PCR technology for screening and quantification of genetically modified organisms (GMOs)

Although PCR technology has obvious limitations, the potentially high degree of sensitivity and specificity explains why it has been the first choice of most analytical laboratories interested in detection of genetically modified (GM) organisms (GMOs) and derived materials. Because the products that laboratories receive for analysis are often processed and refined, the quality and quantity of target analyte (e.g. protein or DNA) frequently challenges the sensitivity of any detection method. Among the currently available methods, PCR methods are generally accepted as the most sensitive and reliable methods for detection of GM-derived material in routine applications. The choice of target sequence motif is the single most important factor controlling the specificity of the PCR method. The target sequence is normally a part of the modified gene construct, for example a promoter, a terminator, a gene, or a junction between two of these elements. However, the elements may originate from wildtype organisms, they may be present in more than one GMO, and their copy number may also vary from one GMO to another. They may even be combined in a similar way in more than one GMO. Thus, the choice of method should fit the purpose. Recent developments include event-specific methods, particularly useful for identification and quantification of GM content. Thresholds for labelling are now in place in many countries including those in the European Union. The success of the labelling schemes is dependent upon the efficiency with which GM-derived material can be detected. We will present an overview of currently available PCR methods for screening and quantification of GM-derived DNA, and discuss their applicability and limitations. In addition, we will discuss some of the major challenges related to determination of the limits of detection (LOD) and quantification (LOQ), and to validation of methods.

Detection and traceability of genetically modified organisms in the food production chain

Both labelling and traceability of genetically modified organisms are current issues that are considered in trade and regulation. Currently, labelling of genetically modified foods containing detectable transgenic material is required by EU legislation. A proposed package of legislation would extend this labelling to foods without any traces of transgenics. These new legislations would also impose labelling and a traceability system based on documentation throughout the food and feed manufacture system. The regulatory issues of risk analysis and labelling are currently harmonised by Codex Alimentarius. The implementation and maintenance of the regulations necessitates sampling protocols and analytical methodologies that allow for accurate determination of the content of genetically modified organisms within a food and feed sample. Current methodologies for the analysis of genetically modified organisms are focused on either one of two targets, the transgenic DNA inserted- or the novel protein(s) expressed- in a genetically modified product. For most DNA-based detection methods, the polymerase chain reaction is employed. Items that need consideration in the use of DNA-based detection methods include the specificity, sensitivity, matrix effects, internal reference DNA, availability of external reference materials, hemizygosity versus homozygosity, extrachromosomal DNA, and international harmonisation. For most protein-based methods, enzyme-linked immunosorbent assays with antibodies binding the novel protein are employed. Consideration should be given to the selection of the antigen bound by the antibody, accuracy, validation, and matrix effects. Currently, validation of detection methods for analysis of genetically modified organisms is taking place. In addition, new methodologies are developed, including the use of microarrays, mass spectrometry, and surface plasmon resonance. Challenges for GMO detection include the detection of transgenic material in materials with varying chromosome numbers. The existing and proposed regulatory EU requirements for traceability of genetically modified products fit within a broader tendency towards traceability of foods in general and, commercially, towards products that can be distinguished from each other. Traceability systems document the history of a product and may serve the purpose of both marketing and health protection. In this framework, segregation and identity preservation systems allow for the separation of genetically modified and non-modified products from "farm to fork". Implementation of these systems comes with specific technical requirements for each particular step of the food processing chain. In addition, the feasibility of traceability systems depends on a number of factors, including unique identifiers for each genetically modified product, detection methods, permissible levels of contamination, and financial costs. In conclusion, progress has been achieved in the field of sampling, detection, and traceability of genetically modified products, while some issues remain to be solved. For success, much will depend on the threshold level for adventitious contamination set by legislation.

Phylogeny and toxigenic potential is correlated in Fusarium species as revealed by partial translation elongation factor 1 alpha gene sequences

