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Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade.

Conceição EC, Refregier G, Gomes HM, Olessa-Daragon X, Coll F, Ratovonirina NH, Rasolofo-Razanamparany V, Lopes ML, van Soolingen D, Rutaihwa L, Gagneux S, Bollela VR, Suffys PN, Duarte RS, Lima KVB, Sola CN.

Infect Genet Evol. 2019 Jun 3;73:337-341. doi: 10.1016/j.meegid.2019.06.001. [Epub ahead of print]


Correction: TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities.

Carey AF, Rock JM, Krieger IV, Chase MR, Fernandez-Suarez M, Gagneux S, Sacchettini JC, Ioerger TR, Fortune SM.

PLoS Pathog. 2019 Jun 4;15(6):e1007846. doi: 10.1371/journal.ppat.1007846. eCollection 2019 Jun.


Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis.

Payne JL, Menardo F, Trauner A, Borrell S, Gygli SM, Loiseau C, Gagneux S, Hall AR.

PLoS Biol. 2019 May 13;17(5):e3000265. doi: 10.1371/journal.pbio.3000265. eCollection 2019 May.


Pathways and associated costs of care in patients with confirmed and presumptive tuberculosis in Tanzania: A cross-sectional study.

Mhalu G, Hella J, Mhimbira F, Said K, Mosabi T, Mlacha YP, Schindler C, Gagneux S, Reither K, de Hoogh K, Weiss MG, Zemp E, Fenner L.

BMJ Open. 2019 Apr 20;9(4):e025079. doi: 10.1136/bmjopen-2018-025079.


Insights into the genetic diversity of Mycobacterium tuberculosis in Tanzania.

Rutaihwa LK, Sasamalo M, Jaleco A, Hella J, Kingazi A, Kamwela L, Kingalu A, Malewo B, Shirima R, Doetsch A, Feldmann J, Reinhard M, Borrell S, Brites D, Reither K, Doulla B, Fenner L, Gagneux S.

PLoS One. 2019 Apr 12;14(4):e0206334. doi: 10.1371/journal.pone.0206334. eCollection 2019.


Revised Interpretation of the Hain Lifescience GenoType MTBC To Differentiate Mycobacterium canettii and Members of the Mycobacterium tuberculosis Complex.

Loiseau C, Brites D, Moser I, Coll F, Pourcel C, Robbe-Austerman S, Escuyer V, Musser KA, Peacock SJ, Feuerriegel S, Kohl TA, Niemann S, Gagneux S, Köser CU.

Antimicrob Agents Chemother. 2019 May 24;63(6). pii: e00159-19. doi: 10.1128/AAC.00159-19. Print 2019 Jun.


Reference set of Mycobacterium tuberculosis clinical strains: A tool for research and product development.

Borrell S, Trauner A, Brites D, Rigouts L, Loiseau C, Coscolla M, Niemann S, De Jong B, Yeboah-Manu D, Kato-Maeda M, Feldmann J, Reinhard M, Beisel C, Gagneux S.

PLoS One. 2019 Mar 25;14(3):e0214088. doi: 10.1371/journal.pone.0214088. eCollection 2019.


Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana.

Otchere ID, van Tonder AJ, Asante-Poku A, Sánchez-Busó L, Coscollá M, Osei-Wusu S, Asare P, Aboagye SY, Ekuban SA, Yahayah AI, Forson A, Baddoo A, Laryea C, Parkhill J, Harris SR, Gagneux S, Yeboah-Manu D.

PLoS One. 2019 Mar 4;14(3):e0209395. doi: 10.1371/journal.pone.0209395. eCollection 2019.


Drug susceptibility testing and mortality in patients treated for tuberculosis in high-burden countries: a multicentre cohort study.

Zürcher K, Ballif M, Fenner L, Borrell S, Keller PM, Gnokoro J, Marcy O, Yotebieng M, Diero L, Carter EJ, Rockwood N, Wilkinson RJ, Cox H, Ezati N, Abimiku AG, Collantes J, Avihingsanon A, Kawkitinarong K, Reinhard M, Hömke R, Huebner R, Gagneux S, Böttger EC, Egger M; International epidemiology Databases to Evaluate AIDS (IeDEA) consortium.

Lancet Infect Dis. 2019 Mar;19(3):298-307. doi: 10.1016/S1473-3099(18)30673-X. Epub 2019 Feb 8.


TB-diabetes co-morbidity in Ghana: The importance of Mycobacterium africanum infection.

