Rapid simultaneous detection and identification of six species Candida using polymerase chain reaction and reverse line hybridization assay

The aim of this study was to develop and evaluate PCR based reverse line blot (RLB) hybridization assay for rapid detection of the most common Candida isolates from clinical specimens. A pair of universal primers targeting the ITS2 region of the gene from 28S rRNA to 5.8S rRNA was designed for PCR amplification of DNA from 6 Candida species (C. albicans, C. tropicalis, C. krusei, C. glabrata, C. parapsilosis, C. dubliniensis), the reverse primer was biotin labeled. PCR products, which were 302-441 bp length, were hybridized with 6 specific oligonucleotides probes immobilized on a nylon membrane. These 6 probes proved specific (they hybridized with only their target molecules). The assay was shown to be sensitive in detecting yeast to a concentration of 10 CFU/ml. This method was used to test 100 isolates and 200 vaginal swabs. The results agreed with those of culture for all but 3 of 100 isolates. Sequencing was performed on these 3 samples and confirmed that the culture results were inaccurate. Our results show the PCR-RLB positive rate (49%) is higher than culture (39%) and smear microscopic screening (27%) (P<0.05). In conclusion, the PCR/RLB developed in this study is specific and offers increased sensitivity compared to culture for the detection of Candida species in swab specimens. Moreover, the improved detection of cases of polycandidal candidiasis is advantageous.     

Detection of Candida species by polymerase chain reaction (PCR) in blood samples of experimentally infected mice and patients with suspected candidemia

In this study, we have established and evaluated a genus-specific polymerase chain reaction (PCR) and species-specific nested PCRs for the detection of Candida species in blood samples of neutropenic mice and patients suspected of candidemia. DNA segments of the gene encoding cytochrome P450 L1A1 were targeted for amplification by using genus and species-specific primers. As compared to the genus-specific PCR, the species-specific nested PCRs improved the sensitivity by 10 times with the detection limit < 10 yeast cells. Of the 18 blood samples tested daily over a period of 8 days following Candida albicans infection in neutropenic mice, four samples were positive by genus-specific PCR and 11 were positive by species-specific nested PCR. The PCR results were correlated with culture findings obtained on blood samples. Two of the three blood culture-positive samples were positive by genus-specific PCR and all the three with species-specific nested PCR. Among 15 mice, which were negative by blood culture but had C. albicans isolated from visceral organs, 2 and 8 mice yielded positive results by genus-specific PCR and species-specific nested PCR, respectively. Consistent with the results of the animal study, species-specific nested PCR yielded much higher positivity as compared to culture (52.2% versus 21.2%) in patients suspected for candidemia. Moreover, 8 specimens which were negative for Candida by genus-specific PCR became positive by species-specific nested PCR. No correlation was apparent between PCR positivity and Candida antigen titers. The results suggest that nested PCR is a sensitive technique for the detection of Candida species from blood samples, and thus it may have application in the diagnosis of suspected cases of candidemia and candidiasis.     

Nanodiagnostic Method for Colorimetric Detection of Mycobacterium tuberculosis 16S rRNA

A nanodiagnostic method using nucleic acid sequence-based amplification (NASBA) and gold nanoparticle probes (AuNP probes) was developed for colorimetric detection of Mycobacterium tuberculosis. The primers targeting 16S rRNA were used for the amplification of mycobacterial RNA by the isothermal NASBA process. The amplicons were hybridized with specific gold nanoparticle probes. The RNA–DNA hybrids were colorimetrically detected by the accumulation of gold nanoparticles. Using this method, 10 CFU ml^?1 of M. tuberculosis was detected within less than 1 h. Results obtained from the clinical specimens showed 94.7% and 96% sensitivity and specificity, respectively. No interference was encountered in the amplification and detection of M. tuberculosis in the presence of non-target bacteria, confirming the specificity of the method.     

