Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms

The emergence of drug-resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole-genome sequencing as a tool to rapidly diagnose resistant infections can transform patient treatment and clinical practice. While resistance mechanisms are we...

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Bibliographic Details
Published inPLoS biology Vol. 20; no. 8; p. e3001755
Main Authors Consortium, The Cryptic, Supply, Philip
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 09.08.2022
Public Library of Science (PLoS)
Subjects
Anti-Infective Agents - pharmacology
Antimicrobial agents
Antimicrobial resistance
Antitubercular Agents - pharmacology
Binding sites
Biology and Life Sciences
Clofazimine
Confidence intervals
Cross-resistance
Drug resistance
Drug resistance in microorganisms
Drugs
Gene sequencing
Genetic aspects
Genetic diversity
Genetic variance
Genome-wide association studies
Genome-Wide Association Study
Genomes
Genomics
Health risks
Heritability
Humans
Isoniazid
Life Sciences
Linezolid
Medicine and Health Sciences
Microbial Sensitivity Tests
Minimum inhibitory concentration
Mutation
Mycobacterium tuberculosis
Mycobacterium tuberculosis - genetics
Oligonucleotides
Phenotypes
Public health
rRNA
rRNA 23S
Short Reports
Tuberculosis
Tuberculosis, Multidrug-Resistant - drug therapy
Tuberculosis, Multidrug-Resistant - genetics
Tuberculosis, Multidrug-Resistant - microbiology
Whole genome sequencing
United Kingdom
Online AccessGet full text

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Abstract The emergence of drug-resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole-genome sequencing as a tool to rapidly diagnose resistant infections can transform patient treatment and clinical practice. While resistance mechanisms are well understood for some drugs, there are likely many mechanisms yet to be uncovered, particularly for new and repurposed drugs. We sequenced 10,228 Mycobacterium tuberculosis (MTB) isolates worldwide and determined the minimum inhibitory concentration (MIC) on a grid of 2-fold concentration dilutions for 13 antimicrobials using quantitative microtiter plate assays. We performed oligopeptide- and oligonucleotide-based genome-wide association studies using linear mixed models to discover resistance-conferring mechanisms not currently catalogued. Use of MIC over binary resistance phenotypes increased sample heritability for the new and repurposed drugs by 26% to 37%, increasing our ability to detect novel associations. For all drugs, we discovered uncatalogued variants associated with MIC, including in the Rv1218c promoter binding site of the transcriptional repressor Rv1219c (isoniazid), upstream of the vapBC20 operon that cleaves 23S rRNA (linezolid) and in the region encoding an α-helix lining the active site of Cyp142 (clofazimine, all p < 10-7.7). We observed that artefactual signals of cross-resistance could be unravelled based on the relative effect size on MIC. Our study demonstrates the ability of very large-scale studies to substantially improve our knowledge of genetic variants associated with antimicrobial resistance in M. tuberculosis.
AbstractList The emergence of drug-resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole-genome sequencing as a tool to rapidly diagnose resistant infections can transform patient treatment and clinical practice. While resistance mechanisms are well understood for some drugs, there are likely many mechanisms yet to be uncovered, particularly for new and repurposed drugs. We sequenced 10,228 Mycobacterium tuberculosis (MTB) isolates worldwide and determined the minimum inhibitory concentration (MIC) on a grid of 2-fold concentration dilutions for 13 antimicrobials using quantitative microtiter plate assays. We performed oligopeptide- and oligonucleotide-based genome-wide association studies using linear mixed models to discover resistance-conferring mechanisms not currently catalogued. Use of MIC over binary resistance phenotypes increased sample heritability for the new and repurposed drugs by 26% to 37%, increasing our ability to detect novel associations. For all drugs, we discovered uncatalogued variants associated with MIC, including in the Rv1218c promoter binding site of the transcriptional repressor Rv1219c (isoniazid), upstream of the vapBC20 operon that cleaves 23S rRNA (linezolid) and in the region encoding an α-helix lining the active site of Cyp142 (clofazimine, all p < 10-7.7). We observed that artefactual signals of cross-resistance could be unravelled based on the relative effect size on MIC. Our study demonstrates the ability of very large-scale studies to substantially improve our knowledge of genetic variants associated with antimicrobial resistance in M. tuberculosis.
The emergence of drug-resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole-genome sequencing as a tool to rapidly diagnose resistant infections can transform patient treatment and clinical practice. While resistance mechanisms are well understood for some drugs, there are likely many mechanisms yet to be uncovered, particularly for new and repurposed drugs. We sequenced 10,228 Mycobacterium tuberculosis (MTB) isolates worldwide and determined the minimum inhibitory concentration (MIC) on a grid of 2-fold concentration dilutions for 13 antimicrobials using quantitative microtiter plate assays. We performed oligopeptide- and oligonucleotide-based genome-wide association studies using linear mixed models to discover resistance-conferring mechanisms not currently catalogued. Use of MIC over binary resistance phenotypes increased sample heritability for the new and repurposed drugs by 26% to 37%, increasing our ability to detect novel associations. For all drugs, we discovered uncatalogued variants associated with MIC, including in the Rv1218c promoter binding site of the transcriptional repressor Rv1219c (isoniazid), upstream of the vapBC20 operon that cleaves 23S rRNA (linezolid) and in the region encoding an α-helix lining the active site of Cyp142 (clofazimine, all p < 10 −7.7 ). We observed that artefactual signals of cross-resistance could be unravelled based on the relative effect size on MIC. Our study demonstrates the ability of very large-scale studies to substantially improve our knowledge of genetic variants associated with antimicrobial resistance in M . tuberculosis .
The emergence of drug-resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole-genome sequencing as a tool to rapidly diagnose resistant infections can transform patient treatment and clinical practice. While resistance mechanisms are well understood for some drugs, there are likely many mechanisms yet to be uncovered, particularly for new and repurposed drugs. We sequenced 10,228 Mycobacterium tuberculosis (MTB) isolates worldwide and determined the minimum inhibitory concentration (MIC) on a grid of 2-fold concentration dilutions for 13 antimicrobials using quantitative microtiter plate assays. We performed oligopeptide- and oligonucleotide-based genome-wide association studies using linear mixed models to discover resistance-conferring mechanisms not currently catalogued. Use of MIC over binary resistance phenotypes increased sample heritability for the new and repurposed drugs by 26% to 37%, increasing our ability to detect novel associations. For all drugs, we discovered uncatalogued variants associated with MIC, including in the Rv1218c promoter binding site of the transcriptional repressor Rv1219c (isoniazid), upstream of the vapBC20 operon that cleaves 23S rRNA (linezolid) and in the region encoding an α-helix lining the active site of Cyp142 (clofazimine, all p < 10−7.7). We observed that artefactual signals of cross-resistance could be unravelled based on the relative effect size on MIC. Our study demonstrates the ability of very large-scale studies to substantially improve our knowledge of genetic variants associated with antimicrobial resistance in M. tuberculosis.
