|
|
PLoS One. 2009; 4(10): e7407. Published online 2009 October 12. doi: 10.1371/journal.pone.0007407. | PMCID: PMC2756628 |
Copyright Niemann et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Genomic Diversity among Drug Sensitive and Multidrug Resistant Isolates of Mycobacterium tuberculosis with Identical DNA Fingerprints Stefan Niemann,#1* Claudio U. Köser,#2 Sebastien Gagneux,3 Claudia Plinke,1 Susanne Homolka,1 Helen Bignell,4 Richard J. Carter,4 R. Keira Cheetham,4 Anthony Cox,4 Niall A. Gormley,4 Paula Kokko-Gonzales,4 Lisa J. Murray,4 Roberto Rigatti,4 Vincent P. Smith,4 Felix P. M. Arends,2 Helen S. Cox,5 Geoff Smith,4 and John A. C. Archer2 1Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany 2Department of Genetics, University of Cambridge, Cambridge, United Kingdom 3Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom 4Illumina Cambridge Limited, Chesterford Research Park, Little Chesterford, Essex, United Kingdom 5Burnet Institute for Medical Research and Public Health, Melbourne, Australia Niyaz Ahmed, Editor University of Hyderabad, India Received July 2, 2009; Accepted September 4, 2009. Background Mycobacterium tuberculosis complex (MTBC), the causative agent of tuberculosis (TB), is characterized by low sequence diversity making this bacterium one of the classical examples of a genetically monomorphic pathogen. Because of this limited DNA sequence variation, routine genotyping of clinical MTBC isolates for epidemiological purposes relies on highly discriminatory DNA fingerprinting methods based on mobile and repetitive genetic elements. According to the standard view, isolates exhibiting the same fingerprinting pattern are considered direct progeny of the same bacterial clone, and most likely reflect ongoing transmission or disease relapse within individual patients. Methodology/Principal Findings Here we further investigated this assumption and used massively parallel whole-genome sequencing to compare one drug-susceptible (K-1) and one multidrug resistant (MDR) isolate (K-2) of a rapidly spreading M. tuberculosis Beijing genotype clone from a high incidence region (Karakalpakstan, Uzbekistan). Both isolates shared the same IS6110 RFLP pattern and the same allele at 23 out of 24 MIRU-VNTR loci. We generated 23.9 million (K-1) and 33.0 million (K-2) paired 50 bp purity filtered reads corresponding to a mean coverage of 483.5 fold and 656.1 fold respectively. Compared with the laboratory strain H37Rv both Beijing isolates shared 1,209 SNPs. The two Beijing isolates differed by 130 SNPs and one large deletion. The susceptible isolate had 55 specific SNPs, while the MDR variant had 75 specific SNPs, including the five known resistance-conferring mutations. Conclusions Our results suggest that M. tuberculosis isolates exhibiting identical DNA fingerprinting patterns can harbour substantial genomic diversity. Because this heterogeneity is not captured by traditional genotyping of MTBC, some aspects of the transmission dynamics of tuberculosis could be missed or misinterpreted. Furthermore, a valid differentiation between disease relapse and exogenous reinfection might be impossible using standard genotyping tools if the overall diversity of circulating clones is limited. These findings have important implications for clinical trials of new anti-tuberculosis drugs. Tuberculosis (TB) is primarily a symptom of poverty and inequality [1], [2], which accounts for its uninterrupted prevalence in most parts of the world [3]. This disparity in TB burden is further exacerbated by the widespread emergence of antibiotic resistance [4]. In Eastern Europe, all of these factors coincide. In Karakalpakstan (Uzbekistan) multi-drug resistant (MDR) Mycobacterium tuberculosis complex (Mtb) strains infect up to 22% of patients never treated and up to 60% of those previously treated [3], [4], [5]. Therefore the most effective antibiotics with the fewest side-effects, isoniazid (INH) and rifampicin (RMP), must, in MDR TB, be replaced by less-effective, more expensive, and more toxic substitutes. In addition to the socio-economic, environmental, and host