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...

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Autores principales:	E. Sodja, N. Toplak, S. Koren, M. Kovač, S. Truden, M. Žolni-Dovč
Formato:	article
Lenguaje:	RU
Publicado:	Sankt-Peterburg : NIIÈM imeni Pastera 2020
Materias:	tuberculosis mycobacterium tuberculosis drug resistant tuberculosis multidrug resistant tuberculosis next-generation sequencing ion torrent phenotypic drug susceptibility testing Infectious and parasitic diseases RC109-216
Acceso en línea:	https://doaj.org/article/0e02e247e9594c8aa40d0c504c6c899a
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spelling	oai:doaj.org-article:0e02e247e9594c8aa40d0c504c6c899a2021-11-22T07:09:53ZNext-generation sequencing of drug resistant <i>Mycobacterium tuberculosis</i> clinical isolates in low-incidence countries2220-76192313-739810.15789/2220-7619-2019-5-6-773-778https://doaj.org/article/0e02e247e9594c8aa40d0c504c6c899a2020-02-01T00:00:00Zhttps://www.iimmun.ru/iimm/article/view/851https://doaj.org/toc/2220-7619https://doaj.org/toc/2313-7398Drug 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.E. SodjaN. ToplakS. KorenM. KovačS. TrudenM. Žolni-DovčSankt-Peterburg : NIIÈM imeni Pasteraarticletuberculosismycobacterium tuberculosisdrug resistant tuberculosismultidrug resistant tuberculosisnext-generation sequencingion torrentphenotypic drug susceptibility testingInfectious and parasitic diseasesRC109-216RUInfekciâ i Immunitet, Vol 9, Iss 5-6, Pp 773-778 (2020)
institution	DOAJ
collection	DOAJ
language	RU
topic	tuberculosis mycobacterium tuberculosis drug resistant tuberculosis multidrug resistant tuberculosis next-generation sequencing ion torrent phenotypic drug susceptibility testing Infectious and parasitic diseases RC109-216
spellingShingle	tuberculosis mycobacterium tuberculosis drug resistant tuberculosis multidrug resistant tuberculosis next-generation sequencing ion torrent phenotypic drug susceptibility testing Infectious and parasitic diseases RC109-216 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
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.
format	article
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
title	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_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_sort	next-generation sequencing of drug resistant <i>mycobacterium tuberculosis</i> clinical isolates in low-incidence countries
publisher	Sankt-Peterburg : NIIÈM imeni Pastera
publishDate	2020
url	https://doaj.org/article/0e02e247e9594c8aa40d0c504c6c899a
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Next-generation sequencing of drug resistant <i>Mycobacterium tuberculosis</i> clinical isolates in low-incidence countries

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