Groundwater central to the country’s future

Source: ESR

Groundwater is central to the future of the country’s freshwater and waterways, says ESR’s chief scientist.

Brett Cowan says the country’s top earners such as tourism, dairy and marine industries are all underpinned by and dependent on water.                

“The cost of not making groundwater a priority is enormous; polluted and dead waterways,” he says.

Groundwater is the enormous collection of water in the pores or cracks in sands, gravel and rocks which flows into our springs, rivers and lakes and is essential for the environment, communities and agricultural productivity.

“For all that, scientists still know relatively little about groundwater, particularly about how it is being affected by increasing demand, pollution and climate change. It’s vital that we build up our scientific knowledge to protect groundwater now and for future generations.”

 The leader of ESR’s groundwater science team, Murray Close, says as the government embarks on huge water reforms, it is critical that groundwater takes its central place, particularly in the face of new challenges such as climate change and emerging organic contaminants such as pesticides.

The health of groundwater, which 40 per cent of New Zealanders rely on for drinking water, is crucial to the quality of surface water.

He and Dr Cowan were commenting following a conference in Christchurch, which, for the first time, brought together about 80 people from all around the country to tackle the management and research of groundwater.

Murray Close says generally groundwater is “out of sight, out of mind”, and only noticed when something goes wrong, such as the widespread illness linked to a contaminated bore two years ago in Havelock North which affected 5,000 New Zealanders.

He says today’s conference was valuable because it is helping to build a broader framework of people working on groundwater, with hopefully a national agenda for what is an overlooked, but valuable resource.

“There needs to be a coherent voice on groundwater because it is so important to the health and economy of the country.”

 “There are 200 major aquifers in the country – we only have geological models for 30, so there’s a lot more we need to know.”

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Measles – not what you want for Easter

Source: ESR



 So far this year there have been 67 cases of measles reported in New Zealand, with most cases linked to outbreaks in Canterbury and the Auckland Region over recent weeks.

In addition to the outbreaks in New Zealand, there have been measles outbreaks reported recently in other countries including the USA, the Philippines and parts of Europe.

In New Zealand measles outbreaks start when measles is brought into the country following international travel.  The virus then spreads to others in the community because our vaccination rates are not high enough to prevent disease spread.

ESR, which tracks all notifiable diseases on behalf of the Ministry of Health, says that with people travelling around the country and around the world over Easter and the school holidays there is an increased risk of cases spreading further around the country and of further measles cases being imported.

ESR Group Leader, Intelligence, Dr Lisa Oakley says people should be mindful of the risks of measles.

“They should also think about the importance of immunisation and of the possibility that they could be exposed to measles, especially if they are travelling, attending events, holiday programmes, camps, or have friends and family travelling to visit them,” Dr Oakley says.  

Measles is a serious and highly infectious disease and immunisation is the best protection to stop the spread of getting measles. For the best protection, people need to have two MMR (measles, mumps, rubella) vaccinations. The MMR is available from your family practice and you should ask if you are eligible for a free vaccination.

Anyone who suspects they may have measles should avoid contact with other people, especially those who aren’t fully immunised, and should phone their GP or call Healthline on 0800 611 116 for advice. It is important to call first because measles is highly infectious, and people with measles can infect others in the waiting room.

Further information including current case numbers is available here: (external link)


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ESR says groundwater critical to large number of drinking supplies

Source: ESR


ESR leading water scientist Murray Close says the country’s groundwater needs urgent attention.

An inaugural conference on groundwater is being held in Christchurch tomorrow (Friday April 5 – see below for details), in a bid to improve understanding and information about a resource which 40 per cent of people in New Zealand rely on for their drinking water supplies.

ESR leading water scientist Murray Close says the country’s groundwater needs urgent attention.

Murray Close says the health of groundwater is crucial to the quality of surface water.

 Groundwater is made up of water in the pores or cracks in sands, gravel and rocks and is essential for the environment, communities and agricultural productivity.

