Monitoring mission of Tuberculosis Whole Genome Sequencing project in Indonesia

The aim of this survey was to evaluate the proportion of TB drug resistance in Indonesia. As a continuation of this survey, 1,604 samples out of the total 3,235 samples in the TB DRS were used for Whole Genome Sequencing (WGS) examination in 2018-2019 for further analysis. As WGS is a relatively new concept in genomic technologies, the country’s capacity of skill and proficiency in WGS laboratory work and data analysis, especially in TB, could be improved. WHO interceded and invited an external TB lab consultant from Italy to monitor the process of WGS and also to review the SOP in relation to the sample processing followed by sequencing. The recommendations were to be taken into account to complement the TB DRS as a whole.

From March 26th-29th 2019, Dr. Andrea Cabibbe visited Indonesia to monitor the process of Whole Genome Sequencing (WGS). Dr. Cabibbe is currently with the TB Supranational Reference Laboratory in Milan, Italy, and is also an external TB lab consultant for WHO Headquarters. During his visit, Dr. Cabibbe along with the WHO Indonesia country team and the TB DRS-WGS core national team visited the two labs that are performing WGS examinations for the TB DRS samples, and one other lab that performed bacterial culture and genomic DNA isolation in preparation for WGS. The two sequencing labs were the Integrated Laboratory of the Faculty of Medicine of University of Indonesia (Laboratorium Terpadu Fakultas Kedokteran Universitas Indonesia) and the National Center for Biomedical Research and Basic Health Technologies laboratory of NIHRD (Laboratorium Nasional Pusat Penelitian dan Pengembangan Biomedis dan Teknologi Dasar Kesehatan, Balitbangkes) and the culture/DNA isolation lab was the Microbiology Laboratory of the Faculty of Medicine of University of Indonesia (Laboratorium Mikrobiologi Fakultas Kedokteran Universitas Indonesia). During his visit, Dr. Cabibbe went through the entire Standard Operating Procedure (SOP) that is used by all the labs and observed the overall workflow of the sample processing inside the labs. His main goal was to identify both the major and minor details and variations that might lead to an inconsistency in the quality of the results.

So far, 517 out of 1604 samples (32.2%) have undergone good quality DNA extraction. Out of the extracted DNA samples, as many as 456 (88.2%) have been successfully sequenced. It is expected that the sequencing for all samples would be completed by the end of June 2019. Afterwards, data analysis and the final reports are expected to be completed by the end of October 2019 and December 2019 respectively.

At the end of his visit, Dr. Cabibbe provided his findings and recommendations to the laboratories and the TB DRS-WGS core national team. His overall impressions were generally positive as both labs have proven to be highly knowledgeable and capable of performing their respective tasks. Dr Cabibbe has given minor remarks to the labs’ SOP based on his own experience, to further improve the quality of the sample output.

This appraisal by Dr. Cabibbe is envisaged to enhance this unprecedented technique of WGS and thereby contribute to the TB DRS.