PCR detection assays for the ochratoxin-producing Aspergillus carbonarius and Aspergillus ochraceus species

Molecular identification and biocontrol of ochratoxigenic fungi and ochratoxin A in animal feed marketed in the state of Qatar

Ochratoxin A (OTA) is a toxic fungal metabolite produced by some Aspergillus and Penicillium species. This work was designed to explore the presence of OTA and ochratoxigenic fungi in feed grains marketed in Qatar and their biological control by a bacterium (Burkholderia cepacia). Significantly higher levels of OTA were detected in mixed grains samples (144.59 ± 6.63 μg/kg), compared to the maize (25.27 ± 1.89 μg/kg) and wheat (3.37 ± 0.11 μg/kg). OTA-producing fungi (A. niger, A. ochraceus, A. westerdijkiae, A. carbonarius and P. verrucosum) were identified on the basis of their morphological features as well as through polymerase chain reaction (PCR). Putative ochratoxigenic polyketide genes in these isolates were evidenced by using primers AoOTA-L/AoOTA-R (in A. ochraceus and A. westerdijkiae), AoPks1/AoPks2 (in A. niger and A. ochraceus) and PenPks1/Penpks2 (in P. verrucosum). On synthetic media, A. westerdijkiae showed the highest OTA synthesis (5913 ± 576 μg/kg) than the closely related A. ochraceus (3520 ± 303 μg/kg), A. carbonarius (3064 ± 289 μg/kg) and P. verrucosum (3030 ± 710 μg/kg). Burkholderia cepacia cells and culture extract showed promising biological control potentials against OTA producing fungi. On the basis of these findings, it can be concluded that animal feed samples are generally contaminated with OTA-producing fungi as well as OTA, and Burkholderia cepacia CS5 exhibits promising antifungal activities.

Aspergillus-bees: A dynamic symbiotic association

Besides representing one of the most relevant threats of fungal origin to human and animal health, the genus Aspergillus includes opportunistic pathogens which may infect bees (Hymenoptera, Apoidea) in all developmental stages. At least 30 different species of Aspergillus have been isolated from managed and wild bees. Some efficient behavioral responses (e.g., diseased brood removal) exerted by bees negatively affect the chance to diagnose the pathology, and may contribute to the underestimation of aspergillosis importance in beekeeping. On the other hand, bee immune responses may be affected by biotic and abiotic stresses and suffer from the loose co-evolutionary relationships with Aspergillus pathogenic strains. However, if not pathogenic, these hive mycobiota components can prove to be beneficial to bees, by affecting the interaction with other pathogens and parasites and by detoxifying xenobiotics. The pathogenic aptitude of Aspergillus spp. likely derives from the combined action of toxins and hydrolytic enzymes, whose effects on bees have been largely overlooked until recently. Variation in the production of these virulence factors has been observed among strains, even belonging to the same species. Toxigenic and non-toxigenic strains/species may co-exist in a homeostatic equilibrium which is susceptible to be perturbed by several external factors, leading to mutualistic/antagonistic switch in the relationships between Aspergillus and bees.

Antifungal activity of Saccharomyces cerevisiae and assessment of ochratoxigenic load on currants by means of Real Time PCR

