Frequent acquisition of bedaquiline resistance by epidemic extensively drug-resistant Mycobacterium tuberculosis strains in Russia during long-term treatment

The emergence and spread of multidrug-resistant extensively drug-resistant (MDR/XDR) Mycobacterium tuberculosis strains require new antituberculosis compounds. Bedaquiline is a novel promising drug, but as with other drugs, bedaquiline resistance can be acquired by M. during long-term treatment. In particular, atpE mutations prevent interaction the drug its target, ATP synthase in efflux pump repressor mmpR (Rv0678) lead to export [1Veziris N. Bernard C. Guglielmetti L. Le Du D. Marigot-Outtandy Jaspard et al.Rapid resistance: lessons avoid repeating past errors.Eur Respir J. 2017; 49: 1601719Crossref PubMed Scopus (59) Google Scholar, 2Peretokina I.V. Krylova L.Y. Antonova O.V. Kholina M.S. Kulagina E.V. Nosova E.Y. al.Reduced susceptibility clinical isolates.J Infect. 2020; 80: 527-535Abstract Full Text PDF (21) 3Melly G. Purdy G.E. MmpL proteins physiology pathogenesis of.M Microorg. 2019; 7: 70Google Scholar].Here we analysed development through whole-genome sequencing multiple consecutive isolates gain comprehensive quantitative perspective on real-time mycobacterial adaptation human host.Kaliningrad (known Königsberg 1255–1945) westernmost Russian region Baltic Sea, separated from mainland Russia Lithuania Poland. characterized high (TB) incidence (38.8/100000) primary MDR TB rate (30.5%). Patients were admitted Kaliningrad Regional Tuberculosis Dispensary 2018–19. Those receiving part their chemotherapy included study. study was approved ethics committee Research Institute Phthisiopulmonology (protocol 31.2 27 February 2017). testing performed using modified proportion method Middlebrook 7H9 liquid culture BACTEC MGIT 960 system. A limitation this that still process wide implementation not available for studied isolates. However, Rv0678c, atpE, pepQ Rv1979c previously reported bedaquiline-resistant or vitro mutants [[1]Veziris Scholar,[2]Peretokina Scholar,[4]Kadura S. King Nakhoul Zhu H. Theron Köser C.U. al.Systematic review associated repurposed drugs bedaquiline, clofazimine, linezolid, delamanid pretomanid.J Antimicrob Chemother. 75: 2031-2043Crossref (48) Scholar], assumed them genotypic proxy resistance.DNA subjected MiSeq NextSeq 500 platforms (Illumina, San Diego, CA, USA). Data deposited National Center Biotechnology Information Sequence Read Archive (projects PRJNA525341 PRJNA635788). short reads aligned complete genome reference strain H37Rv (NC_00962.3) Geneious 9 (Biomatters, Auckland, New Zealand). Protein structures predicted Phyre2 web portal (http://www.sbg.bio.ic.ac.uk/?phyre2/) visualized Chimera tool (http://www.cgl.ucsf.edu/chimera/).Forty-three recovered 11 patients (Supplementary Table S1). All assigned Beijing genotype B0/W148-cluster (‘Russian successful clone’ [[5]Mokrousov I. Insights into origin, emergence, current clone tuberculosis.Clin Microbiol Rev. 2013; 26: 342-360Crossref (81) Scholar]) Central Asia Outbreak clade [[6]Shitikov E. Vyazovaya A. Malakhova Guliaev Bespyatykh Proshina al.Simple assay detection outbreak genotype.J Clin Microbiol. 57: e00215-e00219Crossref (18) Scholar]. total dominance prevalence B0/W148 cluster are noteworthy view more diverse population here [[7]Vyazovaya A.A. Akhmedova G.M. Solovieva N.S. Gerasimova Starkova D.A. Turkin E.N. al.[Molecular epidemiology Russia: 10 years after].Russ J Infect Immun. 367-374Crossref (7) Scholar].Overall, identified ten genes six (Fig. 1(a); Supplementary S2). To our knowledge, most have been described.In one patient, Rv0678 mutation present before start treatment (patient 2 Fig. 1(a)). another patient 1(a)), found 80% first isolate after 13 days Considering relatively slow onset bactericidal effect time frame seems too selection mutation, although 18 described [[2]Peretokina Scholar].In four patients, emerged followed different microevolutionary trajectories (patients 8, 3, 5 Heteroresistance common; wild-type mutant alleles fluctuated over time. Multiple coexisting episodes disrupted 8 same reads; is, they represented subpopulations strain.We further assessed possible protein structure function Frameshift significantly change amino acid sequence and/or truncate protein, arguably resulting loss efflux. effects silico structural analysis electrostatic potential around mutated acids accessible surface area, then light previous studies [[3]Melly Scholar,[8]Radhakrishnan Kumar Wright C.C. Chou T.H. Tringides M.L. Bolla J.R. al.Crystal transcriptional regulator tuberculosis.J Biol Chem. 2014; 289: 16526-16540Abstract (46) Scholar,[9]Salifu Agoni Olotu F.A. Soliman M.E.S. Triple ATP-synthase impedes binding: atomistic perspectives.Comput 85: 107204Crossref (8) Scholar] S2, 1(b)).Taking consideration above analysis, compared outcomes presence mutations. This revealed efficient only whose did harbour Treatment failure observed all cases five without (p 0.03). positive outcome atpE.In conclusion, results suggest frequently treatment, representing main mechanism. common, several months stop (due long half-life bedaquiline). There poor infected bearing mutations, regardless presence, putative structure. epidemic MDR/XDR prevalent rapidly acquire bedaquiline. may result serious negative impact control countries former Soviet Union, where these hypervirulent genotypes dominant.Transparency DeclarationSupported Science Foundation (grant 19-15-00028 ). authors report no conflicts interest relevant article. Here host. resistance. DNA (http://www.cgl.ucsf.edu/chimera/). Forty-three Overall, described. strain. We 1(b)). Taking atpE. dominant. Transparency Supported thank Alexander Shchemelev (St. Petersburg Pasteur Institute, Russia) technical assistance. Appendix dataThe following data article: Download .docx (.03 MB) Help docx files Multimedia component 1