Molecular tools for identification of Penicillium starter cultures used in the food industry

Molecular Identification of Penicillium sp. Isolated from Citrus Fruits

Penicillium is one of the most important postharvest pathogens of citrus fruits worldwide. It induces blue or green mold disease, a decay that can lead to significant economic losses during storage. Based on internal transcribed spacer (ITS) sequences, seven Penicillium species and one closely related Talaromyces variabilis were identified from 30 rotten samples of citrus fruits marketed in Qena. Penicillium expansum was the most common species, recovered from 16.7% of the samples, followed by P. chrysogenum (10%) and P. polonicum (10%). Sixteen isolates were tested through inoculation on healthy citrus fruits; the data exhibited that 68.7% of isolates were highly virulent. A "Specific Gene Random Primer Polymerase Chain Reaction (SGRP-PCR)" marker technique indicated that the genetic similarity among P. expasum ranged from 49.4 to 85.7%, and a relatively correlation was found between SGRP band profile and species origin. Patulin was detected in 40% of P. expansum isolates. This study provided a useful molecular approach to identify different Penicillium species by sequencing ITS region, focus on the pathogenicity, compare between P. expansum isolates and their ability in patulin production.

Dispersion, persistence, and stability of the biocontrol agent Penicillium frequentans strain 909 after stone fruit tree applications

The capacity of dispersion, persistence, and stability from biocontrol agents is essential before these organisms can be developed into a commercial product. Interactions that microorganisms establish with stone fruit trees may be beneficial in the exploitation of trees in agriculture as crop production. The natural background levels of Penicillium frequentans strain 909 dispersion, persistence, and stability were assessed after tree applications and postharvest conditions. A fingerprinting-based approach to trace genetic stability of P. frequentans along stored time and its release in the field was developed. P. frequentans was successfully traced and discriminated. This strain was dispersed well in treated trees, persisting in the ecosystem up to 2 weeks and staying genetically stable after 36 months of storage. However, the dispersal of P. frequentans was very limited on around untreated trees and soil. P. frequentans dispersed randomly into the air, and its presence reduced from the first day to disappear completely at 15-21 days after application. Great losses of P. frequentans and its increased dispersal in open field conditions probably resulted from rainfall. Biological control strategies with Pf909 were discussed.

PCR ITS-RFLP for Penicillium Species and Other Genera

Among numerous molecular methodologies developed for highly specific identification of filamentous fungi isolates, here we describe restriction digestion analysis of the ITS products as an easy method to identify isolates of filamentous fungi. This technique is a rapid and reliable method appropriate for routine identification of filamentous fungi. This can be used to screen large numbers of isolates from various environments in a short time. The use of different endonucleases allowed generating individual restriction profiles. The individual profiles obtained were combined into composite restriction patterns characteristic of a species. Eleven different genera can be differentiated and among them 41 different species.

Geographic variation in mycangial communities of Xyleborus glabratus

Factors that influence fungal communities in ambrosia beetle mycangia are poorly understood. The beetle that is responsible for spreading laurel wilt in SE USA, Xyleborus glabratrus, was examined at three sites along a 500 km N-S transect in Florida, each populated by host trees in the Lauraceae. Fungal phenotypes were quantified in mycangia of individual females that were collected from a site in Miami-Dade County (MDC), 25.8N, with swamp bay (Persea palustris), one in Highlands County (HC), 27.9N, with silkbay (P. humulis) and swamp bay and another in Alachua County (AC), 29.8N, with redbay (P. borbonia). Based on combined LSU, SSU and beta-tubulin datasets the most prominent phenotypes were Raffaelea lauricola (cause of laurel wilt), R. subalba, R. subfusca, R. fusca, R. arxii and an undescribed Raffaelea sp. Mean numbers of colony forming units (CFUs) of R. lauricola varied by location (P < 0.003), and a multivariate analysis, which accounted for the presence and relative abundance of fungal species, indicated that there were significant variations in mycangial communities among the sites; thus climate and vegetation might have affected fungal diversity and the relative abundance of these fungi in the mycangia of X. glabratus Statistically it was unlikely that any of the species influenced the presence and prevalence of another species.