Currants are prone to contamination by ochratoxin during cultivation, processing and storage conditions. Saccharomyces cerevisiae is considered to be among the main species of grape yeast flora able to control antagonistic fungi. In this study, the potential of S. cerevisiae Y₃₃ was investigated to inhibit the growth of several fungal species indigenous to the microbiota of grapes. Moreover, the efficacy of this yeast species was investigated to inhibit OTA by toxin producing fungi both in vitro and in situ. For this purpose thirty-five different fungal species, belonging to the genera Aspergillus, Penicillium, Cladosporium, Fusarium and Alternaria interacted in vitro with S. cerevisiae on Malt Extract agar plates, stored at 25 °C for 14 days. Results showed that the highest OTA producer A. carbonarius F₇₁ was inhibited more than 99% from day 7, in contrast to A. niger strains that presented enhanced OTA production at day 14 due to interaction with S. cerevisiae Y₃₃. Additionally, the antifungal potential of the selected yeast was also studied in situ on currants subjected to different treatments and stored at 25 °C for 28 days. Microbiological analysis was undertaken for the enumeration of the bacterial and fungal flora, together with OTA determination at 7 and 21 days. To quantify A. carbonarius on all treated currant samples, molecular analysis with Real Time PCR was employed. A standard curve was prepared with A. carbonarius DNA. The efficiency of the curve was estimated to 10.416, the slope to -3.312 and the range of haploid genome that could be estimated was from 1.05 to 105∙10⁵. The amount of A. carbonarius DNA in all treated currants samples, where the fungus was positively detected, ranged from as low as 0.08 to 562 ng DNA/g currants. The antifungal activity of S. cerevisiae Y₃₃ was observed in all studied cases, causing inhibition of fungal growth and OTA production.

Colorimetric and chemiluminescence based enzyme linked apta-sorbent assay (ELASA) for ochratoxin A detection

Ochratoxin A (OTA) is one of the most widespread mycotoxin found to contaminate various food products such as cereals, spices, groundnuts, coffee, wine, beer etc. It is also carried over from contaminated feed and fodder to milk, blood, meat, kidney and liver of animals consuming it. Enzyme-linked to biorecognition molecules like antibodies or aptamers are very popular due to their ability to be used as labels or tags in biosensing formats. In this work, OTA aptamer based colorimetric and chemiluminescence biosensing formats were evaluated for the detection of OTA. The colorimetric enzyme linked apta-sorbent assay (Co-ELASA) and chemiluminescence enzyme linked apta-sorbent assay (Cl-ELASA) showed a linear detection range from 1 pg/mL to 1 μg/mL with a limit of detection (LOD) of 0.84 pg/mL for Co-ELASA (limit of quantification (LOQ) = 2.54 pg/mL) and 1.29 pg/mL for Cl-ELASA (LOQ = 3.94 pg/mL) under optimized buffer conditions. Comparison of ELASA methods with sandwich ELISA indicated that the developed techniques had sensitivity similar to the conventional technique which indicated a LOD of 1.13 pg/mL and LOQ of 3.41 pg/mL. Studies in simulated contaminated food samples by spiking OTA in groundnut and coffee bean at concentrations of 0.1, 1 and 10 ppb, indicated recoveries in the range of 50.21 to 113.27% for Co-ELASA, 90.47 to 107.72% for Cl-ELASA and 76.23 to 141.49% for ELISA. Results of the study indicate that Co-ELASA and Cl-ELASA assays could be an alternate approach for ultrasensitive detection of OTA in food samples, which can also be adapted for biosensor development.

Molecular characterization of ochratoxigenic fungi associated with poultry feedstuffs in Saudi Arabia

Fungal and mycotoxins contamination of food and poultry feeds can occur at each step along the chain from grain production, storage, and processing. A total of 200 samples comprising of mixed poultry feedstuffs (n = 100) and their ingredients (n = 100) were collected from Riyadh, Alhassa, Qassium, and Jeddah cities in Saudi Arabia. These samples were screened for contamination by fungi. Penicillium chrysogenum was the predominant species taking into its account and frequency, respectively, in both mixed poultry feedstuff and barley samples (4,561.9 and 687 fungal colony-forming units (CFU)/g) and (66% and 17%). Moisture content was an important indicator for the count of fungi and ochratoxin A. Ochratoxin analysis of plate cultures was performed by a HPLC technique. Sample of mixed poultry feedstuff which was collected from Jeddah displayed the highest level of ochratoxin (14.8 µg/kg) and moisture content (11.5%). Corn grains samples were highly contaminated by ochratoxin A (450 and 423 µg/kg) and recorded the highest moisture contents (14.1 and 14.5%). Ochratoxin A production in fungal species isolated from mixed poultry feedstuff samples were high with P. verrucosum (5.5 μg/kg) and A. niger (1.1 μg/kg). In sorghum and corn grains, the highest ochratoxins producing species were P. viridicatum (5.9 μg/kg) and A. niger (1.3 μg/kg), respectively. Sixty-three isolates of A. niger were ochratoxigenic, and all of them showed the presence of pks genes using PKS15C-MeT and PKS15KS primer pairs. The detection technique of A. niger in poultry feedstuff samples described in the present study was successfully used as a rapid and specific protocol for early detection of A. niger without cultivation on specific media.

