Isolation and characterization of a species-specific DNA fragment for detection of Candida albicans by polymerase chain reaction.

A 2-kbp DNA fragment, EO3, that was present in multiple copies in the Candida albicans genome was isolated for use in developing a detection method for C. albicans by polymerase chain reaction (PCR). Dot blot hybridization revealed that EO3 was specific for the 40 isolates of C. albicans serotypes A and B used. Using a set of primers (20-mer each) derived from the nucleotide sequence of EO3, we performed specific amplification of a 1.8-kbp DNA fragment within EO3 by PCR. All 40 isolates belonging to C. albicans serotypes A and B contained amplifiable 1.8-bkp fragments, although the DNA of the amplified products exhibited small variations in size, yielding three different fragment groups. Southern blot hybridization probed with EO3 showed that these 1.8-kbp fragments were derived from the EO3 region. Conversely, the 1.8-kbp fragment was not amplified from 38 isolates belonging to seven other medically important Candida species or from isolates of Cryptococcus neoformans, Saccharomyces cerevisiae, various bacteria, and a human cell line. The detection limit of the PCR assay for C. albicans with the EO3 fragment was shown to be approximately 2 to 10 cells and 100 cells in saline and human urine, respectively, by ethidium bromide staining and 2 and 10 cells, respectively, by Southern blot analysis. In addition, EO3 was assumed to originate from mitochondrial DNA on the basis of the results of its characterizations. These results indicate that the PCR system using the 1.8-kbp fragment as a target is a reliable method for identifying C. albicans isolates, thereby suggesting its potentials for specific and sensitive detection of C. albicans in samples from patients with candidiasis.     

Identification of Candida species by PCR and restriction fragment length polymorphism analysis of intergenic spacer regions of ribosomal DNA.

The PCR was used to amplify a targeted region of the ribosomal DNA from 84 Candida isolates. Unique product sizes were obtained for Candida guilliermondii, Candida (Torulopsis) glabrata, and Candida pseudotropicalis. Isolates of Candida albicans, Candida tropicalis, Candida stellatoidea, Candida parapsilosis, and Candida krusei could be identified following restriction digestion of the PCR products.     

Restriction fragment length polymorphism analysis of azole-resistant and azole-susceptible Candida albicans strains.

Restriction fragment length polymorphism analysis was performed with the endonucleases EcoRI, BglII, and HinfI on a collection of Candida albicans strains comprising eight strains randomly selected from clinical microbiology laboratory specimens, three reported azole-resistant strains from treatment failures, and several subcultures of the azole-resistant strain NCPF 3310 (also known as the Darlington strain) received from different laboratories. The results demonstrated a diversity of the restriction fragment length polymorphism patterns that were obtained and revealed that two of the proposed Darlington subcultures had patterns distinct from each other and from those of the other Darlington isolates; both were also found to have lost their azole resistance.     

Ploidy and DNA content of Candida stellatoidea cells.

Three isolates of Candida stellatoidea contained approximately the same amount of DNA per blastospore (38.3 to 41.9 fg) as did a known diploid isolate of Candida albicans and about twice as much as did a haploid isolate of Saccharomyces cerevisiae. The diploidy of C. stellatoidea was supported by demonstration of mitotic segregation of an ade marker.     

Isolation and characterization of a species-specific DNA fragment for identification of Candida (Torulopsis) glabrata by PCR

A PCR specific for Candida glabrata that amplifies a mitochondrial rRNA gene fragment was developed by analysis of C. glabrata-specific agarose gel bands, which were generated by arbitrarily primed PCR. The expected PCR product was successfully amplified with genomic DNA from 95 C. glabrata isolates but not from a number of other fungal isolates.     

Restriction fragment analysis of a Candida tropicalis outbreak of sternal wound infections.

An apparent single-source outbreak of Candida tropicalis sternal wound infections in eight patients was investigated by utilizing DNA restriction fragment analysis (RFA) with HindIII and BstNI. All eight outbreak isolates appeared to be identical and were easily differentiated from control isolates by DNA RFA. Compared with an arbitrarily selected reference outbreak isolate, greater than or equal to 95% of the bands in the restriction digests identified by a computerized image analysis system from each of the outbreak isolates were identical versus 13 to 53% of the bands in any of the nine control isolates. Outbreak strains were significantly more likely to match the reference outbreak isolate than were controls (P less than 0.0001). The RFA was greatly facilitated by the use of computerized image analysis and confirmed the epidemiologic link between a scrub nurse and the infected patients.     

