Queensland Health
Health Support Queensland

Forensic and Scientific Services
Annual research report 2016–17

Annual research report
Published by the State of Queensland (Queensland Health), January 2019
This document is licensed under a Creative Commons Attribution 3.0 Australia licence. To view a copy of this licence, visit creativecommons.org/licenses/by/3.0/au © State of Queensland (Queensland Health) 2018. You are free to copy, communicate and adapt the work, as long as you attribute the State of Queensland (Queensland Health).
For more information contact:
Forensic and Scientific Services, 
Research and Development Unit, 
Department of Health,
PO Box 594, Archerfield QLD 4108
Email FSS_Research@health.qld.gov.au
Phone +61 7 3096 2625
An electronic version of this document is available at www.insert.website.here.com
Disclaimer:
The content presented in this publication is distributed by the Queensland Government as an information source only. The State of Queensland makes no statements, representations or warranties about the accuracy, completeness or reliability of any information contained in this publication. The State of Queensland disclaims all responsibility and all liability (including without limitation for liability in negligence) for all expenses, losses, damages and costs you might incur as a result of the information being inaccurate or incomplete in any way, and for any reason reliance was placed on such information.
Table of contents
Foreword
Research and Development Unit
Collaborate with us
Our laboratories have a strong history of collaborative research and partnerships.
Quick facts for 2017
Committee reports
Human Research Ethics Committee
Animal Ethics Committee
Scientific Review Panel
Highlights
Welcome to Forensic and Scientific Services
We are Australia’s most comprehensive forensic and public and environmental health facility. We provide specialist scientific and medical analysis and independent expert advice to private and public sector clients locally, nationally and internationally.
1.0 Public and Environmental Health
We provide analysis and advice supporting the measurement and monitoring of biological, radiological, and chemical markers to help protect the health of the community. We offer a unique capability determining contamination sources, causative agent and relatedness cases, for Queensland Government and private sector clients.
1.1 Inorganic Chemistry
Our staff are experts in analysing metals and elements in environmental samples such as water, soil, sediment, food, blood, urine and other biological tissues.
Research projects
Publications
Lectures and presentations
1.2 Organic Chemistry
State-of-the-art instrumentation allows us to provide an extensive range of testing, research and investigation for environmental and food samples.
Research projects
Publications
Lectures and presentations
1.3 Public Health Microbiology
The Public Health Microbiology team provides expert scientific knowledge and laboratory investigation for notifiable bacterial pathogens and bacterially/toxin-mediated outbreaks.
Research projects
Publications
Lectures and presentations
1.4 Public Health Virology
We perform surveillance testing of viruses and mosquitoes for state and federal authorities allowing for a targeted public health response, and have the capacity to respond to any public health crisis involving emerging or re-emerging viruses and rickettsiae.
Research projects
Publications
Lectures and presentations
1.5 Radiation and Nuclear Science
Our service focus is on the measurement, impact, use and safety of radiation sources, including naturally-occurring radioactive material (NORM), medical and industrial radiation devices and radioactive waste.
Research projects
Publications
Lectures and presentations
2.0 Police Services
We provide forensic DNA analysis and forensic chemistry services for the Queensland Police Service and the Coroners Court of Queensland and private clients.
2.1 Forensic Chemistry
The Forensic Chemistry team provide expert scientific knowledge, laboratory examinations, testing and reporting on items submitted from across the state in relation to alleged offences.
Research projects
Publications
Lectures and presentations
2.2 Forensic DNA Analysis
The Forensic DNA Analysis team provide expert scientific knowledge, laboratory examinations, testing and electronic reporting on items submitted from across the state in relation to alleged offences.
Research projects
Lectures and presentations
3.0 Coronial Services
We provide coronial services, including forensic pathology and forensic toxicology. Our dedicated professionals work closely with the State Coroner, other coroners, coronial staff and police officers, including homicide detectives, police scientists, scenes of crime officers and investigators.
3.1 Forensic Toxicology
Forensic toxicology involves the analysis, detection, identification, measurement and interpretation of alcohol, drugs, poisons and other substances in human samples including blood, urine, saliva and other fluids and tissues.
Research projects
Publications
Lectures and presentations
3.2 Forensic Pathology
We provide specialised forensic services and expert advice to the Queensland Police Service (QPS) and the Coroner’s Court of Queensland.
Research projects
Publications
Lectures and presentations
3.3 Clinical Forensic Medicine
Our medical staff are utilised by the Queensland Police Service, the Office of the Director of Public Prosecutions and the Coroners Court of Queensland.
Research projects
Publications
Lectures and presentations
Collaborations
During 2016–2017 Forensic and Scientific Services has collaborated on research with the following organisations:

Foreword
Welcome to the Forensic and Scientific Services Annual research report. This publication catalogues a wide range of research activities undertaken by our staff.
Forensic and Scientific Services (FSS) provide specialist scientific and medical analysis and expert, independent advice to improve the health and safety of our community. 
We are the only laboratory in Australia to provide both forensic and public and environmental health services in one location. Our research priorities are diverse and encompass areas such as biology, chemistry, radiology, and forensic medicine and science.
We strive for excellence in forensic and public and environmental health services that directly benefits Queensland.
Our research is focused on the health of Queenslanders and is based on real-world problems which influence our local population and environment.
Through embedding research as part of our core function and building our capacity for our business, we are providing opportunities for our staff and ensuring long term health benefits for Queenslanders.
This report highlights the extensive breadth and depth of services we provide, and the expertise we contribute to professional knowledge in forensic and public and environmental health sciences.
Research and Development Unit
The Research and Development Unit is staffed by the Research and Human Ethics Co-ordinator and a Senior Administration Officer. The team coordinate all administrative functions in relation to research conducted within or by staff across Forensic and Scientific Services including administration of the FSS Research and Development (R&D) funding program, and Research Governance and Human Ethics review processes.
The FSS R&D funding program aims to support and strengthen the organisation’s culture of research-led service delivery. In 2017 the R&D funding program distributed over $203,000 to 20 FSS researchers to undertake 49 projects valued at over $2.8 million.
A core responsibility of the research office is governance of the organisation’s research activities. Research governance is the framework by which the organisation and the researcher are accountable for the research undertaken. It encompasses the assessment of legal, financial, regulatory and contractual issues in relation to each research project prior to approval. It also involves the post-approval monitoring of projects to ensure research is conducted, and outcomes reported, in compliance with Queensland Health policy, codes, guidelines and procedures, and related legislation.
The R&D team take a ‘hands on’ approach to assisting researchers who are embarking on the process of seeking approval to commence their research, including contract negotiation with partners external to FSS to cover matters such as confidentiality, intellectual property, financial arrangements, ownership of data, insurance, and indemnity. We provide advice and support for researchers completing ethics applications and education around developing research projects.
Contact us
Research and Development Unit
Email FSS_Research@health.qld.gov.au
Phone +61 7 3096 2609
Fax +61 7 3096 2660
Collaborate with us
Our laboratories have a strong history of collaborative research and partnerships.
We conduct analytical, forensic and applied research in collaboration with other government agencies, universities, industry groups and specialist research organisations across the world and offer a unique selection of research assets. These include an extensive collection of reference and clinical samples, specialised equipment, large datasets and a highly trained and educated work force.
We offer our partners access to state-of-the-art infrastructure, resources, diverse multi-disciplinary teams and individual expertise. Our collaborative approach to delivering forensic and public health solutions and improvements to community safety and wellbeing is encouraged and supported throughout our service models and research activities.
Collaborative opportunities include:
•	forming a long-term strategic alliance
•	sharing resources and expertise
•	joining a science network
•	sponsoring or collaborating on a research project
•	mentoring, advising or coaching students through our student placement program.
Our research themes are focused on translating good science into better public and environmental health outcomes and improving the safety and security of Queenslanders.
These themes include:
•	illicit drugs
•	forensic and environmental toxicology
•	forensic pathology
•	mortuary practice
•	post-mortem CT scanning
•	chemical criminalistics
•	biology and DNA analysis
•	advanced diagnostics
•	allergens in food
•	air, water and food quality
•	radiation investigations
•	phylogenetics and evolution
•	phenotypic, molecular and genomic technologies
•	disease reservoirs and source tracking
•	novel surveillance and control strategies for arboviruses.
We are always looking for opportunities to collaborate on research and development initiatives. If you interested in collaborating or partnering with us, please contact us.
Contact us
Research and Development Unit
Email FSS_Research@health.qld.gov.au 
Phone 1800 000 377
Fax +61 7 3096 2660
Quick facts for 2017
•	49 approved projects
•	$203,000 awarded from R&D funding
•	$2.8 million in project value
•	20 FSS researchers
•	67 published articles and book chapters
•	33 different collaborators
•	35 conference presentations
•	4 students
Committee reports
Human Research Ethics Committee
The Forensic and Scientific Services Human Ethics Committee (FSS-HEC) was established in 1995 to have responsibility for, and particular expertise in, review of research applications involving the use of coronial materials, including data. It was acknowledged by the Brisbane Coroner at the time that ethics review of coronial matters is both sensitive and technical, and should therefore be undertaken by a specialised committee with expert coronial knowledge.
Our committee is composed of 15 volunteers–5 men and 10 women, several of whom have served since the committee’s inception in 1995. Our members include a forensic pathologist, a forensic odontologist, a lawyer, a coronial nurse, an officer of the Coroners Court of Queensland, a minister of religion, an Indigenous leader, a clinical ethicist, a clinical microbiologist, laypeople, and professionals with relevant research experience. Committee members are appointed for their knowledge and experience in considering the particular ethical issues that are related to research involving coronial material and public health.
Associate Professor Charles Naylor has been Chair of the committee since 1995 and in 2018 will hand over his responsibilities to Dr Philip Storey, Forensic Pathologist. Dr Storey is supported by Kate Angus, Coronial Nurse, in the role of Deputy Chair.
The FSS-HEC is registered with the National Health and Medical Research Council (NHMRC) (Registration number EC00305) and is constituted and functions in accordance with the NHMRC’s National Statement on Ethical Conduct in Human Research 2007 (updated May 2015).
Contact us
FSS Human Ethics Committee
Email FSS_HEC@health.qld.gov.au 
Phone +61 7 3096 2609
Animal Ethics Committee
The Animal Ethics Committee (AEC) is responsible for Forensic and Scientific Services’ compliance to the Australian code for the care and use of animals for scientific purposes (2013).
The code encompasses all aspects of the care and use of, or interaction with, animals for scientific purposes in medicine, biology, agriculture, veterinary and other animal sciences, industry and teaching. It includes use in research, teaching, field trials, product testing, diagnosis, the production of biological products and environmental studies.
Researchers must be trained in animal ethics and care before starting any research involving animals.
The FSS AEC committee consists of a number of representatives of the community including a veterinarian, a researcher with animal handling experience, a lay person, and an animal welfare representative. These individuals represent the values of the community with respect to the use of animals for scientific purposes.
The use of animals at FSS is based on the 3R’s– replacement of animals with other methods, reduction in the number of animals used, and refinement of the techniques used during experimentation to minimise the impact on animals.
The functions of the AEC and procedures around the use of animals in Health Support Queensland were examined by an external auditor in 2017, and found to be compliant with the requirements of the code.
Contact us
FSS Animal Ethics Committee
Email ruth.holland@health.qld.gov.au 
Phone +61 7 3096 2702
Scientific Review Panel
The FSS Scientific Review Panel (SRP) is a group of volunteer scientists involved in the peer review and assessment of research proposals in the annual FSS research and development grant pool funding round, managed by the Research and Development Unit.
The purpose of the SRP is to impartially assess the scientific and technical merit of research grant applications and provide recommendations to the Executive Director.
The SRP aims to fairly represent the diversity of age, gender and science streams at FSS and support the continued growth of staff by developing and enhancing research skills.
In the interest of sustaining a diverse and experienced SRP that will continue to facilitate a fair and robust assessment process into the future, the Research and Development Unit trialled an intern program in 2017, with great success. Interns were coached by an experienced member of the SRP and participated in the review and assessment of applications.
If you are interested in becoming a Scientific Review Panel member or intern please contact the Research and Development Unit.
Contact us
Research and Development Unit
Email FSS_Research@health.qld.gov.au 
Phone +61 7 3096 2609
Fax +61 7 3096 2660
Highlights
The purchase of a Liquid Chromatography Mass Spectrometer Orbitrap has enabled testing of unknown and/or untargeted compounds. This has been employed in a collaborative research venture with the Queensland Alliance for Agriculture and Food Innovation (QAAFI), investigating pyrrolizidine alkaloids in honey.
In a joint project with Pathology Queensland and the University of Queensland, staff were awarded a ‘demonstration project’ in round 1 of the Queensland Genomics Health Alliance funding bid, to use whole genome sequencing to rapidly characterise antibiotic resistant microbial pathogens associated with significant morbidity and rapidly increasing healthcare- related costs. The outcomes will help optimise clinical management and enhance infection control interventions.
A major project involved the transition of genomics data and processing to ‘the cloud’ which enables faster processing time and greater opportunities for national and international collaborations.
The Public and Environment Health Organic Chemistry laboratory developed analytical testing methods for perfluorinated alkyl substances (PFAS) in water, soil, blood/serum and seafood in response to an investigation into environmental contamination.
The Public and Environmental Health Organic Chemistry laboratory developed methods using Isotope Ratio Mass Spectrometry for forensic analysis of evidence which enabled FSS to create a state of the art facility for this work and has ensured collaboration with the Australian Federal Police.
Welcome to Forensic and Scientific Services
We are Australia’s most comprehensive forensic and public and environmental health facility. We provide specialist scientific and medical analysis and independent expert advice to private and public sector clients locally, nationally and internationally.
We use the latest technology and methods to investigate and respond to public health threats, epidemics, civil emergencies, criminal investigations and coronial matters.
Forensic and Scientific Services plays a critical role in the government’s response to epidemics, civil emergencies and public health threats.
World-standard management systems are central to our operations. Forensic and Scientific Services is:
•	accredited by the National Association of Testing Authorities, Australia — forensic testing, chemical testing, certified reference materials, proficiency testing, biological testing and medical testing 
•	quality management system certified to International Standards (ISO 9001)
•	licensed by the Therapeutic Goods Administration — analysis and testing
•	approved by the Department of Agriculture and Water Resources (Biosecurity) and Office of the Gene Technology Regulator
•	accredited by World Health Organization, Food and Agricultural Organisation and Office of International Epizooties
•	one of three laboratories that form part of the Analytical Laboratories for the Measurement of Environmental Radioactivity (ALMERA) group under the International Atomic Energy Agency (IAEA).
Our research can be broadly grouped into the following priorities:
Public and Environmental Health
We research diseases, vectors and environmental contaminants which are of public health importance.
Forensic Sciences	
Our police and coronial services teams are at the forefront of forensic science research and emerging trends.
1.0 Public and Environmental Health
We provide analysis and advice supporting the measurement and monitoring of biological, radiological, and chemical markers to help protect the health of the community. We offer a unique capability determining contamination sources, causative agent and relatedness cases, for Queensland Government and private sector clients.
We can provide rapid responses to assist government with emergencies and regulatory compliance across the state. Our diagnostic and reference laboratories are recognised both nationally and internationally and ensure we provide evidence-based research and authoritative scientific advice on state, national and international levels.
Key services 
•	Inorganic Chemistry
•	Organic Chemistry
•	Public Health Microbiology 
•	Public Health Virology 
•	Radiation and Nuclear Science
1.1 Inorganic Chemistry
Our staff are experts in analysing metals and elements in environmental samples such as water, soil, sediment, food, blood, urine and other biological tissues.
We provide analytical and advisory services to Queensland Health’s public health units, hospitals, state and local government departments, universities and private sectors including international clients.
Overview
We are a National Association of Testing Authorities (NATA) accredited laboratory for chemical testing and we are a certified Quarantine Approved Premises (QAP) laboratory.
Testing capabilities and advisory services
•	drinking water quality
•	dialysis water quality
•	fluoride level compliance
•	recycled water assessment
•	desalination water monitoring
•	environmental monitoring
•	lead in paint investigations
•	waste discharge monitoring
•	food compliance and complaint investigations
•	elemental speciation (chromium, arsenic, mercury) monitoring
•	chemical exposure testing
•	environmental level nutrient analysis in freshwater and seawater
•	rapid response to public health events and terrorist threats relating to environmental contamination
•	monitoring of toxic metal discharge of by-products
•	air monitoring (occupational and environmental)
•	country of origin testing.
Ensuring a safe environment and the enduring wellbeing of Queenslanders
The FSS inorganic chemistry laboratory is uniquely placed to enable collaborative research, testing, validation and innovation. The Health Food and Sciences Precinct hosts over 100 scientists from the Department of Agriculture and Fisheries, the Commonwealth Scientific and Industrial Research Organisation (CSIRO), University of Queensland and Queensland Health. Our co-location enables us to make better use of resources, information and expertise that help foster new techniques and ideas, and offers a pathway for clients to access a wide range of relevant research and diagnostic solutions in one location. Our ongoing honey project with the Queensland Alliance for Agriculture and Food Innovation (QAAFI) is a great example.
We have the latest analytical equipment and newly refurbished, quarantine compliant laboratories that support our research and development of new technologies and methodologies. This increases our diagnostic abilities and the efficiency of our testing.
We have recently focussed our research into emerging elemental compounds, trace element pollution of soils and waterways, trace elements in human breast milk and the effect of trace elements on the human biological system, to provide insight to help us understand sources of exposure, distribution of chemicals in the environment and how they accumulate in environmental and biological samples.
Research projects
Speciation of chromium Cr(VI) in water samples by High Performance Liquid Chromatography (HPLC) coupled to Inductively Coupled Plasma-Mass Spectrometer (HPLC-ICPMS)
Although the mineral chromium is naturally occurring, industrial and mining activities causes chromium to leach into waterways. Cr(VI) is known to be carcinogenic and mutagenic. This project developed a more efficient method, for direct determination of Cr(VI) species in water samples. The development of the speciation technique has expanded the service capability of Inorganic Chemistry in line with industry expectations to offer a suite of metal speciation analysis (arsenic, mercury and chromium) and in particular for compliance with the Australian Drinking Water Guidelines for Cr(VI).
Principal researcher: Xiaohong Yang 
Research assistant: Stephan Petry 
Research supervisor: Eugene Lee
Preliminary investigation of elemental content and bioactive components in the native Australian plant, Kakadu plum (Terminalia ferdinandiana)
An Australian native plant, the Kakadu plum, is increasingly being used as a food supplement and it is important to investigate the presence of any possible toxic compounds. A recent study into the safety of Australian plant bushfoods reported significant albeit low levels of oxalic acid, however, any assessment of the adverse effects of oxalic acid must be considered in terms of the oxalate calcium ratio in food. Relatively elevated levels of calcium and oxalic acid were found in the Kakadu plum fruit. Future studies should attempt to clarify the association between increased dietary oxalic acid and calcium intakes and adverse health effects.
Principal researchers: Dr Ujang Tinggi, Madeleine Farrell
Collaborators: Dr Yasmina Sultanbawa, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Dr David J Williams, Department of Agriculture and Fisheries (DAF)
Radiogenic isotope and trace metal analysis of the Tully River
The land within the Tully River catchment is utilised for both human settlement and agriculture, with approximately 76 per cent comprising of natural environments including wetlands, rainforests and mangroves — a significant proportion of which is heritage listed. The catchment is very important to the local economy through agriculture and tourism. The aim of this project is to analyse metal content in water and soil samples from selected sites along the Tully River and demonstrate the applicability of using lead isotopic ratios as a tool in distinguishing mining or other anthropogenic activities from naturally occurring stable isotopes.
Principal researcher: Madeleine Farrell
Research supervisor: Dr Tatiana Komarova
Collaborators: Ms Nina Polaschek, Department of Natural Resources, Mines (DNRM), Mr Alan Hooper, Department of Natural Resources, Mines (DNRM)
Evaluation of mercury transfer from agriculture and mining in soil to freshwater and source identification
Mercury is a neurotoxin. Compounds of mercury have been used as fungicide in agriculture in the past and mercury has also been used in gold mining. There are areas along the Tully River where these activities likely leave residues in soil and sediment. This study will identify the dispersion characteristics of the different forms of mercury along the Tully River system using Diffuse Gradients in Thin Films (DGT’s) and ICP-MS.
Student placement: Marta Turull Lopez, University of Barcelona
Research supervisor: Dr Tatiana Komorova
Analysis of environmental contaminants in Australian/Queensland honey
Honey bees are considered as monitors of environmental contamination and have the potential to transfer such contaminants to honey. Honey and other bee products are widely consumed as food and medicine. In high density urban and industrial environments polycyclic aromatic hydrocarbons and heavy metals can be prevalent, whilst pesticides can have ubiquitous presence in both agricultural and urban areas. Honey hives are traditionally located in rural and forested areas, but there is a growing trend to locate hives in more urban areas. This project will investigate the presence of environmental contaminants in honey samples collected from high density urban, peri-urban and rural areas, and correlate measured contamination with potential sources.
