Next-generation sequencing of drug resistant <i>Mycobacterium tuberculosis</i> clinical isolates in low-incidence countries
Drug resistant tuberculosis (TB), especially multidrug (MDR) and extensively drug-resistant (XDR) TB, is still a serious problem in global TB control. Slovenia and North Macedonia are low-incidence countries with TB incidence rates of 5.4 and 10.4 in 2017, respectively. In both countries, the percen...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | Russian |
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Sankt-Peterburg : NIIÈM imeni Pastera
2020-02-01
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| Series: | Инфекция и иммунитет |
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| Online Access: | https://www.iimmun.ru/iimm/article/view/851 |
| _version_ | 1828081148237971456 |
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| author | E. Sodja N. Toplak S. Koren M. Kovač S. Truden M. Žolni-Dovč |
| author_facet | E. Sodja N. Toplak S. Koren M. Kovač S. Truden M. Žolni-Dovč |
| author_sort | E. Sodja |
| collection | DOAJ |
| description | Drug resistant tuberculosis (TB), especially multidrug (MDR) and extensively drug-resistant (XDR) TB, is still a serious problem in global TB control. Slovenia and North Macedonia are low-incidence countries with TB incidence rates of 5.4 and 10.4 in 2017, respectively. In both countries, the percentage of drug resistant TB is very low with sporadic cases of MDR-TB. However, global burden of drug-resistant TB continues to increase imposing huge impact on public health systems and strongly stimulating the detection of gene variants related with drug resistance in TB. Next-generation sequencing (NGS) can provide comprehensive analysis of gene variants linked to drug resistance in Mycobacterium tuberculosis. Therefore, the aim of our study was to examine the feasibility of a full-length gene analysis for the drug resistance related genes (inhA, katG, rpoB, embB) using Ion Torrent technology and to compare the NGS results with those obtained from conventional phenotypic drug susceptibility testing (DST) in TB isolates. Between 1996 and 2017, we retrospectively selected 56 TB strains from our National mycobacterial culture collection. Of those, 33 TB isolates from Slovenian patients were isolated from various clinical samples and subjected to phenotypic DST testing in Laboratory for Mycobacteria (University Clinic Golnik, Slovenia). The remaining 23 TB isolates were isolated from Macedonian patients and sent to our laboratory for assistance in phenotypic DST testing. TB strains included were either mono-, poly- or multidrug resistant. For control purposes, we also randomly selected five TB strains susceptible to first-line anti-TB drugs. High concordance between genetic (Ion Torrent technology) and standard phenotypic DST testing for isoniazid, rifampicin and ethambutol was observed, with percent of agreement of 77%, 93.4% and 93.3%, sensitivities of 68.2%, 100% and 100%, and specificities of 100%, 80% and 88.2%, respectively. In conclusion, the genotypic DST using Ion Torrent semiconductor NGS successfully predicted drug resistance with significant shortening of time needed to obtain the resistance profiles from several weeks to just a few days. |
| first_indexed | 2024-04-11T03:29:47Z |
| format | Article |
| id | doaj.art-0e02e247e9594c8aa40d0c504c6c899a |
| institution | Directory Open Access Journal |
| issn | 2220-7619 2313-7398 |
| language | Russian |
| last_indexed | 2024-04-11T03:29:47Z |
| publishDate | 2020-02-01 |
| publisher | Sankt-Peterburg : NIIÈM imeni Pastera |
| record_format | Article |
| series | Инфекция и иммунитет |
