Targeting a polyketide synthase gene for Aspergillus carbonarius quantification and ochratoxin A assessment in grapes using real-time PCR

Recent Advances in Mycotoxin Analysis and Detection of Mycotoxigenic Fungi in Grapes and Derived Products

Mycotoxins are secondary metabolites of filamentous fungi that can cause toxic effects in human and animal health. Most of the filamentous fungi that produce these mycotoxins belong to four genera, namely, Aspergillus, Penicillium, Fusarium, and Alternaria. Mycotoxigenic fungi, along with mycotoxins, create a constant and serious economic threat for agriculture in many terms, counting product losses due to crop contamination and food spoilage, as well malnutrition when considering nutritional quality degradation. Given the importance of robust and precise diagnostics of mycotoxins and the related producing fungi in the grape food chain, one of the most important agricultural sectors worldwide, the present review initially delivers a comprehensive presentation of mycotoxin reports on grape and derived products, including a wide range of commodities such as fresh grapes, raisins, wine, juices, and other processed products. Next, based on worldwide regulations’ requirements for mycotoxins, and referring to the relative literature, this work presents methodological approaches for mycotoxin determination, and stresses major methods for the detection of fungal species responsible for mycotoxin production. The principle of function and basic technical background on the available analytical and molecular biology techniques developed—including chromatography, mass spectrometry, immunochemical-based assays, biosensors, and molecular assays—is briefly given, and references for their application to grape and derived product testing are highlighted.

Rapid and accurate identification of black aspergilli from grapes using high-resolution melting (HRM) analysis

BACKGROUND

Aspergillus is a diverse genus of fungi with high economic and social impact. Various species that belong to section Nigri (black aspergilli) are common agents of grape spoilage and potent producers of ochratoxin A (OTA), a mycotoxin associated with various nephrotoxic and immunotoxic effects in humans. Black aspergilli are difficult to classify following only phenotypic criteria; thus chemotaxonomic and molecular methods are employed in parallel with phenotypic ones for species characterization. These approaches, though accurate and replicable, require more than one individual step and are to a certain extent laborious when a rapid identification of these species is required.

RESULTS

The aim of this study was to develop a high-resolution melting polymerase chain reaction (HRM-PCR) assay as a rapid method for identification of Aspergillus spp. section Nigri isolates and their detection in grape samples. Melt curve analysis of amplicons originating from the internal transcribed spacer 2 (ITS2) ribosomal region generated species-specific HRM curve profiles, enabling the accurate differentiation of the analyzed genotypes. Furthermore, the assay was able to identify A. carbonarius, A. tubingensis, A. niger, A. ibericus and A. japonicus in grape samples artificially inoculated with conidia of these fungi.

CONCLUSION

To our knowledge this is the first report on the development of an HRM-PCR assay for the identification of black Aspergillus species in grape samples. © 2018 Society of Chemical Industry.

Mould spoilage of foods and beverages: Using the right methodology

Fungal spoilage of products manufactured by the food and beverage industry imposes significant annual global revenue losses. Mould spoilage can also be a food safety issue due to the production of mycotoxins by these moulds. To prevent mould spoilage, it is essential that the associated mycobiota be adequately isolated and accurately identified. The main fungal groups associated with spoilage are the xerophilic, heat-resistant, preservative-resistant, anaerobic and psychrophilic fungi. To assess mould spoilage, the appropriate methodology and media must be used. While classic mycological detection methods can detect a broad range of fungi using well validated protocols, they are time consuming and results can take days or even weeks. New molecular detection methods are faster but require good DNA isolation techniques, expensive equipment and may detect viable and non-viable fungi that probably will not spoil a specific product. Although there is no complete and easy method for the detection of fungi in food it is important to be aware of the limitation of the methodology. More research is needed on the development of methods of detection and identification that are both faster and highly sensitive.

