Current diagnostic techniques primarily used in veterinary diagnostics of Salmonella

Sensitive detection of internal tandem duplication (ITD) mutation of FLT3 is very important in acute myeloid leukemia. To increase detection sensitivity of FLT3-ITD, we developed new detection algorithm using next generation sequencing (NGS) data. We validated results using nested polymerase chain reaction (PCR) methods. We compared results of NGS data, nested PCR and conventional PCR methods. First, using whole exome sequencing data of 83 AML patients, we applied calling algorithm for FLT3-ITD. Briefly, to detect ITDs with NGS data, the reads are aligned to a reference sequence (UCSC hg19), with BWA which is a read aligner allowing soft-clipping. Some reads can be an indication of the occurrence of ITD and BWA aligns those reads as soft-clipped. Second, we deigned two types of primer for Nested PCR. The first primer was targeted wildly for between exon14 and exon15 of FLT3 gene. Nested PCR primer was deigned to target previously reported regions which are frequently occurred ITD mutation. PCR reactions of two steps were performed using the PCR primers sequentially. In these 83 patients, FLT3-ITD was positive only in 7 patients when tested by conventional PCR methods. When NGS detection method was applied, this resulted in positive FLT3-ITD in 11 patients (11/83, 13%). When validation was performed using nested PCR, FLT3-ITD was confirmed in all of 11 patients. Nested PCR detected additional 4 patient positive for FLT3-ITD in this population. For 68 patients, FLT3-ITD was negative by both NGS and nested PCR method. Overall, NGS method improved sensitivity of FLT3-ITD detection by 57% in this population. And the concordance rate of NGS method and nested PCR was 95.2% (79/83). Then we investigated clinical significance of sensitive FLT3-ITD detection. For this, we performed nested PCR and conventional PCR at the same time in 238 AML patients to detect FLT3-ITD. Positive rate for FLT3-ITD was 20% (48/238) and 10% (24/238) by nested PCR and conventional PCR respectively. When survival analysis was performed, among patients with negative FLT3-ITD result by conventional PCR, patients who showed positive for FLT3-ITD by nested PCR had shorter overall survival compared to those who showed negative for FLT3-ITD by nested PCR. (p = 0.03). This implies that sensitive FLT3-ITD detection using nested PCR is clinically meaningful. Diagnosis of FLT3-ITD is very important genetic factor, leading a therapeutic direction for AML patient. Here we report that we have developed alternative more sensitive detection methods for FLT3-ITD based on nested PCR and NGS. Sensitive detection of FLT3-ITD was clinically meaningful, suggesting that these methods should be incorporated in a future clinical practice. Also, we want to note that, NGS method is capable of quantifying FLT3-ITD size and amount in AML patients. Citation Format: Daeyoon Kim, Yoojin Hong, Youngil Koh, Sung-Soo Yoon, Choong-Hyun Sun, Kwang-Sung Ahn, Seungmook Lee, Hongseok Yun, Suyeon Lee. Improved sensitive detection method of FLT3 (FMS-like tyrosine kinase) internal tandem duplication (ITD) mutation using next-generation sequencing technology and nested PCR. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3186.

Comparable Results of Helicobacter pylori Antibiotic Resistance Testing of Stools vs Gastric Biopsies Using Next-Generation Sequencing

European food production systems have become very efficient in terms of high yield, quality and safety. However, these production systems are not sustainable since, amongst other reasons, a significant proportion of the production is wasted or lost in the supply chain. One of the strategies of the European Union is to achieve climate neutrality by moving towards a circular economy with better waste management. This includes, reducing food waste and losses, and reusing or recycling by-products of the food and feed production systems. A circular economy would greatly improve the sustainability of the European food systems, but attention must be paid to the emergence of (new) food safety hazards. New or not well-known hazards can occur because by-products are reintroduced into the system or new processing steps are used for recycling, and/or known hazards can accumulate in the food production chain due to the reuse of (by-)products. This review addresses food safety hazards in the circular biobased economy, covering the domains of plant production, animal production, aquaculture, and packaging. Instead of an exhaustive list of all potential hazards, example cases of circular food production systems are given, highlighting the known and potential emerging food safety hazards. Current literature covering emerging food safety hazards in the circular economy shows to be limited. Therefore, more research is needed to identify food safety hazards, to measure the accumulation and the distribution of such hazards in the food and feed production systems, and to develop control and mitigation strategies. We advocate a food safety by design approach.

