Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study

Roetzer A, Diel R, Kohl TA, Rückert C, Nübel U, Blom J, Wirth T, Jaenicke S, Schuback S, Rüsch-Gerdes S, Supply P, et al. (2013)
PLoS medicine 10(2): e1001387.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Roetzer, Andreas; Diel, Roland; Kohl, Thomas A; Rückert, ChristianUniBi ; Nübel, Ulrich; Blom, JochenUniBi; Wirth, Thierry; Jaenicke, SebastianUniBi; Schuback, Sieglinde; Rüsch-Gerdes, Sabine; Supply, Philip; Kalinowski, JörnUniBi
Abstract / Bemerkung
BACKGROUND: Understanding Mycobacterium tuberculosis (Mtb) transmission is essential to guide efficient tuberculosis control strategies. Traditional strain typing lacks sufficient discriminatory power to resolve large outbreaks. Here, we tested the potential of using next generation genome sequencing for identification of outbreak-related transmission chains. METHODS AND FINDINGS: During long-term (1997 to 2010) prospective population-based molecular epidemiological surveillance comprising a total of 2,301 patients, we identified a large outbreak caused by an Mtb strain of the Haarlem lineage. The main performance outcome measure of whole genome sequencing (WGS) analyses was the degree of correlation of the WGS analyses with contact tracing data and the spatio-temporal distribution of the outbreak cases. WGS analyses of the 86 isolates revealed 85 single nucleotide polymorphisms (SNPs), subdividing the outbreak into seven genome clusters (two to 24 isolates each), plus 36 unique SNP profiles. WGS results showed that the first outbreak isolates detected in 1997 were falsely clustered by classical genotyping. In 1998, one clone (termed "Hamburg clone") started expanding, apparently independently from differences in the social environment of early cases. Genome-based clustering patterns were in better accordance with contact tracing data and the geographical distribution of the cases than clustering patterns based on classical genotyping. A maximum of three SNPs were identified in eight confirmed human-to-human transmission chains, involving 31 patients. We estimated the Mtb genome evolutionary rate at 0.4 mutations per genome per year. This rate suggests that Mtb grows in its natural host with a doubling time of approximately 22 h (400 generations per year). Based on the genome variation discovered, emergence of the Hamburg clone was dated back to a period between 1993 and 1997, hence shortly before the discovery of the outbreak through epidemiological surveillance. CONCLUSIONS: Our findings suggest that WGS is superior to conventional genotyping for Mtb pathogen tracing and investigating micro-epidemics. WGS provides a measure of Mtb genome evolution over time in its natural host context. Please see later in the article for the Editors' Summary.
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Roetzer A, Diel R, Kohl TA, et al. Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study. PLoS medicine. 2013;10(2): e1001387.
Roetzer, A., Diel, R., Kohl, T. A., Rückert, C., Nübel, U., Blom, J., Wirth, T., et al. (2013). Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study. PLoS medicine, 10(2), e1001387. doi:10.1371/journal.pmed.1001387
Roetzer, Andreas, Diel, Roland, Kohl, Thomas A, Rückert, Christian, Nübel, Ulrich, Blom, Jochen, Wirth, Thierry, et al. 2013. “Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study”. PLoS medicine 10 (2): e1001387.
Roetzer, A., Diel, R., Kohl, T. A., Rückert, C., Nübel, U., Blom, J., Wirth, T., Jaenicke, S., Schuback, S., Rüsch-Gerdes, S., et al. (2013). Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study. PLoS medicine 10:e1001387.
Roetzer, A., et al., 2013. Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study. PLoS medicine, 10(2): e1001387.
A. Roetzer, et al., “Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study”, PLoS medicine, vol. 10, 2013, : e1001387.
Roetzer, A., Diel, R., Kohl, T.A., Rückert, C., Nübel, U., Blom, J., Wirth, T., Jaenicke, S., Schuback, S., Rüsch-Gerdes, S., Supply, P., Kalinowski, J., Niemann, S.: Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study. PLoS medicine. 10, : e1001387 (2013).
Roetzer, Andreas, Diel, Roland, Kohl, Thomas A, Rückert, Christian, Nübel, Ulrich, Blom, Jochen, Wirth, Thierry, Jaenicke, Sebastian, Schuback, Sieglinde, Rüsch-Gerdes, Sabine, Supply, Philip, Kalinowski, Jörn, and Niemann, Stefan. “Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study”. PLoS medicine 10.2 (2013): e1001387.