Principal researchers: Dr Ujang Tinggi, Dr Benjamin Tan
Research team: Madeleine Farrell
Collaborators: Assoc. Prof. Mary Fletcher, QAAFI Dr Natasha Hungerford, QAAFI, UQ, Dr Stephen Were, Biosecurity Queensland, DAF, Dennis Webber, Biosecurity Queensland, DAF
Publications
Journal articles
Fry, B., Carter, J.F., Tinggi, U., Arman, A., Kamal, M., Metian, M., Waduge, V.A., Yaccup, R.B. (2016) Prawn biomonitors of nutrient and trace metal pollution along Asia-Pacific coastlines. Isotopes in Environmental and Health Studies, 52(6):619.32.
Mohd-Taufek, N., Cartwright, D., Davies, M., Hewavitharana, A.K., Koorts, P., McConachy, H., Shaw, P.N., Sumner, R., Whitfield, K. (2016) The effect of pasteurization on trace elements in donor breast milk. Journal of Perinatology, 36(6).
Mohd-Taufek, N., Cartwright, D., Davies, M., Hewavitharana, A.K., Koorts, P., Shaw, P.N., Sumner, R., Lee, E., Whitfield, K. (2016) The simultaneous analysis of eight essential trace elements in human milk by ICP-MS. Food Analytical Methods, 9(7):2068–2075.
Tinggi, U., Sadler, R., Ng, J.C., Noller, B., Seawright, A.A. (2016) Bioavailability study of arsenic and mercury in traditional Chinese medicines (TCM) using an animal model after a single dose exposure. Regulatory Toxicology and Pharmacology, 76:51–56.
Turull, M., Komarova, T.V., Noller, B., Fontas, C., Diez, S. (2017) Evaluation of mercury in a freshwater environment impacted by an organomercury fungicide using diffusive gradient in thin films. Science of the Total Environment, 621:1475–1484.
Williams, D.J., Edwards, D.J., Pun, S., Chaliha, M., Burren, B., Tinggi, U., Sultanbawa, Y. (2016) Organic acids in Kakadu plum (Terminalia ferdinandiana): The good (ellagic), the bad (oxalic) and the uncertain (ascorbic). Food Research International, 89(1):237–244.
Lectures and presentations
Akter, S., Netzel, M., Tinggi, U., Fletcher, M., Williams, D.J., Sultanbawa, Y. (2017) Nutritional and anti-nutritional properties of Terminalia ferdinandiana (Kakadu plum) from the Northern Territory, Australia. In: TropAg 2017, 20–22 November 2017, Brisbane, Queensland. 
Akter, S., Tinggi, U., Netzel, M., Fletcher, M.T., Sultanbawa, Y. (2017) Phytates and oxalates in Kakadu plum (Terminalia ferdinandiana): toxins to be considered. In: 2nd Queensland Annual Chemistry Symposium QACS 2017, 27 November 2017, QUT, Brisbane.
Akter, S., Williams, D.J., Netzel, M., Fletcher, M.T., Tinggi, U., Sultanbawa, Y. (2017) Kakadu plum kernels: a novel nutrition source. In: The Future of Food: 2017 Australian Institute of Food Science and Technology Convention, 17–18 July 2017, Sydney, NSW.
Farrell, M., Komarova, T.V., Cross, M., Sumner, R., Hooper, A., Harper, D., Locastro, T. (2016) Identification of metal contaminants from multiple agro-based activities in the Tully River catchment. In: SETAC-AU, 4–7 October 2016, Hotel Grand Chancellor, Hobart.
Fyfe, S., Netzel, M., Tinggi, U., Biehl, E., Sultanbawa, Y. (2017) Buchanania obovata: an Australian indigenous food for diet diversification. In: TropAg 2017, 20–22 November 2017, Brisbane, Queensland.
Tinggi, U. (2017) Analysis of metals (toxic & essential) in foods and assessment of intakes in selected children. In: RACI Centenary Congress, 23–28 July, 2017, Melbourne, Victoria.
1.2 Organic Chemistry
State-of-the-art instrumentation allows us to provide an extensive range of testing, research and investigation for environmental and food samples.
We provide expert chemical, molecular and scientific advice and analysis services to all levels of government, industry and the private sector.
Overview
Our advice and services are focused on the levels of organic pollutants, contaminants and toxins in public health samples and in the environment. We test water, soil, food, air, vegetation and other samples as requested.
We test water for:
•	disinfection by-products
•	endocrine disrupting compounds
•	hydrocarbons
•	perfluorinated compounds
•	pesticides and herbicides
•	pharmaceuticals and personal care products
•	plasticisers and other manufactured and natural chemicals
•	sewage epidemiology of dangerous or illicit drugs
•	algae identification and enumeration
•	DNA-based detection of toxic blue-green algae
•	freshwater and marine cyanobacterial toxins.
We test food for:
•	food compliance and complaint investigations
•	nutrition panel composition
•	DNA identification of plant, animal, fungal and bacterial species in fresh and processed foods
•	pesticides and other residues
•	toxic alkaloids in honey, herbal teas and plant material
•	toxins in seafood (including ciguatera toxin, paralytic, diarrhetic and amnesic shellfish poison, nodularin)
•	pesticides and perfluorinated compounds in seafood.
We test soil for:
•	hydrocarbons
•	perfluorinated compounds
•	pesticides and herbicides
•	other manufactured and natural chemicals.
We test air for:
•	environmental investigations
•	sick buildings
•	occupational exposure.
We test vegetation and animal tissue (including bees) for:
•	herbicide poisoning
•	spray drift poisoning.
Our specialist testing includes:
•	agricultural dipping/spraying solution testing
•	chemical exposure testing (blood/urine for pesticides, herbicides, PFAS)
•	Chinese and herbal medicine analysis
•	country-of-origin testing (isotope-ratio mass spectrometry)
•	collaborative research into emerging chemical analysis
•	development of new services to respond to our client’s needs
•	mass spectrometry screening and quantitation for unknown chemicals
•	rapid response to public health events including collaboration with Queensland Fire and Emergency Services during chemical emergencies.
New Mass Spectrometer puts Organic Chemistry at the forefront of detecting unknown chemical compounds.
The Organic Chemistry laboratory purchased a state of the art Q Exactive™ Hybrid Quadrupole-Orbitrap™ Mass Spectrometer in 2016. The ‘Orbitrap’ allows extremely high resolution of compounds in complex samples such as foods and environmental samples.
Compounds are first separated by liquid chromatography and then fragmented and ionised — the ions are detected by the Orbitrap. Each ion has a unique spectrum which allows it to be identified by matching it against a huge reference library of compounds.
If a particular spectrum does not match anything in the library, Compound Discoverer software allows the user to perform a search against a live, constantly updated database of compounds.
Steve Carter, the analyst who has been optimising the Orbitrap technology for in-house use, has been able to detect unique compounds in water and explosives and even in physical evidence samples submitted by forensic scientists at FSS.
“This innovative technology is a very powerful tool which will assist us in identifying unknown compounds–therefore enhancing our research capacity and value-adding to the service we provide our clients.” 
Steve Carter
Although it’s also routinely used to resolve and identify herbicides and pesticides in water samples submitted for analysis, the Orbitrap was recently applied to a collaborative research project with the Queensland Alliance for Agriculture and Food Innovation (QAFFI). Steve was able to detect unique pyrrolizidine alkaloids in honey; these toxic compounds are produced in the pollen of some plants species, and can contaminate honey once the pollen has been collected by bees. This technology could also be applied to detecting other contaminants in food products.
Research projects
Proof of concept: atom specific isotypic analysis of amino acids
Under Dr Jim Carter, FSS recently established a facility to measure stable isotope composition. Focus to date has been on determining the country or region of origin of high value consumer products which are easily substituted or counterfeited. Although it is possible to distinguish the country of origin, the classifications when based on protein are very broad. This project aims to develop a method to determine the carbon isotopic ratio (13C/12C) of a specific atom within amino acids, obtained from the hydrolysis of protein materials. It is envisaged that the information obtained will be uncluttered with other signals and provide insight into the metabolic processes involved in the biosynthesis of these compounds. If successful, the methodology may also be extended as a means to study changes in human metabolism as a diagnostic tool for the early onset of disease.
Principal researcher: Dr Jim Carter
Collaborator: Prof. Brian Fry, Griffith University
Profiling and quantifying organic acids in root exudates of native plant species
Many Australian native plants have high tolerance of heavy metal toxicity and have been used to remediate heavy metal contaminated land and mine wastes of base metal mines. However, some plant species are capable of generating large amounts of organic acids which are released into the rhizosphere. These root exudates have potential to mobilise heavy metals in the solid phase into bore water, increasing the risks of heavy metal contamination in seepages and runoffs under high rainfall conditions. Knowing the potential of organic acid production in native plants can help manage heavy metal risks in land remediation programs. The aim of this project is to develop a sensitive method by means of LC-MS/MS to profile and quantify the composition of organic molecules secreted by roots of Australian native plants.
Principal researcher: Steve Carter
Research supervisor: Stewart Carswell
Student placement: Lei (Nicole) Xiong, University of Queensland
Collaborators: Longbin Huang, University of Queensland
Characterisation of potentially toxigenic cyanobacterial (blue-green algae) from diverse environments in north-eastern Australia
The aim of this project is to characterise potentially toxic and ecologically significant cyanobacteria from diverse habitats in Queensland. Cyanobacteria occupy diverse ecological niches in water bodies and consequently their proliferations range from obvious surface blooms to dense mats on the beds of water bodies and even terrestrial formations such as stromatolites. Cyanobacteria are important from a human and animal health perspective because of their ability to produce harmful cyanotoxins in drinking and recreational water. This project has led to the detection and characterisation of the novel saxitoxin- producing species, Scytonema crispum in creeks upstream of Wivenhoe Dam and in the Brisbane River downstream of the dam, suggesting that it may contribute to the presence of saxitoxin in Wivenhoe which presents a significant public health risk in both drinking and recreational water.
Principal researcher: Dr Barbara Sendall 
Research supervisor: Stewart Carswell 
Collaborators: Dr Glenn McGregor, DSITI
Determining the origin of frozen berries through isotopic and trace element analysis
Recent media attention to the finding of Hepatitis virus on imported berries has renewed call for strict enforcement of the Food Standards Code requirements for labelling country of origin. The outcome from this project was a new method to distinguish Australian and imported frozen berries with greater than 80 per cent confidence.
Principal researcher: Dr Jim Carter
Research team: Dr Ujang Tinggi, Inorganic Chemistry Hans Yates, Inorganic Chemistry
Analysis of honey for a range of analytes
The outcome of this project was a new method for analysis of molasses for a range of neonicotinoids — a group of insecticides harmful to bees.
Principal researcher: Kevin Melksham
Research supervisor: Stewart Carswell
A longitudinal study of the isotopic and trace element composition of beers and ciders
Following on from a previous project that demonstrated that a combination of stable isotopic and elemental composition can be used to distinguish the country of origin of beers and ciders, this project was extended to investigate variations in products over time. It was found that the isotopic and elemental composition of some beers and ciders changed significantly over time (production batch) and a contemporary genuine sample will be needed for authentication.
Principal researcher: Dr Jim Carter
Research team: Dr Ujang Tinggi, Inorganic Chemistry, Hans Yates, Inorganic Chemistry
Estimating per capita use and release of chemicals through systematic collection and analysis of sewage treatment plant influent, effluent and biosolids (Australian Research Council funding)
Systematic collection and analysis of wastewater has become an effective tool for estimating population use and abuse of a range of chemicals including illicit drugs, alcohol, pharmaceuticals, specific foods and for assessing markers of population health status. The aim of this project was to undertake a world first synchronised program to sample waste water treatment plants nationwide during the census 2016. Partners covering a wide range of disciplines collaborated in this project, including FSS who provided analytical support.
Lead organisation: University of Queensland
Partner researcher: Steve Carter
Collaborators: Prof. Jochen Mueller, University of Queensland
The risk of pyrrolizidine alkaloids in Queensland honey
Pyrrolizidine alkaloids are natural toxins produced by flowering plants that are transferred through pollen to honey. These alkaloids have been associated with acute and chronic liver damage (even death), and the contamination of honey represents a potential risk to human health. The Australian provisional tolerable daily intake of pyrrolizidine alkaloids is 1 μg/kgbwt/day, but their presence in Queensland honeys has not previously been determined. This project will establish a validated analysis method for measurement of pyrrolizidine alkaloids in honey, and investigate both the identity and level of alkaloids present in honey market survey samples collected across Queensland.
Principal researchers: Kevin Melksham, Steve Carter
Collaborators: Assoc. Prof. Mary Fletcher, QAAFI, UQ, Dr Stephen Were, Biosecurity Queensland, DAF, Dr Ken Yong, Biosecurity Queensland, DAF, Tenille Fort, Health Protection Unit, Queensland Health
Assessment of baseline concentrations and composition of petroleum hydrocarbons in Queensland waters
The aim of this project is to build a library of natural, or baseline, concentrations of hydrocarbons in water and sediment environmental samples around South East Queensland. Analysis of samples from rivers, creeks, drains and around Moreton Bay would provide spatial and temporal variation which will be used to assist the assessment and remediation of petroleum hydrocarbon contamination and other spills.
Principal researcher: Rebecca Catanzariti 
Research supervisor: Scott Turner 
Collaborators: Andrew Moss, DSITI
Development of a method for measuring sunscreens and insect repellents in environmental samples
With potential applications in monitoring of sensitive freshwater streams and coral reefs in popular tourist areas, the aim of this project is to develop robust methods for the analysis of sunscreen and insect repellent active ingredients in groundwater, seawater and sediments.
Principal researcher: Dr Ashley Tronoff
Research supervisor: Scott Turner
Development and validation of Total Oxidisable Precursor Assay (TOPA) in soil and water
Per-and poly-fluoroalkyl substances (PFAS) are perfluorinated chemicals used to make coatings which resist heat, oil, stains, grease and water. They are commonly found in firefighting foam and flame retardants. Many PFAS do not break down readily in the environment and as a result have been found to accumulate in water, soil and biota. TOPA is a standardised pre-treatment of water and soil extracts to expose underlying PFAS. During the pre-treatment the precursors are converted to measurable perfluorinated carboxylic acids, allowing detection. By development and validation of this method, Organic Chemistry can detect the underlying PFAS and comply with the minimum requirements set by the policy of Department of Environment and Science (DES) on the Environmental Management of Firefighting Foams. This method can now be offered to our clients as a validated analytical test on a fee-for-service basis.
Principal researcher: Martie du Plessis
Research supervisor: Scott Turner
Development of rapid moisture measurements in foods
A significant proportion of the work undertaken by the Food Chemistry group is measuring the nutritional composition of foods, to facilitate Public Health Units’ enforcement of legal requirements for nutritional composition and product labelling. The current method for moisture determination is slow (> 3 hours) and labour intensive. This project will enable a rapid instrument based method, using infrared radiation, to replace the existing classical techniques based on oven drying.
Principal researcher: Pam Kahlon, Michael Geyer
Research supervisor: Dr Jim Carter
Authentication of Australian orange juice
Consumers are increasingly prepared to pay more for premium products. Orange juice sold as ‘not from concentrate’ is one such product. The aim of this research is to develop a method to identify the addition of water and/or sugar to fruit juices. The method will be based on carbon isotopic analysis of fruit sugars and sugar free solids (pulp) and on hydrogen and oxygen isotopic analysis of the water.
Principal researcher: Dr Jim Carter
Research team: Dr Ujang Tinggi, Inorganic Chemistry
Development of methods for detection of potential cyanotoxins BMAA and DABA
The putative cyanotoxin BMAA has gained worldwide attention as it has been strongly implicated in the development of the neurodegenerative disease Amyotrophic Lateral Sclerosis (ALS). Many published studies have shown high levels of BMAA in various cyanobacterial species, including many that are commonly found in Queensland. However, it is unknown if BMAA and its structural isomer DABA are present in local cyanobacterial populations or in drinking water. The aim of this project is to develop methods to detect BMAA and DABA in water samples and blue-green algae cultures.
Principal researcher: Rebecca Catanzariti
Research supervisors: Dr Barbara Sendall, Steve Carter
Analysis of environmental contaminants in Australian/Queensland honey
Honey bees are considered as monitors of environmental contamination and have the potential to transfer such contaminants to honey. Honey and other bee products are widely consumed as food and medicine. In high density urban and industrial environments polycyclic aromatic hydrocarbons and heavy metals can be prevalent, whilst pesticides can have ubiquitous presence in both agricultural and urban areas. Honey hives are traditionally located in rural and forested areas, but there is a growing trend to locate hives in more urban areas. This project will investigate the presence of environmental contaminants in honey samples collected from high density urban, peri-urban and rural areas, and correlate measured contamination with potential sources. 
Principal researchers: Dr Benjamin Tan, Dr Ujang Tinggi
Research team: Madeleine Farrell
Collaborators: Assoc. Prof. Mary Fletcher, QAAFI, UQ, Dr Natasha Hungerford, QAAFI, UQ, Dr Stephen Were, Biosecurity Queensland, DAF, Dennis Webber, Biosecurity Queensland, DAF
Development of GCMS methods to detect and quantify regularly detected volatile organic compounds (VOCs) 
VOC’s are organic chemicals with high vapour pressure at room temperature. They are often responsible for taste and odour complaints and have compounding long-term health effects. This project will further develop existing GCMS VOC methods to add 50 to 100 non-target, but regularly detected compounds, for quantitative analysis.
Principal researcher: Jeff Herse
Research supervisor: Vince Alberts
Publications
Journal articles
Banks, A.P.W., Lai, F.Y., Mueller, J.F., Jiang, G., Carter, S., Thai, P.K. (2017) Potential impact of the sewer system on the applicability of alcohol and tobacco biomarkers in wastewater- based epidemiology. Drug Testing and Analysis, 10(3):530–538.
Carter, J.F. (2017) Alcoholic beverages II – spirits, beer, sake and cider. In: Food forensics: stable isotopes as a guide to authenticity and origin. CRC Press, Boca Raton; Florida, pp.207–238.
Carter, J.F. (2017) Fruits and vegetables. In: Food forensics: stable isotopes as a guide to authenticity and origin. CRC Press, Boca Raton; Florida, pp.153–175.
Carter, J.F. (2017) Isotope ratio measurements for food forensics. In: Food forensics: stable isotopes as a guide to authenticity and origin. CRC Press, Boca Raton; Florida, pp. 1–21.
Carter, J.F., Camin, F. (2017) Alcoholic beverages I — wine. In: Food forensics: stable isotopes as a guide to authenticity and origin. CRC Press, Boca Raton; Florida, pp.176–208.
Carter, J.F., Chesson, L.A. (2017) Sampling, sample preparation and analysis. In: Food forensics: stable isotopes as a guide to authenticity and origin. CRC Press, Boca Raton; Florida, pp.22–45.
Dunn, P.J.H., Salouros, H., Carter, J.F., Doyle, S. (2017) Forensic application of stable isotope delta values: proposed minimum requirements for method validation. Rapid Communications in Mass Spectrometry, 31(17):1476–1480.
Fry, B., Carter, J.F., Tinggi, U., Arman, A., Kamal, M., Metian, M., Waduge, V.A., Yaccup, R.B. (2016) Prawn biomonitors of nutrient and trace metal pollution along Asia-Pacific coastlines. Isotopes in Environmental and Health Studies. 52(6):619–32
Gaget, V., Lau, M., Sendall, B.C., Froscio, S., Humpage, A.R. (2017) Cyanotoxins: which detection technique for an optimum risk assessment? Water Research, 118:227–238.
Kabas, S., Saavedra-Mella, F., Huynh, T., Kopittke, P.M., Carter, S., Huang, L. (2017) Metal uptake and organic acid exudation of native Acacia species in mine tailings. Australian Journal of Botany, 65(4).
Lai, F.Y., O’Brien, J.W., Bruno, R., Hall, W., Prichard, J., Kirkbride, P., Gartner, C., Thai, P.K., Carter, S., Lloyd, B., Burns, L., Mueller, J.F. (2016) Spatial variations in the consumption of illicit stimulant drugs across Australia: a nationwide application of wastewater-based epidemiology. Science of the Total Environment, 568:810-818.
Lai, F.Y., O’Brien, J.W., Thai, P.K., Hall, W., Chan, G., Bruno, R., Ort, C., Prichard, J., Carter, S., Anuj, S., Kirkbride, P., Gartner, C., Humphries, M., Mueller, J.F. (2016) Cocaine, MDMA and methamphetamine residues in wastewater: consumption trends (2009– 2015) in South East Queensland, Australia. Science of the Total Environment, 568:803–809.
McGregor, G.B., Sendall, B.C. (2017) Ewamiania thermalis gen. et sp. nov. (Cyanobacteria, Scytonemataceae), a new cyanobacterium from Talaroo thermal springs, north-eastern Australia. Australian Systematic Botany, 30(1):38–47.
McGregor, G.B., Sendall, B.C. (2017) Iningainema pulvinus gen nov., sp nov. (Cyanobacteria, Scytonemataceae) a new nodularin producer from Edgbaston Reserve, north-eastern Australia. Harmful Algae, 62:10–19
Meyer, L., Capper, A., Carter, S., Simpfendorfer, C. (2016) An investigation into ciguatoxin bioaccumulation in sharks. Toxicon, 119:234–243.