Viral Genome Sequencing for Ultrasensitive Detection of Circulating Tumor DNA

Mycoplasma infection is a major problem in veterinary medicine and in poultry production. The pathogen has many strains, so that diagnosis of the disease using culture method is not effective. The objective of this work was to evaluate the prevalence of Mycoplasma gallisepticum (MG) in Kuwait poultry farms using serology and molecular methods in comparison to the culture under specific conditions. A total of 50 swab samples from choanal cleft and tracheal samples and blood samples were obtained from three different local farms, the blood samples were processed for an Enzyme Linked Immunosorbent Assay (ELISA) detection and the swab samples for Polymerase Chain Reaction (PCR) and culture methods detection. A PCR diagnostic kit (VenoMGs) and ELISA diagnostic kit (ProFLOK), were used in comparison to the traditional culture method, to study the spread of this disease in samples from broiler and layer flocks. Fifty chicken samples were tested for mycoplasmosis, samples tested with ELISA gave 24 positive (48%) and 29 were positive by PCR (58%) and only seven (14%) were positive with culture methods. Swab samples obtained from the choanal cleft gave more positive (60%) with PCR than tracheal samples (56.6%). The culture gave 20 and 5% positive, respectively for tracheal and choanal samples. The methods reported here are of high sensitivity and specificity for Mycoplasma. Both the PCR and ELISA methods are superior to culture method for detection of avian mycoplasmosis. This study showed that MG infection is prevalent in commercial broiler and layer chickens in Kuwait poultry farms. The use of these methods for surveillance of the disease will establish data concerning the predominant Mycoplasmosis diseases in Kuwait if done on a large scale.

The aim of this study was to compare the sensitivity and specificity of polymerase chain reaction (PCR) using two primer pairs and combined with blood culture, immunoglobulin M enzyme-linked immunosorbent assay (IgM ELISA), microscopic agglutination test (MAT) and slide agglutination test (SAT) in the diagnosis of human leptospirosis. We analysed 124 serum samples: 60 from patients with confirmed leptospirosis, 20 from patients with other diseases and 44 from healthy individuals. Analysing the first serum sample collected during the first 3-8 days of disease, the sensitivities of the four tests MAT, IgM ELISA, SAT and PCR were, respectively, 69.0%, 79.3%, 72.4% and 62%. In subsequent samples, those same sensitivities were, respectively, 95.4%, 100%, 100% and 72.7% in samples collected from days 9 to 14 and 88.9%, 88.9%, 77.8% and 44.4% in those collected from days 15 to 42. The most specific method (at 100%) was PCR and the least specific (at 89.1%) was IgM ELISA. Although we found PCR to be less sensitive than the serological tests over the course of the disease, our data indicate that PCR was the most sensitive in those initial serum samples presenting no specific antibodies detectable by any of the serological methods tested. We also recommend that PCR can be used in combination with serological tests as we found that this improves the sensitivity of the diagnosis of leptospirosis in the first phase of the disease (93.1-96.5%).

In our review, most techniques (except G-banding) appeared to have good sensitivity (few false negatives) for detection of 1p/19q codeletions in glioma against both FISH and PCR-based LOH as a reference standard. However, we judged the certainty of the evidence low or very low for all the tests. There are possible differences in specificity, with both NGS and SNP array having high specificity (fewer false positives) for 1p/19q codeletion when considered against FISH as the reference standard. The economic analysis should be interpreted with caution due to the small number of studies.