Characterization of Aspergillus section Nigri species populations in vineyard soil using droplet digital PCR

Identification of populations of Aspergillus section Nigri species in environmental samples using traditional methods is laborious and impractical for large numbers of samples. We developed species-specific primers and probes for quantitative droplet digital PCR (ddPCR) to improve sample throughput and simultaneously detect multiple species in each sample. The ddPCR method was used to distinguish Aspergillus niger, Aspergillus welwitschiae, Aspergillus tubingensis and Aspergillus carbonarius in mixed samples of total DNA. Relative abundance of each species measured by ddPCR agreed with input ratios of template DNAs. Soil samples were collected at six time points over two growing seasons from two raisin vineyards in Fresno County, California. Aspergillus section Nigri strains were detected in these soils in the range of 10² -10⁵  CFU g^-1 . Relative abundance of each species varied widely among samples, but in 52 of 60 samples, A. niger was the most abundant species, ranging from 38 to 88% of the total population. In combination with total plate counts, this ddPCR method provides a high-throughput method for describing population dynamics of important potential mycotoxin-producing species in environmental samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study to demonstrate the utility of ddPCR as a means to quantify species of Aspergillus section Nigri in soil. This method eliminates the need for isolation and sequence identification of individual fungal isolates, and allows for greater throughput in measuring relative population sizes of important (i.e. mycotoxigenic) Aspergillus species within a population of morphologically indistinguishable species.

Real-Time PCR Assay Targeting the veA Gene for Quantification of Aspergillus carbonarius in Grapes

In this work, a SYBR Green I real-time PCR method has been developed for the detection and quantification of Aspergillus carbonarius in grapes by targeting the veA gene with a primer pair (veAF4/veAR4) that specifically amplifies a 91-bp PCR product. The quantification of the fungal DNA was performed by generation of standard curves for two A. carbonarius strains, using spectrophotometrically measured DNA quantities (Log) with a linearity range from 50 to 5 × 10(-4) ng of DNA. A high positive correlation (R(2) > 0.99) between exponential increases of DNA and real-time PCR threshold cycles showed a high amplification efficiency for the assay (E values 100.06 and 101.51%, respectively). Quantification of the fungal genomic DNA in grape samples artificially inoculated with A. carbonarius conidia was successfully performed with a minimum threshold of 10(4) conidia per g of grape berry. The assay developed would allow reliable, specific, and efficient detection and quantification of A. carbonarius in grapes.

Quantification of Aspergillus carbonarius in grapes using a real time PCR assay

A study on the representation of Aspergillus carbonarius in the vineyards of the Mesogeia geographical region of Attica, Greece, was conducted. One hundred and twenty five samples of the indigenous drought and disease resistant Savatiano wine grape variety, the most widely planted in Greece, were collected. The sample's total DNA extracts were initially tested for fungal DNA presence by targeting the Internal Transcribed Spacer (ITS) region in end-point Polymerase Chain Reactions. Samples which were proved positive were further subjected to PCR analysis using specific primers targeting an A. carbonarius polycetide synthase (pks) gene. Among ITS positive samples (70%), A. carbonarius was represented in 42% of them. Furthermore, a SYBR Green I Real Time PCR method was used to quantify the amount of this species in the grape samples. The values of the positive samples were estimated in the range of 13 to 50 × 10(3) fungal haploid genomes/g grapes. The significance of this study lies in the applicability of a rapid and culture-independent method to detect and quantify A. carbonarius on grapes.

Development of a real-time PCR assay for Penicillium expansum quantification and patulin estimation in apples

Due to the occurrence and spread of the fungal contaminants in food and the difficulties to remove their resulting mycotoxins, rapid and accurate methods are needed for early detection of these mycotoxigenic fungi. The polymerase chain reaction and the real time PCR have been widely used for this purpose. Apples are suitable substrates for fungal colonization mostly caused by Penicillium expansum, which produces the mycotoxin patulin during fruit infection. This study describes the development of a real-time PCR assay incorporating an internal amplification control (IAC) to specifically detect and quantify P. expansum. A specific primer pair was designed from the patF gene, involved in patulin biosynthesis. The selected primer set showed a high specificity for P. expansum and was successfully employed in a standardized real-time PCR for the direct quantification of this fungus in apples. Using the developed system, twenty eight apples were analyzed for their DNA content. Apples were also analyzed for patulin content by HPLC. Interestingly, a positive correlation (R(2) = 0.701) was found between P. expansum DNA content and patulin concentration. This work offers an alternative to conventional methods of patulin quantification and mycological detection of P. expansum and could be very useful for the screening of patulin in fruits through the application of industrial quality control.