Natusch, D.J.D., Carter, J.F., Aust, P.W., Tri, N.V., Tinggi, U., Mumpunif, M., Riyanto, A., Lyons, J.A. (2017) Serpent’s source: determining the source and geographic origin of traded python skins using isotopic and elemental markers. Biological Conservation, 209:406–414.
O’Brien, D., Lewis, S., Davis, A.,Gallen, C., Smith, R., Turner, R.D., Warne, M.St-J., Turner, S., Carswell, S., Mueller, J.F., Brodie, J. (2016) Spatial and temporal variability in pesticide exposure downstream of a heavily irrigated cropping area: the application of different monitoring techniques. Journal of Agricultural and Food Chemistry, 64(20):3975–3989.
Wynwood, S., Burns, M-A., Graham, G.C., Weier, S.L., McKay, D.B., Craig, S.B. (2016) Serological diagnosis of Leptospirosis in bovine serum samples usinga microsphere immunoassay. Veterinary Record Open, 3:e000148.
Wynwood, S., Burns, M-A., Graham, G.C., Weier, S.L., McKay, D.B., Peck, S., Craig, S.B (2016) Leptospirosis in Tasmanian Devils (Sarcophilus harrisii) in Tasmania, 2008–2012. Journal of Wildlife Diseases, 52(3):636–641.
Lectures and presentations
Banks, A.P.W., Lai, F.Y., Mueller, J.F., Jiang, G., Carter, S., Thai, P.K. (2017) The stability of alcohol and tobacco biomarkers in sewer systems. In: RACI Centenary Congress, 23–28 July, 2017, Melbourne, Victoria.
Carter, J.F. (2017) Food forensics: authenticity and traceability using stable isotopes. In: TropAg 2017, 20–22 November 2017, Brisbane, Queensland.
Fletcher, M.T., Hungerford, N.L., Carter, S., Anuj, S., Martin, C., Yin, M., Melksham, K., Were, S. (2017) Pyrrolizidine alkaloids — natural toxins from flowers to honey. In: RACI Centenary Congress, 23–28 July, 2017, Melbourne, Victoria.
Fry, B., Carter, J.F. (2016) An automated PSIA system for measuring δ13C of carboxyl groups from amino acids. In: 8th International Symposium on Isotopomers, 3–6 October 2016, Nantes, France.
Hungerford, N.L., Martin, C., Fletcher, M.T., Carter, S., Anuj, S., Sharma, E., Yin, M., Melksham, D., Were, S. (2017) Pyrrolizidine alkaloids — natural toxins risk in Queensland honey. In: 2nd Queensland Annual Chemistry Symposium QACS 2017, 27 November 2017, QUT, Brisbane.
Hungerford, N.L., Martin, C., Fletcher, M.T., Carter, S., Anuj, S., Yin, M., Melksham, K., Were, S. (2017) Pyrrolizidine alkaloids—the risk of natural toxins in Queensland honey. In: TropAg 2017, 20–22 November 2017, Brisbane, Queensland.
Melksham, K., du Plessis, M., Patel, R., Carter, S., Anuj, S., Smith, R., King, O.,Turner, R,D., Wallace, R. (2016) Something in the Water. In: Queensland Annual Chemistry Symposium QACS 2016, 25 November 2016, University of Queensland, Brisbane.
Melksham, K., du Plessis, M., Patel, R., Carter, S., Anuj, S., Smith, R., King, O.,Turner, R.D., Wallace, R. (2016) Herbicides/pesticides in Great Barrier Reef Water by direct injection LCMS/MS — beyond residue definitions. In: 5th International Conference on Emerging Contaminants and Micropollutants in the Environment, 20–23 September, 2016, Sydney.
Mueller, J.F., O’Brien, J.W., Thai, P.K., Lai, F.Y., Thomas, K., Ort, C., Covaci, A., Bruno, R., Prichard, J., Gartner, C., Hall, W., Kirkbride, P., Humphries, M., Eaglesham, G.K., Banks, A.P.W., Carter, S., Anuj, S. (2016) Sampling the sh** out of Australia on census. In: SETAC-AU, 4–7 October 2016, Hotel Grand Chancellor, Hobart.
Sendall, B.C., McGregor, G.B. (2016) What lies beneath? Prevalence of toxigenic Scytonema in benthic freshwater habitats in south-east Queensland. In: Emerging cyanobacterial research and its practical application: Fifth National Cyanobacterial Workshop, 29–30 September 2016, Brisbane, Queensland.
Stewart, I., Wickramasinghe, W.A., Carter, S., McGregor, G.B., Davis, B.C., Seawright, A.A. (2016) Acute oral toxicity of deoxy-cylindrospermopsin in male Balb/c mice. In: Emerging cyanobacterial research and its practical application: Fifth National Cyanobacterial Workshop, 29–30 September 2016, Brisbane, Queensland.
1.3 Public Health Microbiology
The Public Health Microbiology team provides expert scientific knowledge and laboratory investigation for notifiable bacterial pathogens and bacterially/toxin-mediated outbreaks.
We use surveillance and epidemiological data to provide high quality reference and diagnostic services to a wide range of public health and clinical clients investigating bacterial outbreaks.
Overview
Our scope can include:
Food—undertaking microbiological surveillance of foods available in the marketplace; investigating and surveying of foodborne illnesses, analysing and identifying moulds and detecting foodborne pathogens and their toxins, national reporting of foodborne disease outbreaks.
Water—investigating water quality and bacterial outbreaks from consuming, ingesting or inhaling contaminated water (e.g. drinking, dialysis, swimming, waste and recycled water).
Molecular epidemiology—genotyping major bacterial pathogens and typing bacteria for identifying and characterising disease outbreaks, transmission sources and emerging diseases.
Leptospirosis—providing expert analysis, advice, diagnostic support and epidemiological data as part of the reference and research laboratory which is part of an international collaborating group.
Bacterial pathogens—providing a reference and referral service for notifiable bacterial pathogens comprising a number of specialty areas including:
•	enteric pathogens
•	Group A Streptococci
•	Neisseria gonorrhoeae and Neisseria meningitidis
•	Streptococcus pneumoniae
•	Legionellae spp.
Innovating service delivery
“Public Health Microbiology reference laboratories fulfil a critical role  in providing testing and surveillance for notifiable, emerging and bacterial pathogens. Our research utilising whole genome sequencing (WGS) to improve molecular epidemiological investigations has led to efficiencies in the routine workflow of the Public Health Microbiology laboratory, enabling the laboratory to replace multiple labour intensive assays, with a single technique of superior typeability and discrimination at an often competitive price.
WGS is deepening our understanding of the epidemiology of a variety of diseases and has the potential to revolutionise clinical management of antibiotic-resistant Neisseria gonorrhoeae for example — we’re very excited, along with our collaborators, to be at the forefront of genomic research.”
Dr Amy Jennison
Scientist, Public Health Microbiology
Research projects
Origins of an emerging pathogen: phylogeny of Shigella flexneri 1c
Shigella causes bacillary dysentery, shigellosis, in over 100 million cases annually and is a notifiable disease in both Australia and New Zealand. In Australia, infections are generally associated with overseas travel or particular community groups such as men who have sex with men and Indigineous populations. The majority of cases in developed countries tend to be of the serotypes Shigella sonnei and Shigella flexneri. A novel serotype S. flexneri 1c — first identified in Bangladesh in the late 1980’s and since isolated from Vietnam, Egypt, Indonesia and Pakistan — has become the major cause of shigellosis in New Zealand and is beginning to emerge in Australia. This study will use whole genome sequencing to determine the epidemiology behind its spread.
FSS researchers: Dr Amy Jennison, Dr Rikki Graham, Christine Doyle, Dr Ning-Xia Fang
Collaborators: Muriel Dufour, Institute of Environmental Science and Research, New Zealand, Mary Vulcanis, University of Melbourne, Naresh Verma, Australian National University
Expanded fever surveillance at provincial hospitals in the Laos PDR
This collaborative work aims to determine the aetiologies of febrile illness at three provincial hospitals in Laos. It is an extension of the study published in Lancet Global Health, Mayxay et al. 2013 of the Xieng Khuang hospital whose staff believed they see significant numbers of patients with leptospirosis but have no diagnostics available to confirm their suspicions. This study aims to investigate what leptospiral serovars are circulating in regions close to our borders. The Laos region is expected to have a number of exotic leptospires not seen in Australia which could possibly be missed on routine screening. This is vital so we can appropriately test patient samples especially from travelers returning from this region with illness.
FSS researcher: Assoc. Prof. Scott Craig
Collaborator: Dr Paul Newton, University of Oxford, UK
Are non-malarial fevers in pregnancy significant causes of under-recognised maternal morbidity and preterm/low birth-weight in Laos? A pilot study
The aim of the project is to investigate the aetiology of fever and its impact in a cohort of ~ 1,000 pregnant women in a district east of Vientiane. This will help define the incidence and impact of leptospirosis in pregnancy in the region and estimate asymptomatic seroconversion. Within Australia, leptospirosis is a public health problem that primarily threatens Queenslanders, visitors to Queensland and the associated tourism and agricultural industries. This is the first cohort study in the tropics of the causes of fever in pregnancy, and the first to explore leptospirosis in such a large population of pregnant women. The findings from this project will engender significant public health considerations for pregnant women and provide the genesis for the development of improved patient monitoring of leptospirosis in pregnant women leading to better obstetric and paediatric outcomes.
FSS researcher: Assoc. Prof. Scott Craig
Collaborator: Dr Paul Newton, University of Oxford, UK
Causes of fever at Mahosot Hospital, Vientiane, Lao PDR 2010–2012
This study will investigate dengue, Japanese encephalitis virus (JEV), rickettsial disease and leptospirosis, diseases common not only in Laos, but also in Queensland. There is a need for clinical, laboratory and public health data on this patient cohort to direct the most appropriate diagnostic and clinical pathways to manage patients with multi-factorial infections.
FSS researcher: Assoc. Prof. Scott Craig
Collaborator: Dr Paul Newton, University of Oxford, UK
Prospective study to compare different methods for the accurate and timely diagnosis of Leptospiral infections
This study aims to conduct a large prospective evaluation of different leptospirosis diagnostics (molecular, culture and serological) at Mahosot hospital over one rainy season. There are many different untested rapid diagnostic tests used in Asia and the main aim of the study is to obtain evidence as to the most accurate and cost-effective.
FSS researcher: Assoc. Prof. Scott Craig
Collaborator: Dr Paul Newton, University of Oxford, UK
Subtyping of ‘Big6’ EHEC strains from Australian cattle and clinical sources
This study aims to explore the diversity and relatedness of the cattle and human clinical ‘Big6’ EHEC isolates using next generation sequencing. The information generated from this work will provide the basis for development of targeted rapid subtyping methods.
FSS researcher: Dr Amy Jennison
Lead organisation: Dr Robert Barlow, CSIRO
Improving Public Health Microbiology outbreak investigations and ensuring molecular epidemiological typing capabilities in the era of culture independent testing
Whole genome sequencing (WGS) is improving bacterial outbreak investigations and disease surveillance. The epidemiological typing for a number of important bacterial illnesses in Queensland could be refined to ensure that outbreaks and chains of transmission can be actively resolved. This project will harness WGS to develop rapid high resolution genotyping tools for Salmonella and Shigella isolates, in order to enhance public health surveillance and investigation. Furthermore, the application of WGS for extrapolating genotyping and antibiotic resistance information from both isolates and clinical specimens will be developed. The capabilities developed by this project will ensure Public Health Microbiology (PHM) can continue to produce genotyping information as pathology laboratories embrace culture independent testing.
Principal researcher: Dr Amy Jennison
Research team: Helen Smith, Dr Rikki Graham, Christine Doyle, Dr Ning-Xia Fang, Lester Hiley
New molecular tools to identify groups of individuals at increased risk of human immunodeficiency virus (HIV) acquisition (HIV Foundation Queensland funded)
Population rates of HIV diagnosis have increased in Queensland despite advances in treatment and prevention. Current HIV programs primarily focus on individual levels and are largely blind to the role of transmission dynamics within and between groups of individuals. This project will combine novel molecular tools with powerful statistical techniques to, for the first time, provide a rigorous investigation of HIV transmission dynamics in Queensland.
FSS researcher: Helen Smith
Lead organisation: Assoc. Prof. David Whiley, University of Queensland
Collaborators: Dr Caroline Lang, Communicable Disease Unit, Queensland Health, Assoc. Prof. Stephen Lambert, Communicable Disease Unit, Queensland Health, Ella Trembizki, University of Queensland
The molecular characterisation of Shigella from Papua New Guinea (PNG) and other Pacific Island nations to better understand the epidemiology, pathogenesis and development of antimicrobial resistance in the Oceania region
The aim of this project is to better understand the epidemiology, pathogenesis and development of antimicrobial resistance of Shigella strains from PNG and neighbouring Pacific Island nations. This will be achieved through the application of culture, molecular and bio-informational techniques to Shigella isolates that originate from Pacific countries.
FSS researcher: Dr Amy Jennison
Lead organisation: Dr Andrew Greenhill, Monash University
Whole genome sequencing (WGS) of clinical invasive Haemophilus influenzae isolates
Haemophilus influenzae is an important aetiological organism of both adult and child respiratory disease. Capsulated strains can be identified in the laboratory using serological techniques as well as capsule gene detection by PCR, however a large proportion of invasive Queensland H. influenzae isolates are non-capsulated and therefore non-typeable by these methods. The incidence of nontypeable Haemophilus influenzae (NTHi) causing invasive disease is increasing in the Queensland population over time. With the implementation of WGS into the Public Health Microbiology laboratory, the capability exists for replacing current molecular techniques with WGS to improve information output and turn-around time. In particular, the data generated from WGS will provide additional genetic resolution and information on H. influenzae isolates for surveillance and characterisation, particularly with NTHi strains, for which no other conventional methods exist.
Principal researcher: Megan Staples
Research supervisor: Dr Amy Jennison
Developing capability in Illumina sequencing and genotyping directly from clinical material
The overall objective of the project is to sequence a variety of positive specimens (viruses or bacteria) either known to contain pathogens or spiked control material, from different sample types using both Ion Torrent Personal Genome Machine (PGM) and Illumina platforms and compare the PGM and Illumina systems and determine whether, most importantly, the latter improves diagnostic sensitivity. Additionally, as bacteria have a DNA genome but viruses of public health importance overwhelmingly have RNA genomes, different methodologies have been developed for sequencing these respective classes of microbes. It would be more time and cost-effective to streamline methodologies into a single workflow for the simultaneous detection of bacteria and viruses. To work towards this longer term goal, an experiment will be conducted to see if library preparations can be combined into a single sample without loss of sensitivity.
FSS researchers: Dr Amy Jennison, Dr David Warrilow
Lead organisation: Assoc. Prof. David Whiley, Pathology Queensland, Queensland Health
Haemophilus influenzae and Streptococcus pneumoniae typing project
This collaborative project is part of a UQCCR research study on isolates from child swabs specimens from vulnerable populations. Bacterial typing was performed on 10 strains of each of H. influenzae and S. pneumoniae as supplied by UQCCR. Typing data obtained will provide increased understanding of carriage versus invasive isolates in children in vulnerable populations.
FSS researchers: Megan Staples, Vicki Hicks
Research supervisor: Dr Amy Jennison
Lead organisation: Dr Hanna E. Sidjabat, University of Queensland Centre for Clinical Research
Establishment of a validated ETEC detection assay and development of an internal control for clinical DNA extract assays
Diarrhoeal disease caused by Escherichia coli is a major health concern worldwide. The aim of this study is to establish a validated assay for detection of enterotoxigenic E. coli, or ETEC — one of the five pathotypes of E. coli — the prevalence of which is unknown in Australia.
Principal researcher: Dr Amy Jennison
Research supervisor: John Bates
Student placement: Stephanie Wilkinson, Griffith University
Understanding the sources of Campylobacter in Australia (NHMRC funding)
Campylobacter causes 96 million foodborne illnesses globally each year, and is the leading foodborne illness in children under five. In Australia, rates of notified cases are among the highest in the developed world. Campylobacteriosis is a zoonotic disease; infections are spread via the faecal oral route following consumption of contaminated food or water, or contact with infected humans, animals or environments. The aim of this study is to transform the understanding of Campylobacter infections through the use of whole genome sequencing. The success of this project lays on the strong inter-disciplinary collaboration between food safety authorities, public health departments and universities.
FSS researchers: Dr Amy Jennison, John Bates
Lead organisation: Assoc. Prof. Martyn Kirk, Australian National University
Collaborators: Dr Craig Shadbolt, NSW Food Authority, Prof. Nigel French, Massey University, Mary Valcanis, University of Melbourne, Dr Russell Stafford, OzFoodNet, Queensland Health
Development of a predictive model to determine the pathogenicity of Staphylococcus epidermidis in patient blood culture bottles
The project focusses on the identification of virulence markers in Staphylococcus epidermis with the aim of developing a predictive model for determining the clinical significance of this isolate upon detection in patient blood cultures. S. epidermidis is the most common bacterium isolated from blood cultures. It harmlessly resides on the skin and commonly colonises indwelling medical devices. Therefore the isolation of S. epidermis from blood cultures may indicate a bloodstream infection, line colonisation or a contaminated blood collection. This presents a clinical dilemma with regards to patient treatment. Analysis of WGS data is anticipated to identify markers that can differentiate between ‘invasive’ and ‘contaminant’ strains.
Principal researcher: Dr Amy Jennison
Student placement: Sharon Kleinschmidt, Queensland University of Technology
Whole genome sequencing to track, treat and prevent nosocomial infections
(Queensland Genomics Health Alliance funding)
Nosocomial (hospital-acquired) infections are common and associated with significant morbidity and high healthcare-related cost. The impact of these infections is exacerbated by rapidly increasing rates of antibiotic resistance. At present we have limited laboratory capacity to track pathogens causing these infections in real time or detect patient-to-patient transmission. This project will use whole genome sequencing to rapidly characterise antibiotic resistant microbial pathogens causing serious infections in patients admitted to the three major Brisbane teaching hospital (RBWH, LCCH, PAH) in order to help optimise clinical management and enhance infection control interventions.
FSS researcher: Dr Amy Jennison
Lead organisation: Prof. David Patterson, University of Queensland Centre for Clinical Research
Collaborators: Dr Patrick Harris, Pathology Queensland, Queensland Health, Prof. Graeme Nimmo, Pathology Queensland, Queensland Health, Assoc. Prof. Scott Beatson, University of Queensland
Assessing the effects of antibiotic choice on gut microbiome — a metagenomic approach
The human gut contains a vast array of micro-organisms that play an essential role in human health and disease. The use of antimicrobials has a detrimental effect on gut microbiota and increased risk for infection or colonisation with resistant pathogens. The gastro intestinal tract is a major reservoir for colonisation with multi-drug resistant pathogens. This study will perform whole genome sequencing on faecal samples from three groups of patients (no antibiotics, piperacillin-tazobactuam or meropenem) over time to describe the relative microbial diversity in each patient set. This work will inform decisions around antibiotic usage and have implications for preventing resistance transfer, ensuring patient recovery of flora and potential to inform on the use of probiotics to manage patient recovery.
FSS researchers: Dr Amy Jennison, Dr Rikki Graham
Lead organisation: Dr Sanmarier Schlebusch, Mater Pathology
Collaborative work with IFM Quality Services
This investigation will compare the degree of genetic similarities in various strains of micro-organisms that are commonly used as control cultures, to report the degree of impact that small differences in control behaviour would have on laboratory practices. A secondary aim is to determine the effect of multiple passages on the genetic and biochemical/morphological characteristics of organisms.
FSS researcher: Dr Amy Jennison
Lead organisation: Ingrid Flemming, IFM Quality Services
Assessing the relationship between phenotypic expression of resistance and genomic resistance markers amongst common bacterial pathogens 
The aim of this study is to utilise next generation sequencing technology to genome sequence bacterial pathogens to assess the relationship between phenotypic expression of resistance and genes present within these pathogens. In addition, we will obtain phenotypic data, proteomic analysis of gene expression and clinical outcome data for patients with isolates from bloodstream infections. This work will provide greater understanding into the application of whole genome sequencing data. The data will contribute to the development of diagnostic strategies to improve both patient care and outbreak responses.
FSS researcher: Dr Amy Jennison
Lead organisation: Dr Andrew Henderson, Pathology Queensland, Queensland Health, Dr Patrick Harris, Pathology Queensland, Queensland Health
Prospective characterisation of carbapenemase-producing Enterobacteriaceae in Queensland using whole genome sequencing
Antibiotic resistance in gram-negative bacteria has emerged as a major public health concern in recent years. We now face the global phenomenon of bacteria increasingly acquiring carbapenemase genes, rendering therapy with carbapenems (one of our ‘last resort’ antibiotics for antibiotic-resistant infections) ineffective. This study will use whole genome sequencing to help elucidate patterns of transmission, enabling rapid identification of future outbreaks.
