Blood culture-negative endocarditis is defined as endocarditis where traditional methods for culturing blood do not yield an organism. BCNE may be classified into three groups [3]:

• Bacterial endocarditis with sterilized blood cultures from previous antibiotic treatment, which accounts for the majority of cases;
• Endocarditis due to fastidious microorganisms, which have historically included the HACEK (Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella) group, nutritionally variant Streptococci, Pasteurella spp., mycobacteria, and fungal organisms;
• “True” BCNE due to infection with intra-cellular organisms that cannot be cultured in blood using traditional techniques but may be diagnosed with serology (e.g., Bartonella sp., Coxiella burnetii) or polymerase chain reaction (PCR) of valvular tissue (e.g., Tropheryma whipplei).

Non-infectious causes of endocarditis, specifically nonbacterial thrombotic endocarditis (NBTE), should also be included in the differential diagnosis of BCNE in the right clinical context. NBTE is associated with hypercoagulable states, e.g., malignancy or autoimmune disease, which may result in the deposition of sterile thrombi on cardiac valves.

A systematic review of 142 studies reporting IE microbiology over five decades from 1960–2010 found a decrease in the incidence of BCNE over that time period from 23.1% to 14.2% [4]. Conversely, Vogkou et al. reviewed 105 studies from 2003 to 2013, with 26.6% of cases classified as BCNE [5]. Accounting for these variations, the incidence of BCNE in modern times is likely in the range of 10–20% [6]. A notable feature of these reviews is the significant variation in the incidence of BCNE in individual studies, with rates ranging from 7.7% to 66% [7,8]. The variation in incidence is attributable to several factors, most notably local variation in the early use of antibiotic therapy prior to obtaining blood cultures but also differences in testing strategies [9] and geographic variation of specific organisms, in particular zoonotic agents [6].

Sepsis is a common clinical presentation of IE, and as a result antibiotics are often administered prior to obtaining blood cultures. In retrospective studies, the prevalence of BCNE attributed to antibiotic administration prior to culture has varied from 35% to 74% [7,10,11]. The microbiological profile in this cohort is similar to that of cases where blood cultures are obtained prior to administration of antibiotics (i.e., streptococci, staphylococci, or enterococci), with the caveat that organisms that are quickly cleared from the bloodstream may be more common.

The HACEK group of organisms and nutritionally variant streptococci (Granulicatella spp., Abiotrophia defectiva) have traditionally been cited as common causes of BCNE due to the difficulty associated with culturing in standard media. However, modern automated culture systems can identify these organisms within 5 days of incubation in the vast majority of cases [12,13].

Fungi account for approximately 1–2% of cases of IE [6]. Candida albicans is the most common cause, accounting for around 25% of cases, and automated culture systems can readily culture this organism along with other yeasts. Invasive mold infections (e.g., IE associated with Aspergillus spp.) and IE associated with endemic fungi, e.g., Histoplasma capsulatum, do not traditionally grow on routine blood cultures, and close attention to risk factors in the history (Table 1) are important when considering these agents as potential etiologies of BCNE.

IE due to Mycobacterial species is most frequently caused by non-tuberculous mycobacteria, with rapidly growing mycobacteria most commonly implicated [20,21]. Blood cultures do not routinely identify Mycobacterial species, and alternative diagnostic methodologies such as histopathologic evaluation of the valve and molecular techniques may be required to establish a diagnosis. IE due to M. tuberculosis is rare, with only a handful of cases reported in the literature. Cardiac surgery, the presence of indwelling prosthetic material, and intravenous drug use have been identified as the most common risk factors for mycobacterial endocarditis [21]. Several outbreaks of M. chimaera prosthetic valve endocarditis have been reported in the United States and Europe over the past decade [19]. These outbreaks have been associated with contaminated heater–cooler units during cardiopulmonary bypass, and this organism should be considered in patients presenting with prosthetic valve endocarditis of insidious onset. The significant lag time from the index surgery and subtle cardiac imaging findings contribute to the significant delay in diagnosis. Mycobacterial blood cultures and molecular detection methods should be performed in suspected cases.

Tropheryma whipplei is a Gram-positive bacterium that causes Whipple’s disease; a chronic multi-systemic disease that predominantly affects middle-aged men and typically causes diarrhea, weight loss, and arthralgias and that may progress to involve the heart, lungs, and central nervous system [22]. Estimates of the frequency of T. whipplei as a causative organism in BCNE have ranged from 0.3% to 3.5% [23,24,25] in studies examining all patients with BCNE and up to 6.3% in patients in whom cardiac tissue was available for analysis [26].

Coxiella burnetii is an obligate intracellular pathogen found worldwide that is associated with exposure to aerosols from infected animals (Table 1). Infection with this organism causes Q fever, a febrile illness associated with myalgias, headaches, and hepatitis and that may progress to endocarditis in the chronic phase if not diagnosed and treated early in the disease course. In the largest prospective studies evaluating cases of BCNE, C. burnetii was identified as the causative pathogen in 37% [24] and 48% [23] of cases. Positive phase 1 IgG titer is considered a major Duke criterion and is considered diagnostic. Coxiella specific PCR performed on the plasma or heart valves can also be used to confirm the diagnosis.

Bartonella spp. are small intracellular Gram-negative bacteria with protean manifestations and have been associated with up to 12.4–28.4% of cases of BCNE [23,24]. Bartonella henselae is associated with cat-scratch disease, and clinicians should be aware of its association with crescentic glomerulonephritis with PR3-ANCA positivity [27]. B. quintana is associated with exposure to the human body louse (Table 1) and has also been associated with BCNE, along with rarer species such as B. elizabethae and B. vinsonii [28,29]. Although most of the literature with respect to B. quintana endocarditis has come out of Europe and Africa, a resurgence in North America has been noted in the past decade [30]. Bartonella serologies are the most commonly used diagnostic tests; Bartonella-specific PCR on peripheral blood specimens or tissue valves could also be used to confirm the diagnosis.

Rare cases of BCNE associated with Legionella spp., Chlamydia spp., and Mycoplasma spp. have been reported in the literature [18,31,32]. Cases of Legionella endocarditis are typically preceded by pneumonia. Diagnosis may be established with histopathological examination of explanted valves or molecular techniques; the role of serological testing is questionable given the rarity of these pathogens [33]. Brucellosis should also be considered in a patient with specific risk factors or returning from an endemic region (Table 1). Although serological testing for Brucella sp. can be added in these cases [34], detection in routine blood cultures is typically achieved within 5 days [35].

In the largest prospective evaluation of cases of BCNE at a tertiary reference center in France, Fournier et al. found a non-infectious cause of BCNE in 2.5% of cases [23]. Specific diagnoses included systemic lupus erythematosus (SLE), also known as Libman–Sacks endocarditis; rheumatoid arthritis; and IE associated with metastatic malignancy, also known as marantic endocarditis. Endocarditis has also been associated with Behçet’s disease [36]. Clinicians should also be aware of the link between endocarditis on porcine bioprosthetic valves and allergy to pork. A handful of cases of recurrent endocarditis on porcine valves in patients with pork allergies has been reported to date in the literature [37], and replacement of the valve with non-porcine material is necessary in these cases.