Asante-Poku A, Asare P, Baddoo NA, Forson A, Klevor P, Otchere ID, Aboagye SY, Osei-Wusu S, Danso EK, Koram K, Gagneux S, Yeboah-Manu D.

PLoS One. 2019 Feb 7;14(2):e0211822. doi: 10.1371/journal.pone.0211822. eCollection 2019.


Whole-Genome Sequencing for Drug Resistance Profile Prediction in Mycobacterium tuberculosis.

Gygli SM, Keller PM, Ballif M, Blöchliger N, Hömke R, Reinhard M, Loiseau C, Ritter C, Sander P, Borrell S, Collantes Loo J, Avihingsanon A, Gnokoro J, Yotebieng M, Egger M, Gagneux S, Böttger EC.

Antimicrob Agents Chemother. 2019 Mar 27;63(4). pii: e02175-18. doi: 10.1128/AAC.02175-18. Print 2019 Apr.


Discovery and Characterization of Mycobacterium basiliense sp. nov., a Nontuberculous Mycobacterium Isolated From Human Lungs.

Seth-Smith HMB, Imkamp F, Tagini F, Cuénod A, Hömke R, Jahn K, Tschacher A, Grendelmeier P, Bättig V, Erb S, Reinhard M, Rütimann G, Borrell S, Gagneux S, Casanova C, Droz S, Osthoff M, Tamm M, Nübel U, Greub G, Keller PM, Egli A.

Front Microbiol. 2019 Jan 8;9:3184. doi: 10.3389/fmicb.2018.03184. eCollection 2018.


A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex.

Brites D, Loiseau C, Menardo F, Borrell S, Boniotti MB, Warren R, Dippenaar A, Parsons SDC, Beisel C, Behr MA, Fyfe JA, Coscolla M, Gagneux S.

Front Microbiol. 2018 Nov 27;9:2820. doi: 10.3389/fmicb.2018.02820. eCollection 2018.


Analysis of potential household transmission events of tuberculosis in the city of Belem, Brazil.

Conceição EC, Guimarães AEDS, Lopes ML, Furlaneto IP, Rodrigues YC, da Conceição ML, Barros WA, Cardoso NC, Sharma A, Lima LNGC, Gomes HM, Duarte RS, Frota C, Rutaihwa LK, Gagneux S, Suffys PN, Lima KVB.

Tuberculosis (Edinb). 2018 Dec;113:125-129. doi: 10.1016/ Epub 2018 Oct 2.


China's tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis.

Liu Q, Ma A, Wei L, Pang Y, Wu B, Luo T, Zhou Y, Zheng HX, Jiang Q, Gan M, Zuo T, Liu M, Yang C, Jin L, Comas I, Gagneux S, Zhao Y, Pepperell CS, Gao Q.

Nat Ecol Evol. 2018 Dec;2(12):1982-1992. doi: 10.1038/s41559-018-0680-6. Epub 2018 Nov 5.


Low sensitivity of the MPT64 identification test to detect lineage 5 of the Mycobacterium tuberculosis complex.

Sanoussi CN, de Jong BC, Odoun M, Arekpa K, Ali Ligali M, Bodi O, Harris S, Ofori-Anyinam B, Yeboah-Manu D, Otchere ID, Asante-Poku A, Anagonou S, Gagneux S, Coscolla M, Rigouts L, Affolabi D.

J Med Microbiol. 2018 Dec;67(12):1718-1727. doi: 10.1099/jmm.0.000846. Epub 2018 Nov 2.


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. 2018 Oct 30;7. pii: e38200. doi: 10.7554/eLife.38200.


Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase.

Ezewudo M, Borens A, Chiner-Oms Á, Miotto P, Chindelevitch L, Starks AM, Hanna D, Liwski R, Zignol M, Gilpin C, Niemann S, Kohl TA, Warren RM, Crook D, Gagneux S, Hoffner S, Rodrigues C, Comas I, Engelthaler DM, Alland D, Rigouts L, Lange C, Dheda K, Hasan R, McNerney R, Cirillo DM, Schito M, Rodwell TC, Posey J.

Sci Rep. 2018 Oct 18;8(1):15382. doi: 10.1038/s41598-018-33731-1.


Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches.

Otchere ID, Coscollá M, Sánchez-Busó L, Asante-Poku A, Brites D, Loiseau C, Meehan C, Osei-Wusu S, Forson A, Laryea C, Yahayah AI, Baddoo A, Ansa GA, Aboagye SY, Asare P, Borrell S, Gehre F, Beckert P, Kohl TA, N'dira S, Beisel C, Antonio M, Niemann S, de Jong BC, Parkhill J, Harris SR, Gagneux S, Yeboah-Manu D.

