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.
Highlights
Mycobacterium tuberculosis (MT), an obligate pathogen that causes tuberculosis (TB), is highly transmissible agent with significant morbidity and mortality
We examined the feasibility of a fulllength gene analysis for the drug resistance related genes using Ion Torrent technology and compared the results with those obtained from conventional phenotypic drug susceptibility testing (DST) in 61
Between 1996 and 2017, we retrospectively selected 33 TB strains that were isolated from various clinical samples of Slovenian patients and subjected to phenotypic DST testing according to routine procedures in Laboratory for Mycobacteria (University Clinic Golnik, Slovenia)
Summary
Mycobacterium tuberculosis (MT), an obligate pathogen that causes tuberculosis (TB), is highly transmissible agent with significant morbidity and mortality. The increasing burden of multidrug resistant (MDR) and extensively drug-resistant (XDR) TB is a serious problem in global TB control. In Slovenia in the period between 1996 and 2017 the average percentage of any drug resistance against isoniazid (INH), rifampicin (RIF), pyrazinamide (PZA), ethambutol (EMB) and streptomycin (SM) was 4.13%, dropping from 6.55% in 1996 to 1.89% in 2017. For North Macedonia, the average percentage of any drug resistance against INH, RIF, EMB and SM (they do not perform DST testing for PZA) was higher and accounted for 10.84%, dropping from 9.93% in 2001 to 5.81% in 2017. During 1996 and 2017 75 MDR-TB cases were observed in North Macedonia with MDRTB cases appearing each year [2,3,4]
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