Whole genome sequencing-based prediction of recurrent tuberculosis etiology for patients involved in a local outbreak

Whole-genome sequencing (WGS) of Mycobacterium tuberculosis (Mtb) is a modern approach in studying tuberculosis (TB) recurrence, which is essential for disease control. Although WGS-based SNP-distance analysis is a current standard in recurrent TB etiology determination, recent studies demonstrated the importance of detailed epidemiological cluster investigation to correctly discriminate between endogenous reactivation and exogenous reinfection. The aim of this research was to delineate the transmission network in the local TB outbreak and predict the cause of clinically confirmed recurrent TB cases. 10 Mtb isolates from 8 epidemiologically linked TB patients diagnosed in 2006-2016 were included in this study; two patients had a recurrent TB episode. WGS of Mtb DNA samples was conducted using Ion Torrent technologies. Bioinformatic analysis of WGS data was performed on the Galaxy web platform, and the median-joining network was constructed using PopArt software. Recurrent TB cases were analysed by determination of pairwise SNP- and network distances between the episodes. All isolates had identical spoligotyping (SIT53) and IS6110 RFLP pattern. The genetic relatedness was confirmed by WGS data, revealing 0-6 SNP distance. Data of specimen collection dates and SNP analysis allowed to predict Mtb transmission chain in the outbreak. Although exhibiting a small difference of 2 SNPs, in the median-joining network, two episodes of the first recurrent TB case showed different clustering mode and were connected via an intermediate node. A 5 SNP-distance was found in the second recurrent case, and the shortest path between the two nodes included a negative step followed by three positive steps. Thus, for both cases, reinfection is thought to be a cause of TB recurrence. This study highlighted the necessity of analysing recurrent TB cases as a part of a cluster investigation for more accurate identification of relapse etiology. This study was supported by RSU grant No. 23030103.