The New Zealand Institute for Public Health and Forensic Science (PHF Science) was formerly named The Institute of Environmental Science and Research (ESR).

Kia Mataara I Surveillence: Te Niwha Research Priority Area

Surveillance Theme Image

Kia Mataara I Surveillance research projects

Wastewater testing at the border and in buildings

Whakarāpopoto Rangahau I Summary of Research 

Testing of sewage for the presence of infectious disease, known as wastewater-based epidemiology, is used to assess disease burden in communities without the need for individualised testing. It allows for cost-effective, non-invasive and unbiased disease screening of whole communities, and can be deployed in areas traditionally underserved by healthcare surveillance. Aotearoa New Zealand has been conducting wastewater-based surveillance for the presence of COVID-19 since early 2020 and recently extended this work to detect other pathogens. 

While the implementation of wastewater-based epidemiology (WBE) in large communities, in Aotearoa New Zealand and internationally has been well established, much less focus has been placed on local-scale WBE. This includes the level of sampling individual buildings. This is a key gap in our pandemic preparedness because it is now well established that wastewater testing can play a hugely important role in monitoring for current and emerging disease threats. 

The ability to roll out wastewater testing at localised scales at the beginning of an outbreak with an established understanding of the sampling methodology and frequency needed would improve likelihood of detection. This is important for smaller, vulnerable communities - especially those that are not connected to large municipal wastewater treatment plants, who could suffer out-sized and inequitable impacts due to undetected disease spread.   

The first and most important step in this project will be to engage with Tāngata Whenua, Pacific Peoples, local communities, airlines, government and public health organisations to establish whether WBE is of value to them. The team will consider the ethical implications, the most appropriate actions to be taken in response to results generated, and the pathways for dissemination of results. There will be tikanga precedents from previous studies on waste, water and data sovereignty in action.   

The practical focus of this mahi rangahau is appropriate and effective means for implementation of wastewater analysis in smaller-scale settings. This sampling closer to the source and of smaller populations could allow new opportunities for early detection of infectious diseases, for confirmation of the elimination of diseases, and for better public health understanding of underrepresented populations.   

Sampling at small scales is potentially controversial, therefore one of the team’s main goals will be to understand the ethical implications of small-scale testing and mitigate the risk of marginalisation or stigmatisation. They will undertake risk assessments from both person-to-person transmission and from the wastewater itself to individuals who come into contact with it.  

Te Hiranga a Rangahau I Research Impact 

WBE made a significant contribution to Aotearoa New Zealand’s response to the COVID-19 pandemic, but was based primarily on analysis of samples collected from wastewater treatment plants. This project will extend that impact to include samples from aircraft and small-scale sites such as individual buildings and facilities. The key outcomes of this mahi will be:   

  • Māori and Pacific People’s views of wastewater testing at different scales are broadly canvassed, recorded and disseminated. 

  • Aotearoa New Zealand and Pacific Nations become integral members of global wastewater efforts focussed on the border (aircraft and airports). 

  • The logistics, detection sensitivity and sampling methodology for wastewater monitoring at small scales in Aotearoa are established, ready for deployment if/when required. 

  • The ethical, social and practical risks and benefits of WBE at various scales are thoroughly investigated. 

  • A true tūhonotanga is established around the future of WBE in Aotearoa New Zealand.   

Together, this aircraft and localised sampling work will seek to overcome a number of technical, social and cultural issues that need to be addressed before WBE can be implemented in these settings, preparing communities to better respond to emerging pandemic and infectious disease threats in a strong and unified way. 

Impact Case Study 

Principal Investigator: Dr Brent Gilpin and Professor Marama Muru-Lanning, PHF Science, Waikato Tainui College for Research and Development. 

Influenza-like illnesses - detection and monitoring in community pharmacies

Whakarāpopoto Rangahau I Summary of Research 

The study aims to assess the feasibility of pharmacies participating in the surveillance of Influenza-like illnesses circulating in the community. Activities will mirror procedures currently in place in the sentinel General Practice surveillance programme led across Aotearoa New Zealand by ESR, whereby patients are invited to have a nose swab for testing and typing of eight respiratory viruses.  

This study will capture surveillance data from a population that has not accessed General Practitioners or Secondary services as a result of their respiratory infection. 

