"Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis.
<h4>Background</h4>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 associa...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2011-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21935448/?tool=EBI |
| _version_ | 1818744252003254272 |
|---|---|
| author | Lukas Fenner Bijaya Malla Béatrice Ninet Olivier Dubuis David Stucki Sonia Borrell Thembela Huna Thomas Bodmer Matthias Egger Sebastien Gagneux |
| author_facet | Lukas Fenner Bijaya Malla Béatrice Ninet Olivier Dubuis David Stucki Sonia Borrell Thembela Huna Thomas Bodmer Matthias Egger Sebastien Gagneux |
| author_sort | Lukas Fenner |
| collection | DOAJ |
| description | <h4>Background</h4>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.<h4>Methods and findings</h4>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.<h4>Conclusions</h4>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. |
| first_indexed | 2024-12-18T02:41:16Z |
| format | Article |
| id | doaj.art-1d58c1b4b5e34a7bbad23176105ba4f7 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-18T02:41:16Z |
| publishDate | 2011-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-1d58c1b4b5e34a7bbad23176105ba4f72022-12-21T21:23:39ZengPublic Library of Science (PLoS)PLoS ONE1932-62032011-01-0169e2473710.1371/journal.pone.0024737"Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis.Lukas FennerBijaya MallaBéatrice NinetOlivier DubuisDavid StuckiSonia BorrellThembela HunaThomas BodmerMatthias EggerSebastien Gagneux<h4>Background</h4>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.<h4>Methods and findings</h4>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.<h4>Conclusions</h4>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.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21935448/?tool=EBI |
| spellingShingle | Lukas Fenner Bijaya Malla Béatrice Ninet Olivier Dubuis David Stucki Sonia Borrell Thembela Huna Thomas Bodmer Matthias Egger Sebastien Gagneux "Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis. PLoS ONE |
| title | "Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis. |
| title_full | "Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis. |
| title_fullStr | "Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis. |
| title_full_unstemmed | "Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis. |
| title_short | "Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis. |
| title_sort | pseudo beijing evidence for convergent evolution in the direct repeat region of mycobacterium tuberculosis |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21935448/?tool=EBI |
| work_keys_str_mv | AT lukasfenner pseudobeijingevidenceforconvergentevolutioninthedirectrepeatregionofmycobacteriumtuberculosis AT bijayamalla pseudobeijingevidenceforconvergentevolutioninthedirectrepeatregionofmycobacteriumtuberculosis AT beatriceninet pseudobeijingevidenceforconvergentevolutioninthedirectrepeatregionofmycobacteriumtuberculosis AT olivierdubuis pseudobeijingevidenceforconvergentevolutioninthedirectrepeatregionofmycobacteriumtuberculosis AT davidstucki pseudobeijingevidenceforconvergentevolutioninthedirectrepeatregionofmycobacteriumtuberculosis AT soniaborrell pseudobeijingevidenceforconvergentevolutioninthedirectrepeatregionofmycobacteriumtuberculosis AT thembelahuna pseudobeijingevidenceforconvergentevolutioninthedirectrepeatregionofmycobacteriumtuberculosis AT thomasbodmer pseudobeijingevidenceforconvergentevolutioninthedirectrepeatregionofmycobacteriumtuberculosis AT matthiasegger pseudobeijingevidenceforconvergentevolutioninthedirectrepeatregionofmycobacteriumtuberculosis AT sebastiengagneux pseudobeijingevidenceforconvergentevolutioninthedirectrepeatregionofmycobacteriumtuberculosis |