DNA sequencing identifies fungal bloodstream infections before cultures turn positive
· Medical Xpressedited by Sadie Harley, reviewed by Robert Egan
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Bloodstream infections are a persistent threat to hospitalized patients, and those caused by fungi are particularly dangerous. Candida species are responsible for most invasive fungal infections worldwide and rank among the leading causes of hospital-acquired bloodstream infections overall. Because different fungal species can respond differently to antifungal drugs, doctors strive to correctly identify the fungus responsible for a given infection before initiating treatment.
However, conventional diagnosis relies on blood cultures, in which a patient's blood is incubated until microorganisms grow to detectable levels. This process, together with subsequent identification tests, can take several days to complete. During this waiting period, clinicians often treat patients with broad-spectrum antifungal drugs or wait longer than ideal to start more targeted therapies.
To address this challenge, a research team led by professor Hiroki Takahashi from the Medical Mycology Research Center at Chiba University in Japan developed a workflow to more rapidly identify fungal pathogens.
Their study, published in the journal Microbiology Spectrum was co-authored by Dr. Isato Yoshioka, Dr. Momotaka Uchida, professor Akira Watanabe and Dr. Takashi Yaguchi, all from Chiba University.
Enriching microbial DNA for real-time sequencing
The proposed workflow comprises three main steps, performed on a blood culture sample collected while it is still incubating and before the automated system flags it as positive.
First, the researchers selectively break down human cells and then degrade human DNA using an enzyme called benzonase, without affecting fungal and bacterial DNA. This greatly increases the proportion of microbial DNA versus human DNA in the sample.
Afterward, the researchers use PCR-based whole-genome amplification to make many copies of DNA fragments from across the genomes present in the sample, generating enough genetic material for sequencing.
The amplified DNA is then loaded onto a portable device for nanopore sequencing, a technique that determines the sequence of DNA molecules as they pass through nanoscale pores. Unlike sequencing approaches that require a completed run before results can be assessed, nanopore sequencing generates DNA sequence data in real time as the run progresses.
The resulting sequences are then compared with a custom-built reference database containing genetic information from a wide range of microorganisms, including fungal and bacterial pathogens associated with bloodstream infections.
"I have a background in sequence analysis and genomics, and I saw an opportunity to apply my expertise to the important clinical challenge of fungal infections," explains Takahashi. "I was particularly motivated by the possibility of using modern genomic technologies to improve our understanding, diagnosis and ultimately treatment of these infections."
Species identification within seven hours
In tests using 48 clinical blood culture samples representing eight fungal species, the proposed workflow achieved species-level identification within approximately seven hours with high accuracy.
The researchers also found that the method could identify a range of fungal pathogens, such as Candida albicans, Nakaseomyces glabratus, Candida parapsilosis, Candida tropicalis and Cryptococcus neoformans. It even detected mixed infections in some samples, including those with two fungal species or both fungi and bacteria.
A key feature of this approach is its speed, as it can identify fungal pathogens directly from blood culture samples before the cultures turn positive in conventional culture systems.
"Our method may enable clinicians to initiate appropriate antifungal treatment earlier, potentially improving outcomes for patients with life-threatening fungal bloodstream infections," remarks Takahashi. Moreover, because the workflow captures the full genome of the pathogen, it can also detect genetic variants in genes associated with drug resistance.
Timing and mixed infections need refinement
The researchers note that further work will be needed to determine the best timing for collecting samples during incubation and to improve detection when heavy bacterial growth masks fungal signals in mixed infections.
With further validation, their strategy could contribute to the development of rapid diagnostic procedures for life-threatening fungal infections, reducing delays in effective therapy and ultimately improving care for affected patients.
More information
Isato Yoshioka et al, Random PCR-based nanopore whole-genome sequencing enables pre-positivity detection of fungal bloodstream infections, Microbiology Spectrum (2026). DOI: 10.1128/spectrum.00478-26
Key medical concepts
Nanopore SequencingBlood Culture
Clinical categories
Infectious diseasesLaboratory medicine Provided by Chiba University Who's behind this story?
Sadie Harley
BSc Life Sciences & Ecology. Microbiology lab background with pharmaceutical news experience in oil, gas, and renewable industries. Full profile →
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