Hopukina I Diagnostics: Te Niwha Priority Research Area

Whakarāpopoto Rangahau I  Summary of Research

There are clear opportunities for rapid point-of-use (POU) testing to reduce inequity and empower communities to take control of their health and environmental resources. Some examples of this may include testing for respiratory viruses, Sexually Transmitted Diseases, monitoring antimicrobial resistance, ensuring safe bathing and drinking water, or monitoring environmental quality.

 We are interested in working with communities to help direct priorities for POU assay development and deployment, and have their input into POU assay design, prototyping and testing in community settings.

Te Hiranga a Rangahau I  Research Impact 

The impact of this project will be an increased capacity for Aotearoa New Zealand to respond to future pandemics and outbreaks by improving the collection of community health information and increasing our ability to respond to this data in remote and under-served communities.

This will help communities take ownership of their health and environment by bringing testing capability to a place and time that works for them - enabling more informed decision making and advocacy.

Impact Case Study 

Principal investigator: Craig Billington, PHF Science

Whakarāpopoto Rangahau I  Summary of Research

Collecting environmental samples such as bird faeces will help understand how and where avian influenza and other potentially devastating viruses could impact Aotearoa New Zealand as the highly infectious H5N1 spreads globally.

Wild aquatic birds carry a panoply of viruses and act as major vectors of virus distribution at a global scale. Although central to biosecurity, the role that such birds play in the transmission of viruses in Aotearoa, and how this may impact human and animal health in the near future, is unclear. These viruses often jump to new hosts and cause disease.

For example, wild aquatic birds such as waterfowl serve as natural reservoirs for influenza A virus, a strain of which is currently killing millions of birds with multiple spillovers to non-avian hosts, including humans. Yet we know little about where, when and how such viruses will emerge here, their reservoir hosts, nor how to prevent them.

This lack of knowledge, combined with very limited surveillance and resources, leaves Aotearoa entirely unprepared for the introduction of highly pathogenic avian influenza virus and its inevitable impacts on wildlife, agriculture and potentially human health.

Using an innovative combination of genomics technologies such as metagenomics, molecular epidemiology and environmental DNA (eDNA), we will determine the transmission networks and evolution of avian influenza strains already present in Aotearoa, demonstrate the use of large-scale environmental sampling for disease surveillance, and quantify the disease risk of such viruses to public health.

Te Hiranga a Rangahau I  Research Impact

This study establishes a framework for broader avian influenza surveillance using advanced genomic techniques. Migratory birds are currently being resampled during the 2024-2025 migration season as New Zealand is currently facing another high-risk migratory period. This work will help assess changes in viral composition between migratory seasons and determine the presence of avian influenza viruses. Nevertheless, the study aims to identify all avian viruses, not just avian influenza virus. Their goal is to track transmission dynamics, evolution, and prevalence of avian viruses in New Zealand. Another research focus for the group is developing environmental monitoring methods. These methods would detect avian influenza virus in samples such as water and sediment, providing a more accessible alternative to direct bird sampling. Ongoing monitoring is critical to detect incursions, track viral evolution, and improve understanding of avian influenza virus in New Zealand.

Impact Case Study

Principal investigators: Professor Jemma Geoghegan (University of Otago) and Dr David Winter (PHF Science, formerly ESR)

Whakarāpopoto Rangahau I  Summary of Research

This project aligns with Te Niwha's mission by supporting world class research to develop diagnostic platforms that can be used to enhance the diagnosis of otherwise hard to diagnose infectious diseases.

Infectious diseases are traditionally diagnosed by culturing the microorganism causing disease. However, in many cases a diagnosis can be difficult to achieve due to the inability of obtaining a suitable sample and the failure to reliably grow the organism in a laboratory environment. The use of quantitative polymerase chain reaction (qPCR) is becoming more widespread in diagnostic laboratories and can offer a platform to diagnose infectious disease quickly and accurately.

When microorganisms invade the body, they release fragments of their own cell-free DNA (mcfDNA) which can be found in the blood and urine of patients. Since blood and urine are routinely obtained from patients during a hospital stay, they are ideal samples for diagnosing infectious diseases. Unfortunately, mcfDNA levels in blood and urine are low, preconcentration is required to increase mcfDNA to levels that are detectable.

• Platform 1 will use special beads to capture the pathogens mcfDNA in urine, which will then be analysed by quantitative polymerase chain reaction (qPCR) to determine if the pathogen is present in the patient. This answer will be achievable within 8 hours.
• Platform 2 will increase the pathogen mcfDNA from a patient sample using PCR, the PCR product is then incubated with a microbe specific CRISPR-Cas reagent which provide a fluorescence read-out if the pathogen mcfDNA is present in the patient sample.

Te Hiranga a Rangahau I  Research Impact

The overall impact of this project will be to improve the diagnosis of currently hard-to-diagnose infections. Both platforms can be used within a laboratory setting without disrupting current workflows. The platforms will allow for faster diagnosis which will improve antimicrobial stewardship as doctors may not need to start empirical treatment. The ability for these two platforms to be utilised in remote areas either within Aotearoa or in the Pacific is promising. A non-invasive diagnostic platform will be a significant advance, especially in diagnosing disease in tamariki where obtaining invasive samples can be very difficult. 

