Researchers and industry meet for annual partners' day by Stephen Fujiwara

On Tuesday the 13th of August we were delighted to host our industry partners for our annual research showcase.

The event included 35+ delegates, 12+ research presentations, three Q&A sessions and two keynote presentations. International guest speaker Professor Keith Warriner provided a wide-ranging review of his food safety experiences in North America. Professor PJ Cullen spoke about the exciting potential applications of cold plasma in food processing and fresh produce.

Research presentations were divided into thematic areas including preharvest, post-harvest and cross-cutting food safety. Student presentations were followed by panel Q&A sessions, facilitated by our industry partners who helped to highlight key findings of relevant to industry and areas for exciting areas for future research.

New ARC Centre to future-proof Australia's fresh food supply by Stephen Fujiwara

Supporting an industry increasingly innovated by scientific advancements, the University of Sydney has launched a specialist training hub which will conduct research into food safety and develop methods to safeguard Australia's fruit and vegetable industries.

The Australian Research Council (ARC) Training Centre for Food Safety in the Fresh Produce Industry has been funded by the Australian Research Council, the NSW Food Authority and eighteen industry partners from agricultural and retail sectors, that have aligned to promote food safety practices across all levels of food production and supply chains.

The centre is administered by the University of Sydney and consists of a multi-disciplinary team of academics with research areas spanning genome editing, water management, horticulture, pathogen detection and food safety.

Officially opening the training centre was Centre Director and Professor of Horticulture Robyn McConchie who highlighted the University’s role in driving high-level research and researcher training that will be used to improve industry practices and standards.

“Working with a multidisciplinary team and a range of industry partners, the centre will be working towards improving commercial food safety practices, whilst minimising and preventing food safety risks such as human pathogen outbreaks,” she said.

Read more at the University of Sydney

Thank you to Dr Pieternel Luning, visiting international guest expert on food quality and safety by Stephen Fujiwara

Dr Pieternel Luning is an Associate Professor in the Food Quality and Design group at Wageningen University & Research in the Netherlands, where she helped to develop the Food Quality Management curriculum. Pieternel and her colleagues developed a techno-managerial approach to food quality and safety that integrates natural science and management science. In addition to teaching, this systems perspective remains the lens through which she conducts research in diverse topics including food safety management, risk-based food integrity management, food safety governance in emerging countries, food consumption quality and waste, food fraud, and food product development.

Pieternel spent three weeks at the University of Sydney, hosted by the ARC Training Centre for Food Safety in the Fresh Produce Industry from 29 October to 16 November. During this time, she met with local researchers, students and industry to share ideas on food and agribusiness curriculum, food safety and quality management, and food safety culture. Some highlights of the visit are outlined below.

Food and agribusiness curriculum

University of Sydney academics met with Pieternel to compare degree structures, discuss opportunities for student exchange, and share experiences related to student recruitment, curriculum development, and academic standards. There is currently some discussion within the Australian food science and technology community on establishing guidelines for higher degrees in food science, so it was interesting to review the Wageningen food programs, which are among the top-ranked in the world.

An exciting new approach to education is the use of Virtual Reality and Augmented Reality technology in blended modes of learning to enhance student engagement, learning, and knowledge retention. Dr Kim-Yen Phan-Thien is working with colleagues to develop some VR scenarios that will be used to teach principles in food quality and safety management. During Pieternel’s visit, the group met with FMCG companies to discuss opportunities to address industry training needs as well as student learning through VR/AR-enhanced modules. Pieternel brought her insights on education and ‘serious gaming’ to the discussion, which will see partnerships with a leading manufacturer to produce a pilot based on beverage processing. Kim is also seeking partners in the fresh produce industry to collaborate in producing VR scenarios.

Food safety and quality management

Pieternel presented on ‘Food Quality Management – A Techno-Managerial Approach’ at the Sydney Institute of Agriculture seminar series on 2 November. The focus of research in our ARC training centre is on the ‘hard science’, e.g. pathogen dynamics, environmental interactions, quantitative models. The techno-managerial approach adds organisational and supply chain characteristics to the understanding of risk and control. This methodology will be explored in Elizabeth Frankish’s PhD project on apple risk assessment, as a complementary framework for evaluating food safety management systems alongside the quantitative risk model that she is developing.

