title: Profiling of the bacteria responsible for pyogenic liver abscess by 16S rRNA gene pyrosequencing.
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.
authors.affiliation: Department of Radiology, Sungkyunkwan University School of Medicine, Changwon, 630-522, Republic of Korea.
authors.forename: Yun Gyu
authors.initials: YG
authors.lastname: Song
authors.forename: Sang Gun
authors.initials: SG
authors.lastname: Shim
authors.forename: Kwang Min
authors.initials: KM
authors.lastname: Kim
authors.forename: Dong-Hae
authors.initials: DH
authors.lastname: Lee
authors.forename: Dae-Soo
authors.initials: DS
authors.lastname: Kim
authors.forename: Sang-Haeng
authors.initials: SH
authors.lastname: Choi
authors.forename: Jae-Young
authors.initials: JY
authors.lastname: Song
authors.forename: Hyung-Lyun
authors.initials: HL
authors.lastname: Kang
authors.forename: Seung-Chul
authors.initials: SC
authors.lastname: Baik
authors.forename: Woo-Kon
authors.initials: WK
authors.lastname: Lee
authors.forename: Myung-Je
authors.initials: MJ
authors.lastname: Cho
authors.forename: Kwang-Ho
authors.initials: KH
authors.lastname: Rhee
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001419:Bacteria / Q000235:genetics*; D005260:Female; D006801:Humans; D046290:Liver Abscess, Pyogenic / Q000382:microbiology*; D008297:Male; D008875:Middle Aged; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S