The SARS-CoV-2 pandemic has brought significant light to the urgent need for rapid, precise, and low-cost diagnosis tools. The scientific community has responded as quickly, overflowing the literature with papers describing interesting biosensors for aiding in the diagnosis of COVID-19.1,2 However, almost none of them, mainly the electrochemical ones have reached the market or never will, with only a few traditional formats used in the daily combat of the virus, including ELISA (enzyme-linked immunosorbent assay), lateral flow assays, and, mainly, PCR (polymerase chain reaction). Although PCR-based methods are currently the gold standard for detecting viruses worldwide, these still present various drawbacks. Usually, the commercial detection of viruses (such as SARS-CoV-2) uses the combination of standard PCR (or RT-PCR) and gel electrophoresis due to its sensitivity, reliability, and low price (if compared to other PCR-based methods such as real-time PCR). This approach relies, mainly, on the use of a standard thermal cycler and an electrophoresis tank by a specialized worker. While electrophoresis tanks can be quite affordable, with some of them costing a few hundred dollars,3 even simple thermal cyclers cost around 5,000 USD4 – significantly enhancing the investment required for testing. Furthermore, the complete analysis of a sample is slow and can take up to six hours to complete, which prevents an effective sanitary barrier at borders and crowded events, for example. The samples need to be transported to the lab, as no reliable portable PCR and gel electrophoresis equipment are available. The results commonly take from two to five days to be generated - an extremely long delay when considering that these can seriously influence the health of a patient and the spread of the virus. Last, standard PCR does not provide quantitative information – which is vital in some cases to aid in diagnosing the severity of an infection. Techniques derived from PCR (such as qPCR, for example), on the other hand, can provide quantitative and more rapid results, but are also more expensive and still require sample transportation. Equipment for performing qPCR ranges from 15,000 USD to 90,000 USD4 and the use of specific reaction kits containing fluorescent markers also corresponds to a significant increase in analysis costs. Other commercially available methods for the detection of viruses, ELISA and lateral flow assays, also present significant drawbacks. While ELISA is time demanding (6 h) and requires specialized professionals and equipment to be adequately performed, some lateral flow assays present results with low precision,5,6 being useful for massive triages in the case of COVID-19, for example. Although presenting such limitations, PCR-based techniques are still the gold standard for the detection of viruses. This is probably due to its sensitive and well-established features, being widespread along with many medical and research centers around the globe. Furthermore, the development of PCR-based diagnosis kits in urgent scenarios, such as the one imposed by SARS-CoV-2, is straightforward and allows rapid responses from health organizations and governments. The technique can also provide low limits of detection (LOD), with a gold standard RT-PCR assay for COVID-19 presenting a LOD of ~100 copies of viral RNA per mL of transport media, for example. It is important to mention, however, that the LOD of currently approved assays for COVID-19 varies over 10,000-fold, which will generate immense false-negative rates.7 Biosensors present interesting properties to overcome some of the drawbacks presented by PCR. Although thousands of papers have been published in the last years based on the detection of several diseases, almost all the material published has focused on the formation of human resources and not on the market (Table I). There are few discussions in the electrochemical meetings and a tremendous demand to produce new selling and profitable devices for the environment, food, medical, and forensic analyses. In this context, portable potentiostats are commonly available on the market at prices that range from a few thousand dollars (2,000 – 3,000 USD) for full desktop equipment8 to a few hundred dollars for equipment devoted to a single analysis. There is also significant research interest in the development of portable, miniaturized, and low-cost potentiostat, as highlighted by some articles published in recent years.9–11 Colorimetric biosensors, in turn, can rely on responses readable with the naked eye or using widespread smartphones. The use of smartphones can also contribute to compiling results and acquiring additional information such as patient location and data. Therefore, if compared to PCR-based techniques, instrumentation costs are decreased while its portability allows point-of-care analysis, significantly increasing the accessibility to tests in remote areas. Analysis time is also greatly diminished as results can be obtained in only a few minutes. Both of these features are of extreme importance when considering healthcare applications that commonly require quick or real-time responses. Furthermore, immunosensors do not require previous sample preparation even when using complex biological fluids, decreasing analysis costs and making it even more rapid. Last, biosensors can be easy to use, usually requiring lower previous preparation from the operator if compared to traditional techniques (Figure 1). Biosensors can also be readily developed in urgent scenarios, as proven with COVID-19. Numerous examples of electrochemical, colorimetric, and mass-sensitive devices for aiding in the diagnosis of the disease were described in the literature only a few months after the start of the pandemic event.1,12,13 Devices are commonly validated in biological samples, providing precise results in a rapid, cheap, and simple manner. So, a relevant question is, why are most of these devices still out of the consumers' reach?

