Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis (original) (raw)
Velayati, A.A. et al. Emergence of new forms of totally drug-resistant tuberculosis bacilli: super extensively drug-resistant tuberculosis or totally drug-resistant strains in Iran. Chest136, 420–425 (2009). ArticlePubMed Google Scholar
Udwadia, Z.F., Amale, R.A., Ajbani, K.K. & Rodrigues, C. Totally drug-resistant tuberculosis in India. Clin. Infect. Dis.54, 579–581 (2012). ArticlePubMed Google Scholar
Migliori, G.B., De Iaco, G., Besozzi, G., Centis, R. & Cirillo, D.M. First tuberculosis cases in Italy resistant to all tested drugs. Euro Surveill.12, E070517.1 (2007). CASPubMed Google Scholar
Gandhi, N.R. et al. Multidrug-resistant and extensively drug-resistant tuberculosis: a threat to global control of tuberculosis. Lancet375, 1830–1843 (2010). ArticlePubMed Google Scholar
David, H.L. Probability distribution of drug-resistant mutants in unselected populations of Mycobacterium tuberculosis. Appl. Microbiol.20, 810–814 (1970). CASPubMedPubMed Central Google Scholar
Ford, C.B. et al. Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat. Genet.10.1038/ng.811 (2011).10.1038/ng.811
Bradford, W.Z. et al. The changing epidemiology of acquired drug-resistant tuberculosis in San Francisco, USA. Lancet348, 928–931 (1996). ArticleCASPubMed Google Scholar
Goble, M. et al. Treatment of 171 patients with pulmonary tuberculosis resistant to isoniazid and rifampin. N. Engl. J. Med.328, 527–532 (1993). ArticleCASPubMed Google Scholar
Pablos-Méndez, A., Knirsch, C.A., Barr, R.G., Lerner, B.H. & Frieden, T.R. Nonadherence in tuberculosis treatment: predictors and consequences in New York City. Am. J. Med.102, 164–170 (1997). ArticlePubMed Google Scholar
Udwadia, Z.F., Pinto, L.M. & Uplekar, M.W. Tuberculosis management by private practitioners in Mumbai, India: has anything changed in two decades? PLoS ONE5, e12023 (2010). ArticleCASPubMedPubMed Central Google Scholar
Johnson, R. et al. Drug-resistant tuberculosis epidemic in the Western Cape driven by a virulent Beijing genotype strain. Int. J. Tuberc. Lung Dis.14, 119–121 (2010). CASPubMed Google Scholar
Streicher, E.M. et al. Genotypic and phenotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from rural districts of the Western Cape Province of South Africa. J. Clin. Microbiol.42, 891–894 (2004). ArticleCASPubMedPubMed Central Google Scholar
Ioerger, T.R. et al. The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa. BMC Genomics11, 670 (2010). ArticleCASPubMedPubMed Central Google Scholar
Sun, G. et al. Dynamic population changes in Mycobacterium tuberculosis during acquisition and fixation of drug resistance in patients. J. Infect. Dis.10.1093/infdis/jis601 (2012).10.1093/infdis/jis601
European Concerted Action on New Generation Genetic Markers and Techniques for the Epidemiology and Control of Tuberculosis. Beijing/W genotype Mycobacterium tuberculosis and drug resistance. Emerg. Infect. Dis.12, 736–743 (2006).
Borrell, S. & Gagneux, S. Infectiousness, reproductive fitness and evolution of drug-resistant Mycobacterium tuberculosis. Int. J. Tuberc. Lung Dis.13, 1456–1466 (2009). CASPubMed Google Scholar
Hershberg, R. et al. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol.6, e311 (2008). ArticleCASPubMedPubMed Central Google Scholar
Comas, I. et al. Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat. Genet.42, 498–503 (2010). ArticleCASPubMedPubMed Central Google Scholar
Glynn, J.R., Whiteley, J., Bifani, P.J., Kremer, K. & Van Soolingen, D. Worldwide occurrence of Beijing/W strains of Mycobacterium tuberculosis: a systematic review. Emerg. Infect. Dis.8, 843–849 (2002). ArticlePubMedPubMed Central Google Scholar
Kato-Maeda, M. et al. Beijing sublineages of Mycobacterium tuberculosis differ in pathogenicity in the guinea pig. Clin. Vaccine Immunol.19, 1227–1237 (2012). ArticleCASPubMedPubMed Central Google Scholar
Drobniewski, F. et al. Drug-resistant tuberculosis, clinical virulence, and the dominance of the Beijing strain family in Russia. J. Am. Med. Assoc.293, 2726–2731 (2005). ArticleCAS Google Scholar
Coscolla, M. & Gagneux, S. Does M. tuberculosis genomic diversity explain disease diversity? Drug Discov. Today Dis. Mech.7, e43–e59 (2010). ArticleCASPubMedPubMed Central Google Scholar
