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Fidler G, Leiter E, Kocsube S, Biro S, Paholcsek M. Validation of a simplex PCR assay enabling reliable identification of clinically relevant Candida species. BMC Infect Dis 2018; 18:393. [PMID: 30103686 PMCID: PMC6090785 DOI: 10.1186/s12879-018-3283-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 07/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fungal bloodstream infections (BSI) may be serious and are associated with drastic rise in mortality and health care costs. Candida spp. are the predominant etiological agent of fungal sepsis. The prompt and species-level identification of Candida may influence patient outcome and survival. The aim of this study was to develop and evaluate the CanTub-simplex PCR assay coupled with Tm calling and subsequent high resolution melting (HRM) analysis to barcode seven clinically relevant Candida species. METHODS Efficiency, coefficient of correlation and the limit of reliable detection were estimated on purified Candida EDTA-whole blood (WB) reference panels seeded with Candida albicans, Candida glabrata, Candida parapsilosis, Candida tropicalis, Candida krusei, Candida guilliermondii, Candida dubliniensis cells in a 6-log range. Discriminatory power was measured on EDTA-WB clinical panels on three different PCR platforms; LightCycler®96, LightCycler® Nano, LightCycler® 2.0. Inter- and intra assay consistencies were also calculated. RESULTS The limit of reliable detection proved to be 0.2-2 genomic equivalent and the method was reliable on broad concentration ranges (106-10 CFU) providing distinctive melting peaks and characteristic HRM curves. The diagnostic accuracy of the discrimination proved to be the best on Roche LightCycler®2.0 platform. Repeatability was tested and proved to be % C.V.: 0.14 ± 0.06 on reference- and % C.V.: 0.14 ± 0.02 on clinical-plates accounting for a very high accuracy. Reproducibility was % C.V.: 0.11 between reference- and % C.V.: 0.12between clinical-panels which is highly acceptable. CONCLUSION Our assay demonstrates recent advances on Tm calling and HRM analysis for the molecular identification of relevant Candida species. This unique, simplex PCR assay may be capable to outperform conventional phenotypic methods by reducing time and providing accurate and reliable results directly from blood (2 h) or from whole blood culture bottles (12-24 h).
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Affiliation(s)
- Gabor Fidler
- Faculty of Medicine, Department of Human Genetics, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - Eva Leiter
- Faculty of Science and Technology, Department of Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
| | - Sandor Kocsube
- Faculty of Science and Informatics, Department of Microbiology, University of Szeged, Szeged, Hungary
| | - Sandor Biro
- Faculty of Medicine, Department of Human Genetics, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - Melinda Paholcsek
- Faculty of Medicine, Department of Human Genetics, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary.
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Freire AKL, dos Santos Bentes A, de Lima Sampaio I, Matsuura ABJ, Ogusku MM, Salem JI, Wanke B, de Souza JVB. Molecular characterisation of the causative agents of Cryptococcosis in patients of a tertiary healthcare facility in the state of Amazonas-Brazil. Mycoses 2012; 55:e145-50. [DOI: 10.1111/j.1439-0507.2012.02173.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Silveira-Gomes F, Sarmento DN, Espírito-Santo EPTD, Souza NDO, Pinto TM, Marques-da-Silva SH. Differentiation between Candida albicans and Candida dubliniensis using hypertonic Sabouraud broth and tobacco agar. Rev Soc Bras Med Trop 2011; 44:457-60. [PMID: 21860890 DOI: 10.1590/s0037-86822011000400011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 04/28/2011] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION Opportunistic fungal infections in immunocompromised hosts are caused by Candida species, and the majority of such infections are due to Candida albicans. However, the emerging pathogen Candida dubliniensis demonstrates several phenotypic characteristics in common with C. albicans, such as production of germ tubes and chlamydospores, calling attention to the development of stable resistance to fluconazole in vitro. The aim of this study was to evaluate the performance of biochemistry identification in the differentiating between C. albicans and C. dubliniensis, by phenotyping of yeast identified as C. albicans. METHODS Seventy-nine isolates identified as C. albicans by the API system ID 32C were grown on Sabouraud dextrose agar at 30°C for 24-48h and then inoculated on hypertonic Sabouraud broth and tobacco agar. RESULTS Our results showed that 17 (21.5%) isolates were growth-inhibited on hypertonic Sabouraud broth, a phenotypic trait inconsistent with C. albicans in this medium. However, the results observed on tobacco agar showed that only 9 (11.4%) of the growth-inhibited isolates produced characteristic colonies of C. dubliniensis (rough colonies, yellowish-brown with abundant fragments of hyphae and chlamydospores). CONCLUSIONS The results suggest that this method is a simple tool for screening C. albicans and non-albicans yeast and for verification of automated identification.
