In silico PCR

Following sequence assembly, several in silico PCRs were performed using an in-house Python script to confirm species identification as well as to look out for SNPs in genomic regions usually targeted by molecular assays. In short, bcsp31, a single-copy locus for identification, IS711, a multi-copy locus for identification, recA [31], a target to discriminate closely related Ochrobactrum from Brucella, BruceLadder [32], a multiplex PCR with specific band patterns after gel electrophoresis to distinguish Brucella species from each other, as well as rpoB [33], a hotspot region for rifampin resistance, were included.