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Enterococcus faecalis

Enterococcus faecalis is a Gram-positive, facultative anaerobic coccus that typically occurs in pairs or short chains and is a ubiquitous commensal bacterium in the human gastrointestinal tract, female genital tract, and oral cavity, as well as in the environment such as soil and water.^[1]^[2]^[3] As part of the normal microbiota, it plays beneficial roles including vitamin production and nutrient metabolism from early in life.^[4] However, it is also an opportunistic pathogen, particularly in healthcare settings, where E. faecalis is responsible for approximately 80–90% of enterococcal infections, causing a range of infections due to its resilience and ability to survive harsh conditions like those on hospital surfaces.^[5]^[6]^[7] The most common infections associated with E. faecalis include urinary tract infections (UTIs), often linked to indwelling catheters, and bacteremia, which can lead to endocarditis and intra-abdominal or pelvic infections.^[1] It is responsible for a significant proportion of nosocomial infections, contributing to higher morbidity and mortality rates, especially in immunocompromised patients or those with underlying conditions.^[8]^[9] Less frequently, it causes wound infections, meningitis, and pneumonia.^[10]^[11] E. faecalis exhibits intrinsic and acquired resistance to multiple antibiotics, making treatment challenging, though it is generally more susceptible than Enterococcus faecium to agents like vancomycin (with only about 10% resistance compared to 80% in E. faecium).^[1] Common treatments involve ampicillin or vancomycin for susceptible strains, but vancomycin-resistant strains (VRE) necessitate alternatives like daptomycin or linezolid.^[12]^[13] Its adaptability, including biofilm formation and intracellular persistence within host cells, further enhances its pathogenic potential and complicates eradication.^[14]^[15]

Taxonomy and Classification

Etymology and Discovery

The genus name Enterococcus originates from the Greek "énteron" (intestine) and "kókkos" (berry or grain), denoting the bacterium's spherical, cocci-shaped morphology and its natural residence in intestinal environments, while the species epithet faecalis derives from the Latin "faex" (dregs or feces), reflecting its isolation from fecal sources.^[16]^[17] Enterococcus faecalis was first described in 1899 by French microbiologist Léon Thiercelin, who isolated a saprophytic diplococcus from human intestinal contents and termed it "entérocoque" to highlight its gut origin.^[1] In 1906, Frederick W. Andrewes and Thomas J. Horder further characterized the organism after isolating it from human feces and a patient with endocarditis, formally naming it Streptococcus faecalis within the Streptococcus genus based on its chain-forming, Gram-positive cocci appearance and association with human disease. This initial classification grouped it with other fecal streptococci, emphasizing its role as a commensal turned opportunistic pathogen. A pivotal reclassification occurred in 1984 when Karl-Heinz Schleifer and Renate Kilpper-Bälz transferred Streptococcus faecalis to the revived genus Enterococcus (nom. rev.), supported by DNA-rRNA hybridization experiments revealing low relatedness (below 70%) to typical streptococci and distinct phenotypic traits such as growth in 6.5% NaCl and at 45°C.^[18] Complementary studies in the 1980s, including 16S rRNA cataloging, confirmed the genetic divergence of enterococci from the Streptococcus genus, solidifying their separate phylogenetic position within the Firmicutes phylum.^[19] Key historical milestones include the 1930s, when James M. Sherman classified enterococci as a distinct physiological division of streptococci based on tolerance to high salt, temperature extremes, and alkaline pH, while Rebecca Lancefield's serologic grouping identified them as group D antigens, linking E. faecalis to urinary tract infections.^[20] By the 1980s, E. faecalis gained recognition as a major nosocomial pathogen, driven by surging reports of antibiotic resistance, particularly to ampicillin and vancomycin, which elevated its clinical significance in hospital settings.^[21]

Phylogenetic Relationships

Enterococcus faecalis belongs to the phylum Bacillota, class Bacilli, order Lactobacillales, and family Enterococcaceae.^[22] This placement reflects its Gram-positive, low-GC content characteristics shared with other lactic acid bacteria. The genus Enterococcus was established in 1984 through reclassification of certain streptococcal species, including S. faecalis, based on 16S rRNA oligonucleotide cataloging and phenotypic traits.^[18] Closest relatives within the genus include Enterococcus faecium, with which E. faecalis shares a common ancestor and exhibits high genomic similarity. Phylogenetic analyses based on 16S rRNA gene sequences place E. faecalis in a distinct clade from Streptococcus species, though both genera belong to the Lactobacillales order; intergenus 16S rRNA sequence similarity is approximately 95%.^[23] Multilocus sequence typing (MLST) using seven housekeeping genes has identified over 1,000 sequence types (STs) for E. faecalis, with ST6 belonging to clonal complex 2 (CC2) and frequently associated with clinical isolates from human infections.^[24] Evolutionary studies using genomic clocks trace the origins of the Enterococcus genus to the Paleozoic era, approximately 425–500 million years ago, coinciding with the emergence of early terrestrial hosts like arthropods.^[25] E. faecalis has acquired numerous mobile genetic elements, such as plasmids and transposons, likely through horizontal gene transfer from environmental bacteria, enhancing its adaptability to diverse niches including the mammalian gut.^[6] Hospital-associated lineages show adaptations predating the modern hospital era, suggesting divergence from commensal populations occurred thousands of years ago.^[26] Comparative genomics reveals that the E. faecalis genome is approximately 3 Mb in size, larger than many Streptococcus genomes (typically 1.8–2.5 Mb), reflecting gene acquisitions for host association. However, it features losses in certain carbohydrate metabolism pathways compared to free-living streptococci, indicating specialization to nutrient-scarce host environments like the intestine.^[27]

Morphology and Physiology

Cell Structure and Morphology

Enterococcus faecalis is a Gram-positive coccus that typically appears in pairs (diplococci) or short chains under microscopic examination. The cells measure approximately 0.5 to 1.5 μm in diameter and exhibit an ovoid shape under certain growth conditions. These bacteria are non-motile and non-spore-forming, lacking flagella or other appendages for locomotion.^[28]^[29]^[30] The cell wall of E. faecalis is characteristic of Gram-positive bacteria, featuring a thick peptidoglycan layer approximately 40 nm in width that provides structural rigidity and protection against osmotic stress. This layer is interspersed with anionic polymers, including wall teichoic acids (WTA) and lipoteichoic acids (LTA), which anchor proteins to the cell surface and contribute to ion homeostasis and adhesion. While most strains lack a true polysaccharide capsule, certain serotypes (C and D) produce capsular polysaccharides or the enterococcal polysaccharide antigen (EPA), which forms a protective layer enhancing immune evasion in some isolates.^[31]^[28]^[32] Ultrastructural analysis via transmission electron microscopy reveals pilus-like structures on the cell surface, particularly in strains like OG1RF, which facilitate adhesion to host tissues and other cells. The underlying cytoplasmic membrane contains cardiolipin lipids, which support membrane fluidity and stability, conferring tolerance to environmental solvents and stresses. These features underscore the bacterium's adaptability in diverse niches.^[33]^[34] For identification, E. faecalis stains Gram-positive and is catalase-negative, distinguishing it from staphylococci. It hydrolyzes esculin, producing a black precipitate on bile-esculin agar, and demonstrates tolerance to 6.5% NaCl and growth at pH 9.6, traits that differentiate it from other Gram-positive cocci like streptococci.^[28]^[35]^[29]

Growth and Metabolic Characteristics

Enterococcus faecalis is a facultative anaerobe capable of growth in both the presence and absence of oxygen.^[36] It exhibits optimal growth at temperatures between 35°C and 37°C, with a broader viable range from 10°C to 45°C.^[17] The bacterium demonstrates remarkable tolerance to environmental stresses, including bile salts up to 0.3% concentration and a pH range of 4.5 to 9.5, enabling survival in the gastrointestinal tract.^[37]^[38] Nutritionally, E. faecalis requires carbohydrates as primary energy sources and ferments sugars such as glucose, lactose, and mannitol through the Embden-Meyerhof-Parnas (glycolytic) pathway, yielding lactic acid as the predominant end product under anaerobic conditions.^[39] This homolactic fermentation supports efficient ATP production via substrate-level phosphorylation, with minimal byproducts like ethanol or formate in standard glucose metabolism.^[40] Under aerobic conditions, E. faecalis can engage in heme-dependent respiration when exogenous heme is available, enhancing growth yield by approximately twofold through oxidative phosphorylation and reducing reliance on fermentation.^[39] Additionally, in nutrient-limited settings, the bacterium utilizes citrate as an energy source via the citrate lyase complex, which cleaves citrate into oxaloacetate and acetate, followed by decarboxylation to pyruvate for further metabolism.^[41] Key adaptations include the expression of pyruvate formate-lyase during strict anaerobiosis, which converts pyruvate to acetyl-CoA and formate, facilitating mixed-acid fermentation and redox balance without external electron acceptors.^[39] For host survival, E. faecalis induces stress responses involving heat shock proteins such as DnaK and GroEL, which maintain protein homeostasis and confer thermotolerance up to 45°C.^[42]

Genetics and Regulation

Genome Organization

The genome of Enterococcus faecalis consists of a single circular chromosome and typically one to several small plasmids. Chromosome sizes range from approximately 2.8 to 3.4 Mb across strains, with a GC content of 37-38%. For example, the vancomycin-resistant clinical isolate V583 features a 3.22 Mb chromosome and three plasmids (pTEF1 at 66 kb, pTEF2 at 58 kb, and pTEF3 at 18 kb), yielding a total genome size of approximately 3.36 Mb. This strain encodes approximately 3,265 protein-coding genes.^[43]^[44] A hallmark of E. faecalis genome organization is the prevalence of mobile genetic elements, which account for about 25% of the DNA in strains like V583 and drive genomic plasticity. These include 38 insertion sequences (IS elements), such as multiple copies of IS256 (an IS3 family member), IS5-family elements, and IS6-family elements, which promote rearrangements, gene disruption, and acquisition of foreign DNA. Plasmids like pTEF1 often carry antibiotic resistance genes, including the vanA operon for vancomycin resistance, and encode conjugation machinery. The chromosome also harbors seven prophage regions and, in V583, a type II CRISPR-Cas system comprising cas genes and spacers that defend against bacteriophages and plasmids. Approximately 20-30% of the coding genes are devoted to transporters (e.g., ABC, phosphotransferase systems) and regulators (e.g., two-component systems), enabling environmental adaptation.^[45]^[46] Genomic organization varies significantly between clinical and commensal strains, reflecting adaptation to host-associated niches. Clinical isolates such as V583 contain extensive mobile elements, prophages, and integrated pathogenicity islands, contributing to over 25% acquired DNA, whereas commensal strains like OG1RF exhibit a more streamlined 2.74 Mb chromosome with fewer IS elements and reduced mobilome content. Functional annotation of E. faecalis genomes indicates that roughly 40% of predicted proteins remain hypothetical or of unknown function, underscoring gaps in understanding. The core genome, defined as genes conserved across diverse strains, comprises approximately 1,800 ORFs that form the foundational metabolic and housekeeping scaffold.^[46]^[47]

