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Updated: Apr 28, 2026
Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
Profiling of the bacteria responsible for pyogenic liver abscess by 16S rRNA gene pyrosequencing
Yun Gyu Song1, Sang Gun Shim, Kwang Min Kim
1Department of Radiology, Sungkyunkwan University School of Medicine, Changwon, 630-522, Republic of Korea.
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.
Insights
This study reveals that 16S rRNA gene sequencing is superior to traditional cultures for identifying bacterial causes of pyogenic liver abscess (PLA). Klebsiella was the most common pathogen found in PLA fluid samples.
Area of Science:
- Microbiology
- Infectious Diseases
- Genomics
Background:
- Pyogenic liver abscess (PLA) is a severe condition with high mortality, often caused by multiple bacteria.
- Accurate identification of causative pathogens is crucial for effective PLA treatment.
Purpose of the Study:
- To profile the bacterial composition in PLA fluid using next-generation sequencing (NGS).
- To identify etiological agents of PLA and provide 16S rRNA sequences for DNA-based diagnostics.
- To compare the efficacy of 16S rRNA gene sequencing with conventional culture methods.
Main Methods:
- Collected PLA fluid from 20 patients undergoing percutaneous catheter drainage.
- Performed 16S ribosomal RNA (rRNA) gene pyrosequencing on abscess fluid DNA.
- Compared sequencing results with abscess and blood culture data.
Main Results:
- 16S rRNA gene sequencing identified known bacterial genera in 90% of PLA fluid samples, with Klebsiella being predominant.
- Conventional cultures were positive in 45% of patients (abscess) and 20% (blood).
- Sequencing revealed a broader spectrum of pathogens, including unassigned bacteria, compared to cultures.
Conclusions:
- 16S rRNA gene sequencing is a more sensitive and accurate method than conventional culture for identifying bacterial pathogens in PLA.
- The findings provide valuable sequence data for developing hospital-based DNA diagnostic techniques for PLA.
