Impact of library preparation-induced low GC sequencing bias on Salmonella serotype prediction using SeqSero2

A recent study by Uezle et al. reported a lack of O antigen prediction by SeqSero2. We found that Nextera XT-prepared genomes in the study were abnormally challenging for O antigen prediction because of unusually high sequencing bias against low GC regions that was not seen in similarly prepared genomes from other laboratories. We recommend that SeqSero2 users be mindful of the GC-related sequencing bias when analyzing Nextera XT-prepared genomes. Although it is unusual for such biases to compromise serotype prediction by SeqSero2 per our knowledge and analysis, it is unknown whether they could affect subtyping and characterization of other low-GC regions, such as Salmonella pathogenicity islands, when genome assembly is affected by such biases.