Using Evolutionary Analyses to Refine Whole-Genome Sequence Match Criteria

Abstract

Whole-genome sequence databases continue to grow. Collection times between samples are also growing, providing both a challenge for comparing recently collected sequence data to historical samples and an opportunity for evolutionary analyses that can be used to refine match criteria. We measured evolutionary rates for 22 Salmonella enterica serotypes. Based upon these measurements, we propose using an evolutionary rate of 1.97 single-nucleotide polymorphisms (SNPs) per year when determining whether genome sequences match.

Keywords: Salmonella enterica; closely related genetically; evolutionary analyses; evolutionary rate; match; outbreak investigation; resident strain; whole-genome sequence.