Tracking a tuberculosis outbreak over 21 years: strain-specific single-nucleotide polymorphism typing combined with targeted whole-genome sequencing. The Journal of Infectious Diseases
Stucki et al. combined strain-specific single-nucleotide polymorphism (SNP) typing and targeted whole-genome sequencing (WGS) to investigate a tuberculosis cluster spanning 21 years in Bern, Switzerland. The authors screened 1’642 M. tuberculosis single patient isolates for the Bernese cluster–specific SNP and identified 71 isolates (4.3%) as belonging to this cluster. Most received a tuberculosis diagnosis in 1991–1995 and two thirds were homeless and/or substance abusers. The strain-specific SNP assay was approximately 15 times less expensive than the current gold standard.
In conclusion, a combined approach using strain-specific SNP genotyping with subsequent targeted WGS could be applied to track bacterial pathogens in real time and at high resolution.