title: Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints.
abstract: 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.
  
  
  RESULTS
  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.
authors.affiliation: Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany. sniemann@fz-borstel.de
authors.forename: Stefan
authors.initials: S
authors.lastname: Niemann
authors.forename: Claudio U
authors.initials: CU
authors.lastname: Köser
authors.forename: Sebastien
authors.initials: S
authors.lastname: Gagneux
authors.forename: Claudia
authors.initials: C
authors.lastname: Plinke
authors.forename: Susanne
authors.initials: S
authors.lastname: Homolka
authors.forename: Helen
authors.initials: H
authors.lastname: Bignell
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Carter
authors.forename: R Keira
authors.initials: RK
authors.lastname: Cheetham
authors.forename: Anthony
authors.initials: A
authors.lastname: Cox
authors.forename: Niall A
authors.initials: NA
authors.lastname: Gormley
authors.forename: Paula
authors.initials: P
authors.lastname: Kokko-Gonzales
authors.forename: Lisa J
authors.initials: LJ
authors.lastname: Murray
authors.forename: Roberto
authors.initials: R
authors.lastname: Rigatti
authors.forename: Vincent P
authors.initials: VP
authors.lastname: Smith
authors.forename: Felix P M
authors.initials: FP
authors.lastname: Arends
authors.forename: Helen S
authors.initials: HS
authors.lastname: Cox
authors.forename: Geoff
authors.initials: G
authors.lastname: Smith
authors.forename: John A C
authors.initials: JA
authors.lastname: Archer
mesh_terms: D000995:Antitubercular Agents / Q000627:therapeutic use; D015373:Bacterial Typing Techniques / Q000379:methods; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000235:genetics*; D016172:DNA Fingerprinting / Q000379:methods; D030541:Databases, Genetic; D024881:Drug Resistance, Bacterial; D018432:Drug Resistance, Multiple; D017353:Gene Deletion; D005821:Genetic Techniques; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000378:metabolism*; D014376:Tuberculosis / Q000235:genetics / Q000382:microbiology
chemical_list: D000995:Antitubercular Agents; D004247:DNA