{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T02:22:20Z","timestamp":1783563740921,"version":"3.55.0"},"reference-count":35,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2018,1,12]],"date-time":"2018-01-12T00:00:00Z","timestamp":1515715200000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"DOI":"10.3389\/fcimb.2017.00539","type":"journal-article","created":{"date-parts":[[2018,1,12]],"date-time":"2018-01-12T04:23:30Z","timestamp":1515731010000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":17,"title":["Comparative Whole-Genomic Analysis of an Ancient L2 Lineage Mycobacterium tuberculosis Reveals a Novel Phylogenetic Clade and Common Genetic Determinants of Hypervirulent Strains"],"prefix":"10.3389","volume":"7","author":[{"given":"Rahim","family":"Rajwani","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wing Cheong","family":"Yam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Kang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barry Kin Chung","family":"Wong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenneth Siu Sing","family":"Leung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kingsley King Gee","family":"Tam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ketema Tafess","family":"Tulu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gilman Kit Hang","family":"Siu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2018,1,12]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"e000062","DOI":"10.1099\/mgen.0.000062","article-title":"Quantitative assessment of insertion sequence impact on bacterial genome architecture","volume":"2","author":"Adams","year":"2016","journal-title":"Microb. Genomics"},{"key":"B2","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1016\/j.tube.2010.12.007","article-title":"Deciphering the role of IS6110 in a highly transmissible Mycobacterium tuberculosis Beijing strain, GC1237","volume":"91","author":"Alonso","year":"2011","journal-title":"Tuberculosis"},{"key":"B3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-1-4939-2450-9_1","article-title":"Whole-genome sequencing for comparative genomics and de novo genome assembly","volume":"1285","author":"Benjak","year":"2015","journal-title":"Methods Mol. Biol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"1165","DOI":"10.1164\/ajrccm.164.7.2101031","article-title":"Epidemiological evidence of the spread of a Mycobacterium tuberculosis strain of the Beijing genotype on Gran Canaria Island","volume":"164","author":"Caminero","year":"2001","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"B5","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1016\/j.tube.2016.04.006","article-title":"Mycobacterium tuberculosis strain 18b, a useful non-virulent streptomycin dependent mutant to study latent tuberculosis as well as for in vivo and in vitro testing of anti-tuberculosis drugs","volume":"99","author":"Campos-Neto","year":"2016","journal-title":"Tuberculosis"},{"key":"B6","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1038\/nmeth.2474","article-title":"Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data","volume":"10","author":"Chin","year":"2013","journal-title":"Nat. Methods"},{"key":"B7","doi-asserted-by":"publisher","first-page":"4812","DOI":"10.1038\/ncomms5812","article-title":"A robust SNP barcode for typing Mycobacterium tuberculosis complex strains","volume":"5","author":"Coll","year":"2014","journal-title":"Nat. Commun."},{"key":"B8","doi-asserted-by":"publisher","first-page":"1592","DOI":"10.1128\/JCM.40.5.1592-1602.2002","article-title":"Variable-number tandem repeat typing of Mycobacterium tuberculosis isolates with low copy numbers of IS6110 by using mycobacterial interspersed repetitive units","volume":"40","author":"Cowan","year":"2002","journal-title":"J. Clin. Microbiol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1007\/978-1-4939-2450-9_8","article-title":"Targeted gene knockout and essentiality testing by homologous recombination","volume":"1285","author":"Gopinath","year":"2015","journal-title":"Methods Mol. Biol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1016\/j.tube.2010.08.004","article-title":"Mycobacterium tuberculosis strains with the Beijing genotype demonstrate variability in virulence associated with transmission","volume":"90","author":"Hanekom","year":"2010","journal-title":"Tuberculosis"},{"key":"B11","doi-asserted-by":"publisher","first-page":"2491","DOI":"10.1128\/JB.00035-10","article-title":"The SigF regulon in Mycobacterium smegmatis reveals roles in adaptation to stationary phase, heat, and oxidative stress","volume":"192","author":"H\u00fcmpel","year":"2010","journal-title":"J. Bacteriol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"88","DOI":"10.3389\/fcimb.2017.00088","article-title":"The Bioinformatics analysis of comparative genomics of Mycobacterium tuberculosis Complex (MTBC) provides insight into dissimilarities between intraspecific groups differing in host association, virulence, and epitope diversity","volume":"7","author":"Jia","year":"2017","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B13","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1128\/JCM.35.4.907-914.1997","article-title":"Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology","volume":"35","author":"Kamerbeek","year":"1997","journal-title":"J. Clin. Microbiol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"1073","DOI":"10.1038\/nprot.2009.86","article-title":"Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm","volume":"4","author":"Kumar","year":"2009","journal-title":"Nat. Protoc."