CanID-PCR - a quick and low-cost PCR tool to identify Candida species on gDNA directly extracted from positive blood bottles

Sep 29, 2026

Upload by Ben

Candida bloodstream infection carries high mortality, with antifungal-resistant species such as Candida auris and C. glabrata increasingly common. CanID-PCR is a simple, low-cost PCR tool that identifies nine common Candida species directly from genomic DNA extracted from positive blood culture bottles, targeting the ACT1 gene. Optimized for direct extraction and tested on 64 patient samples, it achieved 99% concordance with clinical microbiology while revealing polymicrobial infections often overlooked by colony-limited workflows.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages10

Reading Time25 min

AccessFree to download

Abstract

Importance

Keywords

Introduction and Background

Materials and Methods

Assay concept and workflow

| Mycology | Methods and Protocols CanID-PCR: a quick and low-cost PCR tool to identify Candida species on gDNA directly extracted from positive blood bottles Hassan Badrane,1 Cornelius J. Clancy,1,2 M. Hong Nguyen1 AUTHOR AFFILIATIONS See affiliation list on p. 9. ABSTRACT Candida bloodstream infection carries high mortality, and antifungal-resistant species, such as Candida auris and C. glabrata, are increasingly common. Delays in species identification can adversely affect patient outcomes. Conventional workflows by clinical microbiology laboratories require ~24 hours for Candida speciation to allow isolate growth on agar plates. We developed CanID-PCR, a simple, inexpensive PCRbased tool for rapid Candida identification directly from positive blood culture bottles. The assay targets the ACT1 gene, which contains a variable-length intron enabling discrimination among nine common Candida species. CanID-PCR was optimized for genomic DNA extracted directly from positive blood culture bottles and tested on 64 patient samples. Overall, species identification matched the clinical microbiology laboratory with 99% of concordance. One limitation was the inability to distinguish C. parapsilosis from C. metapsilosis, which are highly similar members of the C. parapsilosis complex. The unique discrepancy involved a failure to detect C. tropicalis in a mixed infection with C. glabrata. Among a total of seven samples with two species, one sample had a second species: C. fabianii (Cyberlindnera fabianii), detected only by CanID-PCR, but was missed by the clinical laboratory. These findings demonstrate that CanID-PCR can reveal polymicrobial Candida infections often overlooked when only a few selected colonies are analyzed. CanID-PCR provides rapid, accurate Candida speciation without the need for additional culture, requiring only standard laboratory equipment. This low-cost, straightforward approach is suitable for research laboratories, resource-limited clinical settings, or scenarios where timely species-level identification is critical. IMPORTANCE Identifying species in Candida infections is of utmost importance to clinicians and researchers alike. Here, we describe CanID-PCR: a quick and low-cost PCR tool to identify Candida species on genomic DNA directly extracted from positive blood cultures. This technique uses basic laboratory equipment, and there is no need for high investment in special equipment. The tool allows identification of the nine most prevalent species in candidiasis. The technique is simple and can be used without the need for an additional culture to isolate the cells. It is noteworthy to mention that this tool can detect polymicrobial infections caused by more than one Candida species. KEYWORDS Candida identification, PCR tool C andida is the most common cause of nosocomial fungal bloodstream infection (BSI), a condition associated with high morbidity and mortality. The most common causes of Candida BSI are C. albicans, Nakaseomyces glabratus (previously known as C. glabrata), C. parapsilosis, C. tropicalis, and Pichia kudriavzevii (previously known as C. krusei) (1), although emerging species such as C. auris (Candidozyma auris) are increasingly reported (2) . Rapid and accurate Candida species identification is important in clinical practice, as it informs the likely resistance profiles and guides timely antifungal therapy (3, 4) . It is also important for epidemiological and bench research purposes. Editor Kirsten Nielsen, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia, USA Address correspondence to Hassan Badrane, [hab42@pitt.edu](hab42@pitt.edu). The authors declare no conflict of interest. See the funding table on p. 9. Some of the data here were presented at IDWeek Various approaches, including phenotypic, proteomic, and molecular methods, have been developed to speciate Candida isolates in clinical laboratories (5) . Conventional phenotypic/biochemical meth

FAQs

What problem does CanID-PCR address in Candida bloodstream infections?

It addresses delays in species identification that can worsen patient outcomes, especially when resistant Candida species are involved.

How does CanID-PCR identify Candida species directly from samples?

It performs PCR on genomic DNA extracted from positive blood culture bottles and uses the ACT1 gene intron length to discriminate among nine common species.

What are CanID-PCR’s key performance and limitations based on the study results?

Overall species identification matched the clinical laboratory with 99% concordance, but it could not distinguish C. parapsilosis from C. metapsilosis and showed a discrepancy related to detecting C. tropicalis in a mixed infection.

Sep 29, 2026

Upload by Ben