Revolutionizing Real-Time Genomic Epidemiology in Urban Wastewater Systems

ARC Discovery Project

Human pathogens are one of the major threats to public health and cost the global economy tens of billions of dollars annually. It is also one of the leading causes of death worldwide. Many infected patients require medical treatment or hospitalisation, which entails high costs and loss of productivity. Current approaches to monitor infectious diseases primarily rely on reporting from hospitals or pathology labs. This retrospective approach cannot provide real-time information, which is key to timely intervention. Recent reports by the Australian government indicate that the current epidemiology approach and data are insufficient for timely intervention during outbreaks. With population growth and urbanisation, it is critical to strengthen our capabilities to monitor and prevent the ever-increasing risks of epidemics.

The broad aim of this project is to develop and demonstrate an innovative, real-time, and high-resolution genomic tool to monitor and track pathogenic microbiomes in sewer networks based on the most advanced and portable third-generation sequencing (TGS) platform (MinION nanopore sequencer). The microbiome of pathogens in sewers will be detected by the low-cost, fast sequencing methods within hours. This will allow early warning even before symptoms develop in infected people. Built upon wastewater analysis for pharmaceuticals targeting specific pathogens, this integrated approach of sewage-based epidemiology will greatly enhance public health by achieving early detection and timely intervention of infectious diseases.

Research outputs

Zhang, S., Shi, J., Sharma, E., Li, X., Gao, S., Zhou, X., O'Brien, J., Coin, L., Liu, Y., Sivakumar, M. and Hai, F., 2023. In-sewer decay and partitioning of Campylobacter jejuni and Campylobacter coli and implications for their wastewater surveillance. Water Research233, p.119737.

Guo, Y., Li, J., O'Brien, J., Sivakumar, M. and Jiang, G., 2022. Back-estimation of norovirus infections through wastewater-based epidemiology: A systematic review and parameter sensitivity. Water Research219, p.118610.

Li, X., Kulandaivelu, J., Guo, Y., Zhang, S., Shi, J., O’Brien, J., Arora, S., Kumar, M., Sherchan, S.P., Honda, R. and Jackson, G., 2022. SARS-CoV-2 shedding sources in wastewater and implications for wastewater-based epidemiology. Journal of hazardous materials432, p.128667.

Zhang, S., Li, X., Wu, J., Coin, L., O’brien, J., Hai, F. and Jiang, G., 2021. Molecular methods for pathogenic bacteria detection and recent advances in wastewater analysis. Water13(24), p.3551.

Zhang, S., Li, X., Shi, J., Sivakumar, M., Luby, S., O'Brien, J. and Jiang, G., 2022. Analytical performance comparison of four SARS-CoV-2 RT-qPCR primer-probe sets for wastewater samples. Science of the Total Environment806, p.150572.


Project members

Dr Jake O’Brien

Senior Research Fellow