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Affiliation(s)
- Fabíola Silveira-Gomes
- Programa de Pós-Graduação em Biologia de Agentes Infecciosos e Parasitários, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brasil
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Santos M, Souza E, Junior R, Talhari S, Souza J. Identification of fungemia agents using the polymerase chain reaction and restriction fragment length polymorphism analysis. Braz J Med Biol Res 2010; 43:712-6. [DOI: 10.1590/s0100-879x2010007500065] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 07/06/2010] [Indexed: 11/22/2022] Open
Affiliation(s)
- M.S. Santos
- Fundação de Medicina Tropical do Amazonas, Brasil
| | - E.S. Souza
- Fundação de Medicina Tropical do Amazonas, Brasil
| | | | - S. Talhari
- Fundação de Medicina Tropical do Amazonas, Brasil
| | - J.V.B. Souza
- Fundação de Medicina Tropical do Amazonas, Brasil; Instituto Nacional de Pesquisas da Amazônia, Brasil
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Ferdin J, Cerar T, Strle F, Ruzić-Sabljić E. Evaluation of real-time PCR targeting hbb gene for Borrelia species identification. J Microbiol Methods 2010; 82:115-9. [PMID: 20451566 DOI: 10.1016/j.mimet.2010.04.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Revised: 04/08/2010] [Accepted: 04/22/2010] [Indexed: 11/30/2022]
Abstract
Several molecular methods have been employed for Borrelia species identification. Newly developed technology, real-time polymerase chain reaction (RT-PCR), combines simultaneous amplification, detection and differentiation of strains in one PCR run. The aim of the study was to perform and evaluate RT-PCR for Borreliaburgdorferi sensu lato species identification. Borrelia species identification was accomplished on 374 Borrelia strains using two approaches: 1.) MluI restriction of entire borrelial chromosome (MluI-large restriction fragment patterns, LRFP), and 2.) RT-PCR targeting hbb gene and specific melting temperature (Tm) detection. The results of the two molecular methods were compared. With MluI-RFLP we were able to differentiate all Borrelia species and their subtypes within particular species. RT-PCR based on Tm determination identified unique strains within the species Borreliaafzelii (Tm 66.11 degrees C), B. burgdorferi sensu stricto (Tm 68.18 degrees C), Borreliaspielmanii (Tm 59.45 degrees C) and Borreliavalaisiana (Tm 59.62 degrees C). We were not able to distinguish the last two species that shared almost identical Tm. The large majority of Borreliagarinii strains shared Tm 51.42 degrees C, while subtype Mlg4 was characterized by Tm 56.87 degrees C. Strains of Borrelialusitaniae species also were heterogeneous; human isolate had Tm 63.47 degrees C while two tick isolates shared Tm 61.77 degrees C. Differences inside hbb gene enabled differentiation of the majority of Borrelia species, and revealed two clusters within B. garinii and B. lusitaniae species, respectively, but it was not possible to distinguish B. spielmanii form B. valaisiana. The major advantage of RT-PCR was that it was easy to perform and that the results were obtained within a few hours.