The emergence of drug-resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole-genome sequencing as a tool to rapidly diagnose resistant infections can transform patient treatment and clinical practice. While resistance mechanisms are well understood for some drugs, there are likely many mechanisms yet to be uncovered, particularly for new and repurposed drugs. We sequenced 10,228 Mycobacterium tuberculosis (MTB) isolates worldwide and determined the minimum inhibitory concentration (MIC) on a grid of 2-fold concentration dilutions for 13 antimicrobials using quantitative microtiter plate assays. We performed oligopeptide- and oligonucleotide-based genome-wide association studies using linear mixed models to discover resistance-conferring mechanisms not currently catalogued. Use of MIC over binary resistance phenotypes increased sample heritability for the new and repurposed drugs by 26% to 37%, increasing our ability to detect novel associations. For all drugs, we discovered uncatalogued variants associated with MIC, including in the Rv1218c promoter binding site of the transcriptional repressor Rv1219c (isoniazid), upstream of the vapBC20 operon that cleaves 23S rRNA (linezolid) and in the region encoding an α-helix lining the active site of Cyp142 (clofazimine, all p < 10 −7.7 ). We observed that artefactual signals of cross-resistance could be unravelled based on the relative effect size on MIC. Our study demonstrates the ability of very large-scale studies to substantially improve our knowledge of genetic variants associated with antimicrobial resistance in M . tuberculosis . The emergence of drug resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Phenotyping and sequencing 10,000 Mycobacterium tuberculosis genomes identifies previously uncatalogued genetic variants associated with resistance to thirteen new and repurposed, second line and first line drugs.
The emergence of drug-resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole-genome sequencing as a tool to rapidly diagnose resistant infections can transform patient treatment and clinical practice. While resistance mechanisms are well understood for some drugs, there are likely many mechanisms yet to be uncovered, particularly for new and repurposed drugs. We sequenced 10,228 Mycobacterium tuberculosis (MTB) isolates worldwide and determined the minimum inhibitory concentration (MIC) on a grid of 2-fold concentration dilutions for 13 antimicrobials using quantitative microtiter plate assays. We performed oligopeptide- and oligonucleotide-based genome-wide association studies using linear mixed models to discover resistance-conferring mechanisms not currently catalogued. Use of MIC over binary resistance phenotypes increased sample heritability for the new and repurposed drugs by 26% to 37%, increasing our ability to detect novel associations. For all drugs, we discovered uncatalogued variants associated with MIC, including in the Rv1218c promoter binding site of the transcriptional repressor Rv1219c (isoniazid), upstream of the vapBC20 operon that cleaves 23S rRNA (linezolid) and in the region encoding an α-helix lining the active site of Cyp142 (clofazimine, all p < 10-7.7). We observed that artefactual signals of cross-resistance could be unravelled based on the relative effect size on MIC. Our study demonstrates the ability of very large-scale studies to substantially improve our knowledge of genetic variants associated with antimicrobial resistance in M. tuberculosis.The emergence of drug-resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole-genome sequencing as a tool to rapidly diagnose resistant infections can transform patient treatment and clinical practice. While resistance mechanisms are well understood for some drugs, there are likely many mechanisms yet to be uncovered, particularly for new and repurposed drugs. We sequenced 10,228 Mycobacterium tuberculosis (MTB) isolates worldwide and determined the minimum inhibitory concentration (MIC) on a grid of 2-fold concentration dilutions for 13 antimicrobials using quantitative microtiter plate assays. We performed oligopeptide- and oligonucleotide-based genome-wide association studies using linear mixed models to discover resistance-conferring mechanisms not currently catalogued. Use of MIC over binary resistance phenotypes increased sample heritability for the new and repurposed drugs by 26% to 37%, increasing our ability to detect novel associations. For all drugs, we discovered uncatalogued variants associated with MIC, including in the Rv1218c promoter binding site of the transcriptional repressor Rv1219c (isoniazid), upstream of the vapBC20 operon that cleaves 23S rRNA (linezolid) and in the region encoding an α-helix lining the active site of Cyp142 (clofazimine, all p < 10-7.7). We observed that artefactual signals of cross-resistance could be unravelled based on the relative effect size on MIC. Our study demonstrates the ability of very large-scale studies to substantially improve our knowledge of genetic variants associated with antimicrobial resistance in M. tuberculosis.
The emergence of drug-resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole-genome sequencing as a tool to rapidly diagnose resistant infections can transform patient treatment and clinical practice. While resistance mechanisms are well understood for some drugs, there are likely many mechanisms yet to be uncovered, particularly for new and repurposed drugs. We sequenced 10,228 Mycobacterium tuberculosis (MTB) isolates worldwide and determined the minimum inhibitory concentration (MIC) on a grid of 2-fold concentration dilutions for 13 antimicrobials using quantitative microtiter plate assays. We performed oligopeptide- and oligonucleotide-based genome-wide association studies using linear mixed models to discover resistance-conferring mechanisms not currently catalogued. Use of MIC over binary resistance phenotypes increased sample heritability for the new and repurposed drugs by 26% to 37%, increasing our ability to detect novel associations. For all drugs, we discovered uncatalogued variants associated with MIC, including in the Rv1218c promoter binding site of the transcriptional repressor Rv1219c (isoniazid), upstream of the vapBC20 operon that cleaves 23S rRNA (linezolid) and in the region encoding an α-helix lining the active site of Cyp142 (clofazimine, all p < 10 −7.7 ). We observed that artefactual signals of cross-resistance could be unravelled based on the relative effect size on MIC. Our study demonstrates the ability of very large-scale studies to substantially improve our knowledge of genetic variants associated with antimicrobial resistance in M . tuberculosis .
