PMID- 12454164
OWN - NLM
STAT- MEDLINE
DCOM- 20030225
LR  - 20210526
IS  - 0095-1137 (Print)
IS  - 1098-660X (Electronic)
IS  - 0095-1137 (Linking)
VI  - 40
IP  - 12
DP  - 2002 Dec
TI  - Improvement of differentiation and interpretability of spoligotyping for 
      Mycobacterium tuberculosis complex isolates by introduction of new spacer 
      oligonucleotides.
PG  - 4628-39
AB  - The direct repeat (DR) region in Mycobacterium tuberculosis complex strains is 
      composed of multiple well-conserved 36-bp DRs interspersed with nonrepetitive DNA 
      spacer sequences of similar size. Clinical isolates show extensive polymorphism 
      in this DR region, and this has led to the development of a 43-spacer reversed 
      line blot methodology: spoligotyping. Although this method has contributed 
      significantly to the molecular epidemiology of tuberculosis in the last decade, 
      the discriminatory power and the readability of this method were not found to be 
      optimal. In order to improve the discriminatory power, the usefulness of 43 
      redesigned oligonucleotides and the usefulness of 51 new spacer oligonucleotides 
      were evaluated. For 314 M. tuberculosis complex strains isolated in the central 
      part of The Netherlands over a 5-year period, 264 different IS6110 RFLP types 
      could be distinguished, and 160 different spoligotype patterns were identified by 
      traditional spoligotyping. After the introduction of 51 new spacer 
      oligonucleotides, 14 additional spoligotypes were recognized. This enabled us to 
      split 11 clusters of isolates identified by the traditional spoligotyping. 
      Furthermore, on the basis of the new spacer oligonucleotides a dichotomy was 
      found among the Beijing genotype isolates. Among 76 Mycobacterium bovis strains, 
      20 patterns were found by traditional spoligotyping and 30 patterns were found by 
      novel probe spoligotyping, respectively. Nine M. bovis subsp. caprae isolates 
      yielded six patterns by traditional spoligotyping and eight patterns by novel 
      probe spoligotyping. A part of the redesigned oligonucleotides slightly improved 
      the reading of spoligotype patterns. The reproducibility of spoligotyping, based 
      on internal control probes, invariably yielded a high score; only 4 (1%) of the 
      314 patient isolates gave discrepant results. Analysis of a set of 31 duplicate 
      M. tuberculosis complex strains demonstrated a 10% error rate for the 
      identification of blinded duplicate samples. In a redundancy analysis, 40 
      essential spacer oligonucleotides of the 94-spacer sequences were selected, 
      yielding the same number of spoligotype patterns. We propose to leave the 
      traditional commercialized first-generation membrane for spoligotyping unchanged 
      for current applications and to introduce a second-generation spoligotyping 
      membrane whenever extended discrimination is required, e.g., for low-copy-number 
      IS6110 strains or for phylogenetic studies of Beijing genotype strains.
FAU - van der Zanden, A G M
AU  - van der Zanden AG
AD  - Medical Microbiology and Infectious Diseases, Gelre Hospitals, Location Lukas, 
      Apeldoorn, The Netherlands. agm.vd.zanden@gelre.nl
FAU - Kremer, K
AU  - Kremer K
FAU - Schouls, L M
AU  - Schouls LM
FAU - Caimi, K
AU  - Caimi K
FAU - Cataldi, A
AU  - Cataldi A
FAU - Hulleman, A
AU  - Hulleman A
FAU - Nagelkerke, N J D
AU  - Nagelkerke NJ
FAU - van Soolingen, D
AU  - van Soolingen D
LA  - eng
PT  - Comparative Study
PT  - Evaluation Study
PT  - Journal Article
PL  - United States
TA  - J Clin Microbiol
JT  - Journal of clinical microbiology
JID - 7505564
RN  - 0 (DNA Transposable Elements)
RN  - 0 (Oligonucleotide Probes)
RN  - 0 (Oligonucleotides)
SB  - IM
MH  - Animals
MH  - *Bacterial Typing Techniques
MH  - Base Sequence
MH  - Cattle
MH  - Cattle Diseases/microbiology
MH  - DNA Transposable Elements
MH  - Humans
MH  - Molecular Sequence Data
MH  - Mycobacterium bovis/classification/genetics
MH  - Mycobacterium tuberculosis/*classification/*genetics
MH  - Oligonucleotide Probes/genetics
MH  - Oligonucleotides/*analysis
MH  - Phylogeny
MH  - Polymorphism, Restriction Fragment Length
MH  - Repetitive Sequences, Nucleic Acid/*genetics
MH  - Reproducibility of Results
MH  - Tuberculosis/*microbiology/veterinary
PMC - PMC154657
EDAT- 2002/11/28 04:00
MHDA- 2003/02/26 04:00
PMCR- 2002/12/01
CRDT- 2002/11/28 04:00
PHST- 2002/11/28 04:00 [pubmed]
PHST- 2003/02/26 04:00 [medline]
PHST- 2002/11/28 04:00 [entrez]
PHST- 2002/12/01 00:00 [pmc-release]
AID - 1685 [pii]
AID - 10.1128/JCM.40.12.4628-4639.2002 [doi]
PST - ppublish
SO  - J Clin Microbiol. 2002 Dec;40(12):4628-39. doi: 10.1128/JCM.40.12.4628-4639.2002.