sequencing of mutations in the gene (rpoB)
encoding the RNA polymerase beta subunit
in rifampin-resistant Mycobacterium tuberculosis strains from new York City and Texas. J
Clin Microbiol 32(4):1095
158. 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, Koser
CU, Rodwell TC (2017) A standardised
method for interpreting the association
between mutations and phenotypic drug
resistance in Mycobacterium tuberculosis. Eur
Respir J 50(6). https://doi.org/10.1183/
13993003.01354-2017
159. The CRyPTIC Consortium and the 100000
Genomes
Project,
Allix-Beguec
C,
Arandjelovic I, Bi L, Beckert P, Bonnet M,
Bradley P, Cabibbe AM, Cancino-Munoz I,
Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo
MR, de Neeling H, Diel R, Drobniewski FA,
Faksri K, Farhat MR, Fleming J, Fowler P,
Fowler TA, Gao Q, Gardy J, Gascoyne-BinziD, Gibertoni-Cruz AL, Gil-Brusola A,
Golubchik T, Gonzalo X, Grandjean L,
He G, Guthrie JL, Hoosdally S, Hunt M,
Iqbal Z, Ismail N, Johnston J, Khanzada
FM, Khor CC, Kohl TA, Kong C,
Lipworth S, Liu Q, Maphalala G,
Martinez E, Mathys V, Merker M, Miotto P,
Mistry N, DAJ M, Murray M, Niemann S,
Omar SV, Ong RT, TEA P, Posey JE,
Prammananan T, Pym A, Rodrigues C,
Rodrigues M, Rodwell T, Rossolini GM, Sanchez Padilla E, Schito M, Shen X, Shendure J,
Sintchenko V, Sloutsky A, Smith EG,
Snyder M, Soetaert K, Starks AM, Supply P,
Suriyapol P, Tahseen S, Tang P, Teo YY,
TNT T, Thwaites G, Tortoli E, van
Soolingen D, Walker AS, Walker TM,
Wilcox M, Wilson DJ, Wyllie D, Yang Y,
Zhang H, Zhao Y, Zhu B (2018) Prediction
of susceptibility to first-line tuberculosis
drugs by DNA sequencing. N Engl J Med
379(15):1403–1415.
https://doi.org/10.
1056/NEJMoa1800474
160. Chakravorty S, Kothari H, Aladegbami B,
Cho EJ, Lee JS, Roh SS, Kim H, Kwak H,
Lee EG, Hwang SH, Banada PP, Safi H, Via
LE, Cho SN, Barry CE 3rd, Alland D (2012)
Rapid, high-throughput detection of rifampin
resistance
and
heteroresistance
in
Mycobacterium tuberculosis by use of sloppy
molecular beacon melting temperature coding. J Clin Microbiol 50(7):2194–2202.
https://doi.org/10.1128/JCM.00143-12
161. Ng KC, Meehan CJ, Torrea G, Goeminne L,
Diels M, Rigouts L, de Jong BC, Andre E
(2018) Potential application of digitally
linked tuberculosis diagnostics for real-time
surveillance of drug-resistant tuberculosis
transmission: validation and analysis of test
results. JMIR Med Inform 6(1):e12.
https://doi.org/10.2196/medinform.9309
162. Ng KCS, van Deun A, Meehan CJ, Torrea G,
Driesen M, Gabriels S, Rigouts L, Andre E,
de Jong BC (2018) Xpert ultra can unambiguously identify specific rifampin resistanceconferring mutations. J Clin Microbiol 56
(9):e00686–e00618.
https://doi.org/10.
1128/JCM.00686-18
163. Piddock LJ, Williams KJ, Ricci V (2000)
Accumulation of rifampicin by Mycobacterium
aurum, Mycobacterium smegmatis and Mycobacterium tuberculosis. J Antimicrob Chemother 45(2):159–165. https://doi.org/10.
1093/jac/45.2.159
164. Li XZ, Zhang L, Nikaido H (2004) Efflux
pump-mediated intrinsic drug resistance in
Mycobacterium
smegmatis.
Antimicrob
Agents
Chemother
48(7):2415–2423.
https://doi.org/10.1128/AAC.48.7.24152423.2004
165. Andre E, Goeminne L, Cabibbe A, Beckert P,
Kabamba Mukadi B, Mathys V, Gagneux S,
Niemann S, Van Ingen J, Cambau E (2017)
Consensus numbering system for the rifampicin resistance-associated rpoB gene mutations
in pathogenic mycobacteria. Clin Microbiol
Infect 23(3):167–172. https://doi.org/10.
1016/j.cmi.2016.09.006
166. Meehan CJ, Goig GA, Kohl TA, Verboven L,
Dippenaar A, Ezewudo M, Farhat MR,
Guthrie JL, Laukens K, Miotto P, OforiAnyinam B, Dreyer V, Supply P, Suresh A,
Utpatel C, van Soolingen D, Zhou Y, Ashton
PM, Brites D, Cabibbe AM, de Jong BC, de
Vos M, Menardo F, Gagneux S, Gao Q, Heupink TH, Liu Q, Loiseau C, Rigouts L, Rodwell TC, Tagliani E, Walker TM, Warren RM,
Zhao Y, Zignol M, Schito M, Gardy J, Cirillo
DM, Niemann S, Comas I, Van Rie A (2019)
Whole genome sequencing of Mycobacterium
tuberculosis: current standards and open
issues. Nat Rev Microbiol 17(9):533–545.