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Affiliation(s)
- Jana Ferdin
- Institute of Microbiology and Immunology, University of Ljubljana, Zaloska , 1000 Ljubljana, Slovenia
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Lau A, Chen S, Sleiman S, Sorrell T. Current status and future perspectives on molecular and serological methods in diagnostic mycology. Future Microbiol 2009; 4:1185-222. [DOI: 10.2217/fmb.09.70] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Invasive fungal infections are an important cause of infectious morbidity. Nonculture-based methods are increasingly used for rapid, accurate diagnosis to improve patient outcomes. New and existing DNA amplification platforms have high sensitivity and specificity for direct detection and identification of fungi in clinical specimens. Since laboratories are increasingly reliant on DNA sequencing for fungal identification, measures to improve sequence interpretation should support validation of reference isolates and quality control in public gene repositories. Novel technologies (e.g., isothermal and PNA FISH methods), platforms enabling high-throughput analyses (e.g., DNA microarrays and Luminex® xMAP™) and/or commercial PCR assays warrant further evaluation for routine diagnostic use. Notwithstanding the advantages of molecular tests, serological assays remain clinically useful for patient management. The serum Aspergillus galactomannan test has been incorporated into diagnostic algorithms of invasive aspergillosis. Both the galactomannan and the serum β-D-glucan test have value for diagnosing infection and monitoring therapeutic response.
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Affiliation(s)
- Anna Lau
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia
| | - Sharon Chen
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia and Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Sue Sleiman
- Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Tania Sorrell
- Centre for Infectious Diseases & Microbiology, Westmead Hospital, Darcy and Hawkesbury Roads, Westmead, NSW 2145, Australia
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Bergman A, Fernandez V, Holmström KO, Claesson BEB, Enroth H. Rapid identification of pathogenic yeast isolates by real-time PCR and two-dimensional melting-point analysis. Eur J Clin Microbiol Infect Dis 2007; 26:813-8. [PMID: 17680284 DOI: 10.1007/s10096-007-0369-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
There is a need in the clinical microbiological laboratory for rapid and reliable methods for the universal identification of fungal pathogens. Two different regions of the rDNA gene complex, the highly polymorphic ITS1 and ITS2, were amplified using primers targeting conserved regions of the 18S, 5.8S and 28S genes. After melting-point analysis of the amplified products, the T(m) of the two PCR-products were plotted into a spot diagram where all the 14 tested, clinically relevant yeasts separated with good resolution. Real-time amplification of two separate genes, melting-point analysis and two-dimensional plotting of T(m) data can be used as a broad-range method for the identification of clinical isolates of pathogenic yeast such as Candida and Cryptococcus spp.
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Affiliation(s)
- A Bergman
- Department of Clinical Microbiology, Capio Diagnostik AB, Kärnsjukhuset, Skövde, Sweden.
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Somogyvari F, Doczi I, Serly J, Ahmad S, Nagy E. Rapid discrimination between Candida albicans and Candida dubliniensis by using real-time polymerase chain reaction. Diagn Microbiol Infect Dis 2007; 58:367-9. [PMID: 17376634 DOI: 10.1016/j.diagmicrobio.2007.01.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Revised: 01/15/2007] [Accepted: 01/23/2007] [Indexed: 11/28/2022]
Abstract
Several phenotypic methods have been used for the differentiation of Candida albicans and Candida dubliniensis, but molecular investigations are considered most reliable in their diagnostic value. Here, we suggest a rapid real-time polymerase chain reaction assay where the discrimination was achieved through melting point analysis with the help of the nonspecific fluorescent dye SybrGreen.
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Affiliation(s)
- Ferenc Somogyvari
- Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Szeged 6725, Hungary.
