Publication
Whole-genome sequencing-based surveillance system for Mycobacterium tuberculosis in Portugal
| dc.contributor.author | Pinto, Miguel | |
| dc.contributor.author | Macedo, Rita | |
| dc.date.accessioned | 2025-11-18T12:12:07Z | |
| dc.date.available | 2025-11-18T12:12:07Z | |
| dc.date.issued | 2025-09-12 | |
| dc.description.abstract | To improve TB surveillance and diagnosis, the Portuguese National Reference Laboratory (NRL) began implementing whole-genome sequencing (WGS) for all RR/MDR-TB cases in 2019. Since 2020, this approach has been expanded to indiscriminately include all received isolates. We describe the current WGS-based surveillance system in Portugal, framed in prospective and retrospective data (n = 1171), upgraded for antimicrobial resistance (AMR) prediction and epidemiological analysis. This system relies on three main steps: QC/QA and contamination assessment, with a novel data filtering step; genotyping and AMR prediction; and dynamic SNP-based approach, maximizing variable sites under analysis. While lineage 4 was the most prevalent (84.3 %) followed by lineage 2 (9.1 %), less common EU/EEA sub-lineages (e.g., lineages 3 and 6) showcased cross-border transmissions. Molecular clusters (n = 157) displayed distinct AMR profiles and diverse possible epidemiological contexts. Among the pipeline upgrades, we highlight: i) the novel filtering step that allowed the improvement of 123 out of 128 contaminated samples; ii) tolerating missing data per site more than doubled core variable site resolution; iii) automatic maximization of shared variable sites for in-depth cluster analysis, key for consolidating genetic links in epidemiological investigation. This study highlights the importance of sustained prospective genomic surveillance towards strengthening TB management and diagnosis in Portugal. | eng |
| dc.description.sponsorship | This study was co-funded by the project “Sustainable use and integration of enhanced infrastructure into routine genome-based surveillance and outbreak investigation activities in Portugal” - GENEO (Project no. 101113460) on behalf of the EU4H programme (EU4H-2022-DGA-MS-IBA-01-02). | |
| dc.identifier.citation | Tuberculosis (Edinb). 2025 Dec:155:102691. doi: 10.1016/j.tube.2025.102691. Epub 2025 Sep 12 | |
| dc.identifier.doi | 10.1016/j.tube.2025.102691 | |
| dc.identifier.eissn | 1873-281X | |
| dc.identifier.issn | 1472-9792 | |
| dc.identifier.pmid | 40967101 | |
| dc.identifier.uri | http://hdl.handle.net/10400.18/10619 | |
| dc.language.iso | eng | |
| dc.peerreviewed | yes | |
| dc.publisher | Elsevier | |
| dc.relation | 101113460 | |
| dc.relation.hasversion | https://www.sciencedirect.com/science/article/pii/S1472979225000861?via%3Dihub | |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | |
| dc.subject | Tuberculosis | |
| dc.subject | Mycobacterium Tuberculosis Complex | |
| dc.subject | Antimicrobial Resistance | |
| dc.subject | Whole-Genome Sequencing | |
| dc.subject | Surveillance | |
| dc.subject | Bioinformatics | |
| dc.subject | Resistência aos Antimicrobianos | |
| dc.subject | Portugal | |
| dc.title | Whole-genome sequencing-based surveillance system for Mycobacterium tuberculosis in Portugal | eng |
| dc.type | journal article | |
| dcterms.references | https://www.sciencedirect.com/science/article/pii/S1472979225000861?via%3Dihub#appsec1:~:text=Download%20all%20supplementary%20files%20included%20with%20this%20article | |
| dspace.entity.type | Publication | |
| oaire.citation.startPage | 102691 | |
| oaire.citation.title | Tuberculosis | |
| oaire.citation.volume | 155 | |
| oaire.version | http://purl.org/coar/version/c_970fb48d4fbd8a85 |