Regulatory RNAs

Regulatory RNAs in Enterococcus faecalis were first systematically identified in the early 2010s using high-throughput methods such as tiling microarray analysis and differential RNA sequencing (dRNA-seq). A seminal 2011 study characterized 11 small non-coding RNAs (sRNAs) across the core genome and pathogenicity island of strain V583, revealing their potential roles in gene regulation. Subsequent transcriptomic efforts expanded this repertoire significantly; a 2020 global transcription start site (TSS) mapping via RNA-seq predicted approximately 150 sRNA candidates, with about 22-25% classified as antisense RNAs overlapping protein-coding genes on the opposite strand. Additionally, riboswitches, such as the S-adenosylmethionine (SAM)-binding SMK box, were noted for their role in metabolic sensing, exemplifying the diversity of non-coding elements that include trans-encoded sRNAs, cis-antisense RNAs, and structured regulatory motifs. These sRNAs are distributed throughout the genome, often in intergenic regions or as 5'/3' untranslated regions (UTRs), contributing to fine-tuned post-transcriptional control.^[48]^[49]^[50] sRNAs in E. faecalis primarily function through post-transcriptional mechanisms to regulate virulence factors and stress adaptation, often by base-pairing with target mRNAs to alter translation efficiency or mRNA stability. For instance, a 2015 analysis of six core sRNAs (Efa0750, Efa1371, Efa1477, Efa1593, Efa2843, and Efa3254) demonstrated their control over proteins involved in virulence, such as adhesion and toxin production, as well as responses to oxidative and bile salt stresses; overexpression or deletion of these sRNAs modulated bacterial survival under host-like conditions. In virulence regulation, the antisense sRNA ASwalR targets the walR mRNA of the WalRK two-component system, reducing its expression and thereby suppressing biofilm formation and pathogenicity in endodontic infection models. Regarding stress responses, sRNAs like those studied in 2015 enhance tolerance to oxidative stress by indirectly influencing antioxidant enzyme levels, while the fsr quorum-sensing system—critical for gelatinase (GelE) expression—interacts with sRNA networks to coordinate population-level behaviors during infection. These functions underscore sRNAs' role in enabling E. faecalis to transition from commensal to pathogenic states.^[51]^[52]^[51] Mechanistically, E. faecalis sRNAs exert control via imperfect base-pairing with mRNA targets, frequently in the ribosome-binding or start codon regions, leading to translational repression or mRNA degradation without reliance on canonical RNA chaperones like Hfq, which is absent in enterococci. This Hfq-independent mode highlights evolutionary adaptations in Gram-positive bacteria. In the fsr quorum-sensing pathway, sRNAs contribute by modulating the processing and stability of fsrB-derived signaling peptides, linking density-dependent regulation to virulence gene expression like gelatinase. Recent investigations (2023-2024) have further connected sRNAs to adaptive phenotypes in clinical isolates; for example, differential sRNA expression in multidrug-resistant strains correlates with enhanced biofilm architecture and antibiotic tolerance, as seen in ASwalR-mediated WalRK suppression, which limits cell wall remodeling under sublethal antibiotic exposure. A 2022 gradient sequencing (Grad-seq) study also revealed sRNA-protein complexes involving RNA-binding proteins like KhpB, predicting interactions that bolster tolerance to oxidative and bile stresses in nosocomial settings. These findings position sRNAs as pivotal for E. faecalis persistence in hostile environments.^[49]^[53]

Ecology and Distribution

Natural Habitats and Reservoirs

Enterococcus faecalis primarily resides as a commensal bacterium in the gastrointestinal tracts of humans and various animals, where it plays a role in gut microbiota dynamics. In humans, it is the predominant enterococcal species, accounting for 80-90% of isolates from intestinal samples, with concentrations reaching up to 10^6 colony-forming units (CFU) per gram of feces.^[54] Beyond the intestines, E. faecalis colonizes the oral cavity and vaginal microbiota, contributing to microbial homeostasis in these niches.^[3] In animals, it is similarly prevalent in the guts of domestic species such as poultry, pigs, and cattle, serving as a reservoir that facilitates zoonotic transmission.^[55] The bacterium's presence in animal reservoirs extends into the food chain, where contamination occurs through fecal shedding during slaughter and processing. E. faecalis has been detected in raw meats, particularly poultry and pork, as well as in unpasteurized dairy products, posing risks for foodborne dissemination to humans via undercooked or mishandled foods.^[55] Studies highlight its adaptation to these hosts, with genetic lineages showing host-specific clustering that underscores the role of livestock in maintaining environmental pools of the species.^[56] E. faecalis demonstrates notable persistence in extraintestinal environments, including soil, surface waters, and sewage systems, where it withstands stressors like desiccation, nutrient scarcity, and ultraviolet radiation. This resilience is partly attributed to the production of enterocins, antimicrobial bacteriocins that inhibit competing microbes and enhance survival in harsh conditions.^[57] Transmission primarily follows the fecal-oral route, amplified by foodborne pathways, as evidenced in recent reviews emphasizing the spread through contaminated meats in agricultural settings.^[58]