Partial translation elongation factor 1 alpha (TEF-1alpha) gene and intron sequences are reported from 148 isolates of 11 species of the anamorph genus Fusarium; F. avenaceum (syn. F. arthrosporioides), F. cerealis, F. culmorum, F. equiseti, F.flocciferum, F. graminearum, F. lunulosporum, F. sambucinum, F. torulosum, F. tricinctum and F. venenatum. The sequences were aligned with TEF-1alpha sequences retrieved from 35 isolates of F. kyushuense, F. langsethiae, F. poae and F. sporotrichioides in a previous study, and 39 isolates of F. cerealis, F. culmorum, F. graminearum and F. pseudograminearum retrieved from sequence databases. The 222 aligned sequences were subjected to phylogenetic analyses using maximum parsimony and Bayesian Markov Chain Monte Carlo maximum likelihood statistics. Support for internal branching topologies was examined by Bremer support, bootstrap and posterior probability analyses. The resulting trees were largely congruent. The taxon groups included in the sections Discolor, Gibbosum and Sporotrichiella sensu Wollenweber & Reinking (1935) all appeared to be polyphyletic. All species were monophyletic except F. flocciferum that was paraphyletic, and one isolate classified as F. cfr langsethiae on the basis of morphology that grouped with F. sporotrichioides. Mapping of toxin profiles, host preferences and geographic origin onto the DNA based phylogenetic tree structure indicated that in particular the toxin profiles corresponded with phylogeny, i.e. phylotoxigenic relationships were inferred. A major distinction was observed between the trichothecene and non-trichothecene producers, and the trichothecene producers were grouped into one clade of strictly type A trichothecene producers, one clade of strictly type B trichothecene producers and one clade with both type A and type B trichothecene producers. Furthermore, production of the type A trichothecenes T-2/HT-2 toxins are associated with a lineage comprising F. langsethiae and F. sporotrichioides. The ability to produce zearalenone was apparently gained parallel to the ability to produce trichothecenes, and later lost in a derived sublineage. The ability to produce enniatins is a shared feature of the entire study group, with the exception of the strict trichothecene type B producers and F. equiseti. The ability to produce moniliformin seems to be an ancestral feature of members of the genus Fusarium which seems to have been lost in the clades consisting of trichothecene/zearalenone producers. The aims of the present study were to determine the phylogenetic relationships between the different species of Fusarium commonly occurring on Norwegian cereals and some of their closest relatives, as well as to reveal underlying patterns such as the ability to produce certain mycotoxins, geographic distribution and host preferences. Implications for a better classification of Fusarium are discussed and highlighted.

Testing for genetically modified organisms (GMOs): Past, present and future perspectives

This paper presents an overview of GMO testing methodologies and how these have evolved and may evolve in the next decade. Challenges and limitations for the application of the test methods as well as to the interpretation of results produced with the methods are highlighted and discussed, bearing in mind the various interests and competences of the involved stakeholders. To better understand the suitability and limitations of detection methodologies the evolution of transformation processes for creation of GMOs is briefly reviewed.

Advances in DNA metabarcoding for food and wildlife forensic species identification

Species identification using DNA barcodes has been widely adopted by forensic scientists as an effective molecular tool for tracking adulterations in food and for analysing samples from alleged wildlife crime incidents. DNA barcoding is an approach that involves sequencing of short DNA sequences from standardized regions and comparison to a reference database as a molecular diagnostic tool in species identification. In recent years, remarkable progress has been made towards developing DNA metabarcoding strategies, which involves next-generation sequencing of DNA barcodes for the simultaneous detection of multiple species in complex samples. Metabarcoding strategies can be used in processed materials containing highly degraded DNA e.g. for the identification of endangered and hazardous species in traditional medicine. This review aims to provide insight into advances of plant and animal DNA barcoding and highlights current practices and recent developments for DNA metabarcoding of food and wildlife forensic samples from a practical point of view. Special emphasis is placed on new developments for identifying species listed in the Convention on International Trade of Endangered Species (CITES) appendices for which reliable methods for species identification may signal and/or prevent illegal trade. Current technological developments and challenges of DNA metabarcoding for forensic scientists will be assessed in the light of stakeholders' needs.

Characterization of GM events by insert knowledge adapted re-sequencing approaches

Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-adapted approaches for characterization GM events (TT51-1 and T1c-19 rice as examples) based on paired-end re-sequencing with the advantages of comprehensiveness, accuracy, and automation. The comprehensive molecular characteristics of two rice events were revealed with additional unintended insertions comparing with the results from PCR and Southern blotting. Comprehensive transgene characterization of TT51-1 and T1c-19 is shown to be independent of a priori knowledge of the insert and vector sequences employing the developed approaches. This provides an opportunity to identify and characterize also unknown GM events.