https://doi.org/10.1038/s41579-0190214-5
167. Satta G, Lipman M, Smith GP, Arnold C, Kon
OM, McHugh TD (2018) Mycobacterium
tuberculosis and whole-genome sequencing:
Mycobacterial ID and Characterization Using WGS
453
encoding the RNA polymerase beta subunit
in rifampin-resistant Mycobacterium tuberculosis strains from new York City and Texas. J
Clin Microbiol 32(4):1095
158. 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, Koser
CU, Rodwell TC (2017) A standardised
method for interpreting the association
between mutations and phenotypic drug
resistance in Mycobacterium tuberculosis. Eur
Respir J 50(6). https://doi.org/10.1183/
13993003.01354-2017
159. The CRyPTIC Consortium and the 100000
Genomes
Project,
Allix-Beguec
C,
Arandjelovic I, Bi L, Beckert P, Bonnet M,
Bradley P, Cabibbe AM, Cancino-Munoz I,
Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo
MR, de Neeling H, Diel R, Drobniewski FA,
Faksri K, Farhat MR, Fleming J, Fowler P,
Fowler TA, Gao Q, Gardy J, Gascoyne-BinziD, Gibertoni-Cruz AL, Gil-Brusola A,
Golubchik T, Gonzalo X, Grandjean L,
He G, Guthrie JL, Hoosdally S, Hunt M,
Iqbal Z, Ismail N, Johnston J, Khanzada
FM, Khor CC, Kohl TA, Kong C,
Lipworth S, Liu Q, Maphalala G,
Martinez E, Mathys V, Merker M, Miotto P,
Mistry N, DAJ M, Murray M, Niemann S,
Omar SV, Ong RT, TEA P, Posey JE,
Prammananan T, Pym A, Rodrigues C,
Rodrigues M, Rodwell T, Rossolini GM, Sanchez Padilla E, Schito M, Shen X, Shendure J,
Sintchenko V, Sloutsky A, Smith EG,
Snyder M, Soetaert K, Starks AM, Supply P,
Suriyapol P, Tahseen S, Tang P, Teo YY,
TNT T, Thwaites G, Tortoli E, van
Soolingen D, Walker AS, Walker TM,
Wilcox M, Wilson DJ, Wyllie D, Yang Y,
Zhang H, Zhao Y, Zhu B (2018) Prediction
of susceptibility to first-line tuberculosis
drugs by DNA sequencing. N Engl J Med
379(15):1403–1415.
https://doi.org/10.
1056/NEJMoa1800474
160. Chakravorty S, Kothari H, Aladegbami B,
Cho EJ, Lee JS, Roh SS, Kim H, Kwak H,
Lee EG, Hwang SH, Banada PP, Safi H, Via
LE, Cho SN, Barry CE 3rd, Alland D (2012)
Rapid, high-throughput detection of rifampin
resistance
and
heteroresistance
in
Mycobacterium tuberculosis by use of sloppy
molecular beacon melting temperature coding. J Clin Microbiol 50(7):2194–2202.
https://doi.org/10.1128/JCM.00143-12
161. Ng KC, Meehan CJ, Torrea G, Goeminne L,
Diels M, Rigouts L, de Jong BC, Andre E
(2018) Potential application of digitally
linked tuberculosis diagnostics for real-time
surveillance of drug-resistant tuberculosis
transmission: validation and analysis of test
results. JMIR Med Inform 6(1):e12.
https://doi.org/10.2196/medinform.9309
162. Ng KCS, van Deun A, Meehan CJ, Torrea G,
Driesen M, Gabriels S, Rigouts L, Andre E,
de Jong BC (2018) Xpert ultra can unambiguously identify specific rifampin resistanceconferring mutations. J Clin Microbiol 56
(9):e00686–e00618.
https://doi.org/10.
1128/JCM.00686-18
163. Piddock LJ, Williams KJ, Ricci V (2000)
Accumulation of rifampicin by Mycobacterium
aurum, Mycobacterium smegmatis and Mycobacterium tuberculosis. J Antimicrob Chemother 45(2):159–165. https://doi.org/10.
1093/jac/45.2.159
164. Li XZ, Zhang L, Nikaido H (2004) Efflux
pump-mediated intrinsic drug resistance in
Mycobacterium
smegmatis.
Antimicrob
Agents
Chemother
48(7):2415–2423.
https://doi.org/10.1128/AAC.48.7.24152423.2004
165. Andre E, Goeminne L, Cabibbe A, Beckert P,
Kabamba Mukadi B, Mathys V, Gagneux S,
Niemann S, Van Ingen J, Cambau E (2017)
Consensus numbering system for the rifampicin resistance-associated rpoB gene mutations
in pathogenic mycobacteria. Clin Microbiol
Infect 23(3):167–172. https://doi.org/10.
1016/j.cmi.2016.09.006
166. Meehan CJ, Goig GA, Kohl TA, Verboven L,
Dippenaar A, Ezewudo M, Farhat MR,
Guthrie JL, Laukens K, Miotto P, OforiAnyinam B, Dreyer V, Supply P, Suresh A,
Utpatel C, van Soolingen D, Zhou Y, Ashton
PM, Brites D, Cabibbe AM, de Jong BC, de
Vos M, Menardo F, Gagneux S, Gao Q, Heupink TH, Liu Q, Loiseau C, Rigouts L, Rodwell TC, Tagliani E, Walker TM, Warren RM,
Zhao Y, Zignol M, Schito M, Gardy J, Cirillo
DM, Niemann S, Comas I, Van Rie A (2019)
Whole genome sequencing of Mycobacterium
tuberculosis: current standards and open
issues. Nat Rev Microbiol 17(9):533–545.
https://doi.org/10.1038/s41579-0190214-5
167. Satta G, Lipman M, Smith GP, Arnold C, Kon
OM, McHugh TD (2018) Mycobacterium
tuberculosis and whole-genome sequencing:
Mycobacterial ID and Characterization Using WGS
453