Oral Presentation Australian Society for Microbiology Annual Scientific Meeting 2021

Monitoring diverse enteric pathogens and antimicrobial resistance genes across One Health reservoirs in the RISE Program (#83)

Rachael Lappan 1 2 , Rebekah Henry 3 , Steven L Chown 2 , Stephen P Luby 4 , Ellen E Higginson 5 , Lamiya Bata 3 , Thanavit Jirapanjawat 1 2 , Christelle Schang 3 , John J Openshaw 4 , Joanne O'Toole 6 , Audrie Lin 7 , Autiko Tela 8 , Amelia Turagabeci 8 , Tony H.F Wong 9 , Matthew A French 10 , Rebekah R Brown 10 , Karin Leder 6 , David McCarthy 3 , Chris Greening 1 2
  1. Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
  2. School of Biological Sciences, Monash University, Clayton, VIC, Australia
  3. Department of Civil Engineering, Monash University, Clayton, VIC, Australia
  4. Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
  5. Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
  6. School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
  7. Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
  8. School of Public Health, Fiji National University, Suva, Fiji
  9. Water Sensitive Cities Institute, Monash University, Clayton, VIC, Australia
  10. Monash Sustainable Development Institute, Monash University, Clayton, VIC, Australia

Multiple bacteria, viruses, protists, and helminths cause enteric infections that greatly impact human health and wellbeing. These enteropathogens, as well as antimicrobial resistance (AMR) genes, are continually transmitted across human, animal, and environmental reservoirs and are of particular concern in regions facing compromised water quality, sanitation and hygiene. The Revitalising Informal Settlements and their Environments (RISE) program is a transdisciplinary trial implementing nature-based infrastructure to improve water management in urban informal settlements in Indonesia and Fiji. To evaluate the impact of such interventions on transmission pathways, broad surveillance of AMR and a wide range of enteropathogens across all One Health reservoirs is essential, but rarely implemented.


We comprehensively validated the use of a custom enteric TaqMan Array Card (TAC), a streamlined qPCR format which allows the simultaneous detection of 46 pathogen and faecal indicator targets. We found that it was comparable to standard qPCR assays on a range of samples from urban informal settlements (89% agreement rate, quantitation R2 = 0.82). Standard qPCR prioritises greater sensitivity and quantitation accuracy, while TAC trades small reductions in these for a cost-effective larger enteropathogen panel. This approach provides an avenue for widespread surveillance that surpasses single-pathogen or single-reservoir approaches and reliance on faecal indicator organisms for environmental monitoring. We have additionally evaluated a qPCR array for the simultaneous detection of 87 AMR genes, with preliminary results indicating a high AMR load in Fijian urban informal settlements.


With these techniques, it is increasingly possible to develop a strong and detailed understanding of pathogen levels and resistance traits across a wide range of reservoirs and settings. This in turn allows better resolution of pathogen and antimicrobial resistance exposure pathways, and the design and monitoring of intervention programs, such as RISE, to reduce pathogen and AMR spread.