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Rodrigues Netto MF, Júnior da Silva J, Andrielle da Silva T, Oliveira MC, Höfling JF, de Andrade Bressan E, Vargas de Oliveira Figueira A, Gomes Boriollo MF. DNA microsatellite genotyping of potentially pathogenic Candida albicans and C. dubliniensis isolated from the oral cavity and dental prostheses. Microb Pathog 2020; 149:104548. [PMID: 33059059 DOI: 10.1016/j.micpath.2020.104548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/25/2020] [Indexed: 11/19/2022]
Abstract
This study investigated the incidence, genetic diversity, antifungal sensitivity, and virulence of Candida albicans and C. dubliniensis isolated from subjects using dental prostheses and subjects clinically indicated for the first prosthetic rehabilitation. Subjects were divided into four groups and samples were collected twice: at first rehabilitation by removable partial (A) and total (C) dental prostheses, and replacement of the removable partial (B) and total (D) prostheses. Yeasts were genotyped using DNA microsatellite markers. Microbiological methods were used to screen for azole antifungal resistance and exoenzyme production. In the initial sampling, oral colonization by Candida was observed in 31 (53.4%) subjects in groups A (33.3%), B (68.2%), and D (65%); 20 (47.6%) subjects displayed colonization of prostheses: groups B (50%) and D (45%). The second sampling (±30 days) revealed Candida in 2 (3.4%: oral cavity) and 4 (6.9%: prosthetic) subjects from group B. C. albicans and C. dubliniensis displayed both polyclonal and monoclonal patterns of infection. Azole-resistant C. albicans and SAPs+ strains were prevalent. Related strains were found in one or several oral sites (mucosa and prosthesis), as well as intra- and inter-subject, -gender, -group, and -time of sampling. However, the patterns of clonality can be altered under dental care.
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Affiliation(s)
- Manoel Francisco Rodrigues Netto
- Laboratory of Microbiology and Immunology, Department of Oral Diagnosis, Dental School of Piracicaba, State University of Campinas (FOP/UNICAMP), Piracicaba, SP, 13414-903, Brazil.
| | - Jeferson Júnior da Silva
- Laboratory of Microbiology and Immunology, Department of Oral Diagnosis, Dental School of Piracicaba, State University of Campinas (FOP/UNICAMP), Piracicaba, SP, 13414-903, Brazil.
| | - Thaísla Andrielle da Silva
- Laboratory of Microbiology and Immunology, Department of Oral Diagnosis, Dental School of Piracicaba, State University of Campinas (FOP/UNICAMP), Piracicaba, SP, 13414-903, Brazil.
| | - Mateus Cardoso Oliveira
- Laboratory of Microbiology and Immunology, Department of Oral Diagnosis, Dental School of Piracicaba, State University of Campinas (FOP/UNICAMP), Piracicaba, SP, 13414-903, Brazil.
| | - José Francisco Höfling
- Laboratory of Microbiology and Immunology, Department of Oral Diagnosis, Dental School of Piracicaba, State University of Campinas (FOP/UNICAMP), Piracicaba, SP, 13414-903, Brazil.
| | - Eduardo de Andrade Bressan
- Laboratory of Plant Improvement, Center of Nuclear Energy in Agriculture, University of São Paulo (CENA/USP), Piracicaba, SP, 13400-970, Brazil.
| | - Antonio Vargas de Oliveira Figueira
- Laboratory of Plant Improvement, Center of Nuclear Energy in Agriculture, University of São Paulo (CENA/USP), Piracicaba, SP, 13400-970, Brazil.
| | - Marcelo Fabiano Gomes Boriollo
- Laboratory of Microbiology and Immunology, Department of Oral Diagnosis, Dental School of Piracicaba, State University of Campinas (FOP/UNICAMP), Piracicaba, SP, 13414-903, Brazil.
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Kaur R, Dhakad MS, Goyal R, Haque A, Mukhopadhyay G. Identification and Antifungal Susceptibility Testing of Candida Species: A Comparison of Vitek-2 System with Conventional and Molecular Methods. J Glob Infect Dis 2016; 8:139-146. [PMID: 27942193 PMCID: PMC5126752 DOI: 10.4103/0974-777x.192969] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Background: Candida infection is a major cause of morbidity and mortality in immunocompromised patients; an accurate and early identification is a prerequisite need to be taken as an effective measure for the management of patients. The purpose of this study was to compare the conventional identification of Candida species with identification by Vitek-2 system and the antifungal susceptibility testing (AST) by broth microdilution method with Vitek-2 AST system. Materials and Methods: A total of 172 Candida isolates were subjected for identification by the conventional methods, Vitek-2 system, restriction fragment length polymorphism, and random amplified polymorphic DNA analysis. AST was carried out as per the Clinical and Laboratory Standards Institute M27-A3 document and by Vitek-2 system. Results: Candida albicans (82.51%) was the most common Candida species followed by Candida tropicalis (6.29%), Candida krusei (4.89%), Candida parapsilosis (3.49%), and Candida glabrata (2.79%). With Vitek-2 system, of the 172 isolates, 155 Candida isolates were correctly identified, 13 were misidentified, and four were with low discrimination. Whereas with conventional methods, 171 Candida isolates were correctly identified and only a single isolate of C. albicans was misidentified as C. tropicalis. The average measurement of agreement between the Vitek-2 system and conventional methods was >94%. Most of the isolates were susceptible to fluconazole (88.95%) and amphotericin B (97.67%). The measurement of agreement between the methods of AST was >94% for fluconazole and >99% for amphotericin B, which was statistically significant (P < 0.01). Conclusion: The study confirmed the importance and reliability of conventional and molecular methods, and the acceptable agreements suggest Vitek-2 system an alternative method for speciation and sensitivity testing of Candida species infections.