Te Hiranga a Rangahau I Research Impact 

This project has strong potential to inform local and national preventative measures when integrated with other surveillance systems by: 

  • Identifying changes in prevalence of circulating illnesses by enabling the surveillance of a disadvantaged population  

  • In communities that were disproportionally affected by influenza and SARS-CoV-2 outbreaks, increasing community participation surveillance by offering additional opportunities to participate in surveillance programmes has the potential to detect infection threats sooner, leading to greater opportunities to implement mitigation responses and reduce the burden on the public health system 

  • Explore the potential to expand the role of pharmacies, particularly in rural or remote regions where access to GP services is limited and areas that do not currently have the access to the GP Sentinel Surveillance programme  

  • Increase representation of Māori and Pacific peoples in public health surveillance by building on pharmacist-patient relationships and empowering community driven collaboration. This project will support Māori and Pacific pharmacists and pharmacy students in their research participation as health care leaders.   

This project will support the Aotearoa/New Zealand data that contributes to improving influenza like illnesses surveillance internationally including vaccine development.

Impact Case Study

Principal Investigator: Kyley Kerse, Medical Research Institute of New Zealand (MRINZ). 

A review of infectious disease surveillance in Aotearoa

Whakarāpopoto Rangahau I Summary of Research 

This project will review Aotearoa New Zealand’s current ID surveillance systems and assess their ability to support the prevention and control of important IDs in a timely and equitable manner. 

To ensure New Zealand has a world-class surveillance system to support a highly effective response to important infectious disease threats. 

This project will review Aotearoa New Zealand’s current ID surveillance systems and assess their ability to support the prevention and control of important IDs in a timely and equitable manner. There will be a strong focus on diseases which can cause outbreaks and pandemics, and diseases that particularly affect Māori, Pacific Peoples, and those on low-incomes.

The project will then carry out a ‘gap analysis’ by comparing our current surveillance capacity with what is needed to meet the needs of national agencies, local disease control practitioners and services, Māori decision makers, and communities. The end result will be a well-informed agenda for systems change to give this country the surveillance systems it needs to protect its people from current and emerging ID threats.

Te Hiranga a Rangahau I Research Impact 

Immediate impacts of this research: 

- Systematic stocktake of current surveillance capacity and diverse end user information needs at national and local levels which is likely to help system operators to identify and make immediate system improvements. 

- Shared concepts and vocabulary for discussing information needs from an ID surveillance system which could help to support greater system standardisation and integration. 

- Wider appreciation of the value and power of information for supporting a strengths-based approach to understand and manage ID risk at national and local levels which should support the case for additional resourcing. 

Long-term impacts of this research: 

- Highly effective surveillance systems to meet the requirements of stakeholders. 

- Greater health security from improved pandemic surveillance systems. 

- Robust and relevant information that is available in a timely manner to Māori health organisations, practitioners, and communities to support improved ID management. 

- More equitable management of IDs, with reduced Māori and Pacific rates of infection and serious outcomes that are more in-line with what is seen in the non-Māori non-Pacific population.

Impact Case Study 

 Principal Investigator: Michael Baker, University of Otago. 

Strengthening public health surveillance of emerging diseases for communities and Māori

Whakarāpopoto Rangahau I Summary of Research 

Vibrio infections present as gastroenteritis or tissue infections that can be mild or very serious. These bacteria live naturally in aquatic environments and people become infected from eating contaminated kaimoana (seafood) or coming into contact with contaminated water.   

Aotearoa New Zealand is seeing more Vibrio infections in recent years. Recent outbreaks have involved several cases identifying as Māori who became ill from consuming kaimoana collected in some regions of Aotearoa. Vibrio thrive in warm water, so as climate change brings warmer temperatures, Vibrio could increase in Aotearoa New Zealand, as seen in other countries.  

The burden of infectious disease estimates (based on disability adjusted life years; DALYs) and the cost of illness is dependent on their incidence, the frequency of mortality and the severity of morbidity. Vibrio infections is an example of where infections are only notifiable in some cases such as an outbreak or illness from selected types of Vibrio.  

The current surveillance system, including the database used to record hospitalisations and deaths in Aotearoa, is not capturing all vibriosis cases. This represents an area where under-reporting is likely to be occurring and therefore the burden of disease is also under-estimated.  

