The article investigates the involvement of hypermutation on chronic bacterial infection and its phylogenomic analyses implication. It cites studies which showed that hypermutator isolates increased numbers of single nucleotide polymorphisms (SNPs) and is associated with bacterial resistance as well as nonsynonymous mutations in mismatch repair (MMR)-related. It also mentions the analytical problems in hypermutation and the bias results in the inclusion of hypermutating strains.