Using genomics to better detect outbreaks of Legionnaires’ disease

January 16, 2025 by Liz Farquhar Leave a Comment

Researchers at NSW Health Pathology and the University of Sydney are working together to design a new integrated legionellosis surveillance system, using genomic testing to improve detection of legionella outbreaks.

Legionnaires’ disease is an infection of the lungs that is spread to humans by breathing in droplets of water contaminated with legionella bacteria. The most common sources of this bacteria are air conditioning cooling towers.

There have been several large outbreaks of Legionnaires’ disease in Sydney in the past few years, and public health authorities need better tools to help them control outbreaks more quickly.

A new research project is aiming to bring together the latest in genomics technology and a range of public health organisations to improve how we detect and respond to outbreaks.

NSW Health Pathology (NSWHP) is the host organisation for the project being led by Chief Investigators, Professor Vitali Sintchenko (NSWHP and University of Sydney) and Dr Eby Sim (University of Sydney). (pictured above)

The research team is also partnering with Health Protection NSW, and Public Health Units, in Western Sydney and South East Sydney Local Health Districts.

They’ve been awarded a $500,000 Translational Research Grant through the NSW Office of Health and Medical Research to assess the effectiveness of whole-genome sequencing for integrated surveillance for legionellosis.

A man in a white lab coat sitting a desk with a microscope, smiling up at the camera. — Prof Vitali Sintchenko in the laboratory at Westmead.

“Public Health authorities aim to identify clusters of cases as soon as possible in order to remove the source of infection and prevent further spread in the community,” Vitali explains.

“Growing Legionella in the lab is a complex process, it takes a long time, and cultures are not often available because more cases of legionella infection are diagnosed by PCR testing.

“So, this project is going to use clever genomics that can collect genomic information without culture directly from respiratory samples. That will increase the number of relevant cases that can be investigated without relying on culture.

“The other part of the project is to bring together multiple stakeholders – public health units, specialists in environmental health, clinical and environmental microbiology.

“Our team is focused on a whole-of-system approach so that different types of data can be mapped together, and genomics can hopefully save time by identifying commonalities, or links between cases, that otherwise would not have been recognised as part of a cluster.”

Dr Eby Sim says the genomic sequencing technology being used by the research team at Westmead will significantly streamline the process of searching for matches between samples.

“Legionella is hard to grow in a laboratory, and the culture takes many days,” he said.

A man in a white lab coat sits at a desk with a computer. — Dr Eby Sim in the laboratory.

“Here, we are attempting to bypass the growth of Legionella pneumophila in the laboratory and directly ‘fish out’ its genomic signature from a specimen, which is very helpful for linking cases and clusters together.”

“We also want to make sure that outbreaks don’t keep expanding so we can assist public health units in finding hot spots and responding to them faster,” said Eby.

Vitali says the research project will take two years to complete.

“The success of this competitive grant application is due to our partnership between Health Protection NSW, the University of Sydney and also support from ICPMR and NSW Health Pathology’s Public Health Pathology office.

“What we want to see, if everything goes as we planned, is that NSW Health Pathology’s genomics is integrated into the environmental and public health monitoring and response, reducing the time it takes to identify clusters of legionellosis.”

A large laboratory filled with equipment. — The laboratory where much of the research will be conducted at ICPMR, Westmead.

Mozzies may be carrying Japanese encephalitis this summer. Here’s what to know if you’re spending time outdoors

January 13, 2025 by Liz Farquhar Leave a Comment

A Victorian man is reportedly in a critical condition in hospital after contracting Japanese encephalitis from a mosquito bite. This news comes after both Victoria and New South Wales issued public health alerts in recent weeks warning about the virus.

So what is Japanese encephalitis, and how can you protect yourself and your family if you live, work or are holidaying in mosquito-prone regions this summer?

Mosquito-borne diseases in Australia

Relative to other parts of the world, Australia has traditionally been very low risk for potentially life-threatening mosquito-borne diseases.