Morphological and Molecular Characterization of Toxigenic Aspergillus flavus from Groundnut Kernels in Kenya

Pathogenesis of Aspergillus flavus on important agricultural products is a key concern on human health due to the synthesis and secretion of the hazardous secondary metabolite, aflatoxin. This study identified and further characterized aflatoxigenic A. flavus from groundnuts sampled from sundry shops in Kenya using integrated morphological and molecular approaches. The groundnuts were plated on potato dextrose agar for isolation and morphological observation of A. flavus based on macroscopic and microscopic features. Molecular characterization was done through amplification and comparison of the partial sequence of the ITS1-5.8S-ITS2 region. The expression analysis of aflR, aflS, aflD, aflP, and aflQ genes in the aflatoxin biosynthesis pathways was conducted to confirm the positive identification of A. flavus. The gene expression also aided to delineate toxigenic isolates of A. flavus from atoxigenic ones. Morphologically, 18 isolates suspected to be A. flavus were identified. Out of these, 14 isolates successfully amplified the 500 bp ITS region of A. flavus or Aspergillus oryzae, while 4 isolates were not amplified. All the remaining 14 isolates expressed at least one of the aflatoxigenic genes but only 5 had all the genes expressed. Partial sequencing revealed that isolates 5, 11, 12, 13, and 15 had 99.2%, 97.6%, 98.4%, 97.5%, and 100% homology, respectively, to the A. flavus isolate LUOHE, ITS-5.8S-ITS2, obtained from the NCBI database. The five isolates were accurate identification of atoxigenic A. flavus. Precise identification of toxigenic strains of A. flavus will be useful in establishing control strategies of the fungus in food products.

Mycobiota associated with strawberry fruits, their mycotoxin potential and pectinase activity

Forty-three species and variety belonging to 15 genera were collected from 30 strawberry fruit samples on Glucose-Czapek’s agar medium. Among them, Aspergillus flavus, Aspergillus niger and Penicillium citrinum were the most frequent species recovered from 53.3%, 70.0% and 50.0% of the samples, respectively. According to the ITS rDNA sequence, we confirmed the morphological identification result. Moreover, aflatoxin biosynthesis gene omt-A was detected in A. flavus, while Aopks gene was found in A. niger. Interestingly, we could not detect any aflatoxin or ochratoxin biosynthesis genes in the P. citrinum strain. The concentration of detected aflatoxin was 3.5 ppb produced by A. flavus, while A. niger gave 4.1 ppb as ochratoxin. A. flavus was the most pectinase producer among the selected strains, and the highest amount was obtained at 30°C after 6 days of incubation with initial medium pH 8.

A Comprehensive Study on the Occurrence of Mycotoxins and Their Producing Fungi during the Maize Production Cycle in Spain

Mycotoxin contamination is one of the main problems affecting corn production, due to its significant risk to human and animal health. The Fusarium and Aspergillus species are the main producers of mycotoxins in maize, infecting both pre-harvest and during storage. In this work, we evaluated the presence of mycotoxins and their producing species along maize production cycles in three different stages (anthesis, harvest, and storage) during three consecutive seasons (2016-2018). Fungal occurrences were studied using species-specific PCR protocols, whereas mycotoxin levels were determined by LC-MS/MS. Fumonisin-producing Fusarium species (F. verticillioides and F. proliferatum), as well as the aflatoxin producer Aspergillus flavus, were the most predominant species at all stages; although, during some seasons, the presence of F. graminearum and A. niger aggregate species were also identified. Contrastingly, fumonisins were the only mycotoxins detected and levels were always under legal regulations. The results presented here demonstrate that even when fungal contamination occurs at the early stages of the maize production cycle, the application of good agricultural and storage practices might be crucial to ensure mycotoxin-free grains.

