Direct nanopore sequencing of M. tuberculosis on sputa and rescue of suboptimal results to enhance transmission surveillance

Whole-genome sequencing (WGS) enhances precision in predicting antimicrobial resistance and tracking Mycobacterium tuberculosis (MTB) transmission. Due to MTB’s slow-growing nature, genomic results are delayed; however, few efforts have sought to accelerate them by performing WGS directly on respiratory specimens. Most culture-free efforts have focused on accelerating resistance prediction. The present study provides further evidence to the only preceding study aiming to accelerate precise delineation of transmission, coupling culture-free WGS to a surveillance programme. Our study is distinguished from its predecessor by being the first to apply flexible nanopore sequencing to further accelerate the process. A total of 71 sputa were selected, in which we applied only a procedure to deplete human DNA, thus avoiding costly and cumbersome capture-bait alternatives. Optimal results (>90% genome covered, mean coverage >45× and >70% genome covered >20×) were obtained from 33.8% of cases, allowing the assignment to transmission clusters close to diagnosis of every new case. A further 12.6% of samples yielded suboptimal results (15.5%–90.92% at >10×), which were exploited through a rescue pipeline. This approach was based on identifying informative SNPs acting as markers for relevant transmission clusters in our population. The pipeline enabled pre-allocation of new cases to pre-existing clusters and, in some cases, precise genomic relationships with the preceding cases in the cluster. In summary, this study demonstrates that epidemiologically valuable information can be obtained directly from sputum in approximately half the samples analysed. It represents a new advancement in the pursuit of faster comparative genomics, with epidemiological purposes, at diagnosis.