Environmental Contamination and Indicators

Enterococcus faecalis, a predominant species within the enterococci group, serves as a key indicator of fecal pollution in recreational waters, as recognized by the U.S. Environmental Protection Agency (EPA) and the World Health Organization (WHO). These organizations employ enterococci levels to assess contamination risks in environments such as swimming pools, beaches, and rivers, where the bacteria signal the potential presence of pathogens from human or animal waste. According to 2012 EPA guidelines (current as of the 2023 five-year review), enterococci concentrations should not exceed a geometric mean of 35 CFU per 100 mL or a statistical threshold value of 130 CFU per 100 mL (exceeded no more than 10% of samples in any 30-day interval) in both marine and freshwater to limit health risks, including gastrointestinal illness.^[59] The 2021 WHO guidelines set a threshold of 200 CFU per 100 mL (95th percentile) for intestinal enterococci in recreational waters for low-risk classification.^[60]^[61] In swimming pools, E. faecalis demonstrates notable resilience to standard chlorination levels of 0.5–1 ppm free chlorine, outperforming coliform indicators due to its propensity for cellular clumping, which shields bacteria from disinfectants. This tolerance contributes to persistent contamination, particularly in facilities with inadequate maintenance. Studies from the 2010s have associated recreational water outbreaks—though often involving other pathogens—with poor hygiene practices that facilitate fecal shedding into pools, underscoring E. faecalis as a reliable marker for such vulnerabilities.^[62]^[63]^[64] Asymptomatic human carriers typically carry E. faecalis at concentrations of 10^5–10^7 CFU per gram of feces, with rates amplified following antibiotic exposure due to microbiota disruption favoring enterococcal overgrowth.^[3] Recent investigations, including 2023 analyses of bather impacts, reveal increased post-swim shedding that directly elevates enterococci levels in recreational waters, emphasizing hygiene's role in contamination dynamics. This shedding pattern highlights E. faecalis' utility in tracking anthropogenic fecal inputs.^[65]^[66] Detection of E. faecalis in contaminated environments relies on membrane filtration techniques, where water samples are passed through 0.45-μm filters and incubated on selective chromogenic media such as mEI agar, enabling presumptive enumeration of enterococci through color development. Confirmation and species differentiation from E. faecium involve biochemical assays, including arabinose fermentation (negative for E. faecalis) and pigment production tests, ensuring accurate identification in monitoring programs. These methods align with EPA-approved protocols for rapid and reliable assessment.^[67]^[68]^[69]

Pathogenicity and Virulence

Key Virulence Factors

Enterococcus faecalis employs several key virulence factors that facilitate adhesion, tissue invasion, immune evasion, and coordinated expression of pathogenic traits. Among the adhesins, the enterococcal surface protein (Esp) plays a critical role in binding to host epithelial cells, promoting colonization in urinary tract and endocardial infections. ^[70] Esp expression is associated with increased biofilm formation on abiotic surfaces and enhanced persistence in endocarditis models. ^[71] Another important adhesin is the aggregation substance (Agg), a surface protein that mediates bacterial clumping and adherence to eukaryotic cells, particularly contributing to the development of endocarditis by facilitating platelet-fibrin binding. ^[70] Toxins and enzymes further enable tissue damage and dissemination. Cytolysin, a hemolysin encoded by the cyl operon, exhibits pore-forming activity that lyses host cells, including erythrocytes and neutrophils, thereby aiding in nutrient acquisition and immune suppression during infection. ^[71] Gelatinase (GelE), a zinc metalloprotease, degrades host extracellular matrix components such as collagen and fibrinogen, facilitating bacterial spread and abscess formation; its activity is linked to increased virulence in animal models of peritonitis and endocarditis. ^[70] For immune evasion, capsular polysaccharides shield E. faecalis from phagocytosis by inhibiting opsonization and complement activation, with strains possessing the cps operon showing reduced uptake by macrophages. ^[32] Superoxide dismutase (SodA) neutralizes reactive oxygen species produced by host phagocytes, enhancing intracellular survival and contributing to persistence in inflammatory environments. ^[71] Quorum sensing via the Fsr system regulates virulence factor expression in response to population density. This two-component system activates the transcription of the fsrABDC operon, leading to production of gelatinase and serine protease, which are crucial for biofilm maturation and endodontic persistence; recent 2024 reviews highlight the Fsr system's role in refractory root canal infections by coordinating adaptive responses to host antimicrobials. ^[72] ^[73]

Biofilm Formation and Survival Mechanisms

Enterococcus faecalis forms complex, multilayered biofilms on medical devices such as urinary catheters and heart valves, creating structured communities embedded in an extracellular matrix that enhances persistence in hostile environments.^[74] These biofilms are regulated by quorum sensing systems, particularly the fsrABDC operon, which controls the production of gelatinase (GelE) and serine protease (SprE), promoting biofilm development on abiotic surfaces.^[75] Biofilm formation in E. faecalis proceeds through distinct stages: initial attachment mediated by pili such as the Ebp pilus, which facilitates adherence to host tissues and surfaces; maturation involving the accumulation of extracellular DNA (eDNA) released by autolysin AtlA and polysaccharides that stabilize the matrix structure; and dispersal that promotes detachment and dissemination to new sites.^[76] Specific adhesins like Ebp pili contribute to the initial reversible attachment phase, enabling subsequent irreversible binding.^[76] For survival within biofilms and under stress, E. faecalis employs DNA repair mechanisms, including RecA-dependent homologous recombination, which repairs UV-induced damage and maintains genomic integrity, as evidenced by significantly reduced survival in recA mutants exposed to radiation.^[77] Resistance to oxidative stress is bolstered by the heme-dependent catalase KatA, which degrades hydrogen peroxide, conferring protection when environmental heme is available and enhancing viability in phagocyte-rich environments.^[78] Clinically, E. faecalis biofilms exhibit 100- to 1,000-fold increased tolerance to antibiotics compared to planktonic cells, complicating treatment of infections like endocarditis and catheter-associated urinary tract infections.^[79] As of 2025, studies indicate a global prevalence of biofilm-forming E. faecalis in up to 70% of healthcare-associated infections, underscoring its role in persistent nosocomial outbreaks.^[80] Recent 2025 studies highlight quorum sensing disruption, particularly targeting the fsr system, as a promising therapeutic strategy to inhibit biofilm maturation and restore antibiotic susceptibility.^[72]