Mycoviruses mediate mycotoxin regulation in Aspergillus ochraceus

To date, no demonstration of a direct correlation between the presence of mycoviruses and the quantitative or qualitative modulation of mycotoxins has been shown. In our study, we transfected a virus-free ochratoxin A (OTA)-producing isolate of Aspergillus ochraceus with purified mycoviruses from a different A. ochraceus isolate and from Penicillium aurantiogriseum. Among the mycoviruses tested, only Aspergillus ochraceus virus (AoV), a partitivirus widespread in A. ochraceus, caused a specific interaction that led to an overproduction of OTA, which is regulated by the European Commission and is the second most important contaminant of food and feed commodities. Gene expression analysis failed to reveal a specific viral upregulation of the mRNA of genes considered to play a role in the OTA biosynthetic pathway. Furthermore, AoOTApks1, a polyketide synthase gene considered essential for OTA production, is surprisingly absent in the genome of our OTA-producing isolate. The possible biological and evolutionary implications of the mycoviral regulation of mycotoxin production are discussed.

Mycoflora isolation and molecular characterization of Aspergillus and Fusarium species in Tunisian cereals

Wheat, barley and maize are the mainly consumed cereals in Tunisia. This study aimed to determine the mycoflora of these cereals with special focus on the mycotoxigenic Aspergillus and Fusarium species. Freshly harvested samples and other stored samples of each type of cereal (31 and 34 samples, respectively) were collected in Tunisia and cultured for fungal isolation and identification. Identification of fungal genera was based on morphological features. Aspergillus and Fusarium species were identified by species specific PCR assays complemented with DNA sequencing. Alternaria (70.83%), Eurotium (62.50%), Aspergillus (54.17%) and Penicillium (41.67%) were the most frequent fungi isolated from wheat. Penicillium (75%), Aspergillus (70%), Eurotium (65%) and Alternaria (65%) were the most frequently recovered genera from barley. The predominant genera in maize were Aspergillus (76.19%), Eurotium (42.86%), and Penicillium (38.09%). Aspergilllus, Penicillium, Fusarium and Alternaria were detected in both stored and freshly harvested grain samples. The frequencies of contamination with Aspergillus, Fusarium and Alternaria were higher in freshly harvested samples, whereas Penicillium species were more frequent in stored samples. The predominant Aspergillus species detected were A. flavus and A. niger. The Fusarium species detected were F. equiseti, F. verticillioides, F. nygamai, and F. oxysporum. This study suggested the potential risk for Aflatoxins and, to a lesser extent, for Ochratoxin A in Tunisian cereals. This is the first survey about mycoflora associated with wheat, barley and maize in Tunisia.

Targeting Ochratoxin Biosynthetic Genes

The pathway of ochratoxin A (OTA) biosynthesis has not yet been completely elucidated. Essentially, two kind of genes have been demonstrated to be involved in the biosynthesis of OTA. One of them is the nrps gene encoding a non-ribosomal peptide synthetase (NRPS) which catalyzes the ligation between the isocoumarin group, constituting the polyketide group of OTA molecule, and the amino acid phenylalanine.Here we describe a conventional PCR method developed for the detection of OTA-producing molds belonging to Penicillium and Aspergillus genera by Luque et al. (Food Control 29:270-278, 2013). This method is based on the OTA nrps gene of Penicillium nordicum. It produces a specific amplicon of 459 bp and its functionality in naturally infected samples was also demonstrated.

