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Volumn 1, Issue 10, 2013, Pages 786-792

Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: A retrospective observational study

(20)  Bryant, Josephine M a   Harris, Simon R a   Parkhill, Julian a   Dawson, Rodney b   Diacon, Andreas H c   van Helden, Paul c   Pym, Alex d   Mahayiddin, Aziah A e   Chuchottaworn, Charoen f   Sanne, Ian M g   Louw, Cheryl h   Boeree, Martin J i   Hoelscher, Michael j,k   McHugh, Timothy D l   Bateson, Anna L C l   Hunt, Robert D l   Mwaigwisya, Solomon l   Wright, Laura l   Gillespie, Stephen H m   Bentley, Stephen D k  


Author keywords

[No Author keywords available]

Indexed keywords

ETHAMBUTOL; ISONIAZID; MOXIFLOXACIN; PLACEBO; PYRAZINAMIDE; RIFAMPICIN; BACTERIAL DNA; TUBERCULOSTATIC AGENT;

EID: 84888860825     PISSN: 22132600     EISSN: None     Source Type: Journal    
DOI: 10.1016/S2213-2600(13)70231-5     Document Type: Article
Times cited : (181)

References (33)
  • 1
    • 84870370352 scopus 로고    scopus 로고
    • WHO, World Health Organisation, Geneva
    • Global Tuberculosis Report 2012 2012, WHO, World Health Organisation, Geneva.
    • (2012) Global Tuberculosis Report 2012
  • 2
    • 1442276282 scopus 로고    scopus 로고
    • Patients with active tuberculosis often have different strains in the same sputum specimen
    • Warren RM, Victor TC, Streicher EM, et al. Patients with active tuberculosis often have different strains in the same sputum specimen. Am J Respir Crit Care Med 2004, 169:610-614.
    • (2004) Am J Respir Crit Care Med , vol.169 , pp. 610-614
    • Warren, R.M.1    Victor, T.C.2    Streicher, E.M.3
  • 3
    • 57349104394 scopus 로고    scopus 로고
    • Tuberculosis reinfection rate as a proportion of total infection rate correlates with the logarithm of the incidence rate: a mathematical model
    • Uys PW, van Helden PD, Hargrove JW Tuberculosis reinfection rate as a proportion of total infection rate correlates with the logarithm of the incidence rate: a mathematical model. J R Soc Interface 2009, 6:11-15.
    • (2009) J R Soc Interface , vol.6 , pp. 11-15
    • Uys, P.W.1    van Helden, P.D.2    Hargrove, J.W.3
  • 4
    • 20444401506 scopus 로고    scopus 로고
    • Rate of reinfection tuberculosis after successful treatment is higher than rate of new tuberculosis
    • Verver S, Warren RM, Beyers N, et al. Rate of reinfection tuberculosis after successful treatment is higher than rate of new tuberculosis. Am J Respir Crit Care Med 2005, 171:1430-1435.
    • (2005) Am J Respir Crit Care Med , vol.171 , pp. 1430-1435
    • Verver, S.1    Warren, R.M.2    Beyers, N.3
  • 5
    • 76449113203 scopus 로고    scopus 로고
    • High rates of recurrence in HIV-infected and HIV-uninfected patients with tuberculosis
    • Glynn JR, Murray J, Bester A, Nelson G, Shearer S, Sonnenberg P High rates of recurrence in HIV-infected and HIV-uninfected patients with tuberculosis. J Infect Dis 2010, 201:704-711.
    • (2010) J Infect Dis , vol.201 , pp. 704-711
    • Glynn, J.R.1    Murray, J.2    Bester, A.3    Nelson, G.4    Shearer, S.5    Sonnenberg, P.6
  • 6
    • 76449091261 scopus 로고    scopus 로고
    • Impact of HIV infection on the recurrence of tuberculosis in south India
    • Narayanan S, Swaminathan S, Supply P, et al. Impact of HIV infection on the recurrence of tuberculosis in south India. J Infect Dis 2010, 201:691-703.
    • (2010) J Infect Dis , vol.201 , pp. 691-703
    • Narayanan, S.1    Swaminathan, S.2    Supply, P.3
  • 7
    • 77952841173 scopus 로고    scopus 로고
    • Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved
    • Comas I, Chakravartti J, Small PM, et al. Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat Genet 2010, 42:498-503.
    • (2010) Nat Genet , vol.42 , pp. 498-503
    • Comas, I.1    Chakravartti, J.2    Small, P.M.3
  • 8
    • 79951995822 scopus 로고    scopus 로고
    • Whole-genome sequencing and social-network analysis of a tuberculosis outbreak
    • Gardy JL, Johnston JC, Ho Sui SJ, et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 2011, 364:730-739.
    • (2011) N Engl J Med , vol.364 , pp. 730-739
    • Gardy, J.L.1    Johnston, J.C.2    Ho Sui, S.J.3
  • 9
    • 84872513471 scopus 로고    scopus 로고
    • Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study
    • Walker TM, Ip CLC, Harrell RH, et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis 2013, 13:137-146.
    • (2013) Lancet Infect Dis , vol.13 , pp. 137-146
    • Walker, T.M.1    Ip, C.L.C.2    Harrell, R.H.3
  • 10
