Development of a highly sensitive nested-PCR method using a single closed tube for detection of Fusarium culmorum in cereal samples

A survey of Fusarium species and ADON genotype on Canadian wheat grain

Introduction

Wheat is a staple food that is important to global food security, but in epidemic years, fungal pathogens can threaten production, quality, and safety of wheat grain. Globally, one of the most important fungal diseases of wheat is Fusarium head blight (FHB). This disease can be caused by several different Fusarium species with known differences in aggressiveness and mycotoxin-production potential, with the trichothecene toxin deoxynivalenol (DON) and its derivatives being of particular concern. In North America, the most predominant species causing FHB is F. graminearum, which has two distinct sub-populations that are commonly classified into two main chemotypes/genotypes based on their propensity to form trichothecene derivatives, namely 15-acetyldeoxynivalenol (15-ADON) and 3-acetyldeoxynivalenol (3-ADON).

Materials and methods

We used a panel of 13 DNA markers to perform species and ADON genotype identification for 55, 444 wheat kernels from 7, 783 samples originating from across Canada from 2014 to 2020.

Results and discussion

Based on single-seed analyses, we demonstrate the relationships between Fusarium species and trichothecene chemotype with sample year, sample location, wheat species (hexaploid and durum wheat), severity of Fusarium damaged kernels (FDK), and accumulation of DON. Results indicate that various Fusarium species are present across wheat growing regions in Canada; however, F. graminearum is the most common species and 3-ADON the most common genotype. We observed an increase in the occurrence of the 3-ADON genotype, particularly in the western Prairie regions. Our data provides important information on special-temporal trends in Fusarium species and chemotypes that can aid with the implementation of integrated disease management strategies to control the detrimental effects of this devastating disease.

Omics in the detection and identification of biosynthetic pathways related to mycotoxin synthesis

Mycotoxins are secondary metabolites that are known to be toxic to humans and animals. On the other hand, some mycotoxins and their analogues possess antioxidant as well as antitumor properties, which could be relevant in the fields of pharmaceutical analysis and food research. Omics techniques are a group of analytical tools applied in the biological sciences in order to study genes (genomics), mRNA (transcriptomics), proteins (proteomics), and metabolites (metabolomics). Omics have become a vital tool in the field of mycotoxins, especially contributing to the identification of biomarkers with potential use for the detection of mycotoxigenic species and the gathering of information about the biosynthetic pathways of mycotoxins in different environments. This approach has provided tools for the development of prevention strategies and control measures for different mycotoxins. Additionally, research has revealed important information about the impact of global warming and climate change on the prevalence of mycotoxin issues in society. In the context of foodomics, the aim is to apply omics techniques in order to ensure food safety. The objective of the present review is to determine the state of the art regarding the development of analytical techniques based on omics in the identification of biosynthetic pathways related to mycotoxin synthesis.

Current PCR-based methods for the detection of mycotoxigenic fungi in complex food and feed matrices

Mycotoxins are toxic secondary fungal metabolites produced by certain types of filamentous fungi, such as Aspergillus, Fusarium, and Penicillium spp. Mycotoxigenic fungi and their produced mycotoxins are considered to be an important issue in food and feed safety due to their toxic effects like carcinogenicity, immunosuppression, neurotoxicity, nephrotoxicity, and hepatotoxicity on humans and animals. To boost the safety level of food and feedstuff, detection and identification of toxins are essential at critical control points across food and feed chains. Zero-tolerance policies by the European Union and other organizations about the extreme low level of tolerance of mycotoxins contamination in food and feed matrices have led to an increasing interest to design more sensitive, specific, rapid, cost-effective, and safer to use mycotoxigenic fungi detection technologies. Hence, many mycotoxigenic fungi detection technologies have been applied to measure and control toxins contamination in food and feed substrates. PCR-based mycotoxigenic fungi detection technologies, such as conventional PCR, real-time PCR, nested PCR, reverse transcriptase (RT)-PCR, loop-mediated isothermal amplification (LAMP), in situ PCR, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR DGGE), co-operational PCR, multiplex PCR, DNA arrays, magnetic capture-hybridization (MCH)-PCR and restriction fragment length polymorphism (RFLP), would contribute to our understanding about different mycotoxigenic fungi detection approaches and will enhance our capability about mycotoxigenic fungi identification, isolation and characterization at critical control points across food and feed chains. We have assessed the principles, results, the limit of detection, and application of these PCR-based detection technologies to alleviate mycotoxins contamination problem in complex food and feed substrates. The potential application of these detection technologies can reduce mycotoxins in complex food and feed matrices.

