title: Molecular strain identification of the Mycobacterium tuberculosis complex in archival tissue samples.
abstract: OBJECTIVE
  To investigate the use of different molecular analyses that can identify distinct strains of human pathogenic mycobacteria in formalin fixed and paraffin wax embedded archival tissue samples to see whether it is possible to differentiate between the members of the Mycobacterium tuberculosis complex (M tuberculosis, M bovis, M africanum, M microti, or M canettii) and/or substrains in a high number of samples. This would be of interest for identifying individual infection traits and superinfection by different mycobacterial strains.
  
  
  METHODS
  Forty nine archival tissue samples with clinically and/or histologically suspected tuberculosis infection were subjected to molecular DNA analysis.
  
  
  RESULTS
  The molecular analysis revealed the presence of M tuberculosis complex DNA in 20 samples, whereas acid fast bacilli could be detected by Ziehl-Neelsen staining in only eight samples. All IS6110 positive samples were further characterised by spoligotyping and seven cases provided M tuberculosis specific signatures, whereas M bovis specific signatures were obtained in four cases. The analysis of mtp40, oxyR, and pncA partial gene sequences confirmed the presence of M tuberculosis in six cases and M bovis in one case. The amplification and sequencing of four further genetic regions (katG, gyrA, TbD1, RD9) characterised six "modern" M tuberculosis strains belonging to genetic groups 2 or 3.
  
  
  CONCLUSIONS
  This study provides clear evidence that archival paraffin wax embedded material can be used for further studies on the strain identification of M tuberculosis complex strains and can therefore unequivocally be used for the study of the epidemiology and evolution of tuberculosis pathogens.
authors.affiliation: Institute of Pathology, Academic-Teaching Hospital München-Bogenhausen, D-81925 München, Germany.
authors.forename: A R
authors.initials: AR
authors.lastname: Zink
authors.forename: A G
authors.initials: AG
authors.lastname: Nerlich
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D015373:Bacterial Typing Techniques / Q000379:methods; D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000032:analysis*; D005260:Female; D005798:Genes, Bacterial / Q000235:genetics; D005838:Genotype; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D009163:Mycobacterium bovis / Q000235:genetics / Q000302:isolation & purification; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000302:isolation & purification; D016612:Paraffin Embedding / Q000379:methods; D016133:Polymerase Chain Reaction / Q000379:methods; D014376:Tuberculosis / Q000235:genetics / Q000382:microbiology
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial