journal of Clinical Microbiology"},{"key":"48106_CR61","doi-asserted-by":"publisher","first-page":"1220","DOI":"10.3349\/ymj.2013.54.5.1220","volume":"54","author":"Y Kim","year":"2013","unstructured":"Kim, Y. et al. A simple and efficient multiplex PCR assay for the identification of Mycobacterium genus and Mycobacterium tuberculosis complex to the species level. Yonsei Med J 54, 1220\u20131226, https:\/\/doi.org\/10.3349\/ymj.2013.54.5.1220 (2013).","journal-title":"Yonsei Med J"},{"issue":"Pt 5","key":"48106_CR62","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1099\/00221287-144-5-1189","volume":"144","author":"R Frothingham","year":"1998","unstructured":"Frothingham, R. & Meeker-O\u2019Connell, W. A. Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology 144(Pt 5), 1189\u20131196, https:\/\/doi.org\/10.1099\/00221287-144-5-1189 (1998).","journal-title":"Microbiology"},{"key":"48106_CR63","doi-asserted-by":"publisher","first-page":"1901","DOI":"10.1073\/pnas.98.4.1901","volume":"98","author":"E Mazars","year":"2001","unstructured":"Mazars, E. et al. High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology. Proc. Natl. Acad. Sci. USA 98, 1901\u20131906, https:\/\/doi.org\/10.1073\/pnas.98.4.1901 (2001).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"48106_CR64","doi-asserted-by":"publisher","first-page":"762","DOI":"10.1046\/j.1365-2958.2000.01905.x","volume":"36","author":"P Supply","year":"2000","unstructured":"Supply, P. et al. Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome. Mol Microbiol 36, 762\u2013771 (2000).","journal-title":"Mol Microbiol"},{"key":"48106_CR65","doi-asserted-by":"publisher","first-page":"W326","DOI":"10.1093\/nar\/gkq351","volume":"38","author":"T Weniger","year":"2010","unstructured":"Weniger, T., Krawczyk, J., Supply, P., Niemann, S. & Harmsen, D. MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria. Nucleic Acids Res 38, W326\u2013331, https:\/\/doi.org\/10.1093\/nar\/gkq351 (2010).","journal-title":"Nucleic Acids Res"},{"key":"48106_CR66","doi-asserted-by":"publisher","first-page":"236","DOI":"10.3389\/fmicb.2011.00236","volume":"2","author":"C-Y Hsu","year":"2011","unstructured":"Hsu, C.-Y., Wu, C.-W. & Talaat, A. M. Genome-wide sequence variations among Mycobacterium avium subspecies paratuberculosis isolates: A better understanding of Johne\u2019s disease transmission dynamics. Front Microbiol. 2, 236 (2011).","journal-title":"Front Microbiol."},{"key":"48106_CR67","doi-asserted-by":"publisher","unstructured":"Malone, K. M. et al. Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122\/97. Genome Announc 5, https:\/\/doi.org\/10.1128\/genomeA.00157-17 (2017).","DOI":"10.1128\/genomeA.00157-17"},{"key":"48106_CR68","doi-asserted-by":"publisher","first-page":"3272","DOI":"10.1093\/jac\/dkx316","volume":"72","author":"J Chen","year":"2017","unstructured":"Chen, J. et al. Identification of novel mutations associated with cycloserine resistance in Mycobacterium tuberculosis. J Antimicrob Chemother 72, 3272\u20133276, https:\/\/doi.org\/10.1093\/jac\/dkx316 (2017).","journal-title":"J Antimicrob Chemother"},{"key":"48106_CR69","doi-asserted-by":"publisher","first-page":"1870","DOI":"10.1093\/molbev\/msw054","volume":"33","author":"S Kumar","year":"2016","unstructured":"Kumar, S., Stecher, G. & Tamura, K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 33, 1870\u20131874, https:\/\/doi.org\/10.1093\/molbev\/msw054 (2016).","journal-title":"Mol Biol Evol"},{"key":"48106_CR70","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1016\/j.mbs.2009.12.010","volume":"224","author":"M Falconnet","year":"2010","unstructured":"Falconnet, M. Phylogenetic distances for neighbour dependent substitution processes. Math Biosci 224, 101\u2013108, https:\/\/doi.org\/10.1016\/j.mbs.2009.12.010 (2010).","journal-title":"Math Biosci"},{"key":"48106_CR71","doi-asserted-by":"publisher","first-page":"418","DOI":"10.1093\/oxfordjournals.molbev.a040410","volume":"3","author":"M Nei","year":"1986","unstructured":"Nei, M. & Gojobori, T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3, 418\u2013426, https:\/\/doi.org\/10.1093\/oxfordjournals.molbev.a040410 (1986).","journal-title":"Mol Biol Evol"},{"key":"48106_CR72","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1093\/oxfordjournals.molbev.a040140","volume":"11","author":"T Ota","year":"1994","unstructured":"Ota, T. & Nei, M. Variance and covariances of the numbers of synonymous and nonsynonymous substitutions per site. Mol Biol Evol 11, 613\u2013619, https:\/\/doi.org\/10.1093\/oxfordjournals.molbev.a040140 (1994).","journal-title":"Mol Biol Evol"},{"key":"48106_CR73","doi-asserted-by":"publisher","DOI":"10.1186\/PREACCEPT-2573980311437212","volume":"15","author":"TJ Treangen","year":"2014","unstructured":"Treangen, T. J., Ondov, B. D., Koren, S. & Phillippy, A. M. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol 15, 524, https:\/\/doi.org\/10.1186\/PREACCEPT-2573980311437212 (2014).","journal-title":"Genome Biol"},{"key":"48106_CR74","doi-asserted-by":"publisher","first-page":"251","DOI":"10.5025\/hansen.76.251","volume":"76","author":"Y Sakakibara","year":"2007","unstructured":"Sakakibara, Y., Osana, Y. & Popendorf, K. Development of a large-scale comparative genome system and its application to the analysis of mycobacteria genomes. Nihon Hansenbyo Gakkai Zasshi 76, 251\u2013256 (2007).","journal-title":"Nihon Hansenbyo Gakkai Zasshi"},{"key":"48106_CR75","doi-asserted-by":"publisher","first-page":"1394","DOI":"10.1101\/gr.2289704","volume":"14","author":"AC Darling","year":"2004","unstructured":"Darling, A. C., Mau, B., Blattner, F. R. & Perna, N. T. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14, 1394\u20131403, https:\/\/doi.org\/10.1101\/gr.2289704 (2004).","journal-title":"Genome Res"},{"key":"48106_CR76","doi-asserted-by":"publisher","first-page":"857","DOI":"10.1016\/j.meegid.2011.09.007","volume":"12","author":"NH Smith","year":"2012","unstructured":"Smith, N. H. The global distribution and phylogeography of Mycobacterium bovis clonal complexes. Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 12, 857\u2013865, https:\/\/doi.org\/10.1016\/j.meegid.2011.09.007 (2012).","journal-title":"Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases"},{"key":"48106_CR77","doi-asserted-by":"publisher","first-page":"1951","DOI":"10.1128\/JB.01590-08","volume":"191","author":"B M\u00fcller","year":"2009","unstructured":"M\u00fcller, B. et al. African 1, an epidemiologically important clonal complex of Mycobacterium bovis dominant in Mali, Nigeria, Cameroon, and Chad. Journal of bacteriology 191, 1951\u20131960, https:\/\/doi.org\/10.1128\/JB.01590-08 (2009).","journal-title":"Journal of bacteriology"},{"key":"48106_CR78","doi-asserted-by":"publisher","first-page":"1340","DOI":"10.1016\/j.meegid.2011.04.027","volume":"11","author":"NH Smith","year":"2011","unstructured":"Smith, N. H. et al. European 1: a globally important clonal complex of Mycobacterium bovis. Infect Genet Evol 11, 1340\u20131351, https:\/\/doi.org\/10.1016\/j.meegid.2011.04.027 (2011).","journal-title":"Infect Genet Evol"},{"key":"48106_CR79","doi-asserted-by":"publisher","first-page":"1253","DOI":"10.1093\/molbev\/msn083","volume":"25","author":"D Posada","year":"2008","unstructured":"Posada, D. jModelTest: phylogenetic model averaging. Mol Biol Evol 25, 1253\u20131256, https:\/\/doi.org\/10.1093\/molbev\/msn083 (2008).","journal-title":"Mol Biol Evol"},{"key":"48106_CR80","doi-asserted-by":"publisher","first-page":"2910","DOI":"10.1093\/bioinformatics\/btr481","volume":"27","author":"F Bielejec","year":"2011","unstructured":"Bielejec, F., Rambaut, A., Suchard, M. A. & Lemey, P. SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinformatics 27, 2910\u20132912, https:\/\/doi.org\/10.1093\/bioinformatics\/btr481 (2011).","journal-title":"Bioinformatics"},{"key":"48106_CR81","doi-asserted-by":"publisher","first-page":"e0151816","DOI":"10.1371\/journal.pone.0151816","volume":"11","author":"SA Marcus","year":"2016","unstructured":"Marcus, S. A., Sidiropoulos, S. W., Steinberg, H. & Talaat, A. M. CsoR Is Essential for Maintaining Copper Homeostasis in Mycobacterium tuberculosis. PLoS One 11, e0151816, https:\/\/doi.org\/10.1371\/journal.pone.0151816 (2016).","journal-title":"PLoS One"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-48106-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-48106-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-48106-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,17]],"date-time":"2022-12-17T12:31:36Z","timestamp":1671280296000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-48106-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,8,12]]},"references-count":81,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2019,12]]}},"alternative-id":["48106"],"URL":"https:\/\/doi.org\/10.1038\/s41598-019-48106-3","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,8,12]]},"assertion":[{"value":"22 June 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 July 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 August 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}],"article-number":"11657"}}