There’s no widespread dengue, yellow fever or malaria. But there are still many viruses that local mosquitoes can spread.

About 5,000 cases of mosquito-borne disease are reported in Australia each year. The vast majority of these are due to Ross River virus. The disease this virus causes is not fatal, though it can be severely debilitating.

Disease caused by two other pathogens, Japanese encephalitis virus and Murray Valley encephalitis virus, are much rarer but potentially fatal.

The symptoms of human disease caused by these two viruses are similar.

Most people infected show no symptoms. In mild cases, there may be fever, headache and vomiting. In more serious cases, people may experience neck stiffness, disorientation, drowsiness and seizures. Serious illness can have lifelong neurological complications and, in some cases, the disease is life-threatening.

There’s no specific treatment for either disease, though there is a vaccine for Japanese encephalitis which may be appropriate for certain people at high risk (more on that later).

A close-up photo of a mosquito in a laboratory. — Australian mosquitoes, such as *Culex annulirostris*, can play an important role in the spread of viruses.
A/Prof Cameron Webb/NSW Health Pathology

The influence of weather patterns

Murray Valley encephalitis virus has been known in Australia for many decades. After a significant outbreak across the Murray Darling Basin region in 1974, activity has generally been limited to northern Australia.

Outbreaks in southeastern Australia often accompany flooding brought on by La Niña weather patterns. Floods provide ideal conditions for mosquitoes, as well as the waterbirds that harbour the virus.

Japanese encephalitis virus is closely related to Murray Valley encephalitis virus. Mosquitoes pick up both viruses by biting waterbirds. But Japanese encephalitis virus has only recently become widespread in Australia.

After flooding rains brought on by La Niña in 2020, conditions that persisted for three years, Murray Valley encephalitis virus returned and Japanese encephalitis virus arrived for the first time.

Japanese encephalitis virus was initially discovered in southeastern Australia during the summer of 2021–22, and the boom in mosquito and waterbird populations that followed flooding at the time contributed to its spread.

There have been around 80 cases of disease caused by these two viruses combined over the past four years. This includes seven deaths due to Japanese encephalitis across Queensland, NSW, South Australia and Victoria.

Additional deaths have been reported due to Murray Valley encephalitis in recent years – two each in Western Australia and the Northern Territory.

In the summer of 2023–24, hot and dry summer conditions returned, mosquito numbers declined, and the number of cases of disease caused by Japanese encephalitis virus and Murray Valley encephalitis dropped.

Now both viruses appear to be back. So what’s going on?

What’s different this summer?

This summer, Japanese encephalitis virus has been detected in mosquitoes and feral pigs in NSW. The virus has also been detected in environmental surveillance in northern Victoria, and we know at least one person has been affected there.

Meanwhile, Murray Valley encephalitis virus has been detected in sentinel chicken flocks – which health authorities use to test for increased mosquito-borne disease risk – in NSW and in the Kimberley region of Western Australia.

Chickens can play an important role in helping warn of an increased risk of mosquito-borne disease.

It’s unusual to see activity of these viruses when conditions are relatively dry and mosquito numbers relatively low.

Some regions of Australia may have experienced flooding, but for many regions of the country, conditions have been hot and dry. This is bad news for mosquitoes.

There is no evidence that mosquito numbers are booming like they did back when La Niña brought floods to the Murray-Darling Basin.

There also isn’t any evidence of more waterbird activity. In fact, numbers have declined in recent years.

So why are Japanese encephalitis virus and Murray Valley encephalitis virus active again when the conditions appear to be less favourable?

Despite predictions of a rare mid-summer return of La Niña, there’s still speculation about what this means for temperature and rainfall. We may not see flooding, but there is still likely to be enough water around for mosquitoes.

