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Rusch-Gerdes S, Mokrousov I, Aleksic E,
Allix-Beguec
C,
Antierens
A,
Augustynowicz-Kopec
E,
Ballif
M,
Barletta F, Beck HP, Barry CE 3rd,
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, Lillebaek 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 (2015) Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat
Genet 47(3):242–249. https://doi.org/10.
1038/ng.3195
204. Menardo F, Duchene S, Brites D, Gagneux S
(2019) The molecular clock of Mycobacterium
tuberculosis. PLoS Pathog 15(9):e1008067.
https://doi.org/10.1371/journal.ppat.
1008067
205. Folkvardsen DB, Norman A, Andersen AB,
Michael Rasmussen E, Jelsbak L, Lillebaek T
(2017) Genomic epidemiology of a major
Mycobacterium
tuberculosis
outbreak:
456
Marco A. Riojas et al.
(2):137–146.
https://doi.org/10.1016/
s1473-3099(12)70277-3
193. Lee RS, Radomski N, Proulx JF, Levade I,
Shapiro BJ, McIntosh F, Soualhine H,
Menzies D, Behr MA (2015) Population
genomics of Mycobacterium tuberculosis in
the Inuit. Proc Natl Acad Sci U S A 112
(44):13609–13614.
https://doi.org/10.
1073/pnas.1507071112
194. Glynn JR, Guerra-Assuncao JA, Houben RM,
Sichali L, Mzembe T, Mwaungulu LK,
Mwaungulu JN, McNerney R, Khan P,
Parkhill J, Crampin AC, Clark TG (2015)
Whole genome sequencing shows a low proportion of tuberculosis disease is attributable
to known close contacts in rural Malawi.
PLoS One 10(7):e0132840. https://doi.
org/10.1371/journal.pone.0132840
195. Hatherell HA, Colijn C, Stagg HR,
Jackson C, Winter JR, Abubakar I (2016)
Interpreting whole genome sequencing for
investigating tuberculosis transmission: a systematic review. BMC Med 14:21. https://
doi.org/10.1186/s12916-016-0566-x
196. 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 (2013) Out-of-Africa
migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans.
Nat Genet 45(10):1176–1182. https://doi.
org/10.1038/ng.2744
197. O’Neill MB, Shockey A, Zarley A, Aylward W,
Eldholm V, Kitchen A, Pepperell CS (2019)
Lineage specific histories of Mycobacterium
tuberculosis dispersal in Africa and Eurasia.
Mol Ecol 28(13):3241–3256. https://doi.
org/10.1111/mec.15120
198. Zink AR, Sola C, Reischl U, Grabner W,
Rastogi N, Wolf H, Nerlich AG (2003) Characterization of Mycobacterium tuberculosis
complex DNAs from Egyptian mummies by
spoligotyping. J Clin Microbiol 41
(1):359–367.
https://doi.org/10.1128/
jcm.41.1.359-367.2003
199. Bos KI, Harkins KM, Herbig A, Coscolla M,
Weber N, Comas I, Forrest SA, Bryant JM,
Harris SR, Schuenemann VJ, Campbell TJ,
Majander K, Wilbur AK, Guichon RA, Wolfe
Steadman DL, Cook DC, Niemann S, Behr
MA, Zumarraga M, Bastida R, Huson D,
Nieselt K, Young D, Parkhill J, Buikstra JE,
Gagneux S, Stone AC, Krause J (2014)
Pre-Columbian
mycobacterial
genomes
reveal seals as a source of New World human
tuberculosis. Nature 514(7523):494–497.
https://doi.org/10.1038/nature13591
200. Crispell J, Zadoks RN, Harris SR, Paterson B,
Collins DM, de-Lisle GW, Livingstone P,
Neill MA, Biek R, Lycett SJ, Kao RR, PriceCarter M (2017) Using whole genome
sequencing to investigate transmission in a
multi-host system: bovine tuberculosis in
New Zealand. BMC Genomics 18(1):180.
https://doi.org/10.1186/s12864-0173569-x
201. Crispell J, Benton CH, Balaz D, De Maio N,
Ahkmetova A, Allen A, Biek R, Presho EL,
Dale J, Hewinson G, Lycett SJ, NunezGarcia J, Skuce RA, Trewby H, Wilson DJ,
Zadoks RN, Delahay RJ, Kao RR (2019)
Combining genomics and epidemiology to
analyse bi-directional transmission of Mycobacterium bovis in a multi-host system. elife
8. https://doi.org/10.7554/eLife.45833
202. Merker M, Barbier M, Cox H, Rasigade JP,
Feuerriegel S, Kohl TA, Diel R, Borrell S,
Gagneux S, Nikolayevskyy V, Andres S,
Nubel U, Supply P, Wirth T, Niemann S
(2018) Compensatory evolution drives
multidrug-resistant tuberculosis in Central
Asia. elife 7. https://doi.org/10.7554/
eLife.38200
203. Merker M, Blin C, Mona S, DuforetFrebourg N, Lecher S, Willery E, Blum MG,
Rusch-Gerdes S, Mokrousov I, Aleksic E,
Allix-Beguec
C,
Antierens
A,
Augustynowicz-Kopec
E,
Ballif
M,
Barletta F, Beck HP, Barry CE 3rd,
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, Lillebaek 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 (2015) Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat
Genet 47(3):242–249. https://doi.org/10.
1038/ng.3195
204. Menardo F, Duchene S, Brites D, Gagneux S
(2019) The molecular clock of Mycobacterium
tuberculosis. PLoS Pathog 15(9):e1008067.
https://doi.org/10.1371/journal.ppat.
1008067
205. Folkvardsen DB, Norman A, Andersen AB,
Michael Rasmussen E, Jelsbak L, Lillebaek T
(2017) Genomic epidemiology of a major
Mycobacterium
tuberculosis
outbreak:
456
Marco A. Riojas et al.