Clinical Significance

Associated Infections and Epidemiology

Enterococcus faecalis is a leading cause of several serious infections, particularly in healthcare settings. It is responsible for approximately 10-15% of nosocomial bacteremia cases, often originating from urinary tract or intra-abdominal sources.^[1] Infective endocarditis due to E. faecalis is increasingly prevalent, accounting for 10-14% of all endocarditis cases and predominantly affecting elderly patients with underlying valvular abnormalities or prosthetic valves.^[81] Enterococci are an important cause of community-acquired urinary tract infections (UTIs), accounting for 5-10% of cases, especially in older adults or those with complicating factors such as urinary obstruction.^[82] Beyond these primary sites, E. faecalis contributes to wound infections, particularly surgical site and chronic wounds like diabetic ulcers; meningitis, often in neonates or post-surgical patients; and intra-abdominal abscesses, typically as part of polymicrobial flora.^[83] In endodontics, E. faecalis is frequently implicated in persistent root canal infections, forming part of polymicrobial communities in 24-90% of treatment failure cases.^[84] These virulence factors, such as biofilm production, facilitate tissue invasion and persistence in diverse anatomical sites.^[1] Epidemiologically, E. faecalis accounts for about 9% of all hospital-acquired infections in the United States as of 2021, with higher rates in intensive care units where enterococci rank second or third most common nosocomial pathogens after Staphylococcus aureus and Pseudomonas aeruginosa.^[85] As of 2021, E. faecalis ranked third among HAI pathogens in US hospitals (8.6%), with rising incidence in ICU central line-associated bloodstream infections (12.5%).^[86] Risk factors include indwelling catheters, recent surgery, prolonged hospitalization, and immunosuppression, which compromise host defenses and promote bacterial translocation.^[87] There has been a notable global rise in vancomycin-resistant enterococci (VRE), primarily E. faecium, though rates in E. faecalis remain low at around 10%; regional variations exist, with higher resistance in E. faecium up to 20% in some EU/EEA countries as of 2023.^[88] Demographically, infections are more prevalent among immunocompromised individuals, including those with cancer, transplant recipients, or HIV/AIDS. As of the late 1990s, enterococci caused approximately 110,000 UTIs annually in the United States, with current totals likely higher.^[89] In developing regions, foodborne transmission linked to contaminated meat and dairy products serves as an emerging reservoir, exacerbating community spread in areas with limited sanitation.^[90]

Diagnosis and Prevention Strategies

Diagnosis of Enterococcus faecalis infections typically begins with conventional microbiological techniques, including blood or urine cultures grown on selective media such as bile esculin azide agar, which facilitates the isolation and preliminary identification of enterococci by their ability to hydrolyze esculin in the presence of bile.^[91] These cultures are particularly useful for detecting the bacterium in common infection sites like urinary tract infections and bacteremia.^[91] For rapid species identification and detection of resistance, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is employed directly from positive blood culture bottles, offering results within minutes and high accuracy for distinguishing E. faecalis from other enterococci.^[6] Molecular diagnostics enhance specificity and speed, with polymerase chain reaction (PCR) assays targeting species-specific genes and vancomycin resistance determinants like vanA and vanB to confirm E. faecalis and assess susceptibility profiles early in the diagnostic process.^[92] Additionally, 16S rRNA gene sequencing provides culture-independent identification, especially valuable in cases of fastidious growth or prior antibiotic exposure, by amplifying and sequencing conserved bacterial ribosomal regions for phylogenetic classification.^[93] In suspected endocarditis, transthoracic or transesophageal echocardiography visualizes vegetations on heart valves, while serological antigen tests, such as those detecting the endocarditis-associated antigen (EfaA) or the 112 kDa protein via enzyme-linked immunosorbent assay (ELISA), aid in confirming E. faecalis involvement through antibody responses.^[94]^[95] Prevention strategies emphasize infection control measures in healthcare settings, where hand hygiene with alcohol-based sanitizers or soap and water, combined with proper catheter care protocols—including aseptic insertion, daily review of necessity, and securement to minimize movement—significantly reduce transmission risks associated with indwelling devices.^[96] Antibiotic stewardship programs are critical to limit selective pressure driving resistance, promoting judicious use through guidelines on appropriate prescribing, de-escalation based on culture results, and avoidance of broad-spectrum agents when unnecessary.^[96] In environmental contexts, such as recreational water, maintaining free chlorine levels above 1 ppm at a pH of 7.0–7.8 ensures effective disinfection against E. faecalis, which serves as a fecal contamination indicator, thereby preventing waterborne spread.^[97] Vaccination efforts remain experimental, focusing on polysaccharide-conjugate vaccines that link enterococcal capsular polysaccharides to carrier proteins for enhanced immunogenicity; preclinical and early-phase trials from 2020 onward have demonstrated promise in eliciting protective antibodies against bacteremia in animal models, though human trials are ongoing to evaluate efficacy and safety.^[98]^[99]