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Pedersen MK, Andersen AB, Andersen PH, Svensson E, Jensen SG, Lillebaek T., PLoS One 11(4), 2016
PMID: 27082745
Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock.
Kamath PL, Foster JT, Drees KP, Luikart G, Quance C, Anderson NJ, Clarke PR, Cole EK, Drew ML, Edwards WH, Rhyan JC, Treanor JJ, Wallen RL, White PJ, Robbe-Austerman S, Cross PC., Nat Commun 7(), 2016
PMID: 27165544
Standard Genotyping Overestimates Transmission of Mycobacterium tuberculosis among Immigrants in a Low-Incidence Country.
Stucki D, Ballif M, Egger M, Furrer H, Altpeter E, Battegay M, Droz S, Bruderer T, Coscolla M, Borrell S, Zürcher K, Janssens JP, Calmy A, Mazza Stalder J, Jaton K, Rieder HL, Pfyffer GE, Siegrist HH, Hoffmann M, Fehr J, Dolina M, Frei R, Schrenzel J, Böttger EC, Gagneux S, Fenner L., J Clin Microbiol 54(7), 2016
PMID: 27194683
Nosocomial transmission of Clostridium difficile ribotype 027 in a Chinese hospital, 2012-2014, traced by whole genome sequencing.
Jia H, Du P, Yang H, Zhang Y, Wang J, Zhang W, Han G, Han N, Yao Z, Wang H, Zhang J, Wang Z, Ding Q, Qiang Y, Barbut F, Gao GF, Cao Y, Cheng Y, Chen C., BMC Genomics 17(), 2016
PMID: 27411304
XDR-TB transmission in London: Case management and contact tracing investigation assisted by early whole genome sequencing.
Arnold A, Witney AA, Vergnano S, Roche A, Cosgrove CA, Houston A, Gould KA, Hinds J, Riley P, Macallan D, Butcher PD, Harrison TS., J Infect 73(3), 2016
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Genomic Diversity of Mycobacterium tuberculosis Complex Strains in Cantabria (Spain), a Moderate TB Incidence Setting.
Pérez Del Molino Bernal IC, Lillebaek T, Pedersen MK, Martinez-Martinez L, Folkvardsen DB, Agüero J, Rasmussen EM., PLoS One 11(6), 2016
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Molecular Typing of Mycobacterium Tuberculosis Strains: A Fundamental Tool for Tuberculosis Control and Elimination.
Cannas A, Mazzarelli A, Di Caro A, Delogu G, Girardi E., Infect Dis Rep 8(2), 2016
PMID: 27403266
Whole-Genome Sequencing Analysis of Serially Isolated Multi-Drug and Extensively Drug Resistant Mycobacterium tuberculosis from Thai Patients.
Faksri K, Tan JH, Disratthakit A, Xia E, Prammananan T, Suriyaphol P, Khor CC, Teo YY, Ong RT, Chaiprasert A., PLoS One 11(8), 2016
PMID: 27518818
A Primer on Infectious Disease Bacterial Genomics.
Lynch T, Petkau A, Knox N, Graham M, Van Domselaar G., Clin Microbiol Rev 29(4), 2016
PMID: 28590251
Tracing Mycobacterium tuberculosis transmission by whole genome sequencing in a high incidence setting: a retrospective population-based study in East Greenland.
Bjorn-Mortensen K, Soborg B, Koch A, Ladefoged K, Merker M, Lillebaek T, Andersen AB, Niemann S, Kohl TA., Sci Rep 6(), 2016
PMID: 27615360
Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study.
Casali N, Broda A, Harris SR, Parkhill J, Brown T, Drobniewski F., PLoS Med 13(10), 2016
PMID: 27701423
Tuberculosis in migrants moving from high-incidence to low-incidence countries: a population-based cohort study of 519 955 migrants screened before entry to England, Wales, and Northern Ireland.
Aldridge RW, Zenner D, White PJ, Williamson EJ, Muzyamba MC, Dhavan P, Mosca D, Thomas HL, Lalor MK, Abubakar I, Hayward AC., Lancet 388(10059), 2016
PMID: 27742165
Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages.