For Japanese encephalitis virus, it may be that feral pigs are playing a more important role in its spread. We know numbers are on the rise and with drier conditions, perhaps mosquitoes and feral pigs, and other wildlife, are gathering together where they can find bodies of water.

After its unexpected arrival, it now seems Japanese encephalitis virus is here to stay. But how this virus interacts with local mosquitoes and wildlife, under the influence of increasing unpredictable climatic conditions, requires more research.

How can you reduce your risk this summer?

The public health alerts in Victoria and NSW focus especially on specific regions in northern Victoria and around Griffith and Narromine in NSW where the virus has been detected.

If you live or work in areas at risk of Japanese encephalitis, seek advice from your local health authority to see if you are eligible for vaccination. Residents in specified local government areas in affected regions in both states are currently eligible for a free vaccine.

But there is no vaccine available for Murray Valley encephalitis or Ross River viruses.

Wherever you live, mosquito bite prevention is key. Apply insect repellent when outdoors, especially during dawn and dusk when mosquitoes are most active or at any time of the day if you’re in bushland or wetland areas where numbers of mosquitoes may be high.

You can get better protection by also covering up with a long-sleeved shirt, long pants, and covered shoes.

Cameron Webb, Clinical Associate Professor and Principal Hospital Scientist, University of Sydney and NSW Health Pathology.

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Mosquito-borne diseases are on the rise. Here’s how collecting mozzies in your backyard can help science

January 10, 2025 by Liz Farquhar Leave a Comment

Warm weather is here and mosquitoes are on the rise in Australia. Unseasonably large swarms are causing problems in some parts of Sydney.

Health authorities track mosquitoes across the country to provide an early warning of mosquito-borne disease risk, but they can’t be everywhere. Citizen scientists can step in to help – with excellent success.

Our latest research explored the value of an Australian program called Mozzie Monitors, not just as a surveillance tool but an educational one too.

Citizen scientists are everywhere

Citizen science – when non-scientists help scientists collect data – has become a powerful tool in environmental research. With appropriate training, the community can contribute to scientific discoveries alongside professional scientists.

By combining citizen science data with professionally collected data, everyone benefits. With a greater quantity of reliable data, authorities are more informed when making decisions about environmental protections, wildlife conservation and human health.

People are often drawn to “charismatic” wildlife such as cute mammals, birds or frogs. But our project shows that helping scientists track mosquitoes can improve community understanding of these pesky insects and the public health risks they bring.

Mosquitoes and mosquito-borne disease in Australia

There are hundreds of types of mosquitoes in Australia. Only a dozen or so pose pest and public health risks – but these risks are serious.

Ross River virus infects around 5,000 people every year. The disease it causes isn’t fatal but can be debilitating. There are other viruses spread by mosquitoes that, while very rare, can be deadly.

There are limited opportunities for mosquito control. To prevent disease, raising awareness of mosquito risk and avoiding being bitten are key strategies.

To provide an early warning of elevated public health risks, most state and territory health authorities monitor mosquito and virus activity. But they can only operate so many mosquito traps each season, leading to gaps in coverage.

This is where citizen scientists come in.

Mosquito biting a finger — With hundreds of different types of mosquito in Australia, knowing what’s biting helps determine local health risks.
Cameron Webb/NSW Health Pathology

What’s the Mozzie Monitors program?

Scientists at the University of South Australia started Mozzie Monitors in 2018 to offer an innovative approach to mosquito monitoring. It collects valuable data on mosquito populations and provides participants with useful knowledge.

Participants use low-cost mosquito traps in their backyards to capture mosquitoes. They photograph the collections and send them to researchers for identification.

Citizen scientists also contribute observations through the existing online platform iNaturalist. The beauty of tapping into this platform is that it captures observations by both active participants and casual citizen scientists.

More than 200 people have participated in Mozzie Monitors to date, capturing more than 15,000 mosquitoes and uploading some 8,000 photographs online.

It’s already been shown to be a cost-effective complement to traditional mosquito monitoring programs in Australia. This approach has also been adapted overseas.

