Multikingdom microbial biomarker test for autism risk assessment aids earlier diagnosis & intervention

Researchers from the Chinese University of Hong Kong (CUHK) have developed the world’s first artificial intelligence (AI)–powered multikingdom microbial biomarker test for autism spectrum disorder (ASD) risk assessment. By accurately excluding ASD in low-risk cases, the test may facilitate earlier diagnosis and intervention in high-risk groups.

Negative predictive value >95 percent

“The noninvasive test, which received US FDA’s Breakthrough Device Designation in July 2024, analyzes bacteria, archaea, fungi and viruses, along with their genes and metabolic pathways, in a small faecal sample using patented quantitative polymerase chain reaction technology,” explained Professor Siew Ng of the Department of Medicine and Therapeutics, CUHK. “These data are processed through a validated AI model to generate an ASD risk score. A report is available within approximately 2 weeks.”

The test was developed based on a metagenomic sequencing study involving faecal samples from 1,627 children (age, 1–13 years; female, 24.4 percent) with or without ASD from five independent cohorts. In this study, the CUHK researchers identified differential abundance of 14 archaea, 51 bacteria, 7 fungi and 18 viruses as well as alterations in 27 microbial genes and 12 metabolic pathways in children with ASD compared with neurotypical children. A panel of 31 multikingdom and functional markers demonstrated high diagnostic accuracy (area under the curve, 0.91), with comparable performance for males and females. According to the researchers, the model’s accuracy was driven predominantly by biosynthesis pathways of ubiquinol-7 and thiamine diphosphate, which were reduced in children with ASD. [Nat Microbiol 2024;9:2344-2355]

“Validation of the test in an independent hospital cohort of children with ASD and neurotypical children demonstrated a sensitivity of 91 percent, specificity of 89 percent, and negative predictive value [NPV] higher than 95 percent,” said Ng. [Nat Microbiol 2024;9:2344-2355; MicroSigX, data on file]

“The test’s NPV makes it useful as a first-line tool to effectively exclude ASD in low-risk cases, thus enabling better allocation of medical and social resources to high-risk groups while alleviating parental concerns in low-risk groups,” said Professor Sandra Chan of the Department of Psychiatry, CUHK.

Free testing for 200 eligible preschool children

A pilot programme commencing in January 2026 will offer free access to the test to 200 children 18 months to 4 years of age from low-income families who have suspected ASD symptoms but have not yet received a formal diagnosis. In partnership with nongovernmental organizations and neurodevelopmental experts, a holistic care model will be adopted to provide multidisciplinary support to families in need. Interested parties may contact programme staff at 9495 1894 for enquiries and registration.

Moving forward

“We plan to make the test available to the wider public in Hong Kong in the third quarter of 2026, followed by other regions, including the Greater Bay Area,” said Professor Francis Chan of the Department of Medicine and Therapeutics, CUHK.

An Advancement Centre for Autism will be established at CUHK to provide education programmes for healthcare professionals and caregivers, promote cross-sectional collaboration, translate pioneering research on gut microbiome markers into actionable clinical risk evaluations and early therapeutic interventions, and foster sustainable and comprehensive support for individuals with ASD.