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Alves SH, de Loreto ES, Linares CE, Silveira CP, Scheid LA, Pereira DIB, Santuario JM. Comparison among tomato juice agar with other three media for differentiation of Candida dubliniensis from Candida albicans. Rev Inst Med Trop Sao Paulo 2006; 48:119-21. [PMID: 16847498 DOI: 10.1590/s0036-46652006000300001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The purpose of the present study is to compare the tomato juice agar, a well known medium employed to observe ascospore formation, with niger seed agar, casein agar and sunflower seed agar, applied to a differentiation between C. dubliniensis and C. albicans. After 48 hours of incubation at 30 ºC all 26 (100%) C. dubliniensis isolates tested produced chlamydospores on tomato juice agar as well as in the other three media evaluated. However, when we inoculated all media with C. albicans, the absence of chlamydospores became resulting in the following percents: tomato juice agar (92.47%), niger seed agar (96.7%), casein agar (91.39%), and sunflower seed agar (96.7%). These results indicate that tomato juice agar is another medium which can also be used in the first phenotypic differentiation between C. dubliniensis and C. albicans.
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Affiliation(s)
- Sydney Hartz Alves
- Universidade Federal de Santa Maria, Rua Andradas 1985/201, 97010-033 Santa Maria, RS, Brasil.
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Rakeman JL, Bui U, Lafe K, Chen YC, Honeycutt RJ, Cookson BT. Multilocus DNA sequence comparisons rapidly identify pathogenic molds. J Clin Microbiol 2005; 43:3324-33. [PMID: 16000456 PMCID: PMC1169180 DOI: 10.1128/jcm.43.7.3324-3333.2005] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The increasing incidence of opportunistic fungal infections necessitates rapid and accurate identification of the associated fungi to facilitate optimal patient treatment. Traditional phenotype-based identification methods utilized in clinical laboratories rely on the production and recognition of reproductive structures, making identification difficult or impossible when these structures are not observed. We hypothesized that DNA sequence analysis of multiple loci is useful for rapidly identifying medically important molds. Our study included the analysis of the D1/D2 hypervariable region of the 28S ribosomal gene and the internal transcribed spacer (ITS) regions 1 and 2 of the rRNA operon. Two hundred one strains, including 143 clinical isolates and 58 reference and type strains, representing 43 recognized species and one possible new species, were examined. We generated a phenotypically validated database of 118 diagnostic alleles. DNA length polymorphisms detected among ITS1 and ITS2 PCR products can differentiate 20 of 33 species of molds tested, and ITS DNA sequence analysis permits identification of all species tested. For 42 of 44 species tested, conspecific strains displayed >99% sequence identity at ITS1 and ITS2; sequevars were detected in two species. For all 44 species, identifications by genotypic and traditional phenotypic methods were 100% concordant. Because dendrograms based on ITS sequence analysis are similar in topology to 28S-based trees, we conclude that ITS sequences provide phylogenetically valid information and can be utilized to identify clinically important molds. Additionally, this phenotypically validated database of ITS sequences will be useful for identifying new species of pathogenic molds.
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Affiliation(s)
- Jennifer L Rakeman
- Department of Laboratory Medicine, University of Washington, Box 357110, Seattle, WA 98195, USA
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11
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De Baere T, Van Keerberghen A, Van Hauwe P, De Beenhouwer H, Boel A, Verschraegen G, Claeys G, Vaneechoutte M. An interlaboratory comparison of ITS2-PCR for the identification of yeasts, using the ABI Prism 310 and CEQ8000 capillary electrophoresis systems. BMC Microbiol 2005; 5:14. [PMID: 15774019 PMCID: PMC1082908 DOI: 10.1186/1471-2180-5-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2004] [Accepted: 03/18/2005] [Indexed: 11/11/2022] Open
Abstract
Background Currently, most laboratories identify yeasts routinely on the basis of morphology and biochemical reactivity. This approach has quite often limited discriminatory power and may require long incubation periods. Due to the increase of fungal infections and due to specific antifungal resistence patterns for different species, accurate and rapid identification has become more important. Several molecular techniques have been described for fast and reliable identification of yeast isolates, but interlaboratory exchangeability of identification schemes of molecular techniques has hardly been studied. Here, we compared amplified ITS2 fragment length determination by an ABI Prism 310 (Applied Biosystems, Foster City, Ca.) capillary electrophoresis system with that obtained by a CEQ8000 (Beckman Coulter, Fullerton, Ca.) capillary electrophoresis system. Results Although ITS2 size estimations on both systems differed and separate libraries had to be constructed for each system, both approaches had the same discriminatory power with regard to the 44 reference strains, identical identifications were obtained for 39/ 40 clinical isolates in both laboratories and strains from 51 samples were correctly identified using CEQ8000, when compared to phenotypic identification. Conclusion Identification of yeasts with ITS2-PCR followed by fragment analysis can be carried out on different capillary electrophoresis systems with comparable discriminatory power.
