180. Starks AM, Aviles E, Cirillo DM, Denkinger
CM, Dolinger DL, Emerson C, Gallarda J,
Hanna D, Kim PS, Liwski R, Miotto P,
Schito M, Zignol M (2015) Collaborative
effort for a centralized worldwide tuberculosis relational sequencing data platform. Clin
Infect Dis 61(Suppl 3):S141–S146. https://
doi.org/10.1093/cid/civ610
181. Schito M, Dolinger DL (2015) A collaborative approach for "ReSeq-ing" Mycobacterium
tuberculosis drug resistance: convergence for
drug and diagnostic developers. EBioMedicine 2(10):1262–1265. https://doi.org/10.
1016/j.ebiom.2015.10.008
182. Zignol M, Cabibbe AM, Dean AS, Glaziou P,
Alikhanova N, Ama C, Andres S, Barbova A,
Borbe-Reyes A, Chin DP, Cirillo DM,
Colvin C, Dadu A, Dreyer A, Driesen M,
Gilpin C, Hasan R, Hasan Z, Hoffner S,
Hussain A, Ismail N, Kamal SMM, Khanzada
FM, Kimerling M, Kohl TA, Mansjo ¨ M,
Miotto P, Mukadi YD, Mvusi L, Niemann S,
Omar SV, Rigouts L, Schito M, Sela I,
Seyfaddinova M, Skenders G, Skrahina A,
Tahseen S, Wells WA, Zhurilo A, Weyer K,
Floyd K, Raviglione MC (2018) Genetic
sequencing for surveillance of drug resistance
in tuberculosis in highly endemic countries: a
multi-country population-based surveillance
study. Lancet Infect Dis 18(6):675–683.
https://doi.org/10.1016/s1473-3099(18)
30073-2
183. Comas I (2017) Genomic epidemiology of
tuberculosis. In: Gagneux S (ed) Strain variation in the Mycobacterium tuberculosis complex: its role in biology, Epidemiology and
Control. Springer International Publishing,
Cham, pp 79–93. https://doi.org/10.
1007/978-3-319-64371-7_4
184. Gori A, Bandera A, Marchetti G, Degli
Esposti A, Catozzi L, Nardi GP, Gazzola L,
Ferrario G, van Embden JD, van
Soolingen D, Moroni M, Franzetti F (2005)
Spoligotyping and Mycobacterium tuberculosis. Emerg Infect Dis 11(8):1242–1248.
https://doi.org/10.3201/eid1108.040982
185. Jonsson J, Hoffner S, Berggren I, Bruchfeld J,
Ghebremichael S, Pennhag A, Groenheit R
(2014) Comparison between RFLP and
MIRU-VNTR genotyping of Mycobacterium
tuberculosis strains isolated in Stockholm
2009 to 2011. PLoS One 9(4):e95159.
https://doi.org/10.1371/journal.pone.
0095159
186. Meehan CJ, Moris P, Kohl TA, Pecerska J,
Akter S, Merker M, Utpatel C, Beckert P,
Gehre F, Lempens P, Stadler T, Kaswa MK,
Kuhnert D, Niemann S, de Jong BC (2018)
The relationship between transmission time
and clustering methods in Mycobacterium
tuberculosis epidemiology. EBioMedicine
37:410–416.
https://doi.org/10.1016/j.
ebiom.2018.10.013
187. Wyllie DH, Davidson JA, Grace Smith E,
Rathod P, Crook DW, Peto TEA,
Robinson E, Walker T, Campbell C (2018)
A quantitative evaluation of MIRU-VNTR
typing against whole-genome sequencing for
identifying Mycobacterium tuberculosis transmission: a prospective observational cohort
study. EBioMedicine 34:122–130. https://
doi.org/10.1016/j.ebiom.2018.07.019
188. Jajou R, de Neeling A, van Hunen R, de
Vries G, Schimmel H, Mulder A,
Anthony R, van der Hoek W, van Soolingen
D (2018) Epidemiological links between
tuberculosis cases identified twice as efficiently by whole genome sequencing than
conventional molecular typing: a populationbased study. PLoS One 13(4):e0195413.
https://doi.org/10.1371/journal.pone.
0195413
189. Alaridah N, Hallback ET, Tangrot J,
Winqvist N, Sturegard E, Floren-JohanssonK, Jonsson B, Tenland E, Welinder-Olsson C,
Medstrand P, Kaijser B, Godaly G (2019)
Transmission dynamics study of tuberculosis
isolates with whole genome sequencing in
southern Sweden. Sci Rep 9(1):4931.
https://doi.org/10.1038/s41598-01939971-z
190. Guthrie JL, Strudwick L, Roberts B, Allen M,
McFadzen J, Roth D, Jorgensen D,
Rodrigues M, Tang P, Hanley B, Johnston J,
Cook VJ, Gardy JL (2019) Whole genome
sequencing for improved understanding of
Mycobacterium tuberculosis transmission in a
remote circumpolar region. Epidemiol Infect
147:e188.
https://doi.org/10.1017/
S0950268819000670
191. 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 (2011) Wholegenome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med
364(8):730–739. https://doi.org/10.1056/
NEJMoa1003176
192. Walker TM, Ip CLC, Harrell RH, Evans JT,
Kapatai G, Dedicoat MJ, Eyre DW, Wilson
DJ, Hawkey PM, Crook DW, Parkhill J,
Harris D, Walker AS, Bowden R, Monk P,
Smith EG, Peto TEA (2013) Whole-genome
sequencing to delineate Mycobacterium tuberculosis
outbreaks:
a
retrospective
Mycobacterial ID and Characterization Using WGS
455
CM, Dolinger DL, Emerson C, Gallarda J,
Hanna D, Kim PS, Liwski R, Miotto P,
Schito M, Zignol M (2015) Collaborative
effort for a centralized worldwide tuberculosis relational sequencing data platform. Clin
Infect Dis 61(Suppl 3):S141–S146. https://
doi.org/10.1093/cid/civ610
181. Schito M, Dolinger DL (2015) A collaborative approach for "ReSeq-ing" Mycobacterium
tuberculosis drug resistance: convergence for
drug and diagnostic developers. EBioMedicine 2(10):1262–1265. https://doi.org/10.