genetic determinants [6], strain genetic diversity in Mtb appears to play a more important role than previously believed [7], [8], [9], [10]. Mtb comprises several phylogenetic lineages, some of which have been shown to significantly impact progression from infection to active tuberculosis as well as disease manifestation [11], [12], [13]. In Karakalpakstan and other parts of Eastern Europe, the so-called Beijing lineage of Mtb is mostly responsible for the ongoing MDR epidemic [14]. Some members of this strain lineage have been reported to be hypervirulent in animal models [15], and others have been associated with large outbreaks and extensive transmission of MDR TB in various regions of the world [7], [16], [17]. These findings contradict previous assumptions that resistant Mtb strains in general have a reduced fitness. The fact that MDR variants can even have an enhanced fitness when compared with susceptible progenitor strains, points to the phenomenon of compensatory evolution that can reverse adverse effects on bacterial fitness [18], [19]. Even though genetic diversity appears to influence virulence and immunogenicity of strain of different phylogenetic lineages [9], the overall level of sequence variation in Mtb is low and Mtb is considered to represent the “upper limit of what might be considered genetically monomorphic” [20]. Whole genome comparisons of M. tuberculosis and M. bovis, another species of the M. tuberculosis complex, revealed a maximum diversity of just 2,500 SNPs [21]. M. tuberculosis isolates of the same clone or strain (e.g. characterised by IS 6110 genotyping) are generally considered to be identical and belong to the same outbreak or recent chain of transmission [22]. However, the real level of genomic diversity in rapidly expanding clones from high incidence settings has not been assessed. To address this question, we have applied massively paralleled whole-genome sequencing [23] to two clinical isolates from Karakalpakstan. These isolates were virtually identical with respect to all standard TB genotyping markers, including IS 6110 RFLP, which is the most discriminating test of all standard molecular TB typing tools in use today [22] (). The two isolates, K-1 and K-2, differed in only 1 of 24 Mycobacterial Interspersed Repetitive Units. However, whilst K-1 was fully drug-susceptible, K-2 was resistant to all first line drugs (INH, RMP, ethambutol (EMB), pyrazinamide (PZA) and streptomycin (SM)). Both isolates were part of a large cluster of closely related organisms termed the Beijing K-family that encompasses the dominant, expanding Mtb variant in the region [unpublished results,14]. Genome coverage We generated 23.9 million (K-1) and 33.0 million (K-2) paired 50 bp purity filtered reads corresponding to a mean coverage of 483.5 fold and 656.1 fold respectively which we compared to the genome of the M. tuberculosis reference strain H37Rv (ATCC 27294) [24]. To differentiate true differences from sequencing errors in the original H37Rv reference sequence ( File S1), we also generated 2.7 Gb of sequence data from strain H37Rv (26.7 million paired 50 bp reads, 538.5-fold coverage). The fraction of the H37Rv genome that could not be covered (approximately 2.0%) comprised DNA with a GC content >80% and repeat regions (such as IS 6110 elements) whose sequence could not be uniquely aligned to the reference. This fraction increased to 4.8% for K-1 and 3.4% for K-2 to exclude any areas for which no valid base was called due to insertion or deletions. All the genetic changes we identified are correlated with the existing scientific literature and listed in detail in the Supplementary Information ( File S1). In addition to a tabular output of our results ( File S2) a flexible, graphical representation using Artemis [25] is provided ( Files S3- S6) to allow an exploration of these changes in their genomic context. Errors in reference genome Re-sequencing of H37Rv uncovered 80 SNPs with respect to the published reference genome. 