Antibiotic Resistance

Mechanisms of Resistance Development

Enterococcus faecalis exhibits intrinsic resistance to several antibiotics through inherent structural and biochemical features that limit drug efficacy. One primary mechanism is the low permeability of its cell wall to aminoglycosides, such as gentamicin, due to the absence of a porin-like system that facilitates antibiotic entry in other Gram-positive bacteria.^[100] Additionally, some strains produce beta-lactamase enzymes that hydrolyze beta-lactam antibiotics like penicillin, although this is relatively rare in E. faecalis compared to Enterococcus faecium.^[100] Altered penicillin-binding proteins (PBPs), particularly PBP5, further contribute by reducing the binding affinity of beta-lactams to their targets, thereby decreasing cell wall synthesis inhibition.^[5] Acquired resistance in E. faecalis primarily arises through horizontal gene transfer of mobile genetic elements, enabling the bacterium to adapt rapidly to selective pressures. Conjugation via plasmids and transposons is a key process, with the Tn1546 transposon exemplifying this by carrying the vanA gene cluster, which confers high-level resistance to vancomycin by modifying peptidoglycan precursors to prevent drug binding.^[100] Similarly, point mutations in the gyrA gene alter DNA gyrase, reducing susceptibility to fluoroquinolones like ciprofloxacin.^[100] These elements facilitate the spread of resistance determinants within bacterial populations. The development of resistance is enhanced by pathways such as horizontal gene transfer occurring preferentially in biofilms, where close cell proximity promotes conjugation and transformation efficiency.^[5] Recent reviews highlight environmental acquisition from soil bacteria as a significant reservoir, allowing E. faecalis to integrate resistance genes from diverse ecological niches through transposon-mediated exchanges.^[5] Regulatory mechanisms fine-tune resistance expression in response to antibiotics, with two-component systems playing a central role. The VanS/VanR system, for instance, consists of a membrane-bound sensor kinase (VanS) that detects glycopeptides like vancomycin and autophosphorylates, subsequently transferring the phosphate to the response regulator VanR, which activates transcription of the van operon genes.^[101] This inducible regulation ensures efficient resource allocation for resistance maintenance.

Multidrug Resistance Profiles

Enterococcus faecalis displays notable multidrug resistance (MDR) profiles, particularly in clinical settings where vancomycin-resistant enterococci (VRE) isolates are prevalent. The VanA phenotype, characterized by high-level resistance to vancomycin (MIC ≥64 μg/mL) and teicoplanin (MIC ≥16 μg/mL), is less common in E. faecalis than in E. faecium. In contrast, the VanB phenotype confers moderate vancomycin resistance (MIC 4-64 μg/mL) but susceptibility to teicoplanin, accounting for a significant portion of VRE cases in E. faecalis, with overall VRE prevalence in U.S. healthcare-associated infections reaching about 30% among enterococci, though lower specifically for E. faecalis at approximately 5% as of 2018-2021 CDC data (stable through 2023-2025).^[102]^[103] Resistance to other antibiotics is also common, with ampicillin resistance uncommon (<10%) in clinical E. faecalis isolates globally. High-level gentamicin resistance, leading to loss of synergism with beta-lactams, affects around 30-40% of isolates globally, driven by the aac(6')-Ie-aph(2'')-Ia gene, complicating treatment of serious infections like endocarditis. Emerging linezolid resistance, mediated by the cfr gene encoding 23S rRNA methyltransferase, has been reported in approximately 1-4% of E. faecalis isolates based on 2024-2025 surveillance data, though overall rates remain low at <2% worldwide, with higher incidences in high-use settings.^[104]^[5]^[105]^[106]^[107] Common MDR patterns in E. faecalis involve simultaneous resistance to beta-lactams (e.g., ampicillin), aminoglycosides (e.g., gentamicin), and fluoroquinolones (e.g., ciprofloxacin, up to 60% resistance), often encompassing three or more antibiotic classes. Extensively drug-resistant (XDR) strains, resistant to nearly all available agents except daptomycin, have been documented in clinical isolates, particularly in nosocomial environments, posing severe therapeutic challenges. A brief reference to genetic acquisition, such as plasmid-mediated transfer, underlies these patterns but is detailed elsewhere.^[5]^[108]^[109] Global trends indicate higher MDR prevalence in Asia and Europe compared to North America, with a 2024 systematic review reporting vancomycin resistance rates exceeding 10% in Asian clinical E. faecalis isolates versus ~5% in the Americas. In food isolates, resistance levels are generally lower (e.g., 10-20% MDR), but rising trends have been observed, linked to agricultural antibiotic use, with increasing detection of VRE in animal-derived products. These patterns underscore the need for ongoing surveillance to track evolving resistance.^[5]^[110]^[111]

