Reducing delays in the genomic epidemiology of tuberculosis: a flexible and decentralized analysis of each incident case

Background Genomic analysis has enhanced our understanding of Mycobacterium tuberculosis (MTB) transmission. Short-read sequencing in reference labs ensures full population coverage but delays local data access. We assessed a case-by-case genomic approach using primary cultures from each incident case. Methods We prospectively evaluated 53 TB cases in Almeria, Spain, over two periods: 4 months (March–July 2023) for solid (LJ, 23 cases) and 9 months (April–December 2024) for liquid (MGIT, 30 cases) cultures. DNA was purified from LJ when sufficient growth was observed and from MGIT at positivity. Nanopore sequencing was performed on 1–4 cases per run, with flow-cells reused up to six times. Results In 74% of LJ, adequate growth was reached within 21 days. All LJ cultures achieved optimal genome coverage (> 90% at > 20X), 61% with runs under 2.5 hours. Nearly all MGIT cultures, analyzed at positivity (all but six within 21 days), achieved optimal coverage, despite interfering DNA. Four cases had slightly lower but acceptable coverage (73–88%, > 20X). Same-day classification as clustered or orphan was possible. Nanopore sequencing correlated with high-throughput short-read data, enabling quicker correction of epidemiological errors and identification of transmission links. Conclusions Our strategy offers a flexible, rapid decentralized alternative, accelerating cluster information contact tracing.