Genome sequencing developed to track COVID now protects children in intensive care units from infectious disease

Anyone who has spent time in the neonatal intensive care unit (NICU) knows that it is very intense.

For the tiny babies cared for in these wards, any infection could be fatal. Great measures are taken to prevent the spread of pathogens, but outbreaks still occur.

Traditionally, detection of outbreaks in intensive care units has been done reactively—only after several children became ill at the same time.

Our research advances the use of whole-genome sequencing technologies to detect outbreaks early and eradicate the bacteria before they threaten more children.

From reactive to proactive

Surveillance of outbreaks in intensive care units typically involves monitoring incidence rates and identifying spikes and long-term trends that may indicate pathogen circulation in the unit.

When a potential outbreak is identified, bacteria can be cultured and retrospectively sequenced to determine whether they may be associated with a common source or transmission within the ward.

Wellington Regional Hospital has changed its approach to infection surveillance in intensive care units. Instead of waiting for babies to get sick, they are using the same sequencing technology we developed at the Institute of Environmental Sciences and Research (ESR) to trace genomic contacts during the COVID pandemic.

Diagnostic smears are taken from infants on the unit as part of routine practice. If any key bacteria are cultured from these samples, they are quickly sequenced to identify possible transmission events in near real time. This allows us to closely monitor the situation and quickly respond to emerging outbreaks.

Because not all infants carrying a particular bacterial strain experience severe infection, this proactive approach allows an outbreak to be detected before any infants become ill.

And because whole-genome sequencing deciphers the entire genetic makeup of bacteria, it also provides the ICU team with information about how pathogens are related to each other. This allows them to distinguish isolated cases imported into a unit from any cases circulating within it.

This level of detail allows for accurate infection monitoring and rapid, informed decisions to control outbreaks.

Case study

This shift was recently tested when proactive genomic surveillance revealed that two infants in the NICU had eye infections caused by the same organism, an unusual methicillin-resistant strain. Staphylococcus aureus (MRSA).

MRSA is known to be resistant to common antibiotics, making it especially dangerous in hospitals.

On-site sequencing showed that the two cases were likely related. The priority was to determine whether other babies were affected and to limit the spread of the pathogen as quickly as possible. Screening of infants in the intensive care unit revealed six more carriers of the same strain of MRSA (although none of them had serious illness).

This meant that these infants could be quickly isolated and the outbreak contained before others developed significant infection. ESR’s experience as a genomic contact tracer has helped establish how these infections spread within the department.

Responding to an outbreak requires resources and involves several steps, from initial confirmation of infection and transmission to communication with parents.

This proactive approach to infection surveillance provides an early warning system. This means the ICU team can be confident that an outbreak has already begun and can quickly take action to contain it.

MRSA in New Zealand

The power of genome sequencing extends beyond immediate outbreak control.

By comparing genomic data obtained in the laboratory with data collected through national surveillance projects, our team was able to show that the strain causing the eye infections may have emerged in the early 1990s.

The strain has slowly accumulated genes needed to evade first-choice antibiotics, increasing the risk of antibiotic-resistant bacteria emerging in Aotearoa New Zealand.

We also highlighted the power of genomics to identify connections when we discovered that a strain of MRSA causing illness in an intensive care unit was associated with bacteria collected from cattle. This discovery underscores the concept of “One Health”—the idea that human health, animal health and environmental health are inextricably linked.

The data suggests that bacteria from a cow’s milk reservoir and from babies in a hospital may have shared a common ancestor at some point.

Future Focus

As we continue to unravel the complex world of microbes, tools such as whole-genome sequencing offer hope in the ongoing fight against infectious diseases. Working in Wellington Regional Hospital’s Intensive Care Unit is just the beginning.

From protecting our most vulnerable newborns to identifying unlikely connections between farm animals and hospital patients, genomic technologies are changing the way we fight infectious diseases.

As this technology continues to advance, it promises to play an increasingly important role in protecting public health, one DNA sequence at a time.

In the face of rising antibiotic resistance and the emergence of new pathogens, this proactive, genomics-based approach to infection control may well be our best defense.

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We would like to acknowledge the contributions of Max Bloomfield and the Awanui Labs team, and Emma Voss and the Livestock Improvement Corporation team.

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