Classification of bacteria and fungi in peritoneal dialysis fluids of patients with chronic kidney disease based on metagenomic analysis

Abstract

Chronic kidney disease (CKD) is a long-term condition where sustained damage of the renal parenchyma leads to the chronic deterioration of renal function that may gradually progress to end-stage kidney disease (ESKD). Peritoneal dialysis (PD) is a type of ESKD treatment that is beneficial to improve a patient's quality of life. However, PD-associated peritonitis is a major complication that contributes cause of death, and the detection of the pathogen provided a high culture-negative rate. This study aims to apply metagenomic approaches for identifying the bacteria and fungi in peritoneal dialysis effluent (PDE) of CKD patients based on the full-length 16S ribosomal DNA (rDNA) gene and Internal transcribe spacer (ITS) region, respectively. As a result, the five major bacteria species, including Escherichia coli, Phyllobacterium myrsinacearum, Streptococcus gallolyticus, Staphylococcus epidermidis, and Shewanella algae were observed in PDF samples, whereas the most fungal genera in PDE samples was Wallemia. The results suggested that our metagenomic approach provided a high potential for bacterial and fungal taxonomic identification than the traditional culture method, which would be a practical and alternative culture-independent approach and offers a preventive infectious strategy in CDK patients.