Sci Rep. 2018 Jul 26;8(1):11269. doi: 10.1038/s41598-018-29620-2.


Tuberculosis outbreak investigation using phylodynamic analysis.

Kühnert D, Coscolla M, Brites D, Stucki D, Metcalfe J, Fenner L, Gagneux S, Stadler T.

Epidemics. 2018 Dec;25:47-53. doi: 10.1016/j.epidem.2018.05.004. Epub 2018 May 22.


Reduced transmission of Mycobacterium africanum compared to Mycobacterium tuberculosis in urban West Africa.

Asare P, Asante-Poku A, Prah DA, Borrell S, Osei-Wusu S, Otchere ID, Forson A, Adjapong G, Koram KA, Gagneux S, Yeboah-Manu D.

Int J Infect Dis. 2018 Aug;73:30-42. doi: 10.1016/j.ijid.2018.05.014. Epub 2018 Jun 4.


Interplay of strain and race/ethnicity in the innate immune response to M. tuberculosis.

Nahid P, Jarlsberg LG, Kato-Maeda M, Segal MR, Osmond DH, Gagneux S, Dobos K, Gold M, Hopewell PC, Lewinsohn DM.

PLoS One. 2018 May 22;13(5):e0195392. doi: 10.1371/journal.pone.0195392. eCollection 2018.


Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity.

Menardo F, Loiseau C, Brites D, Coscolla M, Gygli SM, Rutaihwa LK, Trauner A, Beisel C, Borrell S, Gagneux S.

BMC Bioinformatics. 2018 May 2;19(1):164. doi: 10.1186/s12859-018-2164-8.


Anemia in tuberculosis cases and household controls from Tanzania: Contribution of disease, coinfections, and the role of hepcidin.

Hella J, Cercamondi CI, Mhimbira F, Sasamalo M, Stoffel N, Zwahlen M, Bodmer T, Gagneux S, Reither K, Zimmermann MB, Risch L, Fenner L.

PLoS One. 2018 Apr 20;13(4):e0195985. doi: 10.1371/journal.pone.0195985. eCollection 2018.


Hyperglycaemia is inversely correlated with live M. bovis BCG-specific CD4+ T cell responses in Tanzanian adults with latent or active tuberculosis.

Boillat-Blanco N, Tumbo AN, Perreau M, Amelio P, Ramaiya KL, Mganga M, Schindler C, Gagneux S, Reither K, Probst-Hensch N, Pantaleo G, Daubenberger C, Portevin D.

Immun Inflamm Dis. 2018 Jun;6(2):345-353. doi: 10.1002/iid3.222. Epub 2018 Apr 11.


Prevalence and clinical significance of respiratory viruses and bacteria detected in tuberculosis patients compared to household contact controls in Tanzania: a cohort study.

Mhimbira F, Hiza H, Mbuba E, Hella J, Kamwela L, Sasamalo M, Ticlla M, Said K, Mhalu G, Chiryamkubi M, Schindler C, Reither K, Gagneux S, Fenner L.

Clin Microbiol Infect. 2019 Jan;25(1):107.e1-107.e7. doi: 10.1016/j.cmi.2018.03.019. Epub 2018 Mar 23.


Distinct clinical characteristics and helminth co-infections in adult tuberculosis patients from urban compared to rural Tanzania.

Sikalengo G, Hella J, Mhimbira F, Rutaihwa LK, Bani F, Ndege R, Sasamalo M, Kamwela L, Said K, Mhalu G, Mlacha Y, Hatz C, Knopp S, Gagneux S, Reither K, Utzinger J, Tanner M, Letang E, Weisser M, Fenner L.

Infect Dis Poverty. 2018 Mar 24;7(1):24. doi: 10.1186/s40249-018-0404-9.


TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities.

Carey AF, Rock JM, Krieger IV, Chase MR, Fernandez-Suarez M, Gagneux S, Sacchettini JC, Ioerger TR, Fortune SM.

PLoS Pathog. 2018 Mar 5;14(3):e1006939. doi: 10.1371/journal.ppat.1006939. eCollection 2018 Mar. Erratum in: PLoS Pathog. 2019 Jun 4;15(6):e1007846.


High-throughput metabolomic analysis predicts mode of action of uncharacterized antimicrobial compounds.