1016/j.ebiom.2015.10.008
182. Zignol M, Cabibbe AM, Dean AS, Glaziou P,
Alikhanova N, Ama C, Andres S, Barbova A,
Borbe-Reyes A, Chin DP, Cirillo DM,
Colvin C, Dadu A, Dreyer A, Driesen M,
Gilpin C, Hasan R, Hasan Z, Hoffner S,
Hussain A, Ismail N, Kamal SMM, Khanzada
FM, Kimerling M, Kohl TA, Mansjo ¨ M,
Miotto P, Mukadi YD, Mvusi L, Niemann S,
Omar SV, Rigouts L, Schito M, Sela I,
Seyfaddinova M, Skenders G, Skrahina A,
Tahseen S, Wells WA, Zhurilo A, Weyer K,
Floyd K, Raviglione MC (2018) Genetic
sequencing for surveillance of drug resistance
in tuberculosis in highly endemic countries: a
multi-country population-based surveillance
study. Lancet Infect Dis 18(6):675–683.
https://doi.org/10.1016/s1473-3099(18)
30073-2
183. Comas I (2017) Genomic epidemiology of
tuberculosis. In: Gagneux S (ed) Strain variation in the Mycobacterium tuberculosis complex: its role in biology, Epidemiology and
Control. Springer International Publishing,
Cham, pp 79–93. https://doi.org/10.
1007/978-3-319-64371-7_4
184. Gori A, Bandera A, Marchetti G, Degli
Esposti A, Catozzi L, Nardi GP, Gazzola L,
Ferrario G, van Embden JD, van
Soolingen D, Moroni M, Franzetti F (2005)
Spoligotyping and Mycobacterium tuberculosis. Emerg Infect Dis 11(8):1242–1248.
https://doi.org/10.3201/eid1108.040982
185. Jonsson J, Hoffner S, Berggren I, Bruchfeld J,
Ghebremichael S, Pennhag A, Groenheit R
(2014) Comparison between RFLP and
MIRU-VNTR genotyping of Mycobacterium
tuberculosis strains isolated in Stockholm
2009 to 2011. PLoS One 9(4):e95159.
https://doi.org/10.1371/journal.pone.
0095159
186. Meehan CJ, Moris P, Kohl TA, Pecerska J,
Akter S, Merker M, Utpatel C, Beckert P,
Gehre F, Lempens P, Stadler T, Kaswa MK,
Kuhnert D, Niemann S, de Jong BC (2018)
The relationship between transmission time
and clustering methods in Mycobacterium
tuberculosis epidemiology. EBioMedicine
37:410–416.
https://doi.org/10.1016/j.
ebiom.2018.10.013
187. Wyllie DH, Davidson JA, Grace Smith E,
Rathod P, Crook DW, Peto TEA,
Robinson E, Walker T, Campbell C (2018)
A quantitative evaluation of MIRU-VNTR
typing against whole-genome sequencing for
identifying Mycobacterium tuberculosis transmission: a prospective observational cohort
study. EBioMedicine 34:122–130. https://
doi.org/10.1016/j.ebiom.2018.07.019
188. Jajou R, de Neeling A, van Hunen R, de
Vries G, Schimmel H, Mulder A,
Anthony R, van der Hoek W, van Soolingen
D (2018) Epidemiological links between
tuberculosis cases identified twice as efficiently by whole genome sequencing than
conventional molecular typing: a populationbased study. PLoS One 13(4):e0195413.
https://doi.org/10.1371/journal.pone.
0195413
189. Alaridah N, Hallback ET, Tangrot J,
Winqvist N, Sturegard E, Floren-JohanssonK, Jonsson B, Tenland E, Welinder-Olsson C,
Medstrand P, Kaijser B, Godaly G (2019)
Transmission dynamics study of tuberculosis
isolates with whole genome sequencing in
southern Sweden. Sci Rep 9(1):4931.
https://doi.org/10.1038/s41598-01939971-z
190. Guthrie JL, Strudwick L, Roberts B, Allen M,
McFadzen J, Roth D, Jorgensen D,
Rodrigues M, Tang P, Hanley B, Johnston J,
Cook VJ, Gardy JL (2019) Whole genome
sequencing for improved understanding of
Mycobacterium tuberculosis transmission in a
remote circumpolar region. Epidemiol Infect
147:e188.
https://doi.org/10.1017/
S0950268819000670
191. 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 (2011) Wholegenome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med
364(8):730–739. https://doi.org/10.1056/
NEJMoa1003176
192. Walker TM, Ip CLC, Harrell RH, Evans JT,
Kapatai G, Dedicoat MJ, Eyre DW, Wilson
DJ, Hawkey PM, Crook DW, Parkhill J,
Harris D, Walker AS, Bowden R, Monk P,
Smith EG, Peto TEA (2013) Whole-genome
sequencing to delineate Mycobacterium tuberculosis
outbreaks:
a
retrospective
Mycobacterial ID and Characterization Using WGS
455