Next-Generation Sequencing for Characterizing Drug Resistance-Conferring Mycobacterium tuberculosis Genes from Clinical Isolates in the Ukraine

• Published in: Journal of clinical microbiology Vol. 56; no. 6
• Main Authors: Daum, L T, Konstantynovska, O S, Solodiankin, O S, Liashenko, O O, Poteiko, P I, Bolotin, V I, Hrek, I I, Rohozhyn, A V, Rodriguez, J D, Fischer, G W, Chambers, J P, Gerilovych, A P
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 01.06.2018
• Subjects: Adult; Antitubercular Agents - pharmacology; Bacterial Proteins - genetics; DNA-Directed RNA Polymerases - genetics; Drug Resistance, Multiple, Bacterial - genetics; Extensively Drug-Resistant Tuberculosis - epidemiology; Extensively Drug-Resistant Tuberculosis - microbiology; Female; Genes, Bacterial; Genetic Variation; Genome, Bacterial; Genotype; High-Throughput Nucleotide Sequencing; Humans; Male; Microbial Sensitivity Tests; Middle Aged; Mutation; Mycobacteriology and Aerobic Actinomycetes; Mycobacterium tuberculosis - drug effects; Mycobacterium tuberculosis - genetics; Oxidoreductases - genetics; Promoter Regions, Genetic; Real-Time Polymerase Chain Reaction; Sequence Analysis, DNA; Sputum - microbiology; Tuberculosis, Multidrug-Resistant - epidemiology; Tuberculosis, Multidrug-Resistant - microbiology; Ukraine - epidemiology; Ukraine; multidrug resistance; Mycobacterium tuberculosis paratuberculosis; next-generation sequencing; XDR; tuberculosis; MTB; NGS
• ISSN: 0095-1137; 1098-660X
• DOI: 10.1128/JCM.00009-18

The Ukraine ranks among the top 20 countries with the highest number of multidrug-resistant (MDR) and extensively drug resistant (XDR) cases in the world. However, little is known of the genetic diversity, i.e., resistance signatures, in clinical isolates from this region. We analyzed seven of most prevalent MDR/XDR antibiotic resistance-conferring genes from clinical isolates ( = 75) collected from geographically diverse Ukrainian oblasts and the southern Crimean peninsula. Genomic analysis revealed that 6 (8%) were sensitive, 3 (4%) were resistant to at least one antibiotic but were not MDR, 40 (53%) were MDR, and 26 (35%) were XDR. The majority of isolates (81%) were of the Beijing-like lineage. This is the first study to use next-generation sequencing (NGS) of clinical isolates from the Ukraine to characterize mutations in genes conferring drug resistance. Several isolates harbored drug resistance signatures that have not been observed in other countries with high-burden tuberculosis. Most notably, the absence of gene promoter mutations, a diversity of mutation types in the resistance-determining region, and detection of heteroresistance provide a broader understanding of MDR/XDR from this area of the world.