By Ethan Covey
An outbreak of Fusarium solani meningitis among U.S. residents who had undergone surgical procedures with spinal anesthesia in Matamoros, Mexico, during 2023 likely originated from a single point source, according to findings from metagenomic next-generation sequencing (mNGS).
The outbreak included 184 patients in 22 U.S. states who were identified as having potentially been exposed. Twenty-four cases of fungal meningitis were confirmed, and 12 people died (Emerg Infect Dis 2025;31[5]:948-957).
The source of the outbreak is thought to have been a contaminated drug or device used for epidural anesthesia.
Investigators used a novel method called metagenomic multiple extended locus typing, or metaMELT, to perform phylogenetic analysis of concatenated mNGS readings from four patients (P1-P4). The samples, as well as cultured isolates from P1 and another infected individual (P5), showed that strains from all five patients were the same or closely related.
This finding, the researchers said, indicates with a high likelihood that the infections from the five tested individuals—and thus the entire U.S. outbreak—likely came from a single source.
“Being able to characterize the relatedness of strains from different patients is critical to understanding the cause of an outbreak, especially one that is spread out across multiple states and over an extended period,” said lead author Charles Chiu, MD, PhD, a professor of laboratory medicine and medicine in the Division of Infectious Diseases at the University of California, San Francisco School of Medicine. “The main finding of this report, that strains of the fungal pathogen Fusarium solani are genetically similar, supports the current thinking that the outbreak resulted from a common source, such as a contaminated drug used for epidural anesthesia.”
When Can You Use mNGS?
Clinical mNGS is being used to broadly diagnose infections in patients without prior clinical suspicion and can be used to aid in similar investigations.
“We show how mNGS testing can also be leveraged to compare fungal strains from different patients and show that they are genetically related, without having to grow the organism in culture,” Dr. Chiu said. “Thus, a single test can be used to simultaneously diagnose infections and aid in epidemiologic investigations of outbreaks.”
Dr. Chiu noted that a key question regarding mNGS, which will hopefully be answered in future research, relates to the clinical utility or “use cases” for this technology.
“Future clinical studies are needed to determine how the test should be used and deployed to maximize benefit to patients,” he said.
Ensuring greater access to mNGS will likely expand how the technology is used to assist both patients and epidemiological investigators.
“In the long run, I am committed to democratizing mNGS testing so that it becomes cheaper and more widely accessible for critically ill patients who would benefit the most from timely diagnoses followed by effective and appropriate treatment,” Dr. Chiu said. “Given its unbiased nature, mNGS testing also has the potential of being a first-line tool for routine outbreak investigation in public health settings.”
Dr. Chiu reported that he is the founder of Delve Bio; serves on the scientific advisory boards for Biomeme, BiomeSense, Delve Bio, Flightpath Biosciences, Mammoth Biosciences and Poppy Health; and receives research support from Abbott Laboratories and Delve Bio. He also holds a patent for next-generation sequencing used by SURPI+ software.
