RASID, M42 detect rare fungal clade through Abu Dhabi wastewater surveillance

The Reference and Surveillance Intelligence Department (RASID) at the Central Testing Laboratory of the Abu Dhabi Quality and Conformity Council, in partnership with M42, a global health leader powered by artificial intelligence (AI), technology and genomics, has achieved a scientific milestone following the successful detection and isolation of a recently identified and rare genetic clade of Candida auris, an antifungal-resistant fungal pathogen, through Abu Dhabi's wastewater early surveillance system.

The study, published in Communications Medicine, part of Nature Portfolio, reported the first known regional detection of Candida auris Clade VI through wastewater environmental surveillance, based on the data available to researchers at the time of the study. The findings enhance scientific understanding of the pathogen's genetic diversity and support the assessment of emerging health risks.

The findings highlight the importance of wastewater surveillance as an additional and complementary source of information alongside health and clinical surveillance, capable of monitoring pathogens and antimicrobial resistance indicators, including antifungal resistance, to enhance preparedness and proactive response.

The study was based on more than 23,000 wastewater samples collected systematically. Researchers successfully isolated the fungus directly from wastewater and confirmed its identity in the laboratory, rather than simply detecting its genetic traces.

The scientific methodology included identification of the isolates, Whole Genome Sequencing (WGS), genomic and phylogenetic analysis to determine clade classification, antifungal susceptibility testing and investigation of genetic markers associated with resistance.

The analyses identified different genetic clades of the fungus, including Clade VI, and revealed genetic markers and varying patterns associated with resistance to certain antifungal agents.

Candida auris has attracted global attention because of its ability to develop resistance to multiple antifungal agents and the challenges associated with controlling it in certain healthcare environments. The World Health Organisation has classified it within the Critical Priority Group of fungal pathogens.

Samara Bin Salem, Director of RASID, said the scientific value of the achievement lies in the ability of environmental surveillance to capture emerging health indicators and patterns of drug resistance and transform them into information that can be studied and assessed.

She explained that combining laboratory isolation, whole genome sequencing and antifungal susceptibility testing enabled the identification of Clade VI and a more precise understanding of its genomic characteristics and resistance patterns.

Bin Salem said RASID aims to develop a scientific sensing system that goes beyond identifying what is present in samples to understanding population-level changes, emerging risks and indicators that may warrant early preparedness.

Dr. Bhuvanesh Shanmugam, one of the principal researchers involved in the study and Senior Microbiologist and Laboratory Manager at M42, said the identification of Clade VI contributes to scientific knowledge regarding the genetic diversity of Candida auris and its presence beyond clinical settings.

He added that integrating genomic data with antifungal susceptibility testing provides deeper insight into factors associated with resistance and supports monitoring of emerging patterns or genomic changes of potential future significance.

Dr. Grzegorz Brudecki, a researcher involved in the study and Associate Director of Environmental Sciences at M42, said continuous surveillance helps identify changes, trends and unusual signals over time, distinguishing expected patterns from indicators requiring further analysis.

He noted that combining regular surveillance with advanced genomic analysis enhances the scientific value of environmental data and enables the study of changes in pathogens, genomic patterns and resistance indicators.

Sumaya Al Mansoori, one of the principal researchers involved in the study, said the integration of sample collection, continuous surveillance, fungal isolation, whole genome sequencing and antifungal susceptibility testing enabled more precise characterisation and genomic classification of the isolates and their resistance patterns.

She added that the findings demonstrate the potential of wastewater surveillance to provide information on genetic diversity, antimicrobial resistance indicators and emerging risks, supporting more proactive approaches to environmental surveillance.

The achievement reflects RASID's evolution from conventional laboratory testing towards an advanced system integrating environmental surveillance, genomic sciences, data analysis, indicator monitoring, early warning and emerging-risk foresight.

These capabilities support Abu Dhabi's public health system, led by the Department of Health – Abu Dhabi and the Abu Dhabi Public Health Centre, by providing environmental and scientific data that can complement health and clinical information in assessing risks, strengthening preparedness and taking appropriate action.

WAM