Audience Academic
Author The CRyPTIC Consortium Membership of The CRyPTIC Consortium is provided in Supporting information fileS1 Acknowledgments
AuthorAffiliation University of Oxford, Oxford, United Kingdom
Northern Arizona University, UNITED STATES
AuthorAffiliation_xml – name: Northern Arizona University, UNITED STATES
– name: University of Oxford, Oxford, United Kingdom
Author_xml – sequence: 1
  givenname: The Cryptic
  surname: Consortium
  fullname: Consortium, The Cryptic
– sequence: 2
  givenname: Philip
  orcidid: 0000-0003-3690-3853
  surname: Supply
  fullname: Supply, Philip
  organization: Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204
BackLink https://www.ncbi.nlm.nih.gov/pubmed/35944070$$D View this record in MEDLINE/PubMed
https://hal.science/hal-03837098$$DView record in HAL
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Cites_doi 10.1128/AAC.00539-16
10.1038/nrg2813
10.1186/gb-2004-5-2-r12
10.1164/rccm.201909-1819LE
10.1074/jbc.M111.302588
10.1074/jbc.M113.516385
10.1046/j.1365-2958.2003.03425.x
10.1093/jac/dkaa136
10.1164/rccm.201510-2091OC
10.1164/rccm.201910-1960OC
10.1074/jbc.M110.200501
10.1128/JCM.02775-15
10.1038/s41588-017-0029-0
10.1128/JCM.00691-14
10.1128/AAC.49.2.571-577.2005
10.1073/pnas.0505446102
10.1164/rccm.201902-0260LE
10.1021/bi035150b
10.1056/NEJMoa1715849
10.1056/NEJMoa1800474
10.1016/j.ijmm.2019.06.003
10.1128/JB.188.8.2936-2944.2006
10.1038/nmicrobiol.2016.41
10.1016/j.jmb.2012.06.011
10.1007/s12088-015-0511-2
10.1128/JB.187.16.5751-5760.2005
10.1021/bi801595t
10.1128/CMR.00141-20
10.1038/31159
10.1128/AAC.00344-18
10.1093/bioinformatics/btt020
10.1186/s12864-019-5615-3
10.1016/j.molcel.2006.05.044
10.1093/nar/gkv261
10.1016/S1473-3099(15)00062-6
10.1093/cid/ciz039
10.1183/13993003.01354-2017
10.1164/rccm.202001-0201LE
10.1086/423938
10.1007/s00284-012-0215-3
10.5588/ijtld.10.0127
10.1056/NEJMoa0907847
10.1111/1462-2920.12108
10.1093/cid/ciz074
10.1038/ng.2747
10.1101/gr.074492.107
10.1016/S1473-3099(18)30496-1
10.1038/ng.2310
10.1038/ncomms3796
10.1038/ncomms10063
10.1111/febs.14289
10.1016/S2213-2600(15)00466-X
10.1002/pro.2424
10.1016/S0140-6736(11)60438-8
10.1128/mBio.00616-19
10.1056/NEJMoa1604544
10.1128/AAC.06272-11
10.1074/jbc.M110.164293
10.1038/ng.2735
10.1371/journal.pone.0039754
10.1056/NEJMc1413930
10.1128/AAC.02191-12
10.1038/s41598-019-53069-6
10.1111/j.1365-2958.2012.08168.x
10.1016/S1473-3099(17)30123-8
10.1016/j.cmi.2016.10.022
10.1016/j.jgg.2016.10.002
10.1080/15216540701206859
10.1128/AAC.41.8.1677
10.1371/journal.pone.0059414
ContentType Journal Article
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Grandjean, Louis
Nimmo, Camus
Meintjes, Graeme
Knaggs, Jeff
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Hoffmann, Harald
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Plesnik, Sara
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Ozoki, Nana
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Guthrie, Jennifer L
Wilson, Daniel J
Rathod, Priti
Lachapelle, Alexander S
Jarrett, Lisa
Gardy, Jennifer
Lalvani, Ajit
Thuong, Nguyen Thuy Thuong
Millard, James
Ngcamu, Dumisani
Miotto, Paolo
Rakotosamimanana, Niaina
Niemann, Stefan
O’Donnell, Max
Laurenson, Ian F
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content type line 23
Membership of The CRyPTIC Consortium is provided in Supporting information file S1 Acknowledgments.
I have read the journal’s policy and the authors of this manuscript have the following competing interests: E.R. is employed by Public Health England and holds an honorary contract with Imperial College London. I.F.L. is Director of the Scottish Mycobacteria Reference Laboratory. S.N. receives funding from German Center for Infection Research, Excellenz Cluster Precision Medicine in Chronic Inflammation, Leibniz Science Campus Evolutionary Medicine of the LUNG (EvoLUNG)tion EXC 2167. P.S. is a consultant at Genoscreen. T.R. is funded by NIH and DoD and receives salary support from the non-profit organization FIND. T.R. is a co-founder, board member and shareholder of Verus Diagnostics Inc, a company that was founded with the intent of developing diagnostic assays. Verus Diagnostics was not involved in any way with data collection, analysis or publication of the results. T.R. has not received any financial support from Verus Diagnostics. UCSD Conflict of Interest office has reviewed and approved T.R.’s role in Verus Diagnostics Inc. T.R. is a co-inventor of a provisional patent for a TB diagnostic assay (provisional patent #: 63/048.989). T.R. is a co-inventor on a patent associated with the processing of TB sequencing data (European Patent Application No. 14840432.0 & USSN 14/912,918). T.R. has agreed to “donate all present and future interest in and rights to royalties from this patent” to UCSD to ensure that he does not receive any financial benefits from this patent. S.S. is working and holding ESOPs at HaystackAnalytics Pvt. Ltd. (Product: Using whole genome sequencing for drug susceptibility testing for Mycobacterium tuberculosis). G.F.G. is listed as an inventor on patent applications for RBD-dimer-based CoV vaccines. The patents for RBD-dimers as protein subunit vaccines for SARS-CoV-2 have been licensed to Anhui Zhifei Longcom Biopharmaceutical Co. Ltd, China.
