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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. 2016 Jul;54(7):1862-70. doi: 10.1128/JCM.00126-16. Epub 2016 May 18.


Acquired Resistance to Bedaquiline and Delamanid in Therapy for Tuberculosis.

Bloemberg GV, Keller PM, Stucki D, Trauner A, Borrell S, Latshang T, Coscolla M, Rothe T, Hömke R, Ritter C, Feldmann J, Schulthess B, Gagneux S, Böttger EC.

N Engl J Med. 2015 Nov 12;373(20):1986-8. doi: 10.1056/NEJMc1505196. Erratum in: N Engl J Med. 2015 Dec 17;373(25):e29. Stuckia, David [corrected to Stucki, David].


Mycobacterium africanum is associated with patient ethnicity in Ghana.

Asante-Poku A, Yeboah-Manu D, Otchere ID, Aboagye SY, Stucki D, Hattendorf J, Borrell S, Feldmann J, Danso E, Gagneux S.

PLoS Negl Trop Dis. 2015 Jan 8;9(1):e3370. doi: 10.1371/journal.pntd.0003370. eCollection 2015 Jan.


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. 2015 Apr 15;211(8):1306-16. doi: 10.1093/infdis/jiu601. Epub 2014 Oct 30.


KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes.

Steiner A, Stucki D, Coscolla M, Borrell S, Gagneux S.

BMC Genomics. 2014 Oct 9;15:881. doi: 10.1186/1471-2164-15-881.


Evolution of drug resistance in tuberculosis: recent progress and implications for diagnosis and therapy.

Trauner A, Borrell S, Reither K, Gagneux S.

Drugs. 2014 Jul;74(10):1063-72. doi: 10.1007/s40265-014-0248-y. Review.


Evaluation of customised lineage-specific sets of MIRU-VNTR loci for genotyping Mycobacterium tuberculosis complex isolates in Ghana.

Asante-Poku A, Nyaho MS, Borrell S, Comas I, Gagneux S, Yeboah-Manu D.

PLoS One. 2014 Mar 25;9(3):e92675. doi: 10.1371/journal.pone.0092675. eCollection 2014.


Epistasis between antibiotic resistance mutations drives the evolution of extensively drug-resistant tuberculosis.

Borrell S, Teo Y, Giardina F, Streicher EM, Klopper M, Feldmann J, Müller B, Victor TC, Gagneux S.

Evol Med Public Health. 2013 Jan;2013(1):65-74. doi: 10.1093/emph/eot003. Epub 2013 Mar 8.


Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans.

Comas I, Coscolla M, Luo T, Borrell S, Holt KE, Kato-Maeda M, Parkhill J, Malla B, Berg S, Thwaites G, Yeboah-Manu D, Bothamley G, Mei J, Wei L, Bentley S, Harris SR, Niemann S, Diel R, Aseffa A, Gao Q, Young D, Gagneux S.

Nat Genet. 2013 Oct;45(10):1176-82. doi: 10.1038/ng.2744. Epub 2013 Sep 1.


HIV infection disrupts the sympatric host-pathogen relationship in human tuberculosis.

Fenner L, Egger M, Bodmer T, Furrer H, Ballif M, Battegay M, Helbling P, Fehr J, Gsponer T, Rieder HL, Zwahlen M, Hoffmann M, Bernasconi E, Cavassini M, Calmy A, Dolina M, Frei R, Janssens JP, Borrell S, Stucki D, Schrenzel J, Böttger EC, Gagneux S; Swiss HIV Cohort and Molecular Epidemiology of Tuberculosis Study Groups.

PLoS Genet. 2013;9(3):e1003318. doi: 10.1371/journal.pgen.1003318. Epub 2013 Mar 7.


First insights into the phylogenetic diversity of Mycobacterium tuberculosis in Nepal.

Malla B, Stucki D, Borrell S, Feldmann J, Maharjan B, Shrestha B, Fenner L, Gagneux S.

PLoS One. 2012;7(12):e52297. doi: 10.1371/journal.pone.0052297. Epub 2012 Dec 26.


The heterogeneous evolution of multidrug-resistant Mycobacterium tuberculosis.

Müller B, Borrell S, Rose G, Gagneux S.

Trends Genet. 2013 Mar;29(3):160-9. doi: 10.1016/j.tig.2012.11.005. Epub 2012 Dec 13. Review.


Putative compensatory mutations in the rpoC gene of rifampin-resistant Mycobacterium tuberculosis are associated with ongoing transmission.

de Vos M, Müller B, Borrell S, Black PA, van Helden PD, Warren RM, Gagneux S, Victor TC.

Antimicrob Agents Chemother. 2013 Feb;57(2):827-32. doi: 10.1128/AAC.01541-12. Epub 2012 Dec 3.


Prevalence and risk factors for VRE colonisation in a tertiary hospital in Melbourne, Australia: a cross sectional study.

Karki S, Houston L, Land G, Bass P, Kehoe R, Borrell S, Watson K, Spelman D, Kennon J, Harrington G, Cheng AC.

Antimicrob Resist Infect Control. 2012 Oct 8;1(1):31. doi: 10.1186/2047-2994-1-31.


A case of cutaneous tuberculosis in a Buruli ulcer-endemic area.

Bratschi MW, Njih Tabah E, Bolz M, Stucki D, Borrell S, Gagneux S, Noumen-Djeunga B, Junghanss T, Um Boock A, Pluschke G.

PLoS Negl Trop Dis. 2012;6(8):e1751. doi: 10.1371/journal.pntd.0001751. Epub 2012 Aug 28. No abstract available.


Drug resistance-conferring mutations in Mycobacterium tuberculosis from Madang, Papua New Guinea.

Ballif M, Harino P, Ley S, Coscolla M, Niemann S, Carter R, Coulter C, Borrell S, Siba P, Phuanukoonnon S, Gagneux S, Beck HP.

BMC Microbiol. 2012 Sep 4;12:191. doi: 10.1186/1471-2180-12-191.


Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages.

Stucki D, Malla B, Hostettler S, Huna T, Feldmann J, Yeboah-Manu D, Borrell S, Fenner L, Comas I, Coscollà M, Gagneux S.

PLoS One. 2012;7(7):e41253. doi: 10.1371/journal.pone.0041253. Epub 2012 Jul 20.


Genetic diversity of Mycobacterium tuberculosis in Madang, Papua New Guinea.

Ballif M, Harino P, Ley S, Carter R, Coulter C, Niemann S, Borrell S, Fenner L, Siba P, Phuanukoonnon S, Gagneux S, Beck HP.

Int J Tuberc Lung Dis. 2012 Aug;16(8):1100-7. doi: 10.5588/ijtld.11.0779. Epub 2012 Jun 14.


Effect of mutation and genetic background on drug resistance in Mycobacterium tuberculosis.

Fenner L, Egger M, Bodmer T, Altpeter E, Zwahlen M, Jaton K, Pfyffer GE, Borrell S, Dubuis O, Bruderer T, Siegrist HH, Furrer H, Calmy A, Fehr J, Stalder JM, Ninet B, Böttger EC, Gagneux S; Swiss HIV Cohort Study and the Swiss Molecular Epidemiology of Tuberculosis Study Group.

Antimicrob Agents Chemother. 2012 Jun;56(6):3047-53. doi: 10.1128/AAC.06460-11. Epub 2012 Apr 2.


Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes.

Comas I, Borrell S, Roetzer A, Rose G, Malla B, Kato-Maeda M, Galagan J, Niemann S, Gagneux S.

Nat Genet. 2011 Dec 18;44(1):106-10. doi: 10.1038/ng.1038.

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