Enterococcus faecalis and UTIs: Risk factors, diagnostic testing, and treatment options

What is Enterococcus faecalis?

Enterococcus faecalis is a gram-positive bacterium that lives as a normal part of the human gastrointestinal tract in most people. E. faecalis is an opportunistic pathogen, harmless in the gut environment, but capable of causing infection when it ends up elsewhere in the body, including the urinary tract, bloodstream, or heart valves.

Enterococcus species cause an estimated 110,000 UTIs annually in the United States, and E. faecalis accounts for the large majority of those. E. faecalis represents roughly 70–75% of enterococcal urinary isolates, with the closely related Enterococcus faecium responsible for most of the remainder¹. The two species are often discussed together, but they behave differently enough, especially around antibiotic resistance, that it’s worth keeping them distinct.

What causes an Enterococcus faecalis UTI?

Like most UTI-causing bacteria, E. faecalis is thought to reach the urinary tract primarily by migrating from the gastrointestinal tract. Contamination around the urethra by gut bacteria is considered an important route of infection, and this shows up in clinical data: recurrent UTI patients, particularly premenopausal women, have been found to have a higher frequency of infections caused by their own endogenous gut microbes². Beyond the urinary tract specifically, E. faecalis has a few recognized portals of entry into the body: the gastrointestinal tract itself (via translocation through the intestinal lining, often after surgery or illness), the urinary tract (via catheterization or the ascending route just described), and the bloodstream (via central lines)³.

It’s disproportionately involved in complicated UTIs. A few groups of patients experience E. faecalis infection more often:

• People who use urinary catheters, both short- and long-term
• People who are hospitalized or in long-term care, particularly with multiple prior UTIs or antibiotic courses
• People with structural or functional urinary tract abnormalities, including urinary retention or recent urologic instrumentation or surgery
• Older adults

Risks and complications

UTIs caused by E. faecalis carry some distinct risks compared with more typical gram-negative infections.

Biofilm and catheter persistence

E. faecalis isn’t especially aggressive at invading healthy tissue, its strategy is closer to “squatter’s rights.” When a catheter is placed, the body deposits a protein called fibrinogen onto its surface as part of a normal wound-response reaction. E. faecalis uses a structure called a pilus (Ebp) to bind to the fibrinogen, anchoring itself to the catheter and building a protective biofilm from there⁴. Once established, bacteria embedded in that biofilm are considerably harder for antibiotics to reach.

Antibiotic resistance

The Clinical and Laboratory Standards Institute (CLSI) the standards body that defines U.S. laboratory antibiotic susceptibility testing, specifically warns that for Enterococcus species, cephalosporins, low-level aminoglycosides, clindamycin, and trimethoprim-sulfamethoxazole may appear active in a susceptibility test but aren’t effective clinically and shouldn’t be reported as susceptible, regardless of the in vitro result⁵. Unlike its relative E. faecium, most E. faecalis remains ampicillin-susceptible, and while vancomycin-resistant enterococcus (VRE) draws significant attention, surveillance data consistently show the large majority of VRE isolates are E. faecium, not E. faecalis⁶⁷.

Bloodstream spread

E. faecalis can reach the bloodstream by more than one route: directly from the gut, when illness, surgery, or broad-spectrum antibiotics compromise the intestinal lining, or from the urinary tract itself, if an infection ascends to the kidneys. Either route can lead to bacteremia, a more serious systemic infection distinct from an uncomplicated UTI³.

How is Enterococcus faecalis infection detected?

Unlike fastidious organisms such as Aerococcus species, E. faecalis isn’t inherently difficult to grow. It typically grows readily in isolation. In practice, though, detecting it accurately is not always straightforward.

Polymicrobial infections

E. faecalis frequently appears as part of a polymicrobial infection alongside gram-negative bacteria like E. coli. Standard culture protocols aren’t always set up to fully characterize every organism present in a mixed sample, and semi-quantitative reporting thresholds can cause a real but lower-abundance pathogen to go unreported.

Detection gaps in standard culture

In our peer-reviewed clinical validation performed at Biotia’s NYS-CLIA/CLEP-certified laboratory, the BIOTIA-ID Urine Test identified E. faecalis as one of the organisms most frequently missed by standard culture⁸. This isn’t unique to sequencing-based methods: enhanced quantitative urine culture (EQUC), a method that plates larger urine volumes under a wider range of incubation conditions, has independently shown that standard culture detects only a fraction of the non-E. coli uropathogens present in symptomatic urine, with E. faecalis among the organisms most inconsistently recovered between the two techniques⁹. The most likely explanation in both cases is how often E. faecalis shows up in polymicrobial samples and at lower relative abundance, rather than any inherent difficulty growing the organism itself.

Resistance profiling

Knowing an infection involves E. faecalis immediately rules out cephalosporins, per CLSI guidance⁵. If the infection progresses to bacteremia, combination therapy with ampicillin, penicillin, or vancomycin plus an aminoglycoside is often used, so labs run a dedicated high-level aminoglycoside resistance (HLAR) screen ahead of time, typically a high-concentration gentamicin and streptomycin disk or agar screen defined by CLSI standards⁵¹⁰. Documented high-level resistance to both drugs rules out that combination strategy entirely, so getting a fuller picture of resistance markers can help guide antibiotic selection before it’s needed.

Virulence factors

Virulence factors are characteristics or evolutionary strategies of a pathogen that enable it to more efficiently infect a host, evade the immune system, and cause disease. Clinical metagenomic-based tests can identify specific virulence factors a given isolate carries, though more research is needed to know how their presence should change treatment. Virulence factors of E. faecalis are listed in the table below.

How is an E. faecalis UTI treated?

E. faecalis is treated with antibiotics, but susceptibility testing, not assumptions about the species, should drive the choice. Ampicillin or amoxicillin is typically a first-line option for susceptible E. faecalis, since it usually remains ampicillin-susceptible, unlike E. faecium. Nitrofurantoin is another option for uncomplicated cases, though it isn’t appropriate for pyelonephritis or complicated UTI due to poor tissue penetration. For complicated UTI specifically, levofloxacin is FDA-approved as an alternative option, though rising fluoroquinolone resistance in E. faecalis means susceptibility should be confirmed before relying on it¹¹. For more severe infections requiring combination therapy, labs test specifically for high-level aminoglycoside resistance (HLAR), since its presence rules out that strategy.

Catheter-associated and other complicated infections may require additional intervention beyond antibiotics alone. Persistent or recurrent symptoms combined with consistent E. faecalis detection may point to an entrenched biofilm, in which case treatment may include replacing the urological device entirely.

The bottom line

UTIs caused by Enterococcus faecalis are common, particularly for people with catheters, recent hospitalization, or a history of complicated UTI. It typically reaches the urinary tract the same way most UTI-causing bacteria do, traveling from its normal home in the gastrointestinal tract. Once in the urinary tract, its survival strategy relies on biofilm persistence rather than aggressive tissue invasion, which is what makes catheter-associated infections so stubborn. While standard culture usually identifies E. faecalis without difficulty in isolation, Biotia’s own validation data for the BIOTIA-ID Urine Test show it’s still one of the organisms most often missed by urine culture in real-world specimens relative to next-generation sequencing, and when it is found, it’s often part of a polymicrobial infection that benefits from a fuller diagnostic picture.

The BIOTIA-ID Urine Test uses next-generation sequencing to identify over 40 urogenital pathogens, including Enterococcus faecalis, alongside antibiotic resistance markers to help guide treatment.