This scenario is likely be the case for other infectious diseases in Aotearoa as well. More widely, current work within the research team is showing that doctors do have some unconscious bias with Māori patients when they present with gastrointestinal illness at general practices (GPs). 

The current work is focusing on yersinosis (a disease caused by the bacteria Yersinia), but this issue is likely to be the same for Vibrio and other gastrointestinal illnesses too. This unconscious bias, and other factors, may be impacting on multiple actions that need to occur for a case to be diagnosed and thus reported, such as the patient being offered a test or followed up.  

There are likely to be other barriers that make it difficult to understand the burden of gastrointestinal disease for Māori, which impacts on health service decision-making. Furthermore, the pathways of delivering trusted public health messages and alerts of risk to communities (such as in outbreaks) needs further research to improve impact. 

Through fostering relationships and collaborations from different disciplines, we will strive to identify key gaps and seek ways to improve the public health surveillance system for Aotearoa, using Vibrio as an exemplar. We will also continue to explore the barriers that Māori face with testing and follow up of gastrointestinal disease. These relationships will be essential to co-design and co-deliver pathways to deliver trusted public health messages and alerts of risks to communities (such as outbreaks). 

Te Hiranga a Rangahau Research Impact 

Reduce health inequities for Māori who present at a general practice with gastrointestinal illnesses by identifying barriers for Māori in getting tested and followed up by GPs to inform better service delivery to Māori. 

If the notification rates of illness for Māori was to improve, then we would be able to better estimate the true burden of illness, which will help direct important public health resources to key areas. 

Enabling tino rangatiratanga by working with Māori communities to co-design and co-deliver public health messages and alerts of risks to communities that Māori communities will trust and implement. 

Through improvements in enteric disease surveillance, we could better monitor both notifiable and non-notifiable diseases. Such information supports health delivery decision makers. In addition, since emerging diseases are not necessarily notifiable, improved surveillance offers the opportunity for earlier detection.  

Identify areas where improvements in the current surveillance system and DALY methodology is required to support better estimates of burden of disease and the cost of illness for Aotearoa. 

Development of a relationship network that can help design follow on research such as identify the next steps required to improve public health surveillance data for Vibrio and potentially other pathogens. This would include potentially co-design a case-study with sentinel sites in collaboration with key stakeholders (Te Whatu Ora, Ministry for Primary Industries [MPI]), diagnostic laboratories, Māori health providers/advisors and communities. 

Impact Case Study 

Principal Investigator: Lucia Rivas - Senior Scientist and Maria Hepi - Senior Social Scientist, PHF Science.

Community-based carriage study for bacterial species that cause invasive meningococcal disease and invasive pneumococcal disease

Whakarāpopoto Rangahau I Summary of Research 

This project involves a community-based carriage study for bacterial species that cause invasive meningococcal disease and invasive pneumococcal disease, with a focus on households in high prevalence areas. It will help to understand where transmission happens within a household and factors that might influence carriage and transmission. 

The project involves molecular typing and genomic sequencing of bacteria that cause meningococcal disease (IMD, Neisseria meningitidis, meningococcus) and invasive pneumococcal disease (IPD, Streptococcus pneumoniae, pneumococcus) to identify transmission events and get a better understanding of the diversity of circulating meningococci and pneumococci. 

Expected outcomes of the study are: 

  • understanding carriage burden in different populations in Aotearoa New Zealand 

  • identifying factors and behaviours that may influence carriage rate and transmission 

  • a better understanding of the diversity of circulating meningococcus and pneumococcus in Aotearoa New Zealand.

Te Hiranga a Rangahau I Research Impact 

Better understanding of carriage will lead to more evidence-based health policy, immunisation policy and vaccine procurement decision making.  

The relationship between high carriage and disease development is not clear. It is likely dependent on the strain of pathogen being carried. A carriage survey where Māori and Pacific participants are equally represented or enriched, will clarify relationships between carriage and disease in Aotearoa New Zealand. 
 
The study will also identify specific risk factors and devise possible mitigation strategies to reduce transmission.  

Sharing the results with the community could push IMD and IPD awareness to the forefront and create opportunities to increase immunisations. Understanding housing conditions or household behaviour that lessens or exasperates transmission could inform housing standards and contribute to the design of mitigation tools. 

