mNGS to Diagnose Culture-negative Endocarditis

Infective endocarditis is inflammation of endocardium that usually affects heart valves. Mortality rate of the disease is up to  30% in 1st year [1] for many malignant cancers. The most common risk factors for infective endocarditis include previous heart damage, recent heart surgery or poor dental hygiene. According to report of National Organization for Rare Diseases, people over the age of 50 with prosthetic heart valves or cardiac pacemakers are more prone to develop endocarditis. Healthcare contact is major source of infection.

Bacteria account for most cases while fungi are the least common cause of endocarditis. Damaged heart valves and inner lining of the heart is the main risk factor for infective endocarditis because it leaves the tissue susceptible to bacteria overgrowth. Valvular vegetation which is caused by the clumps of bacteria and cells on the heart valves is the classic lesion of infective endocarditis. Untreated endocarditis can cause abscesses beneath valves, heart failure and even death. New regurgitation murmurs may also occur as a result of valvular disorders such as mitral regurgitation, aortic regurgitation or tricuspid regurgitation.  Therefore, early diagnosis is the key to improve clinical outcomes and survival odds. Antibiotics are essential for treatment and are most effective if the disease is caught early. Population at risk and microbiology of endocarditis has changed with advances in healthcare and emergence of antibiotic resistance (Bernard Iung. Presse Med. 2019 May) [3].

Microbiology of endocarditis

The five most common pathogens causing infective endocarditis are Staphylococcus aureus,  Streptococcus viridans,  Staphylococcus epidermidis, Enterococcal endocarditis and Streptococcus bovis. Staphylococcus aureus is the most predominant causative microorganism of endocarditis and mostly attacks tricuspid valve in IV drugs abusers. It is high virulence organism and can also infect intact heart valves. Infection is acute and severe. Staphylococcus aureus prosthetic valve endocarditis (PVE) was found to be one of the most morbid bacterial infections with mortality rate ranging from 40% to 80% (Alicia Galar et al. Clin Microbiol Rev. 2019)[4] .Streptococcus viridans are second most common cause of endocarditis (Vladimír Krčméry et al. 2019) [6]   and presents part of mouth flora, mostly causing endocarditis in people with damaged heart valves (e.g. mitral valve prolapse) after dental procedures. It synthesizes dextran to adhere to platelets and fibrin found in damaged valves resulting in formation of vegetations. Staphylococcus epidermidis is a low virulence, coagulase-negative staphylococcus which found in normal skin flora. Treatment for antibiotic resistant staphylococcus epidermidis is known to be challenging in the clinics. Enterococcal endocarditis is caused by Lancefield group D gram-positive cocci and it is commonly found in older men with genitourinary tract infection (D W Megran. Clin Infect Dis. 1992 Jul) [7]. Streptococcus bovis is also a Lancefield group D gram-positive coccus and part of normal gut flora. All subtypes, especially Streptococcus gallolyticus are associated with colon cancer.


Staphylococcus aureus31
Streptococcus viridans17
Staphylococcus epidermidis11
Enterococcal endocarditis11
Streptococcus bovis7
Other streptococci5
HACEK organisms2
Other gram-negative bacilli2

Table 1. Microbiology of infective endocarditis. Table shows incidence of various causative microorganisms detected in a long-term multicentre study [5].

Culture-negative endocarditis

To identify the causative pathogens for infective endocarditis, in most cases blood culture  is used. However, studies show that 2-7% of endocarditis cases come culture-negative, especially in patients with antibiotics therapy prior to blood collection (Sheibani, H., Salari, M., Azmoodeh, E. et al, 2020) [8].  Culture-negative endocarditis is highly morbid and mortal infection accounts for up to 35% of infective endocarditis (S Subedi et al.2017) [9-10]. Bartonella and coxiella are two of the intracellular organisms most commonly associated with blood culture-negative endocarditis. In addition, HACEK organisms, Tropheryma whipplei and some fungi are commonly found in culture-negative endocarditis patients.

Fast detection of infection is crucial to prevent neurological manifestations of the disease. Next-generation sequencing can prove useful for fast detection and timely treatment of the infection. Even though clinical utility is not wide spread today, application of the diagnostic technique may greatly reduce the chances of misdiagnosis in future. Next-generation sequencing is widely used outside of clinical microbiology laboratories to find the etiology of infectious diseases.

Sishi Cai et al (2021) [11] conducted a research to assess the value of metagenomic next-generation sequencing in diagnosis of infective endocarditis. Total of 49 endocarditis patients were enrolled of which 28 were culture positive and 21 were culture negative. Next-generation sequencing was applied to study the positive detection rate among culture-negative endocarditis patients. Resected valves of 8 patients with non-infective valvular diseases were collected and used as negative control group. Results revealed 100% positive pathogen detection rate by mNGS among culture-negative endocarditis patients. These suggest that mNGS is a valuable tool for diagnosing infective endocarditis, especially culture-negative endocarditis and it can be utilized to guide post-surgical antibiotic treatment.

Devin® filter and Parti-Seq® platform are amongst the newest and most advanced methods developed for the early detection of pathogenic microorganisms from human blood. Devin® Filter filters up to 95% of the patient’s nucleated cells from the blood sample, allowing a passage more than 99% of bacteria and viruses. This filtration process is essential as human genetic information (DNA) in the blood samples that need to be analyzed is a critical holdback in rapidly identifying pathogenic microorganisms. Further, pathogen identification is performed with NGS-based Pathogen Real-Time Identification by Sequencing (PaRTI-Seq®) developed by Micronbrane for rapid pathogen identification within less than 24 hours with a sensitivity of 102 genome copy / ml[12].


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  12. Micronbrane (2021, November 17). [White Paper] Needle in the Haystack: How to Remove Human Background When You Want to Detect Microorganisms.