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Affiliation(s)
- Ravinder Kaur
- Department of Microbiology, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
| | - Megh Singh Dhakad
- Department of Microbiology, Maulana Azad Medical College and Associated Lok Nayak Hospitals, New Delhi, India
| | - Ritu Goyal
- Department of Microbiology, Maulana Azad Medical College and Associated Lok Nayak Hospitals, New Delhi, India
| | - Absarul Haque
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Gauranga Mukhopadhyay
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
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3
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Bai FY. Association of genotypes with infection types and antifungal susceptibilities in Candida albicans as revealed by recent molecular typing strategies. Mycology 2014; 5:1-9. [PMID: 24772369 PMCID: PMC3979442 DOI: 10.1080/21501203.2014.899525] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 02/26/2014] [Indexed: 11/19/2022] Open
Abstract
Candida albicans is a commensal microorganism in the mucosa of healthy individuals, but is also the most common opportunistic fungal pathogen of humans. It causes from benign infections such as oral and vaginal candidiasis to fatal, systematic diseases in immunocompromised or critically ill patients. In addition to improved therapy, the rapid and accurate identification of the disease-causing strains is crucial for diagnosis, clinical treatment and epidemiological studies of candidiasis. A variety of methods for strain typing of C. albicans have been developed. The most commonly used methods with the focus on recently developed molecular typing or DNA-fingerprinting strategies and the recent findings in the association of specific and genetically similar genotypes with certain infection types and the correlation between azole susceptibilities and certain genotypes of C. albicans from China are reviewed.
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Affiliation(s)
- Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Bonfim-Mendonça PDS, Fiorini A, Shinobu-Mesquita CS, Baeza LC, Fernandez MA, Svidzinski TIE. Molecular typing of Candida albicans isolates from hospitalized patients. Rev Inst Med Trop Sao Paulo 2014; 55:385-91. [PMID: 24213190 PMCID: PMC4105085 DOI: 10.1590/s0036-46652013000600003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 04/09/2013] [Indexed: 01/27/2023] Open
Abstract
SUMMARY Introduction: The majority of nosocomial fungal infections are caused
by Candida spp. where C. albicans is the species
most commonly identified. Molecular methods are important tools for assessing the
origin of the yeasts isolated in hospitals. Methods: This is a study on the genetic profifiles of 39 nosocomial
clinical isolates of C. albicans using two typing methods: random
amplifified polymorphic DNA (RAPD) and microsatellite, two different primers for
each technique were used. Results: RAPD provided 10 and 11 different profiles with values for
SAB of 0.84 ± 0.126 and 0.88 ± 0.08 for primers M2 and P4, respectively.
Microsatellite using two markers, CDC3 and HIS3, allowed the observation of six
and seven different alleles, respectively, with combined discriminatory power of
0.91. Conclusions: Although genetic variability is clear, it was possible
to identify high similarity, suggesting a common origin for at least a part of
isolates. It is important to emphasize that common origin was proven from yeasts
isolated from colonization (urine, catheter or endotracheal secretions) and blood
culture from the same patient, indicating that the candidemia must have started
from a site of colonization. The combination of RAPD and microsatellite provides a
quick and efficient analysis for investigation of similarity among nosocomial
isolates of C. albicans.
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Pulcrano G, Roscetto E, Iula VD, Panellis D, Rossano F, Catania MR. MALDI-TOF mass spectrometry and microsatellite markers to evaluate Candida parapsilosis transmission in neonatal intensive care units. Eur J Clin Microbiol Infect Dis 2012; 31:2919-28. [PMID: 22644055 DOI: 10.1007/s10096-012-1642-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 05/09/2012] [Indexed: 10/28/2022]
Abstract
Recent studies on outbreaks of Candida showed an increased incidence of bloodstream infections in neonatal intensive care units (NICUs) caused by C. parapsilosis species, highlighting the need for the proper identification and epidemiology of these species. Several systems are available for molecular epidemiological and taxonomic studies of fungal infections: pulsed-field gel electrophoresis (PFGE) represents the gold standard for typing, but is also one of the most lengthy and expensive, while simple sequence repeats (SSRs) is based on polymerase chain reaction (PCR) amplification and is, therefore, faster. Only recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used to identify and type microorganisms involved in nosocomial outbreaks. In our study, 19 strains of C. parapsilosis isolated from the blood cultures of neonates admitted to the University Hospital Federico II were genotyped by the amplification of eight SSR markers and by MALDI-TOF MS. Electrophoretic and spectrometric profile results were compared in order to identify similarities among the isolates and to study microevolutionary changes in the C. parapsilosis population. The discriminatory power and the unweighted pair group method with arithmetic mean (UPGMA) dendrograms generated were compared in order to evaluate the correlation of the groups established by the analysis of the clusters by both methods. Both methods were rapid and effective in highlighting identical strains and studying microevolutionary changes in the population. Our study evidenced that mass spectroscopy is a useful technique not only for the identification but also for monitoring the spread of strains, which is critical to control nosocomial infections.
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Affiliation(s)
- G Pulcrano
- Department of Cellular and Molecular Biology and Pathology Luigi Califano, Medicine School, University of Naples Federico II, via Pansini, 80131, Naples, Italy.
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Sibley CD, Peirano G, Church DL. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology. INFECTION GENETICS AND EVOLUTION 2012; 12:505-21. [PMID: 22342514 PMCID: PMC7106020 DOI: 10.1016/j.meegid.2012.01.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 12/25/2022]
Abstract
Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.
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Affiliation(s)
- Christopher D. Sibley
- Department of Microbiology, Immunology & Infectious Diseases, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
| | - Gisele Peirano
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
| | - Deirdre L. Church
- Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Department of Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
- Corresponding author. Address: c/o Calgary Laboratory Services, 9-3535 Research Rd. N.W., Calgary, Alta, Canada T2L 2K8. Tel.: +1 403 770 3281; fax: +1 403 770 3347.
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7
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da Costa KRC, Ferreira JC, Lavrador MAS, Baruffi MD, Candido RC. Virulence attributes and genetic variability of oral Candida albicans and Candida tropicalis isolates. Mycoses 2011; 55:e97-e105. [PMID: 22035510 DOI: 10.1111/j.1439-0507.2011.02125.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The wide spectrum of candidiasis and its clinical importance encourage the research with the purpose of clarifying the mechanisms of pathogenicity and identification of virulence factors of Candida sp. Therefore, the aim of this study was to verify the adhesion capacity, protease activity and genotypic diversity of oral C. albicans and C. tropicalis isolates. The adhesion ability to the extracellular matrix glycoproteins laminin and fibronectin was evaluated using the ELISA technique. The research of proteases was carried out in agar plate containing bovine albumin and through a quantitative method in buffer solution containing haemoglobin. Intra and interspecies polymorphisms was verified through random amplified polymorphic DNA (RAPD) technique. All C. albicans and C. tropicalis isolates binded to immobilised laminin and fibronectin. Ca33 and Ct13 isolates had relative adhesion index significantly higher than the other isolates for both glycoproteins (P < 0.001). Protease activity was observed in all isolates of C. albicans using either the semi-quantitative or quantitative assay. The protease activity of C. tropicalis was better detected through the quantitative assay. The genotypic diversity by RAPD revealed a heterogeneous population in both species. Nevertheless, C. tropicalis presented higher genetic variability than C. albicans strains.
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Costa-de-Oliveira S, Sousa I, Correia A, Sampaio P, Pais C, Rodrigues AG, Pina-Vaz C. Genetic relatedness and antifungal susceptibility profile ofCandida albicansisolates from fungaemia patients. Med Mycol 2011; 49:248-52. [DOI: 10.3109/13693786.2010.511633] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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9
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Boriollo MFG, Dias RA, Fiorini JE, Oliveira NDMS, Spolidório DMP, de Souza HMB, Figueira AVDO, Pizzirani-Kleiner AA. Disparity between Multilocus Enzyme Electrophoresis, Microsatellite Markers and Pulsed-Field Gel Electrophoresis in epidemiological tracking of Candida albicans. J Microbiol Methods 2010; 82:265-81. [DOI: 10.1016/j.mimet.2010.06.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 06/29/2010] [Accepted: 06/29/2010] [Indexed: 10/19/2022]
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10
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Abbes S, Sellami H, Sellami A, Makni F, Mahfoudh N, Makni H, Khaled S, Ayadi A. Microsatellite analysis and susceptibility to FCZ of Candida glabrata invasive isolates in Sfax Hospital, Tunisia. Med Mycol 2010; 49:10-5. [PMID: 20586679 DOI: 10.3109/13693786.2010.493561] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have noted that, during the last few years, there has been a redistribution of the most common Candida species with an increase in non-C. albicans Candida species, particularly Candida glabrata. In many countries, the high frequency of Candida glabrata shows the highest resistance rates. The main objective of this investigation was to analyze the genotypic variability of invasive C. glabrata isolates recovered over a period of six years and assess their in vitro susceptibility to fluconazole to determine the possible existence of relationships between genotype and susceptibility. We collected 50 invasive C. glabrata isolates (21.4%) from January 2001 to December 2007. The in vitro susceptibility profiles as determined by the E-test method showed that 8.3% of the isolates were resistant to fluconazole. The typing with three microsatellite markers RPM2, MTI and ERG3 demonstrated 12 multilocus genotypes distributed irregularly with a predominance of G1 (38%). A cluster (G9) was found among isolates collected in the same ward, at the same time period, suggesting cross transmission. Eleven of 13 patients who had previously been colonized by C. glabrata, were infected by their colonizing strains. However, we noted after prolonged treatment with fluconazole that there was an increase of the MIC for an isolate from one patient and in another patient, the selection of a more resistant variant. In our study, we didn't find an association between genotype and susceptibility to fluconazole. In conclusion, the predominance of some genotypes could be explained by nosocomial transmission or a selective ecological advantage rather than an emergence of a resistant isolate.
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Affiliation(s)
- S Abbes
- Laboratoire de Biologie Moléculaire Parasitaire et Fongique, Faculté de Médecine, Sfax, Tunisie
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Abstract
Candida albicans, a diploid yeast commensal and opportunist pathogen, has evolved unusual mechanisms for maintenance of genetic diversity in the absence of a complete sexual cycle. These include chromosomal polymorphisms, mitotic recombination events, and gains and losses of heterozygosity, superimposed on a fundamentally clonal mode of reproduction. Molecular typing of C. albicans strains shows geographical evolutionary associations but these have become partially blurred, probably as a result of extensive human travel. Individual patients usually carry a single C. albicans strain type, but this may undergo microvariation leading to detection of mixtures of closely related types. Associations have been found between clade 1, the most common multilocus sequence typing cluster of related C. albicans strains, and resistance to flucytosine and terbinafine. There are also clade-related associations with lengths of tandem repeats in some cell-surface proteins, but not with virulence or type of infection.
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Affiliation(s)
- Frank C Odds
- Aberdeen Fungal Group, Institute of Medical Sciences, Aberdeen AB25 2ZD, UK.