An important long-term impact of this project is the relationship formed with local Māori and Pacific communities. The goal is to empower communities, build local capability and capacity, increase public health surveillance knowledge, create a trusting approach that allows proactivity and engagement with these services to improve the health and well-being of whānau. Information could also be used at a national level to inform vaccine funding as well as identifying appropriate vaccinations and populations for inclusion in the national immunisation programme. 

Impact Case Study 

Principal Investigator: Xiaoyun (Una) Ren, PHF Science. 

Towards elimination: improving the effectiveness and safety of leprosy treatment in the Pacific

Whakarāpopoto Rangahau I Summary of Research 

Kiribati has one of the highest rates of leprosy in the world and with sea level rise threatening its existence there is likely to be mass migration of i-Kiribati people to neighbouring countries such as Aotearoa New Zealand. 

This project will use a next generation deep sequencing technique to identify drug resistant leprosy and the potential impact of mass treatment of household contacts of those newly-diagnosed with the disease in Kiribati. The project will also explore the degree of susceptibility to severe adverse reactions to common treatments for leprosy. 

Kiribati is a Pacific Island neighbour of Aotearoa New Zealand and has one of the highest rates of leprosy in the world. This stigmatised and neglected mycobacterial disease can cause major disability and is both treatable and preventable. With sea level rise threatening the existence of this low lying atoll, there is likely to be mass migration of i-Kiribati people to countries such as Aotearoa New Zealand in the future and thus a risk of reintroduction of this once-endemic disease.  

Since 2018, the National Leprosy Programme in Kiribati has conducted screening and administration of annual single dose rifampicin chemoprophylaxis for two years for household contacts of newly diagnosed patients with leprosy. Despite this, the rate of leprosy remains extremely high. In 2021, the Ministry of Health and Medical Services in Kiribati (MH&MS) in collaboration with the University of Otago, the University of Sydney and the Pacific Leprosy Foundation (PLF), commenced a leprosy and tuberculosis mass screening and rifamycin-based chemoprophylaxis programme (PEARL + COMBINE) on the most populous island in Kiribati (population ~60,000). (1,2) Such largescale use of rifampicin has the potential to induce resistance in endemic Mycobacterium leprae strains which could have disastrous consequences for leprosy control.  

The researchers have previously set up a pilot M. leprae resistance monitoring programme for Kiribati isolates. This is technically complex as M. leprae cannot be cultured in vitro and testing needs to be done on M. lepraeDNA extracted from skin biopsies that have been transferred from Kiribati to Aotearoa New Zealand. Preliminary data, based on first generation methods, revealed baseline resistance rates to dapsone and rifampicin (both part of the standard leprosy treatment regimen) of 11% (9/83) and 0% respectively.  

Currently, first-generation molecular testing relies on sequencing the rpoB, folP and gyrA genes extracted from skin biopsies of patients with newly diagnosed leprosy in Kiribati. Genoscreen France have developed a next generation deep sequencing technique (Deeplex Myc-Lep®) which targets drug resistance genes, SNPs and variable number of tandem repeats in M. leprae. This platform has been used in other leprosy endemic regions to survey drug resistance. Utilising multiplexed next generation deep sequencing, rather than current methods, should increase the sensitivity of drug-resistance testing, in particular due to additional coverage of parts of the genome recently identified as novel rifampicin resistance targets. The project involves conducting Deeplex sequencing on catalogued biopsy samples to enable comparison of the results of first-generation resistance testing. Researchers will also test prospectively acquired samples taken from patients with presumptive leprosy at the request of the MH&MS while the rifampicin prophylaxis project continues. This will provide valuable information on the impact of mass rifampicin prophylaxis on resistance patterns and will have the added benefit of helping to elucidate transmission pathways of resistant isolates.  

A major concern for the leprosy treatment programme in Kiribati and all other endemic locations is treatment default (i.e. unplanned premature treatment cessation). Treatment default has major potential deleterious consequences including selection and transmission of drug resistant strains and inadequate treatment leading to development of irreversible deformity and disability. One of the major contributors to treatment default is severe adverse reactions to medication. There are two key factors that predispose patients to severe adverse reactions to dapsone, the prevalence of both of which is unknown in Kiribati.  