Aflatoxins and ochratoxin A and their Aspergillus causal species in Tunisian cereals

Occurrence of aflatoxins (AFs) AFB1, AFB2, AFG1, AFG2 and ochra toxin A (OTA) was studied in 65 samples of stored and freshly harvested wheat, barley and maize collected in Tunisia. The mycotoxins were simultaneously extracted and quantified by high performance liquid chromatography. Determination of AF-producing (section Flavi) and OTA-producing Aspergillus species (sections Nigri and Circumdati) was conducted in these samples by species-specific polymerase chain reaction (PCR). Results showed that most of maize samples were contaminated with AFs, data after storage showing lower values than those collected at harvest. All contaminated maize samples contained AFG1 and AFG2, among which 27.78% also had AFB1 and AFB2. This AFs pattern was consistent with the A. parasiticus toxin profile. A. flavus however showed the highest frequency in maize but was also found in barley and wheat where no AFs were detected. In contrast, OTA was neither found in maize nor in barley and only one wheat sample contained OTA. A. niger was the only OTA-producing species detected.

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.

Antifungal effect of eugenol and carvacrol against foodborne pathogens Aspergillus carbonarius and Penicillium roqueforti in improving safety of fresh-cut watermelon

BACKGROUND

Essential oil components eugenol and carvacrol (ranging between 100 and 200 ppm for carvacrol and between 250 and 750 ppm for eugenol) were tested for antifungal activity against foodborne pathogenic fungal species Aspergillus carbonarius A1102 and Penicillium roqueforti PTFKK29 in in vitro and in situ conditions.

MATERIALS AND METHODS

In vitro antifungal activity of eugenol and carvacrol was evaluated by macrobroth method, while watermelon Citrullus lanatus L. Sorento slices were used for antifungal assays in situ.

RESULTS

Selected components, eugenol and carvacrol showed significant inhibitory effect against tested fungi (A. carbonarius A1102 and P. roqueforti PTFKK29) in yeast extract sucrose broth, as well as in in situ conditions. The minimal inhibitory concentration (MIC) of eugenol against A. carbonarius A1102 determined by macrobroth method was 2000 ppm, while against P. roqueforti PTFKK29 determined MIC was 1000 ppm. Carvacrol inhibited growth of A. carbonarius A1102 at minimal concentration of 500 ppm, while against P. roqueforti PTFKK29, MIC was 250 ppm. The assays in real food system watermelon slices for eugenol and carvacrol show that the inhibitory effect against both selected fungal species was concentration dependent. Furthermore, our results showed that antifungal effect of carvacrol as well as eugenol applied on watermelon slices in all concentrations was a result of effective synergy between an active antifungal compound and lower incubation temperature (15°C) in inhibition of A. carbonarius A1102.

CONCLUSION

The present study suggests that the use of eugenol and carvacrol is promising natural alternative to the use of food chemical preservatives, in order to improve safety and quality of fresh-cut and ready-to-eat fruits.

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.

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.

Molecular detection of ochratoxigenic Aspergillus species isolated from coffee beans in Saudi Arabia

Ten fungal isolates from coffee beans were morphologically identified as Aspergillus niger, A. ochraceus and A. carbonari-us (N = 5, 3, and 2, respectively). Only one isolate, morphologically identified as A. niger, was unable to produce ochratoxin A (OTA). This may be a new species in the Aspergillus section Nigri. OTA levels in all the other isolates were above the limit of detection (0.15 mg/kg). Based on microsatellite-primed PCR (MP-PCR) profiles, using three microsatellite primers, three main groups were obtained by UPGMA cluster analysis: A. niger, A. ochraceus and A. carbonarius. A clear-cut association was found between the MP-PCR genotype and the ability to produce OTA. Using the primer pairs OCRA1/OCRA2, a single fragment of about 400 bp was amplified only when genomic DNA from the A. ochraceus isolates was used.

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.

