PMID- 21935448
OWN - NLM
STAT- MEDLINE
DCOM- 20120228
LR  - 20211020
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 6
IP  - 9
DP  - 2011
TI  - "Pseudo-Beijing": evidence for convergent evolution in the direct repeat region 
      of Mycobacterium tuberculosis.
PG  - e24737
LID - 10.1371/journal.pone.0024737 [doi]
LID - e24737
AB  - BACKGROUND: Mycobacterium tuberculosis has a global population structure 
      consisting of six main phylogenetic lineages associated with specific geographic 
      regions and human populations. One particular M. tuberculosis genotype known as 
      "Beijing" has repeatedly been associated with drug resistance and has been 
      emerging in some parts of the world. "Beijing" strains are traditionally defined 
      based on a characteristic spoligotyping pattern. We used three alternative 
      genotyping techniques to revisit the phylogenetic classification of M. 
      tuberculosis complex (MTBC) strains exhibiting the typical "Beijing" 
      spoligotyping pattern. METHODS AND FINDINGS: MTBC strains were obtained from an 
      ongoing molecular epidemiological study in Switzerland and Nepal. MTBC genotyping 
      was performed based on SNPs, genomic deletions, and 24-loci MIRU-VNTR. We 
      identified three MTBC strains from patients originating from Tibet, Portugal and 
      Nepal which exhibited a spoligotyping patterns identical to the classical Beijing 
      signature. However, based on three alternative molecular markers, these strains 
      were assigned to Lineage 3 (also known as Delhi/CAS) rather than to Lineage 2 
      (also known as East-Asian lineage). Sequencing of the RD207 in one of these 
      strains showed that the deletion responsible for this "Pseudo-Beijing" 
      spoligotype was about 1,000 base pairs smaller than the usual deletion of RD207 
      in classical "Beijing" strains, which is consistent with an evolutionarily 
      independent deletion event in the direct repeat (DR) region of MTBC. CONCLUSIONS: 
      We provide an example of convergent evolution in the DR locus of MTBC, and 
      highlight the limitation of using spoligotypes for strain classification. Our 
      results indicate that a proportion of "Beijing" strains may have been 
      misclassified in the past. Markers that are more phylogenetically robust should 
      be used when exploring strain-specific differences in experimental or clinical 
      phenotypes.
FAU - Fenner, Lukas
AU  - Fenner L
AD  - Institute of Social and Preventive Medicine, University of Bern, Bern, 
      Switzerland. lfenner@ispm.unibe.ch
FAU - Malla, Bijaya
AU  - Malla B
FAU - Ninet, Beatrice
AU  - Ninet B
FAU - Dubuis, Olivier
AU  - Dubuis O
FAU - Stucki, David
AU  - Stucki D
FAU - Borrell, Sonia
AU  - Borrell S
FAU - Huna, Thembela
AU  - Huna T
FAU - Bodmer, Thomas
AU  - Bodmer T
FAU - Egger, Matthias
AU  - Egger M
FAU - Gagneux, Sebastien
AU  - Gagneux S
LA  - eng
GR  - R01 AI090928/AI/NIAID NIH HHS/United States
GR  - U01 AI069924/AI/NIAID NIH HHS/United States
GR  - 5U01-AI069924-5/AI/NIAID NIH HHS/United States
GR  - R01AI090928-01/AI/NIAID NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20110913
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
SB  - IM
MH  - *Biological Evolution
MH  - Genotype
MH  - Mycobacterium tuberculosis/classification/*genetics
MH  - Phylogeny
MH  - Repetitive Sequences, Nucleic Acid/*genetics
PMC - PMC3172296
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2011/09/22 06:00
MHDA- 2012/03/01 06:00
PMCR- 2011/09/13
CRDT- 2011/09/22 06:00
PHST- 2011/06/22 00:00 [received]
PHST- 2011/08/16 00:00 [accepted]
PHST- 2011/09/22 06:00 [entrez]
PHST- 2011/09/22 06:00 [pubmed]
PHST- 2012/03/01 06:00 [medline]
PHST- 2011/09/13 00:00 [pmc-release]
AID - PONE-D-11-11180 [pii]
AID - 10.1371/journal.pone.0024737 [doi]
PST - ppublish
SO  - PLoS One. 2011;6(9):e24737. doi: 10.1371/journal.pone.0024737. Epub 2011 Sep 13.