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Affiliation(s)
- Thierry De Baere
- Department of Clinical Chemistry, Microbiology and Immunology, University Hospital Ghent, Belgium
| | | | - Peter Van Hauwe
- Laboratory Microbiology, Onze Lieve Vrouw Ziekenhuis, Aalst, Belgium
| | | | - An Boel
- Laboratory Microbiology, Onze Lieve Vrouw Ziekenhuis, Aalst, Belgium
| | - Gerda Verschraegen
- Department of Clinical Chemistry, Microbiology and Immunology, University Hospital Ghent, Belgium
| | - Geert Claeys
- Department of Clinical Chemistry, Microbiology and Immunology, University Hospital Ghent, Belgium
| | - Mario Vaneechoutte
- Department of Clinical Chemistry, Microbiology and Immunology, University Hospital Ghent, Belgium
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Gutzmer R, Mommert S, Küttler U, Werfel T, Kapp A. Rapid identification and differentiation of fungal DNA in dermatological specimens by LightCycler PCR. J Med Microbiol 2004; 53:1207-1214. [PMID: 15585499 DOI: 10.1099/jmm.0.45779-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aim was to develop a LightCycler PCR method for the rapid detection and differentiation of fungal DNA in dermatological specimens such as skin scales and skin swabs. LightCycler PCR assays were established for seven primer sets specific for fungal DNA. For each primer set LightCycler melting points were defined by amplification of DNA from 21 fungi and sensitivity was determined by amplification of serial dilutions of fungal DNA. A protocol was established that allows detection and differentiation of mould and yeast DNA with one highly sensitive PCR reaction by assessment of LightCycler melting points. Two subsequent LightCycler PCR reactions and one RFLP reaction allowed the differentiation of dermatophytes and non-dermatophyte moulds and the subclassification of yeasts. Analysis of clinical samples from 38 patients with fungal skin diseases provided conclusive new diagnostic information in 9/38 cases (23.7 %) by this PCR protocol that was not equally provided by direct microscopy and mycological culture. Thus the LightCycler PCR protocol established here represents a rapid diagnostic tool that aids in the diagnosis of fungal skin disease in a substantial number of patients.
