Dual DNA Barcoding Could Help Identify Invasive Fungal Infections

Dual DNA barcoding could help identify fungal pathogens and speed up diagnosis and treatment of invasive fungal diseases (IFDs), according to a new study from the Westmead Institute for Medical Research in Sydney, Australia.

The study, published in the journal Frontiers in Microbiology, examined 2 DNA regions—the internal transcribed spacer (ITS) region and the translational elongation factor 1α (TEF1α) to more accurately identify pathogens.

"Identifying the type of fungi that is causing infection will help us administer appropriate treatment faster, reducing harm and, potentially, mortality rates associated with IFDs,” lead investigator Wieland Meyer, PhD, professor of molecular medical mycology at the Westmead Institute for Medical Research, said in a news release. "It may also improve other complications associated with IFDs, such as drug resistance, and the financial impact IFDs can have on both patients and the health care system.”

DNA sequencing from both barcoding regions was added to the International Society of Human and Animal Mycology (ISHAM) Barcoding Database in 2017 to allow the system to be implemented in clinical practice. Previously, DNA barcoding using only the ITS region was able to identify about 75% of fungi. Adding the secondary barcoding region allowed investigators to identify all fungi analyzed.

"Our study is the first to compare the accuracy of the 2 barcoding regions, and to evaluate the effectiveness of ITS and TEF1α combined,” Meyer said in the news release. "We were able to correctly identify all disease-causing fungal species, from the most common human fungal pathogen Candida albicans, to species which rarely cause infections. We found that the primary barcoding region alone could not detect all species—however, the secondary region, as well as the 2 combined, filled in this gap.”

The study generated 270 secondary barcodes and allowed for the expansion of the ISHAM Barcoding Database to include 4091 primary (ITS) and 868 secondary barcode (TEF1α) sequences.

"While we now know that the dual DNA barcoding system is more effective at identifying fungal species, we need to increase the amount of sequences available in reference sequence databases to maximize the number of species we can identify,” Meyer said in the news release. "We are now asking researchers from around the world to submit reference sequences that can be used to identify fungal pathogens.”

Improving the database could allow investigators to speed diagnosis to under 24 hours. IFDs including candidemia and invasive aspergillosis have increased worldwide and are estimated to cause about 1.6 million deaths per year, the study noted.

The spread of fungal pathogens is of particular concern among elderly and immunocompromised populations. Candida auris was first identified 10 years ago and has caused outbreaks, leading investigators to push for better understanding of how the pathogen spreads along with improvements in quickly identifying and treating infections.

The concern drew widespread attention earlier this year, when the The New York Times ran a front-page story about drug-resistant C auris