Genotyping of Yersinia pestis

Abstract

Variation occurs on an individual bacterial genome and then becomes fixed in the population by evolutionary force, including both natural selection and neutral drift, subsequently shaping polymorphism of the species. Genome variations include single-nucleotide mutation, small fragment insertions and deletions (indels), structure variation [also known as SV, including large genome rearrangement (gain and loss)], and copy number variation. By determining these variations, we can identify bacteria strains of different populations and designate their genotypes or even distinguish isolates of different clinical samples during the same epidemic, which provides clues for source tracing in epidemic investigations and supports development of infectious disease control strategies. By comparison with Yersinia pestis reference genome sequences, different types of variations have been detected, and corresponding genotyping methods were developed. These methods included single-nucleotide polymorphism typing that targets single-nucleotide mutations, different region typing that targets the presence/absence of large genome fragments, multiple-locus variable number tandem repeat analysis that targets multiple tandem repeat loci, and clustered regularly interspaced short palindromic repeat (CRISPR) methods that target the composition of repeat-spacer arrays in three CRISPR loci. Here, we summarize these protocols including their experimental operation, data recording, and data analysis.