Whole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug-Resistant Mycobacterium tuberculosis Beijing Strains in Patients

Hdl Handle:
http://hdl.handle.net/10144/311609
Title:
Whole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug-Resistant Mycobacterium tuberculosis Beijing Strains in Patients
Authors:
Merker, Matthias; Kohl, Thomas A; Roetzer, Andreas; Truebe, Leona; Richter, Elvira; Rüsch-Gerdes, Sabine; Fattorini, Lanfranco; Oggioni, Marco R; Cox, Helen; Varaine, Francis; Niemann, Stefan
Journal:
PLoS ONE
Abstract:
Multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains represent a major threat for tuberculosis (TB) control. Treatment of MDR-TB patients is long and less effective, resulting in a significant number of treatment failures. The development of further resistances leads to extensively drug-resistant (XDR) variants. However, data on the individual reasons for treatment failure, e.g. an induced mutational burst, and on the evolution of bacteria in the patient are only sparsely available. To address this question, we investigated the intra-patient evolution of serial MTBC isolates obtained from three MDR-TB patients undergoing longitudinal treatment, finally leading to XDR-TB. Sequential isolates displayed identical IS6110 fingerprint patterns, suggesting the absence of exogenous re-infection. We utilized whole genome sequencing (WGS) to screen for variations in three isolates from Patient A and four isolates from Patient B and C, respectively. Acquired polymorphisms were subsequently validated in up to 15 serial isolates by Sanger sequencing. We determined eight (Patient A) and nine (Patient B) polymorphisms, which occurred in a stepwise manner during the course of the therapy and were linked to resistance or a potential compensatory mechanism. For both patients, our analysis revealed the long-term co-existence of clonal subpopulations that displayed different drug resistance allele combinations. Out of these, the most resistant clone was fixed in the population. In contrast, baseline and follow-up isolates of Patient C were distinguished each by eleven unique polymorphisms, indicating an exogenous re-infection with an XDR strain not detected by IS6110 RFLP typing. Our study demonstrates that intra-patient microevolution of MDR-MTBC strains under longitudinal treatment is more complex than previously anticipated. However, a mutator phenotype was not detected. The presence of different subpopulations might confound phenotypic and molecular drug resistance tests. Furthermore, high resolution WGS analysis is necessary to accurately detect exogenous re-infection as classical genotyping lacks discriminatory power in high incidence settings.
Affiliation:
Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
Publisher:
Public Library of Science
Issue Date:
Dec-2013
URI:
http://hdl.handle.net/10144/311609
DOI:
10.1371/journal.pone.0082551
PubMed ID:
24324807
Language:
en
ISSN:
1932-6203
Appears in Collections:
TB

Full metadata record

DC FieldValue Language
dc.contributor.authorMerker, Matthiasen_GB
dc.contributor.authorKohl, Thomas Aen_GB
dc.contributor.authorRoetzer, Andreasen_GB
dc.contributor.authorTruebe, Leonaen_GB
dc.contributor.authorRichter, Elviraen_GB
dc.contributor.authorRüsch-Gerdes, Sabineen_GB
dc.contributor.authorFattorini, Lanfrancoen_GB
dc.contributor.authorOggioni, Marco Ren_GB
dc.contributor.authorCox, Helenen_GB
dc.contributor.authorVaraine, Francisen_GB
dc.contributor.authorNiemann, Stefanen_GB
dc.date.accessioned2014-01-20T20:54:31Z-
dc.date.available2014-01-20T20:54:31Z-
dc.date.issued2013-12-
dc.identifier.citationWhole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug-Resistant Mycobacterium tuberculosis Beijing Strains in Patients. 2013, 8 (12):e82551 PLoS ONEen_GB
dc.identifier.issn1932-6203-
dc.identifier.pmid24324807-
dc.identifier.doi10.1371/journal.pone.0082551-
dc.identifier.urihttp://hdl.handle.net/10144/311609-
dc.description.abstractMultidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains represent a major threat for tuberculosis (TB) control. Treatment of MDR-TB patients is long and less effective, resulting in a significant number of treatment failures. The development of further resistances leads to extensively drug-resistant (XDR) variants. However, data on the individual reasons for treatment failure, e.g. an induced mutational burst, and on the evolution of bacteria in the patient are only sparsely available. To address this question, we investigated the intra-patient evolution of serial MTBC isolates obtained from three MDR-TB patients undergoing longitudinal treatment, finally leading to XDR-TB. Sequential isolates displayed identical IS6110 fingerprint patterns, suggesting the absence of exogenous re-infection. We utilized whole genome sequencing (WGS) to screen for variations in three isolates from Patient A and four isolates from Patient B and C, respectively. Acquired polymorphisms were subsequently validated in up to 15 serial isolates by Sanger sequencing. We determined eight (Patient A) and nine (Patient B) polymorphisms, which occurred in a stepwise manner during the course of the therapy and were linked to resistance or a potential compensatory mechanism. For both patients, our analysis revealed the long-term co-existence of clonal subpopulations that displayed different drug resistance allele combinations. Out of these, the most resistant clone was fixed in the population. In contrast, baseline and follow-up isolates of Patient C were distinguished each by eleven unique polymorphisms, indicating an exogenous re-infection with an XDR strain not detected by IS6110 RFLP typing. Our study demonstrates that intra-patient microevolution of MDR-MTBC strains under longitudinal treatment is more complex than previously anticipated. However, a mutator phenotype was not detected. The presence of different subpopulations might confound phenotypic and molecular drug resistance tests. Furthermore, high resolution WGS analysis is necessary to accurately detect exogenous re-infection as classical genotyping lacks discriminatory power in high incidence settings.en_GB
dc.language.isoenen
dc.publisherPublic Library of Scienceen_GB
dc.rightsPublished by Public Library of Science, [url]http://www.plosone.org/[/url] Archived on this site by Open Access permissionen_GB
dc.subjectAntibiotic Resistanceen_GB
dc.subjectTuberculosisen_GB
dc.titleWhole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug-Resistant Mycobacterium tuberculosis Beijing Strains in Patientsen
dc.contributor.departmentMolecular Mycobacteriology, Research Center Borstel, Borstel, Germanyen_GB
dc.identifier.journalPLoS ONEen_GB

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