Development of conventional and real-time NASBA for the detection of Legionella species in respiratory specimens

Isothermal nucleic acid sequence-based amplification (NASBA) was applied to detect Legionella 16S rRNA. The assay was originally developed as a Legionella pneumophila conventional NASBA assay with electrochemiluminescence (ECL) detection and was subsequently adapted to a L. pneumophila real-time NASBA format and a Legionella spp. real-time NASBA using molecular beacons. L. pneumophila RNA prepared from a plasmid construct was used to assess the analytical sensitivity of the assay. The sensitivity of the NASBA assay was 10 molecules of in vitro wild type L. pneumophila RNA and 0.1-1 colony-forming units (CFU) of L. pneumophila. In spiked respiratory specimens, the sensitivity of the NASBA assays was 1-10000 CFU of L. pneumophila serotype 1 depending on the background. After dilution of the nucleic acid extract prior to amplification, 1-10 CFU of L. pneumophila serotype 1 could be detected with both detection methods. Finally, 27 respiratory specimens, well characterized by culture and PCR, collected during a L. pneumophila outbreak, were tested by conventional and real-time NASBAs. All 11 PCR positive samples were positive by conventional NASBA, 9/11 and 10/11 were positive by L. pneumophila real-time NASBA and Legionella spp. real-time NASBA, respectively.     

Improvements of PCR-based identification targeting the DNA topoisomerase II gene to determine major species of the opportunistic fungi Candida and Aspergillus fumigatus

For the simple and rapid detection/identification of major pathogenic fungal species such as Candida albicans, C. tropicalis, C. parapsilosis, C. glabrata and Aspergillus fumigatus, common primers for these species and specific primers for each species, designed on the basis on the genomic nucleotide sequences of the DNA topoisomerase II genes, were prepared and tested for their specificities in PCR amplifications. Twelve specific primers were pooled and designated PsVI. Genomic DNAs were amplified by the common primer pair, and followed by PCR amplification using PsVI. Using PsVI, six unique DNA fragments, all of which corresponded to a Candida or A. fumigatus species, were specifically and acceptably amplified from each template DNA even in the presence of other DNAs. Similarly, the results of identification of clinical samples based on the PCR amplification coincided with those of conventional identification techniques. The sensitivities of the direct PCR and the nested PCR using PsVI were found to be 1,000 and 50 yeast cells, respectively.     

10年肠道真菌培养结果分析

目的探讨浙江大学医学院第一附属医院住院患者肠道真菌分离状况与趋势变化。方法回顾分析2000年1月1日至2009年12月30日10年间在该院送检的住院患者粪便标本的真菌分离率、真菌种类和年度变迁变化特点。结果 10年间从送检全部疑似肠道真菌感染的2 344份粪便标本中共检到真菌1 456株,归属5属19种,每年的检出率在55.7%67.0%。分离菌株中以白色念珠菌（74.0%）占首位,其次是光滑念珠菌（11.4%）,再次是热带念珠菌（7.1%）,光滑念珠菌和热带念珠菌分离率分别从2000年的4.9%、6.6%上升到2009年的16.8%、10.6%,呈上升趋势。结论该院10年间肠道真菌的分离率较高,白色念珠菌的分离率一直位于首位,非白色念珠菌的分离率处于上升趋势。     

Comparison between conventional methods, ChromAgar Candida® and PCR method for the identification of Candida species in clinical isolates

The increase in the incidence of yeast species causing fungemia in susceptible immunocompromised patients in the last two decades and the low sensitivity of conventional blood culture has led to the need to develop alternative approaches for the early detection and identification of causative species. The aim of this study was to compare the usefulness of molecular testing by the polymerase chain reaction (PCR) and conventional methods to identify clinical isolates of different species, using the ID32C ATB system (bioMérieux, France), chromogenic culture Chromagar Candida? (CHROMagar, France) and morphogenesis in corn meal agar. We studied 79 isolates, in which the most prevalent species using the system ID32C and PCR was C. albicans, followed by C. tropicalis, C. glabrata and C .krusei. PCR patterns obtained for the identification of clinical isolates were stable and consistent in the various independent studies and showed good reproducibility, concluding that PCR with species-specific primers that amplify genes ITS1 and ITS2 for rRNA or topoisomerase II primers is a very specific and sensitive method for the identification of C. glabrata, C. krusei, C. albicans, and with less specificity for C. tropicalis.     