},{"key":"B15","doi-asserted-by":"publisher","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/j.chom.2008.01.002","article-title":"Mutation in the transcriptional regulator PhoP contributes to avirulence of Mycobacterium tuberculosis H37Ra strain","volume":"3","author":"Lee","year":"2008","journal-title":"Cell Host Microbe"},{"key":"B17","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"B18","first-page":"1080","article-title":"Genotyping of Mycobacterium tuberculosis over two periods: a changing scenario for tuberculosis transmission","volume":"11","author":"L\u00f3pez-Calleja","year":"2007","journal-title":"Int. J. Tuberculosis Lung Dis."},{"key":"B19","doi-asserted-by":"publisher","first-page":"8136","DOI":"10.1073\/pnas.1424063112","article-title":"Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese","volume":"112","author":"Luo","year":"2015","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B20","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1038\/ng.3195","article-title":"Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage","volume":"47","author":"Merker","year":"2015","journal-title":"Nat. Genet."},{"key":"B21","doi-asserted-by":"publisher","first-page":"3021","DOI":"10.1093\/bioinformatics\/btw369","article-title":"Assemblytics: a web analytics tool for the detection of variants from an assembly","volume":"32","author":"Nattestad","year":"2016","journal-title":"Bioinformatics"},{"key":"B22","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"B23","doi-asserted-by":"publisher","first-page":"2615","DOI":"10.1128\/JCM.00498-14","article-title":"Mycobacterium tuberculosis strains of the modern sublineage of the Beijing family are more likely to display increased virulence than strains of the ancient sublineage","volume":"52","author":"Ribeiro","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"1505","DOI":"10.1128\/JB.01371-06","article-title":"Identification of mycobacterial \u03c3 factor binding sites by chromatin immunoprecipitation assays","volume":"189","author":"Rodrigue","year":"2007","journal-title":"J. Bacteriol."},{"key":"B25","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1016\/j.meegid.2017.07.022","article-title":"Comparative genomic analysis of Mycobacterium tuberculosis Beijing-like strains revealed specific genetic variations associated with virulence and drug resistance","volume":"54","author":"Rodr\u00edguez-Castillo","year":"2017","journal-title":"Infect. Genet. Evol."},{"key":"B26","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1016\/j.meegid.2012.02.010","article-title":"TB-Lineage: an online tool for classification and analysis of strains of Mycobacterium tuberculosis complex","volume":"12","author":"Shabbeer","year":"2012","journal-title":"Infect. Genet. Evol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"15918","DOI":"10.1073\/pnas.2433882100","article-title":"Hypervirulent mutant of Mycobacterium tuberculosis resulting from disruption of the mce1 operon","volume":"100","author":"Shimono","year":"2003","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B28","doi-asserted-by":"publisher","first-page":"6093","DOI":"10.1128\/AAC.03277-14","article-title":"An upstream truncation of the furA-katG operon confers high-level isoniazid resistance in a Mycobacterium tuberculosis clinical isolate with no known resistance-associated mutations","volume":"58","author":"Siu","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"B29","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1016\/j.diagmicrobio.2010.08.021","article-title":"Direct detection of isoniazid-resistant Mycobacterium tuberculosis in respiratory specimens by multiplex allele-specific polymerase chain reaction","volume":"69","author":"Siu","year":"2011","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"B30","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1128\/CMR.16.3.463-496.2003","article-title":"Mycobacterium tuberculosis pathogenesis and molecular determinants of virulence","volume":"16","author":"Smith","year":"2003","journal-title":"Clin. Microbiol. Rev."},{"key":"B31","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1128\/JCM.42.1.212-219.2004","article-title":"IS6110 mediates increased transcription of the phoP virulence gene in a multidrug-resistant clinical isolate responsible for tuberculosis outbreaks","volume":"42","author":"Soto","year":"2004","journal-title":"J. Clin. Microbiol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1186\/s13059-014-0524-x","article-title":"The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes","volume":"15","author":"Treangen","year":"2014","journal-title":"Genome Biol."},{"key":"B33","doi-asserted-by":"publisher","first-page":"W326","DOI":"10.1093\/nar\/gkq351","article-title":"MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria","volume":"38","author":"Weniger","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"B34","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.1128\/CVI.00190-07","article-title":"Molecular characterization of clinical isolates of Mycobacterium tuberculosis and their association with phenotypic virulence in human macrophages","volume":"14","author":"Wong","year":"2007","journal-title":"Clin. Vaccine Immunol."},{"key":"B35","doi-asserted-by":"publisher","first-page":"1255","DOI":"10.1038\/ng.2735","article-title":"Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance","volume":"45","author":"Zhang","year":"2013","journal-title":"Nat. Genet."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"http:\/\/journal.frontiersin.org\/article\/10.3389\/fcimb.2017.00539\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,10,25]],"date-time":"2020-10-25T14:34:09Z","timestamp":1603636449000},"score":1,"resource":{"primary":{"URL":"http:\/\/journal.frontiersin.org\/article\/10.3389\/fcimb.2017.00539\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,1,12]]},"references-count":35,"alternative-id":["10.3389\/fcimb.2017.00539"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2017.00539","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,1,12]]},"article-number":"539"}}