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

Abstract

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.

Two Novel katG Mutations Conferring Isoniazid Resistance in Mycobacterium tuberculosis

“…A genetic analysis by next-generation sequencing performed in Ukraine. Daum et al found a poly-resistant strain of M. tuberculosis containing the amino acid substitutions W341R and R463L in KatG ( Daum et al, 2018 ), which are the same amino acid changes as strain CDC-A. A strain with MIC >1 mg/L found to have mutations at W341G and R463L by DNA sequencing ( Brossier et al, 2006 ); and a group in Brazil found a strain with an INH MIC >32 mg/L harbors KatG W341S ( Cardoso et al, 2004 ).…”

Assessment of Maternal Referral Systems in Dr. Sardjito General Hospital Using Phyo Referral Score: A Single-Center Preliminary Study

“…Numerous challenges had to be addressed in the context of maternal referral process such as inability to communicate with tertiary referral hospital due to a poor cellular network, distance from the referral hospital, lack of a vehicle or ambulance by the referral institution were commonly cited [6,10,11].…”

Improving Multidrug-Resistance Tuberculosis Papua’s Management Using Whole Genome Sequencing

“…Additionally mutations that occur outside of genes that are known to be related to drug resistance can be identified from the entire TB genome. 9,10,15,16 In this paper, we focus on the drug resistance profile from the NGS data. Data analysis is performed using a bioinformatics approach.…”

“…The accumulation of WGS data allows us to assess the genetic diversity across the genome, seeking signatures of selective pressure [5]. Many countries apply WGS for detecting MDR and XDR Tuberculosis [6][7][8][9][10][11][12][13]. Whole-genome sequencing of bacteria has been shown to provide comprehensive data like as prediction of drug susceptibility and resistance, epidemiological analysis and research [14][15][16].…”

“…Implementation of this WGS assay on all cases of MTBC has aided TB control efforts and improved the accuracy of molecular resistance predictions being reported to physicians, resulting in more effective patient management and drug resistance surveillance such as New York State [6,9,10]. This information is crucial for clinicians to make prompt decisions regarding the best therapy to adopt for treatment of multi-and extensively DR-TB (M/XDR-TB) [3,5].…”