| spelling | doaj.art-0e02e247e9594c8aa40d0c504c6c899a2023-01-02T06:38:27ZrusSankt-Peterburg : NIIÈM imeni PasteraИнфекция и иммунитет2220-76192313-73982020-02-0195-677377810.15789/2220-7619-2019-5-6-773-778815Next-generation sequencing of drug resistant <i>Mycobacterium tuberculosis</i> clinical isolates in low-incidence countriesE. Sodja0N. Toplak1S. Koren2M. Kovač3S. Truden4M. Žolni-Dovč5University Clinic of Respiratory and Allergic Diseases GolnikOmega d.o.o., LjubljanaOmega d.o.o., LjubljanaOmega d.o.o., LjubljanaUniversity Clinic of Respiratory and Allergic Diseases GolnikUniversity Clinic of Respiratory and Allergic Diseases GolnikDrug resistant tuberculosis (TB), especially multidrug (MDR) and extensively drug-resistant (XDR) TB, is still a serious problem in global TB control. Slovenia and North Macedonia are low-incidence countries with TB incidence rates of 5.4 and 10.4 in 2017, respectively. In both countries, the percentage of drug resistant TB is very low with sporadic cases of MDR-TB. However, global burden of drug-resistant TB continues to increase imposing huge impact on public health systems and strongly stimulating the detection of gene variants related with drug resistance in TB. Next-generation sequencing (NGS) can provide comprehensive analysis of gene variants linked to drug resistance in Mycobacterium tuberculosis. Therefore, the aim of our study was to examine the feasibility of a full-length gene analysis for the drug resistance related genes (inhA, katG, rpoB, embB) using Ion Torrent technology and to compare the NGS results with those obtained from conventional phenotypic drug susceptibility testing (DST) in TB isolates. Between 1996 and 2017, we retrospectively selected 56 TB strains from our National mycobacterial culture collection. Of those, 33 TB isolates from Slovenian patients were isolated from various clinical samples and subjected to phenotypic DST testing in Laboratory for Mycobacteria (University Clinic Golnik, Slovenia). The remaining 23 TB isolates were isolated from Macedonian patients and sent to our laboratory for assistance in phenotypic DST testing. TB strains included were either mono-, poly- or multidrug resistant. For control purposes, we also randomly selected five TB strains susceptible to first-line anti-TB drugs. High concordance between genetic (Ion Torrent technology) and standard phenotypic DST testing for isoniazid, rifampicin and ethambutol was observed, with percent of agreement of 77%, 93.4% and 93.3%, sensitivities of 68.2%, 100% and 100%, and specificities of 100%, 80% and 88.2%, respectively. In conclusion, the genotypic DST using Ion Torrent semiconductor NGS successfully predicted drug resistance with significant shortening of time needed to obtain the resistance profiles from several weeks to just a few days.https://www.iimmun.ru/iimm/article/view/851tuberculosismycobacterium tuberculosisdrug resistant tuberculosismultidrug resistant tuberculosisnext-generation sequencingion torrentphenotypic drug susceptibility testing |
| spellingShingle | E. Sodja N. Toplak S. Koren M. Kovač S. Truden M. Žolni-Dovč Next-generation sequencing of drug resistant <i>Mycobacterium tuberculosis</i> clinical isolates in low-incidence countries Инфекция и иммунитет tuberculosis mycobacterium tuberculosis drug resistant tuberculosis multidrug resistant tuberculosis next-generation sequencing ion torrent phenotypic drug susceptibility testing |
| title | Next-generation sequencing of drug resistant <i>Mycobacterium tuberculosis</i> clinical isolates in low-incidence countries |
| title_full | Next-generation sequencing of drug resistant <i>Mycobacterium tuberculosis</i> clinical isolates in low-incidence countries |
| title_fullStr | Next-generation sequencing of drug resistant <i>Mycobacterium tuberculosis</i> clinical isolates in low-incidence countries |
| title_full_unstemmed | Next-generation sequencing of drug resistant <i>Mycobacterium tuberculosis</i> clinical isolates in low-incidence countries |
| title_short | Next-generation sequencing of drug resistant <i>Mycobacterium tuberculosis</i> clinical isolates in low-incidence countries |
| title_sort | next generation sequencing of drug resistant i mycobacterium tuberculosis i clinical isolates in low incidence countries |
| topic | tuberculosis mycobacterium tuberculosis drug resistant tuberculosis multidrug resistant tuberculosis next-generation sequencing ion torrent phenotypic drug susceptibility testing |
| url | https://www.iimmun.ru/iimm/article/view/851 |
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