The development of genetic and molecular markers to register and commercialize Penicillium rubens (formerly Penicillium oxalicum) strain 212 as a biocontrol agent

Penicillium oxalicum strain 212 (PO212) is an effective biocontrol agent (BCA) against a large number of economically important fungal plant pathogens. For successful registration as a BCA in Europe, PO212 must be accurately identified. In this report, we describe the use of classical genetic and molecular markers to characterize and identify PO212 in order to understand its ecological role in the environment or host. We successfully generated pyrimidine (pyr-) auxotrophic mutants. In addition we also designed specific oligonucleotides for the pyrF gene at their untranslated regions for rapid and reliable identification and classification of strains of P. oxalicum and P. rubens, formerly P. chrysogenum. Using these DNA-based technologies, we found that PO212 is a strain of P. rubens, and is not a strain of P. oxalicum. This work presents PO212 as the unique P. rubens strain to be described as a BCA and the information contained here serves for its registration and commercialization in Europe.

Screening, morphological and molecular characterization of fungi producing cystathionine γ-lyase

The potency for production of cystathionine γ-lyase (CGL) by the fungal isolates was screened. Among the tested twenty-two isolates, Aspergillus carneus was the potent CGL producer (6.29 U/mg), followed by A. ochraceous (6.03 U/mg), A. versicolor (2.51 U/mg), A. candidus (2.12 U/mg), A. niveus and Penicillium notatum (2.0 U/mg). The potent six isolates producing CGL was characterized morphologically, A. carneus KF723837 was further molecularly characterized based on the sequence of 18S-28S rDNA. Upon sulfur starvation, the yield of A. carneus extracellular CGL was increased by about 1.7- and 4.1-fold comparing to non-sulfur starved and L-methionine free medium, respectively. Also, the uptake of L-methionine was duplicated upon sulfur starvation, assuming the activation of specific transporters for L-methionine and efflux of CGL. Also, the intracellular thiols and GDH activity of A. carneus was strongly increased by S starvation, revealing the activation of in vivo metabolic antioxidant systems. Upon irradiation of A. carneus by 2.0 kGy of γ-rays, the activity of CGL was increased by two-fold, regarding to control, with an obvious decreases on its yield upon further doses. Practically, CGL activity from the solid A. carneus cultures, using rice bran as substrate, was increased by 1.2-fold, comparing to submerged cultures, under optimum conditions.

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.

PCR ITS-RFLP: A useful method for identifying filamentous fungi isolates on grapes

Restriction digestion analysis of the ITS products was tested as an easy method to identify isolates of filamentous fungi on grapes. Endonucleases SduI, HinfI, MseI, HaeIII were used. Endonucleases BfmI, Cfr9I, Hpy188I, MaeII or PspGI were used as necessary to complete discrimination. The 43 species studied generated 42 different composite profiles. Only the species P. thomii and P. glabrum gave the same composite profile. 96.3% strains tested could be differentiated to the species level with only four enzymes. Hundred ninety nine strains of filamentous fungi were isolated from various vineyards in Burgundy and identified by this method. Penicillium (58.5%) was the genus the most frequently isolated and no strains of the genus Aspergillus was isolated. P. spinolusum was the most isolated species of Penicillium (22.70%). The species C. cladiosporioides, B. cinerea, E. nigrum, A. alternata, T. koningiopsis, P. diplodiella, C. herbarum, A. alternatum, T. cucumeris and F. oxysporum were also isolated. This technique is a rapid and reliable method appropriate for routine identification of filamentous fungi. This can be used to screen large numbers of isolates from various environments in a short time. This is the first exhaustive study of fungal diversity at species level in vineyard.

Microsatellite loci to recognize species for the cheese starter and contaminating strains associated with cheese manufacturing

We report the development of 17 microsatellite markers in the cheese fungi Penicillium camemberti and P. roqueforti, using an enrichment protocol. Polymorphism and cross-amplification were explored using 23 isolates of P. camemberti, 26 isolates of P. roqueforti, and 2 isolates of each of the P. chrysogenum and P. nalgiovense species, used to produce meat fermented products. The markers appeared useful for differentiating species, both using their amplification sizes and the sequences of their flanking regions. The microsatellite locus PC4 was particularly suitable for distinguishing contaminant species closely related to P. camemberti and for clarifying the phylogenetic relationship of this species with its supposed ancestral form, P. commune. We analyzed 22 isolates from different culture collections assigned to the morphospecies P. commune, most of them occurring as food spoilers, mainly from the cheese environment. None of them exhibited identical sequences with the ex-type isolate of the species P. commune. They were instead distributed into two other distinct lineages, corresponding to the old species P. fuscoglaucum and P. biforme, previously synonymized respectively with P. commune and P. camemberti. The ex-type isolate of P. commune was strictly identical to P. camemberti at all the loci examined. P. caseifulvum, a non toxinogenic species described as a new candidate for cheese fermentation, also exhibited sequences identical to P. camemberti. The microsatellite locus PC4 may therefore be considered as a useful candidate for the barcode of these economically important species.