Food Science and TechnologyVolume 36, Issue 4 p. 42-45 SpotlightFree Access Networking to reduce microbial risk in foods First published: 01 December 2022 https://doi.org/10.1002/fsat.3604_11.xAboutSectionsPDF ToolsExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Matthew Gilmour and Maria Traka of the Quadram Institute introduce the new UK Food Safety Research Network, which is aiming to Improve the safety of UK foods by harnessing expertise across the food chain in collaborative research and training activities. The challenging ecology of foodborne microbes Preventing microbial pathogens from entering the food chain is challenging due to the multitude of environmental and agricultural niches in which they thrive. Pathogens like Salmonella and Listeria are expert at being carried in and adapting to farm and food production settings, leading to contamination of diverse meat and plant-based foods. The challenges to control these microbes are only becoming more complex as food production systems and consumer preferences evolve and global factors, such as climate change, impact the ecology of food systems. The UK is strongly committed to food safety, with food manufacturers focusing on ensuring foods are healthy and safe for their customers. There are many programmes in place that regulate how food is produced and monitor for hazards that might contaminate foods; some initiatives come from government and some from the food industry itself. However, we also know from UK research that it is common for people to visit their GP with food-associated illness and that about a quarter of the UK population have diarrhoea each year1. The causes of food-associated illness are not always determined; of the estimated £9bn annual cost to the UK of these illnesses, £6bn are from unknown causes. Therefore, some microbial hazards are not only challenging to prevent from entering the food chain, but also to detect in foods and food settings. In studies that examined these cases more closely, the cause was often a microbial pathogen that had been carried over into food from the environment or from livestock or even from people. A solution to these food safety challenges is to catalyse collaborative research between scientific experts, the food industry and food policy partners to robustly consider and act upon new opportunities to make food safer. Applying science as a collaborative network In association with the Biotechnology and Biological Sciences Research Council of UK Research & Innovation (BBSRC-UKRI) and the Food Standards Agency (FSA), the Quadram Institute in Norwich established the new UK Food Safety Research Network (FSRN)2 in April 2022. Acting as a hub for scientific innovation and collaborative research that addresses complex challenges, the Network is creating a community from amongst representatives of the food industry, government departments and academia and developing a shared vision and plan for research that can improve the safety of foods now and in the future. The specific remit of the Network is to address microbial risks in the food chain; as the Network was created it became increasingly clear that more than just ‘microbiology’ was going to be in scope. Interviews with Network members and stakeholders during our establishment stages highlighted that there is a ‘new edge’ to biological research in foods based on new technologies and the dynamic economic and environmental sustainability drivers that are currently shaping food system transformations and which transcend traditional biological questions on food hygiene. At this edge, it is possible to pursue research and training that benefits the food system by collectively harnessing interdisciplinary expertise for cutting-edge technologies, rich food system data and theory, and an existing understanding of social and economic factors. The goal of the UK's FSRN is to take a multi-stakeholder approach to apply science to the food safety challenges prioritised within this community. The focus will be areas where collaborative research or training can build new capacity or knowledge that benefits food safety. Within the Network, policy and industry sectors are now coming together with scientific researchers via: exercises that define food safety problems, funded collaborative research projects and food safety training fora. It is important that the FSRN develops successful pathways to curate new relationships between academic researchers and food stakeholders, who are directly facing and motivated to address the evolving risks and challenges in the food system. We have learned that many in the food industry recognise the need for research and developmental activities that address food safety challenges. However, for some producers (often small and medium sized enterprises) there is little bandwidth beyond the operational challenges of their business to participate in such research. The FSRN is providing a platform for food industry members and academic researchers to make these connections and expedite adoption of effective food safety solutions by directly supporting and resourcing co-designed collaborative projects. Building a community to identify ‘problems worth solving’ that increase the safety of UK foods To scope the key food safety risks that would have a meaningful impact on UK foods if pursued in collaborative projects, we are engaging with members of our community of experts that represent primary food producers, food retailers and food sector trade associations. In a series of one-on-one interviews, we documented members’ experiences and perspectives about what they considered to be the contemporary, emerging and perceived food safety challenges that, if addressed, would bring value to their products and for which they could foresee a route to impact within the food system. Scientific perspectives on food safety risks and challenges were simultaneously sought from stakeholders from across scientific disciplines representing the environment, animals and human health. These included veterinarians, virologists, data scientists and social scientists. Perspectives were also sought from: government institutes, knowledge transfer networks and professional bodies specialising in food system studies, policy and training. It is from this multi-disciplinary and multi-sector community that an ability to address complex food safety issues emerges. A broad view of the issues affecting food safety The food system comprises many social, environmental and political factors that together can affect the foods that are produced and those that are sought by consumers. In our initial problem definition interviews, many of these ‘macro’ factors were repeatedly cited by stakeholders as conceivably having a significant consequence to food safety and shelf life because changes to how foods are produced and stored can impact the ecology of any microbes present. Amongst these extensive and overlapping macro factors, there are multiple points in the food chain at which food safety challenges can emerge and then endure as microbial risks, even those not easily identifiable as risks at the outset. For example, new economic pressures, such as those introduced by COVID-19 and Brexit, that affect supply and distribution networks introduce changes to the sourcing and availability of food ingredients; as food ingredients change so do the standards used to produce them, potentially impacting both the microbial composition and safety profile of individual ingredients. Likewise, economic pressures have resulted in other market shifts, such as the availability of CO2 supplies and operational costs related to the energy crisis. Supplies of CO2 have a direct impact on the ability to introduce modified atmosphere packaging (MAP), which is a preservative that inhibits both pathogenic and spoilage microbes. If food storage temperatures are increased to save on energy costs (e.g. during refrigeration), then basic microbial control measures that are currently effective will be compromised and could lead to altered microbial risk profiles. Food storage conditions were also highlighted from an environmental perspective. As our climate changes so does the ability to maintain optimal storage temperatures in some settings. In addition, global impacts to the environment and agriculture have increasingly led to changes in water, carbon and temperature cycles with direct effects on microbial ecology, e.g. microbial profiles in irrigation waters. As microbial composition changes in this critical agricultural resource, it was easy for our interviewees to conceive how the overall risk of pathogen transmission during primary plant and livestock production could increase. Further ‘upstream’ in the food chain, our stakeholders commonly felt that changes in consumer preference and regulation of food categories sold in retail settings could also conceivably impact food safety. For example, the demand for new plant-based foods means food producers are developing product lines that use new ingredients (e.g. alternative proteins, micro-and macro-algae), new culturing technologies, or new processing techniques, while the overall knowledge of microbial risks for food safety and shelf life of these new categories may be lagging behind their arrival on retail shelves. Furthermore, consumers are also seeking food packaging that reduces plastic