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Evaluation of whole-genome sequencing of Mycobacterium tuberculosis isolates in clinical laboratory

E Sodja(1) S Truden(1) M Žolnir-Dovc(1)

1:University Clinic Golnik

Rapid development of whole-genome sequencing (WGS) has facilitated the interpretation of genetic patterns underlying phenotypic resistance in Mycobacterium tuberculosis (MT). To evaluate WGS in Laboratory for Mycobacteria (University Clinic Golnik, Slovenia), we retrospectively selected 66 MT isolates with suspected drug resistance from the National Mycobacterial Strain Collection in years 1996-2020. Additionally, 125 MT isolates from years 2021-2023 were prospectively included.

In retrospective cohort with high percent of resistant MT isolates (64/66; 97%), we observed different levels of agreement between phenotypic drug susceptibility testing (pDST) and WGS for different antibiotics (rifampicin 98.5%, ethambutol 92.3%, pyrazinamide 90.9%, ethionamide 84.1%, isoniazid 81.8%). One possible explanation for lower agreement between methods for detecting isoniazid resistance is that 9/66 (14%) were phenotypically sensitive to INH, where promoter mutation–57c>t in oxyR-ahpC was detected using WGS. For other antibiotics, such comparison was limited due to low number of MT isolates tested with pDST and due to detection of lesser-known mutations with yet unknown impact on resistance.

Prospectively, only six MT isolates (6/125; 5%) harboured different mutations linked to drug resistance. Resistance for all six MT isolates was confirmed with pDST leading to 100% with WGS. Most prevalent mutation was c-15t in fabG1, which was detected in four MT isolates with ETH and low level INH resistance.

To summarize, WGS proved to be useful in detecting resistance at the least for the first line antibiotics. To strengthen the power of WGS, the inclusion of isolates from different geographical regions in WHO mutation catalogue is necessary. 

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