FSS researcher: Dr Amy Jennison
Lead organisation: Dr Claire Heney, Pathology Queensland, Queensland Health, Dr Patrick Harris, Pathology Queensland, Queensland Health, Assoc. Prof. David Whiley, Pathology Queensland, Queensland Health
Collaborators: Assoc. Prof. Scott Beatson, University of Queensland, Prof. Mark Schembri, University of Queensland
New genomic methods to improve management of Staphylococcus aureus infections in Queensland
Staphylococcus aureus remains a leading cause of hospital-acquired infection but weaknesses inherent in currently available typing methods impede effective infection prevention and control. Whole genome sequencing allows clinical isolates of S. aureus to be compared with each other down to a resolution of a single nucleotide difference. This allows greater precision in describing and defining different lineages and offers the potential for an outbreak investigator to determine unambiguously the relatedness of isolates. Combined with epidemiological data it is then possible to better target infection control resources.
FSS researcher: Dr Amy Jennison
Lead organisation: Prof. Graeme Nimmo, Pathology Queensland, Queensland Health, Assoc. Prof. David Whiley, Pathology Queensland, Queensland, Haakon Bergh, Pathology Queensland
Phage type converting plasmids in Salmonella Typhimurium
This project has the prospect of adding to the present stock of knowledge about phage type conversion by plasmids as well possibly defining the precise elements which are the agents of conversion. It would also help to explain some of the mysteries of phage typing results and could provide alternative tests for the molecular unit at Public Health Microbiology to discriminate between isolates when phage typing is discontinued. This would help epidemiologists to understand better the relationship between phage type and genotype when investigating possible outbreaks.
FSS researchers: Lester Hiley, Dr Rikki Graham
Research supervisor: Dr Amy Jennison
Collaborators: Dr Seamus Fanning, University College Dublin, Assoc. Prof. Scott Beatson, University of Queensland
Understanding STEC epidemiology and the predominance of O157: H-negative in Australia: genetic characterisation and virulence assessment of STEC isolates
Shiga-toxigenic Escherichia coli (STEC), a cause of gastroenteritis typically associated with bloody diarrhoea is a notifiable disease in Australia. STEC strains of O157 serogroup are typically reported as being the most prevalent for causing human disease and life threatening complications such haemolytic uremic syndrome (HUS) worldwide, with O157: H7 the most frequent serotype to be isolated from HUS cases. Australia however has a unique STEC epidemiology where HUS cases are typically associated with non-O157 strains and the majority of O157 strains isolated from Australian patients are O157: H-negative. This project will explore the reasons behind the O157: H-negative phenotype predominant in Australia, while also marrying genetic data and expression data to inform on the lower virulence demonstrated by these strains.
FSS researchers: Dr Amy Jennison, Dr Irani Rathnayake, Christine Guiglielmino
Student placement: Alex Pintara, QUT
Collaborator: Prof. Flavia Huygens, QUT QIMR Berghofer
Phase variation studies in non-typeable invasive Haemophilus influenzae (NTHi collection)
Haemophilus influenzae is an important aetiological organism of both adult and child respiratory disease, characterised largely by the presence or absence of a polysaccharide capsule. The number of non-typeable (NTHi) invasive H. influenzae isolates referred to the Queensland Public Health Microbiology Laboratory has increased notably year by year. Little is known about which virulence genes or mechanisms contribute to these un-encapsulated strains being able to invade, colonise and cause disease in the human host. Based on the Atack research groups previous studies, the study proposes to examine invasive NTHi isolates for both gene presence and expression status to futher understanding into virulence mechanisms specific to NTHi.
FSS researcher: Dr Amy Jennison
Lead organisation: John Atack, Griffith University Institute for Glycomics
Bacterial aetiology of severe febrile illness in Yangon, Myanmar
Febrile illness is one of the most common reasons to seek healthcare in the tropics. Malaria has been the febrile illness most frequently over-diagnosed, and febrile patients without malaria have case fatalities ratios that equal or exceed those with malaria. Our WHO Leptospirosis laboratory join leaders in febrile illness research to investigate the aetiology and resistance patterns of leptospirosis and rickettsial pathogens in Laos.
FSS researcher: Assoc. Prof. Scott Craig
Collaborators: Prof. Paul Newton, University of Oxford, Prof. John Crump, University of Otago, Dr Ohn Myat, University of Medicine, Yangon
Use of molecular typing and genomics to enhance surveillance of Neisseria gonorrhoeae and associated antimicrobial resistance in Queensland
Current gonorrhoea management programs are effectively blind to the role of population level transmission dynamics that underpin infection rates and antimicrobial resistance. This project will apply the latest genomic techniques to, for the first time, assess gonorrhoea transmission dynamics within Queensland. We will collaborate with sexual clinicians to ensure that results are to be presented in a way that is understandable and useable. These new tools will have important public health implications, including planning and monitoring effective interventions and preparing clinical care and treatment guidelines.
FSS researchers: Dr Amy Jennison, Helen Smith, Dr Rikki Graham, Christine Guglielmino, Irani Rathnayake, Dr Ning-Xia Fang
Collaborators: Assoc. Prof. David Whiley, Pathology Queensland, Queensland Health, Dr Ella Trembizki, University of Queensland, Dr Graham Neilsen, Metro North Sexual Health Service and HIV Service, Dr Julian Langton-Lockton, Metro North Sexual Health Service and HIV Service Dr Diane Rowling, Metro North Sexual Health Service and HIV Service, Dr Theo van Lieshout, Metro North Sexual Health Service and HIV Service
Publications
Journal articles
Abady, N.R., Guglielmino, C.J., Graham, R.M.A., Adelskov, J., Smith, H.V., Patel, B.K.C., Jennison, A.V. (2017)  Genetic characterization of a Neisseria meningitidis cluster in Queensland, Australia. Canadian Journal of Microbiology, July 2017 63(7):644–647.
Allcock, R., Jennison, A.V., Warrilow, D. (2017) Towards a universal molecular microbiological test. Journal of Clinical Microbiology, 55(9).
Bates, J.R. (2017) Public Health Laboratory Network. Microbiology Australia, 38(4).
Buckley, C., Trembizki, E., Donovan, B., Chen, M., Freeman, K., Guy, R., Lahra, M.M., Kundu, R., Regan, D., Smith, H.V., Whiley, D.M. (2016) Real-time PCR detection of Neisseria gonorrhoeae susceptibility to penicillin. Journal of Antimicrobial Chemotherapy. 71(11):3090–3095.
Chansamouth, V., Thammasack, S., Phetsouvanh, R., Keolouangkot, V., Moore, C.E., Blacksell, S.D., Castonguay-Vanier, J., Dubot-Peres, A., Tangkhabuanbutra, J., Tongyoo, N., Souphaphonh, P., Sengvilaipaseuth, O., Vongsouvath, M., Phommasone, K., Sengdethka, D., Seurbsanith, A., Craig, S.B., Hermann, L., Strobel, M., Newton, P.N. (2016) The aetiologies and impact of fever in pregnant inpatients in Vientiane, Laos. PLoS Neglected Tropical Diseases, 10(4):e0004577.
Dittrich, S., Rudgard, W.E., Woods, K.L., Silisouk, J., Phuklia, W., Davong, V., Vongsouvath, M., Phommasone, K., Rattanavong, S., Knappik, M., Craig, S.B., Weier, S.L., Tulsiani, S.M., Dance, D.A.B., Newton, P.N. (2016) The utility of blood culture fluid for the molecular diagnosis of Leptospira: a prospective evaluation. The American Journal of Tropical Medicine and Hygiene 94(4):736–40.
Doyle, C.J., Mazins, A., Graham, R.M.A., Fang, N-X. (2017) Sequence analysis of toxin gene-bearing Corynebacterium diphtheriae strains, Australia. Emerging Infectious Diseases, 23(1):105–107.
Fu, S., Hiley, L.A., Octavia, S., Tanaka, M.M., Sintchenko, V., Lan, R. (2017) Comparative genomics of Australian and international isolates of Salmonella Typhimurium: correlation of core genome evolution with CRISPR and prophage profiles. Scientific Reports, 7(1):9733.
Gallo, J.G., Woods, M., Graham, R.M.A., Jennison, A.V. (2017) A severe transmissible Majocchi’s granuloma in an immunocompetent returned traveler. Medical Mycology Case Reports, 18:5–7.
Graham, R.M.A., Donohue, S., McMahon, J., Jennison, A.V. (2017) Detection of spotted fever group Rickettsia DNA by deep sequencing. Emerging Infectious Diseases, 23(11):1911–1913.
Graham, R.M.A., Doyle, C.J., Jennison, A.V. (2017) Epidemiological typing of Neisseria gonorrhoeae and detection of markers associated with antimicrobial resistance directly from urine samples using next generation sequencing. Sexually transmitted infections, 93(1):65–67.
Jennison, A.V. (2017) Impact of whole genome sequencing in Public Health reference laboratories. Microbiology Australia, 38(4).
Jennison, A.V., Masson, J.J., Fang, N-X., Graham, R.M.A., Bradbury, M.I., Fegan, N., Gobius, K.S., Graham, T.M., Guglielmino, C.J., Brown, J.L., Fox, E.M. (2017) Analysis of the Listeria monocytogenes population structure among isolates from 1931 to 2015 in Australia. Frontiers in Microbiology, 8:603.
Lau, C.L., Watson, C.H., Lowry, J.H., David, M.C., Craig, S.B., Wynwood, S., Kama, M., Nilles, E.J. (2016) Human Leptospirosis infection in Fiji: an eco-epidemiological approach to identifying risk factors and environmental drivers for transmission. PLoS Neglected Tropical Diseases, 10(1):e0004405.
McCarthy, K.L., Jennison, A.V., Wailan, A.M., Paterson, D.L. (2017) Draft genome sequence of an IMP-7-producing Pseudomonas aeruginosa bloodstream infection isolate from Australia. Genome announcements, 5(27):e00596–17.
McCarthy, K.L., Jennison, A.V., Wailan, A.M., Paterson, D.L. (2017) Draft genome sequences of two Pseudomonas aeruginosa bloodstream infection isolates associated with rapid patient death. Genome announcements, 5(33):e00597–17.
Mowlaboccus, S., Perkins, T.T., Smith, H.V., Sloots, T.P., Tozer, S.J., Prempeh, L-J., Tay, C.Y., Peters, F., Speers, D., Keil, A.D., Kahler, C.M. (2016) Temporal changes in BEXSERO® Antigen sequence type associated with genetic lineages of Neisseria meningitidis over a 15-Year period in Western Australia. PLoS One, 11(6):e0158315.
Robertson, G.J., Koehler, A.V., Gasser, R.B., Watts, M., Norton, R., Bradbury, R.S. (2017) Application of PCR-based tools to explore Strongyloides infection in people in parts of Northern Australia. Tropical Medicine and Infectious Disease, 2(4):62.
Shaban, R.Z., Maloney, S., Gerrard, J., Collignon, P., Macbeth, D., Cruickshank, M., Hume, A., Jennison, A.V., Graham, R.M.A., Bergh, H., Wilson, H.L., Derrington, P. (2017) Outbreak of health care-associated Burkholderia cenocepacia bacteremia and infection attributed to contaminated sterile gel used for central line insertion under ultrasound guidance and other procedures. American Journal of Infection Control, 45(9):954–958
Smith, H.V. (2016) When ‘Spanish flu’ came to Brisbane. In: Brisbane diseased: contagions, cures and controversy. Papers (Brisbane History Group) (25). Boolarong Press, Moorooka, Qld., pp. 149–167.
Smith, H.V. (2017) Public Health. Microbiology Australia, 38(4):155.
Smith, H.V., Jennison, A.V. (2017) Changing epidemiology of invasive meningococcal disease in Australia 1994–2016. Microbiology Australia, 38(4).
Staples, M., Graham, R.M.A., Jennison, A.V. (2017) Characterisation of invasive clinical Haemophilus influenzae isolates in Queensland, Australia using whole-genome sequencing. Epidemiology and Infection, 145(8):1727–1736.
Staples, M., Fang, N-X., Graham, R.M.A., Smith, H.V., Jennison, A.V. (2017) Evaluation of the SHIGA TOXIN QUIK CHEK and ImmunoCard STAT! EHEC as screening tools for the detection of Shiga toxin in fecal specimens. Diagnostic Microbiology and Infectious Disease, 87(2):95–99.
Staples, M., Graham, R.M.A., Hicks, V., Strachan, J., Goncalves da Silva, A., Peverall, J., Wicks, V., Jennison, A.V. (2017) Discovery of Streptococcus pneumoniae serogroup 35 variants in Australian patients. Clinical Microbiology and Infection, 23(7).
Trembizki, E., Wand, H., Donovan, B., Chen, M., Fairley, C.K., Freeman, K., Guy, R., Kaldor, J., Lahra, M.M., Lawrence, A., Lau, C.L., Pearson, J., Regan, D., Ryder, N., Smith, H.V., Stevens, K., Su, J-Y., Ward, J., Whiley, D.M. (2016) The molecular epidemiology and antimicrobial resistance of Neisseria gonorrhoeae in Australia: a nationwide cross-sectional study, 2012. Clinical Infectious Diseases, 63(12):1591–1598.
Vasant, B.R., Stafford, R.J., Jennison, A.V., Bennett, S., Bell, R.J., Doyle, C.J., Young, J.R., Vlack, S.A., Titmus, P., El Saadi, D., Jarvinen, K., Coward, P., Barrett, J., Staples, M., Graham, R.M.A., Smith, H.V., Lambert, S.B. (2017) Mild illness during outbreak of shiga toxin−producing Escherichia coli O157 infections associated with agricultural Show, Australia. Emerging Infectious Diseases, 23(10).
Watkinson, A.J., Micalizzi, G.R., Bates, J.R., Costanzo, S.D. (2017) Occurrence of antimicrobial resistant Escherichia coli in waterways of southeast Queensland, Australia. Medical Research Archives, 5(9).
Woods, K.L., Nic-Fhogartaigh, C., Arnold, C., Boutthasavong, L., Phuklia, W., Lim, C., Chanthongthip, A., Tulsiani, S.M., Craig, S.B., Burns, M-A., Weir, S.L., Davong, V., Sihalath, S., Limmathurotsakul, D., Dance, D.A.B., Shetty, N., Zambon, M., Newton, P.N., Dittrich, S. (2017) A comparison of two molecular methods for diagnosing leptospirosis from three different sample types in patients presenting with fever in Laos. Clinical Microbiology and Infection, 2017 26 October, In press.
Wynwood, S., Burns, M-A., Graham, G.C., Weier, S.L., McKay, D.B., Craig, S.B. (2016) Serological diagnosis of Leptospirosis in bovine serum samples using a microsphere immunoassay. Veterinary Record Open, 3:e000148.
Wynwood, S., Burns, M-A., Graham, G.C., Weier, S.L., McKay, D.B., Peck, S., Craig, S.B. (2016) Leptospirosis in Tasmanian Devils (Sarcophilus harrisii) in Tasmania, 2008–2012. Journal of Wildlife Diseases, 52(3):636–641.
Lectures and presentations
Bates, J.R. (2016) The impact of CIDT on public health lab surveillance. In: Foodborne diseases: changing epidemiology and disease control research symposium, 1 September 2016, Westmead Hospital, Sydney.
Fang, N-X., Doyle, C.J., Graham, R.M.A., Staples, M., Jennison, A.V. (2016) Genotyping of Group A Streptococcus by whole genome sequencing. In: The 5th Annual Molecular Microbiology Meeting, March 2–3, 2016, Waterview, Bicentenial Park NSW Australia.
Graham, R.M.A. (2017) Salmonella Enteritidis genomic surveillance in Queensland. In: ASM Clinical Microbiology Special Interest Group Meeting, 29 November 2017, Coopers Plains, Qld.
Graham, R.M.A., Jennison, A.V. (2017) Deep sequencing of clinical extracts for pathogen discovery and molecular epidemiological surveillance. In: 6th Applied Bioinformatics and Public Health Microbiology conference, 17–19 May 2017, Cambridge, UK.
Jennison, A.V. (2016) Jumping in the deep end: direct deep sequencing of clinical samples in the Public Health Microbiology laboratory. In: Microbiology in Mt Tamborine, 19 November 2016, Mount Tamborine, Queensland.
Jennison, A.V. (2016) The detection of N. gonorrhoeae directly from urine samples using NGS. In: Advances in Microbial Genomics for Public Health and Clinical Microbiology Symposium, 15 November 2016, Doherty Centre for Applied Microbial Genomics, Melbourne, Victoria.
Jennison, A.V. (2017) Genomics guided pathogen detection and surveillance. In: Microbial Genomics for Public Health and Clinical Microbiology Symposium, 20 October 2017, Westmead, Sydney, NSW.
Jennison, A.V. (2017) Genomics in Public Health microbiology. In: Practical Microbial Genomics Workshop, 4 November 2017, UQ Centre for Clinical Research (UQCCR), Royal Brisbane and Women’s Hospital, Herston.
Jennison, A.V. (2017) Practical applications of whole genome sequencing in a Public Health Laboratory. In: Pathogen Genomics for Public Health, 26 June 2017, Melbourne, Victoria.
Jennison, A.V. (2017) Whole genome sequencing for solving microbial outbreaks and disease surveillance. In: Illumina Ignite Event, 19 September 2017, USQ, Toowoomba, Qld.
Jennison, A.V. (2017) Whole genome sequencing in Queensland. In: Communicable Diseases Workshop–NSW Health, 14 November 2017, Sydney, NSW.
Jennison, A.V. (2017) Whole Genome Sequencing of bacteria, how it is routinely used in Public Health/hospital settings, and applications in the study of Gonorrhoea and associated antimicrobial resistance. In: 2017 Australasian Sexual Health Conference (ASHM), 7–9 November 2017, Canberra, ACT.
Lau, C.L., Watson, C.H., Lowry, J.H., David, M.C., Craig, S.B.,Wynwood, S., Kama, M., Nilles, E.J. (2016) Mapping leptospirosis hotspots in Fiji: an eco-epidemiological approach to identifying environmental and socio-demographic drivers of zoonotic disease emergence. In: International Congress for Tropical Medicine and Malaria, 18–22 September, 2016, Brisbane, Qld.
Micalizzi, G.R. (2017) Public Health investigations — enteric pathogens. In: ASM Clinical Microbiology Special Interest Group Meeting, 29 November 2017, Coopers Plains, Qld.
Mowlaboccus, S., Perkins, T.T., Smith, H.V., Sloots, T.P., Tozer, S.J., Prempeh, L-J., Tay, C. Y., Peters, F., Speers, D., Keil, A.D., Richmond, P., Howden, B.P., Kahler, C.M. (2016) Transcontinental changes in the population structure of Neisseria meningitidis and coverage of the BEXSERO® vaccine in Australia. In: 20th International Pathogenic Neisseria Conference, 4–9 September, 2016, Manchester, United Kingdom.
Rathnayake, I.U., Doyle, C.J., Graham, R.M.A., Fang, N-X., Smith, H.V., Jennison, A.V. (2017) Whole–genome sequencing (WGS) provides genomic insight into diphtheria in Queensland. In: 26th annual RBWH Healthcare Symposium, 12–14 September 2017, Herston, Qld.
Smith, H.V. (2017) Changing Meningococcal epidemiology in Australia. In: ASM Clinical Microbiology Special Interest Group Meeting, 29 November 2017, Coopers Plains, Qld.
Tozer, S.J., Whiley, D.M., Smith, H.V., Rockett, R., Jennison, A.V., Doyle, C.J., Graham, R.M.A., Gilchrist, S., Orlandi, L., Frosi, G., Boccadifuoco, G., Medini, D., Serruto, D., Borrow, R., Findlow, J., Pizza, M., Nissen, M.D., Sloots, T.P. (2016) Use of the meningococcal antigen typing system to assess the Australian meningococcal strain coverage with a multicomponent serogroup B vaccine. In: 20th International Pathogenic Neisseria Conference, 4–9 September, 2016, Manchester, UK
1.4 Public Health Virology
We perform surveillance testing of viruses and mosquitoes for state and federal authorities allowing for a targeted public health response, and have the capacity to respond to any public health crisis involving emerging or re-emerging viruses and rickettsiae.
We provide a state-wide diagnostic and tertiary referral service for viral and rickettsial diseases. Our service also investigates outbreaks of virus diseases of public health significance in Queensland.
Overview
Our facility includes high containment laboratories certified by the Department of Agriculture and Water Resources and the Office of the Gene Technology Regulatory. This allows us to work with viruses that cannot be handled within a normal laboratory or that are exotic to Australia.
We also conduct research into zoonoses, emerging viruses and arboviruses, including studies into the potential for native and exotic vectors to transmit arboviral diseases.
Key testing services include:
Measles—samples from suspected measles cases (usually swabs and/or urine) are tested for the presence of the virus. Results can indicate whether the patient has a wild-type measles infection or vaccine-strain infection.
Norovirus—faecal samples are collected from outbreaks of vomiting and diarrhoea which often occur in nursing homes or childcare centres. These are tested for the presence of norovirus which causes viral gastroenteritis.
Dengue—samples are collected from patients who may have been exposed. Blood samples are tested for the presence
of virus and antibodies to the dengue virus. If the virus or antibodies are detected it is often possible to determine the serotype of the infecting dengue virus. Genotyping can be used to track sources of infections to know hot spots around the globe and to monitor the spread of outbreaks.