use; this requires the introduction of new materials or new methods of packaging (e.g. vacuum packing versus MAP). In addition, governments are regulating for reduced contents of salt, sugar and fat. Each of these changes potentially shifts the ecology and risk of microbes present on foods. Factors impacting food safety and microbial contamination more locally within particular food production settings were also discussed during our stakeholder interviews. For example, cleaning and hygiene is a cornerstone of food safety yet the effectiveness of some disinfection and sanitising agents is uncertain and there can be engineering issues associated with food contact surfaces that make them challenging to clean or maintain at controlled temperatures. Stakeholders also cited that there are knowledge gaps on microbial risks in food product categories or gaps in the ability to implement best food safety practices conceivably exacerbated by labour shortages, which aligns with global economic and political pressures. All of these challenges represent an opportunity for research and for the identification of new knowledge to inform interventions or policies that could improve the safety of food. They also provide a view on emerging food safety risks that require participation from a multitude of stakeholders and scientific disciplines if they are to be appropriately studied and effectively addressed. Brokering project partnerships around priority areas of applied food safety research Following our broad scoping of food safety challenges, the next key activity of the FSRN was to coordinate distribution of resources that supported both innovation and collaboration. We understood that many in our community had not directly participated in collaborative research activities previously, and that for some, Network support would be needed to broker partnerships and develop project plans that could draw on collective insights, data and technologies from across the Network. We also understood that some members were already tuned into food safety research around microbial risk and were ready to act with their partners. In August 2022, we opened the FSRN's first call for proposals. Using a streamlined application process, project applications could be submitted that were either ‘ready to fund and ready to act’ or were ‘expressions of interest’ for projects that needed further time to develop. As a guide to all applicants we publicised three prioritised areas as a framework for collaborative projects based on the earlier stakeholder feedback (Figure 1). Figure 1Open in figure viewerPowerPoint The Food Safety Research Network's priority areas. As a guide to all applicants we publicised three prioritised areas as a framework for collaborative projects based on the earlier stakeholder feedback. Firstly, to address known microbial risks, we sought new evidence for interventions that reduce pathogens, such as Salmonella, Campylobacter or Listeria, which continue to be problematic in some foods and food production settings. Secondly, to increase our understanding of the perceived microbial risk in new food categories and production systems, we sought studies on alternative proteins and new plant-based foods. Lastly, to improve the safety of ready-to-eat (RTE) foods, we sought to develop new ways to apply food safety knowledge and new tools to address this established high-risk food category. As an outcome of our first call for proposals, the successful ‘ready to act’ projects included activities that will develop and assess applications of bacteriophage for control of Salmonella and Listeria contamination in settings such as aquaculture and raw pet food production. Our prioritised area of research on novel foods was represented in a project that will profile the microbial communities of crickets (Acheta domesticus) and assess the production systems for this alternative protein, while other projects will test the efficacy of novel biocide combinations and develop new diagnostic technologies that will support pathogen environmental monitoring programmes. Fried crickets For the ‘expression of interest’ stream we received proposals from industry Network members from across the food chain, ranging from animal producers and primary producers to trade associations; we also received proposals from government departments with mandates outside the food chain. From the successful proposals we are facilitating planning with the applicants, other stakeholders and funders to develop these ideas towards large collaborative projects; further information will be forthcoming from the FSRN on these opportunities and the fora (such as stakeholder workshops) that will be used to progress them. Examples of the areas that were prioritised for additional collaborative work include: conducting focal studies on pathogen transmission in livestock production and the spill-over of microbes into meat-based foods; establishing and promoting fit-for-purpose best practices that improve the safety and shelf life of RTE foods; advancing bacteriophage applications to provide evidence to move beyond existing regulatory barriers; understanding the food safety implications of climate change; filling a gap in certification and guidance on food safety for primary producers; facilitating the availability of microbial testing data amongst partners to enhance trend analyses and overall horizon scanning on microbial risks; developing new methods for investigating foodborne viruses (e.g. norovirus; hepatitis E). As project applications and expressions of interest were received during our call for proposals, we realised that not only can the Network provide partners with essential financial resources to conduct collaborative studies, but also a legitimate entry point to communicate ideas and identify partners. Thus, the FSRN has established a framework for collaborative processes where members become mutually aware of food safety networking and research opportunities. Further, there is also the opportunity to connect with other UK food system network programmes, such as the Transforming UK Food Systems Strategic Partnership Fund3, FSA's PATH-SAFE4 and Innovate UK's KTN Food5, to amplify food safety objectives across multiple partners. Mobilising food safety knowledge Paraphrasing from our stakeholder interviews, key findings from industry were that ‘we need simple tools to interpret test results and their implication for food safety’ and that ‘what we don't need is an expensive list of microbes that we don't know what to do with’. These were powerful sentiments and we understand that for some food industry members their capacity to take new action and adopt scientific advancements supporting their food safety aims can be limited due to accessibility and practicality of scientific information or technologies. As such, the ultimate goal of the FSRN is to bring forward Network discoveries that are game changing by working directly with food producers and other food industry members in a manner that is continually informed by their perspectives and ensures their active involvement in piloting or demonstration of new technologies or knowledge. We have also identified that not all knowledge that should be acted upon needs to be new knowledge. Stakeholders asked that FSRN members exploit existing studies, platforms and experiences within the Network's collaborative projects and promote their accessibility. This would create opportunities to upcycle existing data sets that have value for contemporary food safety challenges but which have not been broadly applied by scientific or stakeholder communities. This would also create long-term impact and value from previously funded research. Further, the FSRN plans to publicly promote and extend the impactful methods and knowledge developed in our collaborative research programmes. We will host a series of training events and sponsor the exchange of scientists and food industry employees between Network member sites. A goal is for our programmes to actively support skills development around food safety and interoperability between Network partners. These include professional groups, such as veterinarians and environmental health officers, and our partners in the food industry, who all have key roles in enhancing the safety of UK foods. Matthew W. Gilmour and Maria H. Traka, UK Food Safety Research Network, Quadram Institute Bioscience, Norwich, UK email foodsafetynetwork@quadram.ac.uk web quadram.ac.uk/food-safety-research-network/ References 1 Food Standards Agency. 2020. Foodborne disease estimates for the United Kingdom in 2018. Available from: https://www.food.gov.uk/research/foodborne-disease/foodborne-disease-estimates-for-the-united-kingdom-in-2018 2 Quadram Institute. 2020. Food safety research network. Available from: https://quadram.ac.uk/food-safety-research-network/ 3 Global Food Security. 2022. Transforming UK food systems SPF. Available from: https://www.foodsecurity.ac.uk/research/foodsystems-spf/ 4 Food Standards Agency. 2022. Pathogen surveillance in agriculture, food and environment programme. Available from: https://www.food.gov.uk/our-work/pathogen-surveillance-in-agriculture-food-and-environment-programme 5Innovate UK, KTN. 2022. Food. Available from: https://ktn-uk.org/agrifood/food/ Volume36, Issue4December 2022Pages 42-45 FiguresReferencesRelatedInformation