Development of a novel quantitative PCR assay as a measurement for the presence of geosmin-producing fungi

AIMS

To provide an efficient technique for monitoring the off-flavoured fungal compound geosmin.

METHODS AND RESULTS

Geosmin-associated gpe1 gene of Penicillium expansum displayed ≥99% similarity to cytochrome P450 gene of geosmin-producing P. restrictum, but ≤40% similarities to geosmin biosynthesis, non-cytochromic gene of Streptomyces avermitilis and cytochrome P450 genes of non-geosmin-producing Neotyphodium lolii, Phoma betae and P. paxilli. Serial 10-fold dilutions of P. expansum's DNA was subjected to a previously reported qPCR assay (Atoui et al. 2007), utilizing gpe1 specific primer pair 'SNgpe1F/SNgpe1R'. A linear relationship between DNA quantity and Cycle Threshold (Ct ), with strong correlative coefficient, was observed. Using the available physico-chemical method, geosmin was quantified in 188 grape samples. Penicillium spp's DNA was quantified in these samples, utilizing the developed qPCR assay. A strong positive correlation (R(2)  = 0·97) between Penicillium's DNA and geosmin concentration was observed. Furthermore, <50 ng μl(-1) Penicillium's DNA corresponds to geosmin level below the permitted intensity limit i.e. 4, for 'Flavour Profile Analysis'.

CONCLUSIONS

Penicillium spp., genomic DNA level can provide an efficient way to quantify geosmin.

SIGNIFICANCE AND IMPACT OF THE STUDY

This particular qPCR technique can be utilized in numerous food industries, for the timely detection and monitoring of geosmin contamination.

Detection and discrimination of four Aspergillus section Nigri species by PCR

Species of Aspergillus section Nigri are not easily distinguished by traditional morphological techniques, and typically are identified by DNA sequencing methods. We developed four PCR primers to distinguish between Aspergillus niger, Aspergillus welwitschiae, Aspergillus carbonarius and Aspergillus tubingensis, based on species-conserved differences in the calmodulin gene sequence. PCR amplification from total DNA using these primers was species specific; no amplification occurred from nontarget species DNA for each primer pair. Species-specific PCR could distinguish between species in mixed DNA templates, indicating a utility in determining culture uniformity of isolated Aspergillus strains. In addition, with these primer sets, each species could be detected in soil following mixed-species inoculation with Aspergillus spores. This indicates that PCR with these species-specific primers may be useful in determining the distribution of Aspergillus species in environmental samples without the need for species identification from isolated strains, as well as detecting species that may be infrequently isolated by culture-based methods.

Quantification of polyketide synthase genes in tropical urban soils using real-time PCR

Polyketide synthases (PKSs) catalyze the biosynthesis of polyketides and may contribute to the natural production of antibiotics and pose selective pressure for the development of antibiotic resistant bacteria in the environment. Although conventional PCR have been developed to detect the presence of PKS genes, no previous studies have been done to quantify the abundance of PKS genes in environmental samples. In this study, two sets of degenerate real-time PCR (qPCR) primers (PKS1-F/PKS1-R, PKS2-F/PKS2-R) with high specificity and sensitivity were developed to quantify PKS type I and type II genes. These primers were subsequently used to quantify PKS genes in tropical urban soils, and both PKS genes were widely detected in all soil samples. The absolute abundance of PKS type I ranged from 1.7×10(6) to 4.7×10(6) copies per gram of soil and the absolute abundance of PKS type II genes ranged from 2.4×10(5) to 1.5×10(6) per gram of soil, and the abundance of PKS type I gene was consistently higher than that of PKS type II gene. The relative abundance of PKS type I gene was positively correlated with that of PKS type II gene (p<0.01). Regression analyses indicate that PKS gene abundance was negatively correlated with environmental factors, such as selected antibiotics, sulfate, and metals (p<0.05), but was not correlated with land use type. The studies on the correlation between environmental factors and PKS genes could provide useful information to understand natural production of antibiotics and its associated environmental risks.