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12
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Abdel-Rahman SM. Strain Differentiation of Dermatophytes. Mycopathologia 2008; 166:319-33. [DOI: 10.1007/s11046-008-9108-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 01/15/2008] [Accepted: 01/30/2008] [Indexed: 10/22/2022]
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13
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14
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Li J, Bai FY. Single-strand conformation polymorphism of microsatellite for rapid strain typing of Candida albicans. Med Mycol 2008; 45:629-35. [PMID: 17885945 DOI: 10.1080/13693780701530950] [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: 10/22/2022] Open
Abstract
Single-strand conformation polymorphisms (SSCP) of Candida albicans' microsatellite CAI were characterized. Among the 76 clinical isolates recovered from different patients (independent strains), 60 distinct CAI SSCP patterns were recognized, resulting in a discriminatory power of 0.993. The multiple isolates recovered sequentially from the same or different body locations of the same patient showed exactly the same CAI SSCP pattern. The reliability of the SSCP analysis was confirmed by GeneScan and sequence analyses. From the same set of independent strains, 59 distinct CAI genotypes were identified by GeneScan analysis. Sequence comparison showed the advantage of SSCP over GeneSan analysis in the detection of point mutations in the microsatellite. The results indicated that PCR SSCP analysis of CAI microsatellite is a powerful and economical approach for rapid strain typing of C. albicans in clinical laboratories, especially in the detection of microevolutionary changes in microsatellites and in large-scale epidemiological investigation.
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Affiliation(s)
- Juan Li
- Systematic Mycology and Lichenology Laboratory, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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15
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Barada G, Basma R, Khalaf RA. Microsatellite DNA Identification and Genotyping of Candida albicans from Lebanese Clinical Isolates. Mycopathologia 2008; 165:115-25. [DOI: 10.1007/s11046-008-9089-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 01/07/2008] [Indexed: 11/30/2022]
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Pires-Gonçalves RH, Miranda ET, Baeza LC, Matsumoto MT, Zaia JE, Mendes-Giannini MJS. Genetic relatedness of commensal strains of Candida albicans carried in the oral cavity of patients' dental prosthesis users in Brazil. Mycopathologia 2007; 164:255-63. [PMID: 17906942 DOI: 10.1007/s11046-007-9052-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2007] [Accepted: 08/29/2007] [Indexed: 10/22/2022]
Abstract
The aim of this study is to describe the degree of yeast-colonization in diabetic and hemodialysed-users of dental prostheses. Individuals (306) were examined using an oral rinse technique in order to evaluate the incidence of yeast-carriage, and genotype of C. albicans. Yeasts were isolated from 68.4% (91/133) individual's dental prostheses users. Dental prostheses were found to be a significant factor for the yeast colonization (P < 0.05). Overall, the intensity of carriage was higher in diabetic patients as compared with health and hemodialysed individuals (P < 0.05). The isolation rates were: C. albicans (51.7%), C. parapsilosis (20.9%), C. tropicalis (14.3%), C. glabrata (6.6%), C. krusei (3.3%), C. rugosa (1.1%), and Pichia (Pichia ohmeri, 2.2%). Ready-To-Go RAPD Analysis Beads were used and primer OPJ 6 distinguished the C. albicans isolates found in prostheses users. All the isolates were grouped into 11 RAPD profiles in four main clusters and, the average S (AB) for the entire collection of 47 C. albicans isolates were 0.779 +/- 0.178. Over 85% of isolates had a similarity level higher than or equal to 0.8 reinforcing the idea that the use of dental prostheses, independently of the host's clinical condition, probably provides the necessary conditions for these strains to gain a growth-specific advantage over others.
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Manfredi M, McCullough MJ, Al-Karaawi ZM, Vescovi P, Porter SR. Analysis of the strain relatedness of oral Candida albicans in patients with diabetes mellitus using polymerase chain reaction-fingerprinting. ACTA ACUST UNITED AC 2007; 21:353-9. [PMID: 17064392 DOI: 10.1111/j.1399-302x.2006.00303.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
To increase our understanding of Candida pathogenicity, the identification of those strains most frequently associated with infections is of paramount importance. Polymerase chain reaction (PCR)-based methods are extremely effective in differentiating and determining reproducibility, they require minimum starting material and are rapid and simple to perform. In this study, the genetic relatedness of Candida albicans was assessed for two geographically different patient groups (London, UK and Parma, Italy) affected by diabetes mellitus. C. albicans samples from the oral cavities of non-diabetic healthy subjects were also examined by PCR fingerprinting to evaluate the possible genetic differences among endogenous strains in individuals with and without diabetes mellitus. PCR fingerprinting, with subsequent phylogenetic analysis of C. albicans isolates from the diabetic patients from London and Italy and from the non-diabetic subjects, revealed that there were significant differences (P < 0.0001) between C. albicans isolates indicative of the distinct ecological niches that occur in the oral cavities of these patient cohorts. The most diverse group comprised the isolates from the diabetic patients in the UK, possibly reflecting the antifungal treatment that these patients had received. Further studies that include isolates from patient cohorts with systemic diseases other than diabetes mellitus, and from more diverse geographic localities are required to explain the relatedness of C. albicans isolates in the mouth.
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Affiliation(s)
- M Manfredi
- Oral Medicine, Division of Infection and Immunity, Eastman Dental Institute, UCL, University of London, London, UK.
