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.

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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, 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), p 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, pp. 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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Hawken SE, Snitkin ES., Ann N Y Acad Sci 1435(1), 2019
PMID: 29604079
Whole genome sequencing-based analysis of tuberculosis (TB) in migrants: rapid tools for cross-border surveillance and to distinguish between recent transmission in the host country and new importations.
Abascal E, Pérez-Lago L, Martínez-Lirola M, Chiner-Oms Á, Herranz M, Chaoui I, Comas I, El Messaoudi MD, Cárdenas JAG, Santantón S, Bouza E, García-de-Viedma D., Euro Surveill 24(4), 2019
PMID: 30696526
Investigation of false-positive Mycobacterium tuberculosis culture tests using whole genome sequencing.
Min J, Kim K, Choi H, Kang ES, Shin YM, An JY, Choe KH, Lee KM., Ann Thorac Med 14(1), 2019
PMID: 30745941
Mycobacterial genomics and structural bioinformatics: opportunities and challenges in drug discovery.
Waman VP, Vedithi SC, Thomas SE, Bannerman BP, Munir A, Skwark MJ, Malhotra S, Blundell TL., Emerg Microbes Infect 8(1), 2019
PMID: 30866765
Simplified Model to Survey Tuberculosis Transmission in Countries Without Systematic Molecular Epidemiology Programs.
Domínguez J, Acosta F, Pérez-Lago L, Sambrano D, Batista V, De La Guardia C, Abascal E, Chiner-Oms Á, Comas I, González P, Bravo J, Del Cid P, Rosas S, Muñoz P, Goodridge A, García de Viedma D., Emerg Infect Dis 25(3), 2019
PMID: 30789134
Molecular and genomic typing for tuberculosis surveillance: A survey study in 26 European countries.
Andrés M, van der Werf MJ, Ködmön C, Albrecht S, Haas W, Fiebig L, Survey study group., PLoS One 14(3), 2019
PMID: 30865640
Assessment of the use and need for an integrated molecular surveillance of tuberculosis: an online survey in Germany.
Sanchini A, Andrés M, Fiebig L, Albrecht S, Hauer B, Haas W., BMC Public Health 19(1), 2019
PMID: 30885160
Rapid cell division of Staphylococcus aureus during colonization of the human nose.
Szafrańska AK, Junker V, Steglich M, Nübel U., BMC Genomics 20(1), 2019
PMID: 30894139
Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden.
Alaridah N, Hallbäck ET, Tångrot J, Winqvist N, Sturegård E, Florén-Johansson K, Jönsson B, Tenland E, Welinder-Olsson C, Medstrand P, Kaijser B, Godaly G., Sci Rep 9(1), 2019
PMID: 30894568
An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome.
Gomez-Gonzalez PJ, Andreu N, Phelan JE, de Sessions PF, Glynn JR, Crampin AC, Campino S, Butcher PD, Hibberd ML, Clark TG., Sci Rep 9(1), 2019
PMID: 30914757
Epidemiology of transmissible diseases: Array hybridization and next generation sequencing as universal nucleic acid-mediated typing tools.
Michael Dunne W, Pouseele H, Monecke S, Ehricht R, van Belkum A., Infect Genet Evol 63(), 2018
PMID: 28943408
Patterns of chronic hand eczema: a semantic map analysis of the CARPE registry data.
Cazzaniga S, Apfelbacher C, Diepgen T, Ofenloch RF, Weisshaar E, Molin S, Bauer A, Mahler V, Elsner P, Schmitt J, Ballmer-Weber BK, Spring P, Naldi L, Borradori L, Simon D, CARPE study groups of Germany and Switzerland., Br J Dermatol 178(1), 2018
PMID: 28498524
A cluster of multidrug-resistant Mycobacterium tuberculosis among patients arriving in Europe from the Horn of Africa: a molecular epidemiological study.
