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

A rationalized molecular and genomic strategy to get a snapshot of the tuberculosis peri-pandemic transmission in Madrid | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article A rationalized molecular and genomic strategy to get a snapshot of the tuberculosis peri-pandemic transmission in Madrid Cristina Rodriguez, Guadalupe Bernal, Rosalia Palomino, Alvaro Martínez, and 10 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6135966/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version 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. tuberculosis clusters MIRU-VNTR WGS targeted sequencing Full Text Additional Declarations The authors declare no competing interests. The collection protocol was approved by the Research Ethics Commission of Gregorio Marañón Hospital and consent was not considered necessary due to the nature of the study. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6135966","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":422734404,"identity":"68f33bc8-ce80-4551-a328-43e1b5430423","order_by":0,"name":"Cristina Rodriguez","email":"","orcid":"","institution":"","correspondingAuthor":false,"prefix":"","firstName":"Cristina","middleName":"","lastName":"Rodriguez","suffix":""},{"id":422734481,"identity":"1ae4899e-ff0c-44dc-b39c-7f8922f4d331","order_by":1,"name":"Guadalupe 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