Stucki D, Brites D, Jeljeli L, Coscolla M, Liu Q, Trauner A, Fenner L, Rutaihwa L, Borrell S, Luo T, Gao Q, Kato-Maeda M, Ballif M, Egger M, Macedo R, Mardassi H, Moreno M, Tudo Vilanova G, Fyfe J, Globan M, Thomas J, Jamieson F, Guthrie JL, Asante-Poku A, Yeboah-Manu D, Wampande E, Ssengooba W, Joloba M, Henry Boom W, Basu I, Bower J, Saraiva M, Vaconcellos SEG, Suffys P, Koch A, Wilkinson R, Gail-Bekker L, Malla B, Ley SD, Beck HP, de Jong BC, Toit K, Sanchez-Padilla E, Bonnet M, Gil-Brusola A, Frank M, Penlap Beng VN, Eisenach K, Alani I, Wangui Ndung'u P, Revathi G, Gehre F, Akter S, Ntoumi F, Stewart-Isherwood L, Ntinginya NE, Rachow A, Hoelscher M, Cirillo DM, Skenders G, Hoffner S, Bakonyte D, Stakenas P, Diel R, Crudu V, Moldovan O, Al-Hajoj S, Otero L, Barletta F, Jane Carter E, Diero L, Supply P, Comas I, Niemann S, Gagneux S., Nat Genet 48(12), 2016
PMID: 27798628
Molecular Strain Typing of Mycobacterium tuberculosis: a Review of Frequently Used Methods.
Ei PW, Aung WW, Lee JS, Choi GE, Chang CL., J Korean Med Sci 31(11), 2016
PMID: 27709842
Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999-2009.
Brown TS, Narechania A, Walker JR, Planet PJ, Bifani PJ, Kolokotronis SO, Kreiswirth BN, Mathema B., BMC Genomics 17(1), 2016
PMID: 27871225
Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis.
Eldholm V, Pettersson JH, Brynildsrud OB, Kitchen A, Rasmussen EM, Lillebaek T, Rønning JO, Crudu V, Mengshoel AT, Debech N, Alfsnes K, Bohlin J, Pepperell CS, Balloux F., Proc Natl Acad Sci U S A 113(48), 2016
PMID: 27872285
Diagnosing tuberculosis in the 21st century - Dawn of a genomics revolution?
Jeanes C, O'Grady J., Int J Mycobacteriol 5(4), 2016
PMID: 27931678
Totally drug-resistant tuberculosis and adjunct therapies.
Parida SK, Axelsson-Robertson R, Rao MV, Singh N, Master I, Lutckii A, Keshavjee S, Andersson J, Zumla A, Maeurer M., J Intern Med 277(4), 2015
PMID: 24809736
Tracking a tuberculosis outbreak over 21 years: strain-specific single-nucleotide polymorphism typing combined with targeted whole-genome sequencing.
Stucki D, Ballif M, Bodmer T, Coscolla M, Maurer AM, Droz S, Butz C, Borrell S, Längle C, Feldmann J, Furrer H, Mordasini C, Helbling P, Rieder HL, Egger M, Gagneux S, Fenner L., J Infect Dis 211(8), 2015
PMID: 25362193
Added value of whole-genome sequencing for management of highly drug-resistant TB.
Outhred AC, Jelfs P, Suliman B, Hill-Cawthorne GA, Crawford AB, Marais BJ, Sintchenko V., J Antimicrob Chemother 70(4), 2015
PMID: 25492392
Whole genome sequencing: a new paradigm in the surveillance and control of human tuberculosis.
Hasnain SE, O'Toole RF, Grover S, Ehtesham NZ., Tuberculosis (Edinb) 95(2), 2015
PMID: 25586521
Current and emerging Legionella diagnostics for laboratory and outbreak investigations.
Mercante JW, Winchell JM., Clin Microbiol Rev 28(1), 2015
PMID: 25567224
Meningococcal vaccine antigen diversity in global databases.
Brehony C, Hill DM, Lucidarme J, Borrow R, Maiden MC., Euro Surveill 20(49), 2015
PMID: 26676305
Reemergence and amplification of tuberculosis in the Canadian arctic.
Lee RS, Radomski N, Proulx JF, Manry J, McIntosh F, Desjardins F, Soualhine H, Domenech P, Reed MB, Menzies D, Behr MA., J Infect Dis 211(12), 2015
PMID: 25576599
Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread.
