Nanopore sequencing cuts time needed to identify fungal bloodstream infections

Bloodstream infections caused by fungi present clinical microbiology laboratories with a difficult combination of urgency and technical complexity. Appropriate antifungal treatment depends upon knowing which organism is responsible for the infection, yet conventional identification requires sufficient microbial growth to occur before the laboratory can move to more definitive testing.

 

By Tim Sandle 

 

Researchers at Chiba University in Japan have developed a genomic workflow intended to shorten this diagnostic interval. In a study published in Microbiology Spectrum, the researchers report species-level identification of fungal pathogens from blood culture samples in approximately seven hours, and importantly, before automated blood culture systems indicated that the samples were positive. The research is described by Chiba University.

 

This development is significant because rapid organism identification represents an important component of effective management of bloodstream infection. Different fungal species can respond differently to antifungal agents, making accurate identification relevant to the selection of appropriate treatment.

Getting ahead of blood culture positivity

Conventional blood culture depends upon microorganisms multiplying until their growth can be detected. According to the Chiba University researchers, culture followed by identification testing can take several days to complete. The new method takes a different approach. Instead of waiting for the culture instrument to signal positivity, the scientists remove a sample while the blood culture is still incubating and seek to recover and characterize microbial DNA directly.

 

The workflow developed by the group led by Hiroki Takahashi, Professor at the Medical Mycology Research Center, Chiba University, consists of three principal stages.

 

The first challenge is that blood contains a large quantity of human material. The researchers selectively break down human cells before using benzonase to degrade the released human DNA, while leaving fungal and bacterial DNA unaffected. This increases the relative proportion of microbial DNA available for subsequent analysis. The second stage uses PCR-based whole-genome amplification. This produces multiple copies of DNA fragments from across the genomes contained within the specimen and provides sufficient genetic material for sequencing. 

 

Finally, the amplified material undergoes nanopore sequencing. Rather than requiring the entire sequencing run to finish before analysis can begin, nanopore technology produces sequence data continuously. The resulting sequences are compared with a purpose-built reference database containing genomic information for fungal and bacterial organisms associated with bloodstream infections. This combination of sample preparation, amplification and real-time sequencing is what enables the researchers to seek an identification before conventional blood culture positivity.

Testing clinical blood cultures

The researchers evaluated the process using 48 clinical blood culture samples covering eight fungal species. Chiba University reports that species-level identification was achieved in approximately seven hours with high accuracy. Organisms identified included Candida albicans, Candida parapsilosis, Candida tropicalis, Cryptococcus neoformans and Nakaseomyces glabratus. The last organism is particularly familiar to laboratories under its former name, Candida glabrata, although the Chiba report uses the currently accepted Nakaseomyces nomenclature.

 

 

A further interesting feature was the ability to recognize more complicated specimens. The researchers detected mixed infections in some samples, including cultures containing two fungal species and others containing fungal and bacterial organisms. This is potentially important for diagnostic microbiology because a dominant organism can complicate the detection of other microorganisms within a mixed population. That difficulty has not been completely overcome. The researchers specifically identify heavy bacterial growth masking fungal signals in mixed infections as an area requiring further work. They also need to establish the optimum point during blood-culture incubation at which a specimen should be taken for genomic analysis. 

 

These limitations are important. The work demonstrates the potential of the approach, but it should not yet be interpreted as a replacement for established diagnostic workflows.

 

Genomics provides another layer of information

Species identification is not the only information potentially available from the sequencing process. Because the method obtains genomic information from the pathogen, the researchers state that it can identify genetic variants in genes associated with antifungal drug resistance. This presents an interesting direction for clinical microbiology. Rapidly determining the likely organism is valuable, but coupling identification with genomic information associated with resistance could make sequencing more useful for antimicrobial stewardship.

 

Phenotypic susceptibility testing and genomic resistance detection do not, however, answer precisely the same question. Consequently, the practical value will depend upon how reliably particular genetic markers predict clinically meaningful antifungal resistance and how genomic information is incorporated into validated laboratory procedures. The study itself is titled Random PCR-based nanopore whole-genome sequencing enables pre-positivity detection of fungal bloodstream infections and was published online on August 21, 2026, in Microbiology Spectrum.

Why speed matters

The technological advance needs to be considered in the context of treatment decisions. Until the causative microorganism is known, clinicians may need to make treatment decisions with incomplete microbiological information. Chiba University notes that during the conventional diagnostic interval patients may receive broad antifungal treatment, while more targeted therapy has to await further information. 