Walker TM, Merker M, Knoblauch AM, Helbling P, Schoch OD, van der Werf MJ, Kranzer K, Fiebig L, Kröger S, Haas W, Hoffmann H, Indra A, Egli A, Cirillo DM, Robert J, Rogers TR, Groenheit R, Mengshoel AT, Mathys V, Haanperä M, Soolingen DV, Niemann S, Böttger EC, Keller PM, MDR-TB Cluster Consortium., Lancet Infect Dis 18(4), 2018
PMID: 29326013
Occurrence and Nature of Double Alleles in Variable-Number Tandem-Repeat Patterns of More than 8,000 Mycobacterium tuberculosis Complex Isolates in The Netherlands.
Jajou R, Kamst M, van Hunen R, de Zwaan CC, Mulder A, Supply P, Anthony R, van der Hoek W, van Soolingen D., J Clin Microbiol 56(2), 2018
PMID: 29142049
A complex scenario of tuberculosis transmission is revealed through genetic and epidemiological surveys in Porto.
Rito T, Matos C, Carvalho C, Machado H, Rodrigues G, Oliveira O, Ferreira E, Gonçalves J, Maio L, Morais C, Ramos H, Guimarães JT, Santos CL, Duarte R, Correia-Neves M., BMC Infect Dis 18(1), 2018
PMID: 29370774
Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5],12:i:.
Saltykova A, Wuyts V, Mattheus W, Bertrand S, Roosens NHC, Marchal K, De Keersmaecker SCJ., PLoS One 13(2), 2018
PMID: 29408896
When are pathogen genome sequences informative of transmission events?
Campbell F, Strang C, Ferguson N, Cori A, Jombart T., PLoS Pathog 14(2), 2018
PMID: 29420641
Spatial overlap links seemingly unconnected genotype-matched TB cases in rural Uganda.
Chamie G, Kato-Maeda M, Emperador DM, Wandera B, Mugagga O, Crandall J, Janes M, Marquez C, Kamya MR, Charlebois ED, Havlir DV., PLoS One 13(2), 2018
PMID: 29438413
Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population-based study.
Jajou R, de Neeling A, van Hunen R, de Vries G, Schimmel H, Mulder A, Anthony R, van der Hoek W, van Soolingen D., PLoS One 13(4), 2018
PMID: 29617456
Risk of tuberculosis transmission among healthcare workers.
Diel R, Niemann S, Nienhaus A., ERJ Open Res 4(2), 2018
PMID: 29637080
Genetic profiling of Mycobacterium bovis strains from slaughtered cattle in Eritrea.
Ghebremariam MK, Hlokwe T, Rutten VPMG, Allepuz A, Cadmus S, Muwonge A, Robbe-Austerman S, Michel AL., PLoS Negl Trop Dis 12(4), 2018
PMID: 29664901
Automated IS6110-based fingerprinting of Mycobacterium tuberculosis: Reaching unprecedented discriminatory power and versatility.
Dekhil N, Skhairia MA, Mhenni B, Ben Fradj S, Warren R, Mardassi H., PLoS One 13(6), 2018
PMID: 29856789
Genetic Diversity of Mycobacterium tuberculosis Isolates in the Metropolitan Area of Rome.
Cannas A, Camassa S, Sali M, Butera O, Mazzarelli A, Sanguinetti M, Di Caro A, Delogu G, Girardi E., Chemotherapy 63(3), 2018
PMID: 29902788
Insights into the processes that drive the evolution of drug resistance in Mycobacterium tuberculosis.
Nguyen QH, Contamin L, Nguyen TVA, Bañuls AL., Evol Appl 11(9), 2018
PMID: 30344622
A Quantitative Evaluation of MIRU-VNTR Typing Against Whole-Genome Sequencing for Identifying Mycobacterium tuberculosis Transmission: A Prospective Observational Cohort Study.
Wyllie DH, Davidson JA, Grace Smith E, Rathod P, Crook DW, Peto TEA, Robinson E, Walker T, Campbell C., EBioMedicine 34(), 2018
PMID: 30077721
Investigating spillover of multidrug-resistant tuberculosis from a prison: a spatial and molecular epidemiological analysis.
