Ann Lab Med 2020; 40(1): 63-67  https://doi.org/10.3343/alm.2020.40.1.63
Comparison of 16S Ribosomal RNA Targeted Sequencing and Culture for Bacterial Identification in Normally Sterile Body Fluid Samples: Report of a 10-Year Clinical Laboratory Review
In Young Yoo, M.D.1, On-Kyun Kang, M.T.1, Myoung-Keun Lee, M.T.1, Yae-Jean Kim, M.D.2, Sun Young Cho, M.D.3,4, Kyungmin Huh, M.D.3, Cheol-In Kang, MD.3, Doo Ryeon Chung, M.D.3,4, Kyong Ran Peck , M.D.3, Hee Jae Huh, M.D.1, and Nam Yong Lee, M.D.1
1Department of Laboratory Medicine and Genetics, 2Division of Infectious Diseases, Department of Pediatrics, 3Division of Infectious Diseases, Department of Medicine, 4Center for Infection Prevention and Control, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
Corresponding author: Hee Jae Huh, M.D.
Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Korea
Tel: +82-2-3410-1836 Fax: +82-2-3410-2719 E-mail: pmhhj77@gmail.com

Nam Yong Lee, M.D.
Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Korea
Tel: +82-2-3410-2706 Fax: +82-2-3410-2719 E-mail: micro.lee@samsung.com
Received: April 24, 2019; Revised: June 2, 2019; Accepted: August 7, 2019; Published online: January 1, 2020.
© Korean Society for Laboratory Medicine. All rights reserved.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
As 16S ribosomal RNA (rRNA)-targeted sequencing can detect DNA from non-viable bacteria, it can be used to identify pathogens from clinical samples even in patients pretreated with antibiotics. We compared the results of 16S rRNA-targeted sequencing and culture for identifying bacterial species in normally sterile body fluid (NSBF): cerebrospinal, pericardial, peritoneal and pleural fluids. Over a 10-year period, a total of 312 NSBF samples were evaluated simultaneously using 16S rRNA-targeted sequencing and culture. Results were concordant in 287/312 (92.0%) samples, including 277 (88.8%) negative and 10 (3.2%) positive samples. Of the 16 sequencing-positive, culture-negative samples, eight showed clinically relevant isolates that included Fusobacterium nucleatum subsp. nucleatum, Streptococcus pneumoniae, and Staphylococcus spp. All these samples were obtained from the patients pretreated with antibiotics. The diagnostic yield of 16S rRNA-targeted sequencing combined with culture was 11.2%, while that of culture alone was 6.1%. 16S rRNA-targeted sequencing in conjunction with culture could be useful for identifying bacteria in NSBF samples, especially when patients have been pretreated with antibiotics and when anaerobic infection is suspected.
Keywords: 16S ribosomal RNA, Sequencing, Culture, Diagnostic yield, Normally sterile body fluid



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