Impact Case Study

Principal investigators: Dr Amy Scott-Thomas, University of Otago, Christchurch

Whakarāpopoto Rangahau I Summary of Research

This collaborative project brings together internationally recognised TB-research leaders in Aotearoa New Zealand to focus on TB prevention (through public health measures, vaccination and improving treatment options for antimicrobial resistant organisms) and diagnosis.

The research team will develop a strong, integrated, multi-faceted programme dedicated to reducing inequities in TB outcomes for Māori and Pacific people, who are disproportionately affected by the disease.

This collaborative proposal brings together four University of Otago-based tuberculosis (TB) research teams, with expertise covering the areas of microbiology, immunology, bioinformatics, diagnostics, surveillance, public health and social science. Together, these teams will undertake research to decrease transmission of the infectious disease by:

• Integrating economic and social network analyses to inform appropriate public health measures to eliminate TB 
• Improving diagnostics and antimicrobial resistant M. tuberculosis surveillance in the Pacific and understanding links to Aotearoa New Zealand
• Improving measurements of protective immunity to infection with M. tuberculosis that will aid in vaccine efficacy testing 
• Developing an artificial intelligence framework to combat antimicrobial resistance.

The project consists of four parts.

Part A: TB transmission and economic analysis:

• In-depth Māori social network research to identify epidemiological patterns of transmission.

• Economic analysis of the TB elimination approach to inform policy decisions

Part B: TB diagnostics and surveillance in Pacific peoples in the Pacific and Aotearoa New Zealand:

• Explore TB transmission in the Pacific and how this is linked to TB cases in Māori and Pasifika communities in Aotearoa

• Diagnose drug-resistance patterns and lineages of M. tuberculosis in Aotearoa and the Pacific

• Develop real time genotypic resistance testing of M. tuberculosis

Part C: Signatures of vaccine-induced protection against TB: a bench-to-bedside approach:

• Identify BCG vaccine-induced markers of immune protection that can be easily measured in the clinic

• Understand how Lineage 2 strains of M. tuberculosis can evade BCG-induced protection

Part D: Developing an Artificial Intelligence framework to combat antimicrobial resistance

• Generate an open access repository showing how genes, proteins and metabolites are differentially regulated across drug-susceptible and resistant clinical isolates of M. tuberculosis

• Develop a machine-learning-framework to identify therapeutic vulnerabilities in M. tuberculosis strains

Te Hiranga I Research Impact

This collaborative proposal brings together internationally recognised TB-research leaders in Aotearoa to focus on TB prevention (through public health measures, vaccination and improving treatment options for antimicrobial resistant organisms) and diagnosis.

The main outcomes of this project are to:

• Develop culturally-appropriate strategies to combat TB transmission

• Improve diagnosis of TB in Aotearoa New Zealand

• Develop improved vaccines and increase uptake of these preventative measures

• Understand the best treatment options for TB

The research leaders involved in this project have a proven record providing critical guidance and direction at a national and international level during the COVID-19 pandemic and will be mentoring the next generation of infectious diseases research leaders, including postdoctoral fellows and postgraduate students.

Presently, there are very few Aotearoa-based Māori or Pacific TB senior researchers in this field. The research team is committed to mentoring future Māori and Pacific research leaders to build capability for infectious diseases research and pandemic preparedness.

Impact Case Study Part A

Impact Case Study Part B

Impact Case Study Part C

Impact Case Study Part D

Principal investigator: Associate Professor Jo Kirman, University of Otago 

Whakarāpopoto Rangahau I Summary of Research

Gonorrhoea is a common sexually transmitted infection (STI) that is becoming increasingly difficult to treat due to rising antibiotic resistance. At the same time, infection rates are increasing in Aotearoa New Zealand and globally. Early diagnosis is critical to limit transmission and reduce unnecessary antibiotic use, but current tests require laboratory processing and results can take several days. This project aims to develop the foundations for a rapid, clinic-based test for gonorrhoea similar to a COVID-19 RAT. We are designing small, highly-specific molecules called nanobodies that bind to conserved surface antigens on Neisseria gonorrhoeae, enabling its detection. We will evaluate their stability and binding performance to identify the best candidates for diagnostic development. The long-term goal is to support faster diagnosis and treatment, reduce the spread of gonorrhoea, and improve sexual health, especially for communities that face barriers to accessing STI testing.

Te Hiranga a Rangahau I  Research Impact

This project will have significant research and translational impact by combining synthetic and biological approaches to identify robust, highly specific nanobodies for a rapid, strain-independent point-of-care (POC) test for gonorrhoea. The resulting diagnostic will improve detection, treatment, and surveillance, particularly in low-resource and community settings, by enabling fast, low-cost, and accurate testing using minimally processed samples.

Beyond diagnostic development, the project will advance fundamental understanding of Neisseria gonorrhoeae biology through new insights into key gonorrhoea antigens to inform future therapeutic and vaccine research.

Impact Case Study

Principal investigator: Dr Jonna Hicks and Dr William Kelton, University of Waikato