Warren JL, Grandjean L, Moore DAJ, Lithgow A, Coronel J, Sheen P, Zelner JL, Andrews JR, Cohen T., BMC Med 16(1), 2018
PMID: 30071850
Epidemiological and genomic determinants of tuberculosis outbreaks in First Nations communities in Canada.
Doroshenko A, Pepperell CS, Heffernan C, Egedahl ML, Mortimer TD, Smith TM, Bussan HE, Tyrrell GJ, Long R., BMC Med 16(1), 2018
PMID: 30086755
A Major Mycobacterium tuberculosis outbreak caused by one specific genotype in a low-incidence country: Exploring gene profile virulence explanations.
Folkvardsen DB, Norman A, Andersen ÅB, Rasmussen EM, Lillebaek T, Jelsbak L., Sci Rep 8(1), 2018
PMID: 30089859
Harmonized Genome Wide Typing of Tubercle Bacilli Using a Web-Based Gene-By-Gene Nomenclature System.
Kohl TA, Harmsen D, Rothgänger J, Walker T, Diel R, Niemann S., EBioMedicine 34(), 2018
PMID: 30115606
Genome-based transmission modelling separates imported tuberculosis from recent transmission within an immigrant population.
Ayabina D, Ronning JO, Alfsnes K, Debech N, Brynildsrud OB, Arnesen T, Norheim G, Mengshoel AT, Rykkvin R, Dahle UR, Colijn C, Eldholm V., Microb Genom 4(10), 2018
PMID: 30216147
The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology.
Meehan CJ, Moris P, Kohl TA, Pečerska J, Akter S, Merker M, Utpatel C, Beckert P, Gehre F, Lempens P, Stadler T, Kaswa MK, Kühnert D, Niemann S, de Jong BC., EBioMedicine 37(), 2018
PMID: 30341041
Methods used in the spatial analysis of tuberculosis epidemiology: a systematic review.
Shaweno D, Karmakar M, Alene KA, Ragonnet R, Clements AC, Trauer JM, Denholm JT, McBryde ES., BMC Med 16(1), 2018
PMID: 30333043
Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia.
Merker M, Barbier M, Cox H, Rasigade JP, Feuerriegel S, Kohl TA, Diel R, Borrell S, Gagneux S, Nikolayevskyy V, Andres S, Nübel U, Supply P, Wirth T, Niemann S., Elife 7(), 2018
PMID: 30373719
Genomic sequencing is required for identification of tuberculosis transmission in Hawaii.
Koster KJ, Largen A, Foster JT, Drees KP, Qian L, Desmond E, Wan X, Hou S, Douglas JT., BMC Infect Dis 18(1), 2018
PMID: 30509214
Mycobacterium tuberculosis Next-Generation Whole Genome Sequencing: Opportunities and Challenges.
Iketleng T, Lessells R, Dlamini MT, Mogashoa T, Mupfumi L, Moyo S, Gaseitsiwe S, de Oliveira T., Tuberc Res Treat 2018(), 2018
PMID: 30631597
Whole genome sequencing for M/XDR tuberculosis surveillance and for resistance testing.
Walker TM, Merker M, Kohl TA, Crook DW, Niemann S, Peto TE., Clin Microbiol Infect 23(3), 2017
PMID: 27789378
The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee.
Ellington MJ, Ekelund O, Aarestrup FM, Canton R, Doumith M, Giske C, Grundman H, Hasman H, Holden MTG, Hopkins KL, Iredell J, Kahlmeter G, Köser CU, MacGowan A, Mevius D, Mulvey M, Naas T, Peto T, Rolain JM, Samuelsen Ø, Woodford N., Clin Microbiol Infect 23(1), 2017
PMID: 27890457
A joint cross-border investigation of a cluster of multidrug-resistant tuberculosis in Austria, Romania and Germany in 2014 using classic, genotyping and whole genome sequencing methods: lessons learnt.
Fiebig L, Kohl TA, Popovici O, Mühlenfeld M, Indra A, Homorodean D, Chiotan D, Richter E, Rüsch-Gerdes S, Schmidgruber B, Beckert P, Hauer B, Niemann S, Allerberger F, Haas W., Euro Surveill 22(2), 2017
PMID: 28106529
Translating Omics to Food Microbiology.
