CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis

Price, Valerie; Huo, Wenwen; Sharifi, Ardalan; Palmer, Kelli L.

doi:10.1128/msphere.00064-16

Cited by 111 publications

(166 citation statements)

References 63 publications

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“…We generated pAM771 transconjugants in a CRISPR3 cas9 deletion mutant of E. faecalis T11, and a derivative of this strain expressing CRISPR1- cas9 and tracrRNA (referred to as T11CR1 [Price et al, 2016]). These ermB -encoding transconjugants were then used as recipients for conjugation with pCR2 and pCR2- ermB .…”

Section: Resultsmentioning

confidence: 99%

Exploiting CRISPR-Cas to manipulate Enterococcus faecalis populations

Hullahalli

Rodrigues

Palmer

2017

eLife

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CRISPR-Cas provides a barrier to horizontal gene transfer in prokaryotes. It was previously observed that functional CRISPR-Cas systems are absent from multidrug-resistant (MDR) Enterococcus faecalis, which only possess an orphan CRISPR locus, termed CRISPR2, lacking cas genes. Here, we investigate how the interplay between CRISPR-Cas genome defense and antibiotic selection for mobile genetic elements shapes in vitro E. faecalis populations. We demonstrate that CRISPR2 can be reactivated for genome defense in MDR strains. Interestingly, we observe that E. faecalis transiently maintains CRISPR targets despite active CRISPR-Cas systems. Subsequently, if selection for the CRISPR target is present, toxic CRISPR spacers are lost over time, while in the absence of selection, CRISPR targets are lost over time. We find that forced maintenance of CRISPR targets induces a fitness cost that can be exploited to alter heterogeneous E. faecalis populations.DOI: http://dx.doi.org/10.7554/eLife.26664.001

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Section: Resultsmentioning

confidence: 99%

Exploiting CRISPR-Cas to manipulate Enterococcus faecalis populations

Hullahalli

Rodrigues

Palmer

2017

eLife

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“…However, the acquisition and maintenance of MGEs by E. faecalis depends on a variety of adaptive strategies that were not investigated here. These adaptations include the presence of CRISPR‐Cas in the chromosome (Palmer and Gilmore, ; Price et al ., ), restriction‐modification (RM) and anti‐RM systems, which would act against certain plasmids (e.g. pCF10); or lineage‐specific bacteriocins carried by pheromone‐responsive plasmids (Kurushima et al ., ) or conjugative transposons (Tn 916 ‐like elements) that might influence the transfer of genetic material within and between lineages (Manson et al ., ; Laverde Gomez et al ., ; León‐Sampedro et al ., ; Price et al ., ).…”

Section: Discussionmentioning

confidence: 99%

Phylogenomics of Enterococcus faecalis from wild birds: new insights into host‐associated differences in core and accessory genomes of the species

León‐Sampedro

Campo

Rodríguez-Baños

et al. 2019

Environmental Microbiology

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Summary Wild birds have been suggested to be reservoirs of antimicrobial resistant and/or pathogenic Enterococcus faecalis (Efs) strains, but the scarcity of studies and available sequences limit our understanding of the population structure of the species in these hosts. Here, we analysed the clonal and plasmid diversity of 97 Efs isolates from wild migratory birds. We found a high diversity, with most sequence types (STs) being firstly described here, while others were found in other hosts including some predominant in poultry. We found that pheromone‐responsive plasmids predominate in wild bird Efs while 35% of the isolates entirely lack plasmids. Then, to better understand the ecology of the species, the whole genome of fivestrains with known STs (ST82, ST170, ST16 and ST55) were sequenced and compared with all the Efs genomes available in public databases. Using several methods to analyse core and accessory genomes (AccNET, PLACNET, hierBAPS and PANINI), we detected differences in the accessory genome of some lineages (e.g. ST82) demonstrating specific associations with birds. Conversely, the genomes of other Efs lineages exhibited divergence in core and accessory genomes, reflecting different adaptive trajectories in various hosts. This pangenome divergence, horizontal gene transfer events and occasional epidemic peaks could explain the population structure of the species.

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“…Unmethylated incoming DNA is degraded by restriction enzymes produced by the cell, while the genome of the host remains protected due to methylation by the cognate methyltransferase. RM systems carried by ICEs of S. salivarius could protect their host from invasion by other genetic elements such as phages, thus playing a role in "cellular defense" as described for other bacteria (38)(39)(40). RM systems also turn out to be selfish mobile elements themselves (41).…”

Section: Resultsmentioning

confidence: 99%

Diversity of Integrative and Conjugative Elements of Streptococcus salivarius and Their Intra- and Interspecies Transfer

Dahmane

Libante

Charron-Bourgoin

et al. 2017

Appl Environ Microbiol

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Integrative and conjugative elements (ICEs) are widespread chromosomal mobile genetic elements which can transfer autonomously by conjugation in bacteria. Thirteen ICEs with a conjugation module closely related to that of ICESt3 of Streptococcus thermophilus were characterized in Streptococcus salivarius by wholegenome sequencing. Sequence comparison highlighted ICE evolution by shuffling of 3 different integration/excision modules (for integration in the 3= end of the fda, rpsI, or rpmG gene) with the conjugation module of the ICESt3 subfamily. Sequence analyses also pointed out a recombination occurring at oriT (likely mediated by the relaxase) as a mechanism of ICE evolution. Despite a similar organization in two operons including three conserved genes, the regulation modules show a high diversity (about 50% amino acid sequence divergence for the encoded regulators and presence of unrelated additional genes) with a probable impact on the regulation of ICE activity. Concerning the accessory genes, ICEs of the ICESt3 subfamily appear particularly rich in restriction-modification systems and orphan methyltransferase genes. Other cargo genes that could confer a selective advantage to the cell hosting the ICE were identified, in particular, genes for bacteriocin synthesis and cadmium resistance. The functionality of 2 ICEs of S. salivarius was investigated. Autonomous conjugative transfer to other S. salivarius strains, to S. thermophilus, and to Enterococcus faecalis was observed. The analysis of the ICE-fda border sequence in these transconjugants allowed the localization of the DNA cutting site of the ICE integrase.IMPORTANCE The ICESt3 subfamily of ICEs appears to be widespread in streptococci and targets diverse chromosomal integration sites. These ICEs carry diverse cargo genes that can confer a selective advantage to the host strain. The maintenance of these mobile genetic elements likely relies in part on self-encoded restrictionmodification systems. In this study, intra-and interspecies transfer was demonstrated for 2 ICEs of S. salivarius. Closely related ICEs were also detected in silico in other Streptococcus species (S. pneumoniae and S. parasanguinis), thus indicating that diffusion of ICESt3-related elements probably plays a significant role in horizontal gene transfer (HGT) occurring in the oral cavity but also in the digestive tract, where S. salivarius is present.

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CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis

Cited by 111 publications

References 63 publications

Exploiting CRISPR-Cas to manipulate Enterococcus faecalis populations

Exploiting CRISPR-Cas to manipulate Enterococcus faecalis populations

Phylogenomics of Enterococcus faecalis from wild birds: new insights into host‐associated differences in core and accessory genomes of the species

Diversity of Integrative and Conjugative Elements of Streptococcus salivarius and Their Intra- and Interspecies Transfer

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