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Simplified strategy to update tuberculosis transmission situation in Madrid by rationalizing molecular and genomic sequential analysis

C Rodríguez-Grande(1,2) G Bernal(2) R Palomino-Cabrera(1,2) A Martínez(1,2) A Sanz-Pérez(1,2) A García-Toledo(1,2) S Buenestado-Serrano(1,2) D Peñas-Utrilla(1,2) B Plata-Barril(1,2) A Molero-Salinas(1,2) M Herranz-Martín(1,2) M J Ruíz-Serrano(1,2) P Muñoz(1,2,3,4) L Pérez-Lago(1,2) D García de Viedma(1,2,3)

1:Instituto de Investigación Sanitaria Gregorio Marañón; 2:Hospital General Universitario Gregorio Marañón; 3:CIBERES; 4:Universidad Complutense de Madrid

Molecular/genomic strategies provide a precise understanding of Mycobacterium tuberculosis transmission dynamics. We aim to evaluate an alternative strategy to faster update the epidemiological situation in Madrid, where systematic molecular/genomic surveillance is not running, through a rationalised use of MIRU-VNTR and whole genome sequencing (WGS). A three-step strategy was performed by sequential application of: i) preliminary screening of potential clusters by a 6 loci-MIRU reduced panel (MIRU6) on TB cases diagnosed in 2019 and 2021, ii) extended genotyping (MIRU24), applied exclusively on the MIRU6-defined clusters and iii) WGS on the MIRU24-defined clusters. The application of MIRU6 on 206 and 248 MTB isolates from 2019 and 2021, respectively, classified 220 (48.5%) as orphan. The remaining 234 cases were analysed by MIRU24; 59 (25%) were considered as involved in likely clusters and, finally, WGS confirmed 43 (73%) of them, with 76.5% of the clusters corresponding to recent transmissions (≤5 SNPs). 15 strain-marker SNPs for eight of the confirmed clusters (1-2 SNPs per cluster) were coupled in a multiplex-PCR and analysed by nanopore sequencing. Prospective targeted sequencing was performed in all the new TB cases along a 6-month period in Madrid (N=207). No new cases involving the targeted strains were identified. The application of a three-step sequential molecular/genomic strategy in Madrid reduced in 87% the strains to be characterized genomically to identify transmission clusters. Targeting strain-marker SNPs by multiplex-PCR and nanopore sequencing could mean an alternative to optimize and accelerate the prospective identification of selected strains.

Funding: ISCIII, IiSGM, COST Action-AdvanceTB, co-financed by ERDF.

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