Characterization and Pathogenicity of Fusicladium eriobotryae, the Fungal Pathogen Responsible for Loquat Scab

To characterize the fungal pathogen responsible for loquat scab and establish differences in pathogenicity in loquat, eight strains identified as Fusicladium eriobotryae were isolated from either loquat leaves or fruit showing scab symptoms in Spain. Loquat plants belonging to the cv. Peluche were infected via a newly developed infection system that was based on spraying susceptible loquat plants with fungal spore suspensions, keeping the plants for 1 week in 100% humidity, and then transferring the plants to ambient relative humidity in greenhouses. Scab symptoms were analyzed and pathogenic characterization of all F. eriobotryae strains revealed different degrees of aggressiveness. Based on infection progression and severity of scab symptoms, strain ST1 was confirmed as the most aggressive in cultivars in the Mediterranean region. Strain ST1, which even caused chlorotic spots in loquat stems, is so aggressive it can be used to identify highly resistant cultivars using this in vivo system. Molecular characterization of internal transcribed spacer ribosomal DNA and, particularly, the glyceraldehyde 3-phosphate dehydrogenase gene, clearly distinguished loquat strains from Venturia inaequalis. Moreover, random amplified polymorphic DNA (RAPD) and microsatellite-primed polymerase chain reaction techniques were used to qualitatively discriminate between species and report the variations within fungal populations. Molecular variability was checked by comparing all the different strains and enabled the specific identification of F. eriobotryae. Although no association was observed between any pattern and phenotypic traits, such as aggressiveness, RAPD provided a specific profile that allowed fungal identification.

Molecular characterization of the niaD and pyrG genes from Penicillium camemberti, and their use as transformation markers

Genetic manipulation of the filamentous fungus Penicillium camemberti has been limited by a lack of suitable genetics tools for this fungus. In particular, there is no available homologous transformation system. In this study, the nitrate reductase (niaD) and orotidine-5'-monophosphate decarboxylase (pyrG) genes from Penicillium camemberti were characterized, and their suitability as metabolic molecular markers for transformation was evaluated. The genes were amplified using PCR-related techniques, and sequenced. The niaD gene is flanked by the nitrite reductase (niiA) gene in a divergent arrangement, being part of the putative nitrate assimilation cluster in P. camemberti. pyrG presents several polymorphisms compared with a previously sequenced pyrG gene from another P. camemberti strain, but almost all are silent mutations. Southern blot assays indicate that one copy of each gene is present in P. camemberti. Northern blot assays showed that the pyrG gene is expressed in minimal and rich media, and the niaD gene is expressed in nitrate, but not in reduced nitrogen sources. The functionality of the two genes as transformation markers was established by transforming A. nidulans pyrG- and niaD-deficient strains. Higher transformation efficiencies were obtained with a pyrG-containing plasmid. This is the first study yielding a molecular and functional characterization of P. camemberti genes that would be useful as molecular markers for transformation, opening the way for the future development of a non-antibiotic genetic transformation system for this fungus.

Development of an efficient fungal DNA extraction method to be used in random amplified polymorphic DNA-PCR analysis to differentiate cyclopiazonic acid mold producers

A variety of previously established mechanical and chemical treatments to achieve fungal cell lysis combined with a semiautomatic system operated by a vacuum pump were tested to obtain DNA extract to be directly used in randomly amplified polymorphic DNA (RAPD)-PCR to differentiate cyclopiazonic acid-producing and -nonproducing mold strains. A DNA extraction method that includes digestion with proteinase K and lyticase prior to using a mortar and pestle grinding and a semiautomatic vacuum system yielded DNA of high quality in all the fungal strains and species tested, at concentrations ranging from 17 to 89 ng/microl in 150 microl of the final DNA extract. Two microliters of DNA extracted with this method was directly used for RAPD-PCR using primer (GACA)4. Reproducible RAPD fingerprints showing high differences between producer and nonproducer strains were observed. These differences in the RAPD patterns did not differentiate all the strains tested in clusters by cyclopiazonic acid production but may be very useful to distinguish cyclopiazonic acid producer strains from nonproducer strains by a simple RAPD analysis. Thus, the DNA extracts obtained could be used directly without previous purification and quantification for RAPD analysis to differentiate cyclopiazonic acid producer from nonproducer mold strains. This combined analysis could be adaptable to other toxigenic fungal species to enable differentiation of toxigenic and non-toxigenic molds, a procedure of great interest in food safety.