Coscolla M, Barry PM, Oeltmann JE, Koshinsky H, Shaw T, Cilnis M, Posey J, Rose J, Weber T, Fofanov VY, Gagneux S, Kato-Maeda M, Metcalfe JZ., J Infect Dis 212(2), 2015
PMID: 25601940
Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage.
Merker M, Blin C, Mona S, Duforet-Frebourg N, Lecher S, Willery E, Blum MG, Rüsch-Gerdes S, Mokrousov I, Aleksic E, Allix-Béguec C, Antierens A, Augustynowicz-Kopeć E, Ballif M, Barletta F, Beck HP, Barry CE, Bonnet M, Borroni E, Campos-Herrero I, Cirillo D, Cox H, Crowe S, Crudu V, Diel R, Drobniewski F, Fauville-Dufaux M, Gagneux S, Ghebremichael S, Hanekom M, Hoffner S, Jiao WW, Kalon S, Kohl TA, Kontsevaya I, Lillebæk T, Maeda S, Nikolayevskyy V, Rasmussen M, Rastogi N, Samper S, Sanchez-Padilla E, Savic B, Shamputa IC, Shen A, Sng LH, Stakenas P, Toit K, Varaine F, Vukovic D, Wahl C, Warren R, Supply P, Niemann S, Wirth T., Nat Genet 47(3), 2015
PMID: 25599400
Mycobacterial DNA extraction for whole-genome sequencing from early positive liquid (MGIT) cultures.
Votintseva AA, Pankhurst LJ, Anson LW, Morgan MR, Gascoyne-Binzi D, Walker TM, Quan TP, Wyllie DH, Del Ojo Elias C, Wilcox M, Walker AS, Peto TE, Crook DW., J Clin Microbiol 53(4), 2015
PMID: 25631807
Childhood BCG vaccination does not influence control of Mycobacterium tuberculosis growth by human bronchoalveolar lavage cells.
Herzmann C, Sotgiu G, Schaberg T, Ernst M, Stenger S, Lange C, TB or not TB Consortium., Tuberculosis (Edinb) 95(3), 2015
PMID: 25794470
Tuberculosis and HIV co-infection-focus on the Asia-Pacific region.
Trinh QM, Nguyen HL, Nguyen VN, Nguyen TV, Sintchenko V, Marais BJ., Int J Infect Dis 32(), 2015
PMID: 25809776
Fighting an old disease with next-generation sequencing.
Dippenaar A, Warren RM., Elife 4(), 2015
PMID: 25732038
Clonality and micro-diversity of a nationwide spreading genotype of Mycobacterium tuberculosis in Japan.
Wada T, Iwamoto T, Tamaru A, Seto J, Ahiko T, Yamamoto K, Hase A, Maeda S, Yamamoto T., PLoS One 10(3), 2015
PMID: 25734518
Mathematical Modelling and Tuberculosis: Advances in Diagnostics and Novel Therapies.
Zwerling A, Shrestha S, Dowdy DW., Adv Med 2015(), 2015
PMID: 26556559
Construction of a virtual Mycobacterium tuberculosis consensus genome and its application to data from a next generation sequencer.
Okumura K, Kato M, Kirikae T, Kayano M, Miyoshi-Akiyama T., BMC Genomics 16(), 2015
PMID: 25879806
Predominant Mycobacterium tuberculosis Families and High Rates of Recent Transmission among New Cases Are Not Associated with Primary Multidrug Resistance in Lima, Peru.
Barletta F, Otero L, de Jong BC, Iwamoto T, Arikawa K, Van der Stuyft P, Niemann S, Merker M, Uwizeye C, Seas C, Rigouts L., J Clin Microbiol 53(6), 2015
PMID: 25809979
A microbiological revolution meets an ancient disease: improving the management of tuberculosis with genomics.
Wlodarska M, Johnston JC, Gardy JL, Tang P., Clin Microbiol Rev 28(2), 2015
PMID: 25810419
Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities.
Moran-Gilad J, Sintchenko V, Pedersen SK, Wolfgang WJ, Pettengill J, Strain E, Hendriksen RS, Global Microbial Identifier initiative’s Working Group 4 (GMI-WG4)., BMC Infect Dis 15(), 2015
PMID: 25887164
Whole genome sequence analysis of multidrug-resistant Mycobacterium tuberculosis Beijing isolates from an outbreak in Thailand.