74 SNPs were shared with the Beijing isolates sequenced in this study (), all of which were also detected in one or more studies of H37Ra, the avirulent form of H37 ( File S1), by the following different experimental methodologies: a microarray-based comparative approach [26], re-sequencing [27] and a complete genome sequence ( CP000611.1) from a shotgun library [28]. In contrast, the 6 H37Rv specific SNPs did not feature in any of these studies. Re-examination of the electropherograms of the original H37Rv sequence revealed that 44 of these SNPs were errors in the reference strain H37Rv data ( File S1). The remaining differences might represent micro-evolutionary events that occurred while culturing of the different H37 variants in separate laboratories. Genomic diversity Next, we compared K-1 and K-2 to H37Rv. Both Beijing isolates shared a common pool of 1,209 single-nucleotide-polymorphisms (SNPs) () and five large scale deletions compared to H37Rv ( Table 1). These Beijing-specific differences were congruent with a set of variants reported previously ( File S1). An overview about all previously described SNPs is given in File S1. We found that the majority of the SNPs in K-1 and K-2 were non-synonymous (57% in both cases), which confirms previous findings [29] and is consistent with reduced purifying selection acting on Mtb [10] (). | Table 1Large chromosomal deletions detected in both Beijing isolates K-1 and K-2 [57]. |
In addition to this common backbone of Beijing specific variation, we identified 130 SNPs and one deletion that differentiated K-1 and K-2 ( and ), although both isolates were identical with respect to IS 6110 typing (). Compared to H37Rv, the susceptible isolate K-1 encoded 55 specific SNPs and one specific deletion, while the MDR variant K-2 had 75 specific SNPs, including the five resistance-conferring mutations in the katG, rpoB, embB, pncA, and rpsL genes that are known to be altered in resistance to INH, RIF, EMB, PZA, and SM, respectively [30] ( Table 2, ). Importantly, the observed level of diversity was independent of the MDR phenotype of K-2, as we detected comparable numbers of SNPs in both the drug-susceptible K-1 and the MDR K-2. | Table 2SNPs in K-2 responsible for antibiotic resistances. |
We then investigated the diversity between different lineages. Despite the fact that the total number of differences we observed between the Beijing isolates K-1/K-2 and the laboratory strain H37Rv was in the same range of the DNA variation described earlier between H37Rv and the clinical strain CDC1551 [29], a comparison to the whole genome sequences of CDC1551 ( AE000516.2), F11 ( CP000717.1) and M. bovis ( BX248333.1) revealed that more than half of the SNPs in K-1 were in fact unique to the Beijing genotype (). Early sequencing studies of M. tuberculosis showed an extremely high level of clonality and conservation [31], [32]. As a consequence, standard molecular markers that are based on mobile or repetitive elements (IS 6110 RFLP, spoligotyping and MIRU-VNTR typing) are presumed to provide a high enough discriminatory power to accurately reconstruct transmission chains as part of epidemiological studies. Based on these standard criteria, our isolates K-1 and K-2 that exhibit the same molecular fingerprint can be considered as belonging to the same “outbreak clone” that is rapidly expanding in the study area by extensive transmission [22]. Therefore, we expected to find a low amount of genetic diversity. By contrast, we observed a strikingly high genomic diversity among two isolates sharing the same DNA fingerprint. These findings challenge the “identical fingerprints – same strain” dogma and have important implications for the investigation of disease dynamics, especially in high incidence regions such as Eastern Europe where the Beijing genotype is dominant and the population diversity (e.g. among MDR strains) is significantly reduced [unpublished results,14,33]. The fact that strains with identical genotyping patterns can accumulate significant amounts of genetic diversity indicates that epidemiological links between isolates with identical genotyping data can be more remote and are likely to represent older transmission events rather than