Incidence of Type II CRISPR1-Cas Systems in Enterococcus Is Species-Dependent

Abstract

CRISPR-Cas systems, which obstruct both viral infection and incorporation of mobile genetic elements by horizontal transfer, are a specific immune response common to prokaryotes. Antiviral protection by CRISPR-Cas comes at a cost, as horizontally-acquired genes may increase fitness and provide rapid adaptation to habitat change. To date, investigations into the prevalence of CRISPR have primarily focused on pathogenic and clinical bacteria, while less is known about CRISPR dynamics in commensal and environmental species. We designed PCR primers and coupled these with DNA sequencing of products to detect and characterize the presence of cas1, a universal CRISPR-associated gene and proxy for the Type II CRISPR1-Cas system, in environmental and non-clinical Enterococcus isolates. CRISPR1-cas1 was detected in approximately 33% of the 275 strains examined, and differences in CRISPR1 carriage between species was significant. Incidence of cas1 in E. hirae was 73%, nearly three times that of E. faecalis (23.6%) and 10 times more frequent than in E. durans (7.1%). Also, this is the first report of CRISPR1 presence in E. durans, as well as in the plant-associated species E. casseliflavus and E. sulfureus. Significant differences in CRISPR1-cas1 incidence among Enterococcus species support the hypothesis that there is a tradeoff between protection and adaptability. The differences in the habitats of enterococcal species may exert varying selective pressure that results in a species-dependent distribution of CRISPR-Cas systems.

Frequency of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in non-clinical Enterococcus faecalis and Enterococcus faecium strains

“…To fecal strains, the results are partial in agreement with Lyons et al 2015 andKatyal et al 2003 that reported CRISPRs in E. faecalis isolated from fecal specimens. Although Lyons et al (2015) described a high frequency of CRISPR1-cas in Enterococcus spp. isolates from animal fecal samples; CRISPR1-cas was not detected in E. faecalis strains.…”

“…The high frequency of CRISPRs in E. faecalis strains isolated from animal fecal samples, especially in fecal samples of wild animal could be related with low frequency of antibiotic resistance genes in these strains (Santestevan et al, 2015;Prichula et al, 2016). To fecal strains, the results are partial in agreement with Lyons et al 2015 andKatyal et al 2003 that reported CRISPRs in E. faecalis isolated from fecal specimens. Although Lyons et al (2015) described a high frequency of CRISPR1-cas in Enterococcus spp.…”

“…Differences in the distribution and the frequency of the Type II CRISPRs (CRISPR1-cas, CRISPR2, and CRISPR3-cas) in non-clinical E. faecalis and E. faecium were observed. These differences observed in CRISPRS distributions among enterococci species were reported before by Gilmore (2010), Lindenstrauß et al (2011), Katyal et al (2013), Hullahalli et al (2015) and Lyons et al (2015). The incidence of CRISPR1-cas gene in Enterococcus species is recognized; sometimes cas sequences are distinctly different from each other, showing species-level evolution.…”

“…Hullahalli et al (2015) showed that CRISPR2 locus is ubiquitous in E. faecalis. Until today, there are only a few reports evaluating the distribution of CRISPRs in non-clinical enterococci strains, isolated from food and animals fecal samples (Katyal et al, 2013;Lindenstrauß et al, 2011;Lyons et al, 2015). It is the first report of the presence of CRISPRs in E. faecalis and E. faecium isolates from fecal samples of wild marine animals.…”

“…The distribution of CRISPRs in clinical enterococci strains have been studied (Palmer and Gilmore, 2010;Lindenstrauß et al, 2011;Burley and Sedgley, 2012;Hullahalli et al, 2015), however, in non-clinical strains are still poorly studied (Katyal et al, 2013;Lyons et al, 2015). Therefore, the goal of this study was to determine the distribution and frequency of CRISPR1-cas, orphan CRISPR2 and CRISPR3-cas in E. faecalis and E. faecium strains isolated from food and fecal samples, including wild marine animals.…”