 “While our rivers and the state of their health are rightly regarded as important taonga, little attention is given to the groundwater that sustains the flows in most of our rivers and streams.”

 He says most of the time groundwater is out of sight, out of mind.

 “When we do notice it, it’s when something goes wrong, such as the widespread illness linked to a contaminated bore that took place two years ago in Havelock North,” he says.

 With more than five thousand people affected, the contamination of water supplies in Havelock North was regarded as one of the worst public health outbreaks in the western world.

 “For all that, scientists still know relatively little about groundwater, particularly about how it might be affected by increasing demand, pollution and climate change. It’s vital that we build up our scientific knowledge to protect groundwater now and for future generations.”

 The government has introduced two major water initiatives, the Three Waters Review and the Essential Freshwater programme.

 A report on the Three Waters Review released late last year, said in many parts of the country, communities could not be certain that drinking water is safe.

 It also said the events that led to the Havelock North contamination, have demonstrated that the existing system does not adequately safeguard against the

risk of catastrophic contamination incidences, or drive improving compliance with the drinking water standards.

 “The Inquiry into Havelock North Drinking Water observed there is little understanding amongst the New Zealand public about the large numbers of people who become ill every year by consuming unsafe drinking water,” the report said.

 Murray Close says as the government embarks on huge water reforms, it is critical that groundwater is not forgotten, particularly in the face of new challenges such as climate change and emerging organic contaminants.

 Conference information

 GroundsWell 2019: Symposium on Groundwater Management and Research

 WHEN: Friday, April 5, 2019 from 9:30am – 4:30pm

 WHERE:  University of Canterbury Students’ Association’s Event Centre, 90 Illam Road, Christchurch 

 WHO: Keynote speakers include Ken Taylor, Director, Our Land and Water National Science Challenge, Tina Porou, Poipoi Limited, Tim Davie, Chief Scientist, Environment Canterbury, Graham Sevicke-Jones, Manaaki Whenua Landcare Research

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Almost 50 cases of measles have been confirmed this year.

Source: ESR

Almost 50 cases of measles have been confirmed this year, with almost two thirds of the cases linked to the current outbreak in Canterbury.

ESR, the science agency which tracks all notifiable diseases on behalf of the Ministry of Health, says there have been 49 cases to date this year, with outbreaks also in Waikato and the Bay of Plenty. 

That compares with seven for the same time last year.

Two years ago, New Zealand won international praise for successfully eliminating endemic measles – meaning the virus was no long circulating in New Zealand.

Prior to that, for three years, the only reported measles cases were imported, or spread from someone bringing the virus into the country.

ESR public health physician Jill Sherwood says outbreaks only occur now when someone with the disease arrives here, and it starts to spread.  

“Once here, it can then be easily transmitted if there is a high enough proportion of unimmunised people,” she says.

“That’s why health authorities urge vigilance and stress the need to continue to improve vaccination rates.”

Dr Sherwood says there is always a risk importation of the disease will lead to outbreaks and a return to a situation where measles could become endemic again.

After the introduction of the measles vaccine in 1969, measles continued to occur every year until 1980, with a pattern of “low” years (an average of approximately 100 hospitalisations per year) alternating with “high” or “epidemic” years (an average of 300 hospitalisations per year).

That was because vaccination rates were not high enough to prevent outbreaks.

 Increased uptake of the measles vaccine, which is thought to have reached 70 per cent or more by 1980, resulted in this epidemic cycle becoming more accentuated, with fewer cases and longer periods between epidemics.

Dr Sherwood says measles virtually disappeared between the epidemic years which began to occur less frequently – 1984/85, 1991 and 1997. There were 400 hospitalisations in the 1984/85 outbreak, and a total of 943 hospitalisations in the 1991 and 1997 epidemics, with seven deaths in 1991.  No deaths occurred in 1997.

She says as vaccination coverage increased, outbreaks have been generally confined to a particular region and have been of shorter duration that the epidemics of the past.

“An outbreak in 2009 was probably stopped and an epidemic prevented by the enhanced immunisation programme that was implemented.”