de Jong, B.C. et al. Progression to active tuberculosis, but not transmission, varies by Mycobacterium tuberculosis lineage in The Gambia. J. Infect. Dis.198, 1037–1043 (2008). ArticlePubMed Google Scholar
Pang, Y. et al. Spoligotyping and drug resistance analysis of Mycobacterium tuberculosis strains from national survey in China. PLoS ONE7, e32976 (2012). ArticleCASPubMedPubMed Central Google Scholar
Vadwai, V., Shetty, A., Supply, P. & Rodrigues, C. Evaluation of 24-locus MIRU-VNTR in extrapulmonary specimens: study from a tertiary centre in Mumbai. Tuberculosis (Edinb.)92, 264–272 (2012). ArticleCAS Google Scholar
Huang, H.Y. et al. Mixed infection with Beijing and non-Beijing strains and drug resistance pattern of Mycobacterium tuberculosis. J. Clin. Microbiol.48, 4474–4480 (2010). ArticleCASPubMedPubMed Central Google Scholar
Taype, C.A. et al. Genetic diversity, population structure and drug resistance of Mycobacterium tuberculosis in Peru. Infect. Genet. Evol.12, 577–585 (2012). ArticleCASPubMed Google Scholar
Mestre, O. et al. Phylogeny of Mycobacterium tuberculosis Beijing strains constructed from polymorphisms in genes involved in DNA replication, recombination and repair. PLoS ONE6, e16020 (2011). ArticleCASPubMedPubMed Central Google Scholar
de Steenwinkel, J.E.M. et al. Drug susceptibility of Mycobacterium tuberculosis Beijing genotype and association with MDR TB. Emerg. Infect. Dis.18, 660–663 (2012). ArticlePubMedPubMed Central Google Scholar
Werngren, J. Drug-susceptible Mycobacterium tuberculosis Beijing genotype does not develop mutation-conferred resistance to rifampin at an elevated rate. J. Clin. Microbiol.41, 1520–1524 (2003). ArticleCASPubMedPubMed Central Google Scholar
Luria, S.E. & Delbrück, M. Mutations of bacteria from virus sensitivity to virus resistance. Genetics28, 491–511 (1943). CASPubMedPubMed Central Google Scholar
Lang, G.I. & Murray, A.W. Estimating the per-base-pair mutation rate in the yeast Saccharomyces cerevisiae. Genetics178, 67–82 (2008). ArticleCASPubMedPubMed Central Google Scholar
Stewart, F.M. Fluctuation tests: how reliable are the estimates of mutation rates? Genetics137, 1139–1146 (1994). CASPubMedPubMed Central Google Scholar
Stewart, F.M., Gordon, D.M. & Levin, B.R. Fluctuation analysis: the probability distribution of the number of mutants under different conditions. Genetics124, 175–185 (1990). CASPubMedPubMed Central Google Scholar
Akaike, H. A new look at the statistical model identification. IEEE Trans. Automat. Contr.19, 716–723 (1974). Article Google Scholar
Burnham, K.P. Multimodel inference: understanding AIC and BIC in model selection. Sociol. Methods Res.33, 261–304 (2004). Article Google Scholar
Bergval, I.L., Schuitema, A.R.J., Klatser, P.R. & Anthony, R.M. Resistant mutants of Mycobacterium tuberculosis selected in vitro do not reflect the in vivo mechanism of isoniazid resistance. J. Antimicrob. Chemother.64, 515–523 (2009). ArticleCASPubMedPubMed Central Google Scholar
Gardy, J.L. et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N. Engl. J. Med.364, 730–739 (2011). ArticleCASPubMed Google Scholar
Drummond, A.J., Suchard, M.A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol.29, 1969–1973 (2012). ArticleCASPubMedPubMed Central Google Scholar
Walker, T.M. et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect. Dis.13, 137–146 (2013). ArticleCASPubMedPubMed Central Google Scholar
Colijn, C., Cohen, T., Ganesh, A. & Murray, M.B. Spontaneous emergence of multiple drug resistance in tuberculosis before and during therapy. PLoS ONE6, e18327 (2011). ArticleCASPubMedPubMed Central Google Scholar
Portevin, D., Gagneux, S., Comas, I. & Young, D.B. Human macrophage responses to clinical isolates from the Mycobacterium tuberculosis complex discriminate between ancient and modern lineages. PLoS Pathog.7, e1001307 (2011). ArticleCASPubMedPubMed Central Google Scholar
Rocha, E.P.C. et al. Comparisons of d_N_/d_S_ are time dependent for closely related bacterial genomes. J. Theor. Biol.239, 226–235 (2006). ArticleCASPubMed Google Scholar
Hall, L.M.C. & Henderson-Begg, S.K. Hypermutable bacteria isolated from humans—a critical analysis. Microbiology152, 2505–2514 (2006). ArticleCASPubMed Google Scholar