ORCID 0000-0003-3690-3853
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References M Islam (pbio.3001755.ref008) 2016; 44
C Boehme (pbio.3001755.ref015) 2011; 377
A Reeves (pbio.3001755.ref046) 2013; 57
TM Walker (pbio.3001755.ref025) 2015; 15
S Kadura (pbio.3001755.ref086) 2020; 75
L Pankhurst (pbio.3001755.ref010) 2016; 4
J Zhao (pbio.3001755.ref052) 2019; 309
KE Dooley (pbio.3001755.ref070) 2020; 201
P Bradley (pbio.3001755.ref079) 2015; 6
R Coler (pbio.3001755.ref041) 2018; 3
YP Lai (pbio.3001755.ref036) 2020
The CRyPTIC Consortium and the 100,000 Genomes Project (pbio.3001755.ref011) 2018; 379
S Kurtz (pbio.3001755.ref084) 2004; 5
X Zhou (pbio.3001755.ref032) 2012; 44
K Kranzer (pbio.3001755.ref005) 2019; 200
A Cavazos (pbio.3001755.ref064) 2012; 422
R Morris (pbio.3001755.ref045) 2005; 102
T Monshupanee (pbio.3001755.ref051) 2012; 85
CC Boehme (pbio.3001755.ref014) 2010; 363
S Cole (pbio.3001755.ref083) 1998; 393
World Health Organization (pbio.3001755.ref003) 2020
H Zhang (pbio.3001755.ref019) 2013; 45
C Maus (pbio.3001755.ref048) 2005; 49
TR Blower (pbio.3001755.ref034) 2016; 113
R Cipollone (pbio.3001755.ref054) 2007; 59
AL Price (pbio.3001755.ref026) 2010; 11
World Health Organization (pbio.3001755.ref004) 2019
S Andres (pbio.3001755.ref006) 2020; 201
TM Walker (pbio.3001755.ref012) 2017; 17
T Decroo (pbio.3001755.ref071) 2020; 201
World Health Organization (pbio.3001755.ref027) 2018
FB Jamieson (pbio.3001755.ref085) 2014; 52
P. Ortiz de Montellano (pbio.3001755.ref059) 2018; 180
T Phong (pbio.3001755.ref055) 2015; 55
S Malik (pbio.3001755.ref076) 2012; 7
R Colangeli (pbio.3001755.ref068) 2018; 379
J Burian (pbio.3001755.ref043) 2012; 287
A Disratthakit (pbio.3001755.ref075) 2016; 60
M Farhat (pbio.3001755.ref022) 2019; 10
MB Nair (pbio.3001755.ref021) 2018; 50
NS Shah (pbio.3001755.ref002) 2017; 376
S Ramón-García (pbio.3001755.ref044) 2013; 288
S Polsfuss (pbio.3001755.ref007) 2019; 69
P Rancoita (pbio.3001755.ref030) 2018; 62
SG Earle (pbio.3001755.ref020) 2016; 1
CM Sassetti (pbio.3001755.ref056) 2003; 48
T Yano (pbio.3001755.ref061) 2011; 286
M Driscoll (pbio.3001755.ref057) 2010; 285
pbio.3001755.ref077
KG Papavinasasundaram (pbio.3001755.ref065) 2005; 187
FA Sirgel (pbio.3001755.ref073) 2013; 8
The CRyPTIC Consortium (pbio.3001755.ref078) 2021
MH Hunt (pbio.3001755.ref080) 2021
J van Ingen (pbio.3001755.ref072) 2011; 15
K Winther (pbio.3001755.ref067) 2013; 4
H Ouellet (pbio.3001755.ref060) 2009; 48
N Kumar (pbio.3001755.ref038) 2014; 23
E Sanchez-Padilla (pbio.3001755.ref016) 2015; 372
P Miotto (pbio.3001755.ref017) 2017; 50
A Dixit (pbio.3001755.ref037) 2019; 9
DR Zerbino (pbio.3001755.ref081) 2008; 18
A Deep (pbio.3001755.ref066) 2017; 284
KF Walsh (pbio.3001755.ref069) 2019; 69
The CRyPTIC Consortium. (pbio.3001755.ref031) 2021
YEA Oppong (pbio.3001755.ref023) 2019; 20
N Hicks (pbio.3001755.ref047) 2019; 10
K Bhattacharyya (pbio.3001755.ref042) 2020; 20
AN Meza (pbio.3001755.ref053) 2019; 9
T Schön (pbio.3001755.ref028) 2017; 23
MR Farhat (pbio.3001755.ref074) 2016; 54
pbio.3001755.ref001
S Goossens (pbio.3001755.ref009) 2020; 34
S Johansen (pbio.3001755.ref049) 2006; 23
G Rizk (pbio.3001755.ref082) 2013; 29
S Sreevatsan (pbio.3001755.ref029) 1997; 41
E García-Fernández (pbio.3001755.ref058) 2013; 15
MR Farhat (pbio.3001755.ref018) 2013; 45
M Farhat (pbio.3001755.ref024) 2016; 194
K Sharma (pbio.3001755.ref063) 2006; 188
NA Makhado (pbio.3001755.ref013) 2018; 18
G Sharma (pbio.3001755.ref035) 2015; 43
P Chakhaiyar (pbio.3001755.ref040) 2004; 190
A Pantel (pbio.3001755.ref033) 2012; 56
K Wang (pbio.3001755.ref039) 2013; 66
V Molle (pbio.3001755.ref062) 2003; 42
NE Arenas (pbio.3001755.ref050) 2011; 11
References_xml – volume: 60
  start-page: 5189
  issue: 9
  year: 2016
  ident: pbio.3001755.ref075
  article-title: Role of gyrB Mutations in Pre-extensively and Extensively Drug-Resistant Tuberculosis in Thai Clinical Isolates
  publication-title: Antimicrob Agents Chemother
  doi: 10.1128/AAC.00539-16
  contributor:
    fullname: A Disratthakit
– volume: 11
  start-page: 459
  issue: 7
  year: 2010
  ident: pbio.3001755.ref026
  article-title: New approaches to population stratification in genome-wide association studies
  publication-title: Nat Rev Genet
  doi: 10.1038/nrg2813
  contributor:
    fullname: AL Price
– volume: 5
  start-page: R12
  issue: 2
  year: 2004
  ident: pbio.3001755.ref084
  article-title: Versatile and open software for comparing large genomes
  publication-title: Genome Biol
  doi: 10.1186/gb-2004-5-2-r12
  contributor:
    fullname: S Kurtz
– year: 2019
  ident: pbio.3001755.ref004
  publication-title: Rapid Communication: Key changes to the treatment of drug-resistant tuberculosis
  contributor:
    fullname: World Health Organization
– volume: 20
  issue: 223
  year: 2020
  ident: pbio.3001755.ref042
  article-title: Correlation of drug resistance with single nucleotide variations through genome analysis and experimental validation in a multi-drug resistant clinical isolate of M. tuberculosis
  publication-title: BMC Microbiol
  contributor:
    fullname: K Bhattacharyya
– volume: 201
  issue: 12
  year: 2020
  ident: pbio.3001755.ref006
  article-title: Bedaquiline-Resistant Tuberculosis: Dark Clouds on the Horizon
  publication-title: Am J Respir Crit Care Med
  doi: 10.1164/rccm.201909-1819LE
  contributor:
    fullname: S Andres
– volume: 287
  start-page: 299
  issue: 1
  year: 2012
  ident: pbio.3001755.ref043
  article-title: The mycobacterial transcriptional regulator whiB7 gene links redox homeostasis and intrinsic antibiotic resistance
  publication-title: J Biol Chem
  doi: 10.1074/jbc.M111.302588
  contributor:
    fullname: J Burian
– volume: 288
  start-page: 34514
  issue: 48
  year: 2013
  ident: pbio.3001755.ref044
  article-title: WhiB7, an Fe-S-dependent transcription factor that activates species-specific repertoires of drug resistance determinants in actinobacteria
  publication-title: J Biol Chem
  doi: 10.1074/jbc.M113.516385
  contributor:
    fullname: S Ramón-García
– year: 2020
  ident: pbio.3001755.ref036
  article-title: Exploiting Homoplasy in Genome-Wide Association Studies to Enhance Identification of Antibiotic-Resistance Mutations in Bacterial Genomes.