 

Faster microbiological identification therefore has the potential to reduce some of this uncertainty. “Our method may enable clinicians to initiate appropriate antifungal treatment earlier, potentially improving outcomes for patients with life-threatening fungal bloodstream infections,” Hiroki Takahashi states.

 

The word “may” is important. The present study demonstrates analytical and diagnostic potential. It does not, on the evidence reported by the university, demonstrate improved patient outcomes resulting from use of the workflow.

From proof of concept to routine microbiology

For pharmaceutical and clinical microbiologists, perhaps the most interesting aspect of the research is how several existing molecular technologies have been integrated around a particular diagnostic bottleneck. The significant step is not nanopore sequencing in isolation. It is the complete sample-to-identification strategy: removing unwanted host DNA, increasing microbial genomic material through amplification and exploiting real-time sequencing sufficiently early in blood-culture incubation to obtain information before the automated culture signal. 

 

There are still questions to address before such an approach could progress toward broader routine use. Chiba University says further validation is needed, together with work to optimize the sampling time and improve fungal detection where substantial bacterial growth is present. 

 

Nevertheless, the study illustrates a broader change taking place within diagnostic microbiology. Culture remains enormously important, but genomic technologies are increasingly creating opportunities to obtain actionable information without waiting for all of the traditional microbiological process to be completed.

 

For fungal bloodstream infections, where identifying the infectious agent is particularly important to choosing suitable antifungal therapy, moving identification even a day earlier could prove valuable. The Chiba University work suggests that it may be possible to move considerably further upstream, interrogating the microbial genome while the blood culture bottle is still incubating.

 

Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

The billion-year reign of fungi that predated plants and made Earth livable

Image designed by Tim Sandle
 

Fungi may have shaped Earth’s landscapes long before plants appeared. By combining rare gene transfers with fossil evidence, researchers have traced fungal origins back nearly a billion years earlier than expected. These ancient fungi may have partnered with algae, recycling nutrients, breaking down rock, and creating primitive soils. Far from being silent background players, fungi were ecosystem engineers that prepared Earth’s surface for plants, fundamentally altering the course of life’s history. 

New research from Okinawa Institute of Science and Technology.

Complex multicellular life -- organisms made of many cooperating cells with specialized jobs -- evolved independently in five major groups: animals, land plants, fungi, red algae, and brown algae. On a planet once dominated by single-celled organisms, a revolutionary change occurred not once, but at least five separate times: the evolution of complex multicellular life. Understanding when these groups emerged is fundamental to piecing together the history of life on Earth."

Emergence here was not simply a matter of cells clumping together; it was the dawn of organisms, where cells took on specialized jobs and were organized into distinct tissues and organs, much like in our own bodies. This evolutionary leap required sophisticated new tools, including highly developed mechanisms for cells to adhere to one another and intricate systems for them to communicate across the organism, and arose independently in each of the five major groups.

The difficulties of dating evolutionary divergence

For most of these groups, the fossil record acts as a geological calendar, providing anchor points in deep time. For example, red algae show up possibly as early as about 1.6 billion years ago (in candidate seaweed-like fossils from India); animals appear by around 600 million years ago (Ediacaran fossils such as the quilted pancake like Dickinsonia); land plants take root roughly 470 million years ago (tiny fossil spores); and brown algae (kelp-like forms) diversified tens to hundreds of millions of years later still. Based on this evidence, a chronological picture of life's complexity emerges.

There is, however, a notable exception to this fossil-based timeline: fungi. The fungal kingdom has long been an enigma for paleontologists. Their typically soft, filamentous bodies mean they rarely fossilize well. Furthermore, unlike animals or plants, which appear to have a single origin of complex multicellularity, fungi evolved this trait multiple times from diverse unicellular ancestors, making it difficult to pinpoint a single origin event in the sparse fossil record.

Reading the genetic clock

To overcome the gaps in the fungal fossil record, scientists use a "molecular clock." The concept is that genetic mutations accumulate in an organism's DNA at a relatively steady rate over generations, like the ticking of a clock. By comparing the number of genetic differences between two species, researchers can estimate how long ago they diverged from a common ancestor.

However, a molecular clock is uncalibrated; it can reveal relative time but not absolute years. To set the clock, scientists need to calibrate it with "anchor points" from the fossil record. Given the scarcity of fungal fossils, this has always been a major challenge. The OIST-led team addressed this by incorporating a novel source of information: rare gene "swaps" between different fungal lineages, a process known as horizontal gene transfer (HGT).