Walsh AM, Crispie F, Claesson MJ, Cotter PD., Annu Rev Food Sci Technol 8(), 2017
PMID: 28125344
Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance.
Manson AL, Cohen KA, Abeel T, Desjardins CA, Armstrong DT, Barry CE, Brand J, TBResist Global Genome Consortium, Chapman SB, Cho SN, Gabrielian A, Gomez J, Jodals AM, Joloba M, Jureen P, Lee JS, Malinga L, Maiga M, Nordenberg D, Noroc E, Romancenco E, Salazar A, Ssengooba W, Velayati AA, Winglee K, Zalutskaya A, Via LE, Cassell GH, Dorman SE, Ellner J, Farnia P, Galagan JE, Rosenthal A, Crudu V, Homorodean D, Hsueh PR, Narayanan S, Pym AS, Skrahina A, Swaminathan S, Van der Walt M, Alland D, Bishai WR, Cohen T, Hoffner S, Birren BW, Earl AM., Nat Genet 49(3), 2017
PMID: 28092681
Tuberculosis Outbreak in an Educational Institution in Norway.
Norheim G, Seterelv S, Arnesen TM, Mengshoel AT, Tønjum T, Rønning JO, Eldholm V., J Clin Microbiol 55(5), 2017
PMID: 28202795
New Mycobacterium tuberculosis Complex Sublineage, Brazzaville, Congo.
Malm S, Linguissi LS, Tekwu EM, Vouvoungui JC, Kohl TA, Beckert P, Sidibe A, Rüsch-Gerdes S, Madzou-Laboum IK, Kwedi S, Penlap Beng V, Frank M, Ntoumi F, Niemann S., Emerg Infect Dis 23(3), 2017
PMID: 28221129
Whole-genome analysis of mycobacteria from birds at the San Diego Zoo.
Pfeiffer W, Braun J, Burchell J, Witte CL, Rideout BA., PLoS One 12(3), 2017
PMID: 28267758
The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis.
Dheda K, Gumbo T, Maartens G, Dooley KE, McNerney R, Murray M, Furin J, Nardell EA, London L, Lessem E, Theron G, van Helden P, Niemann S, Merker M, Dowdy D, Van Rie A, Siu GK, Pasipanodya JG, Rodrigues C, Clark TG, Sirgel FA, Esmail A, Lin HH, Atre SR, Schaaf HS, Chang KC, Lange C, Nahid P, Udwadia ZF, Horsburgh CR, Churchyard GJ, Menzies D, Hesseling AC, Nuermberger E, McIlleron H, Fennelly KP, Goemaere E, Jaramillo E, Low M, Jara CM, Padayatchi N, Warren RM., Lancet Respir Med (), 2017
PMID: 28344011
Genomic characterization of Nontuberculous Mycobacteria.
Fedrizzi T, Meehan CJ, Grottola A, Giacobazzi E, Fregni Serpini G, Tagliazucchi S, Fabio A, Bettua C, Bertorelli R, De Sanctis V, Rumpianesi F, Pecorari M, Jousson O, Tortoli E, Segata N., Sci Rep 7(), 2017
PMID: 28345639
Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks.
Didelot X, Fraser C, Gardy J, Colijn C., Mol Biol Evol 34(4), 2017
PMID: 28100788
Epidemiology and whole genome sequencing of an ongoing point-source Salmonella Agona outbreak associated with sushi consumption in western Sydney, Australia 2015.
Thompson CK, Wang Q, Bag SK, Franklin N, Shadbolt CT, Howard P, Fearnley EJ, Quinn HE, Sintchenko V, Hope KG., Epidemiol Infect 145(10), 2017
PMID: 28462733
Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory.
Kozyreva VK, Truong CL, Greninger AL, Crandall J, Mukhopadhyay R, Chaturvedi V., J Clin Microbiol 55(8), 2017
PMID: 28592550
SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology.
