Single-nucleotide polymorphism-based epidemiological analysis of Korean isolates.

BACKGROUND

Bovine tuberculosis (TB) is caused by , a well-known cause of zoonotic tuberculosis in cattle and deer, and has been investigated in many physiological and molecular studies. However, detailed genome-level studies of have not been performed in Korea.

OBJECTIVES

To survey whole genome-wide single-nucleotide polymorphism (SNP) variants in Korean field isolates and to define groups in Korea by comparing SNP typing with spoligotyping and variable number tandem repeat typing.

METHODS

A total of 46 field isolates, isolated from laryngopharyngeal lymph nodes and lungs of Korean cattle, wild boar, and Korean water deer, were used to identify SNPs by performing whole-genome sequencing. SNP sites were confirmed via polymerase chain reaction using 87 primer pairs.

RESULTS

We identified 34 SNP sites with different frequencies across isolates, and performed SNP typing and epidemiological analysis, which divided the 46 field isolates into 16 subtypes.

CONCLUSIONS

Through SNP analysis, detailed differences in samples with identical spoligotypes could be detected. SNP analysis is, therefore, a useful epidemiological tracing tool that could enable better management of bovine TB, thus preventing further outbreaks and reducing the impact of this disease.