While genes are normally passed down "vertically" from parent to child, HGT is like a gene jumping "sideways" from one species to another. These events provide powerful temporal clues," he says. "If a gene from lineage A is found to have jumped into lineage B, it establishes a clear rule: the ancestors of lineage A must be older than the descendants of lineage B.

By identifying 17 such transfers, the team established a series of "older than/younger than" relationships that, alongside fossil records, helped to tighten and constrain the fungal timeline.

A new history for an ancient kingdom

The analysis suggests a common ancestor of living fungi dating to roughly 1.4-0.9 billion years ago -- well before land plants. That timing supports a long prelude of fungi-algae interactions that helped set the stage for life on land.

Fungi run ecosystems -- recycling nutrients, partnering with other organisms, and sometimes causing disease. Pinning down their timeline shows fungi were diversifying long before plants, consistent with early partnerships with algae that likely helped pave the way for terrestrial ecosystems.

This revised timeline fundamentally reframes the story of life's colonization of land. It suggests that for hundreds of millions of years before the first true plants took root, fungi were already present, likely interacting with algae in microbial communities. This long, preparatory phase may have been essential for making Earth's continents habitable. By breaking down rock and cycling nutrients, these ancient fungi could have been the first true ecosystem engineers, creating the first primitive soils and fundamentally altering the terrestrial environment. In this new view, plants did not colonize a barren wasteland, but rather a world that had been prepared for them over eons by the ancient and persistent activity of the fungal kingdom.

The research paper reference is:

Lénárd L. Szánthó, Zsolt Merényi, Philip Donoghue, Toni Gabaldón, László G. Nagy, Gergely J. Szöllősi, Eduard Ocaña-Pallarès. A timetree of Fungi dated with fossils and horizontal gene transfers. Nature Ecology, 2025; DOI: 10.1038/s41559-025-02851-z 

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Meet the tiny ocean fungus that kills toxic algae

Algae, image by Tim Sandle
 

Scientists have discovered a newly identified marine fungus that can infect and kill toxic algae responsible for harmful blooms. The microscopic parasite, named Algophthora mediterranea, attacks algae such as Ostreopsis cf. ovata, which produces toxins that can irritate the lungs, skin, and eyes of people exposed during coastal blooms. Remarkably, the fungus can infect several different algae species and even survive on pollen, suggesting it is far more adaptable than most known marine parasites.

Researchers at Yokohama National University in Japan have identified a previously unknown species of marine fungus capable of killing harmful algae that form toxic blooms.

The organism, named Algophthora mediterranea, is a microscopic chytrid fungus that can infect a wide variety of hosts. Chytrids are a diverse group of aquatic fungi, and the discovery suggests they may influence marine ecosystems more strongly than scientists once believed.

The researchers found that this fungus acts as a lethal parasite in Ostreopsis cf. ovata, a species of algae responsible for toxic blooms that can negatively affect human health. The study describing the discovery was published in Mycologia.

Toxic Algae and Their Health Risks

Harmful algal blooms have become an increasing concern in oceans, rivers, and lakes around the world. These outbreaks occur when algae grow rapidly and excessively, often triggered by high nutrient levels and warmer water temperatures. Such blooms can degrade water quality, disrupt ecosystems, and release toxins that threaten both wildlife and people.

Large blooms of Ostreopsis cf. ovata have been reported more frequently in the Mediterranean over recent decades. This alga produces a toxin called ovatoxin (OVTX), which can cause symptoms in humans including runny nose, coughing, shortness of breath, conjunctivitis, itching, and dermatitis.

A Newly Identified Algae Killing Fungus

Algophthora mediterranea was first detected in Spanish seawater in 2021 by scientists from the Institut de Ciències del Mar (ICM) in Spain, led by Dr. E. Garcés and Dr. A. Reñé. The species was later formally described by Professor Maiko Kagami and PhD student Núria Pou-Solà at Yokohama National University.

Genetic analysis confirmed that the organism represents not only a newly identified species but also an entirely new genus. The researchers named the genus Algophthora by combining the word 'alga' with the Greek word 'phthora', meaning 'destruction'.

Scientists observed that the fungus parasitizes cells of O. cf. ovata and can kill them within a few days. Additional experiments showed that it can also infect several other algae species and can even feed on pollen grains.

Studying the Parasite in Detail

To better understand the organism, the researchers isolated the fungus and recorded time-lapse images every ten minutes over a four-day period. They also examined samples using scanning electron microscopy (SEM), a technique in which a focused beam of electrons scans the surface of a specimen to create highly detailed images. The fungus was also analyzed through DNA sampling.