  publication-title: Evol Bioinform Online
  contributor:
    fullname: YP Lai
– volume: 48
  start-page: 77
  year: 2003
  ident: pbio.3001755.ref056
  article-title: Genes required for mycobacterial growth defined by high density mutagenesis
  publication-title: Mol Microbiol
  doi: 10.1046/j.1365-2958.2003.03425.x
  contributor:
    fullname: CM Sassetti
– volume: 75
  start-page: 2031
  year: 2020
  ident: pbio.3001755.ref086
  article-title: Systematic review of mutations associated with resistance to the new and repurposed Mycobacterium tuberculosis drugs bedaquiline, clofazimine, linezolid, delamanid and pretomanid
  publication-title: J Antimicrob Chemother
  doi: 10.1093/jac/dkaa136
  contributor:
    fullname: S Kadura
– volume: 194
  start-page: 621
  issue: 5
  year: 2016
  ident: pbio.3001755.ref024
  article-title: Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value
  publication-title: Am J Respir Crit Care Med
  doi: 10.1164/rccm.201510-2091OC
  contributor:
    fullname: M Farhat
– volume: 201
  issue: 11
  year: 2020
  ident: pbio.3001755.ref070
  article-title: Early Bactericidal Activity of Different Isoniazid Doses for Drug-Resistant Tuberculosis (INHindsight): A Randomized, Open-Label Clinical Trial.
  publication-title: Am J Respir Crit Care Med
  doi: 10.1164/rccm.201910-1960OC
  contributor:
    fullname: KE Dooley
– volume: 286
  start-page: 10276
  issue: 12
  year: 2011
  ident: pbio.3001755.ref061
  article-title: Reduction of clofazimine by mycobacterial type 2 NADH:quinone oxidoreductase: a pathway for the generation of bactericidal levels of reactive oxygen species
  publication-title: J Biol Chem
  doi: 10.1074/jbc.M110.200501
  contributor:
    fullname: T Yano
– volume: 54
  issue: 3
  year: 2016
  ident: pbio.3001755.ref074
  article-title: Gyrase Mutations Are Associated with Variable Levels of Fluoroquinolone Resistance in Mycobacterium tuberculosis
  publication-title: J Clin Microbiol
  doi: 10.1128/JCM.02775-15
  contributor:
    fullname: MR Farhat
– volume: 50
  start-page: 307
  issue: 2
  year: 2018
  ident: pbio.3001755.ref021
  article-title: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis
  publication-title: Nat Genet
  doi: 10.1038/s41588-017-0029-0
  contributor:
    fullname: MB Nair
– volume: 52
  start-page: 2157
  issue: 6
  year: 2014
  ident: pbio.3001755.ref085
  article-title: Profiling of rpoB Mutations and MICs for Rifampin and Rifabutin in Mycobacterium tuberculosis
  publication-title: J Clin Microbiol
  doi: 10.1128/JCM.00691-14
  contributor:
    fullname: FB Jamieson
– volume: 49
  start-page: 571
  issue: 2
  year: 2005
  ident: pbio.3001755.ref048
  article-title: Mutation of tlyA Confers Capreomycin Resistance in Mycobacterium tuberculosis
  publication-title: Antimicrob Agents Chemother
  doi: 10.1128/AAC.49.2.571-577.2005
  contributor:
    fullname: C Maus
– volume: 102
  start-page: 12200
  issue: 34
  year: 2005
  ident: pbio.3001755.ref045
  article-title: Ancestral antibiotic resistance in Mycobacterium tuberculosis
  publication-title: Proc Natl Acad Sci U S A
  doi: 10.1073/pnas.0505446102
  contributor:
    fullname: R Morris
– volume: 200
  issue: 4
  year: 2019
  ident: pbio.3001755.ref005
  article-title: New World Health Organization Treatment Recommendations for Multidrug-Resistant Tuberculosis: Are We Well Enough Prepared?
  publication-title: Am J Respir Crit Care Med
  doi: 10.1164/rccm.201902-0260LE
  contributor:
    fullname: K Kranzer
– volume: 42
  start-page: 15300
  issue: 51
  year: 2003
  ident: pbio.3001755.ref062
  article-title: An FHA Phosphoprotein Recognition Domain Mediates Protein EmbR Phosphorylation by PknH, a Ser/Thr Protein Kinase from Mycobacterium tuberculosis
  publication-title: Biochemistry
  doi: 10.1021/bi035150b
  contributor:
    fullname: V Molle
– volume: 379
  start-page: 823
  issue: 9
  year: 2018
  ident: pbio.3001755.ref068
  article-title: Bacterial Factors That Predict Relapse after Tuberculosis Therapy
  publication-title: N Engl J Med
  doi: 10.1056/NEJMoa1715849
  contributor:
    fullname: R Colangeli
– volume: 379
  start-page: 1403
  issue: 15
  year: 2018
  ident: pbio.3001755.ref011
  article-title: Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.
  publication-title: N Engl J Med
  doi: 10.1056/NEJMoa1800474
  contributor:
    fullname: The CRyPTIC Consortium and the 100,000 Genomes Project
– volume: 180
  issue: 235–245
  year: 2018
  ident: pbio.3001755.ref059
  article-title: Potential drug targets in the Mycobacterium tuberculosis cytochrome P450 system
  publication-title: J Inorg Biochem
  contributor:
    fullname: P. Ortiz de Montellano
– volume: 309
  issue: 7
  year: 2019
  ident: pbio.3001755.ref052
  article-title: Assessing capreomycin resistance on tlyA deficient and point mutation (G695A) Mycobacterium tuberculosis strains using multi-omics analysis.