Currently transgenic plants are grown in more than 20 countries with maize, soybean, canola and cotton being the most predominant crops. Inexperience in the outcomes of the technology and growing public concern necessitates proper detection and regulation of genetically modified organisms (GMOs) from farmland to market. Due to their high specifity and sensitivity, polymerase chain reaction (PCR) based systems are currently the method of choice in detection of genetic modifications. This study compares the efficiency of three different PCR based methods; reverse-transcription PCR (RT-PCR), real-time PCR (qPCR) and conventional PCR in reference with the transgene copy numbers assessed by Southern blot hybridization, in detection of genetic modification. In the study, first generation transgenic lentil (Lens culinaris M.) plants carrying beta-glucuronidase (gus) gene in control of CaMV-35S promoter and A.tumefaciens nos terminator was used. Conventional PCR was used in detection of gus gene signal and RT PCR was performed in detection of gene's expression. qPCR was used to detect expression signals of both 35S promoter and nos terminator. All of the methods were successful in producing amplification signals for each target gene. Although qPCR signal strengths were in consistency with the band intensities obtained by RT-PCR to some extent, outcomes of both PCR-based methods appeared to be independent from copy number of genes detected in Southern blot hybridization. Band intensities obtained by conventional PCR showed no particular correlation with any other PCR-based method. Inconsistency in copy number of gene and qPCR signal strength, even in pure DNA samples may have a contribution for the debates on the influence of various factors on qPCR and reliability of the method in genetic modification quantification.

