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

@article{Zhang2013GenomeSO,
  title={Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance},
  author={Hongtai Zhang and Dongfang Li and Li-li Zhao and Joy Fleming and Nan Lin and Tingting Wang and Zhangyi Liu and Chuanyou Li and Nicholas W. Galwey and Jiao-yu Deng and Ying Zhou and Yuanfang Zhu and Yun-rong Gao and Tong Wang and Shihua Wang and Yufen Huang and Ming Wang and Qiu Zhong and Lin Zhou and Tao Chen and Jie Zhou and Ruifu Yang and Guofeng Zhu and Haiying Hang and Jia Zhang and Fabin Li and Kanglin Wan and Jun Wang and Xian-En Zhang and Li-jun Bi},
  journal={Nature Genetics},
  year={2013},
  volume={45},
  pages={1255-1260}
}
The worldwide emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis threatens to make this disease incurable. Drug resistance mechanisms are only partially understood, 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… 
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References

SHOWING 1-10 OF 66 REFERENCES
Microevolution of extensively drug-resistant tuberculosis in Russia.
TLDR
Molecular fingerprinting of 2348 Mycobacterium tuberculosis isolates collected in Samara Oblast, Russia, revealed that 72% belonged to the Beijing lineage, a genotype associated with enhanced acquisition of drug resistance and increased virulence, indicating that XDR TB is currently not widely transmitted.
Genome Analysis of Multi- and Extensively-Drug-Resistant Tuberculosis from KwaZulu-Natal, South Africa
TLDR
Analysis of polymorphisms among the strains shows that well-known mutations are observed that are correlated with resistance to isoniazid, rifampicin, kanamycin, ofloxacin, ethambutol, and pyrazinamide, supporting the theory that this represents a case of clonal expansion.
Single Nucleotide Polymorphisms in Genes Associated with Isoniazid Resistance in Mycobacterium tuberculosis
TLDR
A variety of single nucleotide polymorphisms in multiple genes are found exclusively in INH-resistant clinical isolates, and these genes either are involved in mycolic acid biosynthesis or are overexpressed as a response to the buildup or cellular toxicity of INH.
Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes
TLDR
A set of compensatory mutations in the RNA polymerase genes of rifampicin-resistant M. tuberculosis strains harboringthese mutations showed a high competitive fitness in vitro and were associated with high fitness in vivo, as determined by examining their relative clinical frequency across patient populations.
Detection of Multidrug Resistance in Mycobacterium tuberculosis
TLDR
A DNA sequencing-based method used to detect mutations in the genome of drug-resistant Mycobacterium tuberculosis is useful for rapid detection of multiple-drug-resistant M. tuberculosis and for identifying novel mutations in drug- resistant M.culosis.
Detection of rifampicin-resistance mutations in Mycobacterium tuberculosis
Whole-Genome Comparison of Mycobacterium tuberculosis Clinical and Laboratory Strains
TLDR
Results demonstrate that polymorphisms among M. tuberculosis strains are more extensive than initially anticipated, and genetic variation may have an important role in disease pathogenesis and immunity.
Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug resistant tuberculosis
TLDR
Interventions to prevent the emergence of drug-resistant tuberculosis should target bacterial as well as treatment-related risk factors, as determined by whole-genome sequencing of clinical isolates.
Overexpression of the chromosomally encoded aminoglycoside acetyltransferase eis confers kanamycin resistance in Mycobacterium tuberculosis
TLDR
Results have important clinical implications in that clinical isolates determined to be resistant to kanamycin may not be cross-resistant to amikacin, as is often assumed.
Impact of Bacterial Genetics on the Transmission of Isoniazid-Resistant Mycobacterium tuberculosis
TLDR
The results show that in addition to host and environmental factors, strain genetic diversity can influence the transmission dynamics of drug-resistant bacteria.
...
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2
3
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...