Countrywide implementation of whole genome sequencing: An opportunity to improve tuberculosis management, surveillance and contact tracing in low incidence countries

In 2014, the World Health Organization (WHO) and European Respiratory Society published a framework for the elimination of tuberculosis (TB) in low incidence countries, describing the priority actions to achieve this goal. These include: investment on new tools for early diagnosis, access to universal drug susceptibility testing (DST), contact investigation and continuous surveillance. A roadmap was recently proposed for Italy as model for low incidence countries, suggesting that TB elimination requires a concerted action fully coordinated at national and regional level. One of the major obstacles is the undetected transmission linked to international travels and migration. Whole genome sequencing (WGS) with the cost of a conventional Mycobacterium tuberculosis DST assay supplies “all-in-one” information required to track transmissions with high resolution and to provide personalised management of TB cases in a timeframe shorter than the standard diagnostic pathway. Here, we describe the results of a centralised WGS-based model for TB diagnosis and surveillance applied at regional level and how this model extended to a national scale in Italy or other low TB incidence countries could bring benefits to public health and patient management, saving costs for the health system.