Whole genome sequencing of multidrug-resistant Mycobacterium tuberculosis isolates collected in the Czech Republic, 2005–2020

Abstract

The emergence and spread of resistant tuberculosis (TB) pose a threat to public health, so it is necessary to diagnose the drug-resistant forms in a clinically short time frame and closely monitor their transmission. In this study, we carried out a first whole genome sequencing (WGS)-based analysis of multidrug resistant (MDR) M. tuberculosis strains to explore the phylogenetic lineages diversity, drug resistance mechanisms, and ongoing transmission chains within the country. In total, 65 isolates phenotypically resistant to at least rifampicin and isoniazid collected in the Czech Republic in 2005–2020 were enrolled for further analysis. The agreement of the results obtained by WGS with phenotypic drug susceptibility testing (pDST) in the determination of resistance to isoniazid, rifampicin, pyrazinamide, streptomycin, second-line injectables and fluoroquinolones was more than 80%. Phylogenetic analysis of WGS data revealed that the majority of MDR M. tuberculosis isolates were the Beijing lineage 2.2.1 (n = 46/65; 70.8%), while the remaining strains belonged to Euro-American lineage. Cluster analysis with a predefined cut-off distance of less than 12 single nucleotide polymorphisms between isolates showed 19 isolates in 6 clusters (clustering rate 29.2%), located mainly in the region of the capital city of Prague. This study highlights the utility of WGS as a high-resolution approach in the diagnosis, characterization of resistance patterns, and molecular-epidemiological analysis of resistant TB in the country.

Tuberculosis in Ukrainian War Refugees and Migrants in the Czech Republic and Slovakia: A Molecular Epidemiological Study

“…DNA extraction and WGS were performed according to the procedure published in our previous study [ 15 ].…”

Transmission of drug-resistant Mycobacterium tuberculosis isolates between Finnish- and foreign-born patients, 2014-2021: a molecular epidemiological study

“…The clustering rate (15.8%) of drug-resistant MTB isolates in this low-incidence setting was lower than that (48.5%) in Thailand, which is a high-incidence setting 22 . Previous studies reported a high clustering rate of MDR isolates in the Czech Republic (29.23%), Spain (48.4%), and EU countries (51.6%) 17,23,24 . The lower clustering rate of drug-resistant MTB in Finland may be due to smaller immigrant populations from high-incidence countries in Finland than that in other EU countries.…”

Xpert MTB/RIF Ultra Trace Results: Decision Support for the Treatment of Extrapulmonary Tuberculosis in Low TB Burden Countries

“…The WHO recently recommended that, when individuals are being evaluated for extrapulmonary TB using cerebrospinal fluid, lymph nodes, and tissue specimens, MTBC detected trace result be considered as bacteriological confirmation of TB (i.e., a true positive result), and these patients should be treated with an appropriate regimen using first-line TB drugs unless the patients are at high risk of having MDR-TB [5]. Direct whole-genome sequencing (DWGS) of M tuberculosis enables the prediction of drug resistance either from bacterial strains or directly from smearpositive sputum samples [13,14]. DWGS has also been applied to smear-negative sputum samples with some success [14].…”