Petkau A, Mabon P, Sieffert C, Knox NC, Cabral J, Iskander M, Iskander M, Weedmark K, Zaheer R, Katz LS, Nadon C, Reimer A, Taboada E, Beiko RG, Hsiao W, Brinkman F, Graham M, Van Domselaar G., Microb Genom 3(6), 2017
PMID: 29026651
Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review.
Tagini F, Greub G., Eur J Clin Microbiol Infect Dis 36(11), 2017
PMID: 28639162
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.
Bruning-Fann CS, Robbe-Austerman S, Kaneene JB, Thomsen BV, Tilden JD, Ray JS, Smith RW, Fitzgerald SD, Bolin SR, O'Brien DJ, Mullaney TP, Stuber TP, Averill JJ, Marks D., J Am Vet Med Assoc 251(2), 2017
PMID: 28671497
Genomic Epidemiology of a Major Mycobacterium tuberculosis Outbreak: Retrospective Cohort Study in a Low-Incidence Setting Using Sparse Time-Series Sampling.
Folkvardsen DB, Norman A, Andersen ÅB, Michael Rasmussen E, Jelsbak L, Lillebaek T., J Infect Dis 216(3), 2017
PMID: 28666374
Transmission is a Noticeable Cause of Resistance Among Treated Tuberculosis Patients in Shanghai, China.
Nsofor CA, Jiang Q, Wu J, Gan M, Liu Q, Zuo T, Zhu G, Gao Q., Sci Rep 7(1), 2017
PMID: 28794425
Disease reservoirs: from conceptual frameworks to applicable criteria.
Hallmaier-Wacker LK, Munster VJ, Knauf S., Emerg Microbes Infect 6(9), 2017
PMID: 28874791
Whole-genome sequencing illuminates the evolution and spread of multidrug-resistant tuberculosis in Southwest Nigeria.
Senghore M, Otu J, Witney A, Gehre F, Doughty EL, Kay GL, Butcher P, Salako K, Kehinde A, Onyejepu N, Idigbe E, Corrah T, de Jong B, Pallen MJ, Antonio M., PLoS One 12(9), 2017
PMID: 28926571
Drivers of Tuberculosis Transmission.
Mathema B, Andrews JR, Cohen T, Borgdorff MW, Behr M, Glynn JR, Rustomjee R, Silk BJ, Wood R., J Infect Dis 216(suppl_6), 2017
PMID: 29112745
Integration of molecular typing results into tuberculosis surveillance in Germany-A pilot study.
Andrés M, Göhring-Zwacka E, Fiebig L, Priwitzer M, Richter E, Rüsch-Gerdes S, Haas W, Niemann S, Brodhun B., PLoS One 12(11), 2017
PMID: 29166403
Tuberculosis: Just the FAQs.
Guinn KM, Rubin EJ., MBio 8(6), 2017
PMID: 29259086
Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis.
Trewby H, Wright D, Breadon EL, Lycett SJ, Mallon TR, McCormick C, Johnson P, Orton RJ, Allen AR, Galbraith J, Herzyk P, Skuce RA, Biek R, Kao RR., Epidemics 14(), 2016
PMID: 26972511
Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study.
Pankhurst LJ, Del Ojo Elias C, Votintseva AA, Walker TM, Cole K, Davies J, Fermont JM, Gascoyne-Binzi DM, Kohl TA, Kong C, Lemaitre N, Niemann S, Paul J, Rogers TR, Roycroft E, Smith EG, Supply P, Tang P, Wilcox MH, Wordsworth S, Wyllie D, Xu L, Crook DW, COMPASS-TB Study Group., Lancet Respir Med 4(1), 2016
PMID: 26669893
Implementation of a Consensus Set of Hypervariable Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat Loci in Mycobacterium tuberculosis Molecular Epidemiology.
Trovato A, Tafaj S, Battaglia S, Alagna R, Bardhi D, Kapisyzi P, Bala S, Haldeda M, Borroni E, Hafizi H, Cirillo DM., J Clin Microbiol 54(2), 2016
PMID: 26659207
The implications of whole-genome sequencing in the control of tuberculosis.