Advancing research through collaboration
The Public Health Virology research team supports the diagnostic team by investigating new technologies and techniques to improve both the quality of the diagnostic service and the speed of results. Our research is about finding quicker ways to detect infectious diseases like Zika and Dengue. 
Where Australia was once somewhat protected through geographical isolation, global trade and ease of travel now means that diseases and viruses previously found only in remote environments are spreading to more populated areas. It’s vital that we maintain our capacity to respond quickly to emerging and exotic diseases. 
In the last 12 months we have explored the ability of custom-designed NanoString probes to detect, type and sub-type seasonal influenza viruses with promising preliminary results, and have embraced whole genome sequencing as a tool to expose divergent and novel viruses. Building collaborative research partnerships is crucial to our ability to act quickly. 
Collaborating with our university and commercial partners enables us to share knowledge and resources, and tap into national and international funding to support our research. As our collective knowledge grows, so too does our ability to inform strategic planning to combat the threat of mosquito-borne disease and viruses.
Research projects
Zika virus as an emerging pathogen — the Australian context
Zika virus (ZIKV) causes disease ranging from a mild febrile illness to severe neurological disease. The virus is transmitted between humans by mosquitoes. Epidemics are ongoing in the western Pacific and South America. Alarmingly, ZIKV infection has been diagnosed in 31 travellers to Queensland from these epidemic regions. This project was the first to assess the potential for Australian mosquito species to transmit ZIKV.
Principal researcher: Assoc. Prof. Andrew van den Hurk
Research team: Dr Alyssa Pyke, Dr Sonja Hall-Mendelin, Jamie McMahon, Carmel Taylor
Characterisation and correlative molecular and phenotypic analysis of an ancestral sylvatic dengue virus from Brunei 2014
This study examined and characterised a previously undetected novel ancestral DENV strain, which underwent a rare spillover event from an animal reservoir to a human via transmission from sylvatic forest dwelling mosquitoes. It was demonstrated that BRUN2014 has the capacity to replicate in Aedes albopictus cells and infect Aedes aegypti mosquitoes at rates similar to an urban outbreak DENV-1 strain, highlighting the transmission potential associated with this strain and its public health related risks.
Principal researcher: Dr Alyssa Pyke
Research team: Assoc. Prof. Andrew van den Hurk, Carmel Taylor, Dr Peter Moore, Dr Sonja Hall-Mendelin
Evolutionary response of chikungunya virus to Wolbachia based biocontrol cell
The introduction of the endosymbiont Wolbachia has become a potential novel biocontrol of RNA viruses transmitted by mosquitoes. Previous research done by QH in collaboration with Monash University shows that chikungunya virus replication in mosquitoes is limited by the presence of Wolbachia. RNA viruses evolve extremely fast however and may adapt to recover replication, rendering this novel biocontrol ineffective. The aim of this project is to use experimental evolution to test whether chikungunya can rapidly recover replication in the face of selection imposed by Wolbachia. Early results have indicated that, unlike dengue virus, CHIKVs can surprisingly overcome the very strong blocking effect of the wMelPop strain of Wolbachia.
FSS researcher: Dr Alyssa Pyke
Lead organisation: Dr Francesca Frentiu, Queensland University of Technology
A rapid field test for detecting infected mosquitoes (Bill and Melinda Gates grant funding)
The primary expected outcome of this project is the development and assessment of simple and inexpensive assays for the detection of arboviruses, malaria parasites and Wolbachia in mosquitoes. These assays will have direct application in the roll-out of disease control strategies in areas where access to specialised diagnostic facilities is limited, such as in remote areas or developing countries. For instance, they could be used by vector control personnel, with no experience in diagnostics, in locations where Wolbachia is being rolled out for potential control of dengue (ie. North Queensland).
FSS researcher: Assoc. Prof. Andrew van den Hurk
Lead organisation: Dr Joanne Macdonald, University of Sunshine Coast
Collaborators: Prof. Roy Hall, University of Queensland, Assoc. Prof. Cheryl Johansen, University of Western Australia, Dr Leon Hugo, QIMR Berghofer
Evolution and emergence of Australian encephalitogenic flaviviruses
This project will help us understand the fundamental scientific question: where do diseases come from? It will give insight into how Australian arboviruses have changed with time, and determine any trends in pathogenicity. The work will focus on the genome sequencing of several flaviviruses: a group of mosquito-borne viruses, a strain of which recently emerged to cause virulent encephalitis in horses. This is a unique opportunity to determine the genome changes that occur as the virus becomes more virulent.
Principal researcher: Dr David Warrilow
Research team: Dr Ben Huang
Tiresome ticks: ecology and transmission of tick-borne disease in Australia (ARC grant funding)
Growing numbers of Australians are diagnosed with a Lyme disease-like illness, presumed to be tick-borne, yet a conclusive diagnosis remains elusive because of uncertainty about its causative agent(s). Building on data from previous research, the project will determine the bacterial, protozoal and viral biodiversity in wildlife ticks and their native mammal hosts, and provide new information about the biology and transmission dynamics of these microorganisms, and their potential to cause disease in wildlife, domesticated animals and humans. This research will lead to improved diagnostic tests and management protocols for tick-borne disease in Australia.
FSS researcher: Dr Sonja Hall-Mendelin
Lead organisation: Prof. Peter J Irwin, Murdoch University, Prof. Una Ryan, Murdoch University
Collaborators: Prof. Roy Hall, University of Queensland
Molecular characterisation of the Ross River virus responsible for the 2015 epidemic in southeast Queensland
Human infection with the mosquito-transmitted Ross River virus (RRV) causes debilitating arthritic disease. In 2014–2015, the largest RRV outbreak ever reported in Australia occurred in Queensland, resulting in 6,372 cases. It was hypothesised that the scale of the outbreak was due to the emergence of a mutated or previously unrecognized virus strain. We analysed 41 RRV nucleotide sequences to ascertain whether the virus strain/s circulating during the 2015 outbreak was different to other local and national sequences. It was revealed that at least 2 lineages of RRV contributed to the outbreak. These lineages have a widespread distribution in eastern Australia. This suggests that the scale of the outbreak was probably not due to the emergence of a mutated RRV strain. Instead, an abundance of immunologically-naïve amplifying hosts such as wallabies and possums, or elevated mosquito populations may have contributed to the scale of the epidemic. This project was the most comprehensive analysis of RRV sequences in Queensland ever undertaken.
Principal researcher: Assoc. Prof. Andrew van den Hurk
Purification of baculovirus expressed Hendra virus nucleocapsid (HeV N) protein for luminex microsphere serological applications
Hendra virus can cause fatal encephalitis in humans and animals and infections have a high rate of morbidity and mortality. Since the discovery and pathogenic emergence of HeV in 1994, there have been seven human cases, four of which were fatal and more than 80 horses have died or been euthanised. In 2011–2012 there was an unprecedented, widespread incidence of HeV infection in horses along the east coast of Queensland and northeast New South Wales. This study aims to address priority 3 of the National HeV Research Program which is to improve the capacity to detect and respond effectively to HeV incidents in susceptible human or animal hosts. The primary objective will be to produce a highly purified protein derivative in order to enhance its performance in a luminex microsphere immunoassay and provide a reliable, continued source of the diagnostic reagent. This will ensure there is adequate laboratory capacity to respond to disease outbreaks or bioterrorist threats in the future.
FSS researcher: Dr Alyssa Pyke
Collaborator: Dr Linda Lua, University of Queensland
Establishment of a mouse model for ZIKV encephalopathy
ZIKV is a globally emerging mosquito disease with Queensland reporting 26 of Australia’s 54 human cases since 2012. Almost nothing is known about the origin or biological mechanisms that cause disease following infection with ZIKV, particular encephalopathy. Encephalopathy does not refer to a single disease, but rather to a syndrome of overall brain dysfunction that can be caused by a number of conditions such as viral infection. The aim of this project is to develop a mouse model for ZIKV encephalopathy to study the nature and development of the disease. To our knowledge no such model exists currently and the only reported mouse studies were undertaken in 1952 and 1971. In 2016 Public Health Virology was the first laboratory in Australia to recover a ZIKV isolate from a clinical patient returned from Tonga. The Tonga strain is closely related to the ZIKV strains currently circulating in the Pacific and the Americas which have been implicated in the severe disease syndromes microcephaly and Guillain-barré syndrome. Provision of the 2016 Tonga ZIKV isolate by PHV will enable ground-breaking ZIKV research and foster new collaborative links with ongoing mutual benefit between QH and the University of Sydney.
FSS researcher: Dr Alyssa Pyke
Lead organisation: Dr Markus J Hofer, University of Sydney
Hitchhikers from the jungle: assessment of evolution, emergence potential and public health implications of rare and divergent dengue viruses
Dengue viruses (DENVs) are the leading cause of mosquito-borne viral disease of humans. They originated from the jungles of Asia and Africa where they continue to circulate in enzootic (sylvatic) transmission cycles between monkeys and mosquitoes. In 2014–2015, we isolated two unique and highly divergent sylvatic DENVs from viraemic travellers. Our published findings for the first of these viruses highlight key public health implications including infection rates of local Aedes aegypti mosquitoes. Further study of these distantly related DENVs, their emergence and transmission is integral for mitigating future disease and highly pertinent for effective vaccines and mosquito management strategies.
Principal researcher: Dr Alyssa Pyke
Research team: Assoc. Prof. Andrew van den Hurk, Dr Sonja Hall-Mendelin, Dr Peter Moore
Collaborators: Prof. Roy Hall, University of Queensland, Dr Jody Hobson-Peters, University of Queensland, Dr Helle Bielefeldt-Ohmann, University of Queensland
Computer analysis of the sequence of new arbovirus field isolates
This project grows a long term collaboration with Professor Roy Hall’s laboratory at the University of Queensland. We will undertake phylogenetic analysis of sequence to determine the taxonomic grouping of a number of potentially novel mosquito viruses.
Principal researcher: Dr David Warrilow
Collaborator: Dr Jody Peters, University of Queensland
Virus infection and replication dynamics influence Zika virus (ZIKV) transmission by Australian mosquitoes
This project extends the experiments undertaken in a previous study, to further incriminate Australian mosquitoes as ZIKV vectors and elucidate intrinsic factors, such as barriers to infection, tissue tropisms, and infection thresholds, which influence whether a species is a competent or incompetent vector of ZIKV. In the Queensland context, the outcomes will inform public health authorities as to which mosquito species to target during disease control programmes. Of interest globally, this study will reveal further insights into the susceptibility, replication and transmission dynamics of ZIKV in mosquitoes.
Principal researcher: Assoc. Prof. Andrew van den Hurk
Research team: Dr Sonja Hall-Mendelin, Dr Alyssa Pyke, Dr Peter Moore
Collaborators: Dr Helle Bielefeldt-Ohmann, University of Queensland
Development and field validation of a dynamic sentinel surveillance systems for detection of Zika (ZIKV) and dengue viruses (DENV) and malaria parasites (Australian Institute of Tropical Health and Medicine grant funding)
Each year across tropical and subtropical regions of the world an estimated 390 million people are infected with DENV, 5 per cent of which develop severe and life threatening dengue haemorrhagic disease. ZIKV is a rapidly emerging global health risk with transmission now detected in 52 countries from 2007 to 2016. Across the world there are over 200 million cases of malaria and up to a million deaths annually. Malaria continues to be a major public health issue in developing countries including those closest to Australia: Papua New Guinea and the Solomon Islands. One of the primary issues plaguing detection and control initiatives is a lack of sensitive arbovirus surveillance devices. It is our goal to remedy this situation by developing a sentinel surveillance device to allow wide-spread, rapid and economical monitoring of viral activity in local mosquito populations.
FSS researcher: Assoc. Prof. Andrew van den Hurk
Lead organisation: Prof. Scott Richie, James Cook University, Dr Brian Johnson, James Cook University
Student placement: Ms Ana Ramirez, James Cook University
NanoString for virus detection and typing
The overall aim of the proposal is to determine, at the level of proof-of-principle, whether a new molecular-based technology called NanoString™ may be a useful diagnostic technique in the Public Health Virology laboratory. NanoString™ offers a number of advantages over existing methods. It is based on nucleic acid probes that specifically detect a complementary target (ie viral RNA). Where it differs from other established methods is that it utilises an optical barcode for each probe which acts as a unique identifier. The hybridisation technology was correctly able to detect, type and subtype influenza A and B virus strains directly from clinical samples in a single reaction without prior isolation or amplification. Whilst currently not as sensitive as amplification-based assays, these results are a first-step towards application of this technology to detection and typing of influenza and other viruses.
Principal researcher: Dr David Warrilow
Assessment and expansion of arbovirus surveillance and monitoring using next generation sequencing.
The specific objectives of this project are to assess various arbovirus sample types using NGS and expand current nucleotide sequencing and phylogenetic analysis for the purpose of improved, rapid and cost-effective monitoring of arbovirus importation and activity and increase our current knowledge and data output for research and diagnostic platforms.
Principal researcher: Dr Alyssa Pyke
Recombinant yellow fever virus antigen expression in baculovirus cells
Yellow fever virus (YFV) is a potentially fatal mosquito-borne disease currently endemic to parts of Africa and South America. Prevention of incursion of YFV into Queensland is a major public health priority as the vector, Aedes aegypti, exists in the north of the state. Production of the antigen is problematic. The aim of this project is to generate a source of recombinant yellow fever virus antigen for use as an alternative and more reliable source of antigen for the flavivirus microsphere immunoassay (MIA) test.
Principal researcher: Carmel Taylor
Research supervisor: Dr David Warrilow
Can mosquito excreta be used to enhance surveillance of Ross River and West Nile viruses?
Detection of circulating mosquito-borne viruses in wild mosquito and vertebrate populations can be used to identify periods of elevated virus activity. In collaboration with James Cook University we have developed a sugar-based arbovirus surveillance system whereby mosquitoes are attracted to purpose-built CO2-baited traps. Within the traps, mosquitoes are allowed to feed on honey-soaked nucleic acid preservation (FTA) cards, which are dispatched to a central diagnostic facility for potential molecular detection of arboviruses expectorated by sugar feeding mosquitoes. We propose to enhance the sensitivity of the sugar-based surveillance system by analysing excreta samples produced from the final stage of the feeding and digestive process. The concept for this study was inspired by a recent study which demonstrated that dengue viruses could be detected in excreta from infected mosquitoes at potentially higher rates than they could be detected in saliva.
FSS researchers: Assoc. Prof. Andrew van den Hurk, Dr Sonja Hall-Mendelin, Dr Alyssa Pyke Jamie McMahon
Collaborator: Prof. Scott Richie, James Cook University
Student placement: Ms Ana Ramirez, James Cook University
New vectors, new diseases: understanding the risk of chikungunya transmission in Australia (NHMRC grant funding)
Chikungunya virus (CHIKV) is a mosquito-borne pathogen and has caused explosive and unpredictable outbreaks over the past decade, with the current epidemic in the Americas affecting over 1.7 million people. CHIKV infection causes chronic and debilitating polyarthritis/polyarthralgia that can last for several years in adults, and more rarely, may lead to death in children and the elderly. CHIKV poses a significant threat to Australia given its prevalence in neighbouring regions and the rapid global expansion of its vectors, Aedes aegypti and Aedes albopictus mosquitoes.This project aims to assess how genetic diversity in CHIKV strains influences vector competence of Aedes aegypti and Aedes albopictus mosquitoes, under temperatures reflective of climates of major Australian cities.
FSS researcher: Dr Alyssa Pyke
Lead organisation: Dr Francesca Frentiu, Queensland University of Technology
Does a newly discovered insect-specific virus reduce the transmission of flavivirus pathogens in populations of culex annulirostris mosquitoes?
Mosquito-borne flaviviruses like Murray Valley encephalitis (MVEV), West Nile virus (WNV) and dengue cause significant disease in man and animals in Australia. However, a novel group of flaviviruses that replicate in mosquitoes but do not infect man or animals — insect-specific flaviviruses (ISFs) — have been reported to reduce the transmission of flavivirus in mosquitoes that carry ISFs. Recently, a new ISF-like virus, Bamaga virus (BgV), was isolated from mosquitoes collected in northern Australia. In this proposal we will determine whether mosquitoes that carry BgV have reduced ability to transmit MVEV and WNV.
FSS researcher: Dr Sonja Hall-Mendelin
Lead organisation: Prof. Roy Hall, University of Queensland, Dr Jody Hobson-Peters, University of Queensland
Collaborator: Cheryl Johansen, Pathwest
Expression and purification of Zika virus (ZIKV) NS1 protein for diagnostic and research applications
The aim of this project is to produce a highly purified derivative of baculovirus expressed ZIKV non-structural protein 1 (NS1) that is suitable for use in diagnostic assays and research. Specifically,  the ZIKV NS1 will be assessed in luminex microsphere serological assays for its ability to provide rapid and specific diagnoses in a multiplexed platform.
FSS researcher: Dr Alyssa Pyke
Collaborator: Assoc. Prof. Linda Lau, University of Queensland
Can mosquito excreta be used to enhance detection of Australian vector-borne diseases? (Hot North grant funding)
Testing for presence of arboviruses usually involves capturing wild mosquitoes and complicated laboratory analyses. These are not only time and labour-intensive but also costly. Virus detection can be made from saliva however, mosquitoes only expel very small amounts which makes detection difficult. We are proposing to use their excreta instead as it is produced in greater quantities than saliva, and shows higher sensitivity in virus detection. In order to explore this proposal we need to know where and when mosquitoes discharge their excreta in the traps. The discharge of excreta could be dependent on a variety of factors such as temperature, time after last meal or time of day/night, type of trap; it may also be species-dependent or it could just be random. These factors need to be examined to ensure maximum collection of excreta. The results will lead to the modification and optimization of existing traps.
FSS researcher: Assoc. Prof. Andrew van den Hurk
Lead organisation: Prof. Scott A. Ritchie, James Cook University, Dr Dagmar Meyer Steiger, James Cook University
Student placement: Ana Ramirez, James Cook University
Collaborator: Nina Kurucz, Department of Health NT
Publications
Journal articles
Arden, K.E., Shaban, B., Nimmo, G., Nissen, M.D., Sloots, T.P., Mackay, I.M. (2017) Detection of Toscana virus from an adult traveller returning to Australia with encephalitis. Journal of Medical Virology 89(10):1861–1864.
Asad, S., Hall-Mendelin, S., Asgari, S. (2016) Downregulation of Aedes aegypti chromodomain helicase DNA binding protein 7/Kismet by Wolbachia and its effect on dengue virus replication. Scientific Reports, 6.
Colmant, A.M.G., Etebari, D., Webb, C.E., Ritchie, S.A., Jansen, C.C., van den Hurk, A.F., Bielefeldt-Ohmann, H., Hobson-Peters, J., Asgari, S., Hall, R.A. (2017) Discovery of new orbiviruses and totivirus from Anopheles mosquitoes in Eastern Australia. Archives of Virology, 162 (11):3529–3534.
Colmant, A.M.G., Bielefeldt-Ohmann, H., Hobson-Peters, J., Suen, W.W., O’Brien, C.A., van den Hurk, A.F., Hall, R.A. (2016) A newly discovered flavivirus in the yellow fever virus group displays restricted replication in vertebrates. Journal of General Virology, 97(5):1087–1093.
Colmant, A.M.G., Hobson-Peters, J., van den Hurk, A.F., Bielefeldt-Ohmann, H., Hall-Mendelin, S., Chow, W.K., Johansen, C.A., Fros, J.J., Simmonds, P., Watterson, D., Cazier, C., Etebari, K., Asgari, S., Schulz, B.L., Beebe, N.W.,Vet, L.J., Piyasena, T.B.H., Nguyen, H-D. (2017) A new clade of insect-specific flaviviruses from Australian Anopheles mosquitoes displays species-specific host restriction. mSphere, 2(4):e00262–17.
Furuya-Kanamori, L., Cox, M., Milinovich, G.J., Magalhaes, R.J., Mackay, I.M., Yakob, L. (2016) Heterogeneous and dynamic prevalence of asymptomatic influenza virus infections. Emerging Infectious Diseases, 22(6):1052–1056.
Gubala, A., Warrilow, D., (2017) Many encephalitis cases still a medical mystery. Australian and New Zealand Journal of Public Health, 42(1):106
Hall, R.A., Hall-Mendelin, S., Hobson-Peters, J., Prow, N., Mackenzie, J.S. (2016) Ecological and epidemiological factors influencing arbovirus diversity, evolution and spread. In: Arboviruses: molecular biology, evolution and control. Caister Academic Press, pp. 135–166.
Hall-Mendelin, S., Hewitson, G.R., Genge, D., Burtonclay, P.J., De Jong, A.J., Pyke, A.T., van den Hurk, A.F. (2017) FTA cards facilitate storage, shipment, and detection of arboviruses in infected Aedes aegypti collected in adult mosquito traps. American Journal of Tropical Medicine and Hygiene, 96(5):1241–1243.
Hall-Mendelin, S., McLean, B.J., Bielefeldt-Ohmann, H., Hobson-Peters, J., Hall, R.A., van den Hurk, A.F. (2016) The insect-specific Palm Creek virus modulates West Nile virus infection in and transmission by Australian mosquitoes. Parasites & Vectors, 9:414.