cases of recent transmission among patients in one RFLP cluster. Under these circumstances, a valid differentiation of relapse and re-infection, that can occur in significant numbers in TB patients undergoing standard treatment in areas with high rates of MDR [34], might not be possible by applying traditional genotyping. One of the key objectives of molecular epidemiology in TB is to distinguish treatment failure/relapse with the same strain from exogenous reinfection with a second strain. This is particularly important given the emergence of MDR and extensively-drug resistant (XDR) TB in many parts of the world [4], [35], [36]. If a TB patient fails treatment, this indicates that the infecting strain might have become drug-resistant, or that the treatment is not effective, for example because of a lack of patient compliance. In the case of clinical trials where new TB drugs are being evaluated, treatment failure may suggest poor drug performance. Large amounts of resources are now being invested into the development of new drugs against TB [3]. Some of these new drug candidates are entering human trials. If during these trials treatment failures are not adequately differentiated from cases of exogenous re-infection, promising new drug candidates may be abandoned erroneously. A large genetic diversity among closely related isolates of Mtb has also implications for our understanding of the evolution of drug resistance. A recent report detected only few differences when comparing the genomes of MDR and XDR Mtb strains from KwaZulu-Natal, South Africa to an isogenic drug-susceptible isolate (11 unique SNPs in the MDR and 15 in the DS and XDR, respectively) [37], [38]; the authors concluded that the evolution of drug resistance might be relatively easy to study [38]. We have previously shown that the fitness of drug-resistant Mtb depends both on the specific drug-resistance-conferring mutations and strain genetic backgrounds, and that compensatory mutations might mitigate the potential deleterious effects of drug resistance on bacterial fitness [8], [18]. Some of the strain specific mutations in K-2 might represent mutations which are compensating for putative fitness effects of the drug resistance-conferring mutations. However, more work is needed to explore this possibility. Finally, the high number of novel SNPs that are unique to the Beijing lineage confirmed that previously sequenced genomes only sampled a small part of the global diversity of Mtb [9]. These findings highlight the importance of current sequencing efforts to capture the full global diversity of Mtb to ensure that both antibiotics and vaccines that are currently undergoing clinical trials [3] are efficacious against all strains. In conclusion, our results showed that genomic diversity in closely related strains of Mtb may be greater than anticipated. Clonal variants can accumulate high levels of genomic diversity, which can lead to different pathogenic properties undetectable by standard genotyping [27]. Methods to accurately index strain diversity are essential for TB control, especially for the evaluation of new drugs, diagnostics and vaccines. Whole genome sequencing is likely to become available soon for routine molecular epidemiology at comparable costs to traditional typing techniques [39]. Instead of having to rely on molecular surrogates with a limited resolution, such an approach would be highly informative both by giving a more accurate picture of ongoing tuberculosis transmission and related epidemiological outcomes such as re-infection and mixed infections, as well as by shedding light on the microevolutionary processes occurring in M. tuberculosis during spread. In clinical settings, such an approach could allow for rapid detection of drug-resistant TB and enhanced disease surveillance. K-1 was isolated from sputum in 11/2001 and K-2 in 09/2004. IS 6110 RFLP fingerprints, spoligotype patterns and MIRU-VNTR profiles were determined as previously described [40], [41], [42], [43]. Antibiotic resistance was determined with the BACTEC MGIT 960 [44], [45]. ~200 bp paired read fragment