Zampieri M, Szappanos B, Buchieri MV, Trauner A, Piazza I, Picotti P, Gagneux S, Borrell S, Gicquel B, Lelievre J, Papp B, Sauer U.

Sci Transl Med. 2018 Feb 21;10(429). pii: eaal3973. doi: 10.1126/scitranslmed.aal3973.


Ecology and evolution of Mycobacterium tuberculosis.

Gagneux S.

Nat Rev Microbiol. 2018 Apr;16(4):202-213. doi: 10.1038/nrmicro.2018.8. Epub 2018 Feb 19. Review.


The Troika Host-Pathogen-Extrinsic Factors in Tuberculosis: Modulating Inflammation and Clinical Outcomes.

Bastos HN, Osório NS, Gagneux S, Comas I, Saraiva M.

Front Immunol. 2018 Jan 9;8:1948. doi: 10.3389/fimmu.2017.01948. eCollection 2017. Review.


A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis.

Miotto P, Tessema B, Tagliani E, Chindelevitch L, Starks AM, Emerson C, Hanna D, Kim PS, Liwski R, Zignol M, Gilpin C, Niemann S, Denkinger CM, Fleming J, Warren RM, Crook D, Posey J, Gagneux S, Hoffner S, Rodrigues C, Comas I, Engelthaler DM, Murray M, Alland D, Rigouts L, Lange C, Dheda K, Hasan R, Ranganathan UDK, McNerney R, Ezewudo M, Cirillo DM, Schito M, Köser CU, Rodwell TC.

Eur Respir J. 2017 Dec 28;50(6). pii: 1701354. doi: 10.1183/13993003.01354-2017. Print 2017 Dec.


The Nature and Evolution of Genomic Diversity in the Mycobacterium tuberculosis Complex.

Brites D, Gagneux S.

Adv Exp Med Biol. 2017;1019:1-26. doi: 10.1007/978-3-319-64371-7_1. Review.


Tuberculosis in Swiss captive Asian elephants: microevolution of Mycobacterium tuberculosis characterized by multilocus variable-number tandem-repeat analysis and whole-genome sequencing.

Ghielmetti G, Coscolla M, Ruetten M, Friedel U, Loiseau C, Feldmann J, Steinmetz HW, Stucki D, Gagneux S.

Sci Rep. 2017 Nov 7;7(1):14647. doi: 10.1038/s41598-017-15278-9.


Evaluation of spoligotyping, SNPs and customised MIRU-VNTR combination for genotyping Mycobacterium tuberculosis clinical isolates in Madagascar.

Rasoahanitralisoa R, Rakotosamimanana N, Stucki D, Sola C, Gagneux S, Rasolofo Razanamparany V.

PLoS One. 2017 Oct 20;12(10):e0186088. doi: 10.1371/journal.pone.0186088. eCollection 2017.


Molecular characterization of bovine tuberculosis strains in two slaughterhouses in Morocco.

Yahyaoui-Azami H, Aboukhassib H, Bouslikhane M, Berrada J, Rami S, Reinhard M, Gagneux S, Feldmann J, Borrell S, Zinsstag J.

BMC Vet Res. 2017 Aug 25;13(1):272. doi: 10.1186/s12917-017-1165-6.


Preservation of sputum samples with cetylpyridinium chloride (CPC) for tuberculosis cultures and Xpert MTB/RIF in a low-income country.

Hiza H, Doulla B, Sasamalo M, Hella J, Kamwela L, Mhimbira F, Reither K, Gagneux S, Jugheli L, Fenner L.

BMC Infect Dis. 2017 Aug 4;17(1):542. doi: 10.1186/s12879-017-2642-z.


Tuberculosis transmission in public locations in Tanzania: A novel approach to studying airborne disease transmission.

Hella J, Morrow C, Mhimbira F, Ginsberg S, Chitnis N, Gagneux S, Mutayoba B, Wood R, Fenner L.

J Infect. 2017 Sep;75(3):191-197. doi: 10.1016/j.jinf.2017.06.009. Epub 2017 Jul 1.


Significant under expression of the DosR regulon in M. tuberculosis complex lineage 6 in sputum.

Ofori-Anyinam B, Dolganov G, Van T, Davis JL, Walter ND, Garcia BJ, Voskuil M, Fissette K, Diels M, Driesen M, Meehan CJ, Yeboah-Manu D, Coscolla M, Gagneux S, Antonio M, Schoolnik G, Gehre F, de Jong BC.

Tuberculosis (Edinb). 2017 May;104:58-64. doi: 10.1016/ Epub 2017 Mar 4.


