A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic

dc.contributor.authorKlopper, Marisaen_ZA
dc.contributor.authorHeupink, Tim Hermanusen_ZA
dc.contributor.authorHill-Cawthorne, Granten_ZA
dc.contributor.authorStreicher, Elizabeth M.en_ZA
dc.contributor.authorDippenaar, Anzaanen_ZA
dc.contributor.authorDe Vos, Margarethaen_ZA
dc.contributor.authorAbdallah, Abdallah Musaen_ZA
dc.contributor.authorLimberis, Jasonen_ZA
dc.contributor.authorMerker, Matthiasen_ZA
dc.contributor.authorBurns, Scotten_ZA
dc.contributor.authorNiemann, Stefanen_ZA
dc.contributor.authorDheda, Keertanen_ZA
dc.contributor.authorPosey, Jamesen_ZA
dc.contributor.authorPain, Arnaben_ZA
dc.contributor.authorWarren, Robin Marken_ZA
dc.identifier.citationKlopper, M., et al. 2020. A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic. BMC Medicine, 18:24, doi:10.1186/s12916-019-1487-2
dc.identifier.issn1741-7015 (online)
dc.descriptionCITATION: Klopper, M., et al. 2020. A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic. BMC Medicine, 18:24, doi:10.1186/s12916-019-1487-2.
dc.descriptionThe original publication is available at
dc.description.abstractBackground: Atypical Beijing genotype Mycobacterium tuberculosis strains are widespread in South Africa and have acquired resistance to up to 13 drugs on multiple occasions. It is puzzling that these strains have retained fitness and transmissibility despite the potential fitness cost associated with drug resistance mutations. Methods: We conducted Illumina sequencing of 211 Beijing genotype M. tuberculosis isolates to facilitate the detection of genomic features that may promote acquisition of drug resistance and restore fitness in highly resistant atypical Beijing forms. Phylogenetic and comparative genomic analysis was done to determine changes that are unique to the resistant strains that also transmit well. Minimum inhibitory concentration (MIC) determination for streptomycin and bedaquiline was done for a limited number of isolates to demonstrate a difference in MIC between isolates with and without certain variants. Results: Phylogenetic analysis confirmed that two clades of atypical Beijing strains have independently developed resistance to virtually all the potent drugs included in standard (pre-bedaquiline) drug-resistant TB treatment regimens. We show that undetected drug resistance in a progenitor strain was likely instrumental in this resistance acquisition. In this cohort, ethionamide (ethA A381P) resistance would be missed in first-line drug-susceptible isolates, and streptomycin (gidB L79S) resistance may be missed due to an MIC close to the critical concentration. Subsequent inadequate treatment historically led to amplification of resistance and facilitated spread of the strains. Bedaquiline resistance was found in a small number of isolates, despite lack of exposure to the drug. The highly resistant clades also carry inhA promoter mutations, which arose after ethA and katG mutations. In these isolates, inhA promoter mutations do not alter drug resistance, suggesting a possible alternative role. Conclusion: The presence of the ethA mutation in otherwise susceptible isolates from ethionamide-naïve patients demonstrates that known exposure is not an adequate indicator of drug susceptibility. Similarly, it is demonstrated that bedaquiline resistance can occur without exposure to the drug. Inappropriate treatment regimens, due to missed resistance, leads to amplification of resistance, and transmission. We put these results into the context of current WHO treatment regimens, underscoring the risks of treatment without knowledge of the full drug resistance profile.en_ZA
dc.format.extent14 pages ; illustrations
dc.publisherBMC (part of Springer Nature)
dc.subjectTuberculosis -- Epidemiologyen_ZA
dc.subjectMultidrug-resistant tuberculosis -- Epidemiologyen_ZA
dc.subjectGenomics -- Researchen_ZA
dc.titleA landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemicen_ZA
dc.description.versionPublisher's version
dc.rights.holderAuthors retain copyright

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