Application of Whole-Genome Sequencing for Distinguishing Relapse from Reinfection in Tuberculosis Patients from Lithuania

Background Tuberculosis (TB) can reoccur even after successful treatment due to endogenous reactivation or exogenous reinfection. Understanding the etiology of TB recurrence might prevent further transmission and development of resistance. The rate of TB reinfection in patients from Lithuania has never been reported, and the underlying causes of TB recurrence remain poorly understood. Therefore, this study aimed to assess the rate of true TB relapses versus reinfection among patients with TB recurrence in Lithuania using whole-genome sequencing (WGS).Methods This study included 62 Mycobacterium tuberculosis complex (MTBC) isolates, recovered from as many pulmonary TB patients who had at least one reported TB recurrence or treatment failure episode and were treated in Vilnius University Hospital Santaros Klinikos between 2016 and 2023. The analysis of WGS results was performed using the MTBseq v1.0.3 bioinformatic pipeline. A cut-off of 5 single nucleotide polymorphisms (SNP) was used to differentiate between relapse and reinfection. A robust bootstrap-supported phylogenetic tree was produced using Randomized Axelerated Maximum Likelihood (RAxML) v.8.2.12 and subsequently visualized via the online interface Interactive Tree of Life (iTOL).Results The majority of all reported relapses were caused by true relapse, while reinfections accounted for 40%. Furthermore, half of the treatment failures were also found to be reinfections. Moreover, to our knowledge, this is the first study to report genotypic resistance to bedaquiline/clofazimine (BDQ/CFZ), delamanid/pretomanid (DLM/PA), and linezolid (LZD) in MTBC strains from Lithuania.Conclusions The risk of reinfection could be underestimated in Lithuania, highlighting the need for more effective infection control measures. Even a small-scale transmission of XDR-TB strains in the local population could have dramatic consequences on TB control in Europe.