Dr Sherwood says large-scale measles epidemics occur when the proportion of the population who are non-immune increases, usually because the immunisation coverage is low.

“It’s been estimated that to prevent recurrent outbreaks of measles, 95 per cent of the population must be immune,” she says.

 Measles is considered to be the most common vaccine-preventable cause of death among children throughout the world.

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The hot and cold of award-winning software STRmix™

Source: ESR

One of the key instigators of STRmix™, ESR principal scientist Dr John Buckleton, says an “aligning of the planets” was key to producing the software that has dramatically increased the reliability of DNA evidence in court.

STRmix™, ESR’s innovative forensic software, has taken out New Zealand’s top science award, The Prime Minister’s Science Prize.

Dr Buckleton says before STRmix™, complex mixtures of DNA profiles – any mixture of two or more people – were unusable.

“You could tell the evidence was there, but there was no manner to express that in court in a sustainable way,” he says.

 “What STRmix™ does is draw an evidential inference from a more complex mixture, whereas previously, there were just not the methods to draw any inference from such evidence.

“STRmix™ can take a person of interest, compare him with a profile from a crime scene and produce an inference whether that person is included or excluded. 

 “We are told we’ve taken usable DNA evidence in the US courts from 40 per cent to 70 per cent so we’re not just exonerating more false donors and convicting more true donors, we’re advancing the cause of justice in the US, and more broadly.”

 Dr Buckleton says STRmix™ uses “big computing” and stock standard maths.

 “What it does is trial a whole lot of solutions –  it’s like a game of hot and cold.  That’s how we teach it and the analogy works really well.”

 He describes being awarded the Prime Minister’s Science Prize as a “great honour”.

 “It is the high point of my career and I am very grateful that we have the whole team recognised – they are a great team and it is fantastic working with them.”

 Dr Buckleton is quick to acknowledge the work of his colleagues, fellow ESR scientist Jo Bright and Duncan Taylor in South Australia. 

 “‘Without these two fantastic co-workers nothing was going to happen.  Their work ethic, their creativity – with Jo and Duncan, it couldn’t fail. Without them, it couldn’t succeed. The planets just aligned.”

  “As well as great colleagues, there was a bit of the number eight wire mentality, a bit of support from management and the government – it all came from that”.

Dr Buckleton, who has won many awards, including being recognised in last year’s Science New Zealand Awards, says he lives, eats and breathes forensics. “It’s my whole life. I wake up and do it, and I dream about it at night. “

 “It’s just fantastic – the problem solving aspects, the camaraderie of working on important issues. 

 “And if I go to my grave thinking, I’ve made some contribution to justice – that would be good.”


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“An urgent challenge” led to development of STRmix™

Source: ESR

STRmix™, innovative forensic software, this year’s winner of the country’s top science award, was “born out of an urgent challenge”.

 One of the key scientists responsible for the ESR software, Dr Jo-Anne Bright, says the closure of a forensic laboratory in Australia sparked the search for a solution that became STRmix™. 

“The lab closed down after using internet software that proved unreliable.  ESR was challenged to help them re-open and we saw that as an opportunity to start investigating software solutions to DNA profile interpretation as well as an opportunity to improve lab testing,” Dr Bright says.

 STRmix™, which has just been named as the recipient of the Prime Minister’s Science Prize, is now the number one software for the interpretation of DNA profiles.

 A survey of laboratories estimated that 100,000 cases worldwide have been interpreted using the product.

 Dr Bright says while there is competition in the field of forensic analysis, the difference with STRmix™, is that it is fully transparent.

 “All the algorithms supporting the software have been published and that transparency is really important for the criminal justice system.

 “It has also helped the uptake –  law enforcement agencies can see that it’s published and accepted in the science community, and, as well, we can teach the science to those agencies wanting to use it.”

 She believes the product benefits from the reputation of her ESR colleague, Dr John Buckleton – seen as one of the foremost forensic scientists in the world –  and she also points to the amount of published research on the software.

