title: A review of methods for subtyping Yersinia pestis: From phenotypes to whole genome sequencing.
abstract: Numerous subtyping methods have been applied to Yersinia pestis with varying success. Here, we review the various subtyping methods that have been applied to Y. pestis and their capacity for answering questions regarding the population genetics, phylogeography, and molecular epidemiology of this important human pathogen. Methods are evaluated in terms of expense, difficulty, transferability among laboratories, discriminatory power, usefulness for different study questions, and current applicability in light of the advent of whole genome sequencing.
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA. Electronic address: Amy.Vogler@nau.edu.
authors.forename: Amy J
authors.initials: AJ
authors.lastname: Vogler
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA; Translational Genomics Research Institute North, Flagstaff, AZ 86001, USA. Electronic address: Paul.Keim@nau.edu.
authors.forename: Paul
authors.initials: P
authors.lastname: Keim
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA. Electronic address: Dave.Wagner@nau.edu.
authors.forename: David M
authors.initials: DM
authors.lastname: Wagner
mesh_terms: D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D058889:Molecular Typing / Q000191:economics / Q000379:methods*; D010641:Phenotype; D010802:Phylogeny; D058974:Phylogeography; D010930:Plague / Q000382:microbiology*; D017422:Sequence Analysis, DNA / Q000379:methods; D015010:Yersinia pestis / Q000145:classification* / Q000235:genetics
keywords: CRISPR; DFR; Genotyping; IS element; LCB linking modes; MLVA; RFLP; SNP; Subtyping; VNTR; Yersinia pestis