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18
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Chong PP, Abdul Hadi SR, Lee YL, Phan CL, Tan BC, Ng KP, Seow HF. Genotyping and drug resistance profile of Candida spp. in recurrent and one-off vaginitis, and high association of non-albicans species with non-pregnant status. INFECTION GENETICS AND EVOLUTION 2007; 7:449-56. [PMID: 17324639 DOI: 10.1016/j.meegid.2007.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Accepted: 01/12/2007] [Indexed: 11/27/2022]
Abstract
Recurrent vulvovaginal candidiasis affects women worldwide and the resistance to azole drugs may be an important factor. The extent of strain-to-strain variation within a species and its relationship to the ability of the organism to colonize the vulvovaginal mucosa is not well established. The aims of this study were to compare: (i) the genotypes of Candida strains in sequential infections in patients with recurrent vaginitis, (ii) the genotypes of strains in patients with only one episode of infection in a period of 1 year and (iii) determine the in vitro antifungal susceptibilities of strains that cause recurrent vaginitis. Fifty-one cultured specimens from six distinct Candida species were genotyped via random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) method using the ERIC1 and ERIC2 primers (ERIC, enterobacterial repetitive intergenic consensus). Statistical analyses allowed three different scenarios to be discerned for recurrent cases: (i) strain maintenance without genetic variation, (ii) strain maintenance with minor genetic variation and (iii) outright strain replacement. The genetic relatedness between strains from patients with recurrent vaginitis and patients with single episode of vaginitis were demonstrated by the dendogramme and the mean pairwise similarity coefficient S(AB) for the intergroup comparison was 0.223. However, intragroup genetic relatedness was slightly higher than intergroup comparison, with mean S(AB) of 0.261 and 0.331 for Groups I and II, respectively. A high proportion of Group I isolates (87.5%) causing recurrent infections were resistant to ketoconazole, whereas 41.7% of these isolates were cross-resistant to both clotrimazole and ketoconazole as shown by the in vitro antifungal susceptibility test, especially for C. glabrata isolates. Pregnancy status of patients displayed a highly significant association with C. albicans species whereas non-albicans species had a markedly higher prevalence in non-pregnant patients (p<0.001). These results may have a profound impact on the management of vaginal candidiasis, especially in recurrent cases.
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Affiliation(s)
- Pei Pei Chong
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
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Lasker BA, Butler G, Lott TJ. Molecular genotyping of Candida parapsilosis group I clinical isolates by analysis of polymorphic microsatellite markers. J Clin Microbiol 2006; 44:750-9. [PMID: 16517850 PMCID: PMC1393075 DOI: 10.1128/jcm.44.3.750-759.2006] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Candida parapsilosis, a pathogenic yeast, is composed of three newly designated genomic species that are physiologically and morphologically indistinguishable. Nosocomial infections caused by group I C. parapsilosis are often associated with the breakdown of infection control practices and the contamination of medical devices, solutions, and indwelling catheters. Due to the low levels of nucleotide sequence variation that are observed, an investigation of the size polymorphisms in loci harboring microsatellite repeat sequences was applied for the typing of C. parapsilosis group I isolates. PCR primer sets that flank the microsatellite repeats for seven loci were designed. Following amplification by PCR, the size of each amplification product was determined automatically by capillary electrophoresis. A total of 42 C. parapsilosis group I isolates were typed by microsatellite analysis, and their profiles were compared to the hybridization profiles obtained by use of the Cp3-13 DNA probe. A high degree of discrimination (discriminatory power = 0.971) was observed by microsatellite analysis. The number of different alleles per locus ranged from 14 for locus B to 5 for locus C. Microsatellite analysis detected 30 different microsatellite genotypes, with 24 genotypes represented by a single isolate. Comparison of the genotypes obtained by microsatellite analysis and those obtained by analysis of the Cp3-13 hybridization profiles showed that they were similar, and these methods were able to identify related and unrelated isolates. Some discrepancies were observed between the methods and may be due to higher mutation rates and/or homoplasy by microsatellite markers. Identical results were observed between microsatellite analysis and Cp3-13 DNA hybridization profile analysis for C. parapsilosis isolates obtained from two patients, demonstrating the reproducibilities of the methods in vivo. Identical microsatellite profiles were observed for isolates displaying different phenotypic switching morphologies. Indistinguishable Cp3-13 DNA hybridization profiles were observed for six epidemiologically related isolates; however, only three of six primary isolates had identical microsatellite profiles. Size variation at a single locus was observed for three of six isolates obtained either after the outbreak period or from a different body site, suggesting the potential of the method to detect microevolutionary events. Interestingly, for most loci a single allele per strain was observed; in contrast, two alleles per locus were observed for some strains, and consistent with the findings for natural isolates, some isolates may be aneuploid. Due to the potential for high throughput, reproducibility, and discrimination, microsatellite analysis may provide a robust and efficient method for the genotyping of large numbers of C. parapsilosis group I isolates.
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Affiliation(s)
- Brent A Lasker
- Mycotic Diseases Branch, Division of Bacterial and Mycotic Diseases, National Centers for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Mailstop G-11, Atlanta, GA 30333.
