Volume 10,Issue 1
Fall 2025
Application of 16S rRNA Gene-Targeted Next-Generation Sequencing for Bacterial Pathogen Detection in Continuous Ambulatory Peritoneal Dialysis Peritonitis
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°C 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 the diagnosis of CAPD peritonitis. The etiology of culture-negative CAPD peritonitis can be better defined in NGS. Furthermore, it also helped in the detection of anaerobic bacteria.
1.Salzer WL, 2018, Peritoneal Dialysis-Related Peritonitis: Challenges and Solutions. Int J Nephrol Renovasc Dis, 11: 173–186.
2. Ahmadi SH, Neela V, Hamat RA, et al., 2013, Rapid Detection and Identification of Pathogens in Patients with Continuous Ambulatory Peritoneal Dialysis (CAPD) Associated Peritonitis by 16S rRNA Gene Sequencing. Trop Biomed, 30: 602–607.
3. Sung H, Kim MN, 2008, Reliability of Sequence-Based Identification of Microorganism. Infect Chemother, 40: 355–356.
4. Motro Y, Moran-Gilad J, 2017, Next-Generation Sequencing Applications in Clinical Bacteriology. Biomol Detect Quantif, 14: 1–6.
5. Rossen JWA, Friedrich AW, Moran-Gilad J, et al., 2018, Practical Issues in Implementing Whole-Genome-Sequencing in Routine Diagnostic Microbiology. Clin Microbiol Infect, 24: 355–360.
6. Sabat AJ, van Zanten E, Akkerboom V, et al., 2017, Targeted Next-Generation Sequencing of the 16S–23S rRNA Region for Culture-Independent Bacterial Identification – Increased Discrimination of Closely Related Species. Sci Rep, 7: 3434.
7. Grumaz S, Stevens P, Grumaz C, et al., 2016, Next-Generation Sequencing Diagnostics of Bacteremia in Septic Patients. Genome Med, 8: 73.
8. Horiba K, Kawada JI, Okuno Y, et al., 2018, Comprehensive Detection of Pathogens in Immunocompromised Children with Bloodstream Infections by Next-Generation Sequencing. Sci Rep, 8: 3784.
9. Li PK, Szeto CC, Piraino B, et al., 2016, ISPD Peritonitis Recommendations: 2016 Update on Prevention and Treatment. Perit Dial Int, 36: 481–508.
10. Ghali JR, Bannister KM, Brown FG, et al., 2011, Microbiology and Outcomes of Peritonitis in Australian Peritoneal Dialysis Patients. Perit Dial Int, 31: 651–662.
11. Fahim M, Hawley CM, McDonald SP, et al., 2010, Culture Negative Peritonitis in Peritoneal Dialysis Patients in Australia: Predictors, Treatment, and Outcomes in 435 cases. Am J Kidney Dis, 55: 690–697.
12. Pak TR, Kasarskis A, 2015, How Next-Generation Sequencing and Multiscale Data Analysis Will Transform Infectious Disease Management. Clin Infect Dis, 61: 1695–1702.
13. Ivy MI, Thoendel MJ, Jeraldo PR, et al., 2018, Direct Detection and Identification of Prosthetic Joint Infection Pathogens in Synovial Fluid by Metagenomic Shotgun Sequencing. J Clin Microbiol, 56: 402–418.
14. Martins AR, Branco P, Gaspar A, 2016, Lactobacillus casei Peritonitis in Peritoneal Dialysis: A Rare Case and Literature Review. Ther Apher Dial, 20: 90–92.
15. Sanyal D, Bhandari S, 1992, CAPD Peritonitis Caused by Lactobacillus rhamnosus. J Hosp Infect, 22: 325–327.
16. Neef PA, Polenakovik H, Clarridge JE, et al., 2003, Lactobacillus paracasei Continuous Ambulatory Peritoneal Dialysis-Related Peritonitis and Review of the Literature. J Clin Microbiol, 41: 2783–2784.
17. Schleifer CR, Benz RL, McAlack R, et al., 1989, Lactobacillus acidophilus Peritonitis in CAPD. Perit Dial Int, 9: 222–223.
18. Sims D, Brettin T, Detter JC, et al., 2009, Complete Genome Sequence of Kytococcus sedentarius Type Strain (541T). Stand Genomic Sci, 1: 12–20.
19. Durand GA, Pham T, Ndongo S, et al., 2017, Blautia massiliensi ssp. nov., Isolated from a Fresh Human Fecal Sample and Emended Description of the Genus Blautia. Anaerobe, 43: 47–55.
20. Gomez-Arango LF, Barrett HL, Wilkinson SA, et al., 2018, Low Dietary Fiber Intake Increases Collinsella Abundance in the Gut Microbiota of Overweight and Obese Pregnant Women. Gut Microbes, 9: 189–201.
21. Nachimuthu S, Visconti EB, Pannone JB, et al., 2001, Bacteroides Peritonitis Associated with Colon Cancer in a Continuous Ambulatory Peritoneal Dialysis Patient. South Med J, 94: 1021–1022.
22. Denis M, Tommasi L, Teyssier G, et al., 1986, Clostridium butyricum and Bacteroides distasonis Peritonitis in a Child Treated by Peritoneal Dialysis. Usefulness of Anaerobic Culture after Filtration. Presse Med, 15: 2168.
23. Alfa MJ, Degagne P, Olson N, et al., 1997, Improved Detection of Bacterial Growth in Continuous Ambulatory Peritoneal Dialysis Effluent by Use of BacT/Alert FAN Bottles. J Clin Microbiol, 35: 862–866.