There have been reports of increasing numbers of cases of malaria among migrants and travelers. Although microscopic examination of blood smears remains the "gold standard" in diagnosis, this method suffers from insufficient sensitivity and requires considerable expertise. To improve diagnosis, a multiplex real-time PCR was developed. One set of generic primers targeting a highly conserved region of the 18S rRNA gene of the genus Plasmodium was designed; the primer set was polymorphic enough internally to design four speciesspecific probes for P. falciparum, P. vivax, P. malarie, and P. ovale. Real-time PCR with species-specific probes detected one plasmid copy of P. falciparum, P. vivax, P. malariae, and P. ovale specifically. The same sensitivity was achieved for all species with real-time PCR with the 18S screening probe. Ninety-seven blood samples were investigated. For 66 of them (60 patients), microscopy and real-time PCR results were compared and had a crude agreement of 86% for the detection of plasmodia. Discordant results were reevaluated with clinical, molecular, and sequencing data to resolve them. All nine discordances between 18S screening PCR and microscopy were resolved in favor of the molecular method, as were eight of nine discordances at the species level for the species-specific PCR among the 31 samples positive by both methods. The other 31 blood samples were tested to monitor the antimalaria treatment in seven patients. The number of parasites measured by real-time PCR fell rapidly for six out of seven patients in parallel to parasitemia determined microscopically. This suggests a role of quantitative PCR for the monitoring of patients receiving antimalaria therapy.

Molecular approaches are now being developed to provide a more rapid and objective identification of fungi compared to traditional phenotypic methods. Ribosomal targets, especially the large-subunit RNA gene (D1-D2 region) and internal transcribed spacers 1 and 2 (ITS1 and ITS2 regions), have shown particular promise for the molecular identification of some fungi. We therefore conducted an assessment of these regions for the identification of 13 medically important Aspergillus species: Aspergillus candidus, Aspergillus (Eurotium) chevalieri, Aspergillus (Fennellia) flavipes, Aspergillus flavus, Aspergillus fumigatus, Aspergillus granulosus, Aspergillus (Emericella) nidulans, Aspergillus niger, Aspergillus restrictus, Aspergillus sydowii, Aspergillus terreus, Aspergillus ustus, and Aspergillus versicolor. The length of ribosomal regions could not be reliably used to differentiate among all Aspergillus species examined. DNA alignment and pairwise nucleotide comparisons demonstrated 91.9 to 99.6% interspecies sequence identities in the D1-D2 region, 57.4 to 98.1% in the ITS1 region, and 75.6 to 98.3% in the ITS2 region. Comparative analysis using GenBank reference data showed that 10 of the 13 species examined exhibited a <1-nucleotide divergence in the D1-D2 region from closely related but different species. In contrast, only 5 of the species examined exhibited a <1-nucleotide divergence from sibling species in their ITS1 or ITS2 sequences. Although the GenBank database currently lacks ITS sequence entries for some species, and major improvement in the quality and accuracy of GenBank entries is needed, current identification of medically important Aspergillus species using GenBank reference data seems more reliable using ITS query sequences than D1-D2 sequences, especially for the identification of closely related species.Aspergillus species are an increasingly important cause of invasive fungal infections in immunocompromised patients (31, 59). Unfortunately, there are few specific clinical signs of invasive aspergillosis and current methods for laboratory diagnosis are less than ideal, particularly in the early stages of the disease (8,49). Given the recent reports of reduced antifungal drug susceptibilities among some Aspergillus species (21, 26, 50), the timely and accurate identification of aspergilli to the species level has become especially important (10). Species identification is also important for epidemiological purposes and as a guide to clinical management (29,47,48).The current laboratory identification of Aspergillus species is based on macroscopic colonial and microscopic morphological characteristics (7,20,45). Over 180 different species in at least 16 subgeneric groups or sections can be distinguished (35,37,38), including approximately 30 species which are recognized as opportunistic pathogens of humans (7). Many clinical laboratories use traditional phenotypic methods of identification and can differentiate only the more common Aspergillus species; the delineation of less common species must b...

The 165-235 rDNA intergenic spacer region of organisms identical with or closely related to ' Tropheryma whippelii', the uncultivated causative agent of Whipple's disease, was analysed directly from 38 clinical specimens of 28 patients using a specific nested PCR followed by direct sequencing. As compared to the reference sequence in public databases, two novel ' T. whippelii' spacer types were recognized. In the absence of DNA-DNA hybridization data it is uncertain whether the three types found represent subtypes of a single species or three different but closely related species. Methods were developed to detect all three variants by single-strand conformation polymorphism analysis and by type-specif ic PCR assays, thus allowing the screening of large numbers of specimens. Further studies may provide a clue to the possible associations between the type of infecting strain and the various clinical presentations of Whipple's disease.

Tropheryma whippelii is the causative agent of Whipple's disease, a difficult to diagnose systemic illness. Amplification of part of its 16S ribosomal RNA gene(s) has become a standard diagnostic method because of increased sensitivity as compared to classical histopathological analysis. Recently, we demonstrated the presence of T. whippelii DNA by PCR in duodenal biopsies and/or gastric juice of a considerable fraction of individuals without clinical signs of Whipple's disease. In this follow-up study, saliva and dental plaques of the same patients were screened for the presence of T. whippelii DNA. Six out of the 14 previously PCR-positive persons but none of the 17 controls had T. whippelii DNA in their saliva. Our results suggest that Whipple bacteria are ubiquitous environmental or commensal organisms causing Whipple's disease only in a particular subset of individuals, possibly those with an as yet uncharacterized immunological defect.