A rationalized molecular and genomic coupled strategy to get a snapshot of the tuberculosis transmission in Madrid

Genomic epidemiology has improved our understanding of tuberculosis (TB) transmission beyond MIRU-VNTR analyses, but long-term genomic analysis required to identify transmission clusters remains unfeasible in many settings. Our objective is to evaluate an alternative strategy for obtaining a rapid snapshot of TB-transmission in populations without molecular/genomic systematic surveillance, using Madrid as a model. A total of 454 isolates (2019–2021) were analysed through a three-step sequential approach: (i) Preliminary screening of potential clusters, by a 6-loci MIRU panel; (ii) extended MIRU-24 exclusively on the MIRU-6-clusters; and (iii) WGS applied solely on the MIRU-24-clusters. This process progressively excluded orphan cases, reducing WGS to 13% of total isolates and confirming 17 transmission clusters. Genomic data from six clusters were used to identify strain-marker single-nucleotide-polymorphisms (SNPs), enabling the design of a multiplex-PCR assay followed by targeted nanopore sequencing of the amplicons. This approach allowed the rapid exclusion of cluster involvement in new incident and retrospective cases without requiring WGS. Our strategy based on the identification of clusters by a retrospective sequential application of progressively enhanced discriminatory molecular/genomic methods, coupled with targeted sequencing of amplicons harbouring strain-marker SNPs, may contribute to a more rationalised use of resources and facilitate timely updates on TB-transmission, where universal long-term WGS cannot be assured.

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Publication Details

Journal
Scientific Reports
Published
2026-07-22
DOI
https://doi.org/10.1038/s41598-026-59054-0
Primary Topic
Tuberculosis Research and Epidemiology
Type
article
Field-Weighted Citation Impact
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article

A rationalized molecular and genomic coupled strategy to get a snapshot of the tuberculosis transmission in Madrid

Cristina Loras, João Valverde, Laura Barrado, Beatriz Rodríguez-Ponga et al.
Scientific Reports
Tuberculosis Research and Epidemiology
article

A rationalized molecular and genomic coupled strategy to get a snapshot of the tuberculosis transmission in Madrid

Cristina Loras, João Valverde, Laura Barrado, Beatriz Rodríguez-Ponga, Paula López-Roa, Irene Díaz de la Torre, Laura Viñuela, Sara Hernández Egido, Vega Zamora, Jaime Esteban, María Simón Sacristán, María Jesús Ruiz‐Serrano, Carlos Toro Rueda, Diego Domingo, Andrea Marcos-Abellán, Guadalupe Bernal, María Jesús Ruiz Serrano, Felipe Pérez-García, Sergio Buenestado-Serrano, Laura Pérez-Lago, Jesús García Martínez, Darío García de Viedma, Marta Tato Diez, Patricia Muñoz, Álvaro Martínez, Mycobacteria Infections Madrid Study Group, Cristina Rodríguez-Grande, María Cabrera
article en

Abstract

Genomic epidemiology has improved our understanding of tuberculosis (TB) transmission beyond MIRU-VNTR analyses, but long-term genomic analysis required to identify transmission clusters remains unfeasible in many settings. Our objective is to evaluate an alternative strategy for obtaining a rapid snapshot of TB-transmission in populations without molecular/genomic systematic surveillance, using Madrid as a model. A total of 454 isolates (2019–2021) were analysed through a three-step sequential approach: (i) Preliminary screening of potential clusters, by a 6-loci MIRU panel; (ii) extended MIRU-24 exclusively on the MIRU-6-clusters; and (iii) WGS applied solely on the MIRU-24-clusters. This process progressively excluded orphan cases, reducing WGS to 13% of total isolates and confirming 17 transmission clusters. Genomic data from six clusters were used to identify strain-marker single-nucleotide-polymorphisms (SNPs), enabling the design of a multiplex-PCR assay followed by targeted nanopore sequencing of the amplicons. This approach allowed the rapid exclusion of cluster involvement in new incident and retrospective cases without requiring WGS. Our strategy based on the identification of clusters by a retrospective sequential application of progressively enhanced discriminatory molecular/genomic methods, coupled with targeted sequencing of amplicons harbouring strain-marker SNPs, may contribute to a more rationalised use of resources and facilitate timely updates on TB-transmission, where universal long-term WGS cannot be assured.

Scientific Reports
Universidad Complutense de Madrid (ES), Universidad de Alcalá (ES), Hospital Universitario La Paz (ES), Hospital General Universitario Gregorio Marañón (ES), Hospital Clínico San Carlos (ES), Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (ES), Hospital Universitario Fundación Alcorcón (ES), Hospital Universitario 12 De Octubre (ES), Hospital Universitario de Getafe (ES), Hospital Universitario Puerta de Hierro Majadahonda (ES), Hospital Universitario Príncipe de Asturias (ES), Hospital Universitario Fundación Jiménez Díaz (ES), Hospital Universitario de La Princesa (ES), Hospital Universitario de Fuenlabrada (ES), Hospital Universitario de Móstoles (ES), Hospital Universitario Severo Ochoa (ES), Hospital Universitario Infanta Sofía (ES), Instituto de Investigación de Enfermedades Raras (ES), Hospital Universitario Ramón y Cajal (ES), Hospital Central de la Defensa Gómez Ulla (ES), Universidad Autónoma de Madrid (ES)
Instituto de Salud Carlos III
Good health and well-being
Openalex Percentile: Top 9%
Tuberculosis Research and Epidemiology
DOIOpen Access PDFOpenAlex
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