The first of these is deficiency of glucose-6-phosphate dehydrogenase (G6PD - the most common enzymopathy globally) which predisposes to severe dapsone-induced haemolytic anaemia. The second is presence of the HLA-B*13:01 allele which predisposes to the potentially fatal dapsone hypersensitivity syndrome. This project will measure the prevalence of G6PD deficiency and the HLA-B*13:01 allele in the Kiribati population to help determine the utility of implementing pre-treatment screening of patients diagnosed with leprosy. Removal of dapsone from treatment regimens for patients who are positive for either condition should dramatically improve patient adherence and overall treatment effectiveness with consequent reduction in risk of resistance development. 

The laboratory in Kiribati currently does not have capacity for G6PD testing, HLA-B13*01 allele detection or molecular detection of M. leprae or resistance-conferring mutations. A cornerstone of this work is to enhance laboratory capacity in Kiribati to enable in-country diagnostic testing to assist with clinical decision-making and potentially also local transmission hotspot investigation. The G6PD testing equipment used in the research (SD Biosensor®) lends itself well to bedside use in resource-poor settings and will facilitate ongoing use. Researchers also aim to begin preliminary development of a highly sensitive CRISPR molecular assay for M. leprae and drug resistance detection that would be suitable for use in Kiribati.  

Te Hiranga a Rangahau I Research Impact 

The impact of the project will be an improved understanding of the risks associated with a major chemoprophylaxis programme for an epidemic disease currently threatening a Pacific Island partner and which is already spreading to neighbouring countries, including Aotearoa New Zealand. This will help inform other countries and regions of the considerations needed when implementing mass chemoprophylaxis. Given rifampicin resistance in M. leprae has already been reported in other regions, the risk of promoting the development of resistance cannot be dismissed. Molecular drug resistance signatures will also provide information on local pathways of transmission which ultimately could inform leprosy screening and prevention activities. Establishing the presence of G6PD deficiency and/or the HLA-B13*01 allele associated with dapsone-induced haemolytic anaemia and dapsone hypersensitivity syndrome respectively, has the potential to reduce treatment defaults which in turn should reduce leprosy treatment failure, accrual of disability and selection of resistance mutations. There will be knowledge transfer from New Zealand to Kiribati through frequent visits and educational sessions as well as enhancement of local laboratory capacity through facilitation and development of suitable assays for G6PD deficiency and detection of M. leprae DNA and molecular markers of drug resistance. This project will significantly enhance the knowledge and research skills of Dr Patrick Campbell, a young Aotearoa New Zealand infectious diseases physician who will be conducting the bulk of this research during his PhD studies. 

Impact Case Study 

Principal Investigator: Dr Nick Douglas and Professor Steve Chambers, University of Otago. 

The role of improved surveillance and modelling to support prevention and control of infectious diseases in Aotearoa

Whakarāpopoto Rangahau I Summary of Research

 The overarching aim of this project is to identify opportunities for using infectious disease modelling and enhanced surveillance to improve the prevention and control of infectious diseases in Aotearoa. 

To achieve this aim, this project will consider two key perspectives: 

  • How disease modelling can answer infectious disease concerns of Māori communities. 

  • How infectious disease surveillance needs to be enhanced to support effective disease modelling. 

Te Hiranga a Rangahau I Research Impact 

This project will help bridge two existing Te Niwha projects: 

  1. Review of infectious disease surveillance in Aotearoa  

  1. Developing an indigenous-led framework for infectious disease preparedness and response in Aotearoa: addressing critical data needs through whānau ora 

Doing so would enhance the value of both projects, begin discussions around what communities would like to see and find useful from infectious disease surveillance efforts and the disease modelling that would be required to provide solutions for communities. 

Impact Case Study  

Principal Investigator: Dr Sarah Pirikahu, University of Otago.

AMR reference laboratory and pathogen genomics capability for Fiji

Whakarāpopoto Rangahau I Summary of Research 

This strategic Rapid Response Research project will address the rise of antimicrobial resistance (AMR) in Fiji and the Pacific. The research team will be building capability and capacity for genomic testing in Fiji, generate a Fijian national antibiogram and determine the antimicrobial susceptibility pattern of WHO critical AMR pathogens to new antimicrobials.

