Whole-Genome Sequencing of Mycobacterium tuberculosis Provides Insight into the Evolution and Genetic Composition of Drug-Resistant Tuberculosis in Belarus

Kurt R. WollenbergaChristopher A. DesjardinsbAksana ZalutskayacVervara SlodovnikovacAndrew J. OleraMariam QuiñonesaThomas AbeelbSinead B. ChapmanbMichael TartakovskyaAndrei GabrielianaSven HoffnerdAliaksandr SkrahineBruce W. BirrenbAlexander RosenthalaAlena Skrahinacand Ashlee M. Earlb

aOffice of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
bThe Broad Institute of MIT & Harvard, Cambridge, Massachusetts, USA
cRepublican Scientific and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
dDepartment of Microbiology, The Public Health Agency of Sweden, Solna, Sweden
eBelarusian State Medical University, Minsk, Belarus
Karen C. Carroll, Editor
The Johns Hopkins University School of Medicine

The emergence and spread of drug-resistant Mycobacterium tuberculosis (DR-TB) are critical global health issues. Eastern Europe has some of the highest incidences of DR-TB, particularly multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. To better understand the genetic composition and evolution of MDR- and XDR-TB in the region, we sequenced and analyzed the genomes of 138 M. tuberculosis isolates from 97 patients sampled between 2010 and 2013 in Minsk, Belarus. MDR and XDR-TB isolates were significantly more likely to belong to the Beijing lineage than to the Euro-American lineage, and known resistance-conferring loci accounted for the majority of phenotypic resistance to first- and second-line drugs in MDR and XDR-TB. Using a phylogenomic approach, we estimated that the majority of MDR-TB was due to the recent transmission of already-resistant M. tuberculosis strains rather than repeated de novo evolution of resistance within patients, while XDR-TB was acquired through both routes. Longitudinal sampling of M. tuberculosis from 34 patients with treatment failure showed that most strains persisted genetically unchanged during treatment or acquired resistance to fluoroquinolones. HIV+ patients were significantly more likely to have multiple infections over time than HIV− patients, highlighting a specific need for careful infection control in these patients. These data provide a better understanding of the genomic composition, transmission, and evolution of MDR- and XDR-TB in Belarus and will enable improved diagnostics, treatment protocols, and prognostic decision-making.