Typing of Enterococcus species by DNA restriction fragment analysis.

Enterococci are a frequent cause of hospital-acquired infection, being associated with urinary tract infections, wound sepsis, bacteremia, and endocarditis. The source of infection is usually thought to be endogenous, but some evidence points to cross-infection between patients. A better understanding of the epidemiology of enterococci has been limited by the lack of a good discriminatory typing system. This report describes the application of two DNA-based typing methods to Enterococcus faecalis and Enterococcus faecium: comparison of restriction fragments from total DNA by conventional electrophoresis and comparison of restriction fragments hybridizing to an rRNA gene probe (ribotyping). Comparison of restriction fragments (from SstI digestion) by conventional electrophoresis was simple and highly discriminatory. The results of analysis of blood culture isolates and of repeat isolates from individual patients are reported. Ribotyping (with BscI digestion) was more applicable at the level of species discrimination.     

Estimation of DNA restriction fragment size using a PC.

A computer program developed by Duggleby et al. (R. G. Duggleby, H. Kinns and J. I. Rood, A computer program for determining the size of DNA restriction fragments. Analytical Biochemistry 110, 49 (1981)) for determining DNA restriction fragment size was rewritten for the IBM compatible PC. Accuracy of curve fit was examined for molecular size range 22 to 0.6 kb. It showed a better fit of the data involving molecular size range 22 to 2 kb, or 2 to 0.6 kb, rather than for 22 to 0.6 kb, irrespective of agarose gel concentrations and electrophoretic running times. Thus, greater accuracy of DNA fragment size could be estimated by using two calibration ranges, i.e. 22 to 2 kb, or 2 to 0.6 kb, depending on the fragment size.     

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.     

DNA fingerprinting of Candida rugosa via repetitive sequence-based PCR.

A repetitive sequence-based PCR (rep-PCR) technique was developed to characterize the genotypic relatedness among Candida rugosa isolates. Two repetitive sequences, viz., Care-2 and Com29 from Candida albicans, were used to design primers Ca-21, Ca-22, and Com-21, respectively. When used alone or in combination, these primers generated discriminatory fingerprints by amplifying the adjacent variable regions of the genome. Twenty-three isolates from burn patients, eight from other human sources, and four C. rugosa isolates pathogenic in animals were placed into nine fingerprinting groups. Different primers placed these isolates into identical groups, indicating that rep-PCR is a specific and reproducible technique for molecular characterization of C. rugosa. Moreover, these primers unequivocally discriminated among other important Candida species such as C. albicans, C. glabrata, C. tropicalis, C. krusei, C. parapsilosis, C. kefyr, and C. lusitaniae. These data confirm the conservation of repetitive sequences in Candida species. Because of its ease and sensitivity, rep-PCR offers a relatively rapid and discriminatory method for molecular typing of C. rugosa in outbreaks.     

Colonizing populations of Candida albicans are clonal in origin but undergo microevolution through C1 fragment reorganization as demonstrated by DNA fingerprinting and C1 sequencing.

The genetic homogeneity of nine commensal and infecting populations of Candida albicans has been assessed by fingerprinting multiple isolates from each population by Southern blot hybridization first with the Ca3 probe and then with the 0.98-kb C1 fragment of the Ca3 probe. The isolates from each population were highly related, demonstrating the clonal origin of each population, but each population contained minor variants, demonstrating microevolution. Variation in each case was limited to bands of the Ca3 fingerprint pattern which hybridized with the 0.98-kb C1 fragment. The C1 fragment was therefore sequenced and demonstrated to contain an RPS repetitive element. The C1 fragment also contained part or all of a true end of the RPS element. These results, therefore, demonstrate that most colonizing C. albicans populations in nonimmuno-suppressed patients are clonal, that microevolution can be detected in every colonizing population by C1 hybridization, and that C1 contains the repeat RPS element.     