 “We publish a lot of papers in this field; we are actively developing improvements to the software, always trying to find more ways we can get more value out of DNA profiles.”  

 Dr Bright says her team is honoured to be recognised by the award. . 

 “Really excited – there is a real sense of pride that we have created something that so many labs all around the world are using every day in their crime sample interpretation.

 “We’re this small science team at the bottom of the world that’s become world leaders in forensic interpretation.”

 The $500,000 prize money will be used to further develop the science behind STRmix™.

 “We’ll look at ways we can use new technology to get more value out of DNA profiles, such as looking at artificial intelligence, or machine learning, to see if we can dynamically read a profile and that will lead to quicker turnaround times and improved work flows in a laboratory.”

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ESR scientists keeping ahead of the game

Source: ESR

The key to the success of STRmix™, the ESR forensic software that has won the Prime Minister’s Science Prize, is the quality of the team that developed it and the quality of the research, says ESR’s STRmix™ Manager, Bjorn Sutherland.

 He says internationally, STRmix™ is acknowledged as world leading, with law enforcement agencies using the software to solve problems, really understanding they are working with a world leading organisation when they are working with ESR.

 “And we want to be the leading software for the interpretation of complex DNA profiles worldwide,” Mr Sutherland says.

 “We’ve certainly made very good steps in North America and we’re starting to move into the Middle East, Asia, the UK and Europe. There is a lot of interest from parts of the world that we haven’t historically worked with.”

 STRmix™, which has been used in casework since 2012, could not be seen just as a software in isolation as it required a very extensive amount of training as well as support and mentoring through the process of validation.

 “That’s what a forensic lab needs to do to prove the software does what it says it does before they start using it in casework.

 “We had to create a model that took not just really fantastic innovative software, underpinned by sensational science research, but one that also allowed us to provide the training and support to ensure labs could succeed with STRmix™.”

 Mr Sutherland believes ESR’s very agile and hardworking scientific team can stay at the forefront with their world leading scientific research.

“They are innovators. New Zealanders are innovators. We like to implement technologies early.  We have that in the team and we will continue to do that world leading research and implement that in STRmix™. That is the key to our success.”

He says what ESR has done with STRmix™ over the past eight years has been somewhat under the radar in New Zealand because it has been so internationally focused.

“What this prize means to us is recognition at home of the success we have had overseas and the success we will continue to have.”

0800 ESR MEDIA (0800 377 633) or

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STRmix™ a “powerful tool”, making the complicated simple

Source: ESR

Winner of the Prime Minister’s Science Prize, the DNA analysis software, “STRmix™, has been used internationally to interpret DNA evidence in more than 100,000 cases since 2012.

“STRmix™ is a very powerful tool,” says Dr David Foran from the Forensic Biology Laboratory at Michigan State University.

“It takes something that is potentially very complicated, a mixture of several people’s DNAs, and simplifies it for the DNA analyst from the crime lab and it also simplifies it for the jury and judge,” he says.

STRmix™ has been used successfully in numerous US court cases, including 28 successful admissibility hearings. It is used by more than 40 US laboratories and is also in various stages of installation, validation, and training in a further 70.

It is currently being used in all nine state and territory labs in Australia and New Zealand, as well as 11 forensic labs in England, Scotland, Ireland, Finland, Dubai, and Canada.

It has been successfully used to get convictions in murder trials, produce breakthroughs in sexual assault and rape cases and help to resolve cold cases.

To read more, follow these links: -new-dna-analysis-software#stream/0 (external link) (external link) (external link) (external link) (external link) (external link)

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ESR experience and expertise behind win of top science prize

Source: ESR

Winning the country’s top science award is a feather in the cap for ESR scientists and comes only one year after the Crown Research Institute celebrated its 25th anniversary.

ESR was formed in 1992 after the reorganisation of the behemoth Department of Scientific and Industrial Research (DSIR) and the setting up of individual Crown Research Institutes.