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Chong PP, Chieng DCS, Low LY, Hafeez A, Shamsudin MN, Seow HF, Ng KP. Recurrent candidaemia in a neonate with Hirschsprung's disease: fluconazole resistance and genetic relatedness of eight Candida tropicalis isolates. J Med Microbiol 2006; 55:423-428. [PMID: 16533990 DOI: 10.1099/jmm.0.46045-0] [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: 11/18/2022] Open
Abstract
The incidence of candidaemia among immunocompromised patients in Malaysia is increasing at an alarming rate. Isolation of clinical strains that are resistant to fluconazole has also risen markedly. We report here the repeated isolation of Candida tropicalis from the blood of a neonatal patient with Hirschsprung's disease. In vitro fluconazole susceptibility tests of the eight isolates obtained at different time points showed that seven of the isolates were resistant and one isolate was scored as susceptible dose-dependent. Random amplification of polymorphic DNA fingerprinting of the isolates using three primers and subsequent phylogenetic analysis revealed that these isolates were highly similar strains having minor genetic divergence, with a mean pairwise similarity coefficient of 0.893+/-0.041. The source of the infectious agent was thought to be the central venous catheter, as culture of its tip produced fluconazole-resistant C. tropicalis. This study demonstrates the utility of applying molecular epidemiology techniques to complement traditional mycological culture and drug susceptibility tests for accurate and appropriate management of recurrent candidaemia and highlights the need for newer antifungals that can combat the emergence of fluconazole-resistant C. tropicalis strains.
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Affiliation(s)
| | | | | | - Asma Hafeez
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 59100 Kuala Lumpur, Malaysia
| | | | | | - Kee Peng Ng
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 59100 Kuala Lumpur, Malaysia
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Neppelenbroek KH, Campanha NH, Spolidorio DMP, Spolidorio LC, Seó RS, Pavarina AC. Molecular fingerprinting methods for the discrimination between C. albicans and C. dubliniensis. Oral Dis 2006; 12:242-53. [PMID: 16700733 DOI: 10.1111/j.1601-0825.2005.01189.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Opportunistic fungal pathogens are becoming increasingly important causes of both community-acquired and nosocomial infections. The most important fungal pathogens are yeast species belonging to the genus Candida. These species show differences in levels of resistance to antifungal agents and mortality. Consequently, it is important to correctly identify the causative organism to the species level. Identification of Candida dubliniensis in particular remains problematic because of the high degree of phenotypic similarity between this species and Candida albicans. However, as the differences between both are most pronounced at the genetic level, several studies have been conducted in order to provide a specific and rapid identification fingerprinting molecular test. In most candidal infectious, no single DNA fingerprinting technique has evolved as a dominant method, and each method has its advantages, disadvantages and limitations. Moreover, the current challenge of these techniques is to compile standardized patterns in a database for interlaboratory use and future reference. This review provides an overview of most common molecular fingerprinting techniques currently available for discrimination of C. albicans and C. dubliniensis.
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Affiliation(s)
- K H Neppelenbroek
- Department of Dental Materials and Prosthodontics, Araraquara Dental School, São Paulo State University, São Paulo, Brazil
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Sampaio P, Gusmão L, Correia A, Alves C, Rodrigues AG, Pina-Vaz C, Amorim A, Pais C. New microsatellite multiplex PCR for Candida albicans strain typing reveals microevolutionary changes. J Clin Microbiol 2005; 43:3869-76. [PMID: 16081924 PMCID: PMC1233915 DOI: 10.1128/jcm.43.8.3869-3876.2005] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Five new microsatellite loci were described and characterized for use as molecular markers for the identification and genetic differentiation of Candida albicans strains. Following the typing of 72 unrelated clinical isolates, the analysis revealed that they were all polymorphic, presenting from 5 to 30 alleles and 8 to 46 different genotypes. The discriminatory power obtained by combining the information generated by three microsatellites used in a multiplex PCR amplification strategy was 0.99, the highest ever reported. The multiplex PCR was later used to test a total of 114 C. albicans strains, including multiple isolates from the same patient collected from different body locations and along episodes of vulvovaginal infections. Three different scenarios for strain relatedness were identified: (i) different isolates that were revealed to be the same strain, (ii) isolates that were the same strain but that apparently underwent a process of microevolution, and (iii) isolates that corresponded to different strains. Analysis of the microevolutionary changes between isolates from recurrent infections indicated that the genotype alterations observed could be the result of events that lead to the loss of heterozygosity (LOH). In one case of recurrent infection, LOH was observed at the CAI locus, and this could have been related to exposure to fluconazole, since such strains were exposed to this antifungal during treatment. The analysis of microsatellites by a multiplex PCR strategy was found to be a highly efficient tool for the rapid and accurate differentiation of C. albicans strains and adequate for the identification of fine microevolutionary events that could be related to strain microevolution in response to environmental stress conditions.