Lee RS, Behr MA., Ther Adv Infect Dis 3(2), 2016
PMID: 27034776
The transmission of Mycobacterium tuberculosis in high burden settings.
Yates TA, Khan PY, Knight GM, Taylor JG, McHugh TD, Lipman M, White RG, Cohen T, Cobelens FG, Wood R, Moore DA, Abubakar I., Lancet Infect Dis 16(2), 2016
PMID: 26867464
ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections.
Chindelevitch L, Colijn C, Moodley P, Wilson D, Cohen T., PLoS Comput Biol 12(2), 2016
PMID: 26829497
Identification of ITPA on chromosome 20 as a susceptibility gene for young-onset tuberculosis.
Nakauchi A, Wong JH, Mahasirimongkol S, Yanai H, Yuliwulandari R, Mabuchi A, Liu X, Mushiroda T, Wattanapokayakit S, Miyagawa T, Keicho N, Tokunaga K., Hum Genome Var 3(), 2016
PMID: 27081565
Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly.
Love RR, Weisenfeld NI, Jaffe DB, Besansky NJ, Neafsey DE., BMC Genomics 17(), 2016
PMID: 26944054
Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review.
Hatherell HA, Colijn C, Stagg HR, Jackson C, Winter JR, Abubakar I., BMC Med 14(), 2016
PMID: 27005433
Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria.
Jagielski T, Minias A, van Ingen J, Rastogi N, Brzostek A, Żaczek A, Dziadek J., Clin Microbiol Rev 29(2), 2016
PMID: 26912567
Antimicrobial Resistance in Mycobacterium tuberculosis: The Odd One Out.
Eldholm V, Balloux F., Trends Microbiol 24(8), 2016
PMID: 27068531
Occupational Tuberculosis in Denmark through 21 Years Analysed by Nationwide Genotyping.
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
PMID: 27311749
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
PMID: 27315243
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
[High-throughput sequencing: towards a genome-based diagnosis in infectious diseases].
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
PMID: 23943792
Rapid diagnostics of tuberculosis and drug resistance in the industrialized world: clinical and public health benefits and barriers to implementation.
Drobniewski F, Nikolayevskyy V, Maxeiner H, Balabanova Y, Casali N, Kontsevaya I, Ignatyeva O., BMC Med 11(), 2013
PMID: 23987891
"Epidemic clones" of Listeria monocytogenes are widespread and ancient clonal groups.
Cantinelli T, Chenal-Francisque V, Diancourt L, Frezal L, Leclercq A, Wirth T, Lecuit M, Brisse S., J Clin Microbiol 51(11), 2013
PMID: 24006010
Genomics and metagenomics in medical microbiology.
Padmanabhan R, Mishra AK, Raoult D, Fournier PE., J Microbiol Methods 95(3), 2013
PMID: 24200711
Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients.
Merker M, Kohl TA, Roetzer A, Truebe L, Richter E, Rüsch-Gerdes S, Fattorini L, Oggioni MR, Cox H, Varaine F, Niemann S., PLoS One 8(12), 2013
PMID: 24324807

38 References

Daten bereitgestellt von Europe PubMed Central.

The population dynamics and control of tuberculosis.
Dye C, Williams BG., Science 328(5980), 2010
PMID: 20466923

AUTHOR UNKNOWN, 0
The evolution of virulence.
Read AF., Trends Microbiol. 2(3), 1994
PMID: 8156274
Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology.
van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, Gicquel B, Hermans P, Martin C, McAdam R, Shinnick TM., J. Clin. Microbiol. 31(2), 1993
PMID: 8381814
Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology.
Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S, Bunschoten A, Molhuizen H, Shaw R, Goyal M, van Embden J., J. Clin. Microbiol. 35(4), 1997
PMID: 9157152
Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis.
Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rusch-Gerdes S, Willery E, Savine E, de Haas P, van Deutekom H, Roring S, Bifani P, Kurepina N, Kreiswirth B, Sola C, Rastogi N, Vatin V, Gutierrez MC, Fauville M, Niemann S, Skuce R, Kremer K, Locht C, van Soolingen D., J. Clin. Microbiol. 44(12), 2006
PMID: 17005759
The forest behind the tree: phylogenetic exploration of a dominant Mycobacterium tuberculosis strain lineage from a high tuberculosis burden country.
Cardoso Oelemann M, Gomes HM, Willery E, Possuelo L, Batista Lima KV, Allix-Beguec C, Locht C, Goguet de la Salmoniere YO, Gutierrez MC, Suffys P, Supply P., PLoS ONE 6(3), 2011
PMID: 21464915
Epidemiology of tuberculosis in Hamburg, Germany: long-term population-based analysis applying classical and molecular epidemiological techniques.
Diel R, Schneider S, Meywald-Walter K, Ruf CM, Rusch-Gerdes S, Niemann S., J. Clin. Microbiol. 40(2), 2002
PMID: 11825968
DNA fingerprinting of Mycobacterium tuberculosis: from phage typing to whole-genome sequencing.
Schurch AC, van Soolingen D., Infect. Genet. Evol. 12(4), 2011
PMID: 22067515
Molecular epidemiology of tuberculosis among immigrants in Hamburg, Germany.
Diel R, Rusch-Gerdes S, Niemann S., J. Clin. Microbiol. 42(7), 2004
PMID: 15243044
Evaluation of Mycobacterium tuberculosis typing methods in a 4-year study in Schleswig-Holstein, Northern Germany.
Roetzer A, Schuback S, Diel R, Gasau F, Ubben T, di Nauta A, Richter E, Rusch-Gerdes S, Niemann S., J. Clin. Microbiol. 49(12), 2011
PMID: 21998434
Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints.
Niemann S, Koser CU, Gagneux S, Plinke C, Homolka S, Bignell H, Carter RJ, Cheetham RK, Cox A, Gormley NA, Kokko-Gonzales P, Murray LJ, Rigatti R, Smith VP, Arends FP, Cox HS, Smith G, Archer JA., PLoS ONE 4(10), 2009
PMID: 19823582
Whole-genome sequencing and social-network analysis of a tuberculosis outbreak.
Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJ, Brinkman FS, Brunham RC, Tang P., N. Engl. J. Med. 364(8), 2011
PMID: 21345102
Navigating the future of bacterial molecular epidemiology.
Baker S, Hanage WP, Holt KE., Curr. Opin. Microbiol. 13(5), 2010
PMID: 20846899
Recent advances in diagnostic microbiology.
Bravo LT, Procop GW., Semin. Hematol. 46(3), 2009
PMID: 19549577
SNP/RD typing of Mycobacterium tuberculosis Beijing strains reveals local and worldwide disseminated clonal complexes.
Schurch AC, Kremer K, Hendriks AC, Freyee B, McEvoy CR, van Crevel R, Boeree MJ, van Helden P, Warren RM, Siezen RJ, van Soolingen D., PLoS ONE 6(12), 2011
PMID: 22162765
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.
Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE 3rd, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, Quail MA, Rajandream MA, Rogers J, Rutter S, Seeger K, Skelton J, Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG., Nature 393(6685), 1998
PMID: 9634230
Mauve: multiple alignment of conserved genomic sequence with rearrangements.
Darling AC, Mau B, Blattner FR, Perna NT., Genome Res. 14(7), 2004
PMID: 15231754
Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming.
Blom J, Jakobi T, Doppmeier D, Jaenicke S, Kalinowski J, Stoye J, Goesmann A., Bioinformatics 27(10), 2011
PMID: 21450712
BEAST: Bayesian evolutionary analysis by sampling trees.
Drummond AJ, Rambaut A., BMC Evol. Biol. 7(), 2007
PMID: 17996036
A timescale for evolution, population expansion, and spatial spread of an emerging clone of methicillin-resistant Staphylococcus aureus.
Nubel U, Dordel J, Kurt K, Strommenger B, Westh H, Shukla SK, Zemlickova H, Leblois R, Wirth T, Jombart T, Balloux F, Witte W., PLoS Pathog. 6(4), 2010
PMID: 20386717

AUTHOR UNKNOWN, 0
Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains.
Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, Peterson J, DeBoy R, Dodson R, Gwinn M, Haft D, Hickey E, Kolonay JF, Nelson WC, Umayam LA, Ermolaeva M, Salzberg SL, Delcher A, Utterback T, Weidman J, Khouri H, Gill J, Mikula A, Bishai W, Jacobs WR Jr, Venter JC, Fraser CM., J. Bacteriol. 184(19), 2002
PMID: 12218036
Analysis of the proteome of Mycobacterium tuberculosis in silico.
Tekaia F, Gordon SV, Garnier T, Brosch R, Barrell BG, Cole ST., Tuber. Lung Dis. 79(6), 1999
PMID: 10694977
Ongoing outbreak of tuberculosis in a low-incidence community: a molecular-epidemiological evaluation.
Diel R, Meywald-Walter K, Gottschalk R, Rusch-Gerdes S, Niemann S., Int. J. Tuberc. Lung Dis. 8(7), 2004
PMID: 15260277
Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved.
Comas I, Chakravartti J, Small PM, Galagan J, Niemann S, Kremer K, Ernst JD, Gagneux S., Nat. Genet. 42(6), 2010
PMID: 20495566
Rapid pneumococcal evolution in response to clinical interventions.
Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, van der Linden M, McGee L, von Gottberg A, Song JH, Ko KS, Pichon B, Baker S, Parry CM, Lambertsen LM, Shahinas D, Pillai DR, Mitchell TJ, Dougan G, Tomasz A, Klugman KP, Parkhill J, Hanage WP, Bentley SD., Science 331(6016), 2011
PMID: 21273480
Evolution of MRSA during hospital transmission and intercontinental spread.
Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK, Chantratita N, Gardete S, Tavares A, Day N, Lindsay JA, Edgeworth JD, de Lencastre H, Parkhill J, Peacock SJ, Bentley SD., Science 327(5964), 2010
PMID: 20093474
Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection.
Ford CB, Lin PL, Chase MR, Shah RR, Iartchouk O, Galagan J, Mohaideen N, Ioerger TR, Sacchettini JC, Lipsitch M, Flynn JL, Fortune SM., Nat. Genet. 43(5), 2011
PMID: 21516081
Time dependency of molecular rate estimates and systematic overestimation of recent divergence times.
Ho SY, Phillips MJ, Cooper A, Drummond AJ., Mol. Biol. Evol. 22(7), 2005
PMID: 15814826
Variability of infectious aerosols produced during coughing by patients with pulmonary tuberculosis.
Fennelly KP, Jones-Lopez EC, Ayakaka I, Kim S, Menyha H, Kirenga B, Muchwa C, Joloba M, Dryden-Peterson S, Reilly N, Okwera A, Elliott AM, Smith PG, Mugerwa RD, Eisenach KD, Ellner JJ., Am. J. Respir. Crit. Care Med. 186(5), 2012
PMID: 22798319
Epidemiologic consequences of microvariation in Mycobacterium tuberculosis.
Mathema B, Kurepina N, Yang G, Shashkina E, Manca C, Mehaffy C, Bielefeldt-Ohmann H, Ahuja S, Fallows DA, Izzo A, Bifani P, Dobos K, Kaplan G, Kreiswirth BN., J. Infect. Dis. 205(6), 2012
PMID: 22315279
Routine use of microbial whole genome sequencing in diagnostic and public health microbiology.
Koser CU, Ellington MJ, Cartwright EJ, Gillespie SH, Brown NM, Farrington M, Holden MT, Dougan G, Bentley SD, Parkhill J, Peacock SJ., PLoS Pathog. 8(8), 2012
PMID: 22876174
Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains.
Tsolaki AG, Hirsh AE, DeRiemer K, Enciso JA, Wong MZ, Hannan M, Goguet de la Salmoniere YO, Aman K, Kato-Maeda M, Small PM., Proc. Natl. Acad. Sci. U.S.A. 101(14), 2004
PMID: 15024109

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