Ann Clin Microbiol.  2020 Mar;23(1):1-10. 10.5145/ACM.2020.23.1.1.

Application of 16S rRNA Gene-Targeted Next-Generation Sequencing for Bacterial Pathogen Detection in Continuous Ambulatory Peritoneal Dialysis Peritonitis

Affiliations
  • 1Department of Laboratory Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Korea.
  • 2Department of Internal Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Korea.
  • 3Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea. deyong@yuhs.ac
  • 4Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea.

Abstract

BACKGROUND
16S rRNA gene-targeted next-generation sequencing (NGS) can detect microorganisms in a comprehensive reference database. To date, NGS has been successfully applied to samples such as urine, blood, and synovial fluid. However, there is no data for continuous ambulatory peritoneal dialysis (CAPD) fluid. The purpose of this study was to evaluate the clinical usefulness of microbiome analysis of CAPD fluids for the diagnosis of CAPD peritonitis.
METHODS
We included 21 patients with high suspicion of CAPD peritonitis. Routine CAPD fluid culture was performed using a pellet of 50 mL CAPD fluid onto the chocolate and blood agar for two days, and thioglycollate broth for one week. 16S rRNA gene-targeted NGS of pellets, stored at −70℃ was performed with MiSeq (Illumina, USA).
RESULTS
Many colonized or pathogenic bacteria were detected from CAPD fluids using NGS and the microbiomes were composed of 1 to 29 genera with a cut-off 1.0. Compared to the culture results, NGS detected the same pathogens in 6 of 18 valid results (three samples failed with low read count). Additionally, using NGS, anaerobes such as Bacteroides spp. and Prevotella spp. were detected in six patients. In two of five samples in which no bacterial growth was detected, possible pathogens were detected by NGS.
CONCLUSION
To our knowledge, this is the first report about the application of 16S rRNA gene-targeted NGS for diagnosis of CAPD peritonitis. Etiology of culture-negative CAPD peritonitis can be better defined in NGS. Furthermore, it also helped the detection of anaerobic bacteria.

Keyword

Continuous ambulatory peritoneal dialysis; Next-generation sequencing; Peritonitis; Rapid diagnosis; 16S rRNA gene

MeSH Terms

Agar
Bacteria
Bacteria, Anaerobic
Bacteroides
Cacao
Colon
Diagnosis
Humans
Microbiota
Peritoneal Dialysis, Continuous Ambulatory*
Peritonitis*
Prevotella
Synovial Fluid
Agar
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