Treatment Approaches

Conventional Antibiotic Therapies

For susceptible strains of Enterococcus faecalis, defined by minimum inhibitory concentrations (MICs) of ≤8 μg/mL, ampicillin or penicillin G serves as the first-line monotherapy option due to its reliable bactericidal activity against most isolates.^[112]^[113] In cases of beta-lactam allergy, vancomycin is recommended as an alternative, typically dosed at 15-20 mg/kg intravenously every 8-12 hours, adjusted for renal function to maintain therapeutic trough levels of 15-20 μg/mL in serious infections.^[114]^[115] Synergistic combination therapies enhance efficacy, particularly for severe infections like endocarditis. The regimen of ampicillin plus gentamicin achieves clinical cure rates of approximately 80% in E. faecalis endocarditis, though it requires careful monitoring due to potential toxicity.^[116] For vancomycin-resistant enterococci (VRE) bacteremia, daptomycin is a standard choice at doses of 6-10 mg/kg daily, with higher doses (8-12 mg/kg) often preferred for persistent or complicated cases to improve microbiological clearance.^[117]^[118] According to the Infectious Diseases Society of America (IDSA) 2024 guidance on antimicrobial-resistant infections and the 2025 guidelines on complicated urinary tract infections (cUTIs), linezolid at 600 mg twice daily is recommended for skin and soft tissue infections caused by susceptible E. faecalis, offering good tissue penetration and oral bioavailability.^[115]^[119]^[120] For intra-abdominal infections, tigecycline is an appropriate option, dosed at 100 mg loading followed by 50 mg every 12 hours, due to its broad coverage against multidrug-resistant enterococci in polymicrobial settings.^[115]^[83] Despite these options, conventional therapies face limitations, including reduced efficacy against biofilm-associated infections where E. faecalis persistence leads to treatment failure rates exceeding 50% with monotherapy.^[121] Aminoglycosides like gentamicin necessitate renal function monitoring to mitigate nephrotoxicity risks, which occur in up to 20% of prolonged courses.^[122] Resistance patterns, such as vancomycin resistance in approximately 10% of hospital isolates (as of 2024 U.S. data), further influence agent selection.^[123]

Novel and Adjunctive Therapies

Phage therapy has emerged as a promising alternative for combating Enterococcus faecalis infections, particularly those involving biofilms and antibiotic-resistant strains. Lytic bacteriophages, such as EF-P29, have demonstrated efficacy in targeting vancomycin-resistant E. faecalis by preventing bacteremia in murine models through a single intraperitoneal injection, achieving full protection against lethal infections.^[124] Certain lytic bacteriophages exhibit synergy with beta-lactam antibiotics, resensitizing multidrug-resistant clinical isolates of E. faecalis in vitro and enhancing eradication when combined with vancomycin in biofilm models, as shown in 2024 studies.^[125] Similarly, phage vB_EfaS_ZC1 has proven effective against endodontic infections caused by E. faecalis, either alone or in combination with propolis, reducing bacterial loads in root canal models.^[126] These approaches highlight phage therapy's potential to disrupt biofilms and restore antibiotic susceptibility without promoting further resistance. Adjunctive therapies combining antibiotics with non-traditional agents offer reduced toxicity and improved outcomes for E. faecalis infective endocarditis (EFIE). The regimen of ampicillin plus ceftriaxone has shown comparable efficacy to ampicillin plus gentamicin but with lower nephrotoxicity, as evidenced by a 2021 meta-analysis incorporated into 2023 clinical guidelines, supporting its use for native valve EFIE.^[127]^[128] Recent comparisons in 2025 confirm that ceftriaxone maintains synergy with ampicillin, achieving mortality rates similar to traditional combinations while minimizing renal risks in severe cases.^[129] In endodontic applications, nanoparticles enhance the antimicrobial action of calcium hydroxide (Ca(OH)₂); silver nanoparticles (AgNPs) loaded with Ca(OH)₂ effectively eliminate E. faecalis biofilms in root canals, outperforming Ca(OH)₂ alone by disrupting mature biofilms after 7 days of exposure.^[130] Poly(lactic-co-glycolic acid) nanoparticles with Ca(OH)₂ further improve intradental penetration and antibacterial properties against persistent E. faecalis infections.^[131] Natural products provide targeted inhibition of E. faecalis growth and virulence through disruption of key regulatory systems. Aloe vera extracts exhibit strong antibacterial activity against E. faecalis, with minimum inhibitory concentrations (MICs) around 12.5 mg/mL for aqueous extracts, effectively eliminating biofilms in intracanal models superior to saline and comparable to chlorhexidine.^[132] Systematic reviews confirm Aloe vera's efficacy as an intracanal medicament, reducing E. faecalis colony-forming units by over 90% in 4- to 6-week biofilms.^[133] Quorum sensing inhibitors targeting the fsr system further attenuate virulence; polidocanol disrupts fsr-mediated biofilm formation and gelatinase production in E. faecalis, reducing infection severity in vitro without bactericidal effects.^[134] Compounds like siamycin and ambuic acid intercept fsr signaling by blocking the FsrC-FsrA transduction pathway, inhibiting biofilm development and pathogenicity in clinical isolates.^[135] Probiotic modulation using select E. faecalis strains and fecal microbiota transplantation (FMT) leverages microbial competition to control pathogenic overgrowth. Certain E. faecalis isolates, such as CAUM157, demonstrate probiotic potential by surviving gastric conditions, aggregating with pathogens like Listeria, and enhancing gut barrier function in 2025 studies.^[136] Heat-killed E. faecalis EC-12 improves stress resistance and social behaviors in early-life models by modulating gut microbiota and metabolites, reducing E. faecalis-associated deficits.^[137] FMT reduces antimicrobial-resistant Enterococcus colonization, including E. faecalis, by restoring microbial diversity and enabling commensal strains to outcompete pathogens via bacteriocin production from plasmids like pPD1.^[138]^[139] These strategies promote ecological balance in the gut, decreasing E. faecalis translocation and infection risk in high-burden settings.

