Ukraine’s Drug-Resistant Tuberculosis Epidemic Is Driven by a Handful of Dominant Clones

Ukraine carries one of the heaviest burdens of drug-resistant tuberculosis in the WHO European Region, and a new landmark study has now mapped the genetic architecture of that epidemic with unprecedented resolution. Drawing on whole-genome sequencing of more than 4,000 Mycobacterium tuberculosis complex isolates collected from 18 of Ukraine’s 24 regions between December 2019 and November 2023, the multicentre cohort offers the most comprehensive picture yet of how resistance has evolved and spread in a country battered by the COVID-19 pandemic, war, and mass population displacement.

The study, led by Dmytro Butov of Kharkiv National Medical University together with Stefan Niemann and Viola Dreyer of the Research Center Borstel in Germany, enrolled 4,828 patients and successfully sequenced 4,162 isolates after quality-control exclusions. Participants were divided into two groups: a drug-resistant tuberculosis cohort of 3,112 patients with rifampicin-resistant, multidrug-resistant, pre-extensively drug-resistant, or extensively drug-resistant disease, and a comparator cohort of 1,050 patients with non-MDR or drug-susceptible tuberculosis. Within the drug-resistant group, 62.3 percent of isolates were classified as multidrug-resistant, nearly a third as pre-XDR, and 2.5 percent as extensively drug-resistant.

The population structure of the circulating bacteria tells a striking story. Fully 70.6 percent of all sequenced isolates belonged to Lineage 2, the so-called Beijing lineage, which predominates across Eastern Europe and is associated with enhanced transmissibility and a greater propensity to acquire resistance mutations. Among drug-resistant cases, Lineage 2 accounted for 83.7 percent of isolates, rising to 89.7 percent among extensively drug-resistant infections. By contrast, Lineage 4 Euro-American strains, which are more genetically diverse, dominated the comparator cohort, particularly among patients with drug-susceptible disease in western Ukraine.

Even more striking is how little diversity exists within the drug-resistant Lineage 2 population. More than 82 percent of MDR, pre-XDR, and XDR isolates belonged to just four previously described Beijing clades: the Europe/Russia W148 outbreak clone, which alone made up nearly 40 percent of the resistant cohort, the Ukraine outbreak clone, the Central Asia outbreak clone, and the broader Central Asia clade. Geospatial analysis showed Lineage 2 dominance in almost every participating region, with the highest proportions in the central, southern, northern, and eastern parts of the country, while Lineage 4 remained comparatively more common in the west.

Genomic clustering analysis, which identifies isolates separated by five or fewer allelic differences at 2,891 core-genome loci, revealed that nearly half of all isolates belonged to clusters, a signature of recent or ongoing transmission. Clustering was far more frequent in the drug-resistant cohort, affecting 55 percent of isolates, than in the comparator group at 28.9 percent. The three largest clusters, all exclusively Lineage 2, contained 671 drug-resistant isolates, over a fifth of that cohort. Cluster 1, assigned to the Ukraine outbreak clone, comprised 307 isolates, more than half of them pre-XDR or XDR. Cluster 2, the W148 clone, included 296 isolates, mostly MDR, and Cluster 3 contained 76 Central Asia outbreak isolates.

The resistance mutations embedded in these clusters indicate that resistance was largely fixed in common ancestors and propagated through clonal expansion rather than acquired independently. Canonical mutations such as KatG S315T and RpoB S450L, which confer resistance to isoniazid and rifampicin at low fitness cost, dominated all three major clusters. Fluoroquinolone resistance, present in roughly a third of drug-resistant isolates, was driven mainly by GyrA D94G and A90V substitutions, while bedaquiline and clofazimine resistance was linked primarily to loss-of-function variants in Rv0678, notably the 192_ins_g and 141_ins_c frameshift insertions.

