Background:
Non-tuberculous mycobacteria (NTM) are increasingly recognized worldwide as significant causes of chronic pulmonary disease, particularly among individuals with underlying structural lung disorders or immunosuppression. However, data on the epidemiology and clinical management of NTM infections in Eastern Europe remain scarce. In Ukraine, a high-burden country for tuberculosis, NTM infections are often underdiagnosed or misclassified. This two-year prospective observational cohort study aimed to characterize NTM isolated from Ukrainian patients with suspected mycobacterial disease, investigate genetic diversity, and review clinical management practices.
Methods:
Between December 2022 and February 2024, a total of 19,529 clinical specimens from approximately 8,200 patients attending clinics in Zaporizhzhia and Kharkiv region were submitted for mycobacterial culture. Identified NTM isolates were analysed with line probe assays (only Kharkiv) and retrospectively with whole genome sequencing (WGS). Taxonomic classification, core genome multi-locus sequence typing (cgMLST)-based cluster analysis incorporating 4,200 public NTM datasets, and genomic resistance prediction were performed. A threshold of 10 alleles was used to define clusters of closely related isolates. Clinical records were reviewed for age, body mass index, comorbidities, imaging, treatments and outcomes.
Results:
WGS-based analysis of 100 NTM isolates from 99 patients identified one putative novel species and 21 known species, with Mycobacterium kansasii (43%) and Mycobacterium avium (16%) being the most frequently isolated species. Among 41 M. kansasii isolates, six geographically restricted clusters, each comprising 2–4 isolates, were detected. In contrast, 5/13 (39%) M. avium isolates formed one cluster that also contained isolates from another country. No cluster containing more than one Ukrainian isolate was observed among the M. abscessus isolates. However, four of five M. abscessus isolates belonged to known global dominant circulating clones. All patients presented with pulmonary symptoms and radiographic abnormalities in the lung but strict application of the ATS diagnostic criteria was not possible due to diagnostic constraints. Common comorbidities of the patients included chronic obstructive pulmonary disease (n = 20), anaemia (n = 12), HIV infection (n = 6), and tuberculosis (n = 4). While antibiotic therapy was initiated for all patients, treatment regimens often diverged from international recommendations.
Conclusions:
This first systematic, multi-center genomic investigation of NTM in Ukraine reveals a diverse NTM population dominated by M. kansasii and M. avium, with no genomic evidence of large-scale outbreaks. The findings underscore the need to strengthen diagnostic capacity and establish national guidelines for NTM disease confirmation and management, to ensure accurate diagnosis and rational antimicrobial use.