Mosquitoes in a plastic tray. — Scientists identify and count mosquito species to assist local health authorities.
Cameron Webb/NSW Health Pathology

Monitoring mosquitoes and picking up knowledge

We compared data collection by Mozzie Monitors participants in South Australia and Western Australia. There were differences in both the types of mosquitoes collected and their numbers.

While the Australian backyard mosquito (Aedes notoscriptus) and the southern house mosquito (Culex quinquefasciatus) were the most common across both areas, the citizen scientist data also provided insights into the coastal wetland mosquitoes unique to each area.

Mosquito collections were just the start.

We surveyed 26 people about their experience participating in Mozzie Monitors. Their mosquito identification and technical skills significantly improved while taking part in the program. They successfully learned to identify the most common mosquitoes in their backyards while improving their photography skills.

For scientists who received the data, better photos resulted in better specimen identification.

Perhaps most importantly, the study highlighted behavioural changes in citizen scientists that will have public health benefits for themselves, their families and neighbours.

person taking photo of insect with smartphone — Citizen scientists only need a smartphone to collect valuable information on the local environment.
Larissa Braz Sousa (University of Sydney)

Before their participation in Mozzie Monitors, the citizen scientists we surveyed stopped mosquito bites around their properties only by using insect screens. After participating in the program, they were more likely to check their backyards for mosquitoes and eliminate their source (for example, by tipping out water-filled containers).

This change in attitude highlights the program’s power to translate knowledge and skills into actions that can protect participants, and their households, from the health risks of mosquitoes.

Participants had a range of motivations for joining the program. Many were driven by concerns about nuisance or mosquito-borne diseases, while others were motivated by a general interest in science and volunteering.

They appreciated the program’s ease of participation and the opportunity to contribute to valuable research. They also reported improved understanding of mosquito species.

Seen mosquitoes around your home?

Mozzie Monitors shows how citizen science can empower communities to identify common local mosquito species, understand their impact on human health, and take proactive measures to avoid mosquito-borne disease.

By combining knowledge, technical skills and action, the program helps safeguard local communities from the health threats of mosquitoes.

If you’re noticing more mosquitoes around your home, consider sharing photos with scientists by uploading them to iNaturalist. This database makes scientific observations freely available to all. Identifying mosquito species helps us better understand disease risks and nuisance biting, enabling more effective prevention and control efforts.

Mosquitoes may not be the most charismatic of Australia’s wildlife. But by participating in citizen science projects such as Mozzie Monitors, learning about these pests may be the secret to keeping your family safe from their bites this summer.

Cameron Webb, Clinical Associate Professor and Principal Hospital Scientist, University of Sydney; Craig Williams, Professor and Dean of Programs (STEM), University of South Australia; Katherine Baldock, Dean, University of South Australia; Larissa Braz Sousa, Research Fellow at the University of Sydney, University of Sydney, and Stephen Robert Fricker, Manager of Vector Surveillance, University of South Australia

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Harvesting medical-grade maggots for old school wound care

January 6, 2025 by Liz Farquhar Leave a Comment

Maggot therapy has been around for centuries and is still used in our hospitals today to treat particularly troublesome wounds. But where do the maggots come from?

Deep in the basement of Westmead Hospital is a door with a warning sign which reads: Insectary- ensure air curtain is ON while room is in use.

Inside are a series of mesh cages filled with flies and they are carefully looked after by a small team of dedicated scientists.

It’s where NSW Health Pathology’s Medical Entomology team harvests the maggots that are used by hospitals across Australia, and even sent to health services overseas, to treat patients whose wounds are not responding to more conventional medical treatments.

They are the sole suppliers of maggots for medical purposes in Australia.

A man sits at a laboratory fume hood working on a small dish filled with maggots. — Don’t lose count. John Haniotis preparing the vials with the clean fly larvae, which are used in Australian hospitals and have been sent as far away as Japan and Madagascar.