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Affiliation(s)
- Ralf Gutzmer
- Department of Dermatology and Allergology, Hannover Medical University, Ricklinger Str. 5, D-30449 Hannover, Germany
| | - Susanne Mommert
- Department of Dermatology and Allergology, Hannover Medical University, Ricklinger Str. 5, D-30449 Hannover, Germany
| | - Uta Küttler
- Department of Dermatology and Allergology, Hannover Medical University, Ricklinger Str. 5, D-30449 Hannover, Germany
| | - Thomas Werfel
- Department of Dermatology and Allergology, Hannover Medical University, Ricklinger Str. 5, D-30449 Hannover, Germany
| | - Alexander Kapp
- Department of Dermatology and Allergology, Hannover Medical University, Ricklinger Str. 5, D-30449 Hannover, Germany
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Frade JP, Warnock DW, Arthington-Skaggs BA. Rapid quantification of drug resistance gene expression in Candida albicans by reverse transcriptase LightCycler PCR and fluorescent probe hybridization. J Clin Microbiol 2004; 42:2085-93. [PMID: 15131174 PMCID: PMC404661 DOI: 10.1128/jcm.42.5.2085-2093.2004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We developed a rapid, sensitive, and reproducible assay to quantify Candida albicans ACT1, CDR1, CDR2, ERG11, and MDR1 mRNA using a two-step reverse transcription and LightCycler real-time PCR (RT-LightCycler PCR) method with sequence-specific hybridization probes. We compared RT-LightCycler PCR with Northern hybridization for quantitative analysis of gene expression in isolates with various fluconazole susceptibilities. Specificity of each LightCycler PCR was verified by LightCycler melting curve analysis and agarose gel electrophoresis of amplified products. Correlation of quantification results between RT-LightCycler PCR and Northern hybridization yielded correlation coefficients of > or = 0.91 for all genes except MDR1 (0.74). In this case, reduced correlation was due to the inability of Northern hybridization to accurately quantify the high MDR1 expression in a susceptible dose-dependent isolate which was shown by RT-LightCycler PCR to overexpress MDR1 >200-fold relative to the other isolates tested. In four isolates, low levels of CDR2 mRNA were detected by RT-LightCycler PCR but were undetectable by Northern hybridization. mRNA quantification by RT-LightCycler PCR correlates with Northern hybridization and offers additional advantages, including increased sensitivity and speed of analysis, along with lower RNA concentration requirements and an increased dynamic range of signal detection.
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Affiliation(s)
- Joao P Frade
- Department of Microbiology, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
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Graf B, Trost A, Eucker J, Göbel UB, Adam T. Rapid and simple differentiation of C. dubliniensis from C. albicans. Diagn Microbiol Infect Dis 2004; 48:149-51. [PMID: 14972386 DOI: 10.1016/j.diagmicrobio.2003.09.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2003] [Revised: 08/21/2003] [Indexed: 11/24/2022]
Abstract
Differentiation of Candida dubliniensis from C. albicans using biochemical methods is time consuming and may be difficult to achieve because of ambiguous results. Here, we describe a simple, rapid and inexpensive method for unequivocal differentiation of C. dubliniensis from C. albicans using polymerase chain reaction (PCR)/RFLP.
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Affiliation(s)
- Barbara Graf
- Institute for Microbiology and Hygiene, Charité, Humboldt-University, Berlin, Germany
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Trost A, Graf B, Eucker J, Sezer O, Possinger K, Göbel UB, Adam T. Identification of clinically relevant yeasts by PCR/RFLP. J Microbiol Methods 2004; 56:201-11. [PMID: 14744449 DOI: 10.1016/j.mimet.2003.10.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
For molecular diagnosis of fungal disease using DNA amplification procedures in the routine laboratory, choice of appropriate target structures and rapid and inexpensive identification of amplification products are important prerequisites. Most diagnostic procedures described thus far are characterized by limited applicability, considerable cost for laboratory equipment or low power of discrimination between species. This study aimed at identification of a PCR target appropriate for diagnosis of clinically relevant yeasts and an affordable procedure for characterization of the PCR products to the species level. Here, we describe a PCR-based system using amplification of intergenic spacers ITS1 and ITS2 and restriction length polymorphism of PCR products after sequence-specific enzymatic cleavage. We show the evaluation of the system for clinically relevant Candida species. The simple and inexpensive procedure should be instrumental for rapid identification of medically important yeasts.
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Affiliation(s)
- Anja Trost
- Institute for Microbiology and Hygiene, Medical Faculty of Humboldt University, Charité, Dorotheenstr. 96, 10117 Berlin, Germany.