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Vancomycin dosages of 15–20 mg/kg (based on actual body weight) given every 8–12 h are required for most patients with normal renal function to achieve the ...Abstract · Executive Summary · Summary of Recommendations
[114]
IDSA 2024 Guidance on the Treatment of Antimicrobial Resistant ...
Suggested approach: Meropenem, imipenem-cilastatin, or ertapenem are preferred for the treatment of infections outside of the urinary tract caused by ESBL-E.
[115]
A Review of Combination Antimicrobial Therapy for Enterococcus ...
faecalis is often susceptible to ampicillin, treatment failure of 60% and lack of bactericidal activity of cell wall–active agents (ie, penicillin G, ampicillin ...Dual β-Lactam Therapy · In Vitro And Experimental... · Daptomycin Plus β-Lactam...
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Daptomycin | Johns Hopkins ABX Guide
Mar 16, 2025 · USUAL ADULT DOSING · >6 mg/kg is likely needed to treat VRE infections. · Some experts recommend higher doses of 8-10 mg/kg/day for complicated ...
[117]
Comparative Effectiveness and Safety of Standard-, Medium-, and ...
High-dose daptomycin was associated with improved survival and microbiological clearance in VRE-BSI.Abstract · METHODS · RESULTS · DISCUSSION
[118]
Comparison of linezolid and daptomycin for the treatment of ...
Feb 13, 2019 · Guidelines published by the Infectious Diseases Society of America (IDSA) specifically recommend treatment with daptomycin or linezolid for VRE ...
[119]
A Review of Combination Antimicrobial Therapy for Enterococcus ...
Ampicillin plus ceftriaxone is as effective as ampicillin plus gentamicin for treating Enterococcus faecalis infective endocarditis. Clin Infect Dis 2013 ...
[120]
[PDF] infective-endocarditis-in-adults-diagnosis-antimicrobial-therapy-and ...
Oct 16, 2018 · It is reasonable to administer gentamicin every 8 hours with the dose adjusted to achieve a 1-hour serum con- centration of ≈3 µg/mL and a ...
[121]
Prophylactic phage administration provides a time window for ... - NIH
Jan 24, 2025 · A single intraperitoneal injection of the phage EF-P29 was sufficient to protect all mice from bacteremia caused by a vancomycin-resistant E.
[122]
In vitro resensitization of multidrug-resistant clinical isolates of ...
Dec 19, 2024 · Enterococci can develop high-level resistance to vancomycin, a primary treatment. We assessed clinical and laboratory isolates of Enterococcus ...
[123]
Novel strategies for vancomycin-resistant Enterococcus faecalis ...
Apr 13, 2025 · Phage vB_EfaS_ZC1 demonstrates a promising therapy, either individually or in combination with propolis, for addressing challenging endodontic infections ...
[124]
Time to abandon ampicillin plus gentamicin in favour of ... - PubMed
Nov 9, 2021 · Time to abandon ampicillin plus gentamicin in favour of ampicillin plus ceftriaxone in Enterococcus faecalis infective endocarditis? A meta- ...Missing: 2023 | Show results with:2023
[125]
Guidelines for Diagnosis and Management of Infective Endocarditis ...
Jul 31, 2023 · Time to abandon ampicillin plus gentamicin in favour of ampicillin plus ceftriaxone in Enterococcus faecalis infective endocarditis? a meta ...
[126]
Comparison of ceftriaxone versus ceftaroline in combination ... - NIH
May 15, 2025 · Enterococcus faecalis infective endocarditis treatment with ampicillin plus ceftriaxone has not changed the mortality rates by over 30%.
[127]
Antimicrobial Effects of Formulations of Various Nanoparticles and ...
Sep 28, 2024 · According to Afkhami et al., the carrier silver nanoparticles (AgNPs) for Ca(OH)2 were most effective against E. faecalis biofilm in root canal ...
[128]
Antibacterial biodegradable calcium hydroxide nanoparticles in an ...
Dec 15, 2023 · This study aimed to investigate the antibacterial properties of poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) loaded with Ca(OH) 2 for endodontic ...
[129]
[PDF] Effect of Arginine, Protamine, and Aqueous Extracts of Green Tea ...
This result indicates that aqueous extracts of aloe vera were found to be most effective in inhibiting the growth of E. faecalis (MIC=12.5 mg/ml and MBC=100 mg/ ...
[130]
The Efficacy of Aloe vera Against Enterococcus faecalis as an ...
Sep 25, 2024 · This review article seeks to assess the antimicrobial efficacy of Aloe vera (AV) against Enterococcus faecalis in comparison to CaOH as an ...
[131]
Polidocanol inhibits Enterococcus faecalis virulence factors by ...
Oct 16, 2024 · Polidocanol appears to be a promising option for treating of E. faecalis infections by targeting the fsr QS system and exhibiting anti-biofilm activity.Missing: sRNA | Show results with:sRNA
[132]
Interception of Epoxide ring to quorum sensing system in ...
Nov 9, 2023 · Siamycin inhibits the fsr QS system of E. faecalis via the block of FsrC-FsrA two component signal transduction. On the other hand, Ambuic acid ...
[133]
Probiotic potential and safety assessment of bacteriocinogenic ...
Jun 30, 2025 · ... Enterococcus faecalis CAUM157, a bacteriocin-producing strain isolated ... Tolerance to acid and bile salts is an important factor that ...
[134]
Therapeutic potential of heat-killed Enterococcus faecalis (EC-12 ...
Sep 3, 2025 · These findings suggest that heat-killed EC-12 can mitigate early life stress-induced social deficits through microbiota- and metabolite-mediated ...
[135]
Fecal microbiota transplantation promotes reduction of antimicrobial ...
Nov 1, 2023 · Limited studies have shown that fecal microbiota transplantation (FMT) can reduce MDRO colonization, but its mechanisms are poorly understood.
[136]
Microbiota-mediated protection against antibiotic-resistant pathogens
May 4, 2021 · E. faecalis strains that produce bacteriocins from the pPD1 plasmid are able to outcompete non-bacteriocin producing strains in the intestine, ...