Original Article

Ann Lab Med 2017; 37(6): 505-510

Published online November 1, 2017

Copyright © Korean Society for Laboratory Medicine.

Utility of a Direct 16S rDNA PCR and Sequencing for Etiological Diagnosis of Infective Endocarditis

Min-Sun Kim, M.D.1, Jeonghyun Chang, M.D.1, Mi-Na Kim, M.D.1, Sang-Ho Choi, M.D.2, Sung-Ho Jung, M.D.3, Jae-Won Lee, M.D.3, and Heungsup Sung, M.D.1

Departments of Laboratory Medicine1, Internal Medicine2, and Thoracic and Cardiovascular Surgery3, Asan Medical Center and University of Ulsan College of Medicine, Seoul, Korea

Correspondence to: Heungsup Sung
University of Ulsan, College of Medicine and Asan Medical Center, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Korea
Tel: +82-2-3010-4499 Fax: +82-2-478-0884 E-mail:

Received: January 13, 2017; Revised: April 19, 2017; Accepted: July 27, 2017

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.


Background: Cases of infective endocarditis (IE) require prompt etiological diagnosis for effective treatment. Molecular methods can aid in rapid and reliable diagnosis of culture-negative IE cases. We evaluated the utility of 16S rDNA PCR and sequencing in determining the causative agents of IE in valve tissues, especially when specimens were obtained after initiation of antimicrobial therapy.
Methods: We performed 16S rDNA PCR and sequencing in heart valve specimens and medical records review of 80 patients who underwent protocol-based cardiac surgery from 2013 to 2015. One patient did not meet the criteria for IE. Sixty-five (81.3%) and 14 patients (17.5%) were diagnosed as having definite IE and possible IE, respectively. Blood and heart valve biopsy tissue were examined by using routine microbiological methods.
Results: Blood cultures in our hospital were IE-positive for 33 patients (41.8%), whereas 49 patients (62.0%) showed positive blood cultures when initial blood cultures performed at the referring hospital were included. Eighteen (22.8%) and 40 patients (50.6%) were IE-positive in valve tissue cultures and 16S rDNA PCR, respectively. Bacteria in the Streptococcus mitis group (n=26) were the most common etiological agents of IE. Eight (10.1%) culture-negative specimens tested positive by 16S rDNA PCR. In five of eight PCR-positive and culture-negative cases, fastidious or anaerobic organisms were the cause of IE.
Conclusions: Direct 16S rDNA PCR and sequencing can be used as a supplementary method to conventional blood and biopsy culture testing, especially in culture-negative IE cases that are negative for IE by culture.

Keywords: 16S rRNA gene, Infective endocarditis, Utility, PCR, Sequencing