How does maggot therapy work?

Maggot debridement therapy (MDT) involves placing sterile fly larvae (live maggots) on open wounds to assist in the removal of dead and infected tissue.

The maggots are the immature stage of the fly species Lucilia sericata, a common blowfly. It is the main species of fly utilised worldwide for MDT, as the fly’s young have the unique feeding behaviour of devouring devitalised tissue, whilst leaving the surrounding healthy tissue intact. (1)

MDT was once a routine procedure in hospitals throughout Europe, the US and Canada during the 1930s and early 1940s. The medical journals from this era list osteomyelitis, abscesses, carbuncles, burns, cellulitis, gangrene, and leg ulcers as having been successfully treated. But with the advent of antibiotics and the development of new surgical techniques MDT slipped into obscurity.

However, interest was revived when medical trials in the 1980s concluded the therapy still had many benefits to offer patients in the treatment of chronic wounds. Not only do the maggots remove necrotic tissue in a precise manner, but they also assist in controlling infection and promote the regeneration of healthy tissue and healing.

How do we harvest maggots?

The insectary at the Institute of Clinical Pathology and Medical Research at Westmead Hospital’s was established by Merilyn Geary around the year 2000 to provide a disinfected source of maggots for medical purposes.

A gloved hand holding a glass dish containing a piece of liver covered in small white eggs. — Liver is placed inside a cage of flies on which they lay massive numbers of white eggs.

NSW Health Pathology’s Director of Medical Entomology Stephen Doggett (pictured top) says ensuring the maggots are clean is a vital first step in the process.

“Once the flies lay their eggs, we wash the eggs with an antiseptic solution to remove any bacteria,” he said.

“The eggs are then collected and put into a sterile media to grow – we use egg yolk and that’s what they grow in.

“After they hatch there are three larval stages, and we breed them until they hit the second stage. They are then collected and packed into vials, after checks that they are free of bacteria, to send off to where they are needed,” Stephen explained.

Each vial contains about 100 maggots, and they are placed directly onto the patient’s wound.

The wound is then bandaged with special material to keep the maggots in place, while also allowing airflow to the wound. The maggots are left on the wound for two days and after they do their work, they are removed by nursing staff and disposed of.

A white bucket with a small amount of wood shavings in the base. — Part of the process of breeding flies; in the centre well, eggs are placed with meat for the hatching larvae to feed on. The larvae then pupate in the wood shavings, prior to emerging as adult flies.

Is it making a comeback?

Stephen says depending on the size, depth and complexity of the wound, a patient may need more than one application of maggots.

“In most cases simple wounds would only need one application, but we did have a case a few years back when a patient required 45 applications before his wound was under control.

“The treatment was ultimately successful and avoided what would otherwise have almost certainly been the amputation of his foot.”

He thinks it’s a treatment that has found its time again.

“It is taking time to find acceptance in the medical community, but once a patient receives the treatment, they say they would have it again.

“We have a situation where antibiotic resistance is growing. Maggot therapy is cheap, and it works.”

1. Merilyn J Geary, The Broad Street Pump, April 2010

The contribution of NSW Health Pathology to medical research: the first 10 years

January 5, 2025 by Liz Farquhar Leave a Comment

Leading researcher at NSW Health Pathology Prof Emmanuel Favaloro has published an article in the Australian Journal of Medical Science outlining the substantial contribution of the organisation to medical research since its establishment in 2012.

Medical research is integral to improving diagnosis and treatment of disease and as the largest publicly funded pathology organisation in Australia, NSW Health Pathology also undertakes significant research related activities.

Until now there has been no formal broad analysis of these research activities since the statewide organisation was created in 2012.