Reference:

Núria Pou-Solà, Kensuke Seto, Alan Denis Fernández-Valero, Jordina Gordi, Esther Garcés, Albert Reñé, Maiko Kagami. Algophthora mediterranea , gen. et sp. nov.: Novel dinoflagellate- and diatom-infecting generalist marine chytrid from the Mediterranean Sea. Mycologia, 2025; 118 (1): 10 DOI: 10.1080/00275514.2025.2577604 

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

From cursed tomb fungus to cancer cure: Aspergillus flavus yields potent new drug

 Image: Aspergillus flavus by Medmyco - Own work, CC BY-SA 4.0

In a new twist of science, researchers have transformed a fungus long associated with death into a potential weapon against cancer. Found in tombs like that of King Tut, Aspergillus flavus was once feared for its deadly spores. 

Scientists at the University of Pennsylvania School of Engineering and Applied Science have extracted a new class of molecules from it—called asperigimycins—that show powerful effects against leukaemia cells. These compounds, part of a rare group known as fungal RiPPs, were bioengineered for potency and appear to disrupt cancer cell division with high specificity.

"Fungi gave us penicillin," says Sherry Gao, Presidential Penn Compact Associate Professor in Chemical and Biomolecular Engineering (CBE) and in Bioengineering (BE). "These results show that many more medicines derived from natural products remain to be found."

 

From Curse to Cure

 

Aspergillus flavus, named for its yellow spores, has long been a microbial villain. After archaeologists opened King Tutankhamun's tomb in the 1920s, a series of untimely deaths among the excavation team fueled rumors of a pharaoh's curse. Decades later, doctors theorized that fungal spores, dormant for millennia, could have played a role.

In the 1970s, a dozen scientists entered the tomb of Casimir IV in Poland. Within weeks, 10 of them died. Later investigations revealed the tomb contained A. flavus, whose toxins can lead to lung infections, especially in people with compromised immune systems.Now, that same fungus is the unlikely source of a promising new cancer therapy.

 

A Rare Fungal Find

 

The therapy in question is a class of ribosomally synthesized and post-translationally modified peptides, or RiPPs, pronounced like the "rip" in a piece of fabric. The name refers to how the compound is produced -- by the ribosome, a tiny cellular structure that makes proteins -- and the fact that it is modified later, in this case, to enhance its cancer-killing properties.

"Purifying these chemicals is difficult," says Qiuyue Nie, a postdoctoral fellow in CBE and the paper's first author. While thousands of RiPPs have been identified in bacteria, only a handful have been found in fungi. In part, this is because past researchers misidentified fungal RiPPs as non-ribosomal peptides and had little understanding of how fungi created the molecules. "The synthesis of these compounds is complicated," adds Nie. "But that's also what gives them this remarkable bioactivity."

 

Hunting for Chemicals

 

To find more fungal RiPPs, the researchers first scanned a dozen strains of Aspergillus, which previous research suggested might contain more of the chemicals.

By comparing chemicals produced by these strains with known RiPP building blocks, the researchers identified A. flavus as a promising candidate for further study.

Genetic analysis pointed to a particular protein in A. flavus as a source of fungal RiPPs. When the researchers turned the genes that create that protein off, the chemical markers indicating the presence of RiPPs also disappeared.

This novel approach -- combining metabolic and genetic information -- not only pinpointed the source of fungal RiPPs in A. flavus, but could be used to find more fungal RiPPs in the future.

 

A Potent New Medicine

 

After purifying four different RiPPs, the researchers found the molecules shared a unique structure of interlocking rings. The researchers named these molecules, which have never been previously described, after the fungus in which they were found: asperigimycins.

Even with no modification, when mixed with human cancer cells, asperigimycins demonstrated medical potential: two of the four variants had potent effects against leukaemia cells.

Another variant, to which the researchers added a lipid, or fatty molecule, that is also found in the royal jelly that nourishes developing bees, performed as well as cytarabine and daunorubicin, two FDA-approved drugs that have been used for decades to treat leukaemia.

 

Cracking the Code of Cell Entry

 

To understand why lipids enhanced asperigimycins' potency, the researchers selectively turned genes on and off in the leukemia cells. One gene, SLC46A3, proved critical in allowing asperigimycins to enter leukemia cells in sufficient numbers.

That gene helps materials exit lysosomes, the tiny sacs that collect foreign materials entering human cells. "This gene acts like a gateway," says Nie. "It doesn't just help asperigimycins get into cells, it may also enable other 'cyclic peptides' to do the same."

Like asperigimycins, those chemicals have medicinal properties -- nearly two dozen cyclic peptides have received clinical approval since 2000 to treat diseases as varied as cancer and lupus -- but many of them need modification to enter cells in sufficient quantities.