Non-Botrytis grape-rotting fungi responsible for earthy and moldy off-flavors and mycotoxins

The grape microflora is complex and includes filamentous fungi, yeasts and bacteria with different physiological characteristics and effects on wine production. Most studies have focused on the wine microbiota, but a few studies have reported the ecology of grape microorganisms. Some of these organisms - such as non-Botrytis bunch rotting fungi, which greatly influence the safety or sensory quality of wine, due to the production of mycotoxins and off-flavors, respectively - are considered to be spoilage agents. We review here the diversity of filamentous fungi on grapes and the factors influencing their development, such as grape ripening stage, environmental factors (climate, rain and cultivation practices), grape variety and grape health status. We also discuss the pathways by which mycotoxins and off-flavors are produced, the control of the population, the metabolites responsible for wine spoilage and the methods for detecting and characterizing the microorganisms involved.

Identification of ochratoxin A producing Aspergillus carbonarius and A. niger clade isolated from grapes using the loop-mediated isothermal amplification (LAMP) reaction

AIMS

To develop two assays based on the loop-mediated isothermal amplification (LAMP) of DNA for the quick and specific identification of Aspergillus carbonarius and ochratoxigenic strains of the Aspergillus niger clade isolated from grapes.

METHODS AND RESULTS

Two sets of primers were designed based on the polyketide synthase genes involved or putatively involved in ochratoxin A (OTA) biosynthesis in A. carbonarius and A. niger clade. Hydroxynaphthol blue was used as indirect method to indicate DNA amplification. The limit of detection of both assays was comparable to that of a PCR reaction. Specificities of the reactions were tested using DNA from different black aspergilli isolated from grapes. The two LAMP assays were then used to identify A. carbonarius and ochratoxigenic A. niger and A. awamori grown in pure cultures without a prior DNA extraction.

CONCLUSIONS

The two LAMP assays permitted to quickly and specifically identify DNA from OTA-producing black aspergilli, as well as isolates grown in pure culture.

SIGNIFICANCE AND IMPACT OF THE STUDY

Monitoring vineyards for the presence of OTA-producing strains is part of the measures to minimize the occurrence of OTA in grape products. The two LAMP assays developed here could be potentially used to speed the screening process of vineyards for the presence of OTA-producing black aspergilli.

A Saccharomyces cerevisiae wine strain inhibits growth and decreases Ochratoxin A biosynthesis by Aspergillus carbonarius and Aspergillus ochraceus

The aim of this study was to select wine yeast strains as biocontrol agents against fungal contaminants responsible for the accumulation of ochratoxin A (OTA) in grape and wine and to dissect the mechanism of OTA detoxification by a Saccharomyces cerevisiae strain (DISAABA1182), which had previously been reported to reduce OTA in a synthetic must. All of the yeast strains tested displayed an ability to inhibit the growth of Aspergillus carbonarius both in vivo and in vitro and addition of culture filtrates from the tested isolates led to complete inhibition of OTA production. S. cerevisiae DISAABA1182 was selected and further tested for its capacity to inhibit OTA production and pks (polyketide synthase) transcription in A. carbonarius and Aspergillus ochraceus in vitro. In order to dissect the mechanism of OTA detoxification, each of these two fungi was co-cultured with living yeast cells exposed to yeast crude or to autoclaved supernatant: S. cerevisiae DISAABA1182 was found to inhibit mycelial growth and OTA production in both Aspergilli when co-cultured in the OTA-inducing YES medium. Moreover, a decrease in pks transcription was observed in the presence of living cells of S. cerevisiae DISAABA1182 or its supernatant, while no effects were observed on transcription of either of the constitutively expressed calmodulin and β-tubulin genes. This suggests that transcriptional regulation of OTA biosynthetic genes takes place during the interaction between DISAABA1182 and OTA-producing Aspergilli.

Development of a multiplex real-time PCR to quantify aflatoxin, ochratoxin A and patulin producing molds in foods

