4.2. Pathogen selection and prioritisation

A national or regional plan for priority pathogens for sequencing can also be important for introducing WGS into your AMR surveillance system. Thinking about local disease burden, the population’s immunity, case-fatality rates, outbreak risk, transmissibility and drug resistance will help inform this plan (Khoo et al., 2024). Phenotypic data such as antimicrobial-susceptibility profiles can further guide the selection of isolates for sequencing by highlighting unusual resistance patterns or treatment failures. This ensures that sequencing efforts are targeted toward the most clinically and epidemiologically relevant cases.