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.