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.

Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples

“…It is also well established that bacteria deriving from endogenous microbiota are common causative agents of infections in normally sterile body sites (5,6,15,23). In addition, this study and previous studies show that cultivable organisms can also be missed by routine culture (2,15).…”

“…We are not the first to find that molecular techniques can detect bacteria that have not been detected by culture (2) and that these additional species are not necessarily uncultivable species (15). However, studies performed to date did not include a third (and unrelated) comparator technique to further evaluate discrepancies.…”

Fusobacterial liver abscess: a case report and review of the literature

“…Firstly, delays in sample processing have been known to increase the difficulty in identifying anaerobes through conventional culture methods [30], especially in the setting of antimicrobial therapy, which was commenced in advance of abscess drainage. Studies using pyrosequencing of direct samples have shown that pyogenic abscesses are frequently polymicrobial, with the number of aetiologic agents identified significantly exceeding what is achieved using standard culture-based methods [30, 31]. Secondly, many population-based studies accept blood cultures as an appropriate standard in diagnosing causative organisms and in guiding antimicrobial treatment in pyogenic liver abscess [32].…”

Fusobacterium nucleatum in gastroenterological cancer: Evaluation of measurement methods using quantitative polymerase chain reaction and a literature review

“…As a developing research area, the microbiome has been the focus of multiple studies in previous years. The non-spore-forming, anaerobic gram-negative bacterium Fusobacterium nucleatum is part of the normal flora of the human oral cavity and gut mucosa, but is an established opportunistic pathogen in periodontal diseases ( 1 – 4 ) and several inflammatory diseases, including inflammatory bowel disease ( 5 – 8 ), liver abscesses ( 9 , 10 ) and chorioamnionitis ( 11 ). Two previous studies have reported an overabundance of F. nucleatum in colorectal cancer tissues compared with adjacent normal tissues ( 12 , 13 ).…”