OR20
Utility of targeted Nanopore sequencing for the detection of drug-resistant tuberculosis in Kyrgyzstan
A Kulzhabaeva(1) A Iskakova(1,2) G Saparova(2) F Tilekova(2) B Myrzaliev(3,4) M Ahmatov(1,3) A Duishekeeva(1,3) A Soorombaeva(1) A Toktogonova(2) M Sydykova(2) A Slyzkyi(4) N Hermans(4,5) A Kadyrov(2) G Kalmambetova(2) E Tiemersma(4) K Kremer(4)
1:KNCV Tuberculosis Foundation Kyrgyzstan office, Bishkek, Kyrgyzstan; 2:National Center for Phthisiology, Bishkek, Kyrgyzstan; 3:Kyrgyz State Medical Academy, Bishkek, Kyrgyzstan; 4:KNCV Tuberculosis Foundation, The Hague, The Netherlands; 5:National Institute for Public Health and the Environment, Bilthoven, The Netherlands
The utility of the Oxford Nanopore Technologies (ONT) early-access targeted next-generation sequencing (tNGS) tuberculosis (TB) assay (OND-CUST-KIT on MinION MK1B) was evaluated in Kyrgyzstan. The assay targets 24 resistance-associated genes, covering 16 anti-TB drugs, including all BPaL drugs.
For validation, 149/155 (95.5%) smear-positive sputum samples were successfully subjected to ONT-tNGS and Deeplex-Myc-TB-tNGS (GenoScreen, on MiSeq); 135 had complete standard of care drug susceptibility test (SOC-DST) results. Concordance was good for all anti-TB drugs, except pyrazinamid and ethambutol.
In a prospective cohort study from January 2024 to February 2025, of 997 enrolled Xpert TB-positive participants aged ≥18 years, 597 (60%) had complete tNGS and SOC-DST results. Among these, 267 (45%) had TB resistant to ≥1 drug by SOC-DST: 115 (19%) to isoniazid but not rifampicin and 117 (20%) to both rifampicin and isoniazid. Median turnaround times for line probe assay, phenotypic DST and tNGS were 4 (IQR:3–6), 26 (IQR:20–34), and 28 (IQR:15–50) days, respectively. The long turnaround time for tNGS was due to delays in supply of reagents and lack of trained staff during the first months of the study. In times when reagents and staff were available, the turnaround time of tNGS was 6 days (IQR: 5–8). Six patients showed bedaquiline resistance, detected by either tNGS only (n=2), phenotypic DST only (n=1), or by both (n=3). tNGS predicted pretomanid resistance in six cases, while phenotypic DST for pretomanid was not performed.
This ongoing study supports integration of tNGS into routine diagnostic algorithms for accurate and timely treatment decisions.