title: Comparative genomic analysis of Mycobacterium tuberculosis clinical isolates.
abstract: BACKGROUND
  Due to excessive antibiotic use, drug-resistant Mycobacterium tuberculosis has become a serious public health threat and a major obstacle to disease control in many countries. To better understand the evolution of drug-resistant M. tuberculosis strains, we performed whole genome sequencing for 7 M. tuberculosis clinical isolates with different antibiotic resistance profiles and conducted comparative genomic analysis of gene variations among them.
  
  
  RESULTS
  We observed that all 7 M. tuberculosis clinical isolates with different levels of drug resistance harbored similar numbers of SNPs, ranging from 1409-1464. The numbers of insertion/deletions (Indels) identified in the 7 isolates were also similar, ranging from 56 to 101. A total of 39 types of mutations were identified in drug resistance-associated loci, including 14 previously reported ones and 25 newly identified ones. Sixteen of the identified large Indels spanned PE-PPE-PGRS genes, which represents a major source of antigenic variability. Aside from SNPs and Indels, a CRISPR locus with varied spacers was observed in all 7 clinical isolates, suggesting that they might play an important role in plasticity of the M. tuberculosis genome. The nucleotide diversity (Л value) and selection intensity (dN/dS value) of the whole genome sequences of the 7 isolates were similar. The dN/dS values were less than 1 for all 7 isolates (range from 0.608885 to 0.637365), supporting the notion that M. tuberculosis genomes undergo purifying selection. The Л values and dN/dS values were comparable between drug-susceptible and drug-resistant strains.
  
  
  CONCLUSIONS
  In this study, we show that clinical M. tuberculosis isolates exhibit distinct variations in terms of the distribution of SNP, Indels, CRISPR-cas locus, as well as the nucleotide diversity and selection intensity, but there are no generalizable differences between drug-susceptible and drug-resistant isolates on the genomic scale. Our study provides evidence strengthening the notion that the evolution of drug resistance among clinical M. tuberculosis isolates is clearly a complex and diversified process.
authors.forename: Fei
authors.initials: F
authors.lastname: Liu
authors.forename: Yongfei
authors.initials: Y
authors.lastname: Hu
authors.forename: Qi
authors.initials: Q
authors.lastname: Wang
authors.forename: Hong Min
authors.initials: HM
authors.lastname: Li
authors.forename: George F
authors.initials: GF
authors.lastname: Gao
authors.affiliation: CAS key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. liucuihua@im.ac.cn.
authors.forename: Cui Hua
authors.initials: CH
authors.lastname: Liu
authors.forename: Baoli
authors.initials: B
authors.lastname: Zhu
mesh_terms: D000328:Adult; D000368:Aged; D000995:Antitubercular Agents / Q000494:pharmacology; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D005260:Female; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D014644:Genetic Variation; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054643:INDEL Mutation; D008297:Male; D008875:Middle Aged; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D014376:Tuberculosis / Q000382:microbiology*; D018088:Tuberculosis, Multidrug-Resistant / Q000235:genetics; D055815:Young Adult
chemical_list: D000995:Antitubercular Agents