Use of molecular biology methods for diagnosing fungal infections

A total of 130 various clinical materials taken from 48 children with suspected systemic fungal infection were used for the study. Clinical samples were tested by use of classical mycological procedures well as by use of molecular technique (PCR assay). The fragments of 125-bp (EO3) and 317 bp (HSP) specific for C. albicans were used for amplification. Fifty seven samples (48%) were positive for Candida albicans and eighty four (68%) by use of PCR. It should be stressed that 4 blood samples, 21 urine samples and 5 other samples were positive by use of molecular technique, only. PCR is sensitive and rapid method for detection and identification of Candida albicans from clinical materials of children with fungal infection. This technique can be applied for monitoring presence of fungal DNA in tested samples during antifungal therapy.     

Cytodiagnosis of Candida organisms in cervical smears

Cervical smears and cervical scrapings cultured on Sabouraud agar from 31 women suspected of having Candida genital infections were examined in a study of the cytomorphology of this fungal infection in cervical smears. Of the 31 samples, 20 (64.5%) grew C. albicans in culture. One sample (3.2%) grew C. paratropicalis, 2 (6.4%) grew mixed C. albicans and Torulopsis glabrata and 2 (6.4%) grew T. glabrata alone. Of the 25 fungus-positive samples, 20 (80%) had fungus-positive cervical smears and 5 (20%) had fungus-negative smears. There was no instance in which the cervical smear was positive but the culture was negative. Among the cases positive for C. albicans, organisms occurred in two forms: pseudohyphae without blastospores (29.4%) and pseudohyphae with blastospores (70.6%). T. glabrata was present in the smears as budding and nonbudding yeasts. Although the sensitivity of the cervical smear in detecting fungus in culture-positive patients was only 80%, the cervical smear can still be a useful means of rapid identification of C. albicans when blastospores and pseudomycelium are present. The presence of budding or nonbudding yeast without pseudohyphae should strongly suggest a T. glabrata infection.     

Candida glabrata, Candida parapsilosis and Candida tropicalis: biology, epidemiology, pathogenicity and antifungal resistance

The incidence of infections caused by Candida species (candidosis) has increased considerably over the past three decades, mainly due to the rise of the AIDS epidemic, an increasingly aged population, higher numbers of immunocompromised patients and the more widespread use of indwelling medical devices. Candida albicans is the main cause of candidosis; however, non-C. albicans Candida (NCAC) species such as Candida glabrata, Candida tropicalis and Candida parapsilosis are now frequently identified as human pathogens. The apparent increased emergence of these species as human pathogens can be attributed to improved identification methods and also associated with the degree of diseases of the patients, the interventions that they were subjected and the drugs used. Candida pathogenicity is facilitated by a number of virulence factors, most importantly adherence to host surfaces including medical devices, biofilm formation and secretion of hydrolytic enzymes (e.g. proteases, phospholipases and haemolysins). Furthermore, despite extensive research to identify pathogenic factors in fungi, particularly in C. albicans, relatively little is known about NCAC species. This review provides information on the current state of knowledge on the biology, identification, epidemiology, pathogenicity and antifungal resistance of C. glabrata, C. parapsilosis and C. tropicalis.     

Distribution and susceptibility of Candida species isolated in the Medical University of Debrecen

Data of Candida albicans and non-albicans Candida species isolated during the 1997-2000 period in the Medical and Health Science Center of the University of Debrecen are analysed. The number of yeast isolates increased from 408 to 1213 per year during this period. Dominance of C. albicans has been persistent, but a slight increase of C. glabrata and C. krusei could be observed. Distribution of different Candida species isolated from 16 body sites indicates that C. albicans seems to be still the most aggressive Candida species. Investigation of 244 urinary Candida isolates (parallel with bacterial cultures) suggests that tha aetiological role of Candida species in the pathogenesis of urinary tract infections can be hypothesized if colony forming unit (CFU) number of yeasts is higher than 10(4)/ml and bacteria are present in low CFU number or are absent. Antifungal susceptibility testing of C. albicans, C. glabrata, C. tropicalis and C. krusei against Flucytosine, Amphotericin-B, Miconazole, Ketoconazole and Fluconazole suggests that Amphotericin-B is still the most effective antifungal agent. Finally, the problems in judging the aetiological role of isolated Candida species in the pathogenesis of different types of diseases are critically discussed.     