    • 79955460244 scopus 로고    scopus 로고
    • Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection
    • Ford CB, Lin PL, Chase MR, et al. Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat Genet 2011, 43:482-486.
    • (2011) Nat Genet , vol.43 , pp. 482-486
    • Ford, C.B.1    Lin, P.L.2    Chase, M.R.3
  • 11
    • 84874261750 scopus 로고    scopus 로고
    • Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data
    • Bryant JM, Schurch AC, van Deutekom H, et al. Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data. BMC Infect Dis 2013, 13:110.
    • (2013) BMC Infect Dis , vol.13 , pp. 110
    • Bryant, J.M.1    Schurch, A.C.2    van Deutekom, H.3
  • 12
    • 0032508046 scopus 로고    scopus 로고
    • Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
    • Cole ST, Brosch R, Parkhill J, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998, 393:537-544.
    • (1998) Nature , vol.393 , pp. 537-544
    • Cole, S.T.1    Brosch, R.2    Parkhill, J.3
  • 13
    • 26944437440 scopus 로고    scopus 로고
    • Variation of the Mycobacterium tuberculosis PE_PGRS 33 gene among clinical isolates
    • Talarico S, Cave MD, Marrs CF, Foxman B, Zhang L, Yang Z Variation of the Mycobacterium tuberculosis PE_PGRS 33 gene among clinical isolates. J Clin Microbiol 2005, 43:4954-4960.
    • (2005) J Clin Microbiol , vol.43 , pp. 4954-4960
    • Talarico, S.1    Cave, M.D.2    Marrs, C.F.3    Foxman, B.4    Zhang, L.5    Yang, Z.6
  • 14
    • 45849108709 scopus 로고    scopus 로고
    • Mycobacterium tuberculosis PE_PGRS16 and PE_PGRS26 genetic polymorphism among clinical isolates
    • Talarico S, Zhang L, Marrs CF, et al. Mycobacterium tuberculosis PE_PGRS16 and PE_PGRS26 genetic polymorphism among clinical isolates. Tuberculosis 2008, 88:283-294.
    • (2008) Tuberculosis , vol.88 , pp. 283-294
    • Talarico, S.1    Zhang, L.2    Marrs, C.F.3
  • 15
    • 84859342693 scopus 로고    scopus 로고
    • Comparative analysis of Mycobacterium tuberculosis PE and PPE genes reveals high sequence variation and an apparent absence of selective constraints
    • McEvoy CR, Cloete R, Muller B, et al. Comparative analysis of Mycobacterium tuberculosis PE and PPE genes reveals high sequence variation and an apparent absence of selective constraints. PLoS One 2012, 7:e30593.
    • (2012) PLoS One , vol.7
    • McEvoy, C.R.1    Cloete, R.2    Muller, B.3
  • 16
    • 84881369293 scopus 로고    scopus 로고
    • Assessment of the sensitivity and specificity of Xpert MTB/RIF assay as an early sputum biomarker of response to tuberculosis treatment
    • Friedrich SO, Rachow A, Saathoff E, et al. Assessment of the sensitivity and specificity of Xpert MTB/RIF assay as an early sputum biomarker of response to tuberculosis treatment. Lancet Respir Med 2013, 1:462-470.
    • (2013) Lancet Respir Med , vol.1 , pp. 462-470
    • Friedrich, S.O.1    Rachow, A.2    Saathoff, E.3
  • 17
    • 0029133534 scopus 로고
    • Demonstration of homology between IS6110 of Mycobacterium tuberculosis and DNAs of other Mycobacterium spp.?
    • Kent L, McHugh TD, Billington O, Dale JW, Gillespie SH Demonstration of homology between IS6110 of Mycobacterium tuberculosis and DNAs of other Mycobacterium spp.?. J Clin Microbiol 1995, 33:2290-2293.
    • (1995) J Clin Microbiol , vol.33 , pp. 2290-2293
    • Kent, L.1    McHugh, T.D.2    Billington, O.3    Dale, J.W.4    Gillespie, S.H.5
  • 18
    • 33750085449 scopus 로고    scopus 로고
    • Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis
    • Supply P, Allix C, Lesjean S, et al. Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol 2006, 44:4498-4510.
    • (2006) J Clin Microbiol , vol.44 , pp. 4498-4510
    • Supply, P.1    Allix, C.2    Lesjean, S.3
  • 19
    • 84856448155 scopus 로고    scopus 로고
    • Optimal enzymes for amplifying sequencing libraries
    • Quail MA, Otto TD, Gu Y, et al. Optimal enzymes for amplifying sequencing libraries. Nat Methods 2011, 9:10-11.
    • (2011) Nat Methods , vol.9 , pp. 10-11
    • Quail, M.A.1    Otto, T.D.2    Gu, Y.3
  • 20
    • 84859545563 scopus 로고    scopus 로고
    • Microevolution of extensively drug-resistant tuberculosis in Russia
    • Casali N, Nikolayevskyy V, Balabanova Y, et al. Microevolution of extensively drug-resistant tuberculosis in Russia. Genome Res 2012, 22:735-745.
    • (2012) Genome Res , vol.22 , pp. 735-745
    • Casali, N.1    Nikolayevskyy, V.2    Balabanova, Y.3
  • 21
    • 75649084906 scopus 로고    scopus 로고
    • Evolution of MRSA during hospital transmission and intercontinental spread