  publication-title: Int J Med Microbiol
  doi: 10.1016/j.ijmm.2019.06.003
  contributor:
    fullname: J Zhao
– year: 2020
  ident: pbio.3001755.ref003
  article-title: WHO Consolidated Guidelines on Tuberculosis, Module 4: Treatment -. Drug-Resistant Tuberculosis Treatment
  contributor:
    fullname: World Health Organization
– volume: 10
  issue: 2128
  year: 2019
  ident: pbio.3001755.ref022
  article-title: GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions
  publication-title: Nat Commun
  contributor:
    fullname: M Farhat
– volume: 188
  start-page: 2936
  issue: 8
  year: 2006
  ident: pbio.3001755.ref063
  article-title: Transcriptional control of the mycobacterial embCAB operon by PknH through a regulatory protein, EmbR, in vivo
  publication-title: J Bacteriol
  doi: 10.1128/JB.188.8.2936-2944.2006
  contributor:
    fullname: K Sharma
– volume: 1
  start-page: 16041
  issue: 5
  year: 2016
  ident: pbio.3001755.ref020
  article-title: Identifying lineage effects when controlling for population structure improves power in bacterial association studies
  publication-title: Nat Microbiol
  doi: 10.1038/nmicrobiol.2016.41
  contributor:
    fullname: SG Earle
– volume: 422
  start-page: 488
  issue: 4
  year: 2012
  ident: pbio.3001755.ref064
  article-title: Structure of the Sensor Domain of Mycobacterium tuberculosis PknH Receptor Kinase Reveals a Conserved Binding Cleft
  publication-title: J Mol Biol
  doi: 10.1016/j.jmb.2012.06.011
  contributor:
    fullname: A Cavazos
– volume: 55
  start-page: 219
  issue: 2
  year: 2015
  ident: pbio.3001755.ref055
  article-title: Using a Label Free Quantitative Proteomics Approach to Identify Changes in Protein Abundance in Multidrug-Resistant Mycobacterium tuberculosis
  publication-title: Indian. J Microbiol
  doi: 10.1007/s12088-015-0511-2
  contributor:
    fullname: T Phong
– volume: 187
  start-page: 5751
  issue: 16
  year: 2005
  ident: pbio.3001755.ref065
  article-title: Deletion of the Mycobacterium tuberculosis pknH Gene Confers a Higher Bacillary Load during the Chronic Phase of Infection in BALB/c Mice
  publication-title: J Bacteriol
  doi: 10.1128/JB.187.16.5751-5760.2005
  contributor:
    fullname: KG Papavinasasundaram
– volume: 48
  start-page: 863
  issue: 5
  year: 2009
  ident: pbio.3001755.ref060
  article-title: Reaction of Mycobacterium tuberculosis cytochrome P450 enzymes with nitric oxide
  publication-title: Biochemistry
  doi: 10.1021/bi801595t
  contributor:
    fullname: H Ouellet
– volume: 9
  issue: 5602
  year: 2019
  ident: pbio.3001755.ref037
  article-title: Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting
  publication-title: Sci Rep
  contributor:
    fullname: A Dixit
– year: 2021
  ident: pbio.3001755.ref031
  article-title: Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis.
  publication-title: medRxiv
  contributor:
    fullname: The CRyPTIC Consortium.
– volume: 34
  start-page: e00141
  issue: 1
  year: 2020
  ident: pbio.3001755.ref009
  article-title: Mechanisms of Drug-Induced Tolerance in Mycobacterium tuberculosis
  publication-title: Clin Microbiol Rev
  doi: 10.1128/CMR.00141-20
  contributor:
    fullname: S Goossens
– volume: 393
  start-page: 537
  issue: 6685
  year: 1998
  ident: pbio.3001755.ref083
  article-title: Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
  publication-title: Nature
  doi: 10.1038/31159
  contributor:
    fullname: S Cole
– volume: 62
  start-page: e00344
  issue: 9
  year: 2018
  ident: pbio.3001755.ref030
  article-title: Validating a 14-Drug Microtiter Plate Containing Bedaquiline and Delamanid for Large-Scale Research Susceptibility Testing of Mycobacterium tuberculosis
  publication-title: Antimicrob Agents Chemother
  doi: 10.1128/AAC.00344-18
  contributor:
    fullname: P Rancoita
– volume: 29
  start-page: 652
  issue: 5
  year: 2013
  ident: pbio.3001755.ref082
  article-title: DSK: k-mer counting with very low memory usage
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btt020
  contributor:
    fullname: G Rizk
– volume: 20
  start-page: 252
  issue: 1
  year: 2019
  ident: pbio.3001755.ref023
  article-title: Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance
  publication-title: BMC Genom
  doi: 10.1186/s12864-019-5615-3
  contributor:
    fullname: YEA Oppong
– volume: 23
  start-page: 173
  issue: 2
  year: 2006
  ident: pbio.3001755.ref049
  article-title: Capreomycin Binds across the Ribosomal Subunit Interface Using tlyA-Encoded 2′-O-Methylations in 16S and 23S rRNAs
  publication-title: Mol Cell
  doi: 10.1016/j.molcel.2006.05.044
  contributor:
    fullname: S Johansen
– volume: 43
  start-page: 3922
  issue: 8
  year: 2015
  ident: pbio.3001755.ref035
  article-title: The interaction of mycobacterial protein Rv2966c with host chromatin is mediated through non-CpG methylation and histone H3/H4 binding
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkv261
  contributor:
    fullname: G Sharma
– volume: 15
  start-page: 1193
  issue: 10
  year: 2015
  ident: pbio.3001755.ref025
  article-title: Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: A retrospective cohort study
  publication-title: Lancet Infect Dis
  doi: 10.1016/S1473-3099(15)00062-6
  contributor:
    fullname: TM Walker
– volume: 113
  start-page: 1706
  issue: 7
  year: 2016
  ident: pbio.3001755.ref034
  article-title: Structure of tuberculosis quinolone–gyrase complex
  publication-title: Proc Natl Acad Sci U S A
  contributor:
    fullname: TR Blower
– volume: 69
  start-page: 717
  issue: 4
  year: 2019
  ident: pbio.3001755.ref069
  article-title: Improved Outcomes With High-dose Isoniazid in Multidrug-resistant Tuberculosis Treatment in Haiti
  publication-title: Clin Infect Dis
  doi: 10.1093/cid/ciz039
  contributor:
    fullname: KF Walsh
– ident: pbio.3001755.ref077
– volume: 50
  start-page: 1701354
  issue: 6
  year: 2017
  ident: pbio.3001755.ref017
  article-title: A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis
  publication-title: Eur Respir J
  doi: 10.1183/13993003.01354-2017
  contributor:
    fullname: P Miotto
– volume: 201
  issue: 12
  year: 2020
  ident: pbio.3001755.ref071
  article-title: High-Dose First-Line Treatment Regimen for Recurrent Rifampicin-Susceptible Tuberculosis
  publication-title: Am J Respir Crit Care Med
  doi: 10.1164/rccm.202001-0201LE
  contributor:
    fullname: T Decroo
– volume: 190
  start-page: 1237
  issue: 7
  year: 2004
  ident: pbio.3001755.ref040
  article-title: Regions of high antigenicity within the hypothetical PPE major polymorphic tandem repeat open-reading frame, Rv2608, show a differential humoral response and a low T cell response in various categories of patients with tuberculosis
  publication-title: J Infect Dis
  doi: 10.1086/423938
  contributor:
    fullname: P Chakhaiyar
– volume: 66
  start-page: 222
  issue: 3
  year: 2013
  ident: pbio.3001755.ref039
  article-title: The expression of ABC efflux pump, Rv1217c-Rv1218c, and its association with multidrug resistance of Mycobacterium tuberculosis in China
  publication-title: Curr Microbiol
  doi: 10.1007/s00284-012-0215-3
  contributor:
    fullname: K Wang
– volume: 15
  start-page: 990
  issue: 7
  year: 2011
  ident: pbio.3001755.ref072
  article-title: Low-level rifampicin-resistant Mycobacterium tuberculosis strains raise a new therapeutic challenge
  publication-title: Int J Tuberc Lung Dis
  doi: 10.5588/ijtld.10.0127
  contributor:
    fullname: J van Ingen
– volume: 363
  start-page: 1005
  issue: 11
  year: 2010
  ident: pbio.3001755.ref014
  article-title: Rapid Molecular Detection of Tuberculosis and Rifampin Resistance
  publication-title: N Engl J Med
  doi: 10.1056/NEJMoa0907847
  contributor:
    fullname: CC Boehme
– year: 2018
  ident: pbio.3001755.ref027
  article-title: Technical report on critical concentrations for TB drug susceptibility testing of medicines used in the treatment of drug-resistant TB.
