Reconstituting the History of Cronobacter Evolution Driven by Differentiated CRISPR Activity

Abstract

strains harboring the CRISPR-Cas system are important foodborne pathogens causing serious neonatal infections. However, the specific role of the CRISPR-Cas system in bacterial evolution remains relatively unexplored. In this study, we investigated the impact of CRISPR-Cas in evolution and obtained 137 new whole-genome sequences of by next-generation sequencing technology. Among the strains examined (n=240), 90.6% (193/213) of prevalent species ,, and strains had intact CRISPR-Cas systems. Two rare species, (n=2) and (n=6), lacked and preserved the CRISPR-Cas system at a low frequency (1/6), respectively. These results suggest that the presence of one CRISPR-Cas system in is important for the species to maintain genome homeostasis for survival. The ancestral strain was likely to harbored both subtype I-E and I-F CRISPR-Cas systems, during the long evolutionary process, subtype I-E was retained, while subtype I-F selectively degenerated in species and was even lost in the major pathovars. Moreover, significantly higher CRISPR activity was observed in plant-associated species than in the virulence-related species and Similar spacers of CRISPR arrays were rarely found among species, suggesting intensive change through adaptive acquisition and loss. Differentiated CRISPR activity appears to be the product of environmental selective pressure and might contribute to the bidirectional divergence and speciation of This study reports the evolutionary history of under the selective pressure of the CRISPR-Cas system. One CRISPR-Cas system in is important for maintaining genome homeostasis, whereas two types of systems may be redundant and not conducive for acquiring beneficial DNA for environmental adaption and pathogenicity. Differentiated CRISPR activity has contributed to the bidirectional divergence and genetic diversity of This perspective makes a significant contribution to the literature by providing new insights into CRISPR-Cas systems in general, while further expanding the roles of CRISPR beyond conferring adaptive immunity and demonstrating a link to adaptation and species divergence in a genus. Moreover, our study provides new insights into the balance between genome homeostasis and the uptake of beneficial DNA related to CRISPR-based activity in the evolution of .

Evolution of the U.S. Biological Select Agent Rathayibacter toxicus

“…Results presented in this study underscore the importance of phage in the evolutionary and population dynamics of bacteria. NCPPB3778 and the CRISPR immune system are hypothesized to drive the evolution of R. toxicus , which is consistent with recent findings implicating CRISPRs in speciation of bacteria ( 52 ). Whether the low genetic diversity compromises the ability of R. toxicus to migrate from Australia and adapt to new environments is unknown.…”

Prevalence, Antibiotic Susceptibility, and Molecular Characterization of Cronobacter spp. Isolated From Edible Mushrooms in China

“…The source of infections in adults is still unidentified (Joseph and Forsythe, 2012). Some research reports indicated that the principal sources of this organism are associated with soil, water, and vegetables (Ueda, 2017; Zeng et al, 2018b). However, a clear understanding about the epidemiology and reservoirs of Cronobacter spp.…”

Cronobacter sakazakii, Cronobacter malonaticus, and Cronobacter dublinensis Genotyping Based on CRISPR Locus Diversity

“…Moreover, this genus has been isolated from the environment, food, and clinical sources (Ueda, 2017; Yong et al, 2018; Zeng et al, 2018a; Li et al, 2019). Further, C. sakazakii , C. malonaticus , and C. dublinensis are three prevalent species and some reports have indicated that the principal sources of these organisms might be soil, water, and vegetables (Ueda, 2017; Zeng et al, 2018b). However, the epidemiology and reservoirs of Cronobacter spp.…”

“…Unlike subtype I-E, which was commonly detected among Cronobacter strains, subtype I-F was found to be significantly more prevalent in the plant-associated species C. dublinensis than in the human virulence-related species C. sakazakii and C. malonaticus . However, C. condimenti lacked intact CRISPR-Cas system (Zeng et al, 2017, 2018b). At the same time, significantly higher CRISPR activity was also observed in the plant-associated species C .…”