Measuring recent in-country TB transmission using a classification model with whole genome sequencing data
Frederiks, W Anthony, RM de Vries, G
Frederiks, W
Anthony, RM
de Vries, G
Series / Report no.
Open Access
Type
Journal Article
Article
Article
Language
en
Date of publication
2026-05-11
Year of publication
Research Projects
Organizational Units
Journal Issue
Title
Measuring recent in-country TB transmission using a classification model with whole genome sequencing data
Translated Title
Published in
IJTLD Open 2026; 3(5):286-292
Abstract
BACKGROUND: Molecular typing of isolates provides insight into TB transmission by identifying clustering isolates. However, clustering alone does not necessarily indicate ongoing in-country transmission, as infections may have occurred abroad or long ago.
METHODS: We developed a classification model categorising clustering TB patients into three groups: i) likely, ii) possibly, and iii) unlikely to have been recently infected in the Netherlands. The model consists of two stages: i) individual labelling, followed by ii) cluster labelling for the remaining cases, and includes epidemiological, whole genome sequencing (WGS) data, and confirmed epidemiological links based on cluster investigation.
RESULTS: We found that 28% of TB patients with WGS results in 2018-2023 had a clustered isolate. However, when we classified cases by individual labelling (48% of cases) and cluster labelling (52% of cases), only 11% to a maximum of 15% were likely to have been infected within the last 2 years in the Netherlands.
CONCLUSION: Our WGS-based classification model provides a valuable tool for monitoring progress towards TB pre-elimination by enabling estimation of recent in-country transmission. Importantly, our findings indicate that a substantial proportion of clustered cases were likely the result of infections acquired abroad or from non-recent transmission events.