  contributor:
    fullname: World Health Organization
– volume: 15
  start-page: 2342
  issue: 8
  year: 2013
  ident: pbio.3001755.ref058
  article-title: A highly conserved mycobacterial cholesterol catabolic pathway
  publication-title: Environ Microbiol
  doi: 10.1111/1462-2920.12108
  contributor:
    fullname: E García-Fernández
– volume: 69
  start-page: 1229
  issue: 7
  year: 2019
  ident: pbio.3001755.ref007
  article-title: Emergence of Low-level Delamanid and Bedaquiline Resistance During Extremely Drug-resistant Tuberculosis Treatment
  publication-title: Clin Infect Dis
  doi: 10.1093/cid/ciz074
  contributor:
    fullname: S Polsfuss
– volume: 45
  start-page: 1183
  issue: 10
  year: 2013
  ident: pbio.3001755.ref018
  article-title: Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis
  publication-title: Nat Genet
  doi: 10.1038/ng.2747
  contributor:
    fullname: MR Farhat
– volume: 18
  start-page: 821
  issue: 5
  year: 2008
  ident: pbio.3001755.ref081
  article-title: Velvet: algorithms for de novo short read assembly using de Bruijn graphs
  publication-title: Genome Res
  doi: 10.1101/gr.074492.107
  contributor:
    fullname: DR Zerbino
– volume: 18
  start-page: 1350
  issue: 12
  year: 2018
  ident: pbio.3001755.ref013
  article-title: Outbreak of multidrug-resistant tuberculosis in South Africa undetected by WHO-endorsed commercial tests: an observational study
  publication-title: Lancet Infect Dis
  doi: 10.1016/S1473-3099(18)30496-1
  contributor:
    fullname: NA Makhado
– volume: 3
  issue: 34
  year: 2018
  ident: pbio.3001755.ref041
  article-title: The TLR-4 agonist adjuvant, GLA-SE, improves magnitude and quality of immune responses elicited by the ID93 tuberculosis vaccine: first-in-human trial
  publication-title: NPJ Vaccines
  contributor:
    fullname: R Coler
– volume: 44
  start-page: 821
  issue: 7
  year: 2012
  ident: pbio.3001755.ref032
  article-title: Genome-wide efficient mixed-model analysis for association studies
  publication-title: Nat Genet
  doi: 10.1038/ng.2310
  contributor:
    fullname: X Zhou
– volume: 4
  start-page: 2796
  year: 2013
  ident: pbio.3001755.ref067
  article-title: VapC20 of Mycobacterium tuberculosis cleaves the Sarcin–Ricin loop of 23S rRNA.
  publication-title: Nat Commun
  doi: 10.1038/ncomms3796
  contributor:
    fullname: K Winther
– volume: 6
  start-page: 10063
  year: 2015
  ident: pbio.3001755.ref079
  article-title: Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
  publication-title: Nat Commun
  doi: 10.1038/ncomms10063
  contributor:
    fullname: P Bradley
– volume: 284
  start-page: 4066
  year: 2017
  ident: pbio.3001755.ref066
  article-title: Crystal structure of Mycobacterium tuberculosis VapC20 toxin and its interactions with cognate antitoxin, VapB20, suggest a model for toxin–antitoxin assembly.
  publication-title: FEBS J.
  doi: 10.1111/febs.14289
  contributor:
    fullname: A Deep
– volume: 4
  start-page: 49
  issue: 1
  year: 2016
  ident: pbio.3001755.ref010
  article-title: Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study
  publication-title: Lancet Respir Med
  doi: 10.1016/S2213-2600(15)00466-X
  contributor:
    fullname: L Pankhurst
– volume: 11
  issue: 16
  year: 2011
  ident: pbio.3001755.ref050
  article-title: Molecular modeling and in silico characterization of Mycobacterium tuberculosis TlyA: Possible misannotation of this tubercle bacilli-hemolysin
  publication-title: BMC Struct Biol
  contributor:
    fullname: NE Arenas
– volume: 23
  start-page: 423
  issue: 4
  year: 2014
  ident: pbio.3001755.ref038
  article-title: Crystal structure of the transcriptional regulator Rv1219c of Mycobacterium tuberculosis
  publication-title: Protein Sci
  doi: 10.1002/pro.2424
  contributor:
    fullname: N Kumar
– ident: pbio.3001755.ref001
– volume: 377
  start-page: 1495
  issue: 9776
  year: 2011
  ident: pbio.3001755.ref015
  article-title: Feasibility, diagnostic accuracy, and effectiveness of decentralised use of the Xpert MTB/RIF test for diagnosis of tuberculosis and multidrug resistance: a multicentre implementation study
  publication-title: Lancet
  doi: 10.1016/S0140-6736(11)60438-8
  contributor:
    fullname: C Boehme
– volume: 10
  start-page: e00616
  issue: 2
  year: 2019
  ident: pbio.3001755.ref047
  article-title: Bacterial Genome-Wide Association Identifies Novel Factors That Contribute to Ethionamide and Prothionamide Susceptibility in Mycobacterium tuberculosis
  publication-title: MBio
  doi: 10.1128/mBio.00616-19
  contributor:
    fullname: N Hicks
– year: 2021
  ident: pbio.3001755.ref080
  article-title: Minos: graph adjudication and joint genotyping of cohorts of bacterial genomes.