Assessment of Fusarium pseudograminearum and F. culmorum Biomass in Seedlings of Potential Host Cereal Species

Fusarium crown rot is a major disease of wheat and barley worldwide, with the most frequently isolated causal agents being Fusarium pseudograminearum and F. culmorum. This study has successfully designed a quantitative polymerase chain reaction assay that is specific for F. culmorum, which has been used in conjunction with a previously established F. pseudograminearum-specific assay to compare the location and extent of infection by each fungus across a range of potential hosts, including six winter and three summer cereal species. All common winter cereals, excluding oat, demonstrated a similar range of visual and fungal biomass results when inoculated with either F. pseudograminearum or F. culmorum. Oat exhibited the lowest visual disease ratings and fungal biomass values of the winter cereals, while the sorghum, maize, and rice cultivars returned the lowest values overall. The ranking of host species according to visual discoloration was strongly correlated for both pathogens. Visual reactions to F. pseudograminearum were greater than those caused by F. culmorum in all potential hosts trialed; however, fungal biomass results only indicated this trend for barley. These results demonstrate significant variation in the ability of these pathogens to colonize the range of cereal species examined and also suggest differences between the pathogens in their patterns of host colonization.

Verification of the effectiveness of SCAR (sequence characterized amplified region) primers for the identification of Polish strains of Fusarium culmorum and their potential ability to produce B-trichothecenes and zearalenone

Rapid and sensitive methods to detect Fusarium culmorum and trichothecene and zearalenone producing strains in food and feed are valuable in predicting potential contamination. In this study the effectiveness of primers, recommended in the literature, for species identification of F. culmorum and basic genes encoding for mycotoxin production was tested. A total of 68 isolates of F. culmorum were collected from cereals and potato between 2005 and 2008 from different Polish provinces. It was shown that from among the four primer pairs enabling the identification of F. culmorum, and therefore also to establish its presence in the material, only primers Fc01F/Fc01R seem to be fully effective in the case of Polish strains. Determination of material contamination by F. culmorum, however, is only a first step in determining food safety. It is also extremely important to identify genes encoding the potential ability to produce mycotoxins. It was shown that three pairs of primers (tox5-1/tox5-2, HATriF/HATriR and Tri5F/Tri5R) enable a fully effective identification of the presence of the Tri5 gene responsible for producing trichothecenes. Determination of the DON-chemotype, and thus identification of the strains of F. culmorum potentially producing deoxynivalenol, is enabled equally by MinusTri7F/MinusTri7F, Tri7F/Tri7DON and Tri13F/Tri13DONR. However, a determination of the NIV-chemotype, and thus identification of the strains potentially producing nivalenol, is enabled by Tri7F/Tri7R, Tri7F/Tri7NIV and Tri13NIVF/Tri13R. The potential ability of isolates to produce ZEA can be determined to the same degree in assay with PKS4-PS.1/PKS4-PS.2 and F1/R1.

Development of the molecular methods for rapid detection and differentiation of Fusarium oxysporum and F. oxysporum f. sp. niveum in Taiwan

Fusarium wilt, caused by Fusarium oxysporum (Fo), is one of the most important fungal diseases worldwide. Like other plant pathogens, Fo displays specialized forms in association with its hosts. For example, F. oxysporum f. sp. niveum (Fon) is the damaging pathogen causing Fusarium wilt disease on watermelon, whereas F. oxysporum f. sp. cubense is the pathogen that infects banana. A rapid and reliable pathogen identification or disease diagnosis is essential for the integrated disease management practices in many crops. In this study, two new primer sets, Fon-1/Fon-2 and FnSc-1/FnSc-2, were developed to differentiate Fon and Fo, respectively. The PCR method using the novel primer sets has high sensitivity to detect Fon when the DNA concentration was as low as 0.01 pg or when the conidia number was as few as 5. In comparison with the published primer set, the Fon-1/Fon-2 primer set, derived from the sequence of OP-M12 random primer-amplified fragment, produced a 174 bp DNA fragment, and was more specific to Fon in Taiwan. In addition, with optimized PCR parameters, the molecular method using the Fon-1/Fon-2 primer set could directly detect Fon even when watermelon samples were collected in its early stage of disease development.