ESR specialises in sciences relating to people and communities; water and the environment, public health, food safety and forensic science.

The organisation’s expertise in forensic DNA analysis led to the development of STRmix™, world leading software, which has revolutionised the interpretation of complex criminal evidence, and which has just been awarded The Prime Minister’s Science Prize.

ESR chief executive Keith McLea says the award shows ESR is already at the cutting edge of DNA research, and STRmix™ reinforces that New Zealand is right out in front of the world in forensic science.

The software was developed as part of ESR’s drive to increase the effectiveness of its forensic science services to help prevent and solve crime,

ESR is also charged with safeguarding the health of New Zealanders through improvements in the management of biosecurity and threats to public health.

That includes combatting influenza, the nationwide surveillance of infectious diseases, and fighting resistance to antibiotics.

Its scientists also work on researching and improving the safety of freshwater and ground water resources for human use as well as the use of bio-waste.

Some of the research ESR environmental scientists are involved in includes studying how native plant species can help clean up waterways, the effectiveness of denitrification walls in removing nitrates from ground water and the impact of climate change on people’s health.

ESR is also responsible for enhancing the protection of New Zealand’s food-based economy through the management of food safety risks associated with trade goods,

While most of ESR’s business is in service delivery, its research helps it to effectively respond to events of national significance and increases its ability to keep New Zealanders healthy and safe.

The 2016 water contamination crisis in Havelock North showed the breadth of ESR’s expertise and response capability as it tackled what was a major health issue, with 5,500 of Havelock North’s 14,000 residents becoming ill with campylobacteriosis. 

Dr McLea says over the next five years, ESR needs to invest in renewing its science and infrastructure.

“There are rapid changes occurring in science and technology in our focus areas and we need to be prepared for these,” he says.

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ESR hunting down new psychoactive substances

Source: ESR

ESR’s tracking of illicit drugs coming into the country is continuing to turn up a large and varied number of new psychoactive substances.                         

Research led by ESR senior scientist Cameron Johnson into the detection of illegal drugs at the New Zealand border has just been published in the Australian Journal of Forensic Science.

Scientists detected more than 130 such new substances at ESR’s border screening laboratory between 2014 and 2018. In a collaboration with the University of Auckland, analysts were able to use expensive state-of-the-art spectroscopy to assist in identifying these new drugs.

Mr Johnson says more than 730 new psychoactive substances were reported to the United Nations Office on Drugs and Crime between 2009 and 2016, a rate of one a week.

In New Zealand, scientists detected more than 130 such substances at ESR’s border screening laboratory between 2014 and 2018. In a collaboration with the University of Auckland, analysts were able to use expensive state-of-the-art spectroscopy to assist in identifying half of these new drugs.

With the emergence of “party pills” or “legal highs” in the past decade, the Institute of Environmental Health and Science (ESR) says illicit drug manufactures are increasingly “tweaking” designer drugs in a bid to help their products avoid detection when entering the country.

ESR says over the last 10 years, there has been an explosion of new psychoactive substances, or designer drugs, into the drug market.

Cameron Johnson is also leading a project looking to link up all the various parts of ESR’s extensive drug testing capabilities.

 “We have our border screening lab which looks at what’s coming across the border through customs’ seizures, the seizures by the police that are analysed by the ESR drug chemistry team, we see the domestic manufacture of drugs with our clan labs, and we’ve got drug use in the population through our toxicology analysis.

“Although the substances that we see at the border lab have been seized by NZ Customs, it is likely that some importation of that substance may eventually make its way into New Zealand to be used as a psychoactive drug.

“We want all the drug testing capabilities within ESR to be able to detect that substance that was first seen at the border, so the early identification of new substances in the project is crucial to allow that to happen.”

Armed with this new information, ESR laboratories can ensure they have the capability to detect the substances in the analytical tests that are carried out.

“New designer drugs change very rapidly there are lots of different types and along with that comes the challenge in analysing them. They are also so new that they are largely untested so the risk they pose to users is very high,” Mr Johnson says.

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