"Knowing that lipids can affect how this gene transports chemicals into cells gives us another tool for drug development," says Nie.

 

Disrupting Cell Division

 

Through further experimentation, the researchers found that asperigimycins likely disrupt the process of cell division. "Cancer cells divide uncontrollably," says Gao. "These compounds block the formation of microtubules, which are essential for cell division."

Notably, the compounds had little to no effect on breast, liver or lung cancer cells -- or a range of bacteria and fungi -- suggesting that asperigimycins' disruptive effects are specific to certain types of cells, a critical feature for any future medication.

 

Future Directions

 

In addition to demonstrating the medical potential of asperigimycins, the researchers identified similar clusters of genes in other fungi, suggesting that more fungal RiPPS remain to be discovered. "Even though only a few have been found, almost all of them have strong bioactivity," says Nie. "This is an unexplored region with tremendous potential."

The next step is to test asperigimycins in animal models, with the hope of one day moving to human clinical trials. "Nature has given us this incredible pharmacy," says Gao. "It's up to us to uncover its secrets. As engineers, we're excited to keep exploring, learning from nature and using that knowledge to design better solutions."

Reference:

 

Qiuyue Nie, Fanglong Zhao, Xuerong Yu et al. A class of benzofuranoindoline-bearing heptacyclic fungal RiPPs with anticancer activities. Nature Chemical Biology, 2025; DOI: 10.1038/s41589-025-01946-9 

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Tumor-promoting potential in common skin fungus

Image:  AJC1 from UK - Malassezia globosa (CC BY-SA 2.0)

A common skin fungus, Malassezia globosa may invade deep tissues through the skin or by other means, then cause tumor growth, according to a new study. The study results were reported in mBio, an open access journal of the American Society for Microbiology.

"It is important to take care of skin not only for beauty, but also for health. As a factor promoting tumor growth, intertumoral microorganisms need to be paid more attention."

 

Qi-Ming Wang, Ph.D., corresponding study author, professor in the School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Hebei, China

Recently, an increasing number of studies have shown a relationship between fungus and cancer. In the new study, Wang and colleagues subjected mouse breast cancer cells to tumor transplantation and then injected the M. globosa into the mammary gland fat pad. At the end of the experiment, they collected the tumor tissue to measure the tumor size and observe the content of intertumoral M. globosa. The researchers discovered that M. globosa colonizes in breast fat pads leading to tumor growth. As a lipophilic yeast, the breast fat pad may provide an external source of lipids for the development of M. globosa, say the researchers. They also found that the pro-inflammatory cytokine interleukin (IL)-17a/macrophage axis plays a key role in mechanisms involved in M. globosa-induced breast cancer acceleration from the tumor immune microenvironment perspective.

"Although still controversial, the relationship between microbes and cancer is gaining attention. The imbalance of the microflora in the tumor may lead to disorder in the tumor microenvironment," Wang said. "For example, Helicobacter pylori emerged as a potential cause of gastric cancer. In addition, Fusobacterium nucleatum has been identified as a potential colorectal cancer biomarker in stool and is predominantly found in the tumor microenvironment. Bacteria or fungi may play a direct (e.g., toxins) or indirect (e.g., inhibition of anti-tumoral immune responses) role in the tumorigenesis pathways of many of these risk factors. The imbalance of microbial homeostasis in tumors has a certain significance for cancer diagnosis, treatment and prognosis." 

According to Wang, although the researchers found that M. globosa can promote the growth of tumors, the related transmission route is still unclear. 

Source:

American Society for Microbiology

Journal reference:

Liu, M-M., et al. (2024) Breast cancer colonization by Malassezia globosa accelerates tumor growth. mBio. doi.org/10.1128/mbio.01993-24 

 Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Ramble with Sandle: Fungi and cleanrooms

 

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Identifying origin of fungi in cleanrooms

 Image: Tim Sandle

Pharmaceutical product recalls due to fungal contamination have been increasing. These, together with environmental monitoring trend data, highlight several fungal contamination issues associated with pharmaceutical cleanrooms, cold rooms and other controlled areas. Species of filamentous mould include: Cladosporium, Penicillium, Aspergillus, Alternaria, Fusarium, and Paecilomyces).

Read the article free online:

Eckford, C. and Sandle, T.(2023) Identifying origin of fungi in cleanrooms, European Pharmaceutical Review, 22 March 2023: https://www.europeanpharmaceuticalreview.com/news/180833/identifying-origin-of-fungi-in-cleanrooms-fungi-contamination/

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)