Diagnosing infections earlier in preterm babies with real time genomic analysis

16 December 2019

Scientists and clinicians at the Norwich Research Park have pioneered a new method for profiling the microbiome of preterm babies that can significantly speed-up the identification of infections and indicate more effective treatments.

By harnessing next generation sequencing techniques, the team from the Quadram Institute and the Earlham Institute (EI) have shown that they can rapidly and reliably identify the microbes present in a preterm baby’s stool sample that may cause life-threatening conditions such as sepsis or necrotising enterocolitis (NEC). The method also uncovers the presence of antimicrobial resistance genes, vital information needed to select the most effective treatment.

Using Oxford Nanopore Technology’s MinION portable sequencing device coupled with bespoke software to analyse the sequence data in real time, data can be obtained in under 5 hours. With current methods taking up to 48 hours, developing this platform for routine use in a clinical setting would allow faster and tailored antimicrobial treatments to be used.

“Preterm babies are born with underdeveloped gut physiology, immunity, and have an altered gut microbiota, all of which increases risk of life-threatening infections. Time is of the essence in detecting or diagnosing infections” said Dr Lindsay Hall from the Quadram Institute. “Not only could our approach be more effective, it will also reduce the use of antibiotics and help slow the rise of antimicrobial resistance.

Dr Richard Leggett, Group Leader at EI, added: “With the MinION and our own analysis pipeline (NanoOK RT, developed specifically for this work), we can go from faecal sample to pathogen and antimicrobial resistance (AMR) profile in just four to five hours. With these kinds of high-risk patients, time is absolutely critical. We can also take advantage of the MinION’s long DNA reads to place AMR genes within host bacteria, enabling better understanding of antibiotic resistance.”

“Nanopore sequencing is an interesting technology because it provides useful data so quickly. We were excited to see how well it could perform on clinical samples – with our custom software. It hasn’t escaped our attention that because it is cheap, small and low powered it could be uniquely useful in lower and middle-income countries,” said Dr Matthew D. Clark, former Head of Technology Development at EI, now Research Leader at the Natural History Museum London.

To test their platform, the researchers used the portable MinION to carry out shotgun metagenomics on mock microbial communities. Shotgun metagenomics analyses the genomic sequence from a mixed collection of organisms, in this case 20 different microbes. Having confirmed that the approach using the MinION worked, the researchers progressed to using samples obtained from preterm babies.

To assess how well the platform worked in real life situations, the researchers worked with the Norfolk and Norwich University Hospital’s Neonatal Intensive Care Unit (NICU). The clinical research team collected faecal samples from preterm babies, with consent of the parents, as part of a long-term collaboration into the gut health and microbiome in very premature babies.

The method, published in the journal Nature Microbiology, discerned between healthy babies and those diagnosed with NEC or sepsis, with the healthy babies having a strong population of beneficial Bifidobacterium and the others harbouring either E. cloacae or Klebsiella pneumoniae, both of which can cause life-threatening infections.

Prof Paul Clarke, consultant neonatologist and research lead at the Norfolk and Norwich University Hospital NICU and one of the co-authors of the research said: “Preterm babies are a group at high risk of dangerous infection. More that 90% of our preterm babies are presently treated with antibiotics, yet in retrospect most did not need them. This study is important because it raises the hope that we might soon have available the technology that could help us to discern at a much earlier stage which babies really need antibiotics, and which do not need them. This could save many babies from getting antibiotics they did not need and would be an important advance in helping limit AMR.”

Crucially, the system facilitates sampling over a period of time, so that changes in the microbiota profile can be monitored. This is very useful for monitoring pathogenic bacteria, but it also lets researchers see how other interventions affect the microbiome over time. For example, it can monitor the effect of antibiotics on the overall microbial profile or measure the effects of probiotic supplementation.

Shotgun metagenomics doesn’t just profile the species diversity. In this study, the researchers were particularly interested in profiling the genes that confer antibiotic resistance in the microbiome – known as the ‘resistome’. Klebsiella in particular is of concern as it is becoming increasingly resistant to multiple antimicrobials. An expansion of shotgun metagenomics could therefore help in surveillance for AMR in these clinical settings.

The development of this platform for rapid, portable microbiota profiling brings its use in a clinical setting closer but more trials at different locations are needed to prove its utility before it can be adopted as a routine diagnostic tool. However, with the fast pace of improvements in the technology, there is clear potential for its deployment to save lives in the clinical setting, and to protect us all from the threat of AMR.

The research was supported by the Biotechnology and Biological sciences Research Council and the Wellcome Trust.

Notes to editors

If you would like to speak to Dr Richard Leggett, please contact:

Dr Peter Bickerton

Scientific Communications & Outreach Manager, Earlham Institute (EI)

  • +44 (0)1603 450 994

peter.bickerton@earlham.ac.uk

The Earlham Institute (EI) is a world-leading research Institute focusing on the development of genomics and computational biology. EI is based within the Norwich Research Park and is one of eight institutes that receive strategic funding from Biotechnology and Biological Science Research Council (BBSRC) - £5.43m in 2017/18 - as well as support from other research funders. EI operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.

EI offers a state of the art DNA sequencing facility, unique by its operation of multiple complementary technologies for data generation. The Institute is a UK hub for innovative bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. It is also actively involved in developing novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational Bioscience. Additionally, the Institute offers a training programme through courses and workshops, and an outreach programme targeting key stakeholders, and wider public audiences through dialogue and science communication activities.

www.earlham.ac.uk

@EarlhamInst

The Quadram Institute (quadram.ac.uk) is an interdisciplinary research centre at the forefront of a new era of food and health research. It brings together researchers and clinicians under one roof and houses one of Europe’s largest endoscopy units and a clinical trial facility. It focuses on lifelong health – from birth and throughout the lifecourse, increasing healthspan as well as lifespan. It undertakes both fundamental and translational research working with industry to accelerate innovation and bring novel therapeutics and new food products to patients and consumers.

Based on the Norwich Research Park, The Quadram Institute is a partnership between Quadram Institute Bioscience, the Norfolk and Norwich University Hospitals NHS Foundation Trust, the University of East Anglia and the Biotechnology and Biological Sciences Research Council (BBSRC).

Four interconnected interdisciplinary research themes in Quadram Institute Bioscience deliver a pipeline of research in plants, microbes, food and health: microbes in the food chain; the gut and the microbiome; food innovation and population health.

The Natural History Museum exists to inspire a love of the natural world and unlock answers to the big issues facing humanity and the planet. It is a world-leading science research centre, and through its unique collection and unrivalled expertise it is tackling issues such as food security, eradicating diseases and managing resource scarcity. It is the most visited natural history museum in Europe and the top science attraction in the UK; we welcome around five million visitors each year and our website receives over 850,000 unique visitors a month. People come from around the world to enjoy our galleries and events and engage both in-person and online with our science and educational activities through innovative programmes and citizen science projects. www.nhm.ac.uk

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