Dynamics of CRISPR Loci in Microevolutionary Process of Yersinia pestis Strains

Abstract

The potential use of CRISPR loci genotyping to elucidate population dynamics and microevolution of 146 Yersinia pestis strains from different biovars and locations was investigated in this work. The majority of strains from the Orientalis biovar presented specific spacer arrays, allowing for the establishment of a CRISPR signature for their respective isolates. Twenty-one new spacers were found in the Y. pestis strains from plague foci in Brazil. Ninety-three (64%) strains were grouped in the G1 genotype, whereas the others were distributed in 35 genotypes. This study allowed observing a microevolutionary process in a group of Y. pestis isolated from Brazil. We also identified specific genotypes of Y. pestis that were important for the establishment of the bacteria in plague foci in Brazil. The data have provided supporting evidence for the diversity and dynamics of CRISPR loci present in the genome of Y. pestis strains from plague foci in Brazil.

Spontaneous CRISPR loci generation in vivo by non-canonical spacer integration

“…Owing to its potential as a human pathogen, Y. pestis phylogeny has been heavily studied, with many strains of the species whole-genome sequenced 27 . One of the modern Y pestis strains, CO92, is typically used as the reference strain 28 .…”

“…One of the modern Y pestis strains, CO92, is typically used as the reference strain 28 . All but one strain of Y pestis have three active CRISPR loci (YPa, YPb and YPc), and only one of these loci is proximal to a set of Cas genes (YPa) 27 (Figs. 4b and 5a).…”

“…Figure adapted from ref. 27 , PLoS. b , Y. pestis contains three canonical CRISPR arrays (YPa, YPb and YPc) and one set of type I-F Cas genes.…”

Viability of Yersinia pestis subcultures in agar stabs

“…; Barros et al . , ), the nearly ubiquitous presence of these genes in virulent Y. pestis strains (Perry and Fetherston ), and the isolation of these strains during activities associated with surveillance of active disease, suggesting that all of these strains were originally virulent. It should be noted, however, that possession of all four virulence genes is not necessarily required for virulence (Leal‐Balbino et al .…”

“…; Barros et al . , ). In the course of these various studies, most of the original strain cultures were subcultured and the new subculture tubes kept together with the older subcultures, resulting in multiple stored subcultures of each strain created at different times.…”