Rapid identification of Candida species by using nuclear magnetic resonance spectroscopy and a statistical classification strategy

Nuclear magnetic resonance (NMR) spectra were acquired from suspensions of clinically important yeast species of the genus Candida to characterize the relationship between metabolite profiles and species identification. Major metabolites were identified by using two-dimensional correlation NMR spectroscopy. One-dimensional proton NMR spectra were analyzed by using a staged statistical classification strategy. Analysis of NMR spectra from 442 isolates of Candida albicans, C. glabrata, C. krusei, C. parapsilosis, and C. tropicalis resulted in rapid, accurate identification when compared with conventional and DNA-based identification. Spectral regions used for the classification of the five yeast species revealed species-specific differences in relative amounts of lipids, trehalose, polyols, and other metabolites. Isolates of C. parapsilosis and C. glabrata with unusual PCR fingerprinting patterns also generated atypical NMR spectra, suggesting the possibility of intraspecies discontinuity. We conclude that NMR spectroscopy combined with a statistical classification strategy is a rapid, nondestructive, and potentially valuable method for identification and chemotaxonomic characterization that may be broadly applicable to fungi and other microorganisms.     

Application of a unique server-based oligonucleotide probe selection tool toward a novel biosensor for the detection of Streptococcus pyogenes

We developed a software program for the rapid selection of detection probes to be used in nucleic acid-based assays. In comparison to commercially available software packages, our program allows the addition of oligotags as required by nucleic acid sequence-based amplification (NASBA) as well as automatic BLAST searches for all probe/primer pairs. We then demonstrated the usefulness of the program by designing a novel lateral flow biosensor for Streptococcus pyogenes that does not rely on amplification methods such as the polymerase chain reaction (PCR) or NASBA to obtain low limits of detection, but instead uses multiple reporter and capture probes per target sequence and an instantaneous amplification via dye-encapsulating liposomes. These assays will decrease the detection time to just a 20 min hybridization reaction and avoid costly enzymatic gene amplification reactions. The lateral flow assay was developed quantifying the 16S rRNA from S. pyogenes by designing reporter and capture probes that specifically hybridize with the RNA and form a sandwich. DNA reporter probes were tagged with dye-encapsulating liposomes, biotinylated DNA oligonucleotides were used as capture probes. From the initial number of capture and reporter probes chosen, a combination of two capture and three reporter probes were found to provide optimal signal generation and significant enhancement over single capture/reporter probe combinations. The selectivity of the biosensor was proven by analyzing organisms closely related to S. pyogenes, such as other Streptococcus and Enterococcus species. All probes had been selected by the software program within minutes and no iterative optimization and re-design of the oligonucleotides was required which enabled a very rapid biosensor prototyping. While the sensitivity obtained with the biosensor was only 135 ng, future experiments will decrease this significantly by the addition of more reporter and capture probes for either the same rRNA or a different nucleic acid target molecule. This will lead to the possibility of detecting S. pyogenes with a rugged assay that does not require a cell culturing or gene amplification step and will therefore enable rapid, specific and sensitive onsite testing.     

Molecular typing of Candida spp. by random amplification of polymorphic DNA and analysis of restriction fragment length polymorphism of ribosomal DNA repeats

Random amplification of polymorphic DNA (RAPD) using an arbitrary oligonucleotide primer (5'-CGGTGCGACG) and analysis of restriction fragment length polymorphism of ribosomal DNA (rDNA-RFLP) after digestion of genomic DNA with restriction endonuclease EcoRI were investigated as tools for genotypic delineation beyond the species level of 91 Candida clinical isolates and four reference strains including 33 Candida albicans, 19 Candida tropicalis, 22 Candida krusei and 21 Candida (Torulopsis) glabrata. Results indicated that both techniques can be useful for typing isolates of the above species, although showing a variable discriminative potential with different species. As compared to RAPD fingerprinting, the discriminative potential of rDNA-RFLP appeared to be highest for C. albicans and lowest for C. glabrata, being overall similar for C. krusei and identical for C. tropicalis. A comparative analysis of the results obtained with the two typing techniques showed that, except for C. tropicalis, they were able to provide non-redundant information, and that their use in combination could enhance the discriminative potential for delineation among C. glabrata and C. krusei isolates.     