Moulds contaminants on Norwegian dry-cured meat products

Dry-cured meat production has a long tradition in Norway. However, uncontrolled mould growth on the surface of the dry-cured meat products is causing significant quality problems. As some moulds are mycotoxigenic, their growth on the dry-cured meat products could also pose a serious health risk. Such quality problems and potential health risks can be better handled if the types of moulds growing on the products are known. In total, 161 samples were collected from the ripening and packaging stages of production with the aim of identifying moulds contaminating smoked and unsmoked Norwegian dry-cured meat products. Moulds were isolated either by transferring aerial mycelium of each visible mould colonies on the products or by directly plating pieces of meat on suitable agar media. The isolates were identified at a species level by a polyphasic approach. In total, 264 isolates belonging to 20 species and four fungal genera were identified. The genus Penicillium covered 88.3% of the total isolates. This genus contributed to the isolates of smoked and unsmoked products by 91% and 84% respectively. Penicillium nalgiovense was the dominant species isolated from both smoked and unsmoked products and covered 38% of the total isolates. Penicillium solitum and P. commune were the next most frequently isolated species with a contribution of 13% and 10% respectively. Species of Cladosporium and Eurotium contributed to the total isolates by 6% and 4.9% respectively. Smoking seems to affect the growth of these dominating species differently. An increase in the isolation frequency of P. nalgiovense accompanied by the reduction in the occurrence of P. solitum, P. commune and species of Cladosporium was observed on smoked products. The survey showed that the species of Penicillium are associated with Norwegian dry-cured meat products in general. Penicillium nalgiovense, the dominating mould species, is a potential producer of penicillin and its presence could represent a threat to allergic consumers.

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.

Comparison of a randomly amplified polymorphic DNA (RAPD) analysis and ATB ID 32C system for identification of clinical isolates of different Candida species

The objective of this work was to compare the usefulness of a randomly amplified polymorphic DNA (RAPD) assay to that of the ATB ID32C kit (bioMérieux, France) for identification of different species of Candida isolated from clinical specimens. The RAPD-PCR patterns obtained with OPE-18 primer for identification of clinical isolates were consistent, and the different independent assays revealed reproduction of the band patterns. RAPD with the OPE-18 primer is a very specific and sensitive method for identification of Candida glabrata, Candida guilliermondii, Candida tropicalis, Candida pelliculosa, Candida albicans, Candida krusei, and Candida lusitaniae.

Polymerase chain reaction (PCR) identification ofPenicillium brevicompactum, a grape contaminant and mycophenolic acid producer

Penicillium brevicompactum is a ubiquitous fungal species that contaminates diverse substrates and commodities and produces an array of metabolites toxic to human and animals. The present work has obtained evidence, by liquid chromatography (LC)-ion-trap mass spectrometry, of the ability of P. brevicompactum strains isolated from grapes to produce mycophenolic acid, a potent immunosuppressor. In order to facilitate early diagnosis of this species on commodities for human and animal consumption, a rapid, sensitive and specific polymerase chain reaction (PCR) assay for P. brevicompactum was developed. The specific primers were designed based on the ITS1-5.8S-ITS2ITS (Internal Transcribed Spacers of rRNA genes) multicopy region. This method provides a useful aid to detect the presence of this fungal species in grapes and other commodities in order to prevent the toxins produced entering the food chain.

Mutation at β-Tubulin Codon 200 Indicated Thiabendazole Resistance in Penicillium digitatum Collected from California Citrus Packinghouses

Thiabendazole (TBZ) is commonly applied to harvested citrus fruit in packinghouses to control citrus green mold, caused by Penicillium digitatum. Although TBZ is not used before harvest, another benzimidazole, thiophanate methyl, is commonly used in Florida and may be introduced soon in California to control postharvest decay of citrus fruit. Isolates from infected lemons and oranges were collected from many geographically diverse locations in California. Thirty-five isolates collected from commercial groves and residential trees were sensitive to TBZ, while 19 of 74 isolates collected from 10 packinghouses were resistant to TBZ. Random amplified polymorphic DNA analysis indicated that the isolates were genetically distinct and differed from each other. Nineteen TBZ-resistant isolates and a known TBZ-resistant isolate displayed a point mutation in the β-tubulin gene sequence corresponding to amino acid codon position 200. Thymine was replaced by adenine (TTC → TAC), which changed the phenylalanine (F) to tyrosine (Y). In contrast, for 49 TBZ-sensitive isolates that were sequenced, no mutations at this or any other codon positions were found. All of the isolates of P. digitatum resistant to TBZ collected from a geographically diverse sample of California packinghouses appeared to have the same point mutation conferring thiabendazole resistance.

