Integrating epidemiology and genomic sequencing to characterize tuberculosis transmission
Abstract
Tuberculosis (TB) remains a relevant public health challenge in settings characterised by high mobility and rapid population turnover, where independent cases, reactivations, and recent transmission may coexist. Integrating classical epidemiology with whole genome sequencing (WGS) allows recent transmission to be distinguished from unrelated case clustering and improves interpretation of complex events. To characterize a TB event in a high‑turnover reception centre through the integration of clinical, microbiological, epidemiological, and genomic data, and to evaluate how combining WGS and classical epidemiology supports identification of recent transmission. A descriptive observational study was conducted between July and December 2025. Clinical, microbiological, epidemiological, and genomic data were integrated. Cases were classified as genomically confirmed outbreak, outbreak without genomic evidence, or independent cases according to predefined criteria. Contact investigation included tuberculin skin testing (TST), chest radiography, and evaluation of latent TB infection. Seven active TB cases were identified. WGS confirmed a limited genomic outbreak involving two cases with 0 SNP differences and one associated secondary case. A second cluster was classified as an outbreak without genomic evidence, supported by close cohabitation and temporal exposure. Two additional cases were independent. Among 52 contacts evaluated, 43 had a positive TST at baseline, two showed TST conversion, and two secondary TB cases were identified. The event represented a mixed scenario, with genomic and non-genomic outbreaks and independent cases. Combining WGS with epidemiological analysis prevented outbreak overdiagnosis and supported targeted public health response in a high mobility setting.
Key messages: • Combining genomic sequencing with classical epidemiology improves identification of recent tuberculosis transmission and differentiation from unrelated cases in high mobility settings.
• An integrated genomic and epidemiological approach prevents overestimation of outbreaks and enables more targeted tuberculosis control in reception and transit centres.
Related
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BibTeX
@article{aquino2026integrating,
title = {{Integrating epidemiology and genomic sequencing to characterize tuberculosis transmission}},
author = {R Aquino and S Jiménez and MA Arce},
journal = {The European Journal of Public Health},
year = {2026},
month = oct,
doi = {10.1093/eurpub/ckag169.1841},
url = {https://doi.org/10.1093/eurpub/ckag169.1841},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - Integrating epidemiology and genomic sequencing to characterize tuberculosis transmission
AU - R Aquino
AU - S Jiménez
AU - MA Arce
PY - 2026
DA - 2026/10/01
JO - The European Journal of Public Health
DO - 10.1093/eurpub/ckag169.1841
UR - https://doi.org/10.1093/eurpub/ckag169.1841
AB - Tuberculosis (TB) remains a relevant public health challenge in settings characterised by high mobility and rapid population turnover, where independent cases, reactivations, and recent transmission may coexist. Integrating classical epidemiology with whole genome sequencing (WGS) allows recent transmission to be distinguished from unrelated case clustering and improves interpretation of complex events. To characterize a TB event in a high‑turnover reception centre through the integration of clinical, microbiological, epidemiological, and genomic data, and to evaluate how combining WGS and classical epidemiology supports identification of recent transmission. A descriptive observational study was conducted between July and December 2025. Clinical, microbiological, epidemiological, and genomic data were integrated. Cases were classified as genomically confirmed outbreak, outbreak without genomic evidence, or independent cases according to predefined criteria. Contact investigation included tuberculin skin testing (TST), chest radiography, and evaluation of latent TB infection. Seven active TB cases were identified. WGS confirmed a limited genomic outbreak involving two cases with 0 SNP differences and one associated secondary case. A second cluster was classified as an outbreak without genomic evidence, supported by close cohabitation and temporal exposure. Two additional cases were independent. Among 52 contacts evaluated, 43 had a positive TST at baseline, two showed TST conversion, and two secondary TB cases were identified. The event represented a mixed scenario, with genomic and non-genomic outbreaks and independent cases. Combining WGS with epidemiological analysis prevented outbreak overdiagnosis and supported targeted public health response in a high mobility setting. Key messages: • Combining genomic sequencing with classical epidemiology improves identification of recent tuberculosis transmission and differentiation from unrelated cases in high mobility settings. • An integrated genomic and epidemiological approach prevents overestimation of outbreaks and enables more targeted tuberculosis control in reception and transit centres.
SN - 1101-1262
SN - 1464-360X
ER -