Rapid identification of Candida species by DNA fingerprinting with PCR.

DNA polymorphisms in different species and strains of the genus Candida were assessed by amplifying genomic DNA with single nonspecific primers. This PCR method employed an arbitrary primer (the 10-mer AP3), a primer derived from the intergenic spacer regions (T3B), and the microsatellite primers (GTG)5 and (AC)10. Distinctive and reproducible sets of amplification products were observed for 26 different Candida and 8 other fungal species. The numbers and sizes of the amplification products were characteristic for each species. All yeast species tested could be clearly distinguished by their amplification patterns. With all primers, PCR fingerprints also displayed intraspecies variability. However, PCR profiles obtained from different strains of the same species were far more similar than those derived from different Candida species. By comparing species-specific PCR fingerprints of clinical isolates with those of reference strains, clinical isolates could be identified to the species level even if they could not be identified by routine biochemical methods.     

Application of DNA typing methods to epidemiology and taxonomy of Candida species.

Methods are described for extraction of DNA from the yeast form of Candida spp., followed by digestion and electrophoresis of DNA fragments. The resulting gel patterns (greater than 100 bands) were used to type Candida isolates. Four intense bands identified, three of which are present in each isolate (6 to 7, 3.7 or 4.2, and 2.5 to 3 kilobases), appear to be DNA encoding the rRNA. The methods proved to be both simple and reproducible. The patterns were shown to be stable through several hundred doublings from multiple single colonies. A survey of isolates showed that, on the basis of similarity of gel patterns, several Candida species could be sorted into mutually exclusive groups, and subgroups could be created. Analyses of this survey suggested the possible epidemiologic and taxonomic applications of these methods. DNA typing methods appear to offer important potential advantages over phenotyping methods. The methods provide a base for further epidemiologic studies and for further development of techniques, such as the use of cloned probes for studies of DNA homology.     

Differentiation of Campylobacter jejuni and Campylobacter coli strains by using restriction endonuclease DNA profiles and DNA fragment polymorphisms.

The chromosomal DNA fragment patterns from a total of 169 Campylobacter jejuni and Campylobacter coli isolates from poultry and humans were analyzed by using DNA restriction endonucleases ClaI and EcoRV. The DNA restriction patterns produced by ClaI and EcoRV consisted of unique DNA fragments of 9 to 9.5 kb and 3.5 kb generated with ClaI and a single unique fragment of 3.0 kb produced by EcoRV. These patterns were obtained with all strains of C. jejuni tested. The DNA restriction patterns were further examined by Southern blot analysis with a previously constructed DNA probe, pMO2005, which is also able to distinguish between C. jejuni and C. coli spp. (5). Two types of patterns were produced by hybridization with the ClaI-cleaved DNA of C. jejuni strains, one of a single 18.5-kb genomic fragment and the other of 14.5- and 4.0-kb fragments. This indicated the presence of an extra ClaI site in this genomic fragment in the strains with the duplex pattern. The Southern blot analysis of 169 C. jejuni and C. coli isolates from poultry and from humans with DNA probe pMO2005 demonstrated that 78% of C. jejuni strains isolated from chickens hybridized with DNA probe pMO2005 with a characteristic 14.5- and 4.0-kb banding pattern and 22% hybridized with a single 18.5-kb fragment, whereas 71% of human isolates hybridized with the single 18.5-kb fragment and only 29% hybridized with 14.5- and 4.0-kb fragments. These findings suggest that only a small proportion of C. jejuni strains that colonize chickens may cause disease in humans.     

Yeast-specific DNA probes and their application for the detection of Candida albicans.

Two DNA fragments cloned from the genome of Candida albicans ATCC 10261 may be useful in the rapid diagnosis of disseminated candidosis. One sequence (probe EOB1) was specific for C. albicans (positive hybridisation with 45 strains tested). The second sequence (probe EOB2) detected C. albicans, as well as five other pathogenic Candida spp. and Saccharomyces cerevisiae, but did not react with human or bacterial DNA. Both probes were repetitive sequences in the genome of C. albicans. Probe EOB1 was used to detect, without DNA amplification, 500 C. albicans yeast cells in 1 ml of human blood.     

