Whole genome sequencing of 230 Mycobacterium tuberculosis strains from Lithuania and Poland

The objective of this study was to compare the spoligotyping results for M. tuberculosis clinical isolates, produced using in vitro and in silico approaches. The study included 230 M. tuberculosis isolates, recovered from patients from Poland (n=86) and Lithuania (n=144) between 2018 and 2021. In this number were 130 multidrug-resistant (MDR) and 100 drug-susceptible (DS) isolates. Upon in vitro spoligotyping, the isolates produced 66 different profiles split into 22 clusters (n=186, 80.9%, 2-69 isolates per cluster) and 44 (19.1%) unique patterns. Spoligotypes inferred from the WGS data were congruent with in vitro generated profiles in 81.7% (188/230) for lorikeet and 81.3% (187/230) for SpolPred and SpoTyping software tools. All three implemented in silico approaches were similarly efficient in M. tuberculosis spoligotype prediction. However, given a relatively high (ca. 20%) discordance of the in vitro and in silico spoligotyping results, for comparative purposes we advise to perform this genotyping as a conventional, PCR-reverse hybridization assay.