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Affiliation(s)
- Paula Sampaio
- CBUM-Center of Biology, University of Minho, 4710-057 Braga, Portugal, IPATIMUP-Institut of Pathology and Molecular Immunology of Porto University, R. Roberto Frias, s/n 4200 Porto, Portugal, Faculty of Science, University of Porto, Porto, Portugal, Microbiology Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Leonor Gusmão
- CBUM-Center of Biology, University of Minho, 4710-057 Braga, Portugal, IPATIMUP-Institut of Pathology and Molecular Immunology of Porto University, R. Roberto Frias, s/n 4200 Porto, Portugal, Faculty of Science, University of Porto, Porto, Portugal, Microbiology Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Alexandra Correia
- CBUM-Center of Biology, University of Minho, 4710-057 Braga, Portugal, IPATIMUP-Institut of Pathology and Molecular Immunology of Porto University, R. Roberto Frias, s/n 4200 Porto, Portugal, Faculty of Science, University of Porto, Porto, Portugal, Microbiology Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Cíntia Alves
- CBUM-Center of Biology, University of Minho, 4710-057 Braga, Portugal, IPATIMUP-Institut of Pathology and Molecular Immunology of Porto University, R. Roberto Frias, s/n 4200 Porto, Portugal, Faculty of Science, University of Porto, Porto, Portugal, Microbiology Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Acácio G. Rodrigues
- CBUM-Center of Biology, University of Minho, 4710-057 Braga, Portugal, IPATIMUP-Institut of Pathology and Molecular Immunology of Porto University, R. Roberto Frias, s/n 4200 Porto, Portugal, Faculty of Science, University of Porto, Porto, Portugal, Microbiology Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Cidália Pina-Vaz
- CBUM-Center of Biology, University of Minho, 4710-057 Braga, Portugal, IPATIMUP-Institut of Pathology and Molecular Immunology of Porto University, R. Roberto Frias, s/n 4200 Porto, Portugal, Faculty of Science, University of Porto, Porto, Portugal, Microbiology Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - António Amorim
- CBUM-Center of Biology, University of Minho, 4710-057 Braga, Portugal, IPATIMUP-Institut of Pathology and Molecular Immunology of Porto University, R. Roberto Frias, s/n 4200 Porto, Portugal, Faculty of Science, University of Porto, Porto, Portugal, Microbiology Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Célia Pais
- CBUM-Center of Biology, University of Minho, 4710-057 Braga, Portugal, IPATIMUP-Institut of Pathology and Molecular Immunology of Porto University, R. Roberto Frias, s/n 4200 Porto, Portugal, Faculty of Science, University of Porto, Porto, Portugal, Microbiology Department, Faculty of Medicine, University of Porto, Porto, Portugal
- Corresponding author. Mailing address: Departamento de Biologia, Centro de Biologia da Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal. Phone: (351)253604312. Fax: (351)253678980. E-mail:
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Lim S, Notley-McRobb L, Lim M, Carter DA. A comparison of the nature and abundance of microsatellites in 14 fungal genomes. Fungal Genet Biol 2004; 41:1025-36. [PMID: 15465391 DOI: 10.1016/j.fgb.2004.08.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Accepted: 08/06/2004] [Indexed: 11/18/2022]
Abstract
An overview of the character of microsatellites in 14 fungal genomes was obtained by analyzing databases containing complete or nearly complete genome sequences. Low GC content, rather than genome size, was the best predictor of high microsatellite density, although very long iterations of tandem repeats were less common in small genomes. Motif type correlated with %GC in that low-GC genomes were more likely to be dominated by A/T-rich motifs, and vice versa, although some exceptions were noted. The experimentally useful dinucleotide and trinucleotide arrays were analyzed in greater detail. Although these varied in sequence and length among fungal species, some that are likely to be universally useful were identified. This information will be useful for researchers wanting to identify the most useful microsatellites to analyze for the fungi included in this survey and provides a platform for choosing microsatellites to target in fungi that are not yet sequenced.
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Affiliation(s)
- S Lim
- School of Molecular and Microbial Biosciences, University of Sydney, Sydney, Australia
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Lasker BA, Ran Y. Analysis of polymorphic microsatellite markers for typing Penicillium marneffei isolates. J Clin Microbiol 2004; 42:1483-90. [PMID: 15070993 PMCID: PMC387604 DOI: 10.1128/jcm.42.4.1483-1490.2004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Penicillium marneffei is an emerging opportunistic dimorphic fungal pathogen that is endemic in Southeast Asia. A typing method based on the analysis of size polymorphisms in microsatellite loci was investigated. Three loci available from the GenBank database were identified to harbor microsatellites. PCR primers flanking the microsatellite repeats were designed with one primer in the set fluorescently labeled. PCR products were then sized by automated capillary electrophoresis. As expected for a haploid fungus, a single band was observed for each microsatellite locus for all isolates. Polymorphic microsatellite marker (PMM) analysis detected a total of 22 different allelic types for 35 isolates of P. marneffei with a high discriminatory power (D = 0.956). Microsatellites I, II, and III detected 14, 10, and 7 alleles, respectively. The reproducibility of length polymorphisms was confirmed by using different DNA preparations from the same isolate or by repeated runs from the same DNA preparation. PMM profiles for eight isolates passaged in vitro for 7 to 8 weeks were identical to the original culture, demonstrating short-term stability and reproducibility. PCR products were not observed for other dimorphic fungi or human DNA. Comparison of allelic frequencies in isolates obtained from China and Thailand identified distinct allele combinations, suggesting the potential geographic isolation of populations. Due to the high discriminatory power, reproducibility, and potential for high throughput, PMM analysis may provide a good typing method for epidemiologic and surveillance investigations of P. marneffei.
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Affiliation(s)
- Brent A Lasker
- Mycotic Diseases Branch, Division of Bacterial and Mycotic Diseases, National Centers for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
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25
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Humphreys H. Does molecular typing make any contribution to the care of patients with infection? Clin Microbiol Infect 2004; 10:269-71. [PMID: 15059114 DOI: 10.1111/j.1198-743x.2004.00815.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Molecular typing has been used extensively to study the epidemiology of infection, but there are few studies on the role of typing in the clinical management of infected patients. Examples of this include distinguishing relapse of infection from new infection, determining the significance of colonisation with potential pathogens, assessing the capacity of isolates to spread and cause serious illness, and linking changes in antimicrobial resistance with treatment. Further studies in selected patient groups and greater collaboration between molecular microbiologists, clinical microbiologists and infectious disease physicians are required to determine the impact of molecular typing in these and other scenarios.