Blázquez, J. Hypermutation as a factor contributing to the acquisition of antimicrobial resistance. Clin. Infect. Dis.37, 1201–1209 (2003). ArticlePubMed Google Scholar
Oliver, A., Cantón, R., Campo, P., Baquero, F. & Blázquez, J. High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection. Science288, 1251–1254 (2000). ArticleCASPubMed Google Scholar
Mizrahi, V. & Andersen, S.J. DNA repair in Mycobacterium tuberculosis. What have we learnt from the genome sequence? Mol. Microbiol.29, 1331–1339 (1998). ArticleCASPubMed Google Scholar
Springer, B. et al. Lack of mismatch correction facilitates genome evolution in mycobacteria. Mol. Microbiol.53, 1601–1609 (2004). ArticleCASPubMed Google Scholar
Fallow, A., Domenech, P. & Reed, M.B. Strains of the East Asian (W/Beijing) lineage of Mycobacterium tuberculosis are DosS/DosT-DosR two-component regulatory system natural mutants. J. Bacteriol.192, 2228–2238 (2010). ArticleCASPubMedPubMed Central Google Scholar
Huet, G. et al. A lipid profile typifies the Beijing strains of Mycobacterium tuberculosis: identification of a mutation responsible for a modification of the structures of phthiocerol dimycocerosates and phenolic glycolipids. J. Biol. Chem.284, 27101–27113 (2009). ArticleCASPubMedPubMed Central Google Scholar
Schmalstieg, A.M. et al. The antibiotic resistance arrow of time: efflux pump induction is a general first step in the evolution of mycobacterial drug resistance. Antimicrob. Agents Chemother.56, 4806–4815 (2012). ArticleCASPubMedPubMed Central Google Scholar
Louw, G.E. et al. Rifampicin reduces susceptibility to ofloxacin in rifampicin resistant Mycobacterium tuberculosis through efflux. Am. J. Respir. Crit. Care Med.184, 269–276 (2011). ArticleCASPubMed Google Scholar
Adams, K.N. et al. Drug tolerance in replicating mycobacteria mediated by a macrophage-induced efflux mechanism. Cell145, 39–53 (2011). ArticleCASPubMedPubMed Central Google Scholar
Comas, I. et al. Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nat. Genet.44, 106–110 (2012). ArticleCAS Google Scholar
Williams, K. et al. Sterilizing activities of novel combinations lacking first- and second-line drugs in a murine model of tuberculosis. Antimicrob. Agents Chemother.56, 3114–3120 (2012). ArticleCASPubMedPubMed Central Google Scholar
Lienhardt, C. et al. New drugs for the treatment of tuberculosis: needs, challenges, promise, and prospects for the future. J. Infect. Dis.205, S241–S249 (2012). ArticlePubMed Google Scholar
Menzies, D. et al. Standardized treatment of active tuberculosis in patients with previous treatment and/or with mono-resistance to isoniazid: a systematic review and meta-analysis. PLoS Med.6, e1000150 (2009). ArticleCASPubMedPubMed Central Google Scholar
Gelmanova, I.Y. et al. Barriers to successful tuberculosis treatment in Tomsk, Russian Federation: non-adherence, default and the acquisition of multidrug resistance. Bull. World Health Organ.85, 703–711 (2007). ArticleCASPubMedPubMed Central Google Scholar
Seung, K.J. et al. The effect of initial drug resistance on treatment response and acquired drug resistance during standardized short-course chemotherapy for tuberculosis. Clin. Infect. Dis.39, 1321–1328 (2004). ArticleCASPubMed Google Scholar
Helb, D. et al. Rapid detection of Mycobacterium tuberculosis and rifampin resistance by use of on-demand, near-patient technology. J. Clin. Microbiol.48, 229–237 (2010). ArticleCASPubMed Google Scholar
Weyer, K. Laboratory Services in Tuberculosis Control. Part II: Microscopy (World Health Organization, Geneva, 1998).
Dowdy, D.W., Basu, S. & Andrews, J.R. Is passive diagnosis enough? The impact of subclinical disease on diagnostic strategies for tuberculosis. Am. J. Respir. Crit. Care Med.187, 543–551 (2013). ArticlePubMedPubMed Central Google Scholar
Shaw, J.B. & Wynn-Williams, N. Infectivity of pulmonary tuberculosis in relation to sputum status. Am. Rev. Tuberc.69, 724–732 (1954). CASPubMed Google Scholar
Tsolaki, A.G. et al. Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains. Proc. Natl. Acad. Sci. USA101, 4865–4870 (2004). ArticleCASPubMedPubMed Central Google Scholar
Gagneux, S. The competitive cost of antibiotic resistance in Mycobacterium tuberculosis. Science312, 1944–1946 (2006). ArticleCASPubMed Google Scholar