The vegan trend and the microfoundations of institutional change: A commentary on food producers’ sustainable innovation journeys in Europe

Impact of minimal residual disease and next generation sequencing discordance in AML following induction with hypomethylating agent + venetoclax.

The detection of microbial contaminants in food and food products is a cornerstone of public health protection and food safety assurance. As foodborne diseases continue to pose a global burden, with pathogens such as Salmonella, Escherichia coli, Listeria monocytogenes, and norovirus accounting for millions of illnesses annually, the need for robust and reliable detection methodologies has become increasingly urgent. This chapter provides a comprehensive overview of the evolving landscape of microbial detection in food systems. It begins by exploring the sources and pathways of microbial contamination across the “farm-to-fork” continuum, highlighting critical control points and microbial risk factors. Emphasis is placed on sampling strategies, including representative sampling, sample preparation, and enrichment protocols, which form the foundation of accurate microbial detection. The chapter then examines diverse detection strategies, including culture-based methods, immunological assays (such as enzyme-linked immunosorbent assay and lateral flow tests), and molecular techniques like polymerase chain reaction (PCR), quantitative PCR, loop-mediated isothermal amplification, and next-generation sequencing. Emerging technologies such as biosensors, Clustered Regularly Interspaced Short Palindromic Repeats-based diagnostics, and metagenomics are also discussed for their potential to enhance sensitivity, specificity, and rapidity in pathogen detection. Each technique is assessed in terms of sensitivity, specificity, operational feasibility, and its integration into food safety risk management frameworks. Special attention is given to validation standards, harmonization efforts, and the challenges of deploying these technologies in low-resource settings. The chapter concludes by identifying emerging trends, such as artificial intelligence-assisted detection and portable diagnostics, which hold promise for revolutionizing microbial monitoring in food systems. By bridging microbiological principles with practical applications and regulatory contexts, offering critical insights for researchers, food safety practitioners, and policymakers.

