Culture-Negative Infective Endocarditis in the Modern Diagnostic Era: Patient Characteristics and Heterogeneity in a Nationwide Cohort

Background

Infective endocarditis (IE) is a serious infection of the heart’s inner lining or heart valves. It can damage valves, cause heart failure, and send infected clots to the brain, lungs, kidneys, or other organs. In many cases, the infection is identified by blood cultures, but a meaningful subset of patients have culture-negative infective endocarditis (CNIE), meaning routine cultures do not reveal the causative organism.

CNIE has long been a diagnostic and therapeutic problem. A negative culture can happen for several reasons: antibiotics may have been given before blood was drawn, the infecting organism may be slow-growing or difficult to culture, or the pathogen may be one that requires specialized testing. In modern practice, additional tools such as valve tissue culture, polymerase chain reaction (PCR), and positron emission tomography with computed tomography (PET-CT) can help identify the cause and confirm the diagnosis.

This nationwide Danish study, based on the NIDUS registry, offers one of the most detailed modern descriptions of CNIE. It examines who develops CNIE, how these patients present, how their disease differs from culture-positive infective endocarditis (CPIE), and how often advanced imaging contributes to diagnosis.

Study design and population

Researchers included all patients hospitalized in Denmark with first-time left-sided IE from 2016 to 2021. Patients were classified as having CNIE or CPIE based on results from blood cultures, valve tissue cultures, and PCR analyses. Because the study drew from a nationwide registry, it reflects routine clinical practice rather than a highly selected referral population.

A total of 2,875 patients with IE were included, and 212 patients, or 7.4%, had culture-negative disease. This proportion is lower than many earlier reports, suggesting that improved diagnostics and systematic care may be reducing the apparent burden of CNIE or changing how it is detected.

Who developed culture-negative infective endocarditis?

The study found that patients with CNIE were not identical to those with CPIE. Several differences stood out in their medical histories and baseline characteristics.

Patients with CNIE were more likely to have congenital heart disease than patients with CPIE (9.9% versus 2.9%). This matters because abnormal cardiac anatomy, prior procedures, and prosthetic material can create conditions where infection develops and may also make diagnosis more complex.

On the other hand, patients with CNIE were less likely to have a prior history of cancer (9.3% versus 14.7%). The reasons for this difference are not fully clear, but it may reflect differences in overall patient profiles, healthcare exposure, or competing risks.

How did the illness present?

The clinical presentation of CNIE differed from CPIE in important ways.

At admission, CNIE patients were less likely to present with sepsis (7.1% versus 24.6%) and fever (44.3% versus 61.7%). In everyday terms, this means that culture-negative disease may be easier to miss because the “classic” infection signals are less obvious.

At the same time, CNIE patients were more likely to present with embolic events (25.9% versus 10.8%). Embolism occurs when fragments of infected material break off the valve and travel through the bloodstream, potentially causing stroke, limb ischemia, splenic infarction, or other complications. CNIE patients also more often had valvular insufficiency (11.3% versus 7.4%), which reflects leakage of the heart valve due to infection-related damage.

Taken together, these findings suggest that CNIE may be recognized later in the disease course in some patients, when complications have already occurred, even though fever and sepsis are less prominent.

Imaging and valve findings

The median vegetation size was smaller in CNIE than in CPIE (8 mm versus 10 mm). Vegetations are the infected masses that form on valves, and their size can influence embolic risk and treatment decisions. A smaller average size does not mean disease is less serious; even small vegetations can cause major complications.

Rates of prosthetic valve infection were similar between the two groups (22.2% in CNIE versus 23.1% in CPIE). Likewise, valve surgery rates were nearly the same (20.3% versus 21.8%). This indicates that culture negativity did not make the disease less likely to require surgery. Decisions about valve replacement or repair still depended on standard clinical indications such as heart failure, uncontrolled infection, large vegetations, or embolic events.