An assessment of the efficiency of fungal DNA extraction methods for maximizing the detection of medically important fungi using PCR

To date, no single reported DNA extraction method is suitable for the efficient extraction of DNA from all fungal species. The efficiency of extraction is of particular importance in PCR-based medical diagnostic applications where the quantity of fungus in a tissue biopsy may be limited. We subjected 16 medically relevant fungi to physical, chemical and enzymatic cell wall disruption methods which constitutes the first step in extracting DNA. Examination by light microscopy showed that grinding with mortar and pestle was the most efficient means of disrupting the rigid fungal cell walls of hyphae and conidia. We then trialled several published DNA isolation protocols to ascertain the most efficient method of extraction. Optimal extraction was achieved by incorporating a lyticase and proteinase K enzymatic digestion step and adapting a DNA extraction procedure from a commercial kit (MO BIO) to generate high yields of high quality DNA from all 16 species. DNA quality was confirmed by the successful PCR amplification of the conserved region of the fungal 18S small-subunit rRNA multicopy gene.

First Report of Penicillium brasilianum and P. daleae Isolated from Soil in Korea

In this study, a total of 300 isolates of Penicillium and related teleomorphic genera were collected from soils of 17 locations in Korea from April to May, 2004. Ninety four isolates were identified as the species of Penicillium subgenus Furcatum based on cultural and morphological characteristics and β-tubulin gene sequences. Among the species, Korean isolates of P. brasilianum Bat. and P. daleae K. M. Zalessky were phylogenetically identical to the reference species based on DNA sequence of the β-tubulin gene. Here we described and illustrated P. brasilianum and P. daleae that are new in Korea.

Characterization of molds from dry-cured meat products and their metabolites by micellar electrokinetic capillary electrophoresis and random amplified polymorphic DNA PCR

Molds are common contaminants of dry-cured meat products in which mycotoxins could be synthesized if stored under favorable conditions. Thus, efficient and accurate characterization of the toxigenic molds from dry-cured meat products is necessary. A micellar electrokinetic capillary chromatography (MECC) method was tested to analyze secondary metabolites produced by 20 mold strains commonly found in dry-cured meat products. In addition, their random amplified polymorphic DNA (RAPD) genotypes were determined by using a PCR method. Although peak profiles of the secondary metabolites differed among mold strains of different species, they were similar in the same species. MECC analysis showed that 10 of the 20 molds tested produced mycotoxins, including patulin, penicillic acid, cyclopiazonic acid, mycophenolic acid, aflatoxin B1, sterigmatocystin, and griseofulvin. The RAPD analysis yielded a different pattern for each of the mold species tested. However, strains of the same species showed similar RAPD profiles. A high correlation between RAPD analysis and MECC was observed, since strains of the same species that showed similar RAPD patterns had similar profiles of secondary metabolites. RAPD patterns with primer GO2 and MECC profiles, either singly or combined, could be of great interest to distinguish toxigenic from nontoxigenic molds in dry-cured meat products.

Characterization of Penicillium Isolates Associated with Blue Mold on Apple in Uruguay

Blue mold caused by Penicillium spp. is the most important postharvest disease of apple in Uruguay. Fourteen isolates of Penicillium were recovered from rotten apple and pear fruit with blue mold symptoms, and from water from flotation tanks in commercial apple juice facilities. Phenotypic identification to species level was performed, and the isolates were tested for sensitivity to commonly used postharvest fungicides. Genetic characterization of the isolates was performed with restriction fragment length polymorphism of the region including the internal transcribed spacer (ITS) ITS1 and ITS2 and the 5.8SrRNA gene (ITS1-5.8SrRNA gene-ITS2) ribosomal DNA region and with random amplified polymorphic DNA (RAPD) primers. Both techniques were able to differentiate these isolates at the species level. RAPD analysis proved to be an objective, rapid, and reliable tool to identify Penicillium spp. involved in blue mold of apple. In all, 11 isolates were identified as Penicillium expansum and 3 as P. solitum. This is the first report of P. solitum as an apple pathogen in Uruguay.