Rapid advances in DNA sequencing technologies have made it increasingly cost-effective to obtain accurate and timely large-scale genomic sequence data on individuals (short read massively parallel or next generation [next-gen]). A next-gen molecular diagnostic approach that has seen rapid deployment in the clinic over the last year is exome sequencing. Whole exome sequencing covers all protein-coding genes in the genome (≈1.1% of genome), and an exome test for a single patient generates ≈6 gigabases (109 bp) of DNA sequence data. A key challenge facing routine use of next-gen data in patient diagnosis and management is data interpretation. What sequence variant findings are relevant to diagnosis (pathogenic mutations)? What sequence variant findings are relevant to clinical care but not necessarily to patient diagnosis (clinically actionable incidental data)? What sequence information should be stored, and where can it be stored? This review provides a tutorial on current approaches to answering these questions. A recent landmark study showed that application of next-gen sequencing to a large cohort of idiopathic dilated cardiomyopathy patients found ≈27% of patients to show mutations of the titin gene, the most complex gene in the genome (363 exons). We use titin in cardiomyopathy as an exemplar for explaining next-gen sequencing approaches and data interpretation. Decreasing sequencing costs and broad dissemination of next-generation (next-gen) equipment and expertise are increasing availability of massively parallel sequencing of patient DNA samples (short read massively parallel or next-gen sequencing).1,2 Most rapidly expanding is exome sequencing, where all protein-coding sequences (exons) are selected from total genomic DNA and selectively sequenced.3 Alternative approaches to next-gen sequencing include targeted sequencing (TS) and whole genome (complete genome) sequencing. Currently, marketed targeted Sanger sequencing panels using traditional individual exon-by-exon sequencing remain expensive and time consuming, and massively parallel next-gen approaches are beginning to supplant …

For patients with metastatic non-small cell lung cancer (mNSCLC), next-generation sequencing (NGS) biomarker testing has been associated with a faster time to appropriate targeted therapy and more comprehensive testing relative to polymerase chain reaction (PCR) testing. However, the impact on payer costs and clinical outcomes during patients' treatment journeys has not been fully characterized. To assess the costs and clinical outcomes of NGS vs PCR biomarker testing among patients with newly diagnosed de novo mNSCLC from a US payers' perspective. A Markov model assessed costs and clinical outcomes of NGS vs PCR testing from the start of testing up to 3 years after. Patients entered the model after receiving biomarker test results and then initiated first-line (1L) targeted or nontargeted therapy (immunotherapy and/or chemotherapy) depending on actionable mutation detection. A few patients with an actionable mutation were not detected by PCR and inappropriately initiated 1L nontargeted therapy. At each 1-month cycle, patients could remain on treatment with 1L, progress to second line or later (2L+), or die. Literature-based inputs included the rates of progression-free survival (PFS) and overall survival (OS), targeted and nontargeted therapy costs, total costs of testing, and medical costs of 1L, 2L+, and death. Per patient average PFS and OS as well as cumulative costs were reported for NGS and PCR testing. In a modeled population of 100 patients (75% commercial and 25% Medicare), 45.9% of NGS and 40.0% of PCR patients tested positive for an actionable mutation. Relative to PCR, NGS was associated with $7,386 in savings per patient (NGS = $326,154; PCR = $333,540) at 1 year, driven by lower costs of testing, including estimated costs of delayed care and nontargeted therapy initiation before receiving test results (NGS = $8,866; PCR = $16,373). Treatment costs were similar (NGS = $305,644; PCR = $305,283). In the PCR cohort, the per patient costs of inappropriate 1L nontargeted therapy owing to undetected mutations were $6,455, $6,566, and $6,569 over the first 1, 2, and 3 years, respectively. Relative to PCR testing, NGS was associated with $4,060 in savings at 2 years and $1,092 at 3 years. Patients who initiated 1L targeted therapy had an additional 5.4, 8.8, and 10.4 months of PFS and an additional 1.4, 3.6, and 5.3 months of OS over the first 1, 2, and 3 years, respectively, relative to those who inappropriately initiated 1L nontargeted therapy. In this Markov model, as early as year 1, and over 3 years following biomarker testing, patients with newly diagnosed de novo mNSCLC undergoing NGS testing are projected to have cost savings and longer PFS and OS relative to those tested with PCR.