Regmi SM, Chaiprasert A, Kulawonganunchai S, Tongsima S, Coker OO, Prammananan T, Viratyosin W, Thaipisuttikul I., Mol Genet Genomics 290(5), 2015
PMID: 25903079
Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain.
Eldholm V, Monteserin J, Rieux A, Lopez B, Sobkowiak B, Ritacco V, Balloux F., Nat Commun 6(), 2015
PMID: 25960343
What caused the outbreak of ESBL-producing Klebsiella pneumoniae in a neonatal intensive care unit, Germany 2009 to 2012? Reconstructing transmission with epidemiological analysis and whole-genome sequencing.
Haller S, Eller C, Hermes J, Kaase M, Steglich M, Radonić A, Dabrowski PW, Nitsche A, Pfeifer Y, Werner G, Wunderle W, Velasco E, Abu Sin M, Eckmanns T, Nübel U., BMJ Open 5(5), 2015
PMID: 25967999
Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples.
Brown AC, Bryant JM, Einer-Jensen K, Holdstock J, Houniet DT, Chan JZ, Depledge DP, Nikolayevskyy V, Broda A, Stone MJ, Christiansen MT, Williams R, McAndrew MB, Tutill H, Brown J, Melzer M, Rosmarin C, McHugh TD, Shorten RJ, Drobniewski F, Speight G, Breuer J., J Clin Microbiol 53(7), 2015
PMID: 25972414
Direct DNA Extraction from Mycobacterium tuberculosis Frozen Stocks as a Reculture-Independent Approach to Whole-Genome Sequencing.
Bjorn-Mortensen K, Zallet J, Lillebaek T, Andersen AB, Niemann S, Rasmussen EM, Kohl TA., J Clin Microbiol 53(8), 2015
PMID: 26019203
Mycobacterium bovis in Panama, 2013.
Acosta F, Chernyaeva E, Mendoza L, Sambrano D, Correa R, Rotkevich M, Tarté M, Hernández H, Velazco B, de Escobar C, de Waard JH, Goodridge A., Emerg Infect Dis 21(6), 2015
PMID: 25988479
The essential role of SepF in mycobacterial division.
Gola S, Munder T, Casonato S, Manganelli R, Vicente M., Mol Microbiol 97(3), 2015
PMID: 25943244
Whole-genome sequencing in outbreak analysis.
Gilchrist CA, Turner SD, Riley MF, Petri WA, Hewlett EL., Clin Microbiol Rev 28(3), 2015
PMID: 25876885
Whole-genome sequencing targets drug-resistant bacterial infections.
Punina NV, Makridakis NM, Remnev MA, Topunov AF., Hum Genomics 9(), 2015
PMID: 26243131
Clinical value of whole-genome sequencing of Mycobacterium tuberculosis.
Takiff HE, Feo O., Lancet Infect Dis 15(9), 2015
PMID: 26277037
Whole-genome Sequencing for Tracing the Transmission Link between Two ARD Outbreaks Caused by a Novel HAdV Serotype 7 Variant, China.
Qiu S, Li P, Liu H, Wang Y, Liu N, Li C, Li S, Li M, Jiang Z, Sun H, Li Y, Xie J, Yang C, Wang J, Li H, Yi S, Wu Z, Jia L, Wang L, Hao R, Sun Y, Huang L, Ma H, Yuan Z, Song H., Sci Rep 5(), 2015
PMID: 26338697
Utility of Whole-Genome Sequencing of Escherichia coli O157 for Outbreak Detection and Epidemiological Surveillance.
Holmes A, Allison L, Ward M, Dallman TJ, Clark R, Fawkes A, Murphy L, Hanson M., J Clin Microbiol 53(11), 2015
PMID: 26354815
Whole genome sequencing identifies circulating Beijing-lineage Mycobacterium tuberculosis strains in Guatemala and an associated urban outbreak.
Saelens JW, Lau-Bonilla D, Moller A, Medina N, Guzmán B, Calderón M, Herrera R, Sisk DM, Xet-Mull AM, Stout JE, Arathoon E, Samayoa B, Tobin DM., Tuberculosis (Edinb) 95(6), 2015
PMID: 26542222
Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal.