  publication-title: bioRxiv
  contributor:
    fullname: MH Hunt
– volume: 376
  start-page: 243
  issue: 3
  year: 2017
  ident: pbio.3001755.ref002
  article-title: Transmission of Extensively Drug-Resistant Tuberculosis in South Africa
  publication-title: N Engl J Med
  doi: 10.1056/NEJMoa1604544
  contributor:
    fullname: NS Shah
– volume: 56
  start-page: 1990
  issue: 4
  year: 2012
  ident: pbio.3001755.ref033
  article-title: Extending the definition of the GyrB quinolone resistance-determining region in Mycobacterium tuberculosis DNA gyrase for assessing fluoroquinolone resistance in M. tuberculosis
  publication-title: Antimicrob Agents Chemother
  doi: 10.1128/AAC.06272-11
  contributor:
    fullname: A Pantel
– year: 2021
  ident: pbio.3001755.ref078
  article-title: A data compendium of M. tuberculosis antibiotic resistance.
  publication-title: bioRxiv
  contributor:
    fullname: The CRyPTIC Consortium
– volume: 285
  start-page: 38270
  issue: 49
  year: 2010
  ident: pbio.3001755.ref057
  article-title: Structural and biochemical characterization of Mycobacterium tuberculosis CYP142: evidence for multiple cholesterol 27-hydroxylase activities in a human pathogen
  publication-title: J Biol Chem
  doi: 10.1074/jbc.M110.164293
  contributor:
    fullname: M Driscoll
– volume: 45
  start-page: 1255
  issue: 10
  year: 2013
  ident: pbio.3001755.ref019
  article-title: Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance
  publication-title: Nat Genet
  doi: 10.1038/ng.2735
  contributor:
    fullname: H Zhang
– volume: 7
  start-page: e39754
  issue: 6
  year: 2012
  ident: pbio.3001755.ref076
  article-title: New insights into fluoroquinolone resistance in Mycobacterium tuberculosis: functional genetic analysis of gyrA and gyrB mutations
  publication-title: PLoS ONE
  doi: 10.1371/journal.pone.0039754
  contributor:
    fullname: S Malik
– volume: 372
  start-page: 1181
  issue: 12
  year: 2015
  ident: pbio.3001755.ref016
  article-title: Detection of Drug-Resistant Tuberculosis by Xpert MTB/RIF in Swaziland
  publication-title: N Engl J Med
  doi: 10.1056/NEJMc1413930
  contributor:
    fullname: E Sanchez-Padilla
– volume: 57
  start-page: 1857
  issue: 4
  year: 2013
  ident: pbio.3001755.ref046
  article-title: Aminoglycoside cross-resistance in Mycobacterium tuberculosis due to mutations in the 5’ untranslated region of whiB7
  publication-title: Antimicrob Agents Chemother
  doi: 10.1128/AAC.02191-12
  contributor:
    fullname: A Reeves
– volume: 9
  start-page: 16791
  year: 2019
  ident: pbio.3001755.ref053
  article-title: Mycobacterium tuberculosis CysA2 is a dual sulfurtransferase with activity against thiosulfate and 3-mercaptopyruvate and interacts with mammalian cells.
  publication-title: Sci Rep.
  doi: 10.1038/s41598-019-53069-6
  contributor:
    fullname: AN Meza
– volume: 85
  start-page: 1194
  year: 2012
  ident: pbio.3001755.ref051
  article-title: Capreomycin susceptibility is increased by TlyA-directed 2′-O-methylation on both ribosomal subunits
  publication-title: Mol Microbiol
  doi: 10.1111/j.1365-2958.2012.08168.x
  contributor:
    fullname: T Monshupanee
– volume: 17
  start-page: 359
  issue: 4
  year: 2017
  ident: pbio.3001755.ref012
  article-title: Tuberculosis is changing
  publication-title: Lancet Infect Dis
  doi: 10.1016/S1473-3099(17)30123-8
  contributor:
    fullname: TM Walker
– volume: 23
  start-page: 154
  issue: 3
  year: 2017
  ident: pbio.3001755.ref028
  article-title: Mycobacterium tuberculosis drug-resistance testing: challenges, recent developments and perspectives
  publication-title: Clin Microbiol Infect
  doi: 10.1016/j.cmi.2016.10.022
  contributor:
    fullname: T Schön
– volume: 44
  start-page: 21
  issue: 1
  year: 2016
  ident: pbio.3001755.ref008
  article-title: Drug resistance mechanisms and novel drug targets for tuberculosis therapy
  publication-title: J Genet Genomics
  doi: 10.1016/j.jgg.2016.10.002
  contributor:
    fullname: M Islam
– volume: 59
  start-page: 51
  year: 2007
  ident: pbio.3001755.ref054
  article-title: Common themes and variations in the rhodanese superfamily
  publication-title: IUBMB Life
  doi: 10.1080/15216540701206859
  contributor:
    fullname: R Cipollone
– volume: 41
  start-page: 1677
  issue: 8
  year: 1997
  ident: pbio.3001755.ref029
  article-title: Ethambutol resistance in Mycobacterium tuberculosis: critical role of embB mutations
  publication-title: Antimicrob Agents Chemother
  doi: 10.1128/AAC.41.8.1677
  contributor:
    fullname: S Sreevatsan
– volume: 8
  start-page: e59414
  issue: 3
  year: 2013
  ident: pbio.3001755.ref073
  article-title: The Rationale for Using Rifabutin in the Treatment of MDR and XDR Tuberculosis Outbreaks.
  publication-title: PLoS ONE
  doi: 10.1371/journal.pone.0059414
  contributor:
    fullname: FA Sirgel
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Snippet The emergence of drug-resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole-genome sequencing...
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SubjectTerms Anti-Infective Agents - pharmacology
Antimicrobial agents
Antimicrobial resistance
Antitubercular Agents - pharmacology
Binding sites
Biology and Life Sciences
Clofazimine
Confidence intervals
Cross-resistance
Drug resistance
Drug resistance in microorganisms
Drugs
Gene sequencing
Genetic aspects
Genetic diversity
Genetic variance
Genome-wide association studies
Genome-Wide Association Study
Genomes
Genomics
Health risks
Heritability
Humans
Isoniazid
Life Sciences
Linezolid
Medicine and Health Sciences
Microbial Sensitivity Tests
Minimum inhibitory concentration
Mutation
Mycobacterium tuberculosis
Mycobacterium tuberculosis - genetics
Oligonucleotides
Phenotypes
Public health
rRNA
rRNA 23S
Short Reports
Tuberculosis
Tuberculosis, Multidrug-Resistant - drug therapy
Tuberculosis, Multidrug-Resistant - genetics
Tuberculosis, Multidrug-Resistant - microbiology
Whole genome sequencing
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Title Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms
URI https://www.ncbi.nlm.nih.gov/pubmed/35944070
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https://doaj.org/article/80296c89bfd14eec9d46b9d961ee047b
http://dx.doi.org/10.1371/journal.pbio.3001755
Volume 20
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