libraries were prepared from 1 µg of DNA, and sequenced using the Illumina Genome Analyzer as described previously [23]. SNPs were mapped by paired short read alignment of individual reads to their cognate positions in the M. tuberculosis H37Rv genome ( AL123456.2) and called at threshold ≥100 with the Illumina Genome Analyzer Pipeline. Where more than one base was called, only the majority call was accepted when the ratio between the two calls was ≥3. Only positions for which valid base calls were available in all genomes were considered for our assessment of the diversity. The validity of the SNP calls was confirmed by 40 kb of dideoxy chain terminator sequencing (ABI 3130xl) of each isolate. Deletions ≥250 bp were detected using combined paired read data and localised homology mapping across the deletion boundary. Details of the annotation used for the SNP analysis and the graphical representation of the tabular results ( File S2) with Artemis [25] ( Files S3- 6) can be found in the Supplementary Methods ( File S1). File S1 Description of supplementary information Supplementary Tables and Figures as well as Supplementary Methods and Results (1.07 MB PDF) File S2 Supplementary information - Excel file with all SNPs detected (0.30 MB ZIP) File S3 Contains the H37Rv genome ( AL123456.2) and TubercuList R11 annotation, necessary for the graphical representation of all SNPs. (1.96 MB ZIP) File S4 contains the graphical representation of SNPs in H37Rv (0.05 MB ZIP) File S5 Contains the graphical representation of SNPs in K-1 (Section 2.2). (0.05 MB ZIP) File S6 Contains the graphical representation of SNPs in K-2 (Section 2.2). (0.05 MB ZIP) The authors would like to thank I. Radzio, T. Ubben and P. Vock for technical assistance and both national and expatriate staff of Médecins Sans Frontières in Karakalpakstan. Furthermore, M. Cahill, E. Chan, T. Dos Vultos, A. Edwards, S. Godbole, K. Holt, R. Krause, C. Larsen, X. Liu, A. Motiwala, A. Pain, J. Parkhill and K. Rutherford contributed at various stages. We thank P. Supply for critical reading of the manuscript. To N.A.M. 1. Farmer PE, Nizeye B, Stulac S, Keshavjee S. Structural violence and clinical medicine. PLoS Med. 2006;3:e449. [PubMed] 2. Keshavjee S, Gelmanova IY, Pasechnikov AD, Mishustin SP, Andreev YG, et al. Treating multidrug-resistant tuberculosis in Tomsk, Russia: developing programs that address the linkage between poverty and disease. Ann N Y Acad Sci. 2008;1136:1–11. [PubMed] 3. World Health Organization. Geneva: World Health Organization; 2007. WHO Report 2007: Global Tuberculosis Control - Surveillance, Planning, Financing. 4. World Health Organization. Anti-Tuberculosis Drug Resistance In the World. 2008. Report Number 4. Geneva: World Health Organization. 5. Cox HS, Orozco JD, Male R, Ruesch-Gerdes S, Falzon D, et al. Multidrug-resistant tuberculosis in central Asia. Emerg Infect Dis. 2004;10:865–872. [PubMed] 6. Hill AV. Aspects of genetic susceptibility to human infectious diseases. Annu Rev Genet. 2006;40:469–486. [PubMed] 7. Wirth T, Hildebrand F, Allix-Beguec C, Wolbeling F, Kubica T, et al. Origin, spread and demography of the Mycobacterium tuberculosis complex. PLoS Pathog. 2008;4:e1000160. [PubMed] 8. Gagneux S, DeRiemer K, Van T, Kato-Maeda M, de Jong BC, et al. Variable host-pathogen compatibility in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2006;103:2869–2873. [PubMed] 9. Gagneux S, Small PM. Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect Dis. 2007;7:328–337. [PubMed] 10. Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, et al. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol. 2008;6:e311. [PubMed] 11. Caws M, Thwaites G, Dunstan S, Hawn TR, Lan NT, et al. The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis. PLoS Pathog. 2008;4:e1000034. [PubMed] 12. de Jong BC, Hill PC, Aiken A, Awine T, Antonio M, et al. Progression to active tuberculosis, but not transmission, varies by Mycobacterium tuberculosis lineage in The Gambia. J Infect Dis. 2008;198:1037–1043. [PubMed] 13. Thwaites G, Caws M, Chau TT, D'Sa A, Lan NT, et al. Relationship between Mycobacterium tuberculosis genotype and the clinical phenotype of pulmonary and meningeal tuberculosis. J Clin Microbiol. 