DNA signature-based approaches for bacterial detection and identification

During the late eighties, environmental microbiologists realized the potential of the polymerase chain reaction (PCR) for the design of innovative approaches to study microbial communities or to detect and identify microorganisms in diverse and complex environments. In contrast to long-established methods of cultivation-based microbial identification, PCR-based techniques allow for the identification of microorganisms regardless of their culturability. A large number of reports have been published that describe PCR-inspired methods, frequently complemented by sequencing or hybridization profiling, to infer taxonomic and clonal microbial diversity or to detect and identify microorganisms using taxa-specific genomic markers. Typing methods have been particularly useful for microbial ecology-driven studies; however, they are not suitable for diagnostic purposes, such as the detection of specific species, strains or clones. Recently, comprehensive reviews have been written describing the panoply of typing methods available and describing their advantages and limitations; however, molecular approaches for bacterial detection and identification were either not considered or only vaguely discussed. This review focuses on DNA-based methods for bacterial detection and identification, highlighting strategies for selecting taxa-specific loci and emphasizing the molecular techniques and emerging technological solutions for increasing the detection specificity and sensitivity. The massive and increasing number of available bacterial sequences in databases, together with already employed bioinformatics tools, hold promise of more reliable, fast and cost-effective methods for bacterial identification in a wide range of samples in coming years. This tendency will foster the validation and certification of these methods and their routine implementation by certified diagnostic laboratories.

Species-specific fungal DNA in airborne dust as surrogate for occupational mycotoxin exposure?

Possible health risks associated with occupational inhalation of mycotoxin-containing dust remain largely unknown, partly because methods for mycotoxin detection are not sensitive enough for the small dust masses obtained by personal sampling, which is needed for inhalable exposure measurements. Specific and sensitive PCR detection of fungi with mycotoxin-producing potential seem to be a good surrogate for occupational exposure measurements that include all fungal structures independent of morphology and cultivability. Results should, however, be interpreted with caution due to variable correlations with mycotoxin concentrations.

PCR-based diagnosis and quantification of mycotoxin-producing fungi

Mycotoxins are secondary metabolites produced by filamentous fungi which have toxicologically relevant effects on vertebrates if administered in small doses via a natural route. In order to improve food safety and to protect consumers from harmful contaminants, the presence of fungi with the potential to produce such compounds must be checked at critical control points during the production of agricultural commodities as well as during the process of food and feed preparation. Polymerase chain reaction (PCR)-based diagnosis has been applied as an alternative assay replacing cumbersome and time-consuming microbiological and chemical methods for the detection and identification of the most serious toxin producers in the fungal genera Fusarium, Aspergillus, and Penicillium. The current chapter covers the numerous PCR-based assays which have been published since the first description of the use of this technology to detect Aspergillus flavus biosynthesis genes in 1996.

Toxigenic Fusarium spp. as determinants of trichothecene mycotoxins in settled grain dust

Trichothecenes are immunosuppressive mycotoxins produced mainly by Fusarium spp. and often are detected as natural contaminants of grain and other agricultural products. Exposure to trichothecenes through inhalation during grain work may represent possible health risks for grain farmers. We aimed, therefore, to investigate the level of Fusarium spp. and trichothecenes in settled grain dust collected during work on 92 Norwegian farms. Mycotoxins were determined by gas chromatography-mass spectrometry, whereas the Fusarium spp. were identified and quantified both by species-specific semiquantitative polymerase chain reaction (PCR) and by cultivation. All potential trichothecene-producing molds in the grain dust were quantified using a PCR assay specific for tri5, the gene coding for trichodiene synthase that catalyzes the first step in the trichothecene biosynthesis. We performed correlation analysis between mold-DNA and mycotoxins to assess whether the PCR-detected DNA could be used as indicators of the mycotoxins. The methodological problem of detecting small amounts of airborne mycotoxins during grain work may then be avoided. Whereas the trichothecene-producing Fusarium species in grain dust could not be identified or quantified to a sufficient extent by cultivation, all investigated Fusarium spp. could be specifically detected by PCR and quantified from the DNA agarose gel band intensities. Furthermore, we observed a strong correlation between the trichothecenes HT-2 toxin (HT-2) or T-2 toxin (T-2) and DNA specific for tri5 (r = 0.68 for HT-2 and r = 0.50 for T-2; p < 0.001), F. langsethiae (r = 0.77 for HT-2 and r = 0.59 for T-2; p < 0.001), or F. poae (r = 0.41 for HT-2 and r = 0.35 for T-2; p < 0.001). However, only a moderate correlation was observed between the trichothecene deoxynivalenol (DON) and the combination of its producers, F. culmorum and F. graminearum (r = 0.24, p = 0.02), and no significant correlation was observed between DON and tri5. PCR clearly improved the detection of toxigenic Fusaria as potential sources of health risks for farmers inhaling grain dust during work, but the use of Fusarium-DNA as indicators for trichothecenes should be used cautiously.