| Congresso Brasileiro de Microbiologia 2023 | Resumo: 594-1 | ||||
Resumo:Enterococcus faecalis is a commensal gut bacterium of humans and animals and is ubiquitous in natural environments. This species is also a leading cause of nosocomial infections worldwide, but its generalist lifestyle underlies an unclear division between commensal and high-risk strains. The aim of this study was to perform a comparative genomic analysis focusing on CRISPR2 variability in different E. faecalis sequence types (STs) to investigate the potential applicability of this locus in molecular epidemiology approaches. A local set of strains (total of 72) isolated from different sources in Rio de Janeiro state (Brazil) as well as strains of matching STs (total of 242) from diverse isolation and geographical origins and deposited in GenBank were examined. CRISPR2 loci prediction and typing were performed by using complementary bioinformatics tools (in silico PCR; CRISPRCasFinder; CRISPRtionary). Correlations between CRISPR2 type and strain-specific metadata, such as STs, isolation sources, genotypic traits of adaptive value (e.g., antimicrobial resistance genes and CRISPR-Cas functional systems), and core genome-based phylogenetic relatedness were investigated. Phylogeny reconstruction supported the division into two major clades: Clade I, mainly comprising strains from hospitalized human patients (and belonging to STs considered predominant in hospital settings, such as ST6, ST103, and ST525), and Clade II, which was more genetically diverse and included STs known for their ubiquitous distribution (e.g., ST16, ST21, ST40). CRISPR2 typing confirmed the limited diversity within the hospital-associated clade, as strains from closely related STs were assigned to the same CRISPR2 type. Most of these strains were predicted to be vancomycin-resistant enterococci (VRE) based on the detection of vanA or vanB genes. They consistently lacked CRISPR-Cas systems, which may be the reason for their notable ability to acquire mobile DNA. These results support the previous suggestion that CRISPR2 conservation in hospital lineages likely reflects events of DNA exchange in this niche, and such patterns may indicate an ongoing process of ecological specialization. On the other hand, the greater genetic diversity and ubiquity of Clade II were consistent with increased CRISPR2 variability, even among strains belonging to the same ST, such as ST4, ST21, and ST40, which also exhibited heterogeneous VRE and CRISPR-Cas genotypes. This high genetic diversity is likely associated with the generalist properties of these STs, allowing diverse fitness factors in changing environments, as supported by their isolation from humans, animals, food, and environmental sources. In addition, we identified similar CRISPR2 arrays between distantly related strains. For instance, CRISPR2 type 2A, an array suggested to be useful as a diagnostic marker for ST2/ST6 in previous reports, was also identified in three ST21 strains from animal-derived food, which may be an evidence of horizontal gene transfer between STs mainly found in hospitals and STs commonly isolated from food and environmental sources. Our findings confirm that CRISPR2 typing can be a valuable tool to gain insights into the eco-evolutionary dynamics of E. faecalis, which is essential for understanding the factors underlying the emergence and spread of high-risk lineages and for improving surveillance and control strategies in the perspective of One Health. Palavras-chave: CRISPR, Enterococcus faecalis, molecular epidemiology, One health Agência de fomento:CNPq, INPRA, CAPES, FAPERJ | |||||