Study of the phenotypic and genotypic biodiversity of potentially ochratoxigenic black aspergilli isolated from grapes

Ochratoxin A (OTA) is a mycotoxin with nephrotoxic, carcinogenic, teratogenic and immunotoxic effects, naturally found in agricultural products including grapes and wine. Black Aspergillus species (Section Nigri) are mainly responsible for OTA accumulation in wine grapes and in particular Aspergillus carbonarius and Aspergillus niger aggregate. The biodiversity of potentially ochratoxigenic strains of black aspergilli from different French vineyards in the southern Mediterranean region of Languedoc-Roussillon was studied. One hundred and eighty nine black strains were isolated from grapes and studied according to harvest year, production zone, grape variety and pre-harvest treatment of grapevines. The strains were identified and classified in two groups according to macroscopic and microscopic characters; these were called the A. carbonarius representative group and the A. niger aggregate representative group. Members of each group were classified in subgroups based on macroscopic morphological colony characters. Strain biodiversity was studied according to phenotypic and genotypic characterization and to the OTA production of selected strains on PDA medium. After identification was confirmed by specific PCR using primer pair ITS1/CAR and ITS1/NIG, 24 potential ochratoxigenic strains belonging to A. carbonarius and A. niger aggregate were discriminated by RAPD-PCR using 8 different OPC primers. The use of specific primers supported the identification based on phenotypic and morphological characters. RAPD-PCR patterns demonstrated a considerable diversity among the strains. Clustering among A. niger aggregate strains was associated with production zone and harvest year, but not grape variety or pre-harvest treatment. Clustering among A. carbonarius strains was not associated with any of the above parameters. OTA production of strains on culture medium seemed to correlate better with morphological characters than with genotypic profiles. No clear relation could be established between phenotypic and genotypic characters of the studied black aspergilli.

Rapid polymerase chain reaction (PCR)-single-stranded conformational polymorphism (SSCP) screening method for the identification of Aspergillus section Nigri species by the detection of calmodulin nucleotide variations

Single-stranded conformational polymorphism (SSCP) analysis for genetic diversity studies has been widely applied to detect indirectly sequence differences up to a single base in amplified DNA fragments of the same length, representing an alternative to gene sequencing. In this study SSCP analysis was used to detect sequence variations contained in an about 180-bp region of the calmodulin gene in order to identify Aspergillus section Nigri species. The method described shows that fluorescence-based SSCP analysis by capillary electrophoresis is cheaper and faster than direct sequencing, and suitable for computer-assisted analyses allowing discrimination between the Aspergillus species belonging to the Nigri section: A. aculeatus, Aspergillus 'atypic uniseriate', A. brasiliensis, A. carbonarius, A. ellipticus, A. foetidus, A. heteromorphus, A. ibericus, A. japonicus, A. niger, and A. tubingensis.

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.

Detection and quantification of Aspergillus westerdijkiae in coffee beans based on selective amplification of β-tubulin gene by using real-time PCR

Aspergillus westerdijkiae is a new species of fungus that was recently dismembered from Aspergillus ochraceus taxon. Most isolates of A. westerdijkiae are able to produce large amounts of a mycotoxin called ochratoxin A (OA). OA has been found in food and beverages, such as coffee. A. westerdijkiae is very similar to A. ochraceus, and several isolates previously identified as A. ochraceus are now identified as A. westerdijkiae. By using sequences of the beta-tubulin gene, we analyzed several isolates from Brazilian coffee bean samples, previously identified as A. ochraceus, to compare with those of A. westerdijkiae. In fact, most (84%) were identified as A. westerdijkiae. Since this species consistently produces large amounts of OA, we developed a specific primer-pair for detecting and quantifying it in coffee beans by using real-time PCR. The primers Bt2Aw-F 5'TGATACCTTGGCGCTTGTGACG and Bt2Aw-R 5'CGGAAGCCTAAAAAATGAAGAG provided an amplicon of 347 bp in all A. westerdijkiae isolates, and no cross-reaction was observed using DNA from A. ochraceus. The sensitivity of real-time PCR was more than 100 times higher than the cfu technique.