Hall-Mendelin, S., Pyke, A.T., Moore, P.R., Mackay, I.M., McMahon, J., Ritchie, S.A., Taylor, C.T., Moore, F., van den Hurk, A.F. (2016) Assessment of local mosquito species incriminates Aedes aegypti as the potential vector of Zika Virus in Australia. PLoS Neglected Tropical Diseases, 10(9):e0004959.
Harrison, J.J., Warrilow, D., McLean, B.J., Watterson, D., O’Brien, C.A., Colmant, A.M.G., Johansen, C.A., Barnard, R.T., Hall-Mendelin, S., Davis, S.S., Hall, R.A., Hobson-Peters, J. (2016) A new orbivirus isolated from mosquitoes in North-Western Australia shows antigenic and genetic similarity to Corriparta Virus but does not replicate in vertebrate cells. Viruses, 8(5).
He, C., Mackay, I.M., Ramsay, K., Liang, Z., Kidd, T., Knibbs, L.D., Johnson, G., McNeale, D., Stockwell, R., Coulthard, M.G., Long, D.A., Williams, T.J., Duchaine, C., Smith, N., Wainwright, C., Morawska, L. (2017) Particle and bioaerosol characteristics in a paediatric intensive care unit. Environment International, 107:87–99.
Hobson-Peters, J., Warrilow, D., McLean, B.J., Watterson, D., Colmant, A.M.G., van den Hurk, A.F., Hall-Mendelin, S., Hastie, M.L., Gorman, J.J., Harrison, J.J., Prow, N.A., Barnard, R.T., Allcock, R., Johansen, C.A., Hall, R.A. (2016) Discovery and characterisation of a new insect-specific bunyavirus from Culex mosquitoes captured in northern Australia. Virology, 489:269–281.
Huang, B., Allcock, R., Warrilow, D. (2016) Newly characterized arboviruses of Northern Australia. Virology Reports, 6:11–17.
Huang, B., Firth, C., Watterson, D., Allcock, R., Colmant, A.M.G., Hobson-Peters, J., Kirkland, P.D., Hewitson, G.R., McMahon, J., Hall-Mendelin, S., van den Hurk, A.F., Warrilow, D. (2016) Genetic characterization of archived Bunyaviruses and their potential for emergence in Australia. Emerging Infectious Diseases, 22(5).
Huang, B., Harrower, B.J., Burtonclay, P.J., Constantino, T.R., Warrilow, D. (2017) Genome sequences of Coxsackievirus B5 isolates from two children with meningitis in Australia. Genome announcements, 5(41):e01125–17.
Huang, B., Prow, N., van den Hurk, A.F., Allcock, R., Moore, P.R., Doggett, S.L., Warrilow, D. (2016) Archival isolates confirm a single topotype of West Nile Virus in Australia. PLoS Neglected Tropical Diseases, 10(12):e0005159.
Huang, B., Pyke, A.T., McMahon, J., Warrilow, D. (2017) Complete coding sequence of a case of Chikungunya virus imported into Australia. Genome announcements, 5(19):e0031017.
Huang, B., West, N., Vider, J., Cox, A.J., Constantino, T.R., Harrower, B.J., Pyke, A.T., McMahon, J., Northill, J.A., Riordan, T., Warrilow, D. (2017) Diagnosis and typing of influenza using fluorescent barcoded probes. Scientific Reports, 7(18092):1–5.
Lee, M., Etebari, K., Hall-Mendelin, S., van den Hurk, A.F., Hobson-Peters, J., Vatipally, S., Schnettler, E., Hall, R.A., Asgari, S. (2017) Understanding the role of microRNAs in the interaction of Aedes aegypti mosquitoes with an insect-specific flavivirus. Journal of General Virology, 98(7):1892–1903.
Maynard, A.J., Ambrose, L., Cooper, R.D., Chow, W.K., Davis, J.B., Muzari, O.M., van den Hurk, A.F., Hall-Mendelin, S., Hasty, J.M., Burkot, T.R., Bangs, M.J., Reimer, L.J., Butafa, C., Lobo, N.F., Syafruddin, D., Maung Maung, Y.N., Ahmad, R., Beebe, N.W. (2017) Tiger on the prowl: invasion history and spatio-temporal genetic structure of the Asian tiger mosquito Aedes albopictus (Skuse 1894) in the Indo-Pacific. PLoS Neglected Tropical Diseases, 11(4):e0005546.
Montgomery, B.L., Shivas, M.A., Hall-Mendelin, S., Edwards, J., Hamilton, N.A., Jansen, C.C., McMahon, J., Warrilow, D., van den Hurk, A.F. (2017) Rapid Surveillance for Vector Presence (RSVP): development of a novel system for detecting Aedes aegypti and Aedes albopictus. PLoS Neglected Tropical Diseases, 11(3):e0005505.
Moore, P.R., van den Hurk, A.F., Mackenzie, J.S., Pyke, A.T. (2017) Dengue viruses in Papua New Guinea: evidence of endemicity and phylogenetic variation, including the evolution of new genetic lineages. Emerging microbes and infections, 6:e114.
Muzari, O.M., Devine, G.J., Davis, J.B., Crunkhorn, B., van den Hurk, A.F., Whelan, P.I., Russell, R.C., Walker, J.A., Horne, P., Ehlers, G., Ritchie, S.A. (2017) Holding back the tiger: successful control program protects Australia from Aedes albopictus expansion. PLoS Neglected Tropical Diseases, 11(2):e0005286.
Northill, J.A., Finger, M., Lyon, M.J., Mackay, I.M. (2017) Japanese encephalitis virus real-time RT-PCR. Protocols.io, November 2017. 
O’Brien, C.A., McLean, B.J., Colmant, A.M.G., Harrison, J.J., Hall-Mendelin, S., van den Hurk, A.F., Johansen, C.A., Watterson, D., Bielefeldt-Ohmann, H., Newton, N.D., Schulz, B.L., Hall, R.A., Hobson-Peters, J. (2016) Discovery and characterisation of Castlerea Virus, a new species of Negevirus isolated in Australia. Evolutionary Bioinformatics, 2017 Feb 23;13:1176934317691269.
Prow, N., Edmonds, J., Williams, D.T., Setoh, Y.X., Bielefeldt-Ohmann, H., Suen, W.W., Hobson-Peters, J., van den Hurk, A.F., Pyke, A.T., Hall-Mendelin, S., Northill, J.A., Johansen, C.A., Warrilow, D., Wang, J., Kirkland, P.D., Doggett,  S.L., Andrade, C.C., Brault, A.C., Khromykh, A.A., Hall, R.A. (2016) Virulence and evolution of West Nile Virus, Australia, 1960–2012. Emerging Infectious Diseases, 22(8):1353–1362.
Pyke, A.T. (2016) Second dengue infection with a highly divergent sylvatic dengue virus strain — Brisbane, Queensland, Australia. ProMED mail. 
Pyke, A.T., Huang, B., Warrilow, D., Moore, P.R., McMahon, J., Harrower, B.J. (2017) Complete genome sequence of a highly divergent dengue virus type 2 strain, imported into Australia from Sabah, Malaysia. Genome announcements, 5(29):e00546–17.
Pyke, A.T., Moore, P.R., Hall-Mendelin, S., McMahon, J., Harrower, B.J., Constantino, T.R., van den Hurk, A.F. (2016) Isolation of Zika Virus imported from Tonga into Australia. PLoS Currents: Outbreaks, 2016 Sep 7, Edition 1
Pyke, A.T., Moore, P.R., Taylor, C.T., Hall-Mendelin, S., Cameron, J.N., Hewitson, G.R., Pukallus, D., Huang, B., Warrilow, D., van den Hurk, A.F. (2016) Highly divergent dengue virus type 1 genotype sets a new distance record. Scientific Reports, 6:22356.
Rafiei, N., Hajkowicz, K., Redmond, A., Taylor, C.T. (2016) First report of Zika virus infection in a returned traveller from the Solomon Islands. Medical Journal of Australia, 204(5):186.
Sarna, M., Alsaleh, A., Lambert, S.B., Ware, R.S., Mhango, L.P., Mackay, I.M., Whiley, D.M., Sloots, T.P., Grimwood, K. (2016) Respiratory viruses in neonates: a prospective, community-based birth cohort study. Pediatric Infectious Disease Journal, 35(12):1355–1357.
Shrestha, S., Flower, R.L.P., Seed, C.R., Keller, A.J., Harley, R., Chan, H-T., Hoad, V., Warrilow, D., Northill, J.A., Holmberg, J.A., Faddy, H.M. (2016) Hepatitis E virus RNA in Australian blood donations. Transfusion, 56(12):3086–3093.
Si, D., Marquess, J., Donnan, E., Harrower, B.J., McCall, B.J., Bennett, S., Lambert, S.T. (2016) Potential exposures to Australian Bat Lyssavirus notified in Queensland, Australia, 2009–2014. PLoS Neglected Tropical Diseases, 10(12):e0005227.
Teoh, L., Mackay, I.M., Van Asperen, P.P., Acworth, J.P., Hurwitz, M., Upham, J.W., Siew, W.H., Wang, C.Y.T., Sloots, T.P., Neeman, T., Chang, A.B. (2017) Presence of atopy increases the risk of asthma relapse. Archives of Disease in Childhood, Epub 2017 Oct 11.
van den Hurk, A.F. (2016) Dengue and the introduction of mosquito- transmitted viruses into Australia. Microbiology Australia, 37(4):167–169.
van den Hurk, A.F., Hall-Mendelin, S., Jansen, C.C. (2017) Zika virus and Culex quinquefasciatus mosquitoes: a tenuous link. The Lancet. Infectious diseases, 17(10):1014–1016.
van den Hurk, A.F., Jansen, C.C. (2016) Arboviruses of Oceania. In: Neglected Tropical Diseases — Oceania. Neglected Tropical Diseases. Springer International Publishing, pp. 193–235.
van den Hurk, A.F., Nicholson, J., Beebe, N.W., Davis, J.B., Muzari, O.M., Russell, R.C., Devine, G.J., Ritchie, S.A. (2016) Ten years of the Tiger: Aedes albopictus presence in Australia since its discovery in the Torres Strait in 2005.  One Health, 2:19–24.
Vidgen, M.E., Edson, D.W., van den Hurk, A.F., Field, H.E., Smith, C.S. (2016) No evidence of Hendra virus infection in the Australian flying-fox ectoparasite genus Cyclopodia. Zoonoses and Public Health, 64(3):228–231.
Warrilow, D. (2017) Arboviruses. In: Encyclopedia of Microbiology. Elsevier, pp. 313–321.
Warrilow, D., Pyke, A.T. (2016) Archival collections are important in the study of the biology, diversity and evolution of arboviruses. Evolutionary Bioinformatics, 12(S2):27–30.
Ye, Y.H., Chenoweth, S.F., Carrasco, A.M., Allen, S.L., Frentiu, F.D., van den Hurk, A.F., Beebe, N.W., McGraw, E.A. (2016) Evolutionary potential of the extrinsic incubation period of dengue virus in Aedes aegypti. Evolution: International Journal of Organic Evolution, 70(11):2459–2469.
Yin, C., Yang, W., Meng, J., Lv, Y., Wang, J., Huang, B. (2017) Co-infection of Pseudomonas aeruginosa and Stenotrophomonas maltophilia in hospitalised pneumonia patients has a synergic and significant impact on clinical outcomes. European journal of Clinical Microbiology & Infectious Diseases, 36(11):2231–2235.
Lectures and presentations
Colmant, A.M.G., Bielefeldt-Ohmann, H., Hobson-Peters, J., Suen, W.W., O’Brien, C.A., van den Hurk, A.F., Hall, R.A. (2016) A newly discovered flavivirus in the yellow fever virus group displays restricted replication in vertebrates. In: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4–9 September, 2016, Surfers Paradise, Qld.
Colmant, A.M.G., Hobson-Peters, J., Bielefeldt-Ohmann, H., Hall-Mendelin, S., van den Hurk, A.F., Chow, W.K., Schulz, B.L., Beebe, N.W., Watterson, D., Fros, J.J., Simmonds, P., Piyasena, T.B.H., Vet, Laura J and Nguyen, H-D., Barnard, R.T., Hall, R.A. (2016) A newly discovered insect-specific flavivirus clade from Anopheles mosquitoes represents a unique model of flavivirus evolution and biology. In: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4–9 September, 2016, Surfers Paradise, Qld.
Colmant, A.M.G., Hobson-Peters, J., Bielefeldt-Ohmann, H., van den Hurk, A.F., Hall-Mendelin, S., Chow, W.K., Johansen, C.A., Fros, J.J., Simmonds, P., Watterson, D., Cazier, C., Etebari, K., Asgari, S., Schulz, B.L., Beebe, N.W., Nguyen, D.H., Barnard, R.T., Hall, R.A. (2017) Stuck in the gut: a new clade of insect-specific flaviviruses from Australian Anopheles mosquitoes displays species-specific host-restriction. In: 9th Australasian Virology Society Meeting (AVS 2017), 5–8 December 2017, Glenelg, South Australia.
Colmant, A.M.G., Hobson-Peters, J., Bielefeldt-Ohmann, H., van den Hurk, A.F., Hall-Mendelin, S., Fros, J.J., Simmonds, P., Etebari, K., Piyasena, T.B.H., Hall, R.A. (2017) Newly discovered insect-specific flaviviruses from Anopheles mosquitoes are highly specialised for their host mosquito species. In: IUMS Congresses 2017: 15th International Congress of Bacteriology and Applied Microbiology, 15th International Congress of Mycology and Eukaryotic Microbiology and 17th International Congress of Virology, 17–21 July 2017, Singapore.
Colmant, A.M.G., Vet, L.J., Hall-Mendelin, S., van den Hurk, A.F., Bielefeldt-Ohmann, H., O’Brien, C.A., Hobson-Peters, J., Piyasena, T.B.H., Khromykh, A.A., Hall, R.A. (2017) Host-restriction and transmission dynamics of a newly discovered flavivirus in the yellow fever virus group. In: IUMS Congresses 2017: 15th International Congress of Bacteriology and Applied Microbiology, 15th International Congress of Mycology and Eukaryotic Microbiology and 17th International Congress of Virology, 17–21 July 2017, Singapore.
Colmant, A.M.G., Vet, L.J., O’Brien, C.A., Bielefeldt-Ohmann, H., Hall-Mendelin, S., van den Hurk, A.F., Piyasena, T.B.H., Hobson-Peters, J., Khromykh, A.A., Hall, R.A. (2017) Cool hideouts for a hot virus: dissecting Bamaga virus host-restriction. In: 9th Australasian Virology Society Meeting (AVS 2017), 5–8 December 2017, Glenelg, South Australia.
Frentiu, F.D., Phillips, D.A., Pyke, A.T., Young, P.R., McGraw, E.A., O’Neill, S.L. (2016) Evolutionary response of Chikungunya virus to Wolbachia. In: International Congress for Tropical Medicine and Malaria, 18–22 September, 2016, Brisbane, Qld.
Hall, R.A., Hobson-Peters, J., Bielefeldt-Ohmann, H., O’Brien, C.A., McLean, B.J., Colmant, A.M.G., Harrison, J.J., Piyasena, T.B.H., Newton, N.D., Wiseman, W., Mah, M., Prow, N., Suhrbier, A., Warrilow, D., van den Hurk, A.F., Hall-Mendelin, S., Johansen, C.A., Davis, S.S., Chow, W.K., Doggett, S.L., Haniotis, J., Webb, C.E. (2016) Neges, Nidos and Nings — so that’s what’s killing my mossie cells. In: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4–9 September, 2016, Surfers Paradise, Qld.
Hall-Mendelin, S., McLean, B.J., Bielefeldt-Ohmann, H., Webb, C.E., Hobson-Peters, J., Hall, R.A., van den Hurk, A.F. (2016) Insect specific flaviviruses suppress West Nile virus replication and transmission. In: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4–9 September, 2016, Surfers Paradise, Qld.
Hall-Mendelin, S., Pyke, A.T., Moore, P.R., Mackay, I.M., McMahon, J., Ritchie, S.A., Taylor, C.T., Moore, F., van den Hurk, A.F. (2016) From the forests of Uganda to our sunburnt country: incrimination of Australian mosquitoes as Zika virus vectors. In: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4–9 September, 2016, Surfers Paradise, Qld.
Harrison, J., Newton, N.D., Warrilow, D., Piyasena, T.B.H., O’Brien, C.A., Davis, S.S., Hall, R.A., Hobson-Peters, J. (2017) Binjari virus: a new insect-specific flavivirus isolated from Aedes normanensis mosquitoes in Northern Australia. In: IUMS Congresses 2017: 15th International Congress of Bacteriology and Applied Microbiology, 15th International Congress of Mycology and Eukaryotic Microbiology and 17th International Congress of Virology, 17–21 July 2017, Singapore.
Hobson-Peters, J., Colmant, A.M.G., O’Brien, C.A., Harrison, J.J., Zhang, X.S., McLean, B.J., Warrilow, D., van den Hurk, A.F., Hastie, M.L., Gorman, J.J., Watterson, D., Johansen, C.A., Hall, R.A. (2016) The risk of emerging arboviruses: Discovery of a divergent group of bunyaviruses in Australian mosquitoes. In: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4–9 September, 2016, Surfers Paradise, Qld.
Hobson-Peters, J., McLean, B.J., Colmant, A.M.G., O’Brien, C.A., Harrison, J.J., Warrilow, D., van den Hurk, A.F., Watterson, D., Johansen, C.A., Hall, R.A. (2017) The risk of emerging arboviruses: discovery of a divergent group of bunyaviruses in Australian mosquitoes. In: IUMS Congresses 2017: 15th International Congress of Bacteriology and Applied Microbiology, 15th International Congress of Mycology and Eukaryotic Microbiology and 17th International Congress of Virology, 17–21 July 2017, Singapore.
Hobson-Peters, J., McLean, B.J., Hall-Mendelin, S., Webb, C.E., Bielefeldt-Ohmann, H., van den Hurk, A.F., Hall, R.A. (2016) Mosquito-specific viruses can regulate the replication and transmission of Dengue and West Nile viruses. In: International Congress for Tropical Medicine and Malaria, 18–22 September, 2016, Brisbane, Qld.
Huang, B., Prow, N.A., van den Hurk, A.F., Allcock, R., West, N., Vider, J., Moore, P.R., Doggett, S.L., Warrilow, D. (2017) Evolution of West Nile virus in Australia and emergence of a pro-inflammatory phenotype. In: 9th Australasian Virology Society Meeting (AVS 2017), 5–8 December 2017, Glenelg, South Australia.
Jansen, C.C., Lodo, K., McMahon, J., Hall-Mendelin, S., Lyons, S., Davis, J. (2016) Arbovirus surveillance in Queensland 2014–2016. In: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4–9 September, 2016, Surfers Paradise, Qld.
Jansen, C.C., Lodo, K., Pyke, A.T., Hall-Mendelin, S., Montgomery, B.L., Darbro, J.M., Shivas, M.A., van den Hurk, A.F (2016) Epidemiological, entomological and virological investigations of the Ross River virus outbreak in Queensland, 2015. In: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4–9 September, 2016, Surfers Paradise, Qld.
Lee, W.S., van den Hurk, A.F., Herrero, L. (2017) Glycobiology of arboviruses: do glycans affect the transmission of Ross River virus. In: IUMS Congresses 2017: 15th International Congress of Bacteriology and Applied Microbiology, 15th International Congress of Mycology and Eukaryotic Microbiology and 17th International Congress of Virology, 17–21 July 2017, Singapore.
Macdonald, J., Kristoffersen, J., Li, J., Nyari, S., James, A., Denes, A., Simpson, J., Prow, N.,Hall-Mendelin, S., Hall, R.A. (2016) Rapid amplification of flaviviruses using recombinase polymerase amplification and potential for efficient detection using a novel multiplex lateral flow strip. In: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4–9 September, 2016, Surfers Paradise, Qld.
Mackay, I.M. (2016) Middle East respiratory syndrome (MERS): four years on, what do we know? In: Public and Environmental Health Forum, 29 September 2016, Forensic and Scientific Services, Brisbane, Qld.
Mackay, I.M. (2016) Middle East respiratory syndrome (MERS): humans and healthcare facilities. In: International Congress for Tropical Medicine and Malaria, 18–22 September, 2016, Brisbane, Qld.
Mackay, I.M. (2016) Middle East Respiratory syndrome coronavirus: camels, humans and healthcare facilities. In: International Congress for Tropical Medicine and Malaria, 18–22 September, 2016, Brisbane, Qld.
Mackay, I.M. (2016) Point of Care Testing (POCT) for ARIs. In: 3rd Annual Queensland Forum on Antimicrobial Resistance, 14 November, 2016, Royal Brisbane and Women’s Hospital (RBWH) Education Centre, Herston, Qld.
Montgomery, B.L., Shivas, M.A., Hall-Mendelin, S., Edwards, J., Hamilton, N.A., Jansen, C.C., McMahon, J., Warrilow, D., van den Hurk, A.F. (2016) Rapid Surveillance for Vector Presence (RSVP): development of a novel system for detecting invasive mosquito species that can transmit Zika, dengue and chikungunya viruses. In: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4–9 September, 2016, Surfers Paradise, Qld.