Members of the ARC Training Centre accompanied Pieternel to meet with several industry partners to discuss tools for evaluating food safety management, and explore industry considerations in developing these to be relevant and useful to the Australian industry. A key point was that assessment methods needed to be clearly applicable as tools for continual improvement, and not additional compliance requirements. The ARC Training Centre would like to thank GSF Australia, Freshcare, Fresh Produce Group, and Harris Farm for hosting these meetings.

Dr Pieternel Luning and the University of Sydney Sydney team meeting with Freshcare staff

Dr Pieternel Luning and the University of Sydney Sydney team meeting with Freshcare staff

Food safety culture

During Australian Food Safety week, 12-17 November, the Fresh Produce Safety Centre Australia and New Zealand and the ARC Training Centre for Food Safety in the Fresh Produce Industry at the University of Sydney co-hosted a webinar on ‘Food Safety Culture – Take it Seriously’. The webinar was well-attended, with at least 80 participants. Pieternel explained the underpinnings of food safety culture, its importance to food safety management, and how it can be evaluated. The webinar was followed by discussions with industry members. One of the outcomes will be development of new research collaboration on food safety culture, led by Pieternel and Kim. Industry members who are interested to find out more, and possibly participate in this research, are invited to contact Kim.

Dr Pieternel Luning providing overview of tools that can be used for assessing Food Safety Culture to industry audience via co-hosted event with the  Fresh Produce Safety Centre Australia and New Zealand

Dr Pieternel Luning providing overview of tools that can be used for assessing Food Safety Culture to industry audience via co-hosted event with the Fresh Produce Safety Centre Australia and New Zealand


It is always invigorating to host international researchers, for the simple reason that they bring fresh ideas and perspectives to research interests held in common, or stimulate interest in new areas. The break from business-as-usual is energising and promotes creativity for all concerned. Pieternel’s enthusiasm for food safety education and research has been motivating for both our researchers and students, and we are grateful to both the ARC Training Centre for Food Safety in the Fresh Produce Industry and Wageningen University and Research, Food Quality and Design group for supporting her visit.

Sign up to host a University of Sydney intern by Stephen Fujiwara


Save the date: 14 March,  Internship seminar

The University of Sydney is seeking expressions of interest for companies and organisations that can host a Bachelor of Food an Agribusiness intern for a period of 11 weeks later this year.

Who are the interns?

The students are in the 3rd year of a Bachelor of Food and Agribusiness. This has a double major in Food Science and Agribusiness, so students have a broad understanding of the science and technology underpinning food production and processing, as well as the business environment in which this occurs. This means that placements in both technical/production and commercial/office environments may be suitable – as we will have students who are good fits for either or both contexts.

What does the internship involve?

  • Students spend 11 weeks full-time in an industry placement. The allocated period this year is 3 September to 16 November, 2018.
  • Flexible program. Interns can carry out routine activities like other employees or be given specific project tasks within their capabilities. They can be rotated through different divisions in the business or spend the entirety with a particular team. The details of placements can vary widely, depending on what best suits the Host Organisation and the student. The goal is for students to learn about the realities of working in the food and agribusiness sector, and to develop professional skills through immersion in the business.
  • Internships are unpaid. However, some businesses choose to pay students an allowance to assist with travel and living costs, which is also fine.
  • Internships are covered by a standard agreement between the University and the Host Organisation. It contains typical clauses around responsibilities, liability, confidentiality and intellectual property. It is also possible to negotiate amendments to the agreement.
  • Students are covered by University insurance policies including Public Liability, Professional Indemnity and Personal Accident. We’ll provide certificates of currency if you go ahead with the program.