NSW Health Pathology’s Lead Scientist in haemostasis research, located at the Department of Haematology at the Institute of Clinical Pathology and Medical Research, Prof Emmanuel Favaloro, who has just been named in the 2025 Top 250 Researchers list for The Australian Magazine for Haematology, has recently conducted a detailed analysis of medical research output from researchers citing an affiliation with NSW Health Pathology.

His analysis identified a total of 2345 publications citing at least one affiliation as NSW Health Pathology.

He found the yearly publication rate of NSW Health Pathology researchers has grown exponentially since 2012, when there were two publications cited, followed by four and another nine publications respectively in the next two years.

In the four years from 2020 to 2023, NSWHP affiliated researchers published more than 400 PubMed listed papers each year.

“The publications appear in a wide range of journals, the most popular was perhaps unsurprisingly, ‘Pathology’ (link: https://www.pathologyjournal.rcpa.edu.au/ ),” Prof Favaloro said.

Forty-six NSWHP affiliated researchers published in excess of 20 papers each year over the 10 year timeframe, with the lead author publishing nearly 250 publications over this time.

A chart showing a rapid increase in publications over time. — Publications ascribed to authors citing a NSW Health Pathology affiliation and extracted from the PubMed database as published over the years 2012 to 2023 inclusive.

The research also looked at the geographic worksite location of authors and categorised the publications and authors by Clinical Stream or Service.

NSWHP researchers based at Westmead Hospital, Prince of Wales Hospital, Royal Prince Alfred, Royal North Shore Hospital and Newcastle’s John Hunter Hospital were the most prolific publishers of research papers.

Ten ‘service streams’ contributed authorships in excess of 60 each over the data capture period, with Microbiology, Anatomical Pathology and Haematology the leading research areas.

A column graph showing the highest publications were in Microbiology, followed by Anatomical Pathology, Haematology and Genomics. — Publications/authors according to Clinical Stream or other NSW Health Pathology Service (where >60 publications/ authors listed).

“To my knowledge, this is the most comprehensive analysis of publications arising from researchers citing a NSWHP affiliation,” Prof Favaloro said.

“It highlights a broad spread of publications arising from several locations and service streams of NSWHP,” Prof Favaloro said.

“I’m proud to work at an organisation making such a significant contribution to medical research and the furthering of knowledge in these diverse fields of study.”

A man standing at a podium giving a speech. — Leading Haematology researcher Prof Emmanuel Favaloro.

Jobs taskforce hears inspirational stories from NSW Health Pathology

December 23, 2024 by Liz Farquhar Leave a Comment

NSW Health Pathology’s People and Culture leaders attended a recent jobs and skills event in Sydney, sharing some of our employment success stories with the Hon Murray Watt, Federal Minister for Employment and Workplace Relations.

Our People and Culture Acting Director Jessica Lee presented at the Joint Sydney Wide Taskforce event in December 2024.

“It was such an honour to be able to share with the Minister for Employment and Workplace Relations Murray Watt some of the fantastic success stories we have had here at NSW Health Pathology,” Jessica said.

Jessica spoke about the inspiring story of Asraa Al Saadi who she met at a Taskforce event and who went on to secure her dream job with NSW Health Pathology.

“Asraa’s experience is a great example of how job opportunities can transform lives, and as Australia’a largest public pathology provider we know our staff make a positive difference every day in the lives of the communities they serve.”

A woman stands at a podium giving a speech, with a photo of a health worker on a screen in the background. — Jessica Lee giving a presentation at the Joint Sydney Wide Taskforce event in December 2024.

Acting Chief Executive, Dr Deanna Paulin, and Jessica were fortunate to hear many inspiring stories from participants at the event who have overcome numerous obstacles to secure employment, what it meant for them and their families in programs run by the Taskforce.

“The Joint Sydney Wide Taskforce provides vital job opportunities to diverse communities, and we were excited to hear the Minister confirm funding for the Local Jobs program would be extended for an additional 2 years!” Deanna said.

“We are proud to be part of events like these and excited to see how they can help our workforce better reflect the communities we serve every day.”