2008;46:1363–1368. [PubMed] 14. Cox HS, Kubica T, Doshetov D, Kebede Y, Rusch-Gerdess S, et al. The Beijing genotype and drug resistant tuberculosis in the Aral Sea region of Central Asia. Respir Res. 2005;6:134. [PubMed] 15. Reed MB, Domenech P, Manca C, Su H, Barczak AK, et al. A glycolipid of hypervirulent tuberculosis strains that inhibits the innate immune response. Nature. 2004;431:84–87. [PubMed] 16. Cowley D, Govender D, February B, Wolfe M, Steyn L, et al. Recent and rapid emergence of W-Beijing strains of Mycobacterium tuberculosis in Cape Town, South Africa. Clin Infect Dis. 2008;47:1252–1259. [PubMed] 17. Glynn JR, Whiteley J, Bifani PJ, Kremer K, van Soolingen D. Worldwide occurrence of Beijing/W strains of Mycobacterium tuberculosis: a systematic review. Emerg Infect Dis. 2002;8:843–849. [PubMed] 18. Gagneux S, Long CD, Small PM, Van T, Schoolnik GK, et al. The competitive cost of antibiotic resistance in Mycobacterium tuberculosis. Science. 2006;312:1944–1946. [PubMed] 19. Maisnier-Patin S, Andersson D. Adaptation to the deleterious effects of antimicrobial drug resistance mutations by compensatory evolution. Res Microbiol. 2004;155:360–369. [PubMed] 20. Achtman M. Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens. Annu Rev Microbiol. 2008;62:53–70. [PubMed] 21. Garnier T, Eiglmeier K, Camus J, Medina N, Mansoor H, et al. The complete genome sequence of Mycobacterium bovis. Proc Natl Acad Sci U S A. 2003;100:7877–7882. [PubMed] 22. Van Soolingen D, Kremer K, Vynycky E. New perspectives in the molecular epidemiology of tuberculosis. In: Kaufmann S, Hahn H, editors. Mycobacteria and TB. Berlin: Karger; 2003. pp. 17–45. 23. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456:53–59. [PubMed] 24. Cole ST, Barrell BG. Analysis of the genome of Mycobacterium tuberculosis H37Rv. Novartis Found Symp. 1998;217:160–172; discussion 172–167. [PubMed] 25. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, et al. Artemis: sequence visualization and annotation. Bioinformatics. 2000;16:944–945. [PubMed] 26. Frigui W, Bottai D, Majlessi L, Monot M, Josselin E, et al. Control of M. tuberculosis ESAT-6 secretion and specific T cell recognition by PhoP. PLoS Pathog. 2008;4:e33. [PubMed] 27. Lee JS, Krause R, Schreiber J, Mollenkopf HJ, Kowall J, et al. Mutation in the transcriptional regulator PhoP contributes to avirulence of Mycobacterium tuberculosis H37Ra strain. Cell Host Microbe. 2008;3:97–103. [PubMed] 28. Zheng H, Lu L, Wang B, Pu S, Zhang X, et al. Genetic basis of virulence attenuation revealed by comparative genomic analysis of Mycobacterium tuberculosis strain H37Ra versus H37Rv. PLoS ONE. 2008;3:e2375. [PubMed] 29. Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, et al. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol. 2002;184:5479–5490. [PubMed] 30. Zhang Y, Jacobs WRJ. Mechanisms of drug action, drug resistance and drug tolerance in Mycobacterium tuberculosis: Expected phenotypes from evolutionary pressures from a highly successful pathogen. In: Kaufmann SH, Rubin E, editors. Handbook of tuberculosis. Weinheim: Wiley-VCH Verlag; 2008. 31. Sreevatsan S, Pan X, Stockbauer K, Connell N, Kreiswirth B, et al. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci U S A. 1997;94:9869–9874. [PubMed] 32. Musser J, Amin A, Ramaswamy S. Negligible genetic diversity of mycobacterium tuberculosis host immune system protein targets: evidence of limited selective pressure. Genetics. 2000;155:7–16. [PubMed] 33. Pardini M, Niemann S, Varaine F, Iona E, Meacci F, et al. Characteristics of drug-resistant tuberculosis in Abkhazia (Georgia), a high-prevalence area in Eastern Europe. Tuberculosis (Edinb). 