Automated design of outbreak-specific primers from massive pangenome graphs

Genomic surveillance has become standard for outbreak investigations. However, in routine clinical microbiology, sequencing many suspicious isolates from screening can be cost-prohibitive. Ideally, after identifying an outbreak, one would use an inexpensive but specific marker instead. Here, we present a method to design highly specific PCR primers, which target an in-group of genomes while avoiding amplification in a potentially large reference genome collection.