Polymerase chain reaction (PCR) identification of Aspergillus niger and Aspergillus tubingensis based on the calmodulin gene

Aspergillus niger and A. tubingensis, species belonging to section Nigri, are commonly found in plant products and processed food, such as grapes, cereals, coffee, and derived products. These two species are very difficult to differentiate by classical morphological criteria and some isolates are known to produce ochratoxin A. The exact identification of these two species is very important to avoid the overestimation of toxicological contamination and related risks. A polymerase chain reaction (PCR)-based identification and detection assay was developed as a tool to identify A. niger and A. tubingensis, using molecular differences obtained by sequencing the calmodulin gene. Two pairs of species-specific primers were designed and empirically evaluated for PCR identification of A. niger and A. tubingensis. Species-specific PCR products generated by each primer set were 505 bp (A. tubingensis) and 245 bp (A. niger) in length, which could be potentially useful for a multiplex PCR assay. The sensitivity of this assay was about 10 pg DNA in a 25-microl PCR reaction volume, using pure total DNA of the two species. The method described in this study represents a rapid and reliable procedure to assess the presence in food products of two ochratoxigenic species of section Nigri.

Internal amplification controls have not been employed in fungal PCR hence potential false negative results

Polymerase chain reaction (PCR) is subject to false negative results. Samples of fungi with the genes of interest (e.g. a disease or mycotoxin) may be categorized as negative and safe as a consequence. Fungi are eukaryotic organisms that are involved in many fields of human activity such as antibiotic, toxin and food production. Certain taxa are implicated in human, animal and plant diseases. However, fungi are difficult to identify and PCR techniques have been proposed increasingly for this purpose. Internal amplification controls (IACs) will ameliorate the situation and need to become mandatory. These are nucleic acids that posses a sequence which will provide a PCR product (i) using the same primers employed for the target gene, and (ii) that will not coincide on the gel with the product of the target gene. Only one group of workers employed an IAC, to respond to potential inhibition, which was reported in 1995 from this present assessment of numerous reports. Inhibitors in cultures need to be minimized, and secondary metabolites are an obvious source. The fields reviewed herein include medical mycology, mycotoxicology, environmental mycology and plant mycology. The conclusion is that previous reports are compromised because IACs have not been employed in fungal PCR; future research must include this control at an early stage.

Real-Time RT-PCR assay to quantify the expression of fum1 and fum19 genes from the Fumonisin-producing Fusarium verticillioides

Fumonisins are a group of mycotoxins produced by Fusarium species of the Gibberella fujikuroi species complex that contaminate food and feed products, and represent a risk for human and animal health. In this work, we have developed a specific real-time reverse transcription-PCR (RT-PCR) assay to quantify the level of expression of two genes of the fumonisin biosynthetic cluster in F. verticillioides: fum1 (that encodes a polyketide synthase enzyme) and the ABC transporter encoding gene fum19. The level of expression of both genes was compared with the amount of fumonisin B(1) (FB(1)), measured by HPLC, produced by several strains of F. verticillioides in liquid culture. The results indicated a good correspondence between the levels of fum1 and fum19 expression and the production of fumonisin B(1). The analysis described provides a good approach for the rapid and specific detection and characterization of the potential ability of F. verticillioides strains to produce fumonisins.

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

Aspergillus carbonarius is an ochratoxin producing fungus that has been considered to be responsible of the ochratoxin A (OTA) contamination in grapes and wine. In order to monitor and quantify A. carbonarius, a specific primer pair Ac12RL_OTAF/Ac12RL_OTAR has been designed from the acyltransferase (AT) domain of the polyketide synthase sequence Ac12RL3 to amplify 141 bp PCR product. Among the mycotoxigenic fungi tested, only A. carbonarius gave a positive result. This specific primer pair was also successfully employed in real-time PCR conjugated with SYBR Green I dye for the direct quantification of this fungus in grape samples. A positive correlation (R(2)=0.81) was found between A. carbonarius DNA content and OTA concentration in 72 grape samples, allowing for the estimation of the potential risk from OTA contamination. Consequently, this work offers a quick alternative to conventional methods of OTA quantification and mycological detection and quantification of A. carbonarius in grapes.