Generation of DNA probes for detection of microorganisms by polymerase chain reaction fingerprinting

Functional Foods: A Survey of Health Claims, Pros and Cons, and Current Legislation

Functional foods stand for a new category of remarkably promising foods bearing properties (i.e., low cholesterol, antioxidant, anti-aging, anticancer, etc.) that have already rendered them quite appealing. There are many classes offunctionalfoods (pro- and pre-biotics, dietary fiber, low fat, etc.), and their definition is occasionally confused with that of nutraceuticals and novel foods. Consumers' main skepticism regarding functional foods resides in the veracity of health claims and in the low and often inadequate control of their claimed properties. Legislation concerning this matter is progressing at an extremely low pace and currently only Japan, the U.K., U.S.A., and Scandinavian countries have managed to make notable progress. Moreover, the labeling of functional foods is far from informative, providing scanty information about nutritional value, storage, and cooking recipes. It is anticipated that technological advances in the food industry, in conjunction with extensive clinical trials and governmental control, will eventually guarantee the credibility of health claims and ensure consumers' confidence in functional foods.

Molecular approaches to the study of dermatophytes

Dermatophyte species are common keratinophilic fungi responsible for superficial infections called dermatophytosis or ringworm and composed of three anamorphic genera, Trichophyton, Microsporum and Epidermophyton. Through the use of several complementary molecular methods, dermatophytes have been shown to constitute an homogeneous group of species with very low genetic diversity contrasting with high phenotypic heterogeneity. For diagnostic applications, distinction among isolates to the species level was easily performed using polymerase chain reaction-based assays, which could be useful tools in the mycology laboratory, particularly for atypical isolates. In contrast, in all but a few cases distinction between dermatophyte strains has failed, which has hindered the development of molecular-based epidemiological investigations.

Validation of binary typing for Staphylococcus aureus strains

Most of the DNA-based methods for genetic typing of Staphylococcus aureus strains generate complex banding patterns. Therefore, we have developed a binary typing procedure involving strain-differentiating DNA probes which were generated on the basis of randomly amplified polymorphic DNA (RAPD) analysis. We present and validate the usefulness of 15 DNA probes, according to generally accepted performance criteria for molecular typing systems. RAPD analysis with multiple primers was performed on 376 S. aureus strains of which 97% were methicillin resistant (MRSA). Among the 1,128 RAPD patterns generated, 66 were selected which identified 124 unique DNA fragments. From these amplicons, only 12% turned out to be useful for isolate-specific binary typing. The nature of the RAPD-generated DNA fragments was investigated by partial DNA sequence analysis. Several homologies with known S. aureus sequences and with genes from other species were discovered; however, 87% of the probe sequences are of previously unknown origin. The locations of most of the DNA probes on the chromosome of S. aureus NCTC 8325 were determined by hybridization. Seven fragments were randomly dispersed along the genome, five were clustered within the 2500- to 2600-kb position of the genome, and the remaining four did not recognize complementary sequences in S. aureus NCTC 8325. A total of 103 S. aureus strains (69% MRSA) were used for the validation of the binary typing technique. The 15 DNA probes provided stable epidemiological markers, both in vitro (type consistency after serial passages on culture media) and in vivo (comparison of sequential isolates recovered from cases of persistent colonization). The discriminatory power of binary typing (D = 0.998) exceeded that of pulsed-field gel electrophoresis (D = 0.966) and RAPD analysis (D = 0.949). Reproducibility, measured by analyzing multiple strains belonging to a multitude of different epidemiological clusters, was comparable to that of other genotyping techniques used. Contribution of the DNA probes to the discriminatory power of the system was analyzed by comparison of dendrograms. This study demonstrates that binary typing is a robust tool for the genetic typing of S. aureus isolates.

DNA-probes for the differentiation of Capnocytophaga species

We designed oligonucleotides to differentiate between the seven currently known Capnocytophaga species. The oligonucleotides were labelled non-radioactively at the 3' end with digoxigenin. The specificity could be demonstrated in a dot-blot hybridization assay by using the type strains, reference strains, and 37 clinical Capnocytophaga isolates as well as 11 representative strains of other taxa as a template. The sensitivity of the assay was calculated with 10(3) bacteria per dot.

Curie-point pyrolysis mass spectrometry as a tool in clinical microbiology

Pyrolysis mass spectrometry is a well established analytical tool that has received a considerable boost from the development of low cost, dedicated instruments and sophisticated statistical analyses on personal computers. Further analytical developments, especially in the area of neural networks, are pushing the technology to the forefront of methods for the discrimination and identification of microorganisms and their products. The speed and reproducibility of pyrolysis mass spectrometry and its applicability to a wide range of microorganisms make it an attractive method for epidemiological studies. For inter-strain comparisons, the method is at least as discriminatory as conventional typing systems and usually gives discrimination similar to that of nucleic acid fingerprinting techniques. There has been some success in using neural networks to make identifications across pyrolysis mass spectrometric batches. Further development of methods used to handle data from multiple PyMS analyses can be expected to extend the value of pyrolysis mass spectrometry in clinical microbiology.

On the nature and use of randomly amplified DNA from Staphylococcus aureus

Various DNA-based methods have been introduced to genetically type Staphylococcus aureus strains but not a single technique is universally applicable. In order to search for DNA probes suitable for differentiating strains, randomly amplified polymorphic DNA patterns were generated for 243 S. aureus strains and a single isolate of Staphylococcus intermedius. All fingerprints were examined for unique amplicons, and the nature of 42 of these DNA fragments was investigated. Partial DNA sequences were determined, and several homologies were discovered with known S. aureus sequences (plasmid pSH6 DNA with insertion sequences, agrA and agrB sequences, hld genes, the gene for 23S rRNA, the lysyl tRNA synthetase gene, and the threonyl tRNA synthetase gene) and with genes from other species (Haemophilus influenzae bexA and Bacillus subtilis spoF and ctrA). Thirty fragments were of previously unknown origin. In Southern blots containing Eco RI-digested DNA from S. aureus strains and the S. intermedius strain, nine probes demonstrated the capacity to differentiate strains on the basis of the presence or absence of the sequence element in the staphylococcal genome involved. The remainder of the probes displayed restriction fragment length polymorphisms (n = 12), hybridized in a homogeneously positive fashion (n = 13) or hybridized only with their source strains (n = 8) (four of the latter were specific to S. intermedius). Three of the nine strain-specific probes were overlapping, and two of the others were found to display a high level of inconsistency among epidemiologically related strains. Thus, five strain-specific probes remained that, in a 5-digit typing system, accurately distinguished epidemiologically related and unrelated strains of S. aureus. We conclude that application of strain-specific DNA probes, selected on the basis of differing randomly amplified polymorphic DNA patterns, promises to become a technically simple, robust, and reproducible tool that may significantly facilitate the study of the epidemiology of S. aureus infections.