A rationalized molecular and genomic strategy to get a snapshot of the tuberculosis peri-pandemic transmission in Madrid
Listed in
This article is not in any list yet, why not save it to one of your lists.Abstract
Genomic epidemiology has improved our understanding of tuberculosis (TB) transmission, overpassing the lower discriminatory MIRU-VNTR analysis. However, universal long-term genomic analysis is required to properly identify transmission clusters, which is not possible in many settings. We aim to evaluate an alternative strategy to obtain a fast snapshot of TB transmission, where systematic molecular/genomic surveillance is not running, using as a model Madrid, before and after the COVID-19 pandemic. We propose a rationalized use of MIRU-VNTR and whole genome sequencing (WGS) by following a 3-sequential step analytical pipeline: i) preliminary screening of potential clusters by a 6 loci-MIRU reduced panel (MIRU-6), ii) extended MIRU-24 genotyping, exclusively on the MIRU-6-defined clusters and iii) WGS only applied to confirm the MIRU-24-defined clusters. The application of our strategy on 454 isolates (years 2019 and 21), by progressively ruling out the orphan cases, limited the application of WGS to 59 cases (13% of the initial total cases), candidates to be part of 25 MIRU-24 clusters. Seventeen of those clusters were finally confirmed genomically; for eight of them, genomic data were exploited to identify strain marker SNPs. A multiplex PCR amplifying the regions harboring 15 marker SNPs for the selected clustered strains was analyzed by targeted nanopore sequencing. It allowed us to rule out their involvement in 202 new incident cases and, among 96 retrospective cases, identified three candidates to be part of two of the tracked clusters. Our strategy based on identifying clusters by a retrospective sequential application of progressively enhanced discriminatory molecular/genomic methods, coupled with targeted sequencing of amplicons harboring strain-marker SNPs, means a rationalized cost-effective usage of resources to fast update our knowledge on TB transmission, where universal long-term WGS cannot be assured.
