Title Profiling of the Bacteria Responsible for Pyogenic Liver Abscess by 16S rRNA Gene Pyrosequencing
Author Yun Gyu Song1, Sang Gun Shim2, Kwang Min Kim2, Dong-Hae Lee3, Dae-Soo Kim4, Sang-Haeng Choi5, Jae-Young Song3, Hyung-Lyun Kang3, Seung-Chul Baik3, Woo-Kon Lee3, Myung-Je Cho3*, and Kwang-Ho Rhee3
Address 1Department of Radiology, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon 630-522, Republic of Korea, 2Department of Internal Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon 630-522, Republic of Korea, 3Department of Microbiology, Gyeongsang National University School of Medicine, Jinju 660-751, Republic of Korea, 4Human Derived Material Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea, 5Unitech Science Co., Ltd., Daejeon 302-120, Republic of Korea
Bibliography Journal of Microbiology, 52(6),504-509, 2014,
DOI 10.1007/s12275-014-4241-7
Key Words pyogenic liver abscess, abscess culture, metagenomics, 16S rRNA gene sequencing, next generation sequencing
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.