Cohen KA, Abeel T, Manson McGuire A, Desjardins CA, Munsamy V, Shea TP, Walker BJ, Bantubani N, Almeida DV, Alvarado L, Chapman SB, Mvelase NR, Duffy EY, Fitzgerald MG, Govender P, Gujja S, Hamilton S, Howarth C, Larimer JD, Maharaj K, Pearson MD, Priest ME, Zeng Q, Padayatchi N, Grosset J, Young SK, Wortman J, Mlisana KP, O'Donnell MR, Birren BW, Bishai WR, Pym AS, Earl AM., PLoS Med 12(9), 2015
PMID: 26418737
Population genomics of Mycobacterium tuberculosis in the Inuit.
Lee RS, Radomski N, Proulx JF, Levade I, Shapiro BJ, McIntosh F, Soualhine H, Menzies D, Behr MA., Proc Natl Acad Sci U S A 112(44), 2015
PMID: 26483462
TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis Using Short-Read Whole-Genome Sequencing.
Sekizuka T, Yamashita A, Murase Y, Iwamoto T, Mitarai S, Kato S, Kuroda M., PLoS One 10(11), 2015
PMID: 26565975
Phenotypic Heterogeneity Affects Stenotrophomonas maltophilia K279a Colony Morphotypes and β-Lactamase Expression.
Abda EM, Krysciak D, Krohn-Molt I, Mamat U, Schmeisser C, Förstner KU, Schaible UE, Kohl TA, Nieman S, Streit WR., Front Microbiol 6(), 2015
PMID: 26696982
A Novel Tool Improves Existing Estimates of Recent Tuberculosis Transmission in Settings of Sparse Data Collection.
Kasaie P, Mathema B, Kelton WD, Azman AS, Pennington J, Dowdy DW., PLoS One 10(12), 2015
PMID: 26679499
Whole genome sequencing analysis of intrapatient microevolution in Mycobacterium tuberculosis: potential impact on the inference of tuberculosis transmission.
Pérez-Lago L, Comas I, Navarro Y, González-Candelas F, Herranz M, Bouza E, García-de-Viedma D., J Infect Dis 209(1), 2014
PMID: 23945373
Prevalence and molecular characterization of fluoroquinolone-resistant Mycobacterium tuberculosis isolates in China.
Zhang Z, Lu J, Wang Y, Pang Y, Zhao Y., Antimicrob Agents Chemother 58(1), 2014
PMID: 24165186
Proposal of a consensus set of hypervariable mycobacterial interspersed repetitive-unit-variable-number tandem-repeat loci for subtyping of Mycobacterium tuberculosis Beijing isolates.
Allix-Béguec C, Wahl C, Hanekom M, Nikolayevskyy V, Drobniewski F, Maeda S, Campos-Herrero I, Mokrousov I, Niemann S, Kontsevaya I, Rastogi N, Samper S, Sng LH, Warren RM, Supply P., J Clin Microbiol 52(1), 2014
PMID: 24172154
Progenitor “Mycobacterium canettii” clone responsible for lymph node tuberculosis epidemic, Djibouti.
Blouin Y, Cazajous G, Dehan C, Soler C, Vong R, Hassan MO, Hauck Y, Boulais C, Andriamanantena D, Martinaud C, Martin É, Pourcel C, Vergnaud G., Emerg Infect Dis 20(1), 2014
PMID: 24520560
Mycobacterium tuberculosis evolutionary pathogenesis and its putative impact on drug development.
Le Chevalier F, Cascioferro A, Majlessi L, Herrmann JL, Brosch R., Future Microbiol 9(8), 2014
PMID: 25302954
Microevolution during an Anthrax outbreak leading to clonal heterogeneity and penicillin resistance.
Ågren J, Finn M, Bengtsson B, Segerman B., PLoS One 9(2), 2014
PMID: 24551231
PolyTB: a genomic variation map for Mycobacterium tuberculosis.
Coll F, Preston M, Guerra-Assunção JA, Hill-Cawthorn G, Harris D, Perdigão J, Viveiros M, Portugal I, Drobniewski F, Gagneux S, Glynn JR, Pain A, Parkhill J, McNerney R, Martin N, Clark TG., Tuberculosis (Edinb) 94(3), 2014
PMID: 24637013
Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007-12, with whole pathogen genome sequences: an observational study.