    • Harris SR, Feil EJ, Holden MT, et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 2010, 327:469-474.
    • (2010) Science , vol.327 , pp. 469-474
    • Harris, S.R.1    Feil, E.J.2    Holden, M.T.3
  • 22
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 23
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078-2079.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3
  • 24
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821-829.
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 25
    • 84864111704 scopus 로고    scopus 로고
    • Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages
    • Stucki D, Malla B, Hostettler S, et al. Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages. PLoS One 2012, 7:e41253.
    • (2012) PLoS One , vol.7
    • Stucki, D.1    Malla, B.2    Hostettler, S.3
  • 26
    • 0030911908 scopus 로고    scopus 로고
    • Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology
    • Kamerbeek J, Schouls L, Kolk A, et al. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol 1997, 35:907-914.
    • (1997) J Clin Microbiol , vol.35 , pp. 907-914
    • Kamerbeek, J.1    Schouls, L.2    Kolk, A.3
  • 27
    • 0027498478 scopus 로고
    • Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology
    • van Embden JD, Cave MD, Crawford JT, et al. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol 1993, 31:406-409.
    • (1993) J Clin Microbiol , vol.31 , pp. 406-409
    • van Embden, J.D.1    Cave, M.D.2    Crawford, J.T.3
  • 28
    • 70350719440 scopus 로고    scopus 로고
    • Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints
    • Niemann S, Koser CU, Gagneux S, et al. Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints. PLoS One 2009, 4:e7407.
    • (2009) PLoS One , vol.4
    • Niemann, S.1    Koser, C.U.2    Gagneux, S.3
  • 29
    • 70649084195 scopus 로고    scopus 로고
    • Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies
    • Comas I, Homolka S, Niemann S, Gagneux S Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies. PLoS One 2009, 4:e7815.
    • (2009) PLoS One , vol.4
    • Comas, I.1    Homolka, S.2    Niemann, S.3    Gagneux, S.4
  • 30
    • 79953839838 scopus 로고    scopus 로고
    • Evaluation of the inaccurate assignment of mixed infections by Mycobacterium tuberculosis as exogenous reinfection and analysis of the potential role of bacterial factors in reinfection
    • Martin A, Herranz M, Navarro Y, et al. Evaluation of the inaccurate assignment of mixed infections by Mycobacterium tuberculosis as exogenous reinfection and analysis of the potential role of bacterial factors in reinfection. J Clin Microbiol 2011, 49:1331-1338.
    • (2011) J Clin Microbiol , vol.49 , pp. 1331-1338
    • Martin, A.1    Herranz, M.2    Navarro, Y.3
  • 31
    • 0018832013 scopus 로고
    • Quality control in tuberculosis bacteriology. 2. The origin of isolated positive cultures from the sputum of patients in four studies of short course chemotherapy in Africa
    • Mitchison DA, Keyes AB, Edwards EA, Ayuma P, Byfield SP, Nunn AJ Quality control in tuberculosis bacteriology. 2. The origin of isolated positive cultures from the sputum of patients in four studies of short course chemotherapy in Africa. Tubercle 1980, 61:135-144.
    • (1980) Tubercle , vol.61 , pp. 135-144
    • Mitchison, D.A.1    Keyes, A.B.2    Edwards, E.A.3    Ayuma, P.4    Byfield, S.P.5    Nunn, A.J.6
  • 32
    • 0018836103 scopus 로고
    • Quality control in tuberculosis bacteriology. 1. Laboratory studies on isolated positive cultures and the efficiency of direct smear examination
    • Aber VR, Allen BW, Mitchison DA, Ayuma P, Edwards EA, Keyes AB Quality control in tuberculosis bacteriology. 1. Laboratory studies on isolated positive cultures and the efficiency of direct smear examination. Tubercle 1980, 61:123-133.
    • (1980) Tubercle , vol.61 , pp. 123-133
    • Aber, V.R.1    Allen, B.W.2    Mitchison, D.A.3    Ayuma, P.4    Edwards, E.A.5    Keyes, A.B.6
  • 33
    • 0036840826 scopus 로고    scopus 로고
    • Estimation of the rate of unrecognized cross-contamination with mycobacterium tuberculosis in London microbiology laboratories
    • Ruddy M, McHugh TD, Dale JW, et al. Estimation of the rate of unrecognized cross-contamination with mycobacterium tuberculosis in London microbiology laboratories. J Clin Microbiol 2002, 40:4100-4104.
    • (2002) J Clin Microbiol , vol.40 , pp. 4100-4104
    • Ruddy, M.1    McHugh, T.D.2    Dale, J.W.3


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