Singapore researchers discover new candida auris – a possible global public health threat

Singapore, 13 August 2024 – Researchers from the Singapore General Hospital (SGH), A*STAR’s Genome Institute of Singapore (GIS) and Yong Loo Lin School of Medicine at National University of Singapore (NUS Medicine) have discovered a new clade (or type) of Candida auris, bringing the number of clades known globally to a total of six.

Candida auris, or C. auris, is a fungus that is highly transmissible and hard to eradicate. It mostly affects patients with severe underlying medical conditions. Those with invasive medical devices like breathing or feeding tubes and catheters tend to be at higher risk of getting C. auris and developing a range of infections from superficial to more severe, life-threatening ones.

The World Health Organization listed C. auris as a critical priority for research and public health action in 2022. The U.S. Centers for Disease Control and Prevention has also declared the fungus as an ‘urgent antimicrobial resistance threat’ as it has become increasingly difficult to treat, further emphasising the need to understand and mitigate this public health threat.

“The implications of this discovery extend far beyond the laboratory. Now that we have discovered the sixth Candida auris clade, there is a pressing need to improve surveillance capability or develop new methods to augment current surveillance strategies so that healthcare facilities can keep a close watch on its emergence and contain the spread once found,” said Dr Karrie Ko, co-first author of the study. She is also Consultant, Department of Microbiology, SGH, and Genomics Director of the Pathology Academic Clinical Programme under SingHealth and Duke-NUS Medical School.

The new clade was detected in 2023 after an SGH patient tested positive for C. auris, which is commonly associated with overseas travel. The patient, however, had remained in Singapore for two years prior, which prompted further investigations. Scientists from A*STAR’s GIS developed a machine-learning technique to keep track of a potential new C. auris clade. They then reconstructed the C. auris genomes and performed an in-depth characterisation of the genomes to confirm the emergence of a new clade.

Upon discovering that the patient had C. auris belonging to a clade that was genetically different from the other five, the team looked through the Hospital’s archive and found two other patient cases. Their discovery was documented in “Detection and characterisation of a sixth Candida auris clade in Singapore: a genomic and phenotypic study”, which was published in the peer-reviewed medical journal, The Lancet Microbe, in July 2024.

SGH has an active surveillance programme which screens high-risk patients for C. auris through a routine swab upon admission. Patients who are tested positive are immediately isolated and all inpatients who shared the same ward or room will be screened as part of the Hospital’s strategy to contain its spread.

The team is now working on a proof-of-concept machine learning approach that can automatically detect new clades early. This is particularly important for regional hubs like Singapore, which receives high number of international visitors, to monitor and identify emerging public health threats early.

“This study demonstrated that machine learning approach can improve surveillance capabilities by automatically detecting unusual outlier genomes. Our human-in-the-loop machine learning workflow facilitates continuous learning from new data, so that we can detect and investigate potential novel genomes as early as possible. This has the potential to strengthen surveillance against emerging public health threats,” said co-first author of the study, Dr Chayaporn Suphavilai, Senior Scientist, A*STAR’s GIS.

"Genomic surveillance is essential for understanding emerging pathogens. By integrating genomics, metagenomics, and collaborative efforts among researchers and clinicians, we can continually enhance our pandemic preparedness and response to public health threats," said senior author of the study, Associate Professor Niranjan Nagarajan, from the Infectious Diseases Translational Research Programme at NUS Medicine, and Associate Director, Genome Architecture, and Senior Group Leader, Laboratory of Metagenomic Technologies and Microbial Systems at A*STAR’s GIS.

The study was supported by the Duke-NUS Academic Medical Center Nurturing Clinician Researcher Scheme and the Genedant-GIS Innovation Program.

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About Singapore General Hospital (SGH)

Singapore General Hospital, established in 1821, is the largest tertiary hospital in Singapore and ranked among the world’s best. It provides the most comprehensive patient-centred care with over 50 clinical specialties on its campus. As an Academic Medical Centre, it takes pride in training healthcare professionals and conducting cutting edge research to meet evolving needs of the nation as well as the region. Driven by a strong sense of purpose, SGH is committed to give of its best to heal and bring hope, as it has for over 200 years. For more information, please visit www.sgh.com.sg

About the Agency for Science, Technology and Research (A*STAR)

The Agency for Science, Technology and Research (A*STAR) is Singapore's lead public sector R&D agency. Through open innovation, we collaborate with our partners in both the public and private sectors to benefit the economy and society. As a Science and Technology Organisation, A*STAR bridges the gap between academia and industry. Our research creates economic growth and jobs for Singapore, and enhances lives by improving societal outcomes in healthcare, urban living, and sustainability. A*STAR plays a key role in nurturing scientific talent and leaders for the wider research community and industry. A*STAR’s R&D activities span biomedical sciences to physical sciences and engineering, with research entities primarily located in Biopolis and Fusionopolis. For ongoing news, visit www.a-star.edu.sg.

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About A*STAR’s Genome Institute of Singapore (GIS)

The Genome Institute of Singapore (GIS) is an institute of the Agency for Science, Technology and Research (A*STAR). It has a global vision that seeks to use genomic sciences to achieve extraordinary improvements in human health and public prosperity. Established in 2000 as a centre for genomic discovery, the GIS pursues the integration of technology, genetics, and biology towards academic, economic and societal impact, with a mission to "read, reveal and (ω)rite DNA for a better Singapore and world".

Key research areas at the GIS include Precision Medicine & Population Genomics, Genome Informatics, Spatial & Single Cell Systems, Epigenetic & Epitranscriptomic Regulation, Genome Architecture & Design, and Sequencing Platforms. The genomics infrastructure at the GIS is also utilised to train new scientific talent, to function as a bridge for academic and industrial research, and to explore scientific questions of high impact. For more information about GIS, please visit www.a-star.edu.sg/gis.

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About National University of Singapore, Yong Loo Lin School of Medicine

The NUS Yong Loo Lin School of Medicine is Singapore’s first and largest medical school. Our enduring mission centres on nurturing highly competent, values-driven and inspired healthcare professionals to transform the practice of medicine and improve health around the world. The School is the oldest institution of higher learning in the National University of Singapore and a founding institutional member of the National University Health System. It is one of the leading medical schools in Asia and ranks among the best in the world (Times Higher Education World University Rankings 2024 by subject and the Quacquarelli Symonds (QS) World University Rankings by subject 2023). For more information about NUS Medicine, please visit https://medicine.nus.edu.sg/