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Profiling of the bacteria responsible for pyogenic liver abscess by 16S rRNA gene pyrosequencing

Journal of Microbiology volume 52, pages 504–509 (2014)Cite this article

Abstract

Pyogenic liver abscess (PLA) is a severe disease with considerable mortality and is often polymicrobial. Understanding the pathogens that cause PLA is the basis for PLA treatment. Here, we profiled the bacterial composition in PLA fluid by pyrosequencing the 16S ribosomal RNA (rRNA) gene based on next-generation sequencing (NGS) technology to identify etiological agents of PLA and to provide information of their 16S rRNA sequences for application to DNA-based techniques in the hospital. Twenty patients with PLA who underwent percutaneous catheter drainage, abscess culture, and blood culture for isolates were included. Genomic DNAs from abscess fluids were subjected to polymerase chain reaction and pyrosequencing of the 16S rRNA gene with a 454 GS Junior System. The abscess and blood cultures were positive in nine (45%) and four (20%) patients, respectively. Pyrosequencing of 16S rRNA gene showed that 90% of the PLA fluid samples contained single or multiple genera of known bacteria such as Klebsiella, Fusobacterium, Streptococcus, Bacteroides, Prevotella, Peptostreptococcus, unassigned Enterobacteriaceae, and Dialister. Klebsiella was predominantly found in the PLA fluid samples. All samples that carried unassigned bacteria had 26.8% reads on average. We demonstrated that the occurrence of PLA was associated with eight known bacterial genera as well as unassigned bacteria and that 16S rRNA gene sequencing was more useful than conventional culture methods for accurate identification of bacterial pathogens from PLA.

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Affiliations

  1. Department of Radiology, Sungkyunkwan University School of Medicine, Changwon, 630-522, Republic of Korea

    Yun Gyu Song

  2. Department of Internal Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, 630-522, Republic of Korea

    Sang Gun Shim & Kwang Min Kim

  3. Korea Research Institute of Bioscience and Biotechnology, Human Derived Material Center, Daejeon, 305-806, Republic of Korea

    Dae-Soo Kim

  4. Unitech Science Co., Ltd., Daejeon, 302-120, Republic of Korea

    Sang-Haeng Choi

  5. 5Department of Microbiology, Gyeongsang National University School of Medicine, Jinju, 660-751, Republic of Korea

    Dong-Hae Lee, Jae-Young Song, Hyung-Lyun Kang, Seung-Chul Baik, Woo-Kon Lee, Myung-Je Cho & Kwang-Ho Rhee

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  1. Yun Gyu Song
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  2. Sang Gun Shim
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  3. Kwang Min Kim
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  4. Dong-Hae Lee
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  7. Jae-Young Song
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  10. Woo-Kon Lee
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Correspondence to Myung-Je Cho.

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Song, Y.G., Shim, S.G., Kim, K.M. et al. Profiling of the bacteria responsible for pyogenic liver abscess by 16S rRNA gene pyrosequencing. J Microbiol. 52, 504–509 (2014). https://doi.org/10.1007/s12275-014-4241-7

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  • DOI: https://doi.org/10.1007/s12275-014-4241-7

Keywords

  • pyogenic liver abscess
  • abscess culture
  • metagenomics
  • 16S rRNA gene sequencing
  • next generation sequencing