Molecular Typing of Mycobacterium tuberculosis Strains in Gifu Prefecture, Japan, Using Variable Number Tandem Repeat Analysis

To investigate the molecular epidemiological characteristics of Mycobacterium tuberculosis strains collected from patients in Gifu Prefecture, Japan, 483 M. tuberculosis clinical isolates were analyzed using Japan Anti-Tuberculosis Association (JATA) 18-variable number tandem repeats (VNTR) between 2015 and 2019. To evaluate the lineage of M. tuberculosis strains, JATA18-VNTR profiles were applied to a maximum a posteriori method. The results revealed that the ancient Beijing subfamily, accounting for 57.3% (277/483) of the strains was the most prevalent M. tuberculosis strain. Furthermore, 18 clusters (GC-1-18) were found by minimum spanning tree analysis. The proportion of clustering strains was 9.9% (48/483), and epidemiological links to these clusters were unclear without GC-6 and GC-18. Meanwhile, interestingly, VNTR profiles of GC-7-9 and GC-14 were indistinguishable from the regional epidemic strains of Nagoya City, which has a strong socioeconomic relationship with Gifu Prefecture, but did not match the nationwide epidemic strains. This study suggests that coordinated analyses within the prefectures with strong socioeconomic relationships are important.