Role of PET-CT and modern diagnostics

One of the most important findings of the study was the frequent use of PET-CT. This imaging test was used in 67% to 68% of patients in both groups, showing that it has become a routine part of modern IE workup in Denmark, especially when prosthetic material is involved or when conventional tests are inconclusive.

PET-CT was diagnostic in 13.1% of CNIE cases and 10.7% of CPIE cases. Although this may sound modest, it is clinically important because PET-CT can identify active infection around prosthetic valves, help confirm the diagnosis, and sometimes detect other infectious foci or embolic complications.

The diagnostic yield was especially striking in patients with prosthetic valve CNIE, where PET-CT was helpful in almost 50% of cases. This suggests that in suspected prosthetic valve endocarditis, especially when cultures are negative, PET-CT can provide decisive evidence and should be considered early in the diagnostic process.

Modern diagnostic strategies for CNIE also often include prolonged culture incubation, serologic testing for difficult-to-culture organisms, molecular methods such as PCR on blood or valve tissue, and careful multidisciplinary review. Although this study focused on registry-based clinical practice, its findings support the value of combining imaging with microbiology and pathology rather than relying on blood cultures alone.

What the findings mean clinically

This nationwide cohort shows that CNIE is less common than older studies may have suggested, at least in a contemporary system with broad access to advanced diagnostics. However, the condition remains highly relevant because it presents differently and may be harder to recognize quickly.

Clinicians should be alert to CNIE when a patient has signs of IE but lacks fever, sepsis, or positive blood cultures, especially if embolic complications, valvular dysfunction, congenital heart disease, or prosthetic valves are present. A negative blood culture does not exclude IE. In the right clinical setting, persistent suspicion should prompt further testing, including imaging, valve tissue analysis if surgery occurs, and targeted molecular workup.

The study also reinforces that culture-negative disease is not one single entity. Rather, it is likely a mixed group of conditions with different causes, host factors, and diagnostic pathways. Some patients may have received antibiotics before cultures were drawn, while others may harbor fastidious organisms such as Bartonella, Coxiella burnetii, Tropheryma whipplei, or certain fungi and intracellular bacteria. Others may have noninfectious mimics or partially treated infections that blur the picture. This heterogeneity helps explain why CNIE cannot be understood well as one uniform phenotype.

Practical implications for care

In practice, the study supports several important principles:

First, blood cultures should be obtained before antibiotics whenever possible in suspected IE. This remains one of the most effective ways to identify the organism.

Second, if cultures are negative but clinical suspicion remains high, clinicians should move quickly to additional diagnostic tools rather than waiting for spontaneous clarification.

Third, PET-CT has an increasingly important role, especially in prosthetic valve cases and in patients with complex or ambiguous presentations.

Fourth, embolic events in a patient without fever should still raise concern for IE, including CNIE, particularly if there are cardiac risk factors.

Finally, management should be individualized and ideally coordinated by an endocarditis team that includes cardiology, infectious diseases, cardiac surgery, radiology, and microbiology specialists.

Study limitations and interpretation

As with any registry study, the findings should be interpreted in context. Registry data can be limited by missing information, variation in local practice, and dependence on what is recorded in clinical systems. Also, some CNIE cases may still have been misclassified if the causative organism was never identified despite extensive testing.

Even so, the study’s strength lies in its large, nationwide, unselected cohort and its reflection of real-world modern diagnostics. This makes the findings especially useful for everyday clinical care.

Conclusion

In this large Danish nationwide study of first-time left-sided infective endocarditis, culture-negative disease accounted for 7.4% of cases, a lower proportion than often reported previously. Compared with culture-positive IE, CNIE was associated with congenital heart disease, fewer fevers and septic presentations, more embolic complications, and similar rates of prosthetic valve infection and surgery.

PET-CT was widely used and proved particularly valuable in prosthetic valve CNIE. Overall, the study shows that culture-negative IE is not a single uniform syndrome but a heterogeneous group of conditions. For clinicians, the key message is clear: when cultures are negative, suspicion should remain high, and diagnosis should rely on a broad, modern toolkit that includes imaging, pathology, and molecular testing.