title: A single-step sequencing method for the identification of Mycobacterium tuberculosis complex species.
abstract: BACKGROUND
  The Mycobacterium tuberculosis complex (MTC) comprises closely related species responsible for strictly human and zoonotic tuberculosis. Accurate species determination is useful for the identification of outbreaks and epidemiological links. Mycobacterium africanum and Mycobacterium canettii are typically restricted to Africa and M. bovis is a re-emerging pathogen. Identification of these species is difficult and expensive.
  
  
  RESULTS
  The Exact Tandem Repeat D (ETR-D; alias Mycobacterial Interspersed Repetitive Unit 4) was sequenced in MTC species type strains and 110 clinical isolates, in parallel to reference polyphasic identification based on phenotype profiling and sequencing of pncA, oxyR, hsp65, gyrB genes and the major polymorphism tandem repeat. Inclusion of M. tuberculosis isolates in the expanding, antibiotic-resistant Beijing clone was determined by Rv0927c gene sequencing. The ETR-D (780-bp) sequence unambiguously identified MTC species type strain except M. pinnipedii and M. microti thanks to six single nucleotide polymorphisms, variable numbers (1-7 copies) of the tandem repeat and two deletions/insertions. The ETR-D sequencing agreed with phenotypic identification in 107/110 clinical isolates and with reference polyphasic molecular identification in all isolates, comprising 98 M. tuberculosis, 5 M. bovis BCG type, 5 M. canettii, and 2 M. africanum. For M. tuberculosis isolates, the ETR-D sequence was not significantly associated with the Beijing clone.
  
  
  CONCLUSIONS
  ETR-D sequencing allowed accurate, single-step identification of the MTC at the species level. It circumvented the current expensive, time-consuming polyphasic approach. It could be used to depict epidemiology of zoonotic and human tuberculosis, especially in African countries where several MTC species are emerging.
authors.affiliation: Unité des Rickettsies CNRS UMR6020, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France.
authors.forename: Zoheira
authors.initials: Z
authors.lastname: Djelouadji
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
authors.forename: Mamadou
authors.initials: M
authors.lastname: Daffé
authors.forename: Michel
authors.initials: M
authors.lastname: Drancourt
mesh_terms: D000818:Animals; D015373:Bacterial Typing Techniques / Q000379:methods*; D004269:DNA, Bacterial / Q000235:genetics; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics*; D010641:Phenotype; D011110:Polymorphism, Genetic / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods; D014376:Tuberculosis / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial