Molecular identification of pathogens from excised heart valves of infective endocarditis cases

Main Article Content

Akiko Miyazato Kotaro Mitsutake


Infective endocarditis is a life-threatening disease and identification of the pathogenic organisms is crucial for better prognosis. However, in some conditions, such as previous antibiotic usage or infection with fastidious organisms, obtaining positive cultures results is difficult. In addition to conventional culture methods, a molecular approach has been developed over several decades, such as broad-range 16S rRNA gene PCR and sequencing using excised tissues, to detect the pathogens. The current consensus is that this method is useful for the diagnosis and management of infective endocarditis patients and it has been suggested that these molecular results should be included as a new Deke criterion. Although molecular technique cannot replace culture methods and should be interpreted carefully, broad-range 16S rRNA/sequencing has great value in complementing conventional methods. Tissue samples from infective endocarditis cases should be examined by this method for better management of the patients. 

Article Details

How to Cite
MIYAZATO, Akiko; MITSUTAKE, Kotaro. Molecular identification of pathogens from excised heart valves of infective endocarditis cases. Medical Research Archives, [S.l.], v. 5, n. 6, june 2017. ISSN 2375-1924. Available at: <>. Date accessed: 29 may 2023.
Infective endocarditic, broad-range 16S rRNA gene PCR/sequencing, pathogenic organisms, excised heart valves, blood culture
Review Articles


Baddour LM, Wilson WR, Bayer AS, Fowler VG, Tleyjeh IM, Rybak MJ, Barsic B, Lockhart PB, Gewitz MH, Levison ME, Bolger AF, Steckelberg JM, Baltimore RS, Fink AM, O’Gara P, Taubert KA; on behalf of the American Heart Association Committee on Rheumatic Fever, Endocarditis, and Kawasaki Disease of the Council on Cardiovascular Disease in the Young, Council on Clinical Cardiology, Council on Cardiovascular Surgery and Anesthesia, and Stroke Council. Infective endocarditis in adults: diagnosis, antimicrobial therapy, and management of complications. A scientific statement for healthcare professionals from the American Heart Association. Circulation. 2015;132:1435-1486.

Benett JE, Dolin R, Blaser MJ. Endocarditis and Intravascular Infection. Principles and Practice of Infectious Disease. 7th Edition. Churchill Livingstone. 2011.

Brouqui P and Raoul D. New insight into the diagnosis of fastidious bacterial endocarditis. FEMS Immunolo Med Microbiol. 2006;47:1-13.

Brouqui P and Raoul D. Endocarditis due to rare and fastidious bacteria. Clin Microbiol Rev. 2001;14:177-207.

Cambau E, Durand-Zaleski I, Bretagne S, Buisson CB, Cordonnier C, Duval X, Herwegh S, Pottecher J, Courcol R, Bastuji-Garin S; EVAMICA study team. Performance and economic evaluation of the moleculer detection of pathogens for patients with severe infections: the EVAMICA open-label, cluster-randomised, interventional crossover trial. Intensive Care Med. 2017. doi: 10.1007/s00134-017-4766-4.

Chen K, Neimark H, Rumore P, Steinman CR. Broad range DNA probes for detecting and amplifying eubacterial nucleic acids. FEMS Microbiol Lett. 1989;57:19-24.

Edouard S, Nabet C, Lepidi H, Fournier PE, Raoult D. Bartonella, a common cause of endocarditis: a report on 106 cases and review. 2015;53:824-829.

Edwards U, Rogall T, Blöcker H, Emde m, Böttger EC. Isolation and direct complete nucleotide determination of entire genes. Characterization of gene coding for 16S ribosomal RNA. Nucleic Acids Res. 1989;17:7843-7853.

Fernandez-Guerrero ML. Zoonotic endocarditis. Infect Dis Clin North Am. 1993;7:135-152.

Fournier PE, Thuny F, Richet H, LepidiH, Casalta JP, Arzouni JP, Maurin M, Célard M, Mainardi JL, Caus T, Collart F, Habib G, Raoult D. Comprehensive diagnostic strategy for blood culture-negative endocarditis: A prospective study of 819 new cases. Clin Infect Dis. 2010;51:131-140.

Fukuchi T, Iwata K. Failure of early diagnosis of infective endocarditis in Japan – a retrospective descriptive analysis. Medicine. 2014;93;e237.

Gauduchon V, Chalabreysse L, Etienne J, Célard M, Benito Y, Lepidi H, Thivolet-Béjui F, Vandenesch F. Molecular diagnosis of infective endocarditis by PCR amplification and direct sequencing of DNA from valve tissue. J Clin Microbiol. 2003;41:763-766.

Geiβdörfer W, Moos V, Moster A, Loddenkemper C, Jansen A, Tandler R, Morguet AJ, Fenollar F, Raoult D, Bogdan C, Schneider T. High frequency of Tropheryma whipplei in culture-negative endocarditis. J Clin Microbiol. 2012;50:216-22.

Goldenberger D, Künzli A, Vogt P, Zbinden R, Altwegg M. Molecular diagnosis of bacterial endocarditis by broad-range PCR amplification and direct sequencing. J Clin Microbiol. 1997;35(11):2733-2739.

Gould FK, Denning DW, Elliott TSJ, Foweraker J, Perry JD, Prendergast BD, Sandoe JAT, Spry MJ, Watkin RW. Guidelines for the diagnosis and antibiotic treatment of endocarditis in adults: a report of the working party of the British Society for Antimicrobial Chemotherapy. J Antimicrob Chemother. 2012;67:269-289.

Habib G, Lancellotti P, Antunes MJ, Bongiorni MG, Casalta JP, Del Zotti F, Dulgheru R, Khoury GE, Erba PA, Lung B, Miro JM, Mulder BJ, Plonska-Gosciniak E, Price S, Roos-Hesselink J, Snygg-Martin U, Thuny F, Tornos Mas P, Vilacosta I, Luis Zamorano J. 2015 ESC Guidelines for the management of infective endocarditis: The task force for the management of infective endocarditis of the European Society of Cardiology (ESC). Endorsed by: European Association for cardio-thoracic surgery (EACTS), the European Association of Nuclear Medicine (EANM). Eur Heart J. 2015;36:3075-3128.

Harris KA, Yam T, Jalili S, Williams OM, Alshafi K, Gouliouris T, Munthali P, NiRiain U, Hartley JC. Service evaluation to establish the sensitivity, specificity and additional value of infective endocarditis from resected endocardial material in patients from eight UK and Ireland hospitals. Eur J Clin Microbiol Infect Dis. 2014;33:2061-2066.

Hoen B, Alla F, Selton-Stuy C, Béguinot I, Bouvet A, Briançon S, Casalta JP, Danchin N, Delahaye F, Etienne J, Le Moing V, Leport C, Mainardi JL, Ruimy R, Vandenesch F. Changing profile of infective carditis: results of a 1-year survey in France. JAMA. 2002;288:75-81.

Houpikian P, Raoult D. Blood culture-negative endocarditis in a reference center. Etiologic diagnosis of 348 cases. Medicine. 2005;84:162-173.

Jalava J, Kotilainen P, Nikkari S, Skurnik M, Vänttinen E, Lehtonen OP, Eerola E, Toivanen P. Use of the polymerase chain reaction and DNA sequencing for detection of Bartonella quintana in the aortic valve of a patient with culture-negative infective endocarditis. Clin Infect Dis. 1995;21(4):891-6.

Leli C, Moretti A, Pasticci MB, Cenci E, Bistoni F, Mencacci A. A commercially available multiplex real-time PCR for detection of pathogens in cardiac valves from patients with infective endocarditis. Diagn Microbiol Infect Dis. 2014;79:98-101.

Li JS, Sexton DJ, Mick N, Nettles R, Fowler VG Jr, Ryan T, Bashore T, Corey GR. Proposed modifications to the Duke criteria for the diagnosis of infective endocarditis. Clin Infect Dis. 2000;30:633–638.

Marin M, Muñoz P, Sánchez M, del Rosal M, Alcala L, Rodriguez-Créixems M, Bouza E, the Group for the management of infective endocarditis of the Gregorio Marañón Hospital (GAME). Molecular diagnosis of infective endocarditis by real-time broad-range polymerase chain reaction (PCR) and sequencing directly from heart valve tissue. Medicine. 2007;86:195-202.

Marsch G, Orszag P, Mashaqi B, Kuehen C, Haverich A. Antibiotic therapy following polymerase chain reaction diagnosis of infective endocarditis: a single centre experience. Interact Cardiovasc Thorac Surg. 2015;20:589-593.

Menacacci A, Leli C, Montagna P, Cardaccia A, Meucci M, Bietolini C, Cenci E, Pasticci MB, Bisoni F. Diagnosis of infective endocarditis: comparison of the LightCycler SeptiFast real-time PCR with blood culture. J Med Microbiol. 2012;88:1-3.

Millar B, Moore J, Mallon P, Xu J, Crowe M, Mcclurg R, Raoult D, Earle J, Hone R, Murphy P. Molecular diagnosis of infective endocarditis—a new Duke’s criterion. Scand J Infect Dis. 2001;33:673-80.

Miller R, Chow B, Pillai D, Church D. Development and evaluation of a novel fast broad-range 16S ribosomal DNA PCR and sequencing assay for diagnosis of bacterial infective endocarditis: multi-year experience in a large Canadian healthcare zone and a literature review. BMC Infect Dis. 2016;16:146. doi: 10.1186/s12879-016-1476-4.

Miyazato A, Ohkusu K, Ishi S, Sasaoka T, Ikeda M, Niinami H, Ezaki T, Mitsutake K. A case of infective Aerococcus urinae endocarpditis successfully treated by aortic valve replacement. J J A Inf D. 2011;85:678-681.

Miyazato A, Ohkus K, Tabata M, Uwabe K, Kawamura T, Tachi Y, Ezaki T, Niinami H, Mitsutake K. Comparative molecular and microbiological diagnosis of 19 infective endocarditis cases in which causative microbes were identified by PCR-based DNA sequencing from the excised heart valves. J Infect Chemother. 2012;18:318-323.

Miyazato A, Ohkusu K, Tachi Y, Hashikita G, Ezaki T, Mitsutake K. Two cases of infective endocarditis caused by Streptococcus tigurinus. J J A Inf D. 2014;88:304-306.

Morel AS, Dubourg G, Purdent E, Edouard S, Gouriet F, Casalta JP, Fenollar F, Fournier PE, Drancourt M, Roult D. Complemantarity between targeted real-time specific PCR and conventional broad-range 16S rDNA PCR in the syndrome-driven diagnosis of infectious diseases. Eur J Clin Microbiol Infect Dis. 2015;34:561-570.

Moter A, Musci M, Schmiedel D. Molecular methods for diagnosis of infective endocarditis. Curr Infect Dis Rep. 2010;12:244-252.

Mühlemann K, Matter L, Meyer B, Schopfer K. Isolation of Coxiella burnetii from heart valves of patients treated for Q fever endocarditis. J clin Microbiol. 1995;33:428-431.

Mylonakis E, Calderwood SB. Infective endocarditis in adults. N Engl J Med. 2001;345:1318-30.

Nakatani S, Mitustake K, Ohara T, Kokubo Y, Yamamoto H, Hanai S; CADRE investigators. Recent picture of infective endocarditis in Japan – Lessons from Cardiac Disease Registration (CADRE-IE). Circ J. 2013;77(6):1558-64.

Raoult D, Birg ML, Scola BL, Fournier PE, Enea M, Lepidi H, Roux V, Piette JC, Vandenesch F, Vital-Durand D, Marrie TJ. Cultivation of the bacillus of Whipple’s disease. N Engl J Med. 2000;342:620-5.

Relman DA, Loutit JS, Schmidt TM, Falkow S, Tompkins LS. The agent of bacillary angiomatosis. An approach to the identifyion of uncultured pathogens. N Engl J Med. 1990;323:1573-1580.

Relman DA, Schmidt TM, MacDermott RP, Falkow S. Identification of the uncultured bacillus of Whipple’s disease. N Engl J Med. 1992;327:293-301.

Rovery C, Greub G, Lepidi H, Casalta JP, Habib G, Gollart F, Raoult D. PCR detection of bacteria on cardiac valves of patients with treated bacterial endocarditis. J Clin Microbiol. 2005;43:163-7.

Ruoff KL. Nutritionally variant Streptococci. Clin Microbiol Review. 1991;4:184-190.

Takayama Y, Okamoto R, Sunakawa K. Definite infective endocarditis: clinical and microbialogical features of 155 episodes in one Japanese university hospital. J Formos Assoc. 2010;109:788.

Tornos P, Lung G, Permanyer-Miralda G, Baron G, Dlahaye F, Gohlke-Bärwolf, Butchart EG, Ravaud P, Vahanian A. Infective endocarditis in Europe: lessons from the euro heart survey. Heart. 2005;92:571-575.

Vogkou C, Vlachogiannis NI, Palaiodimos L, KousoulisAA. The causative agents in infective endocarditis: a systematic review comprising 33,214 cases. Eur J Clin Microbiol Infect Dis.2016;35:1227-1245.

Voldstedlund M, Norum Pedersen L, Baandrup U, Klaaborg KE, Fuursted K. Broad-range PCR and sequencing in routine diagnosis of infective endocarditis. Acta Pathol Microbiol Immunol Scand. 2008;116:190-8.

Werner M, Andersson R, Olaison L, Hogevik H. A clinical study of 
culture-negative endocarditis. Medicine. 2003;82:263–273.

Wilson KH, Blitchington RB, Greene RC. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. 1990;28:1942-1946.

Wilson KH, Blitchngon R, Frothingham R, Wilson JA. Phylogeny of the Whipple’s-disease-associated bacterium. Lancet. 1991;338:474-5.