top of page


Experiences from a demonstration study on Nanopore sequencing for the diagnosis of drug-resistant tuberculosis in low-middle-income countries

A Slyzkyi(1) A Iskakova(2,3) A Kulzhabaeva(2,10) T Maya(4,5) N Thanh(6) B Myrzaliev(1,10) L Mtei(4) H Nguyen(7) N Hermans(1,8) L Manrho(9) P Lempens(1) D Luong(6) S Mfinanga(5) A Kadyrov(3) E Tiemersma(1) K Kremer(1)

1:KNCV Tuberculosis Foundation, The Hague, The Netherlands; 2:KNCV Tuberculosis Foundation Kyrgyzstan office, Bishkek, Kyrgyzstan; 3:National Center for Phthisiology, Bishkek, Kyrgyzstan; 4:KNCV Tuberculosis Foundation Tanzania office, Dar Es Salaam; 5:National Institute for Medical Research, Dar Es Salaam, Tanzania; 6:National Tuberculosis Program, Hanoi, Vietnam; 7:KNCV Tuberculosis Foundation Vietnam office, Hanoi, Vietnam; 8:National Institute for Public Health and the Environment, Bilthoven, The Netherlands; 9:Laboratory Microbiology Twente Achterhoek, Hengelo, The Netherlands; 10:Kyrgyz State Medical Academy, Bishkek, Kyrgyzstan

We are implementing a project to investigate the utility of nanopore sequencing for the diagnosis and surveillance of drug-resistant tuberculosis (DR-TB) and other lung diseases in national and decentralized laboratories in low-middle-income countries. We aim to generate evidence on the performance, patient-important outcomes, feasibility, acceptability, implementation costs and budget impact of using nanopore sequencing for this purpose. Here we present our first experiences with the implementation of this study.

The Oxford Nanopore Technologies (ONT, United Kingdom) targeted next-generation sequencing (tNGS) TB assay (OND-CUST-KIT) on MinION MK1B sequencers with wf-tb-amr (v2.0.0-beta.2) EPI2ME analysis workflow was implemented in Kyrgyzstan and Tanzania. Implementation is planned for Vietnam. Two two-weeks trainings were provided to the laboratory staff.

Sequencing is ongoing in Kyrgyzstan and Tanzania for validation purposes (n=200 samples tested) and for the investigation of patient-important outcomes in Kyrgyzstan (75/782 planned Xpert-positive TB patients enrolled). Implementation was delayed due to lengthy procedures for agreements, procurement and importation, and delays in delivery of equipment and reagents. Practical challenges included transcription errors in the preparation of the sample sheet for EPI2ME software analysis, lower sequencing capacity/flow cell than anticipated, and difficulties with updating the EPI2ME software (due to unstable internet connection).

Implementation of the ONT tNGS TB assay proved to be feasible with limited training. The recent workflow update improved the functionality and display of results of the EPI2ME analysis pipeline. The challenges and critical issues highlighted in this study will guide future development and scale-up of Nanopore sequencing for the detection of DR-TB.

bottom of page