A multiplex real-time PCR (qPCR) method to quantify aflatoxin, ochratoxin A (OTA) and patulin producing molds in foods was developed. For this, the primer pairs F/R-omt, F/R-npstr and F/R-idhtrb and the TaqMan probes, OMTprobe, NPSprobe and IDHprobe targeting the omt-1, otanpsPN and idh genes involved in aflatoxin, OTA and patulin biosynthesis, respectively, were used. The functionality of the developed qPCR method was demonstrated by the high linear relationship of the standard curves constructed with the omt-1, otanpsPN and idh gene copies and threshold cycle (Ct) values for the respective producing molds tested to quantify aflatoxin, OTA and patulin producing molds. The ability of the optimized qPCR protocol to quantify producing molds was evaluated in different artificially inoculated foods (fruits, nuts, cereals and dry-ripened meat and cheese products). Efficiency values ranged from 81 to 110% in all inoculated foods. The detection limit was between 3 and 1logcfu/g for aflatoxin, OTA and patulin producing molds. The developed multiplex qPCR was shown be an appropriate tool for sensitive quantification of growth of toxigenic fungi in foods throughout the incubation time. Thus, the multiplex qPCR is a useful, rapid and efficient method to quantify simultaneously aflatoxin, OTA and patulin producing molds in food products.

Quantification of Fusarium graminearum and Fusarium culmorum by real-time PCR system and zearalenone assessment in maize

Zearalenone (ZEA) is a mycotoxin produced by some species of Fusarium, especially by Fusarium graminearum and F. culmorum. ZEA induces hyperoestrogenic responses in mammals and can result in reproductive disorders in farm animals. In the present study, a real-time PCR (qPCR) assay has been successfully developed for the detection and quantification of Fusarium graminearum based on primers targeting the gene PKS13 involved in ZEA biosynthesis. A standard curve was developed by plotting the logarithm of known concentrations of F. graminearum DNA against the cycle threshold (Ct) value. The developed real time PCR system was also used to analyze the occurrence of zearalenone producing F. graminearum strains on maize. In this context, DNA extractions were performed from thirty-two maize samples, and subjected to real time PCR. Maize samples also were analyzed for zearalenone content by HPLC. F. graminearum DNA content (pg DNA/ mg of maize) was then plotted against ZEA content (ppb) in maize samples. The regression curve showed a positive and good correlation (R²=0.760) allowing for the estimation of the potential risk from ZEA contamination. Consequently, this work offers a quick alternative to conventional methods of ZEA quantification and mycological detection and quantification of F. graminearum in maize.

Duplex real-time PCR method with internal amplification control for quantification of verrucosidin producing molds in dry-ripened foods

Verrucosidin, which is a tremorgenic mycotoxin responsible for neurological diseases, has been detected in different dry-ripened foods as consequence of the growth of toxigenic molds. To improve food safety, the presence of verrucosidin producing molds in these kind foods should be quantified. The aim of this study was to design a duplex real-time PCR (qPCR) protocol based on TaqMan methodology with an internal amplification control (IAC). Eleven verrucosidin producing and 11 non producing strains belonging to different species often reported in food products were used. Verrucosidin production was tested by micellar electrokinetic capillary electrophoresis (MECE) and high-pressure liquid chromatography-mass spectrometry (HPLC-MS). A primer pair (VerF1/VerR1) and a TaqMan probe (Verprobe) were designed from the SVr1 probe sequence of a verrucosidin producing Penicillium polonicum. The conserved regions of the β-tubulin gene were used to design primers (TubF1/TubR1) and probe (Tubprobe) of the non-competitive IAC. The functionality of the developed method was demonstrated by the high linear relationship of the standard curves which relating Ct values and DNA template of the tested verrucosidin producers using the verrucosidin and IAC primers. The ability to quantify verrucosidin producers of the developed TaqMan assay in all artificially inoculated food samples was successful, with a minimum detection limit of 1 log cfu per gram of food. This qPCR protocol including an IAC could be very useful to quantify verrucosidin producing molds in dry-ripened foods avoiding false negative results. This method should be proposed to monitor the target molds in HACCP programs to prevent the risk of verrucosidin formation and consequently avoid its presence in the food chain.

Diagnostic tools to identify black aspergilli

The present taxonomy of the black aspergilli reveals that there are 19 accepted taxa. However the identification of species of Aspergillus section Nigri is often problematic in spite of the existence of numerous methods proposed. An overview is provided of phenotypic and molecular methods to identify the accepted species of the black aspergilli. Colony morphology, conidial size and ornamentation of the ex type cultures is presented in a pictorial overview. The temperature range of all species is given and their growth characteristics on creatine agar and boscalid agar, a medium which was developed as a selective medium for the isolation of A. carbonarius are also shown. The extrolites produced by each species are listed while the response of the Ehrlich reaction is described. The literature on the various molecular methods to be used for species identification is reviewed and a critical evaluation of the usefulness of various techniques and genomic loci for species identification of black aspergilli is presented.