Key dates

  • Wednesday, 14 March, 1:00-2:30 pm – Internship seminar – An opportunity for host organisations to meet students and give a 5-10 min talk to introduce the business to them. Our agenda is to demonstrate the scope of food and agribusiness to students, to encourage them to be open-minded and expose them to opportunities that they may not have been aware of.
  • 21 Mar – We advertise placement opportunities to students. A placement description template is used to capture basic details.
  • 21 Mar-6 Apr – Application and shortlisting process. We are happy to work with your criteria.
  • 9 Apr-4 May – Host organisations evaluate/interview shortlisted students. You let us know if any applicants are suitable.
  • 7 May-1 June – Students allocated to placements based on feedback from interviews. Placement agreements and schedules finalised.
  • 3 Sep-16 Nov – Internship period

For further information or to express interest in hosting an intern, please contact:
Dr Kim-yen Phan-Thien
Lecturer in Food Science
Degree Coordinator, Bachelor of Food and Agribusiness

Blog: Fresh produce food safety in the post-genomic era by Stephen Fujiwara

Dr Mark Bradbury
Post-doctoral fellow

This post discusses some of the opportunities and challenges presented by the expanding use of High Throughput DNA Sequencing (HTS) in microbiology, particularly with respect to microbial food safety in the fresh produce industry. The application of HTS (sometimes termed “next generation sequencing”) has revolutionised the way microbiology, indeed all biology, is performed. From a food safety perspective, HTS has transformed our capacity to track and characterise foodborne pathogens and their genomes (genetic makeup). Indeed we can now interrogate the composition and behaviour of entire microbial communities across the food chain. I use the term ’post-genomic era’ to describe the approaching period where genomic analysis transitions from being a specialist research method to a routine assay.


This technology is rapidly reducing in cost and being deployed now

Like many new technologies, the initial development and use of HTS has been confined to academia. However, with rapidly decreasing costs and increasing standardisation of methods, sequencing in clinical settings is becoming more common and we are starting to see these techniques implemented in the food industry. There are many examples highlighting the ubiquitous role that HTS has taken in food systems such as the collaboration between IBM and Mars Inc. in "Sequencing the Food Supply Chain" and the establishment of the distributed laboratory ‘GenomeTrakr’ network for whole genome sequencing (WGS) by the US Food and Drug Administration (FDA). GenomeTrakr will host WGS data in public databases for real time analyses that promise to expedite foodborne outbreak investigations [].

Current high throughput sequencing (HTS) devices fit on a lab bench, and are being deployed in collaborative, large scale survelliance such as the GenomeTrakr network. Photo:   Konrad Förstner /   (CC0 1.0)

Current high throughput sequencing (HTS) devices fit on a lab bench, and are being deployed in collaborative, large scale survelliance such as the GenomeTrakr network. Photo:  Konrad Förstner / (CC0 1.0)

The evolution of HTS technologies is startling. To put it into perspective, the Human Genome Project completed in 2003 at an estimated cost of between $0.5 and 1 billion and required the concerted efforts of 20 laboratories across six countries. Less than 15 years later, whole genome sequencing (WGS) has become essentially routine. Particularly in the bacterial, to where cost has dropped to the point where some researchers have started to envision the $1 bacterial genome in the future. Just as amazing is the potential capability to sequence bacteria in the field, outside of the strictly controlled lab environment. With some current generation of sequencing devices shrinking to the size of a thumbdrive. Soon, it may soon be possible for producers themselves to sequence the microbiome of their crops and upload the data to a global network.

Wetterstrand KA / . DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program

Wetterstrand KA / DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program


Reviewing the state of all HTS techniques is beyond the scope of this post and, at the current rate of advancements, would undoubtedly be out of date within a year. However, it is important for producers and quality managers to understand the two most common HTS techniques of immediate relevance to food safety: WGS of pure bacterial cultures and environmental community profiling (or microbiome screening).

Whole genome sequencing provides powerful datasets that will be widely shared

 In WGS, individual bacteria isolated from products have their entire genetic code mapped and digitised. This is in contrast to traditional methods, which involve the identification of bacterial cultures based on specific traits (i.e., growth on differential media or production of a toxin). This electronic fingerprint provides not just the identity of bacteria, but also the entire genetic code. From this information, it is possible to identify the presence or absence of genes responsible for the antimicrobial resistance, persistence in the environment, and virulence. Just as importantly for quality managers and factory hygienists, the relationship of one bacteria to another bacteria isolated from other sources can be identified.