The Modular Analytical Procedure and Validation Approach and the Units of Measurement for Genetically Modified Materials in Foods and Feeds

Food and feed analysts are confronted with a number of common problems, irrespective of the analytical target. The analytical procedure can be described as a series of successive steps: sampling, sample processing, analyte extraction, and ending, finally, in interpretation of an analytical result produced with, e.g., real-time polymerase chain reaction. The final analytical result is dependent on proper method selection and execution and is only valid if valid methods (modules) are used throughout the analytical procedure. The final step is easy to validate—the measurement uncertainty added from this step is relatively limited and can be estimated with a high degree of precision. In contrast, the front-end sampling and processing steps have not evolved much, and the corresponding methods are rarely or never experimentally validated according to internationally harmonized protocols. In this paper, we outlined a strategy for modular validation of the entire analytical procedure, using an upstream validation approach, illustrated with methods for genetically modified materials that may partially apply also to other areas of food and feed analyses. We have also discussed some implications and consequences of this approach in relation to reference materials, measurement units, and thresholds for labelling and enforcement, and for application of the validated methods (modules) in routine food and feed analysis.

Structural characteristics and possible horizontal transfer of group I introns between closely related plant pathogenic fungi

We have characterized structural features and the distribution pattern of nuclear group I introns found in ribosomal DNA (rDNA) of closely related plant pathogenic fungi of the family Sclerotiniaceae. Sixteen introns, at two distinct positions in the small-subunit (SSU) and large-subunit (LSU) rDNA, were sequenced and analyzed among the 29 taxa included in the initial screening. Genera found to contain introns were Botrytis, Dumontinia, Encoelia, Grovesinia, Myriosclerotinia, and Sclerotinia. Secondary-structure analyses of the group I introns concluded that all belong to the common IC1 subclass. Interestingly, the SSU rDNA intron from Myriosclerotinia caricisampullacea contains an insertion-like sequence extension which may be a relic of an open reading frame. Incongruent branching patterns of intron-based and rDNA-based (internal transcribed spacer) phylogenetic trees suggest that the fungal host genomes and the group I introns do not share a common evolutionary history. A model to explain how horizontal intron transfers may have occurred among the closely related fungal taxa is proposed.

High Throughput Sequencing for Detection of Foodborne Pathogens

High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data. The influence of sample processing, nucleic acid extraction and purification, harmonized protocols for generation and interpretation of data, and properly annotated and curated reference databases including non-pathogenic "natural" strains are other major obstacles to the realization of the full potential of HTS in analytical food surveillance, epidemiological and outbreak investigations, and in complementing preventive approaches for the control and management of foodborne pathogens. Despite significant obstacles, the achieved progress in capacity and broadening of the application range over the last decade is impressive and unprecedented, as illustrated with the chosen examples from the literature. Large consortia, often with broad international participation, are making coordinated efforts to cope with many of the mentioned obstacles. Further rapid progress can therefore be prospected for the next decade.

Phylogenetic analyses of the Fusarium poae, Fusarium sporotrichioides and Fusarium langsethiae species complex based on partial sequences of the translation elongation factor-1 alpha gene

Phylogenetic relationships between four Fusarium species were studied using parts of the nuclear translation elongation factor-1 alpha (EF-1alpha) gene as a phylogenetic marker. Sequences from 12 isolates of Fusarium poae, 10 isolates of Fusarium sporotrichioides and 12 isolates of Fusarium langsethiae yielded 4, 5 and 5 haplotypes, respectively. In addition, we included one isolate of Fusarium kyushuense. The aligned sequences were subjected to neighbor-joining (NJ), maximum parsimony and maximum likelihood (ML) analyses. The results from the different analyses were highly concordant. The EF-1alpha-based phylogenies support the classification of F. langsethiae as a separate taxon in the section Sporotrichiella of Fusarium, as the closest sister taxon to F. sporotrichioides, while F. kyushuense is the sister taxon to F. poae. This corresponds well with the ability of F. langsethiae and F. sporotrichioides to produce T-2 and HT-2 toxins. In contrast, morphological characters indicate a closer relationship between F. langsethiae and F. poae on the one hand, and between F. sporotrichioides and F. kyushuense on the other hand.

Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples

DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories. A DNA metabarcoding method was developed that makes use of 12 DNA barcode markers that have demonstrated universal applicability across a wide range of plant and animal taxa and that facilitate the identification of species in samples containing degraded DNA. The DNA metabarcoding method was developed based on Illumina MiSeq amplicon sequencing of well-defined experimental mixtures, for which a bioinformatics pipeline with user-friendly web-interface was developed. The performance of the DNA metabarcoding method was assessed in an international validation trial by 16 laboratories, in which the method was found to be highly reproducible and sensitive enough to identify species present in a mixture at 1% dry weight content. The advanced multi-locus DNA metabarcoding method assessed in this study provides reliable and detailed data on the composition of complex food products, including information on the presence of CITES-listed species. The method can provide improved resolution for species identification, while verifying species with multiple DNA barcodes contributes to an enhanced quality assurance.

