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Title:Next-generation sequencing of drug resistant Mycobacterium tuberculosis clinical isolates in low-incidence countries
Authors:Sodja, Eva (Author)
Toplak, Nataša (Author)
Koren, Simon (Author)
Kovač, Minka (Author)
Truden, Sara (Author)
Ilievska Poposka, Biljana (Author)
Žolnir-Dovč, Marija (Author)
Language:English
Tipology:1.01 - Original Scientific Article
Organisation:Logo UKPBAG - University Clinic of Respiratory and Allergic Diseases Golnik
Abstract: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.
Keywords:drug resistant tuberculosis, next-generation sequencing, low-incidence countries, phenotypic drug susceptibility testing
Year of publishing:2019
Publisher:Saint-Petersburg Pasteur Institute
Source:Rusija
COBISS_ID:13128195 Link is opened in a new window
UDC:616-002
ISSN on article:2313-7398
OceCobissID:525094169 Link is opened in a new window
DOI:10.15789/2220-7619-2019-5-6-773-778 Link is opened in a new window
Note:Nasl. z nasl. zaslona; Soavtorji iz Slovenije: N. Toplak, S. Koren, M. Kovač, S. Truden, M. Žolnir-Dovč; Opis vira z dne 29. 4. 2020;
Views:1153
Downloads:550
Files:.pdf PDF - Presentation file, download (144,02 KB)
URL URL - Source URL, visit https://www.iimmun.ru/iimm/article/view/851/883
 
Journal:Infekc. immun.
NIIÈM imeni Pastera
 
Metadata:XML RDF-CHPDL DC-XML DC-RDF
Rights:Sodja E. et al., 2019
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License:CC BY 4.0, Creative Commons Attribution 4.0 International
Link:http://creativecommons.org/licenses/by/4.0/
Description:This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
Licensing start date:24.07.2020

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