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Updated: Aug 17, 2026
Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
Rapid detection and identification of pathogens in patients with continuous ambulatory peritoneal dialysis (CAPD)
S H Ahmadi1, V Neela1, R A Hamat1
1Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
Abstract:
Peritonitis still remains a serious complication with high rate of morbidity and mortality in patients on CAPD. Rapid and accurate identification of pathogens causing peritonitis in a CAPD patient is essential for early and optimal treatment. The aim of this study was to use 16S rRNA and ITS gene sequencing to identify common bacterial and fungal pathogens directly from the peritoneal fluid without culturing. Ninety one peritoneal fluids obtained from 91 different patients on CAPD suspected for peritonitis were investigated for etiological agents by 16S rRNA and ITS gene sequencing. Data obtained by molecular method was compared with the results obtained by culture method. Among the 45 patients confirmed for peritonitis based on international society of peritoneal dialysis (ISPD) guidelines, the etiological agents were identified in 37(82.2%) samples by culture method, while molecular method identified the etiological agents in 40(88.9%) samples. Despite the high potential application of the 16S rRNA and ITS gene sequencing in comparison to culture method to detect the vast majority of etiological agents directly from peritoneal fluids; it could not be used as a standalone test as it lacks sensitivity to identify some bacterial species due to high genetic similarity in some cases and inadequate database in Gene Bank. However, it could be used as a supplementary test to the culture method especially in the diagnosis of culture negative peritonitis.
Insights
Molecular sequencing accurately identifies more pathogens in continuous ambulatory peritoneal dialysis (CAPD) peritonitis cases than traditional culture. This method aids in diagnosing culture-negative peritonitis, improving patient treatment outcomes.
Area of Science:
- Medical Microbiology
- Nephrology
- Molecular Diagnostics
Background:
- Peritonitis is a severe complication in patients undergoing continuous ambulatory peritoneal dialysis (CAPD), leading to significant morbidity and mortality.
- Timely and precise pathogen identification is crucial for effective peritonitis management in CAPD patients.
Purpose of the Study:
- To evaluate the utility of 16S rRNA and ITS gene sequencing for direct pathogen identification from peritoneal fluid in CAPD peritonitis.
- To compare the diagnostic yield of molecular methods against conventional culture techniques.
Main Methods:
- Analysis of 91 peritoneal fluid samples from CAPD patients suspected of peritonitis.
- Direct identification of bacterial and fungal pathogens using 16S rRNA and ITS gene sequencing.
- Comparison of molecular results with traditional culture-based methods.
Main Results:
- Molecular sequencing identified etiological agents in 88.9% of peritonitis cases, compared to 82.2% by culture.
- The molecular method demonstrated a higher detection rate for pathogens than culture.
- Limitations include sensitivity issues with certain bacteria and database limitations.
Conclusions:
- 16S rRNA and ITS gene sequencing offers a valuable adjunct to culture methods for diagnosing CAPD peritonitis.
- Molecular techniques are particularly beneficial for identifying pathogens in culture-negative peritonitis cases.
- It is recommended as a supplementary diagnostic tool rather than a standalone test.