2009;89:317–324. [PubMed] 34. Cox H, Sibilia K, Feuerriegel S, Kalon S, Polonsky J, et al. Emergence of extensive drug resistance during treatment for multidrug-resistant tuberculosis. N Engl J Med. 2008;359:2398–2400. [PubMed] 35. Shah NS, Wright A, Bai GH, Barrera L, Boulahbal F, et al. Worldwide emergence of extensively drug-resistant tuberculosis. Emerg Infect Dis. 2007;13:380–387. [PubMed] 36. Zignol M, Hosseini MS, Wright A, Weezenbeek CL, Nunn P, et al. Global incidence of multidrug-resistant tuberculosis. J Infect Dis. 2006;194:479–485. [PubMed] 37. Jassal M, Bishai W. Extensively drug-resistant tuberculosis. Lancet Infect Dis. 2009;9:19–30. [PubMed] 38. Koenig R. Tuberculosis. Few mutations divide some drug-resistant TB strains. Science. 2007;318:901–902. [PubMed] 39. Service RF. Gene sequencing. The race for the ![[light shade]](/corehtml/pmc/pmcents/x2591.gif) 1000 genome. Science. 2006;311:1544–1546. [PubMed] 40. van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, et al. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol. 1993;31:406–409. [PubMed] 41. Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, et al. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol. 1997;35:907–914. [PubMed] 42. Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rusch-Gerdes 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. [PubMed] 43. Oelemann MC, Diel R, Vatin V, Haas W, Rusch-Gerdes S, et al. Assessment of an optimized mycobacterial interspersed repetitive- unit-variable-number tandem-repeat typing system combined with spoligotyping for population-based molecular epidemiology studies of tuberculosis. J Clin Microbiol. 2007;45:691–697. [PubMed] 44. Pfyffer GE, Palicova F, Rusch-Gerdes S. Testing of susceptibility of Mycobacterium tuberculosis to pyrazinamide with the nonradiometric BACTEC MGIT 960 system. J Clin Microbiol. 2002;40:1670–1674. [PubMed] 45. Bemer P, Palicova F, Rusch-Gerdes S, Drugeon HB, Pfyffer GE. Multicenter evaluation of fully automated BACTEC Mycobacteria Growth Indicator Tube 960 system for susceptibility testing of Mycobacterium tuberculosis. J Clin Microbiol. 2002;40:150–154. [PubMed] 46. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics. 2009;25:119–120. [PubMed] 47. Cole ST. Learning from the genome sequence of Mycobacterium tuberculosis H37Rv. FEBS Lett. 1999;452:7–10. [PubMed] 48. Zhang Y, Heym B, Allen B, Young D, Cole S. The catalase-peroxidase gene and isoniazid resistance of Mycobacterium tuberculosis. Nature. 1992;358:591–593. [PubMed] 49. Abe C, Kobayashi I, Mitarai S, Wada M, Kawabe Y, et al. Biological and molecular characteristics of Mycobacterium tuberculosis clinical isolates with low-level resistance to isoniazid in Japan. J Clin Microbiol. 2008;46:2263–2268. [PubMed] 50. Telenti A, Imboden P, Marchesi F, Lowrie D, Cole S, et al. Detection of rifampicin-resistance mutations in Mycobacterium tuberculosis. Lancet. 1993;341:647–650. [PubMed] 51. Telenti A, Philipp WJ, Sreevatsan S, Bernasconi C, Stockbauer KE, et al. The emb operon, a gene cluster of Mycobacterium tuberculosis involved in resistance to ethambutol. Nat Med. 1997;3:567–570. [PubMed] 52. Ramaswamy SV, Amin AG, Goksel S, Stager CE, Dou SJ, et al. Molecular genetic analysis of nucleotide polymorphisms associated with ethambutol resistance in human isolates of Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2000;44:326–336. [PubMed] 53. Scorpio A, Zhang Y. Mutations in pncA, a gene encoding pyrazinamidase/nicotinamidase, cause resistance to the antituberculous drug pyrazinamide in tubercle bacillus. Nat Med. 1996;2:662–667. [PubMed] 54. Lee KW, Lee JM, Jung KS. Characterization of pncA mutations of pyrazinamide-resistant Mycobacterium tuberculosis in Korea. J Korean Med Sci. 2001;16:537–543. [PubMed] 55. Chan RC, Hui M, Chan EW, Au TK, Chin ML, et al. Genetic and phenotypic characterization of drug-resistant Mycobacterium tuberculosis isolates in Hong Kong. J Antimicrob Chemother. 2007;59:866–873. [PubMed] 56. Nair J, Rouse D, Bai G, Morris S. The rpsL gene and streptomycin resistance in single and multiple drug-resistant strains of Mycobacterium tuberculosis. Mol Microbiol. 1993;10:521–527. [PubMed] 57. Tsolaki AG, Gagneux S, Pym AS, Goguet de la Salmoniere YO, Kreiswirth BN, et al. Genomic deletions classify the Beijing/W strains as a distinct genetic lineage of Mycobacterium tuberculosis. J Clin Microbiol. 2005;43:3185–3191. [PubMed]
|
This article has been 