DNA probes for the rapid identification of medically important Candida species using a multianalyte profiling system

Recently, a new flow cytometric technology to detect multiple DNA target sequences in a single microtiter well plate was developed [multianalyte profiling (MAP) System, Luminex Corp., Austin, TX]. DNA probes, directed to the internal transcribed spacer 2 region of ribosomal DNA, were therefore designed to detect and differentiate PCR amplicons from six medically important Candida species using this system. Each probe was covalently linked to one of 100 available microsphere (bead) sets. Biotinylated PCR amplicons were then hybridized to the complementary probe on each bead set. Bound amplicons were detected fluorometrically using a streptavidin-linked reporter dye, R-phycoerythrin. Specific hybridization was noted for all six Candida species probes (mean sample-to-background ratio+/-standard error: Candida albicans, 58.7+/-1.2; Candida tropicalis, 53.2+/-3.8; Candida glabrata, 46.9+/-2.1; Candida parapsilosis, 59.9+/-1.6; Candida krusei, 54.7+/-3.7 vs. 0.9+/-0.03 for all heterologous Candida species DNA targets and vs. 1.0+/-0.1 for samples containing water instead of DNA; P < 0.001). The limit of test sensitivity was 0.5 pg of DNA. A sample could be processed and analyzed within 1 h post-PCR amplification. Therefore, the multianalyte profiling system was rapid, sensitive and specific for the detection and differentiation of the most medically important species of Candida.     

医院内深部真菌感染分布及耐药性分析

目的探讨大连医科大学附属第一医院深部真菌感染的常见菌种,临床病区分布及其耐药性。方法对2008年1月1日至2008年12月31日749例住院患者深部真菌感染进行分析。结果常见菌种为白色假丝酵母菌,热带假丝酵母菌,近平滑假丝酵母菌,克柔假丝酵母菌,光滑球拟酵母菌。主要病区为ICU。从标本的来源看,痰标本中真菌检出率最高,占61.1%。两性霉素B抗菌作用最强,耐药率只有3.6%。结论医院内深部真菌感染分布广泛,非白色假丝酵母菌感染明显增多,耐药菌株增多,部分治疗需联合用药。     

Yeast-like fungi as etiologic agents of blood infections in patients hospitalized in 1998-1999

The aim of the study was the analysis of frequency of yeast-like fungi as etiological agents of fungemias in patients hospitalized in operative and conservative wards of Medical Academy Central Clinical Hospital in Warsaw in 1998-1999. Peripheral blood samples and collected from vascular catheters were incubated in BacT/Alert system(Organon Teknika, USA). Positive blood samples were inoculated on Sabouraud medium with chloramphenicol (bioMerieux, France) (the time of cultivation from 48 h to 7 days at 30 C) and on chromogenic medium BBL CHROMagar Candida (Becton Dickinson, USA). Fungal strains were identified by standard mycological procedures using ID 32 C strips (ATB system, bioMerieux, France) and tests of Sanofi Diagnostics Pasteur (France). The total number of positive blood cultures was 1724. Fifty eight fungal strains were isolated from blood samples (3.36%). Strains belonged to 4 genera: Candida (55), Trichosporon (1), Saccharomyces (1) and Pichia (1). Thirty eight fungal strains were isolated from peripheral blood samples. Forty seven fungal strains were cultured from patients hospitalized in operative wards. Among fungi isolated from peripheral blood samples C. albicans (10), C. glabrata (9) and C. parapsilosis (5) strains dominated. From blood samples collected from vascular catheters most often C. albicans (7), C. glabrata (4) and C. parapsilosis (3) were isolated.     