The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy.

Trauner A, Liu Q, Via LE, Liu X, Ruan X, Liang L, Shi H, Chen Y, Wang Z, Liang R, Zhang W, Wei W, Gao J, Sun G, Brites D, England K, Zhang G, Gagneux S, Barry CE 3rd, Gao Q.

Genome Biol. 2017 Apr 19;18(1):71. doi: 10.1186/s13059-017-1196-0.


The Influence of HIV on the Evolution of Mycobacterium tuberculosis.

Koch AS, Brites D, Stucki D, Evans JC, Seldon R, Heekes A, Mulder N, Nicol M, Oni T, Mizrahi V, Warner DF, Parkhill J, Gagneux S, Martin DP, Wilkinson RJ.

Mol Biol Evol. 2017 Jul 1;34(7):1654-1668. doi: 10.1093/molbev/msx107.


Antimicrobial resistance in Mycobacterium tuberculosis: mechanistic and evolutionary perspectives.

Gygli SM, Borrell S, Trauner A, Gagneux S.

FEMS Microbiol Rev. 2017 May 1;41(3):354-373. doi: 10.1093/femsre/fux011. Review.


Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420.

Blondiaux N, Moune M, Desroses M, Frita R, Flipo M, Mathys V, Soetaert K, Kiass M, Delorme V, Djaout K, Trebosc V, Kemmer C, Wintjens R, Wohlkönig A, Antoine R, Huot L, Hot D, Coscolla M, Feldmann J, Gagneux S, Locht C, Brodin P, Gitzinger M, Déprez B, Willand N, Baulard AR.

Science. 2017 Mar 17;355(6330):1206-1211. doi: 10.1126/science.aag1006. Epub 2017 Mar 16.


Prevalence and clinical relevance of helminth co-infections among tuberculosis patients in urban Tanzania.

Mhimbira F, Hella J, Said K, Kamwela L, Sasamalo M, Maroa T, Chiryamkubi M, Mhalu G, Schindler C, Reither K, Knopp S, Utzinger J, Gagneux S, Fenner L.

PLoS Negl Trop Dis. 2017 Feb 8;11(2):e0005342. doi: 10.1371/journal.pntd.0005342. eCollection 2017 Feb.


The First population structure and comparative genomics analysis of Mycobacterium africanum strains from Ghana reveals higher diversity of Lineage 5.

Otchere ID, Harris SR, Busso SL, Asante-Poku A, Osei-Wusu S, Koram K, Parkhill J, Gagneux S, Yeboah-Manu D.

Int J Mycobacteriol. 2016 Dec;5 Suppl 1:S80-S81. doi: 10.1016/j.ijmyco.2016.09.051. Epub 2016 Nov 11.


Within Host Evolution Selects for a Dominant Genotype of Mycobacterium tuberculosis while T Cells Increase Pathogen Genetic Diversity.

Copin R, Wang X, Louie E, Escuyer V, Coscolla M, Gagneux S, Palmer GH, Ernst JD.

PLoS Pathog. 2016 Dec 14;12(12):e1006111. doi: 10.1371/journal.ppat.1006111. eCollection 2016 Dec.


Association between tuberculosis, diabetes and 25 hydroxyvitamin D in Tanzania: a longitudinal case control study.

Boillat-Blanco N, Bovet P, Ramaiya KL, Mganga M, Minja LT, Saleh L, Imboden M, Schindler C, Gagneux S, Daubenberger C, Reither K, Probst-Hensch N.

BMC Infect Dis. 2016 Nov 3;16(1):626.


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. 2016 Dec;48(12):1535-1543. doi: 10.1038/ng.3704. Epub 2016 Oct 31.


Consensus numbering system for the rifampicin resistance-associated rpoB gene mutations in pathogenic mycobacteria.

Andre E, Goeminne L, Cabibbe A, Beckert P, Kabamba Mukadi B, Mathys V, Gagneux S, Niemann S, Van Ingen J, Cambau E.

Clin Microbiol Infect. 2017 Mar;23(3):167-172. doi: 10.1016/j.cmi.2016.09.006. Epub 2016 Sep 21. Review.


Spatio-Temporal Distribution of Mycobacterium tuberculosis Complex Strains in Ghana.

Yeboah-Manu D, Asare P, Asante-Poku A, Otchere ID, Osei-Wusu S, Danso E, Forson A, Koram KA, Gagneux S.

PLoS One. 2016 Aug 26;11(8):e0161892. doi: 10.1371/journal.pone.0161892. eCollection 2016.

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