Abstract: Conventional diagnostic techniques used in a clinical microbiology laboratory include culturing of microorganisms, pathogen-specific antibodies/antigen detection and applications of various techniques for the detection of target nucleic acids. Thousands of microorganisms are known to cause human diseases, but only a fraction are readily identifiable using traditional microbiology-based diagnostic methods and the success of identification also depends on a priory knowledge of the possible aetiology. Most clinically relevant pathogens grow within 24 to 48 h in vitro, but several species require a much longer time and some can not be cultured in vitro and thus often avoid timely detection. Rapid and accurate identification of the etiological agents and prediction of other clinically relevant phenotypes such as antimicrobial resistance is of paramount importance for determining the clinical course of treatment. Clinical metagenomics provides the “one for all” approach, which can characterize all DNA or RNA molecules present in a sample, enabling an analysis of the entire meta-organism that aid in precise diagnosis and clinical decision making. Our aim is to make KAUST a major hub for providing training to healthcare professionals in conducting research on applications of Clinical Metagenomics in healthcare settings within KSA under the KAUST Smart Health Initiative (KSHI). We will present a few selected case studies on the applications of Clinical Metagenomics involving KAUST and Infectious Disease Physicians at the partner hospitals in Saudi Arabia.

Bio: Prof. Pain received his PhD from the University of Cambridge, U.K., working on microbial pathogenesis in a bacterial pathogen of cultivated mushrooms. He had his postdoctoral training at the Weatherall Institute of Molecular Medicine (WIMM) in Oxford, U.K. where he focused on cell biology and virulence-associated phenotypes in the human malaria parasite Plasmodium falciparum. After spending five years in Oxford, he moved back to Cambridge and joined the Pathogen Sequencing Unit (PSU) at the Wellcome Trust Sanger Institute (WTSI) as a Senior Scientist. In WTSI, he took a leading role in coordinating several genome and transcriptome projects of several major species of malaria and other related apicomplexan parasites of humans and animals. In 2010, he moved to Saudi Arabia to join the Biological and Environmental Sciences and Engineering (BESE) Division at King Abdullah University of Science and Technology (KAUST) as a member of the founding faculty to establish and lead a research program on Pathogen Genomics – primarily focusing on pathogens of regional and global relevance. Since 2015, he has had an appointment as a Distinguished Professor at the international Institute for Zoonosis Control, Hokkaido University in Sapporo, Japan. Currently, he also serves as an Honorary Professor at the Liverpool School of Tropical Medicine (LSTM) in the U.K.

Prof. Pain’s research group uses a combination of high-throughput sequencing, comparative and functional genomics protocols and bioinformatic analysis tools to study pathogenicity determinants in selected parasitic protists, bacteria and more recently in SARS-CoV-2.