Restriction fragment length polymorphism of the DNA of typhus group rickettsiae.

The DNA of 10 strains of Rickettsia prowazekii, 5 strains of Rickettsia typhi and 1 strain of Rickettsia canada was investigated by restriction fragment length polymorphism analysis. Interspecies differences were characterized by a great number of noncomigrating bands. Using the endonuclease HindIII and PstI fragments comigration as a quantitative criterion, genetic similarity coefficient was calculated for the pair Rickettsia prowazekii/Rickettsia typhi-32.0%, for Rickettsia prowazekii/Rickettsia canada-22.7%, and for Rickettsia typhi/Rickettsia canada-23.5%. Intraspecies differences expressed are very subtle and concern 1-2 noncomigrating fragments. The investigated strains of Rickettsia prowazekii and Rickettsia typhi can be divided into 2 groups without any correlation to the source and period of isolation, or to strain passage history.     

Identification of restriction fragment length polymorphisms in DNA from Mycobacterium paratuberculosis.

DNAs from 34 mycobactin-dependent isolates of Mycobacterium paratuberculosis and 1 isolate of M. paratuberculosis 18 were digested with four restriction endonucleases. Southern hybridization experiments were performed with a 32P-labeled oligonucleotide DNA probe derived from the sequence of IS900, an insertion sequence present in 15 to 20 copies per M. paratuberculosis chromosome. The probe hybridized with DNA from each of the mycobactin-dependent isolates, and restriction fragment length polymorphisms were detected among the isolates with each restriction endonuclease used. Restriction fragment length polymorphism analysis may permit identification of various strains of M. paratuberculosis, which has not been possible with other techniques.     

Flow cytometric analysis of the DNA synthetic cycle of Candida species.

The total DNA per cell and DNA synthetic cycle phases were determined by flow cytometry in five Candida isolates including three species: Candida albicans 208R1, Candida tropicalis ATCC 750, and Candida parapsilosis 970, 3138, and ATCC 22019. The cells were prepared for flow cytometry by fixation in Carnoy fixative followed by staining with mithramycin. Marked but stable and reproducible inter- and intraspecific differences in total DNA per cell of stationary-phase cultures were found which did not correlate directly to diphenylamine estimates of the same parameter. This discrepancy was resolved by mathematically converting flow cytometry data into diphenylamine data. The reason for the discrepancy was found in studies of the DNA synthetic cycle of these yeasts: a large but isolate-specific variable proportion of the population is arrested in the S and G2-M phases after the culture passes from exponential to stationary phase. Histograms of exponential-growth-phase Candida isolates demonstrate that the majority of the population is in the G2-M phase of the DNA synthetic cycle. The DNA content of the C. tropicalis and C. parapsilosis isolates studied is as high as or higher than that of C. albicans. Extranuclear fluorescent particles were observed in the C. tropicalis isolate. No equivalent particles could be detected in the other four Candida isolates. The nature of the particles is unknown.     

Candida orthopsilosis and Candida metapsilosis spp. nov. to replace Candida parapsilosis groups II and III

Two new species, Candida orthopsilosis and C. metapsilosis, are proposed to replace the existing designations of C. parapsilosis groups II and III, respectively. The species C. parapsilosis is retained for group I isolates. Attempts to construct a multilocus sequence typing scheme to differentiate individual strains of C. parapsilosis instead revealed fixed DNA sequence differences between pairs of subgroups in four genes: COX3, L1A1, SADH, and SYA1. PCR amplicons for sequencing were obtained for these four plus a further seven genes from 21 group I isolates. For nine group II isolates, PCR products were obtained from only 5 of the 11 genes, and for two group III isolates PCR products were obtained from a different set of 5 genes. Three of the PCR products from group II and III isolates differed in size from the group I products. Cluster analysis of sequence polymorphisms from COX3, SADH, and SYA1, which were common to the three groups, consistently separated the isolates into three distinct sets. All of these differences, together with DNA sequence similarities <90% in the ITS1 sequence, suggest the subgroups should be afforded species status. The near absence of DNA sequence variability among isolates of C. parapsilosis and relatively high levels of sequence variability among isolates of C. orthopsilosis suggest that the former species may have evolved very recently from the latter.