1108. A comparison between next generation sequencing and bacterial culture for the detection of bacteria in clinical specimen
Session: Poster Abstract Session: Molecular and Nucleic Acid Testing Diagnostics
Friday, October 9, 2015
Room: Poster Hall
Background: Until now, culture study has been the gold standard in diagnosis of infectious diseases. But advancement in next-generation sequencing (NGS) has allowed the medical field to develop a new diagnostic tool in detecting pathogens. In our study, we compared NGS with bacterial culture in the detection of bacteria in clinical specimens.

Methods: Sputum and stool specimens from ICU patients were collected between April 2014 and March 2015 at Severance Hospital, a 2000-bed tertiary care hospital in Seoul, Korea. NGS and bacterial culture were performed to identify the genus of bacteria in each of the specimens. In NGS, the V1-V3 region of 16S rRNA amplified from genomic DNA was sequenced using the pyrosequending method. We compared the results of NGS and bacterial culture.

Results: Ten specimens from 7 patients were analyzed. Six and four specimens included stools and sputa respectively. In 7 specimens, NGS results included all genera found in bacterial cultures, in addition to the genera which had not been identified in bacterial cultures. In the other 3 specimens, NGS and bacterial culture results contained both intersectional and different portions. Numerous genera detected in NGS were not identified in bacterial cultures. The genera which were not identified in NGS but only in bacterial cultures were Aeromonas, Chryseobacterium and Staphylococcus. The sensitivity, specificity and predictive values of NGS for detecting major bacterial pathogens were calculated in comparison with bacterial culture. The sensitivity was 100% in Acinetobacter, Enterococcus, Escherichia and Klebsiella, and 33% in Staphylococcus. The specificity was 67% in Acinetobacter and Enterococcus, 57% in Escherichia and Klebsiella, and 43% in Staphylococcus. The positive predictive value was 25% in Acinetobacter, 88% in Enterococcus, 50% in Escherichia and Klebsiella, and 20% in Staphylococcus. The negative predictive value was 100% in Acinetobacter, Enterococcus, Escherichia and Klebsiella, and 60% in Staphylococcus.

Conclusion: In our study, NGS technique significantly improved the detection limit of bacterial genera level compared to the conventional protocol indicating that DNA-based culture-independent method will provide a new insight into bacterial detection in clinical samples.

Yong Duk Jeon, MD1, Young Soun Lim, M.S2, Soohyun Lee, M.S3, Kyung Mo Kim, PhD3, Choong-Min Ryu, PhD3, In Young Jung, MD1, Mi-Young Ahn, MD1, Hea Won Ann, MD1, Jin Young Ahn, MD1,2, Nam Su Ku, MD1,2, Dongeun Yong, MD, PhD4, Kyungwon Lee, MD, PhD4, June Myung Kim, MD, PhD1,2 and Jun Yong Choi, MD, PhD1,2, (1)Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea, (2)AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea, (3)Super-Bacteria Research Center, Korean Research institute of Bioscience and Biotechnology, Deajeon, South Korea, (4)Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea


Y. D. Jeon, None

Y. S. Lim, None

S. Lee, None

K. M. Kim, None

C. M. Ryu, None

I. Y. Jung, None

M. Y. Ahn, None

H. W. Ann, None

J. Y. Ahn, None

N. S. Ku, None

D. Yong, None

K. Lee, None

J. M. Kim, None

J. Y. Choi, None

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