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Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance

Nature Genetics volume 45, pages 1255–1260 (2013)Cite this article

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Abstract

The worldwide emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis threatens to make this disease incurable1,2. Drug resistance mechanisms are only partially understood3,4,5, and whether the current understanding of the genetic basis of drug resistance in M. tuberculosis is sufficiently comprehensive remains unclear. Here we sequenced and analyzed 161 isolates with a range of drug resistance profiles, discovering 72 new genes, 28 intergenic regions (IGRs), 11 nonsynonymous SNPs and 10 IGR SNPs with strong, consistent associations with drug resistance. On the basis of our examination of the dN/dS ratios of nonsynonymous to synonymous SNPs among the isolates6,7,8, we suggest that the drug resistance–associated genes identified here likely contain essentially all the nonsynonymous SNPs that have arisen as a result of drug pressure in these isolates and should thus represent a near-complete set of drug resistance–associated genes for these isolates and antibiotics. Our work indicates that the genetic basis of drug resistance is more complex than previously anticipated and provides a strong foundation for elucidating unknown drug resistance mechanisms.

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Figure 1: Phylogenetic analysis of M. tuberculosis isolates.
Figure 2: Genomic locations of the 85 drug resistance–associated genes.
Figure 3: IGR SNPs alter the expression level of downstream genes.
Figure 4: The 84 drug resistance–associated protein-encoding genes identified in this study contain essentially all the nonsynonymous SNPs that have arisen as a result of drug pressure in this set of isolates and antibiotics.

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Acknowledgements

We would like to thank S.M. Wang for helpful discussions and input and the anonymous reviewers for their constructive comments. We thank D. Chatterji (Indian Institute of Science) for the pSD5B vector. L.B. was supported by the National Natural Science Foundation of China (grant 31170132), the National Basic Research Program of China (grants 2009CB825402 and 2012CB518703), the Chinese Academy of Sciences (grant KSZD-EW-Z-006) and the Key Project Specialized for Infectious Diseases of the Chinese Ministry of Health (grants 2012ZX10003002 and 2013ZX10003006).

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Author notes

  1. Hongtai Zhang, Dongfang Li, Lili Zhao and Joy Fleming: These authors contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China

    Hongtai Zhang, Joy Fleming, Ting Wang, Nicholas Galwey, Ying Zhou, Yunrong Gao, Ming Wang, Haiying Hang, Jia Zhang & Lijun Bi

  2. State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China

    Hongtai Zhang & Xian-En Zhang

  3. BGI-Shenzhen, Shenzhen, China

    Dongfang Li, Zhangyi Liu, Yuanfang Zhu, Tong Wang, Yufen Huang, Ruifu Yang & Jun Wang

  4. Shenzhen Key Laboratory of Unknown Pathogen Identification, Shenzhen, China

    Dongfang Li

  5. National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China

    Lili Zhao & Kanglin Wan

  6. State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China

    Lili Zhao & Kanglin Wan

  7. College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China

    Nan Lin & Shihua Wang

  8. Beijing Chest Hospital, Capital Medical University, Beijing, China

    Chuanyou Li

  9. State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China

    Jiaoyu Deng & Xian-En Zhang

  10. Center for Tuberculosis Control of Guangdong Province, Guangzhou, China

    Qiu Zhong, Lin Zhou & Tao Chen

  11. The Fourth People's Hospital, Foshan City, China

    Jie Zhou

  12. Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China

    Guofeng Zhu

  13. Heilongjiang Center for Tuberculosis Control and Prevention, Harbin, China

    Fabin Li

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  1. Hongtai Zhang
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Contributions

H.Z. conducted the experiments. D.L., J.F., H.Z., N.L., Y.H., Z.L., Y. Zhu, S.W., M.W., Y. Zhou, J.D., J.W., R.Y., G.Z., N.G., H.H., L. Zhao, J. Zhou and J. Zhang contributed to data analysis. K.W., L. Zhao, C.L., Q.Z., L. Zhou, T.C. and F.L. collected the isolates. Y.G., H.Z., L. Zhao, N.L. and T.C. cultured the isolates and prepared DNA samples. Tong Wang performed genome sequencing and assembly. H.Z. and Ting Wang performed the IGR promoter experiments. J.F. and H.Z. wrote and revised the manuscript. X.-E.Z. directed part of the work, and L.B. conceived, designed and provided overall direction for the project.

Corresponding authors

Correspondence to Kanglin Wan, Jun Wang, Xian-En Zhang or Lijun Bi.

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Zhang, H., Li, D., Zhao, L. et al. Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance. Nat Genet 45, 1255–1260 (2013). https://doi.org/10.1038/ng.2735

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