Nicholson, J., Johnson, B., Ritchie, S.A., Hall-Mendelin, S., van den Hurk, A.F., Lindsay, M.D., Wong, S., Chidlow, G., Johansen, C.A. (2016) The use of sugar-based surveillance for arbovirus detection in WA: past, present and future. In: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4–9 September, 2016, Surfers Paradise, Qld.
O’Brien, C.A., Hall-Mendelin, S., Hobson-Peters, J., Lew-Tabor, A., Rodriguez-Valle, M., Barker, S., Deliyannis, G., Allen, A., Hall, R.A. (2016) Virus discovery in Ixodes holocyclus. In: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4–9 September, 2016, Surfers Paradise, Qld.
Pyke, A.T., Moore, P.R., Hall-Mendelin, S., Cameron , J.N., Hewitson, G.R., Pukallus, D., Huang, B., Warrilow, D., (2016) Hitchhikers from the jungle: assessment of evolution, emergence potential and public health implications of rare and divergent dengue viruses. In: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4–9 September, 2016, Surfers Paradise, Qld.
van den Hurk, A.F. (2016) A tale of yellow fever, Zika and the Asian Tiger mosquito [seminar]. In: Australian Institute of Tropical Health and Medicine seminar, 20 May 2016, James Cook University, Cairns.
Vet, L.J., Colmant, A.M.G., Piyasena, T.B.H., Setoh, Y.X., Khromykh, A.A., van den Hurk, A.F., Bielefeldt-Ohmann, H., Hobson-Peters, J., Hall, R.A. (2016) Investigating the host-restriction of Bamaga virus in vitro. In: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4–9 September, 2016, Surfers Paradise, Qld.
1.5 Radiation and Nuclear Science
Our service focus is on the measurement, impact, use and safety of radiation sources, including naturally-occurring radioactive material (NORM), medical and industrial radiation devices and radioactive waste.
We are a ISO9001systems certified public, occupational and environmental health group providing professional advice and assessment, monitoring and surveillance services to all levels of government and private sector clients. Research is a fundamental and important part of our service portfolio.
Overview
Our services and facilities include:
•	health physics consultancy programs including radiation safety training, regulatory surveillance and monitoring, radiation assessments and surveys, advisory and compliance certification
•	a modern, purpose designed radiochemistry and radio-analytical laboratory with the capability to quantify radioactivity in water, soils, sediments and solid materials, air, biota and food 
•	highly specialised instrumentation, including alpha and gamma spectrometry, radon monitoring and other advanced instrumentation
•	emergency response, either in a first responder, urgent radioanalytical or post incident remediation role.

Our staff hold licences to use and transport radiation sources under the Queensland Radiation Safety Act 1999, and are accredited for certifying radiation devices and facilities.
We actively participate in state (Queensland Health), national (Australian Radiation Protection and Nuclear Safety Agency), and international (Atomic Energy Agency’s Analytical Laboratories for the Measurement of Environmental Radioactivity) emergency response networks.
Embedding research in Radiation and Nuclear Sciences (RNS) — just part of the job
“Research is an integral part of the RNS business model, a necessity to develop our staff and provide them with the tools to better promote and provide a safe, healthy Queensland.
We develop new ways of measuring and monitoring radiation sources with outcomes targeted at reducing the effects of radiation on our communities, in the workplace and upon our environment, while acknowledging and exploiting the properties of radiation as a scientific, medical and industrial tool benefiting us all in everyday life.
I’m proud of the passion and commitment that all my staff have to research. I have always fostered, supported and driven an environment of on-going learning and study, questioning why we do things, how they are done and what we could do better to fulfil our role as a provider of specialised scientific services. I feel RNS constantly achieves well above expectations in providing radiation science solutions to our varied client base – this, to me, is research and development in practice, and at its best.”
Dr Ross Kleinschmidt
Principal Health Physicist, Radiation and Nuclear Sciences Adjunct Associate Professor, Science and Engineering Faculty, QUT
Research projects
Queensland drinking water survey
The aim of this survey is to determine the ability of the current Australian Drinking Water Guidelines (ADWG) to appropriately assess what is safe, good quality water in terms of radioactivity content, for the Australian community.
Principal researcher: Megan Cook
Research assistant: Sian Patterson, Sarah Mullins, Dimitri Nikolakopaoulos
Collaborators: Peter Medley, Environmental Research Institute of the Supervising Scientist (ERISS), Sandra Sdraulig, Australian Radiation Protection and Nuclear Safety Agency (ARPANSA), Atun Zawadzki, Australian Nuclear Science and Technology Organisation (ANSTO)
Accumulation of anthropogenic radionuclides in king prawns along the Queensland coastline
To determine the migration of anthropogenic radionuclides from the Fukushima nuclear incident in the southern hemisphere oceans using prawns as an indicator the research team developed a novel sequential extraction procedure for several radioactive isotopes in water, biota and sediment. The new data generated provides historical background levels of radioactivity along the Queensland coastline. An invitation to participate in the National Project Team for the IAEA “Enhancing Regional Capabilities for marine radioactivity monitoring and assessment of the potential impact of radioactive releases from nuclear facilities in Asia-Pacific marine ecosystems” project and collaborations with the international IAEA ALMERA network were two of the outcomes from this research.
Principal researcher: Megan Cook
Research assistant: Sian Patterson, Sarah Mullins
Transport and migration of fissile materials in the Australian ecosystem
The consequences to public health from the release of plutonium isotopes into the environment during a nuclear incident are significant as demonstrated in failure of the nuclear power plant in Fukushima. Fissile materials are an incredible risk to human and environmental health causing deterioration of cells, acute and chronic radiation poisoning and death. A baseline study will provide information to decision makers of the impact and possible consequences a nuclear incident could cause for the Australian public health. With the increase in use of nuclear power in the southern hemisphere and serious discussion around the installation of a nuclear waste repository in Australia this research is imperative and timely.
Principal researcher: Dr Ross Kleinschmidt
Research supervisor: Dr Ross Kleinschmidt
Student placement: Megan Cook (PhD Student), Monash University, Talia Enright, University of Queensland Madison Hoffman, University of Queensland
Collaborator: Dr Vanessa Wong, Monash University
Portable X-ray fluorescence user dosimetry
Portable X-ray fluorescence instruments (pXRF) are hand held X-ray emitting devices designed for in-situ compositional analysis of materials, enabling immediate real-time measurements of materials. To be portable, pXRF’s do not incorporate the same amount of radiation shielding as laboratory X-ray apparatus. The aim of this research is to assess the radiation dose received by users of portable X-ray fluorescence instruments. This evidence-based research will inform radiation regulatory governance.
Principal researcher: Drew Watson
Research supervisor: Dr Ross Kleinschmidt
Collaborators: Simon Critchley, Health Protection Branch, Paula Veevers, Health Protection Branch
Development of a passive thoron progeny monitor based on TASL platform
Exposure to the radioactive gas radon is the second highest cause of lung cancer after smoking. It is only recently that the radon isotope radon-220, also known as thoron, has been identified as a significant contributor to radon dose. This project will develop and validate a passive thoron progeny monitor based on the RNS TASL CR39 track etch platform.
Principal researcher: Dr Ross Kleinschmidt
Research assistant: Kathy Coles
Naturally occurring radioactive materials (NORM) in mineral processing slag dumps — assessing a possible building material resource
NORM are associated with all mineral resource extraction processes, and in many cases NORM — including uranium and thorium parent and progeny materials — are preferentially concentrated in furnace slags. These large stockpiles of slag are currently being assessed for reuse in a number of industries including concrete, roads, railway ballast and other construction materials. The purpose of this project is to characterise the NORM content, and disequilibria between parent and progeny radionuclides that may be present, with a view to gaining knowledge of potential hazards in reuse of these waste materials.
Principal researcher: Dr Ross Kleinschmidt
Research team: Pushpendra Chauhan
Primordial radionuclide disequilibria in sediments — a tool for discrimination between natural and anthropogenic contaminant sources
While uranium mining in Queensland currently remains banned, monitoring and surveillance activities continue for exploration and historical sites. Compliance monitoring may be complicated at these sites where both natural and anthropogenic sources of contaminants co-exist. Radioelement tracers may be employed to assess and monitor compliance of resource sector operations, minimising detrimental impacts to community health and the environment. Radioisotopic ratio methods will be developed to establish if discrimination between naturally occurring, and anthropogenically modified sources of environmental uranium radionuclides in sediment and water samples is feasible, and can be used as a compliance monitoring tool to determine the source of contaminants.
Principal researcher: Dr Ross Kleinschmidt
Research team: Megan Cook, Sian Patterson, Pushpendra Chauhan, Kathy Coles
Collaborators: Tania Hall, Department of Natural Resources and Mines
Radium: profiling and radioecology near Cooby Dam
This project will measure the profile of radium concentrations throughout sediment and biota along a creek bed formerly used for discharging bore water to augment Cooby Dam water levels. The mobility and potential impact of this radium-rich sediment is of great interest for radiation protection and radioecology and will contribute to global radioecology modelling tools.
Principal researchers: Drew Watson, Sian Patterson
Research supervisor: Dr Ross Kleinschmidt
Publications
Journal articles
Kleinschmidt, R. (2017) Reference natural radionuclide concentrations in Australian soils and derived terrestrial air Kerma rate. Journal of Environmental Radioactivity 172:160–162.
Kleinschmidt, R., Watson, D.M. (2016) Terrestrial gamma radiation baseline mapping using ultra low density sampling methods. Journal of Environmental Radioactivity, 151(3):609–622.
Kleinschmidt, R., Watson, D.M. (2017) Mine animation — Underground at Bamford Hill. [Video] 
Wallace, J.D. (2016) Establishing a NORM based radiation calibration facility. Journal of Environmental Radioactivity, 155–156:84–88.
Watson, D.M. (2016) Baseline Radiological Mapping of Queensland. EIANZ News. 
Zawadzki, A., Cook, M.L., Cutmore, B., Evans, F., Fierro, D., Gedz, A., Harrison, J.J., Loosz, T., Medley, P., Mokhber- Shahin, L., Mullins, S., Sdraulig, S. (2017) Comparison of radium-228 determination in water among Australian laboratories. Journal of Environmental Radioactivity, 178–179:411–418.
Lectures and presentations
Kleinschmidt R. (2017) Overview of Radiation and Nuclear Science General Facilities & Capabilities, Current Research Areas. Radiation Safety Officers User Group meeting, 5 May 2017, Brisbane, Australia.
Mullins, S., Cook, M.L. (2017) The comparison of two liquid scintillation instruments for analysis of highly quenched samples. In: LSC 2017: an international conference on advances in Liquid Scintillation Spectrometry, 1–5 May 2017, Copenhagen, Denmark.
Wallace, J.D. (2016) An improved NORM based planar radiation calibration facility. In: 41st Annual Conference of the Australasian Radiation Protection Society, 11–14 September 2016, Adelaide Convention Centre, South Australia.
2.0 Police Services
We provide forensic DNA analysis and forensic chemistry services for the Queensland Police Service and the Coroners Court of Queensland and private clients.
We:
•	assist with missing persons and victims of disasters
•	provide impartial expert evidence in all levels of the judicial system 
•	provide training and advice to the Queensland Police Service, the Office of the Director for Public Prosecutions and the Coroners Court of Queensland.
Our forensic DNA analysis services include:
•	Examining and testing biological items delivered from alleged crime scenes to generate a DNA profile
•	Comparing and reporting interpretations of DNA profiles, including the use of the National Criminal Investigation DNA Database on behalf of the Queensland Police Service
•	Preparing of court documents and the provision of expert evidence in court 
Our forensic chemistry services include:
•	Examining, testing and reporting on seized items related to pills, powders, liquids, food and utensils suspected to be associated with dangerous drugs
•	Providing information to law enforcement agencies on emerging drug trends and new drug types
•	Providing on-call assistance to the Queensland Police Service to dismantle and collect evidence from hazardous crime scenes which involve a clandestine drug laboratory
•	Analytical testing, reporting and expert evidence on items related to the manufacturing of suspected dangerous drugs or illicit drug material
•	Testing and reporting on cases; comparison of items such as fibres, textiles, oils, and identification of unknown items such as explosives and chemical warfare agents
2.1 Forensic Chemistry
The Forensic Chemistry team provide expert scientific knowledge, laboratory examinations, testing and reporting on items submitted from across the state in relation to alleged offences.
Overview
We provide services to a variety of agencies including the Queensland Police Service, the Australian Criminal Intelligence Commission, Australian Border Force, Maritime Safety Queensland, Australian Federal Police and Queensland Health
•	Analytical testing of illicit drugs and advice in relation to the production of dangerous drugs
•	Providing advice, collecting evidence and safely dismantling chemically hazardous crime scenes
•	Testing and reporting on samples collected from alleged criminal incidents.
Research that supports customer needs Forensic Chemistry — Beyond reasonable doubt
“Good science always needs sound, supportive, peer-reviewable evidence. But few disciplines exist where the need to confirm a scientific outcome, beyond reasonable doubt, is as critical as it is within our forensic chemistry group.
Sole evidence, accurate results, and scientifically supported evidence may often be the only discriminator between a person being found guilty or innocent of a crime.
Our research focus is on developing new methods and incorporating new emerging technologies to be at the cutting edge to identify new drugs, new processes used to illicitly produce drugs, and comparative methods for fibres, oils, explosives and other trace evidence, as well as developing the means to carry out specialised testing in the field as well as the laboratory.
Our research is often specific and critical for a case before the courts. Without determining a novel suspected illicit drug manufacturing process works within our laboratory for example, we can only give a theoretically based opinion rather than the factual unambiguous results we do provide.
I would consider our team to be one of the best nationally if not internationally in the field of forensic chemistry. Our team are dedicated, committed and always willing to go that extra mile, to ensure we have the best possible scientific outcome we can provide to support justice, law enforcement and health.”
Dr Peter Culshaw
Chief Chemist, Forensic Chemistry, Police Services
Research projects
Investigation of DSA-TOF for the forensic analysis of drugs and explosives
The potential of Direct Sample Analysis — Time of Flight (DSA-TOF) instrumentation to rapidly screen for drugs and explosives will be investigated. DSA-TOF has the potential to screen for target compounds in 30 seconds. This capability could enable the rapid exclusion of negative samples and allow more specific analysis of samples indicated to contain target compounds. However extensive investigation is required to determine whether the capability of this emerging technology, with real forensic exhibits in a high-throughput environment, can actually deliver efficiency improvements.
Principal researcher: Jenny McGowan
Research supervisor: Methsiri Edirisinghe
Research team: Dr Sarah Atkinson, Karen Blakey, Simon Collett, Andrew Stewart, Dr Paul Venz
Rapid analysis of pharmaceutical products using DSA-TOF
The diversion of legitimate pharmaceutical products into the illicit drug market as potential drugs of abuse or as chemical precursors for the synthesis of methylamphetamine is a widely reported outcome. The aim of this project was to determine whether DSA-TOF can provide sufficient characterisation of the formulation components present to support the identification and reporting of pharmaceutical products, in a fraction of the time that current analytical processes take, in order to contribute to efficiency gains within the Forensic Chemistry, Illicit Drug Group. The project was valuable in differentiating promised capability of an instrument with actual operation in a functioning and high throughput laboratory.
Principal researcher: Jenna Wolf
Research supervisor: Karen Blakey
Student placement: Simone Burge, Griffith University
Use of Isotope Ratio Mass Spectrometry (IRMS) for forensic analysis study of methylamphetamine (MA) seizures
IRMS is an integral part of testing done to determine the composition of and similarities between illicit drug seizures. This project developed a new method for the measurement of hydrogen isotopic composition and established a searchable database of MA seizures isotopic compositions. It is expected that extending the database will lead to a better understanding of links between illicit drug seizures, the production of MA, as well as provide intelligence on potential distribution networks.
Principal researcher: Simon Collett
Research supervisor: Dr Jim Carter
Collaborator: Dr Sarah Cresswell, Griffith University
Student: Joe Meikle, Griffith University
The Neber rearrangement in the synthesis of cathinones and amphetamines
The aim of this project is to explore potential alternative synthetic routes that could be used to illegally produce substances such as cathinones and amphetamines, and to produce analytical profiles of the precursors, intermediates, reaction mixtures and final products of this particular synthetic route should it be successful. The information generated by this project will serve to inform Queensland legislative and law enforcement agencies on illicit drug manufacturing.
Principal researcher: Dr Urs Wermuth
Research supervisor: Dr Peter Culshaw
Collaborators: Dr Sarah Cresswell, Griffith University, Dr Sue Boyd, Griffith University
Student: Ebony Shand, Griffith University
Procedures for the safe handling and analysis of illicit drug samples containing low-dose opioids and other high-risk drugs
The increasing availability and detection of low-dose opioids, fentanyl and its analogues for example, in the illicit drug market is a concern to health and law enforcement agencies worldwide. The aim of this project is to develop the analytical capability for the Forensic Chemistry laboratory to detect low-dose opioids and other high-risk compounds in seized drug exhibits, as well as investigate the best practices to implement in the laboratory to minimise any risk to laboratory staff in the handling of these exhibits.
Principal researcher: Karen Blakey
Research supervisor: Jenny McGowan
Developing capability in scheduled peptide analysis
The number of seizures of protein and peptide drugs submitted to the laboratory has significantly increased in the last five years. Some of the seized materials are legitimate pharmaceutical products including growth hormone and insulin; however there are a number of peptide compounds, advertised as performance and image enhancing drugs available from online suppliers, of which the manufacture is not regulated. This project will develop the laboratories capacity to definitively identify peptide compounds scheduled in the Poisons Standard (SUSMP).
Principal researcher: Dr Sarah Atkinson
Research supervisor: Jenny McGowan
Develop capacity to analyse low level cannabinoids in various matrices
This project seeks to develop a method to accurately and reliably quantify low levels of various cannabinoids found in complex matrices, often encountered in Queensland Police Service and Queensland Health Environmental Health Officer exhibits submitted for analysis. This is a timely project in respect to the introduction of the Public Health (Medicinal Cannabis) Act 2016 and the proposed addition of hemp as a food ingredient under the ANZ Food Standards.
Principal researcher: Aaron Schulze 
Research team: Melanie Fuenzalida 
Research supervisor: Dr Sarah Atkinson
The synthesis of 3, 4-Methylenedioxyphenyl-2-propanone (MDP2P) from helional
The aim of this project is to investigate the synthesis of MDP2P from helional via a novel synthetic pathway.
Principal researcher: Sean Davis
Research supervisor: Dr Peter Culshaw
Collaborators: Peter Vallely, ACIC, Dr Sarah Cresswell, Griffith University
Investigation of emerging drugs and novel psychoactive substances (NPS) on the illicit drug market
Since 2006, there has been continued growth in the number of new compounds emerging on the international illicit drug market. This trend has been reflected in Queensland, with more than 200 new compounds encountered since 2011. The diversity and ever-increasing number of new compounds encountered on the illicit drug market has proved challenging to forensic laboratories worldwide as they strive to acquire sufficient data and analytical capabilities. This project will enhance the capability of the laboratory to identify emerging drugs and NPS in the illicit drug market and contribute vital information to law enforcement and health agencies.
Principal researcher: Karen Blakey
Research supervisor: Jenny McGowan
Publications
Journal articles
Blakey, K., Boyd, S., Atkinson, S., Wolf, J., Slottje, P.M., Goodchild, K., McGowan, J. (2016) Identification of the novel synthetic cannabimimetic 8-quinolinyl 4-methyl-3-(1-piperidinylsulfonyl) benzoate (QMPSB) and other designer drugs in herbal incense. Forensic Science International, 260:40–53.
Cawley, A.T., Blakey, K., Waller, C.C., McLeod, M.D., Boyd, S., Heather, A., McGrath, K.C., Handelsman, D.J., Willis, A.C. (2016) Detection and metabolic investigations of a novel designer steroid: 3-chloro-17α-methyl-5α-androstan-17β-ol. Drug Testing and Analysis, 8(7):621–632.
Davis, S (2017) Fentanyl Volume 3 — Analysis of Fentanyl and its Analogues, CLIC Monograph. 
Davis, S., Vallely, P. (2017) Short Communication: A Novel Synthesis of 3, 4-Methylenedioxyphenyl-2-propanone (MDP2P) from Helional, JCLIC, 27(3):21.
Smith, G., Wermuth, U.D. (2016) Crystal structure and hydrogen bonding in the water-stabilized proton-transfer salt brucinium 4-aminophenylarsonate tetrahydrate. Acta crystallographica. Section E, Crystallographic communications, 72(5):751–755.
Smith, G., Wermuth, U.D. (2017) The coordination complex structures and hydrogen bonding in the three- dimensional alkaline earth metal salts (Mg, Ca, Sr and Ba) of (4-aminophenyl) arsonic acid. Acta Crystallographica Section C, C73(1):61–67.
Thai, P.K., Lai, F.Y., Edirisinghe, M., Hall, W., Bruno, R., O’Brien, J.W., Prichard, J., Kirkbride, P., Mueller, J.F. (2016) Monitoring temporal changes in use of two cathinones in a large urban catchment in Queensland, Australia. Science of the Total Environment, 545–546:250–255.
