Evaluation of SNP-based genotyping to monitor tuberculosis control in a high MDR-TB setting

Mycobacterium tuberculosis (Mtb) lineage identification and typing of clinical isolates in general is performed only retrospectively. The results are rarely linked to drug susceptibility testing (DST) or patient data. Consequently, the association between Mtb lineage, (multi)drug resistance and treatment history is not fully explored at the local level. Here we evaluated a new SNP based typing assay. We furthermore assessed the added value of genotyping of Mtb isolates for epidemiological purposes and guidance of tuberculosis (TB) control. Mtb lineage, DST profile and treatment history were determined for 399 samples at the National TB Reference Laboratory (NRL) in Tbilisi, Georgia by local staff. Data was shared electronically and analysis was performed remotely. Out of 399 isolates, 74 (74/399, 18.5%) were at least multidrug resistant (MDR)-TB, of which 63 (63/74, 85.1%) were members of three different Mtb Beijing lineages. Previous treatment was reported in 38/74 (51.4%) MDR(+) patients. The availability of this data allows associations with lineages. Notably, multidrug resistant TB was more strongly associated with the Beijing lineage than treatment history. Of all MDR-TB Beijing strains 56.7% (42/74) were members of a genetic cluster. This is most easily explained by (ongoing) MDR-TB transmission rather than drug resistance amplification. This knowledge is useful when designing intervention strategies for MDR-TB. Our study provides an example that on-site integrated Mtb genotyping is realistic and could support TB control activities.