UNMASKING HIDDEN PATHOGENS: NANOPORE ITS SEQUENCING REVEALS SITE-SPECIFIC MICROBIAL SIGNATURES IN HEMODIALYSIS CATHETERS

 

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UNMASKING HIDDEN PATHOGENS: NANOPORE ITS SEQUENCING REVEALS SITE-SPECIFIC MICROBIAL SIGNATURES IN HEMODIALYSIS CATHETERS

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Talerngsak
Kanjanabuch
Thunvarat Saejew thunvarat.p@gmail.com Center of Excellence in Kidney Metabolic Disorders Faculty of Medicine, Chulalongkorn University Bangkok Thailand -
Suthida Visedthorn tangsuthida.chula@gmail.com Medical Biochemistry Program Department of Biochemistry, Faculty of Medicine, Chulalongkorn University Bangkok Thailand - Center of Excellence in Systems Microbiology Faculty of Medicine, Chulalongkorn University Bangkok Thailand
Pavit Klomkliew pavit.kw@gmail.com Center of Excellence in Systems Microbiology Faculty of Medicine, Chulalongkorn University Bangkok Thailand -
Vorthon Sawaswong vorthon007.giftedcru@gmail.com Medical Biochemistry Program Department of Biochemistry, Faculty of Medicine, Chulalongkorn University Bangkok Thailand - Center of Excellence in Systems Microbiology Faculty of Medicine, Chulalongkorn University Bangkok Thailand
Pavaret Sivapornnukul Pavaret.S@alumni.chula.ac.th Center of Excellence in Systems Microbiology Faculty of Medicine, Chulalongkorn University Bangkok Thailand -
Prangwalai Chanchaem puiiprang.ch@gmail.com Center of Excellence in Systems Microbiology Faculty of Medicine, Chulalongkorn University Bangkok Thailand -
Preeyarat Pavatung preeyarat648@gmail.com Center of Excellence in Kidney Metabolic Disorders Faculty of Medicine, Chulalongkorn University Bangkok Thailand -
Sunchai Payungporn sp.medbiochemcu@gmail.com Center of Excellence in Systems Microbiology Faculty of Medicine, Chulalongkorn University Bangkok Thailand - Department of Biochemistry Faculty of Medicine, Chulalongkorn University Bangkok Thailand
Talerngsak Kanjanabuch golfnephro@hotmail.com Center of Excellence in Kidney Metabolic Disorders Faculty of Medicine, Chulalongkorn University Bangkok Thailand * Division of Nephrology Department of Internal Medicine, Faculty of Medicine, Chulalongkorn University Bangkok Thailand CAPD Excellence Center King Chulalongkorn Memorial Hospital Bangkok Thailand
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Catheter-related bloodstream infections (CRBSIs) remain a major complication in hemodialysis (HD). Conventional culture methods frequently miss fastidious or biofilm-associated pathogens, particularly fungi, limiting diagnostic accuracy. Oxford Nanopore Technologies (ONT) sequencing provides rapid, culture-independent pathogen identification and can detect difficult-to-culture organisms. Viewing the HD catheter as a cumulative infection recorder—analogous to HbA1c for glycemic exposure—this study aimed to characterize site-specific microbial communities within HD catheters and explore their association with CRBSI pathogenesis.

This multicenter observational study analyzed 70 tunneled HD catheters removed from adult patients (≥18 years) between [Jan 2023–May 2024]. Patients were classified into CRBSI (n = 27) and non-CRBSI (n = 43) groups according to IDSA criteria. Each catheter was sectioned into arterial (site A) and venous (site V) lumens. Biofilm was scraped aseptically and divided for culture and DNA extraction. Standard aerobic, anaerobic, and fungal cultures were performed using blood agar, MacConkey, and Sabouraud dextrose agar. Culture positivity was recorded as /, with results pending analysis. DNA extraction was performed using the ZymoBIOMICS™ DNA Miniprep Kit, followed by amplification of the ITS1–ITS2 region using fungal-specific primers. Sequencing was carried out on the Oxford Nanopore MinION platform. Raw reads were processed using QIIME2 and taxonomic classification performed with the SILVA databases. Relative abundance, alpha diversity (Chao1, Shannon), and beta diversity (PERMANOVA) were assessed between site A and site V, and between CRBSI and non-CRBSI catheters.

All samples yielded amplifiable ITS sequences. Sequencing positivity was 66% (46/70) for site A and 79% (55/70) for site V, markedly higher than culture detection (36% vs. 36%). Beta diversity showed significant differences in microbial composition between sites (p=0.001), while alpha diversity revealed greater richness at site V. Site A was dominated by human-associated fungi, including Candida albicans (22%) and Candida tropicalis (13%), suggesting endogenous colonization. In contrast, site V showed enrichment with environmental fungi, including Wallemia canadensis (31%), Aureobasidium leucospermi (15%), and Lodderomyces elongisporus (13%), implying exogenous contamination possibly related to breaches in aseptic technique. CRBSI catheters demonstrated higher fungal loads and reduced community evenness compared with non-CRBSI samples.

Nanopore ITS sequencing provides comprehensive, site-specific profiling of microbial communities in HD catheters, uncovering diverse fungal and environmental pathogens missed by conventional culture. Distinct arterial and venous microbial patterns indicate dual infection pathways—endogenous and environmental—offering new insights to enhance prevention and management of catheter-related infections in HD practice.

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