Development of real-time PCR methods to quantify patulin-producing molds in food products

Patulin is a mycotoxin produced by different Penicillium and Aspergillus strains isolated from food products. To improve food safety, the presence of patulin-producing molds in foods should be quantified. In the present work, two real-time (RTi) PCR protocols based on SYBR Green and TaqMan were developed. Thirty four patulin producers and 28 non-producers strains belonging to different species usually reported in food products were used. The patulin production was tested by mycellar electrokinetic capillary electrophoresis (MECE) and high-pressure liquid chromatography-mass spectrometry (HPLC-MS). A primer pair F-idhtrb/R-idhtrb and the probe IDHprobe were designed from the isoepoxydon dehydrogenase (idh) gene, involved in patulin biosynthesis. The functionality of the developed method was demonstrated by the high linear relationship of the standard curves constructed with the idh gene copy number and Ct values for the different patulin producers tested. The ability to quantify patulin producers of the developed SYBR Green and TaqMan assays in artificially inoculated food samples was successful, with a minimum threshold of 10 conidia g(-1) per reaction. The developed methods quantified with high efficiency fungal load in foods. These RTi-PCR protocols, are proposed to be used to quantify patulin-producing molds in food products and to prevent patulin from entering the food chain.

Differentiation between Aspergillus flavus and Aspergillus parasiticus from pure culture and aflatoxin-contaminated grapes using PCR-RFLP analysis of aflR-aflJ intergenic spacer

Aflatoxins (AFs) represent the most important single mycotoxin-related food safety problem in developed and developing countries as they have adverse effects on human and animal health. They are produced mainly by Aspergillus flavus and A. parasiticus. Both species have different aflatoxinogenic profile. In order to distinguish between A. flavus and A. parasiticus, gene-specific primers were designed to target the intergenic spacer (IGS) for the AF biosynthesis genes, aflJ and aflR. Polymerase chain reaction (PCR) products were subjected to restriction endonuclease analysis using BglII to look for restriction fragment length polymorphisms (RFLPs). Our result showed that both species displayed different PCR-based RFLP (PCR-RFLP) profile. PCR products from A. flavus cleaved into 3 fragments of 362, 210, and 102 bp. However, there is only one restriction site for this enzyme in the sequence of A. parasiticus that produced only 2 fragments of 363 and 311 bp. The method was successfully applied to contaminated grapes samples. This approach of differentiating these 2 species would be simpler, less costly, and quicker than conventional sequencing of PCR products and/or morphological identification.

Allergens/Antigens, toxins and polyketides of important Aspergillus species

The medical, agricultural and biotechnological importance of the primitive eukaryotic microorganisms, the Fungi was recognized way back in 1920. Among various groups of fungi, the Aspergillus species are studied in great detail using advances in genomics and proteomics to unravel biological and molecular mechanisms in these fungi. Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Aspergillus parasiticus, Aspergillus nidulans and Aspergillus terreus are some of the important species relevant to human, agricultural and biotechnological applications. The potential of Aspergillus species to produce highly diversified complex biomolecules such as multifunctional proteins (allergens, antigens, enzymes) and polyketides is fascinating and demands greater insight into the understanding of these fungal species for application to human health. Recently a regulator gene for secondary metabolites, LaeA has been identified. Gene mining based on LaeA has facilitated new metabolites with antimicrobial activity such as emericellamides and antitumor activity such as terrequinone A from A. nidulans. Immunoproteomic approach was reported for identification of few novel allergens for A. fumigatus. In this context, the review is focused on recent developments in allergens, antigens, structural and functional diversity of the polyketide synthases that produce polyketides of pharmaceutical and biological importance. Possible antifungal drug targets for development of effective antifungal drugs and new strategies for development of molecular diagnostics are considered.