A genome mapped as a circular ("circos") plot. Image:  Lalita Kaplish / Sanger Institute /   (CC BY 4.0)

A genome mapped as a circular ("circos") plot. Image: Lalita Kaplish / Sanger Institute / (CC BY 4.0)

The positive impacts of WGS are immense both for public health surveillance and the fresh produce industry as whole. The comparison of isolates from clinical, environmental and food sources can reveal contamination pathways and improve the surveillance of food safety systems. The fresh produce industry involves complex supply chains with a multitude of stakeholders, so the ability to share genetic information across multiple stakeholders offers great benefits. On the other hand, there are important questions to resolve regarding the use of WGS. For example, will it be permissible to use WGS data in litigation of foodborne outbreaks and what are the implications of this? What platforms will be available for sharing of sequencing information? Will sequencing and testing standards be imposed upon supply chains? Proactive engagement across research organisations, regulatory bodies, and the industry will be critical to promote the uptake and sharing of information to maximise the benefits for the industry as a whole.  

Community profiling will shine a light on the microbiome

Photo: © Oleg Shakirov / Shutterstock

Photo: © Oleg Shakirov / Shutterstock

In addition to WGS of pure cultures, the burgeoning area of community profiling or microbiome research has exploded with advances in HTS. Community profiling involves surveys of all the microbial DNA extracted from an environmental sample. These methods are particularly powerful as they are culture-independent. In other words, microbes don’t need to be grown and isolated on petri dishes, as is done traditionally, which saves a great deal in time and labour. Community profiling characterises the composition of an entire microbial community, rather than a fingerprint of a single strain. Currently, the most commonly applied approaches use a single marker gene. This does not provide sufficient resolution to unambiguously detect pathogens, however it may provide complementary methods by detection of groups of indicator organisms. The less commonly applied technique of shotgun metagenomics may however improve the resolution to identification of specific virulence marker genes. Community profiling is becoming incredibly routine and have widespread applications in human health and environmental monitoring. For fresh produce growers, community profiling offers particular benefits in the monitoring and profiling of soil microbiomes, which may present approaches to improve crop yield and quality.

Interpreting data will be challenging and have legal implications

The new HTS techniques are extremely powerful in comparison to traditional culture-dependent methods. So, what challenges arise from a food safety assessment perspective? Problems with these techniques are predominantly interpretative, due to the fact these techniques are non-targeted with a high degree of sensitivity. How will we define a potential foodborne microbial contaminant in the future? A bacteria, virus or fungi defined by our previous culture-based approaches and a history of foodborne illness, or those that carry identifiable genetic markers associated with virulence? Whilst these aren’t particularly new questions for food microbiologists and regulators, such questions will come to the fore as the diversity of microbial ecosystems are systemically explored. To avoid such issues, we will need stricter definitions and consensus on whether genetic data is evidence of a microbial hazard or not, and clearer guidelines on how to handle such results. This will assist producers to assess possible foodborne pathogenic contaminants and increase preparedness to employ microbial community profiling in environmental monitoring systems.

Distinctions between pathogens and beneficials may become less clear

One of the unexpected challenges from the explosion in microbiome research is the emergence of foodborne pathogens, not previously identified, that contribute to gut health. The human gut is recognised increasingly as a nexus for diverse chronic diseases ranging from mental health conditions to allergies. The food we eat and the bacteria that we introduce to this system are increasingly seen as indicators for human health. Whilst the positive effects of fresh produce on the gut microbiome are well established, further evidence of the impact of differing groups of fresh produce will undoubtedly be described in the future. In turn, segments of the indigenous microbiome previously thought to be benign in fruits and vegetables may turn out to be associated with positive or negative gut health. 

With the glut of data being generated from HTS technologies, curation of data and contextualisation of results must be prioritised. The democratisation of sequencing brings benefits and challenges. Just as the world of journalism has had to undergo radical changes with the advent of the internet, we will need to adjust to changes in the world of microbial testing. The harmonisation of baseline practices for applications will help to ensure that producers, buyers and consumers have confidence in the approaches taken to monitor foods. The development of well thought out risk communication strategies will also be essential to manage the increased quantity of microbial data shared across a broad range of stakeholders.

Despite the revolution in the way microbiologists are testing food, some things won’t change. A well-designed, proactive food safety management system and culture must remain the core focus for ensuring the safety of our fresh produce, rather than microbial end-point testing. Microbial testing should predominately be applied as a means for process monitoring and verification ensuring efficacy of sanitation. Further to this, communication and collaboration across the entire supply chain remains key in ensuring the maintenance of the safety of fresh produce and retaining consumer confidence.