Walker TM, Lalor MK, Broda A, Ortega LS, Morgan M, Parker L, Churchill S, Bennett K, Golubchik T, Giess AP, Del Ojo Elias C, Jeffery KJ, Bowler ICJW, Laurenson IF, Barrett A, Drobniewski F, McCarthy ND, Anderson LF, Abubakar I, Thomas HL, Monk P, Smith EG, Walker AS, Crook DW, Peto TEA, Conlon CP., Lancet Respir Med 2(4), 2014
PMID: 24717625
eCAMBer: efficient support for large-scale comparative analysis of multiple bacterial strains.
Wozniak M, Wong L, Tiuryn J., BMC Bioinformatics 15(), 2014
PMID: 24597904
Supersize me: how whole-genome sequencing and big data are transforming epidemiology.
Kao RR, Haydon DT, Lycett SJ, Murcia PR., Trends Microbiol 22(5), 2014
PMID: 24661923
Profiling of rpoB mutations and MICs for rifampin and rifabutin in Mycobacterium tuberculosis.
Jamieson FB, Guthrie JL, Neemuchwala A, Lastovetska O, Melano RG, Mehaffy C., J Clin Microbiol 52(6), 2014
PMID: 24740074
Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology.
Chernyaeva EN, Shulgina MV, Rotkevich MS, Dobrynin PV, Simonov SA, Shitikov EA, Ischenko DS, Karpova IY, Kostryukova ES, Ilina EN, Govorun VM, Zhuravlev VY, Manicheva OA, Yablonsky PK, Isaeva YD, Nosova EY, Mokrousov IV, Vyazovaya AA, Narvskaya OV, Lapidus AL, O'Brien SJ., BMC Genomics 15(), 2014
PMID: 24767249
Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach.
Kohl TA, Diel R, Harmsen D, Rothgänger J, Walter KM, Merker M, Weniger T, Niemann S., J Clin Microbiol 52(7), 2014
PMID: 24789177
A multicenter study of cross-priming amplification for tuberculosis diagnosis at peripheral level in China.
Ou X, Song Y, Zhao B, Li Q, Xia H, Zhou Y, Pang Y, Wang S, Zhang Z, Cheng S, Liu C, Zhao Y., Tuberculosis (Edinb) 94(4), 2014
PMID: 24880705
Whole-genome sequencing to detect recent transmission of Mycobacterium tuberculosis in settings with a high burden of tuberculosis.
Luo T, Yang C, Peng Y, Lu L, Sun G, Wu J, Jin X, Hong J, Li F, Mei J, DeRiemer K, Gao Q., Tuberculosis (Edinb) 94(4), 2014
PMID: 24888866
Four year longitudinal study of Mycobacterium tuberculosis complex isolates in a region of North-Eastern Italy.
Fallico L, Couvin D, Peracchi M, Pascarella M, Franchin E, Lavezzo E, Rassu M, Manganelli R, Rastogi N, Palù G., Infect Genet Evol 26(), 2014
PMID: 24820340
Validation of high throughput sequencing and microbial forensics applications.
Budowle B, Connell ND, Bielecka-Oder A, Colwell RR, Corbett CR, Fletcher J, Forsman M, Kadavy DR, Markotic A, Morse SA, Murch RS, Sajantila A, Schmedes SE, Ternus KL, Turner SD, Minot S., Investig Genet 5(), 2014
PMID: 25101166
Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar enteritidis.
den Bakker HC, Allard MW, Bopp D, Brown EW, Fontana J, Iqbal Z, Kinney A, Limberger R, Musser KA, Shudt M, Strain E, Wiedmann M, Wolfgang WJ., Emerg Infect Dis 20(8), 2014
PMID: 25062035
A glimpse into the past and predictions for the future: the molecular evolution of the tuberculosis agent.
Boritsch EC, Supply P, Honoré N, Seemann T, Stinear TP, Brosch R., Mol Microbiol 93(5), 2014
PMID: 25039682
Whole-genome sequencing to control antimicrobial resistance.
Köser CU, Ellington MJ, Peacock SJ., Trends Genet 30(9), 2014
PMID: 25096945
Temporal dynamics of Mycobacterium tuberculosis genotypes in New South Wales, Australia.