Polyphasic re-examination of Yarrowia lipolytica strains and the description of three novel Candida species: Candida oslonensis sp. nov., Candida alimentaria sp. nov. and Candida hollandica sp. nov

The type strain of Yarrowia lipolytica and 38 strains identified as Yarrowia lipolytica, four strains of Candida deformans, including the type and two subcultures of the type, two strains of Candida galli and six unidentified strains that resembled Y. lipolytica were examined by PCR fingerprints using primers M13 and (GAC)5. The same strains, together with four strains of the recently introduced Candida yakushimensis nom. inval., were sequenced for the D1/D2 domain of the 26S rRNA gene and parts of the ITS domain and also studied for their physiological properties. Of the strains identified previously as Y. lipolytica, CBS 2076 had the same fingerprint as the type of C. deformans and strain CBS 4855 was distinct from all other strains. The six strains that resembled Y. lipolytica were separated into two groups distinct from any of the other clades. A total of six groups obtained by fingerprint and sequence data were evaluated by performing DNA reassociation reactions. Mating experiments among the 35 strains of Y. lipolytica sensu stricto showed that 15 strains represented one mating type and 16 strains represented the opposite mating type, while four strains were self-sporulating. Teleomorph states were not produced by C. deformans, C. galli or any of the unidentified isolates. However, positive mating reactions were rarely observed in crosses among C. galli and some strains of Y. lipolytica and C. deformans. Consequently, sharing the same mating type system, C. deformans and C. galli could be considered anamorphs of unnamed Yarrowia species. Results from PCR fingerprints, sequencing and mating studies support the grouping of the studied strains into Y. lipolytica, C. galli, C. deformans, C. yakushimensis nom. inval. and three novel species in the Yarrowia clade: Candida oslonensis sp. nov. (type strain CBS 10146T =NRRL Y-48252T; Mycobank number MB 510769), Candida alimentaria sp. nov. (type strain CBS 10151T =NRRL Y-48253T; Mycobank number MB 510770) and Candida hollandica sp. nov. (type strain CBS 4855T =NRRL Y-48254T; Mycobank number MB 510771).

Morphological, chemical and molecular differentiation of Fusarium equiseti isolated from Norwegian cereals

The morphological variation, secondary metabolite profiles and restriction fragment length polymorphisms (RFLPs) of PCR amplified intergenic spacer (IGS) ribosomal DNA (rDNA) were studied in 27 isolates of Fusarium equiseti, 25 isolated from Norwegian cereals and 2 from soil obtained from the IBT culture collection (BioCentrum, Technical University of Denmark). All 27 isolates were tested for production of fusarochromanone (FUSCHR), zearalenone (ZEA) and the trichothecenes: 15-monoacetoxy-scirpentriol (MAS), diacetoxy-scirpenol (DAS), T-2 and HT-2 toxins, T2-triol, neosolaniol (NEO), deoxynivalenol (DON), nivalenol (NIV) and 4-acetylnivalenol (Fus-X). The trichothecenes were analysed by GC-MS in a selected ion monitoring mode, while FUSCHR was determined by ion pair HPLC with fluorometric detection and production of ZEA by TLC. For amplification of IGS rDNA primers CNL12 and CNS1 were applied. IGS rDNA was digested with the four restriction enzymes: AvaII, CfoI, EcoRI and Sau3A. In addition, we sequenced the IGS rDNA region of three of the Norwegian isolates. There were two morphological types among the Norwegian strains of F. equiseti, type I with short apical cells (dominating) and type II with long apical cells, with four haplotypes identified based on the RFLP data. Variation in secondary metabolite profiles within and between the morphological groups was observed and the levels of produced toxins were: FUSCHR 3000-42,500 and 25-30 ng/g, NIV 20-2500 and 120-700 ng/g, FUS-X 20-15,000 and 0 ng/g, DAS 30-7500 and 0-600 ng/g, and MAS 10-600 and 0-500 ng/g, for strains with short and long apical cells, respectively. NEO was detected in 16/27 strains tested (all morphotype I). All but four strains of type I (these four lacked a restriction site for EcoRI) had identical RFLP profiles. The isolates of type II had two haplotypes. The IGS sequence similarity data indicated differences between these morphotypes corresponding to two separate lineages apparently at the species level.