Identification of Candida spp. by randomly amplified polymorphic DNA analysis and differentiation between Candida albicans and Candida dubliniensis by direct PCR methods

Because Candida species have innately highly variable antifungal susceptibilities, the availability of a fast and reliable species identification test is very important so that suitable and effective therapeutic measures may be taken. Using three oligonucleotide primers, we established a randomly amplified polymorphic DNA (RAPD) analysis method that enabled direct identification of the most common opportunistic pathogenic Candida species. RAPD analysis revealed a characteristic molecular fingerprint for each Candida species. Differences between the profiles for Candida albicans and C. dubliniensis were evident. RAPD analysis is a relatively easy, reproducible, and reliable technique that can be useful in providing genetic fingerprints for the identification of strains. In addition, a collection of different C. albicans strains was identified by a specific PCR based on multiple secreted aspartic proteinase (SAP) genes and the dipeptidyl aminopeptidase (DAP2) gene. Our findings demonstrate that PCR based upon the SAP and DAP2 sequences is a simple, rapid, clear, and direct technique for the identification and differentiation of C. albicans and C. dubliniensis.

Application of random amplified polymorphic DNA (RAPD) analysis for identification of grouper (Epinephelus guaza), wreck fish (Polyprion americanus), and Nile perch (Lates niloticus) fillets

A random amplified polymorphic DNA (RAPD) method was developed for the specific identification of grouper (Epinephelus guaza), wreck fish (Polyprion americanus), and Nile perch (Lates niloticus) fillets. Using two different reaction primers (S1 and L1), RAPD analysis produced clear fingerprints from which the three fish species could be easily identified. This approach is rapid and reliable and offers the potential to detect fraudulent or unintentional mislabeling of these species in routine seafood authentication analysis.

Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens

Advances in molecular technology show great potential for the rapid detection and identification of fungi for medical, scientific and commercial purposes. Numerous targets within the fungal genome have been evaluated, with much of the current work using sequence areas within the ribosomal DNA (rDNA) gene complex. This section of the genome includes the 18S, 5.8S and 28S genes which code for ribosomal RNA (rRNA) and which have a relatively conserved nucleotide sequence among fungi. It also includes the variable DNA sequence areas of the intervening internal transcribed spacer (ITS) regions called ITS1 and ITS2. Although not translated into proteins, the ITS coding regions have a critical role in the development of functional rRNA, with sequence variations among species showing promise as signature regions for molecular assays. This review of the current literature was conducted to evaluate clinical approaches for using the fungal ITS regions as molecular targets. Multiple applications using the fungal ITS sequences are summarized here including those for culture identification, phylogenetic research, direct detection from clinical specimens or the environment, and molecular typing for epidemiological investigations. The breadth of applications shows that ITS regions have great potential as targets in molecular-based assays for the characterization and identification of fungi. Development of rapid and accurate amplification-based ITS assays to diagnose invasive fungal infections could potentially impact care and improve outcome for affected patients.

Comparison of statistical methods for identification of Streptococcus thermophilus, Enterococcus faecalis, and Enterococcus faecium from randomly amplified polymorphic DNA patterns

Thermophilic streptococci play an important role in the manufacture of many European cheeses, and a rapid and reliable method for their identification is needed. Randomly amplified polymorphic DNA (RAPD) PCR (RAPD-PCR) with two different primers coupled to hierarchical cluster analysis has proven to be a powerful tool for the classification and typing of Streptococcus thermophilus, Enterococcus faecium, and Enterococcus faecalis (G. Moschetti, G. Blaiotta, M. Aponte, P. Catzeddu, F. Villani, P. Deiana, and S. Coppola, J. Appl. Microbiol. 85:25-36, 1998). In order to develop a fast and inexpensive method for the identification of thermophilic streptococci, RAPD-PCR patterns were generated with a single primer (XD9), and the results were analyzed using artificial neural networks (Multilayer Perceptron, Radial Basis Function network, and Bayesian network) and multivariate statistical techniques (cluster analysis, linear discriminant analysis, and classification trees). Cluster analysis allowed the identification of S. thermophilus but not of enterococci. A Bayesian network proved to be more effective than a Multilayer Perceptron or a Radial Basis Function network for the identification of S. thermophilus, E. faecium, and E. faecalis using simplified RAPD-PCR patterns (obtained by summing the bands in selected areas of the patterns). The Bayesian network also significantly outperformed two multivariate statistical techniques (linear discriminant analysis and classification trees) and proved to be less sensitive to the size of the training set and more robust in the response to patterns belonging to unknown species.