Candidemia at selected Canadian sites: results from the Fungal Disease Registry, 1992-1994

BACKGROUND: Candida species are important bloodstream pathogens that are being isolated with increasing frequency. Despite the availability of effective antifungal therapy, the mortality rate associated with Candida infection remains high. With the objective of describing the epidemiology of candidemia, the Canadian Infectious Disease Society conducted a study of candidemia in Canada. METHODS: Fourteen medical centres across Canada identified all patients with candidemia from March 1992 to February 1994 through blood culture surveillance for Candida spp. Patient-related data for invasive fungal infection were compiled retrospectively by chart review using a standardized data-recording form developed for the Fungal Disease Registry of the Canadian Infectious Disease Society. Cases of Candidemia were studied in relation to underlying medical conditions, predisposing factors, concurrent infection, antimicrobial agents, antifungal treatment and deaths. RESULTS: In total, 415 cases of candidemia were identified, 48 (11.6%) in children and 367 (88.4%) in adults. The causative pathogens were C. albicans in 286 cases (68.9%), C. parapsilosis in 43 (10.4%), C. glabrata in 34 (8.2%), C. tropicalis in 27 (6.5%) and other Candida species in 18 (4.3%); polymicrobial candidemia occurred in 7 cases (1.7%). The overall mortality rate was 46%, and the rate of deaths clinically related to candidemia was 19%. However, only 13 (27%) of the children died. A univariate analysis indicated that significant risk factors for death were age greater than 60 years, therapy for concomitant bacterial infection, stay in an intensive care unit, concurrent malignant disease, cytotoxic chemotherapy and granulocytopenia, although only age and stay in an intensive care unit emerged as significant risk factors in the multivariate analysis. After adjustment for other predictors of death, only infection with C. parapsilosis was associated with a lower mortality rate than infection with C. albicans. Treatment was given in 352 (84.8%) of cases. Amphotericin B was the preferred agent in 244 cases (69.3% of those treated); fluconazole was used in 101 cases (28.7%) and ketoconazole in 5 cases (1.4%). INTERPRETATION: Candidemia in Canada is caused predominantly by C. albicans. The mortality rate associated with candidemia is high, but it varies with the species of Candida and is lower in children than in adults. Age greater than 60 years and stay in an intensive care unit were the most significant risk factors for overall mortality.     

Rapid identification of Candida glabrata using a new commercial kit

Candida glabrata is an emergent pathogen with diminished susceptibility to azoles, thus a rapid identification of this yeast could be of help to choose the appropriate treatment. GLABRATA RTT (Fumouze Diagnostics, France) is a new C. glabrata identification test. To evaluate its utility in the clinical laboratory daily routine, we prospectively tested 168 yeasts isolated in our hospital. GLABRATA RTT results had a sensitivity of 98.4% and a specificity of 100%. The combination of CHROMagar Candida isolation medium and GLABRATA RTT test allowed the identification of the four most common species in the clinical practice (Candida albicans, Candida tropicalis, Candida krusei and C. glabrata).     

Evolutionary relationships among pathogenic Candida species and relatives.

Small subunit rRNA sequences have been determined for 10 of the most clinically important pathogenic species of the yeast genus Candida (including Torulopsis [Candida] glabrata and Yarrowia [Candida] lipolytica) and for Hansenula polymorpha. Phylogenetic analyses of these sequences and those of Saccharomyces cerevisiae, Kluyveromyces marxianus var. lactis, and Aspergillus fumigatus indicate that Candida albicans, C. tropicalis, C. parapsilosis, and C. viswanathii form a subgroup within the genus. The remaining significant pathogen, T. glabrata, falls into a second, distinct subgroup and is specifically related to S. cerevisiae and more distantly related to C. kefyr (psuedotropicalis) and K. marxianus var. lactis. The 18S rRNA sequence of Y. lipolytica has evolved rapidly in relation to the other Candida sequences examined and appears to be only distantly related to them. As anticipated, species of several other genera appear to bear specific relationships to members of the genus Candida.