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letter
. 2024 Jul 1;1(7):320–322. doi: 10.5588/ijtldopen.24.0147

Table.

Summary of the implementation of WGS for MTB at the Vietnam National TB Reference Laboratory.

No Contents and descriptions
1. Sequencing platform:
Miniseq Illumina platform – whole-genome sequencing
2. Timeline:

  • A research grant-based implementation in 2020–2022 during COVID-19 outbreak which led to delays

  • 2020 for preparation step

  • 2021–2022 for sample collection, sequencing and data analysis
4. Cost:

  • Foreseen fixed start-up: USD122,907

  • Cost per sequenced sample: USD163
4. Human resources and training:

  • 1 clinical microbiologist and 3 laboratory technicians who had a basic background in medical laboratory sciences and more than 4 years’ experience in TB diagnostics.

  • Total 5 training courses provided: 1 for basic principles of NGS (3 days), 2 for DNA extraction, library preparation and sequencing (4 days each in OUCRU and NTRL), 1 for bioinformatics (1 day).

  • Remote technical support via Zoom call, chat provided by OUCRU when necessary
5. Major technical challenges Further solutions
The complexity of WGS protocol and workflow Received close technical support from OUCRU HCM team to set-up a sequencing laboratory and build staff capacity
Disrupted online pipeline to predict drug resistance Implemented the Clockwork pipeline on a specially purchased local high-performance computer
Some sequencing running errors were caused by improper placement of the sequencing device. Identified a separate and better temperature and humidity-controlled place for sequencing devices
Challenges with storing the large amounts of data from WGS Established a local server for data sequencing storage
6. Future plan

  • Training more staff to mitigate against employee turnover

  • Improving bioinformatics skills to make best use of the sequencing data

  • Procuring another sequencing platform with a larger capacity and a freezer with back-up power supply

  • Participating in a proficiency testing programme

WGS = whole-genome sequencing; MTB = M. tuberculosis; NGS = next-generation sequencing; OUCRU = Oxford University Clinical Research Unit; HCM = Ho Chi Minh.