Repeated evolution of bedaquiline resistance in Mycobacterium tuberculosis is driven by truncation of mmpR5

The antibiotic Bedaquiline (BDQ) is a key component of new WHO regimens for drug resistant tuberculosis (TB) but predicting BDQ resistance (BDQ-R) from genotypes remains challenging. We analysed a collection (n=505) of Mycobacterium tuberculosis from two high prevalence areas in South Africa (Cape Town and Johannesburg, 2019-2020), and found 53 independent acquisitions of 31 different mutations within the mmpR5 regulatory gene, with a particular enrichment of truncated MmpR5 in BDQ-R isolates by either frameshift or introduction of an insertion element. Truncations occurred across three M. tuberculosis lineages, impacting 66% of BDQ-R isolates. Extending our analysis to 1,961 isolates with minimum inhibitory concentrations (MICs) revealed that mmpR5-disrupted isolates had a median BDQ MIC of 0.25 mg/L, compared to the wild-type median of 0.06 mg/L. By matching mmpR5-disrupted isolates with phylogenetically close control isolates without the disruption, we were able to estimate the impact on MIC of individual mutations. In conclusion, as the MIC increase borders the ECOFF threshold for BDQ-R, we recommend the continued use of MICs and detection of MmpR5 truncations to identify modest shifts in BDQ-R.

[1]  N. Ismail,et al.  Bedaquiline-Resistant Tuberculosis Associated with Rv0678 Mutations. , 2022, The New England journal of medicine.

[2]  G. Maartens,et al.  Assessment of epidemiological and genetic characteristics and clinical outcomes of resistance to bedaquiline in patients treated for rifampicin-resistant tuberculosis: a cross-sectional and longitudinal study. , 2021, The Lancet. Infectious diseases.

[3]  Joshua J Carter.  Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach , 2021, bioRxiv.

[4]  M. Schatz,et al.  Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes , 2021, bioRxiv.

[5]  L. Freschi,et al.  Role of Epistasis in Amikacin, Kanamycin, Bedaquiline, and Clofazimine Resistance in Mycobacterium tuberculosis Complex , 2021, Antimicrobial agents and chemotherapy.

[6]  Z. Iqbal,et al.  Deciphering Bedaquiline and Clofazimine Resistance in Tuberculosis: An Evolutionary Medicine Approach , 2021, bioRxiv.

[7]  P. Bork,et al.  Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation , 2021, Nucleic Acids Res..

[8]  Thomas M. Keane,et al.  Twelve years of SAMtools and BCFtools , 2020, GigaScience.

[9]  F. Balloux,et al.  Population-level emergence of bedaquiline and clofazimine resistance-associated variants among patients with drug-resistant tuberculosis in southern Africa: a phenotypic and phylogenetic analysis , 2020, The Lancet. Microbe.

[10]  C. Köser,et al.  Systematic review of mutations associated with resistance to the new and repurposed Mycobacterium tuberculosis drugs bedaquiline, clofazimine, linezolid, delamanid and pretomanid. , 2020, The Journal of antimicrobial chemotherapy.

[11]  Z. Iqbal,et al.  Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe , 2019, Wellcome open research.

[12]  Randle Aaron M. Villanueva,et al.  ggplot2: Elegant Graphics for Data Analysis (2nd ed.) , 2019, Measurement: Interdisciplinary Research and Perspectives.

[13]  Srinivas Aluru,et al.  Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems , 2019, 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS).

[14]  G. Maartens,et al.  Effect of bedaquiline on mortality in South African patients with drug-resistant tuberculosis: a retrospective cohort study. , 2018, The Lancet. Respiratory medicine.

[15]  K. Dheda,et al.  Long-term bedaquiline-related treatment outcomes in patients with extensively drug-resistant tuberculosis from South Africa , 2018, European Respiratory Journal.

[16]  Jia Gu,et al.  fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.

[17]  Dennis Andersson,et al.  A retrospective cohort study , 2018 .

[18]  Thomas K. F. Wong,et al.  ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates , 2017, Nature Methods.

[19]  Julian Parkhill,et al.  ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads , 2017, bioRxiv.

[20]  L. Rigouts,et al.  Unexpected high prevalence of resistance-associated Rv0678 variants in MDR-TB patients without documented prior use of clofazimine or bedaquiline , 2016, The Journal of antimicrobial chemotherapy.

[21]  Simon R. Harris,et al.  SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments , 2016, bioRxiv.

[22]  David J. Edwards,et al.  ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data , 2015, BMC Genomics.

[23]  Thomas Abeel,et al.  Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal , 2015, PLoS medicine.

[24]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[25]  B. D. de Jong,et al.  Acquired Resistance of Mycobacterium tuberculosis to Bedaquiline , 2014, PloS one.

[26]  S. Cole,et al.  Cross-Resistance between Clofazimine and Bedaquiline through Upregulation of MmpL5 in Mycobacterium tuberculosis , 2014, Antimicrobial Agents and Chemotherapy.

[27]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[28]  Jon Cohen,et al.  Infectious disease. Approval of novel TB drug celebrated--with restraint. , 2013, Science.

[29]  Gil McVean,et al.  High-throughput microbial population genomics using the Cortex variation assembler , 2012, Bioinform..

[30]  K. Andries,et al.  Randomized Pilot Trial of Eight Weeks of Bedaquiline (TMC207) Treatment for Multidrug-Resistant Tuberculosis: Long-Term Outcome, Tolerability, and Effect on Emergence of Drug Resistance , 2012, Antimicrobial Agents and Chemotherapy.

[31]  Hadley Wickham,et al.  The Split-Apply-Combine Strategy for Data Analysis , 2011 .

[32]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[33]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[34]  Geoffrey J. Barton,et al.  Jalview Version 2—a multiple sequence alignment editor and analysis workbench , 2009, Bioinform..

[35]  Hinrich W. H. Göhlmann,et al.  A Diarylquinoline Drug Active on the ATP Synthase of Mycobacterium tuberculosis , 2005, Science.