Given the rise of antimicrobial resistance (AMR) in Fiji and the Pacific, it is crucial to enhance AMR surveillance and diagnostics to assist with the identification of outbreaks, to inform infection prevention and control interventions, to break the chain of transmission, and to inform selection of appropriate first and second-line treatment options for patient management. 

Next generation sequencing (NGS) is a powerful new tool for pathogen genomics that has the potential to transform culture independent diagnostics and to enable rapid identification of transmission networks and outbreaks. Our previous work has demonstrated the utility of pathogen genomics for the identification of a previously unrecognised outbreak of carbapenem-resistant Acinetobacter baumannii in the Pacific Islands. The study combined work on bacterial isolates from Fiji, Samoa, Aotearoa, Australia, and India. We were able to identify separate connections between isolates across the Pacific and to India based on genomic analyses, suggesting the need for coordinated AMR surveillance in the region. Moreover, our prospective study revealed prolonged, unrecognised outbreaks of multiple clones of carbapenem resistant Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae within and between healthcare facilities in Fiji. These studies highlighted the critical need for advanced AMR genomic surveillance in the Pacific region and are helping to foster the establishment of a Pacific-wide research network. 

Traditionally, next-generation sequencing (NGS) has been restricted to specialized facilities due to high equipment costs and the need for extensive bioinformatics expertise. Indeed, our previous studies utilised sequencing facilities in Aotearoa and in Asia. However, recent technological advancements have significantly reduced these barriers. The Oxford Nanopore Technologies MinION platform exemplifies this shift, offering an affordable, portable solution for long-read sequencing. Additionally, advances in bioinformatics have led to the development of streamlined analysis pipelines that do not require extensive expertise. These innovations enable pathogen genomics both in the laboratory and in the field, making advanced genomic analysis more accessible and practical for regions with limited resources. We have already initiated work to establish MinION sequencing in Fiji and have used it to perform whole genome sequencing on patient carbapenem-resistant Acinetobacter baumannii isolates. 

Research goals: 

  • Through whole genome sequencing, identify outbreaks and potential transmission pathways of WHO critical AMR pathogens (extended spectrum beta-lactamase [ESBL] and carbapenemase-producing gram negative organisms) in Fijian hospitals 

  • Generate a Fijian national antibiogram 

  • Determine the antimicrobial susceptibility pattern of WHO critical AMR pathogens to new antimicrobials 

Te Hiranga a Rangahau I Research Impact 

The research team’s recent study has highlighted the transnational spread of resistant bacteria between the Pacific and New Zealand (Baleivanualala et al., 2023). By enhancing our understanding of this transmission, this project aims to empower researchers, health professionals, and communities in the Pacific to develop effective prevention strategies and control measures against resistant bacteria. Given the rising number of Pacific patients seeking medical treatment in Aotearoa, this project has the potential to address and reduce inequitable health outcomes in both the Pacific and Aotearoa. 

This project will develop cutting-edge real-time pathogen genomic solutions to address antimicrobial resistance (AMR) by establishing AMR genomic surveillance which will lead to the establishment of an AMR reference laboratory in Fiji that serves the Pacific. By centralising this lab in Fiji, we aim to enhance regional collaboration and data sharing, including with Aotearoa. 

AMR is a silent pandemic recognized by the WHO as a critical threat to human health and well-being, especially in low-resource settings like the Pacific. Next-generation sequencing has proven effective in identifying and tracking AMR pathogens both internationally and in Aotearoa. This project will build real-time sequencing capabilities in Fiji, integrating epidemiological data to enable rapid identification and characterisation of resistant pathogens. It will facilitate early detection of outbreaks, support effective treatment, and ensure swift implementation of control strategies, leading to a better understanding of AMR patterns across the Pacific. 

This project will build research capacity and expertise in AMR surveillance and molecular diagnostics, contributing to the global fight against AMR. The establishment of the AMR reference laboratory will serve as a hub for cutting-edge research and training, fostering the development of innovative solutions to address AMR. This initiative will also ensure a coordinated and effective response to AMR threats in the broader Pacific region and in Aotearoa. 

Impact Case Study 

Principal Investigators: Professor James Ussher and Saki Baleivanualala, University of Otago.