The postfire discomycete Geopyxis carbonaria (Ascomycota) is a biotrophic root associate with Norway spruce (Picea abies) in nature

The hypothesis that the postfire discomycete Geopyxis carbonaria (Ascomycota, Pezizales, Pyronemataceae) has a biotrophic association with roots of Norway spruce (Picea abies) in nature was tested by isolation of fungal strains from fresh, brown, smooth mycorrhiza-like root tips of Norway spruce collected from below the depth of detrimental heat penetration in a postfire site. The morphology of seven culture isolates originating from the smooth mycorrhiza-like root tips of two different spruce trees was congruent with the morphology of axenic culture isolates obtained from ascospores of G. carbonaria. DNA sequences of the nuclear ribosomal internal transcribed spacers ITS1 and ITS2 from these root-derived cultures and the ascosporic G. carbonaria culture isolates were found to be identical, further supporting the conclusion that the isolates were conspecific. The extensive ascocarp and ascospore formation of G. carbonaria which succeeds a forest fire may be explained in terms of a fungal escape from a moribund tree associate. Possible ecological adaptations of G. carbonaria to the pre- and postfire community are discussed.

Influence of storage temperature on gene expression and virulence potential of Listeria monocytogenes strains grown in a salmon matrix

Little is understood about the impact of environmental conditions on the virulence plasticity of Listeria monocytogenes strains grown in food. In this report, we monitored changes in the virulence properties of one high virulent (CCUG 3998) and one low virulent (442) L. monocytogenes strains grown on raw salmon (Salmo salar L.). The effect of temperature exposures (0 degrees C, 4 degrees C and 20 degrees C) on the expression levels of virulence genes (hlyA, actA, inlA and prfA), invasion into Caco-2 cells and in vivo mouse infection was analysed. Our results showed that L. monocytogenes virulence genes are differentially expressed when salmon is stored at different temperatures. Of the four virulence genes, the transcript levels for inlA were strongly affected, which correlated with the strain's virulence capacity as assessed by Caco-2 cells. In contrast to CCUG 3998, the virulence of strain 442 was altered with tested conditions. This strain maintains its low virulence status as far as salmon is stored at lower temperatures, but increases its virulence at higher temperatures. These results lead to the indication that exposure to abuse temperature conditions might influence the virulence potential of low pathogenic L. monocytogenes strains in salmon.

Coherence between legal requirements and approaches for detection of genetically modified organisms (GMOs) and their derived products

Analytical methods for the qualitative and quantitative detection of genetically modified (GM) products may serve multiple purposes. Legal requirements differ among jurisdictions, ranging from no requirements to mandatory use of event-specific quantitation and implementation of production chain traceability. Although efforts have been taken to harmonize the analytical methodology at national, regional, and international levels, no normative international standards have yet been established. Lack of coherence between analytical methodologies and their applicabilities, on the one hand, and legislation, on the other hand, is a major problem. Here, key points where coherence is lacking are discussed. These include the definition of units of measurements, expression of GM material quantities, terminology, and inconsistent legal status of products derived from related but slightly different transformation routes. Finally, recommendations to improve the coherence are brought forward, including guidance to stakeholders for prediction of product-specific GM material quantities from gene ratios in the originating seed.

Detection and quantification of the crayfish plague agent in natural waters: direct monitoring approach for aquatic environments

Aphanomyces astaci, a specialised parasite of North American freshwater crayfish, is the disease agent of crayfish plague that is lethal to European freshwater crayfish. The life cycle of A. astaci has been inferred from experimental laboratory studies, but less is known about its natural sustainability and ecology. To address such questions, tools for monitoring of A. astaci directly in aquatic environments are needed. Here, we present an approach for detecting and quantifying A. astaci directly from water samples using species-specific TaqMan minor groove binder real-time PCR. Samples of a 10-fold dilution series from approximately 10(4) to approximately 1 spore of A. astaci were repeatedly tested, and reliable detection down to 1 spore was demonstrated. Further, to simulate real-life samples from natural water bodies, water samples from lakes of various water qualities were spiked with spores. The results demonstrated that co-extracted humic acids inhibit detection significantly. However, use of bovine serum albumin or the TaqMan Environmental Master Mix largely removes this problem. The practical application of the approach was successfully demonstrated on real-life water samples from crayfish farms in Finland hosting infected North American signal crayfish Pacifastacus leniusculus. Direct monitoring of A. astaci from aquatic environments may find application in the management of wild noble crayfish Astacus astacus stocks, improved aquaculture practices and more targeted conservation actions. The approach will further facilitate studies of A. astaci spore dynamics during plague outbreaks and in carrier crayfish populations, which will broaden our knowledge of the biology of this devastating crayfish pathogen.

Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products

The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.