Resistance to the newer Group A agents central to modern all-oral therapy remained uncommon, offering a measure of reassurance. WGS-inferred bedaquiline resistance was detected in only 90 isolates overall, about 2.8 percent of the drug-resistant cohort, and linezolid resistance in just 33 isolates, or 1.1 percent. Yet the researchers identified 11 isolates carrying variants associated with combined resistance to fluoroquinolones, bedaquiline, and linezolid, a combination that would compromise both BPaL and BPaLM regimens. Notably, seven bedaquiline-resistant XDR isolates carried atpE variants, six of them in Lineage 2 strains scattered across different clades, suggesting independent acquisition. Comparative analysis showed the Ukrainian atpE-mutant isolates were separated by at least 28 SNPs from publicly available Russian genomes, ruling out a single shared clone and pointing to a possible regional propensity for this resistance mechanism that the authors say warrants urgent investigation.

Temporal analysis across four consecutive 12-month intervals revealed significant declines in resistance to moxifloxacin and levofloxacin, each falling from around 41 percent in 2019–2020 to roughly 28 percent in 2022–2023, with pyrazinamide resistance also declining modestly. The fluoroquinolone trends held up in sensitivity analyses restricted to the 12 consistently sampled regions and within the pooled major genomic clusters. In parallel, recorded treatment success rose from 59.6 percent to 73.4 percent over the study period. The authors, however, caution strongly against causal interpretation: the trends coincided with changes in regional sampling after the February 2022 invasion, population displacement, diagnostic disruptions, evolving treatment policies, and the pandemic, and individual-level regimen data were unavailable.

The study also highlights the social epidemiology of the epidemic. Patients with drug-resistant disease were younger and more often male, and more frequently reported recurrent tuberculosis, previous treatment failure, homelessness, drug use, incarceration, HIV infection, and viral hepatitis. Lineage 2 infection was independently associated with rifampicin-resistant or MDR status, fluoroquinolone resistance, and genomic clustering in multivariable models adjusted for demographic, clinical, social, temporal, and regional factors.

The authors conclude that sustained genomic surveillance of drug-resistant tuberculosis in Ukraine and neighbouring countries is essential, particularly for dominant Lineage 2 clones and for resistance to fluoroquinolones, bedaquiline, and linezolid. They call for systematic fluoroquinolone testing before deployment of shorter all-oral regimens, targeted phenotypic confirmation of bedaquiline and linezolid susceptibility, integration of whole-genome sequencing into routine care, and cross-border data sharing to track tuberculosis among displaced, migrant, and refugee populations. As Ukraine continues to rebuild its health system amid ongoing conflict, the genomic record preserved in this cohort provides both a warning about the entrenched clones fuelling the epidemic and a template for surveillance elsewhere in Eastern Europe.

Subject of Research: Genomic surveillance of drug-resistant Mycobacterium tuberculosis in Ukraine from 2019 to 2023

Article Title: Drug-resistance profiles, population structure, genomic clustering, and temporal trends in drug resistance among Mycobacterium tuberculosis complex isolates in Ukraine, 2019–2023: a multicentre cohort study

Article References: Butov, D., Butova, T., Miasoiedov, V., Feshchenko, Y., Nakonechna, O., Kuzhko, M., Rosenthal, A., Grinev, A., Hoppes, D., Kilmnick, J., Levandovska, D., Hryhorieva, A., Vekshyn, V., Abramova, L., Niemann, S., & Dreyer, V. (2026). Drug-resistance profiles, population structure, genomic clustering, and temporal trends in drug resistance among Mycobacterium tuberculosis complex isolates in Ukraine, 2019–2023: a multicentre cohort study. The Lancet Regional Health – Europe, 70, Article 101865. https://doi.org/10.1016/j.lanepe.2026.101865

Image Credits: AI Generated

DOI: 10.1016/j.lanepe.2026.101865

Keywords: tuberculosis, drug resistance, whole-genome sequencing, Lineage 2 Beijing, MDR-TB, Ukraine, fluoroquinolone, bedaquiline, linezolid, genomic clustering, outbreak clones, public health surveillance