Gurjav U, Jelfs P, McCallum N, Marais BJ, Sintchenko V., BMC Infect Dis 14(), 2014
PMID: 25149181
Impact and cost-effectiveness of current and future tuberculosis diagnostics: the contribution of modelling.
Dowdy DW, Houben R, Cohen T, Pai M, Cobelens F, Vassall A, Menzies NA, Gomez GB, Langley I, Squire SB, White R, TB MAC meeting participants., Int J Tuberc Lung Dis 18(9), 2014
PMID: 25189546
Age-specific risks of tuberculosis infection from household and community exposures and opportunities for interventions in a high-burden setting.
Zelner JL, Murray MB, Becerra MC, Galea J, Lecca L, Calderon R, Yataco R, Contreras C, Zhang Z, Grenfell BT, Cohen T., Am J Epidemiol 180(8), 2014
PMID: 25190676
Diversity and evolution of Mycobacterium tuberculosis: moving to whole-genome-based approaches.
Niemann S, Supply P., Cold Spring Harb Perspect Med 4(12), 2014
PMID: 25190252
KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes.
Steiner A, Stucki D, Coscolla M, Borrell S, Gagneux S., BMC Genomics 15(), 2014
PMID: 25297886
Prospective genotyping of Mycobacterium tuberculosis from fresh clinical samples.
Bidovec-Stojkovič U, Seme K, Žolnir-Dovč M, Supply P., PLoS One 9(10), 2014
PMID: 25313883
Strain classification of Mycobacterium tuberculosis isolates in Brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism.
Vasconcellos SE, Acosta CC, Gomes LL, Conceição EC, Lima KV, de Araujo MI, Leite Mde L, Tannure F, Caldas PC, Gomes HM, Santos AR, Gomgnimbou MK, Sola C, Couvin D, Rastogi N, Boechat N, Suffys PN., PLoS One 9(10), 2014
PMID: 25314118
An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella.
Pettengill JB, Luo Y, Davis S, Chen Y, Gonzalez-Escalona N, Ottesen A, Rand H, Allard MW, Strain E., PeerJ 2(), 2014
PMID: 25332847
Evolution of extensively drug-resistant Mycobacterium tuberculosis from a susceptible ancestor in a single patient.
Eldholm V, Norheim G, von der Lippe B, Kinander W, Dahle UR, Caugant DA, Mannsåker T, Mengshoel AT, Dyrhol-Riise AM, Balloux F., Genome Biol 15(11), 2014
PMID: 25418686
Marked microevolution of a unique Mycobacterium tuberculosis strain in 17 years of ongoing transmission in a high risk population.
Mehaffy C, Guthrie JL, Alexander DC, Stuart R, Rea E, Jamieson FB., PLoS One 9(11), 2014
PMID: 25405861
Clinical detection and characterization of bacterial pathogens in the genomics era.
Fournier PE, Dubourg G, Raoult D., Genome Med 6(11), 2014
PMID: 25593594
Dissemination of cephalosporin resistance genes between Escherichia coli strains from farm animals and humans by specific plasmid lineages.
de Been M, Lanza VF, de Toro M, Scharringa J, Dohmen W, Du Y, Hu J, Lei Y, Li N, Tooming-Klunderud A, Heederik DJ, Fluit AC, Bonten MJ, Willems RJ, de la Cruz F, van Schaik W., PLoS Genet 10(12), 2014
PMID: 25522320
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Audebert C, Hot D, Lemoine Y, Caboche S., Med Sci (Paris) 30(12), 2014
PMID: 25537045
The need for improved tuberculosis control.
Hoffner SE, Jonsson J., Lancet Infect Dis 13(9), 2013
PMID: 23759448
Metagenomic analysis of tuberculosis in a mummy.
Chan JZ, Sergeant MJ, Lee OY, Minnikin DE, Besra GS, Pap I, Spigelman M, Donoghue HD, Pallen MJ., N Engl J Med 369(3), 2013
PMID: 23863071
Unravelling parasitic nematode natural history using population genetics.
Gilabert A, Wasmuth JD., Trends Parasitol 29(9), 2013
PMID: 23948430
Sequencing the human microbiome in health and disease.
Cox MJ, Cookson WO, Moffatt MF., Hum Mol Genet 22(r1), 2013
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Rapid diagnostics of tuberculosis and drug resistance in the industrialized world: clinical and public health benefits and barriers to implementation.
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