Lectures and presentations
Blakey, K. (2016) Synthetic cannabinoids: key fragments and structural characteristics In: ANZFSS 23rd International Symposium on the Forensic Sciences, 18–22 September, 2016, Auckland, New Zealand. 
Blakey, K., Atkinson, S., White, R., Adebajo, A. (2016) Novel steroids in the Queensland drug market: identification and analytical challenges. In: ANZFSS 23rd International Symposium on the Forensic Sciences, 18–22 September, 2016, Auckland, New Zealand.
Blakey, K., Boyd, S., Atkinson, S., Schulze, A., Adebajo, A. (2016) The continuing evolution of synthetic cannabinoids in Queensland. In: ANZFSS 23rd International Symposium on the Forensic Sciences, 18–22 September, 2016, Auckland, New Zealand.
Croft, S., McGowan, J. (2016) Illicit drug trends from Queensland, Australia. In: ANZFSS 23rd International Symposium on the Forensic Sciences, 18–22 September, 2016, Auckland, New Zealand.
Morey, S., Thompson, A., Little, D., Adebajo, A. (2016) ‘Not so herbal’ weight loss pills: case study of a Sibutramine death. In: 54th TIAFT meeting, 28 August 2016–1 September 2016, Brisbane, Queensland.
Thompson, A., Schulze, A. (2016) Pentobarbitone in disguise: a series of pentobarbitone related deaths in Queensland, Australia. In: 54th TIAFT meeting, 28 August 2016–1 September 2016, Brisbane, Queensland.
Wolf, J., Blakey, K., McGowan, J.,Edirisinghe, M. (2016) Investigation of Direct Sample Analysis — Time of Flight mass spectrometry (DSA-TOF) for the forensic analysis of seized drugs. In: ANZFSS 23rd International Symposium on the Forensic Sciences, 18–22 September, 2016, Auckland, New Zealand.
2.2 Forensic DNA Analysis
The Forensic DNA Analysis team provide expert scientific knowledge, laboratory examinations, testing and electronic reporting on items submitted from across the state in relation to alleged offences.
Overview
Services to the Queensland Police Service include:
•	assisting with missing persons cases and victims of disaster incidents
•	analysing and profiling 30,000 forensic DNA samples annually from alleged criminal investigations
•	examining and testing biological items from alleged crime scenes to generate a DNA profile
•	maintaining the reference sample database of persons associated with alleged offences.
Research projects
Massively parallel sequencing (MPS) as an investigative tool
The aim of this project is to assess whether ancestry and externally visible characteristics generated through MPS will assist Queensland Police Service in eliminating or including suspects during an active criminal investigation.
Principal researcher: Luke Ryan
Research team: Megan Mathieson
Collaborators: Thermo Fisher Scientific, Queensland Police Service
Lectures and presentations
Caunt, E., Morgan, R. (2016) Development of guidelines for determination of number of contributors to mixed DNA profiles. In: ANZFSS 23rd International Symposium on the Forensic Sciences, 18–22 September, 2016, Auckland, New Zealand.
3.0 Coronial Services

We provide coronial services, including forensic pathology and forensic toxicology. Our dedicated professionals work closely with the State Coroner, other coroners, coronial staff and police officers, including homicide detectives, police scientists, scenes of crime officers and investigators.
We are supported by mortuary and administration teams and other specialists who provide medical services such as histology, forensic dentistry, neuropathology, disaster victim identification and post-mortem CT-scanning services. We can provide advice on mortuary practices and the operation of anatomy schools and propose amendments to medico-legal legislation.
3.1 Forensic Toxicology
Forensic toxicology involves the analysis, detection, identification, measurement and interpretation of alcohol, drugs, poisons and other substances in human samples including blood, urine, saliva and other fluids and tissues.
Overview
Our two main services include:
•	testing of samples from autopsies ordered by the coroners
•	testing of samples from living subjects for the Queensland Police Service, such as alcohol and drugs in drivers and specialist testing for drugs in assault victims.

This information is used to report on substances that may or may not have contributed to an accident or death, impaired behaviour, such as in drivers or been involved in a criminal offence.
Our services include:
•	performing expedited analysis in coronial cases where an obvious drug overdose is indicated
•	analysing blood samples provided by the QPS under the Transport Operations (Road Use Management) Act 1995
•	analysing blood and urine samples of alleged perpetrators and victims of crime
•	performing workplace drug testing
•	preparing certified reference materials for the QPS breath analysis unit
•	providing expert opinion and advice on issues relating to forensic toxicology.
Research projects
The analysis of histamine and metabolites in biological specimens
Assisting the Queensland Coroner in determining that cause of death of an individual by the analysis of post-mortem specimens for drugs and/or poisons is a significant role of the Forensic Toxicology unit. Histamine, whilst not a drug or poison, is a compound in which positive identification in a post-mortem sample can provide the coroner with information that may subsequently rule anaphylaxis as the cause of death. This project developed a method for identification of histamine and its metabolites in biological specimens.
Principal researcher: Sarah Morey
Research supervisor: Mark Stephenson
Analysis of β-phenylethylamine in post-mortem blood samples
The aim of this project is to measure the level of β-phenylethylamine (PEA) in a series of post-mortem blood samples with varying degrees of decomposition, and assess whether any correlation exists between the level of β-phenylethylamine and the degree of composition. PEA is a naturally occurring substance present in blood and urine, with levels known to increase after death, but can also be ingested as a drug to induce amphetamine like effects. There is currently very little information in the literature on the levels of PEA seen in post-mortem blood samples. While it is unusual to see cases of ingestion, the lack of information makes it difficult to assess whether any PEA detected is due to ingestion or merely present as a result of decomposition.
Principal researcher: Amanda Thompson
Research supervisor: Mark Stephenson
Development of identification methods for the analysis of fentanyl derivatives and novel opioids 
Deaths related to fentanyl derivatives and novel opioid derivatives have been increasingly reported in the US and Europe. In Australia, the threat posed by these drugs is an immediate one, with carfentanil for example — a drug 10,000 times more potent than morphine — being identified in border seizures. This project will enable the early detection and confirmation of fentanyl derivatives and novel opioid derivatives in Queensland toxicology cases and illicit drug seizures by developing methods for the characterisation and analysis of these compounds.
Principal researcher: Andrew Griffiths
Research supervisor: Mark Stephenson
A review of pregabalin involvement in coronial cases
Pregabalin is an anticonvulsant and analgesic designed to treat neuropathic pain and partial seizures, and since the drug was listed on the PBS in 2013 has had a large increase in prescription rates within Australia. This study will report on the rise of pregabalin use, abuse, and overdose and will contribute to the limited number of published studies on the levels of pregabalin found in post-mortem cases.
Principal researchers:  Sarah Morey, Andrew Griffiths Amanda Thompson
Research supervisor: Mark Stephenson
The determination of baseline concentrations of histamine and metabolites in post-mortem blood
The aim of this project is to establish baseline concentration ranges for histamine and its metabolites in post-mortem blood specimens in order to assist forensic pathologists, coroners and other scientists in determining if the cause of death was contributed to or due to anaphylaxis.
Principal researcher: Sarah Morey
Research supervisor: Mark Stephenson
The forensic toxicology of the synthetic cannabinoid AB-CHMINACA
AB-CHMINACA is one of several new synthetic cannabinoids identified in Australian seizures in recent years. This study will examine cases where AB-CHMINACA was identified in the blood of drivers suspected of impaired driving and in coronial cases, to present an overall toxicological profile.
Principal researcher:  Andrew Griffiths
Research supervisor: Mark Stephenson
Investigation of several cannabinoids (THC, THCCOOH, 11OHTHC, CBN, CBD, Δ8THC and THCV) in preserved blood specimens
With recent legislative changes in Australia towards the legalisation of medicinal cannabis and low-THC hemp food products, this project aims at examining the above cannabinoids to gain insight into their prevalence, distribution and levels in biological matrixes. The results of the study may provide pathologists with additional, useful information for the interpretation of cannabinoid levels, particularly in post-mortem specimens.
Principal researcher: Julie Bergeon
Research supervisor: Mark Stephenson
Publications
Journal articles
Griffiths, A., Leonars, R., Hadley, L.M., Stephenson, M., Teale, R. (2017) Smoke on the water − oral fluid analysis at sea. Forensic Science International. 278: 361–366.
Stephenson, M. (2016) Meet the lab — Forensic Toxicology Brisbane, QLD, Australia. TIAFT Bulletin, 46(2): 28–31.
Lectures and presentations
Griffiths, A. (2017) The forensic toxicology of the synthetic cannabinoid AB-CHMINACA. In: FACTA 2017 — Forensic & Clinical Toxicology Association Inc., 19–22 November 2017, Melbourne, Victoria.
Griffiths, A., Griffin, A. (2016) A series of cases involving AB-CHMINACA in the blood of drivers suspected of impaired driving in Queensland, Australia. In 54th TIAFT meeting, 28 August 2016–1 September 2016, Brisbane, Queensland.
Griffiths, A., Leonars, R., Hadley, L.M., Stephenson, M., Teale, R. (2016) Smoke on the water — oral fluid analysis at sea. In: 54th TIAFT meeting, 28 August 2016–1 September 2016, Brisbane, Queensland.
Griffiths, A., Scuderi, G., Hadley, L.M. (2016) Novel psychoactive substances in Queensland drivers. In: 54th TIAFT meeting, 28 August 2016–1 September 2016, Brisbane, Queensland.
Morey, S. (2017) Determination of baseline concentration ranges for histamine and metabolites in post-mortem blood. In: FACTA 2017 — Forensic & Clinical Toxicology Association Inc., 19–22 November 2017, Melbourne, Victoria.
Morey, S., Olumbe, A., Stephenson, M. (2016) The analysis of histamine and metabolites in blood. In: 54th TIAFT meeting, 28 August 2016–1 September 2016, Brisbane, Queensland.
Morey, S., Thompson, A., Little, D., Adebajo, A. (2016) ‘Not so herbal’ weight loss pills: case study of a Sibutramine death. In: 54th TIAFT meeting, 28 August 2016–1 September 2016, Brisbane, Queensland.
Thompson, A., Morey, S., Griffiths, A. (2017) The rise of pregabalin and its involvement in coronial cases in Queensland. In: FACTA 2017 — Forensic & Clinical Toxicology Association Inc., 19–22 November 2017, Melbourne, Victoria.
Thompson, A., Schulze, A. (2016) Pentobarbitone in disguise: a series of pentobarbitone related deaths in Queensland, Australia. In: 54th TIAFT meeting, 28 August 2016–1 September 2016, Brisbane, Queensland.
Thompson, A., Stephenson, M. (2016) B-Phenylethylamine: production or ingestion? In: 54th TIAFT meeting, 28 August 2016–1 September 2016, Brisbane, Queensland.
3.2 Forensic Pathology
We provide specialised forensic services and expert advice to the Queensland Police Service (QPS) and the Coroner’s Court of Queensland.
We also provide services such as disaster victim identification, anthropology and forensic dentistry. We provide advice on mortuary practices, posthumous sperm donation, proposed amendments to medico-legal legislation and inspect anatomy schools.
Overview
•	Forensic Pathology includes a broad range of services including:
•	conducting autopsies and examinations ordered by coroners
•	providing specialist forensic medical services such as histology, neuropathology and post-mortem CT scanning
•	facilitating the issue of Cause of Death Certificates in non-suspicious natural deaths
•	providing expert opinions about causes and circumstances of death
•	interpreting autopsy test results, including alcohol, drugs and poisons
•	providing court evidence in inquests and trials and advice to prosecuting and defence counsel
•	advising and supporting families bereaved by deaths reported to coroners
•	training of medical specialists in forensic pathology accredited by the Royal College of Pathologists Australasia.
Research projects
Polarising amyloid deposition under H&E staining
Amyloid is the deposition of proteinaceous material in extracellular space. The condition can occur as an incidental finding at autopsy or it could be the primary cause of death in individuals. The aim of the study is to explore the possibility of visualising amyloid deposition in tissue under polarised light of the microscope without the need of additional staining.
Principal researcher: Dr Rohan Samarasinghe
Student placement: Cherry Pun, University of Queensland
Survivability of identifying features on pacemakers in fires
Fire related deaths can render human bodies unrecognisable. Medical devices such as pacemakers and dentures that have unique identifying numbers could be used to confirm an individual’s identification. The aim is to assess the survivability of pacemakers and denture material in fires.
Principal researcher: Dr Nathan Milne 
Research team: Dr Alistair Soon 
Research supervisor: Dr Beng Ong
Collaborators: Chris Markwell, Qld Fire and Emergency Services, Gordon Hemphrey, Qld Fire and Emergency Services, Sven Diga, Qld Fire and Emergency Services
Prevalence of air embolism in trauma related deaths
Air embolism is a complication of traumatic injuries and its presence may alter interpretation of the forensic aspect of a case. Currently, air embolism is frequently missed when it’s extent is mild or moderate, or when the sustained injuries are severe enough to account for the cause of death without seeking the presence of air embolism during post mortem examination. As air embolism can only be diagnosed in post mortem examinations when specifically tested for, it may be missed if the prior index of suspicion is low. As a result, air embolism may be currently underdiagnosed in forensic pathology practice. It is hoped that utilising post mortem CT imaging prior to post mortem examinations will prompt more testing for, and enable more reliable diagnosis of air embolus. The researchers aim to review post mortem CT imaging of all trauma related deaths investigated at Forensic and Scientific Services in 2016 to identify the number of deaths that were positive for air embolus.
Principal researcher: Dr Beng Ong
Research team: Trevor Watkins, Matt Meredith, Dr Chris Day
Publications
Journal articles
Agrawal, N.K., Dahal, S., Wasti, H., Soon, A.S. (2017) Application of ultraviolet light in dental identification of avalanche victims. Journal of Nepal Health Research Council, 15(2): 193–196.
Bagnall, R.D., Weintraub, R.G., Ingles, J., Duflou, J., Yeates, L., Lam, L., Davis, A.M., Thompson, T., Connell, V., Wallace, J., Naylor, C., Crawford, J., Love, D.R., Hallam, L., White, J., Lawrence, C., Lynch, M., Morgan, N., James, P., du Sart, D., Puranik, R., Langlois, N., Vohra, J., Winship, I., Atherton, J., McGaughran, J., Skinner, J.R., Semsarian, C. (2016) A prospective study of sudden cardiac death among children and young adults. The New England Journal of Medicine, 374: 2441–2452.
Ellis, P., Wright, R. (2016) War crimes: site investigation. In: Encyclopedia of Forensic and Legal Medicine. Elsevier, London, UK, pp. 665–671.
Forrest, A., Milne, N., Soon, A.S. (2016) Hereditary angioedema: death after a dental extraction. Australian Dental Journal, 62(1): 107–110.
Forrest, A., Soon, A.S. (2016) Bite marks. In: Forensic odontology: principles and practice. Wiley-Blackwell, Chichester, West Sussex., pp. 228–285.
Ong, B.B., Milne, N. (2016) Injury, fatal and nonfatal: burns and scalds. In: Encyclopedia of Forensic and Legal Medicine. Elsevier, London, UK, pp. 173–181.
Ong, B.B., Milne, N. (2016) Sudden natural death: central nervous system and miscellaneous causes. In: Encyclopedia of Forensic and Legal Medicine. Elsevier, London, UK, pp. 469–476.
Ong, B.B., Milne, N. (2017) Vertebral artery trauma. In: Essentials of autopsy practice: reviews, updates and advances. Springer International Publishing, pp. 23–41.
Phillips, B. (2016) SUDI: a modern approach. Pathology, 48((S1)): s21.
Phillips, B., Little, D. (2016) Fatal arachnophobia. Pathology, 48(Supplement): s93–s94.
Phillips, B., Milne, N. (2016) Vehicle assisted ligature strangulation. Pathology, 48(1).
Reid, A., Samarasinghe, R. (2017) Sudden and unexpected death due to a rare case of endocarditis. Pathology, 49 (Supplement 1): s102–s103.
Reynolds, M.S., MacGregor, D.M., Barry, M.D., Lottering, N., Wilson, L.J., Meredith, M., Gregory, L.S. (2017) Technical note: Standardized anthropological measurement of postcranial bones using three- dimensional models in CAD software. Forensic Science International. 278: 381.
Lectures and presentations
Ong, B.B., Watkins, R., Day, C., Meredith, M. (2017) Diagnosis of venous air embolism with the use of post-mortem CT scan. In: International Society for Forensic Radiology and Imaging (ISFRI), 11–13 May 2017, Copenhagen.
Morey, S., Thompson, A., Little, D., Adebajo, A. (2016) ‘Not so herbal’ weight loss pills: case study of a Sibutramine death. In: 54th TIAFT meeting, 28 August 2016–1 September 2016, Brisbane, Queensland.
3.3 Clinical Forensic Medicine
Our medical staff are utilised by the Queensland Police Service, the Office of the Director of Public Prosecutions and the Coroners Court of Queensland.
We examine and treat victims and alleged perpetrators in criminal investigations. Our service operates 24 hours a day, 7 days a week.
Overview
Our scope includes:
•	collecting and interpreting medical evidence for court
•	documenting and interpreting injuries
•	providing toxicological advice to the Coroner
•	providing evidence and advice in healthcare-related death investigations.

We provide medical advice at death and crime scenes. We also provide expert clinical and medico-legal opinions in court relating to:
•	fitness to appear or to be interviewed
•	traffic medicine
•	clinical effects and toxicology of alcohol and drugs
•	expert opinions regarding medical issues for the legal system including criminal prosecutions, coronial investigations, medical board investigations and civil litigation.
Research projects
A comparison of methylamphetamine levels with indicia in individuals charged with Driving Under the Influence of Drugs (DUID) in Queensland
Forensic physicians are often asked how a particular blood level of methylamphetamine may effect an individual. The interpretation of methylamphetamine levels is problematic due to individual variability in terms of tolerance, dependence, timing and size of dose, pattern of use and genetic variability in metabolism. Therefore, it can be difficult to state with any certainty what the effects of the drug will be based upon blood levels alone. This study proposes to determine if a significant relationship exists between methylamphetamine blood levels and central nervous system indicia described by police and witnesses through the examination of DUID cases from 2011 to 2016.
Principal researcher: Dr Natalie MacCormick
Research team: Dr Adam Griffin
Publications
Journal articles
Crilly, J., Greenslad, J., Lincoln, C.A., Timms, J., Fisher, A. (2016) Measuring the impact of the working environment on emergency department nurses: A cross-sectional pilot study. International Emergency Nursing, 31: 9–14.
Lincoln, C.A., Crilly, J., Scuffham, P., Timms, J., Becker, K., van Buuren, N., Fisher, A., Murphy, D., Green, D. (2016) Reducing risks and improving health outcomes for prisoners in watch houses: Do emergency department nurses in the custodial setting make a difference? Pathology, 48 (Supplement 1): S24–S25.
Robinson, K., Prins, J., Venkatesh, B. (2016) Adipokines in critical illness. In: The stress response of critical illness: metabolic and hormonal aspects. Springer International Publishing, pp. 169–183.
Lectures and presentations
Griffin, A., Kirkegaard, A. (2016) Prevention in practice. In: 2016 Asia Pacific Coroners’ Society Conference: Pathways to Prevention, 8–11 November 2016, Perth, WA.
Griffiths, A., Griffin, A. (2016) A series of cases involving AB-CHMINACA in the blood of drivers suspected of impaired driving in Queensland, Australia. In: 54th TIAFT meeting, 28 August 2016–1 September 2016, Brisbane, Queensland.
Collaborations
During 2016–2017 Forensic and Scientific Services has collaborated on research with the following organisations:
Australian Criminal Intelligence Commission (ACIC)
Australian Federal Police Australian National University
Australian Nuclear Science and Technology Organisation (ANSTO)
Australian Radiation Protection and Nuclear Safety Agency (ARPANSA)
Biosecurity Queensland, Department of Agriculture and Fisheries, Queensland (DAF)
Commonwealth Scientific and Industrial Research Organisation (CSIRO)
Department of Health, Northern Territory
Department of Natural Resources and Mines, Queensland (DNRM)
Department of Science, Information Technology and Innovation, Queensland (DSITI)
Environmental Research Institute of the Supervising Scientist (ERISS)
Griffith University
Griffith University Institute for Glycomics Institute of Environmental Science
and Research, New Zealand (ESR)
James Cook University Massey University Mater Pathology
Metro North Sexual Health Service and HIV Service
Monash University Murdoch University
Novartis Vaccines and Diagnostics SRL, Italy
NSW Food Authority Pathology Queensland PathWest
Queensland Alliance for Agriculture and Food Innovation (QAAFI)
Queensland Fire and Emergency Services, Scientific Branch
Queensland Health, Communicable Disease Unit
Queensland Health, Health Protection Branch
Queensland Institute of Medical Research (QIMR) Berghofer
Queensland Police Services (QPS) Queensland University of Technology Sanaria, USA
Synthaur LLC, Russia Thermo Fisher Scientific
University of Barcelona, student placement
University College Dublin University of Medicine, Yangon University of Melbourne University of Otago
University of Oxford, UK University of Queensland
University of Queensland Centre for Clinical Research (UQCCR)
University of Sunshine Coast University of Sydney