Early detection of Aspergillus carbonarius and A. niger on table grapes: a tool for quality improvement

Aspergillus carbonarius and A. niger aggregate are the main fungal contaminants of table grapes. Besides their ability to cause black rot, they can produce ochratoxin A (OTA), a mycotoxin that has attracted increasing attention worldwide. The objective of this work was to set up a simple and rapid molecular method for the early detection of both fungi in table grapes before fungal development becomes evident. Polymerase chain reaction (PCR)-based assays were developed by designing species-specific primers based on the polyketide synthases (PKS(S)) sequences of A. carbonarius and A. niger that have recently been demonstrated to be involved in OTA biosynthesis. Three table grape varieties (Red globe, Crimson seedless, and Italia) were inoculated with A. carbonarius and A. niger aggregate strains producing OTA. The extracted DNA from control (non-inoculated) and inoculated grapes was amplified by PCR using ACPKS2F-ACPKS2R for A. carbonarius and ANPKS5-ANPKS6 for A. niger aggregate. Both primers allowed a clear detection, even in symptomless samples. PCR-based methods are considered to be a good alternative to traditional diagnostic means for the early detection of fungi in complex matrix for their high specificity and sensitivity. The results obtained could be useful for the definition of a 'quality label' for tested grapes to improve the safety measures taken to guarantee the production of fresh table grapes.

Ochratoxin a: general overview and actual molecular status

Ochratoxin A (OTA) is a mycotoxin produced by several species of Aspergillus and Penicillium fungi that structurally consists of a para-chlorophenolic group containing a dihydroisocoumarin moiety that is amide-linked to L-phenylalanine. OTA is detected worldwide in various food and feed sources. Studies show that this molecule can have several toxicological effects such as nephrotoxic, hepatotoxic, neurotoxic, teratogenic and immunotoxic. A role in the etiology of Balkan endemic nephropathy and its association to urinary tract tumors has been also proved. In this review, we will explore the general aspect of OTA: physico-chemical properties, toxicological profile, OTA producing fungi, contaminated food, regulation, legislation and analytical methods. Due to lack of sufficient information related to the molecular background, this paper will discuss in detail the recent advances in molecular biology of OTA biosynthesis, based on information and on new data about identification and characterization of ochratoxin biosynthetic genes in both Penicillium and Aspergillus species. This review will also cover the development of the molecular methods for the detection and quantification of OTA producing fungi in various foodstuffs.

Characterisation of a pks gene which is expressed during ochratoxin A production by Aspergillus carbonarius

Aspergillus carbonarius is considered the main fungus responsible for ochratoxin A (OTA) contamination in grapes. OTA is a potent nephrotoxin and a possible human carcinogen with a polyketide derived structure. Fungal polyketide synthases (PKSs) have recently been demonstrated to be involved in OTA biosynthesis in both Penicillium and Aspergillus species. We report here on the identification and characterisation of part of a novel polyketide synthase gene, ACpks from A. carbonarius. The sequence appears to encode conserved ketosynthase and acyl transferase domains, which are characteristic of previously characterised PKS enzymes. Expression of the ACpks gene is differentially regulated, with transcription being observed when the fungus was grown on synthetic grape medium and on OTA permissive medium (MM) whereas no transcription was detected when the fungus was grown on OTA restrictive medium (YES). ACpks expression was also observed when A. carbonarius was grown at low pH, with concomitant increases in OTA production. This correlation between ACpks gene expression and OTA production suggests the likely involvement for the product of this gene in ochratoxin A biosynthesis in the fungus. From a preliminary screening of Aspergillus isolates with ACpks specific primers, ACpks gene homologues appear to be present in A. sclerotioniger and A. ibericus, two species of section Nigri which are closely related to A. carbonarius.

Detection of Aspergillus carbonarius and other black aspergilli from grapes by DNA OLISA microarray

Black aspergilli, and particularly Aspergillus carbonarius, are responsible for ochratoxin A production in grapes. Correct identification of these species is essential for toxicological risk assessment in grape and wine. A low-complexity oligonucleotide microarray (OLISA, Apibio, F) based on DNA oligonucleotides probes, obtained from sequences of the calmodulin gene, was set up in order to detect A. carbonarius, A. japonicus/A. aculeatus and A. ibericus isolated from grape. The designed microarray distinguished all Aspergillus species and the detection limit for A. carbonarius was 3.2 pg of DNA as a template for the PCR reaction. This microarray offers a quick and parallel analysis to detect individual Aspergillus species in pure cultures and in naturally contaminated grape samples.

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.