Whole genome sequencing of mono-resistant and poly-resistant TB. Resistance patterns and transmission of mono- and poly-resistant tuberculosis in low-incidence tuberculosis countries: is it under the control?

Tuberculosis (TB), especially drug-resistant (DR) forms, are still a global medical emergency. The global prevalence of mono- and polyresistant strains is almost 17%. The detection and rapid diagnosis of these cases is neccessary to prevent the development of multidrug-resistant TB. The aim of the study was to perform whole genome sequencing to determine the rate of false positivity and negativity of phenotypic drug susceptibility testing (pDST), characterize the molecular mechanisms of resistance and transmission of mono- and poly-resistant Mycobacterium tuberculosis (Mtb) strains. This cohort study performed whole genome sequencing (WGS) on 78 mono- and polyresistant Mtb isolates characterized by pDST. The data showed the variable sensitivity and specificity of WGS in the identification of gene variants encoding drug resistance: izoniazid 92.7% and 92.3% ; streptomycin 41.9% and 100.0%; pyrazinamide 15% and 94.8%, ethambutol 75.0% and 98.6%. We found the novel mutations potentially encoding the resistance to streptomycin (in the gidB) and pyrazinamide (in the KefB). Also, we have identified several mutations classified in Group 3: Uncertain significance and Group 5: Not associated with resistance in the WHO catalogue in phenotypic resistant isolates. Most isolates belonged to lineage 4 (80.1%) followed by lineage 2 (17.9%) and the overall clustering rate was 21.8%. In this study, we identified a relatively high frequency of false pDSTs, thus emphasizing the need to apply WGS in a clinical setting to prevent the development and spread of DR-TB. Also, our results highlight the clinical potential of the WHO catalogue in setting the correct treatment regimen.