Metagenomic next-generation sequencing has emerged as a promising approach for diagnosing transplant infectious disease (TID). During the session Challenging Cases in HCT And Cellular Therapy Viral, Fungal, Metagenomic Next Generation Sequencing in TID, experts presented cases that highlighted the promises and challenges of this approach.

Diagnosing invasive fungal infections in immunocompromised patients poses numerous challenges, including slow culture growth that results in low sensitivity and a lack of specificity in fungal markers, explained Yeon Joo Lee, MD, MPH, infectious diseases specialist at Memorial Sloan Kettering Cancer Center. Additionally, patients are at risk of multiple pathogens that can lead to high mortality and morbidity. Metagenomic next-generation sequencing might help address some of these hurdles.

“Next-generation sequencing results can be very fast,” Lee said. “It is unbiased and noninvasive. It can also provide species-level identification.”

There are three commercially available metagenomic next-generation sequencing tests. Karius Test can detect bacteria, DNA, fungi, mycobacterium, and parasites from blood samples within three days. NeXGen Fungal can detect fungi and acid-fast bacteria from blood samples within three days. MicroGenDX can detect fungi, acid-fast bacteria, and bacteria from various specimens within three and a half days.

There are several challenges associated with this kind of sequencing for fungal infections, Lee noted, including the unknown negative predictive value, the need for additional clinical data, its inability to provide susceptibility information, and uncertainty regarding the optimal testing time.

Diego Hijano, MD, MSc, assistant member of the pediatric TID faculty at St. Jude Children’s Research Hospital, discussed how metagenomic sequencing and bronchoalveolar lavage (BAL) testing impact clinical care.

There are several limitations to plasma microbial cell-free DNA sequencing (mcfDNA-seq), he explained. First, a negative test does not rule out infection, and RNA viruses cannot be detected. Further, determining the clinical significance of these results can be quite challenging.

Hijano outlined how BAL and plasma mcfDNA-seq impact clinical care. Most of the time, BAL has a high clinical impact with positive outcomes. From his data, BAL testing led to antimicrobial discontinuation in 50% of patients, targeted antimicrobial initiation in 40%, and avoidance of antimicrobial initiation in 25%. The clinical impact of plasma mcfDNA-seq is limited, and only 10-14% of patients will have a clinical change based on it.

“Plasma mcfDNA-seq has a low, often negative clinical impact and should never be a replacement in these situations,” Hijano said. “BAL performs well, and always remember it’s the right test for the right patient for the right action.”

Augusto Dulanto Chiang, MD, assistant professor of medicine at Vanderbilt University Medical Center, discussed the diagnostic value of metagenomic next-generation sequencing.

Chiang highlighted two studies assessing the diagnostic value of metagenomic next-generation sequencing tests. One study performed weekly omics on 70 stem cell transplant patients. Out of 32 infection cases diagnosed by both regular testing and genomics, metagenomic next-generation sequencing testing detected infection 12 days earlier than regular testing. This study found that five of these 32 cases would have been actionable, a low number but significant result.

Another study did serial cell-free metagenomics in patients at risk for invasive fungal infections. This study found that in the majority of patients who were diagnosed with an invasive fungal infection, the organism could have been detected before clinical diagnosis.

“So why are we not using this more often? Of course, there are many challenges. This test is expensive, and overall, articles report an aggregate usefulness between 5-15%,” Chiang said.

Further, there are still challenges in determining if an organism detected is a pathogen or commensal. There is also a need for standardizing methods, not just bioinformatics but also the timing of testing during the clinical course.

In addition to the discussion highlighted above, the panelists presented challenging cases and weighed in on the appropriate course of action.

This and other sessions at the 2025 Tandem Meetings | Transplantation & Cellular Therapy Meetings of ASTCT® and CIBMTR® will be available for on-demand viewing for registered attendees following the live presentation.