By Dr Rhys White, ESR Scientist, Genomics and Bioinformatics Team
The challenge in neonatal intensive care units
Every infection in a neonatal intensive care unit (NICU) is a significant threat. Newborn infants (or neonates) in these facilities are often premature or have underlying health issues. As such, their immune systems are highly vulnerable. Early detection of bacterial infections can help doctors and nurses intervene quickly and save lives. Fortunately, a cutting-edge technology has the potential to transform how infections are managed in NICUs, providing quicker and more accurate detection of outbreaks.
The power of whole-genome sequencing
Whole-genome sequencing is a powerful tool that can be used to decode the genetic makeup of bacteria. This information provides us a more in-depth understanding into how infections spread, what their sources might be and whether they carry antibiotic-resistant genes. This higher level of detail enables health professionals to monitor infections with unprecedented precision and adjust their responses accordingly. What’s more, whole-genome sequencing offers a deeper understanding of the specific bacterial strains impacting at-risk patients.
Nanopore sequencing: a game-changing technology
At the forefront of this shift, the Institute for Environmental Science and Research (ESR) and Wellington Regional Hospital are collaborating to use nanopore sequencing, a transformative technology that brings high-resolution genomic testing directly into the hands of frontline healthcare workers.
Around 20 years ago, genome sequencing machines were as large as refrigerators and needed enough power to run a coffee shop. Today, handheld DNA sequencers, about the size of a smartphone, have the potential to become a first line of defence in detecting deadly outbreaks. While colleagues at Wellington Regional Hospital manage real-time whole-genome sequencing using hand-held Oxford Nanopore Technologies devices, my role is to enhance these efforts by delivering high-resolution genomic analyses.
High-resolution genomic analyses involve digging deeper into the genetic data produced by sequencing. It allows us to identify minor differences in the DNA of bacteria that could indicate how an infection is spreading, whether it is resistant to antibiotics, or even where it may have come from.
This level of detail helps track outbreaks more accurately and tailor treatments to target infections more effectively. This adds critical value to the computational species identification and multi-locus sequence typing (MLST) performed on-site, so we can get a clearer, more complete picture of what is happening at the genetic level.
Faster results, bigger impact
Traditional methods of identifying hospital outbreaks can take days, sometimes weeks. With Oxford Nanopore Technologies, results can get back to clinical decision-makers in hours. A recent outbreak of methicillin-resistant Staphylococcus aureus (commonly known as MRSA – this can result in conditions from boils to serious bloodstream and flesh-eating infections) in Wellington’s NICU was detected after just two cases, allowing hospital staff to quickly contain it.
This sort of quick turnaround helps protect the most vulnerable patients and reduces the risk of larger outbreaks. In contrast, Staphylococcus capitis strain NRCS-A, first isolated in Dunedin Hospital’s NICU in 2007 from a neonate with a bloodstream infection, had persisted despite traditional containment efforts, including after the relocation of NICU services to a renovated facility in 2014.
Speed and accuracy are beneficial when it comes to identifying outbreaks among infants. MRSA outbreaks have previously meant closing parts of the NICU to get things under control. As seen with this recent outbreak in Wellington, rapid detection limited the outbreak to 10 infants, none of whom developed an invasive infection. This swift action also meant there was no need to close parts of the ward to gain control, and there was minimal service disruption.
As technology advances, we are moving from reactive to proactive infection control, preventing outbreaks from happening in the first place. This in turn means better patient outcomes, while contributing to reduced infection prevention costs.
Power to the people
It is not just about speed. This technology is democratising advanced genomic surveillance – in other words, making it accessible to a wider range of healthcare settings. Traditionally, due to the infrastructure, cost and expertise required, whole-genome sequencing was limited to large, centralised facilities, such as New Zealand’s reference laboratories.
Now, with more affordable, portable devices, the ability to conduct high-resolution genomic testing could soon be put in more hands on the frontline. This decentralisation of sequencing is a game-changer, especially in smaller hospitals, rural clinics and resource-limited settings.
Through this technology, these places have the potential identify pathogens and make critical decisions on-site, reducing the need for delays associated with sending samples to central labs in the future. The ability to perform genomic sequencing anywhere, at any time, transforms how we respond to infectious diseases, improving patient care and reducing the spread of infections.
Hidden threats made visible
An additional benefit of the genomics sequencing collaboration between ESR and Wellington Regional Hospital has been its ability to uncover hidden threats. What were initially believed to be Klebsiella pneumoniae infections turned out to be Klebsiella variicola. In simple terms, these two bacterial species are closely related and can cause similar infections, but K. variicola is harder to detect with traditional methods because it is often mistaken for its ‘cousin’, K. pneumoniae.
While the treatment for both species is often the same, the real challenge in this case was that K. variicola, an apparently ‘normal’ bacteria with no obvious antibiotic resistance, was silently spreading in the unit. Whole-genome sequencing allowed us to identify the species, uncover this hidden threat quickly, track its spread, and take swift action. Understanding these subtle differences can sometimes help improve patient outcomes and help us better understand our local situation.
This research is also tracking how bacteria evolve and spread, providing insights into potential links between human and animal diseases – critical in an agricultural country like New Zealand. Furthermore, genomics not only uncovers these silent threats but also enables proactive measures to curb them before they escalate. With more widespread adoption of this technology, a future is possible where routine genomic surveillance in NICUs becomes the norm, significantly reducing the risk of uncontrolled infections.
Challenges and considerations for widespread adoption
However, challenges remain. While these handheld devices hold great promise, the costs and expertise needed for effective implementation in resource-poor areas still need to be addressed. Healthcare workers require specific training to use this technology and interpret the results effectively. Ethical considerations, such as ensuring proper management of bacterial genetic data and protecting patient privacy, must also be carefully navigated. Additionally, regulatory hurdles exist, as health authorities need to approve these devices for clinical use and establish clear guidelines for their application in healthcare settings. Continued development of cost-effective models and training is critical to ensure the widespread adoption of this technology.
Looking ahead
The future looks promising. We are rapidly moving from reacting to outbreaks to preventing them. By combining Oxford Nanopore Technologies sequencing with computational tools and methods that can correct mistakes in the sequence data, this collaboration has the potential to develop a cost-effective model that could change infection control globally. Saving lives, improving patient outcomes, and ensuring health spending can be invested in increasingly impactful ways.
By sharing our genomic data publicly, we are helping build a global resource that will drive healthcare innovations far beyond New Zealand. And as the technology evolves, the impact grows – not just for reacting to outbreaks, but for preventing them entirely. The ability to perform real-time genomic sequencing anywhere, at any time, is transforming how we respond to infectious diseases, improving patient care, and ultimately saving lives.
This tiny technology is having a big impact, and it is just the beginning for New Zealand. As we look to the future, one thing is clear: the power to save lives is in our hands – quite literally.
Further reading
- Oxford nanopore next generation sequencing in a front-line clinical microbiology laboratory without on-site bioinformaticians
- Early identification of a ward-based outbreak of Clostridioides difficile using prospective multilocus sequence type-based Oxford Nanopore genomic surveillance
- Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit using nanopore sequencing