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Selvarangan R, Bui U, Limaye AP, Cookson BT. Rapid identification of commonly encountered Candida species directly from blood culture bottles. J Clin Microbiol 2004; 41:5660-4. [PMID: 14662958 PMCID: PMC309003 DOI: 10.1128/jcm.41.12.5660-5664.2003] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report a rapid-cycle, real-time PCR method for identifying six Candida spp. directly from BACTEC blood culture bottles. Target sequences in the noncoding internal transcribed spacer regions of the rRNA operon were simultaneously amplified and interrogated with fluorescent probes to identify Candida albicans, C. glabrata, C. parapsilosis, C. tropicalis, C. krusei, and C. lusitaniae; these account for 88% of the yeast species isolated from positive blood cultures in our laboratory. Any of the first four species can be identified in a single reaction using two fluorescent hybridization probe sets. The antifungal-resistant species C. krusei and C. lusitaniae are detected in a second reaction, also with two probe sets. The assay was validated with DNA extracted from BACTEC blood culture bottles positive for yeasts (n = 62) and was 100% concordant with culture identification based on biochemical and morphological features of C. albicans (n = 22), C. parapsilosis (n = 10), C. tropicalis (n = 1) C. glabrata (n = 22), C. krusei (n = 2), and C. lusitaniae (n = 1). No cross-reactivity was observed in blood culture samples growing yeasts other than the above-mentioned species (n = 4), in those growing bacteria (n = 12), or in the absence of microbial growth. Our assay allows rapid (</=2 h) and specific detection of the most common Candida spp. directly from positive blood cultures and may facilitate delivery of optimal antifungal therapy.
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Affiliation(s)
- Rangaraj Selvarangan
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington 98195-7110, USA
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Sullivan DJ, Moran GP, Pinjon E, Al-Mosaid A, Stokes C, Vaughan C, Coleman DC. Comparison of the epidemiology, drug resistance mechanisms, and virulence of and. FEMS Yeast Res 2004; 4:369-76. [PMID: 14734017 DOI: 10.1016/s1567-1356(03)00240-x] [Citation(s) in RCA: 164] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Candida dubliniensis is a pathogenic yeast species that was first identified as a distinct taxon in 1995. Epidemiological studies have shown that C. dubliniensis is prevalent throughout the world and that it is primarily associated with oral carriage and oropharyngeal infections in human immunodeficiency virus (HIV)-infected and acquired immune deficiency syndrome (AIDS) patients. However, unlike Candida albicans, C. dubliniensis is rarely found in the oral microflora of normal healthy individuals and is responsible for as few as 2% of cases of candidemia (compared to approximately 65% for C. albicans). The vast majority of C. dubliniensis isolates identified to date are susceptible to all of the commonly used antifungal agents, however, reduced susceptibility to azole drugs has been observed in clinical isolates and can be readily induced in vitro. The primary mechanism of fluconazole resistance in C. dubliniensis has been shown to be overexpression of the major facilitator efflux pump Mdr1p. It has also been observed that a large number of C. dubliniensis strains express a non-functional truncated form of Cdr1p, and it has been demonstrated that this protein does not play a significant role in fluconazole resistance in the majority of strains examined to date. Data from a limited number of infection models reflect findings from epidemiological studies and suggest that C. dubliniensis is less pathogenic than C. albicans. The reasons for the reduced virulence of C. dubliniensis are not clear as it has been shown that the two species express a similar range of virulence factors. However, although C. dubliniensis produces hyphae, it appears that the conditions and dynamics of induction may differ from those in C. albicans. In addition, C. dubliniensis is less tolerant of environmental stresses such as elevated temperature and NaCl and H(2)O(2) concentration, suggesting that C. albicans may have a competitive advantage when colonising and causing infection in the human body. It is our hypothesis that a genomic comparison between these two closely-related species will help to identify virulence factors responsible for the far greater virulence of C. albicans and possibly identify factors that are specifically implicated in either superficial or systemic candidal infections.
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Affiliation(s)
- Derek J Sullivan
- Microbiology Research Unit, Department of Oral Medicine, Oral Surgery and Oral Pathology, Dublin Dental School and Hospital, University of Dublin, Trinity College, Dublin 2, Ireland.
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Current awareness on yeast. Yeast 2003; 20:455-62. [PMID: 12728936 DOI: 10.1002/yea.943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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