Rapid Respiratory Response in Rural and Remote Regions

RRR²: Using rapid DNA sequencing to improve respiratory infection care in rural and remote communities

RRR² is testing whether portable DNA sequencing can help clinicians understand respiratory infections faster in children with bronchiectasis living in regional, rural, and remote communities.

The Rapid Respiratory Response in Rural and Remote Regions study, or RRR², is an observational research project focused on improving how respiratory infections are understood in children and young people with bronchiectasis.

Bronchiectasis is a chronic lung condition where repeated infection and inflammation cause permanent airway damage. Children with bronchiectasis can experience recurrent respiratory flare-ups, often requiring antibiotics, hospital care, and, in severe cases, transfer away from their home community for treatment.

RRR² is developing and testing new ways to rapidly identify the bacteria, viruses, and antimicrobial resistance genes present in respiratory samples. By using portable DNA sequencing technologies, the study aims to understand whether more detailed microbial information can be generated closer to the patient, faster than conventional laboratory pathways, and in a way that may ultimately support better clinical decision-making.

Why this study is needed

Respiratory infections are a major health issue for children living in regional, rural, and remote communities. Bronchiectasis is especially important because repeated infections can contribute to progressive and irreversible lung damage.

Current clinical testing usually relies on culture-based microbiology. These tests are important, but they can take days to weeks to return results, and they may not detect all organisms present in a respiratory sample. This delay can be particularly challenging in outreach and remote healthcare settings, where children and families may have returned home before results are available.

RRR² addresses this gap by exploring whether metagenomic sequencing can provide a more complete picture of respiratory infections. Instead of looking only for selected organisms, metagenomics reads the genetic material in a sample and can identify bacteria, viruses, resistance markers, and other microbial features that may be relevant to infection and treatment.

What we are doing

RRR² will collect respiratory samples, such as sputum or bronchoalveolar lavage where clinically available, from children and young people with bronchiectasis who are receiving care through participating clinical sites.

The project focuses on three main goals:

1. Understanding respiratory microbiomes in bronchiectasis

We will use DNA sequencing to describe the bacteria, viruses, and microbial genes present in respiratory samples from children with bronchiectasis. This will help us understand how airway microbial communities differ between patients and how they may change during respiratory exacerbations.

2. Testing rapid sequencing workflows

We will evaluate portable sequencing approaches, including Oxford Nanopore sequencing, to determine whether respiratory samples can be processed and analysed within clinically useful timeframes. The long-term aim is to support a workflow that could help clinicians receive more detailed microbial information while care decisions are still being made.

3. Comparing sequencing with standard clinical microbiology

Sequencing results will be compared with routine clinical information, including standard microbiology reports and relevant clinical metadata. This will help determine where metagenomic sequencing provides additional information, particularly for complex or culture-negative samples.

Where the study is taking place

RRR² brings together clinicians, microbiologists, bioinformaticians, Aboriginal health expertise, and community partners across South Australia and the Northern Territory.

The approved study sites include:

Women’s and Children’s Hospital
Limestone Coast Local Health Network
Alice Springs Hospital

We are working with clinicians and researchers from:

Women’s and Children’s Hospital
Flinders University
Royal Adelaide Hospital
Mount Gambier Hospital
Alice Springs Hospital
Adelaide University
SA Pathology
Black Ochre Data Labs

The project includes regional and remote clinical settings where timely access to advanced diagnostic testing can be difficult, and where new approaches to respiratory infection monitoring may have substantial benefit.

Working with communities

RRR² is being conducted with strong attention to culturally safe research practice, community engagement, and Indigenous data governance.

The study team is working with Aboriginal Health Workers, Aboriginal liaison teams, Indigenous researchers, and community partners to support respectful engagement with children, families, and local health services. Study materials and consent processes are being developed to support clear communication and informed participation.

The project has ethics approval from the Women’s and Children’s Health Network Human Research Ethics Committee, the Aboriginal Health Research Ethics Committee, and reciprocal approval through the Human Research Ethics Committee of NT Health and Menzies School of Health Research for the Alice Springs Hospital site.

What makes RRR² different?

RRR² combines clinical respiratory care, portable genomics, microbiome science, and bioinformatics in a real-world rural and remote healthcare setting.

The project is designed to move beyond laboratory-based discovery and ask a practical question: can rapid metagenomic sequencing be used in settings where faster, more complete microbial information is most needed?

The study is not changing patient treatment directly. Instead, it is generating evidence about whether rapid sequencing can provide useful information that may support future diagnostic pathways, antimicrobial stewardship, and respiratory care for children with bronchiectasis.

Our long-term vision

The long-term goal of RRR² is to help reduce preventable lung damage by improving the speed and precision of respiratory infection diagnosis.

By building a portable, culturally safe, and clinically relevant sequencing workflow, the project aims to create a foundation for future diagnostic tools that can be used closer to home for children and families in regional, rural, and remote communities.

Project team

RRR² is led by a multidisciplinary team including respiratory clinicians, microbiologists, bioinformaticians, Aboriginal health leaders, and researchers with expertise in Indigenous data governance.

The project is supported by the Women’s and Children’s Hospital Foundation Bloom Research Program and involves collaboration between clinical services and research groups across South Australia and the Northern Territory.

Information for participants and families

Before joining the RRR² study, children and families will be given information about the study and asked to decide whether they would like to take part. Participation is voluntary, and choosing not to take part will not affect a child’s medical care.

The approved study documents are available below.

Parent/Guardian Information Sheet

This information sheet is for parents and guardians of children who may be invited to take part in the RRR² study. It explains why the study is being done, who can participate, what samples and health information will be used, and how privacy will be protected.

The sheet explains that the study will use mucus or spit samples that are already collected as part of routine care, so there are no extra tests, procedures, or physical risks for the child. The research team will study the DNA of germs in the sample, such as bacteria and viruses, but will not study the child’s DNA.

It also explains how study findings will be shared. Individual results will not be provided; instead, families and communities will receive overall study updates, and results will be shared with Elders and community leaders before being made public.

Download: Parent/Guardian Information Sheet

Child/Participant Information Sheet

This information sheet is written for children and young people. It explains the study in simpler language, including why doctors are trying to find faster ways to identify the germs that cause lung infections.

The child information sheet explains that the study uses spit or mucus samples already given to the doctor as part of usual care, and that children do not need to do anything extra. It also explains that taking part is optional, that saying no will not change their care, and that they can change their mind later.

The sheet also describes how samples and information will be kept private, how de-identified data will be stored securely, and how children and families can hear about the overall results of the study.

Download: Child/Participant Information Sheet

This form is completed by a parent or guardian if they agree for their child to take part in the RRR² study. It confirms that the parent or guardian has read, or had read to them, the information sheet and understands what participation involves.

The consent form covers key choices, including whether the child’s mucus or spit sample can be used in the study, whether de-identified data can be used in future ethically approved research, whether leftover de-identified samples can be stored until the end of the study, whether the research team can access relevant electronic medical records, and whether the family would like to be contacted about related future research.

The form also gives families the option to receive study updates by email or post. These updates will describe combined findings from all participants, not individual results for the child.

Download: Parent/Guardian Consent Form

Child/Participant Agreement Form

This form is for children and young people who are able to give their own agreement to take part. It is written in child-friendly language and gives the participant the opportunity to say whether they agree to be involved.

The agreement form explains that joining the study is the child’s choice, that they can stop at any time, that leaving the study will not change their medical care, and that no extra samples or tests are required. It also explains that information will be kept private and that any leftover samples will be respectfully and safely disposed of when the study finishes.

The form asks the participant to agree to specific parts of the study, including use of their sample, use of results in this project and future ethically approved research, access to electronic medical records, and possible future contact about related research studies.

Download: Child/Participant Agreement Form

Questions about the study

For more information about the RRR² study, please contact:

Dr Thomas Goddard Principal Investigator Women’s and Children’s Hospital Phone: (08) 8161 7000

For concerns or complaints about the study, families can contact the relevant ethics committee listed in the information sheets.

Information for researchers

RRR² will generate respiratory metagenomic and clinical research datasets under approved ethical and governance frameworks. Data sharing will follow participant consent, institutional requirements, and Indigenous data governance principles.