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26
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Bayliss CD, Dixon KM, Moxon ER. Simple sequence repeats (microsatellites): mutational mechanisms and contributions to bacterial pathogenesis. A meeting review. ACTA ACUST UNITED AC 2004; 40:11-9. [PMID: 14734181 DOI: 10.1016/s0928-8244(03)00325-0] [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: 10/26/2022]
Abstract
This review summarises the presentations and discussions that took place during a European Science Foundation-funded workshop whose purpose was to gain current perspectives on the mutational mechanisms of simple sequence repeats and the contribution of localised hypermutation in such repeats to bacterial pathogenesis. In vitro biophysical and biochemical assays of mutational mechanisms were covered as well as genetic studies in various eukaryotic and prokaryotic organisms. Presentations on bacterial pathogenesis elaborated investigations of the use of repeats for typing of strains, epidemiological investigations of mutation rates and functions of loci whose expression is controlled by simple sequence repeats. This review tabulates current perspectives on the cis- and trans-acting factors for mutation of simple sequence repeats and the orientations of mononucleotide repeats in some bacterial species that utilise repeats for adaptation.
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Affiliation(s)
- Christopher D Bayliss
- Molecular Infectious Diseases Group, Weatherall Institute for Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
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27
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Chong PP, Lee YL, Tan BC, Ng KP. Genetic relatedness of Candida strains isolated from women with vaginal candidiasis in Malaysia. J Med Microbiol 2003; 52:657-666. [PMID: 12867559 DOI: 10.1099/jmm.0.04973-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aims of this study were to compare the genetic relatedness of: (i) sequential and single isolates of Candida strains from women with recurrent vaginal candidiasis (RVC); and (ii) Candida strains from women who had only one episode of infection within a 1-year period. In total, 87 isolates from 71 patients were cultured, speciated and genotyped by random amplification of polymorphic DNA (RAPD) analysis. Patients were categorized into three groups, namely those with: (i) a history of RVC from whom two or more yeast isolates were obtained (group A); (ii) a history of RVC from whom only a single isolate was obtained (group B); and (iii) a single episode of vaginal candidiasis within a 1-year period (group C). Six yeast species were detected: Candida albicans, Candida glabrata, Candida lusitaniae, Candida famata, Candida krusei and Candida parapsilosis. Interestingly, the prevalence of non-albicans species was higher in group A patients (50 %) than in patients in groups B (36 %) or C (18.9 %). Eighty RAPD profiles were observed, with a total of 61 polymorphic PCR fragments of distinct sizes. Clustering analysis showed that, overall, the majority of patients in group A had recurrent infections caused by highly similar, but not identical, sequential strains [mean pairwise similarity coefficient (S(AB)) = 0.721 +/- 0.308]. The range of mean S(AB) values for intergroup comparisons for C. albicans isolates alone was 0.50-0.56, suggesting that there was no significant relatedness between strains from different groups. Genetic similarity of C. albicans isolates from patients in group A was lower than that of C. albicans isolates from patients in group C (mean S(AB) = 0.532 +/- 0.249 and 0.636 +/- 0.206, respectively); this difference was statistically significant (P = 0.036). These results demonstrate that the cause of recurrent infections varies among individuals and ranges between strain maintenance, strain microevolution and strain replacement; the major scenario is strain maintenance with microevolution. They also show that C. albicans strains that cause recurrent infections are less similar to each other than strains that cause one-off infections, suggesting that the former may represent more virulent subtypes.
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Affiliation(s)
- Pei Pei Chong
- Department of Biomedical Sciences1 and Gynaecology and Obstetrics Unit2, Faculty of Medicine and Health Sciences, University Putra Malaysia, Selangor, Malaysia 3Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 59100 Kuala Lumpur, Malaysia
| | - Yee Lean Lee
- Department of Biomedical Sciences1 and Gynaecology and Obstetrics Unit2, Faculty of Medicine and Health Sciences, University Putra Malaysia, Selangor, Malaysia 3Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 59100 Kuala Lumpur, Malaysia
| | - Boon Chong Tan
- Department of Biomedical Sciences1 and Gynaecology and Obstetrics Unit2, Faculty of Medicine and Health Sciences, University Putra Malaysia, Selangor, Malaysia 3Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 59100 Kuala Lumpur, Malaysia
| | - Kee Peng Ng
- Department of Biomedical Sciences1 and Gynaecology and Obstetrics Unit2, Faculty of Medicine and Health Sciences, University Putra Malaysia, Selangor, Malaysia 3Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 59100 Kuala Lumpur, Malaysia
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28
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Forche A, May G, Beckerman J, Kauffman S, Becker J, Magee PT. A system for studying genetic changes in Candida albicans during infection. Fungal Genet Biol 2003; 39:38-50. [PMID: 12742062 DOI: 10.1016/s1087-1845(02)00585-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Candida albicans is a diploid yeast with a dimorphic life history. It exists commensally in many healthy humans but becomes a potent pathogen in immunocompromised hosts. The underlying genetic mechanisms by which C. albicans switches from a commensal to a pathogenic form in the host are not well understood. To study the evolution of virulence in mammalian hosts, we used GAL1 as selectable marker system that allows for both positive and negative selection in selective media. We show that the deletion of one or both copies of GAL1 in the C. albicans genome does not change virulence in a systemic mouse model. We obtained estimates for the frequency of mitotic recombination at the GAL1 locus during systemic infection. Our observations suggest that genetic changes such as mitotic recombination and gene conversion occur at a high enough frequency to be important in the transition of C. albicans from a commensal to a pathogenic organism.
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Affiliation(s)
- A Forche
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA.
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29
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Samaranayake YH, Samaranayake LP, Dassanayake RS, Yau JYY, Tsang WK, Cheung BPK, Yeung KWS. 'Genotypic shuffling' of sequential clones of Candida albicans in HIV-infected individuals with and without symptomatic oral candidiasis. J Med Microbiol 2003; 52:349-359. [PMID: 12676875 DOI: 10.1099/jmm.0.04972-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although HIV-infected individuals harbour multiple strains of oral Candida albicans, little is known of their micro-evolution over time. Therefore, a prospective study was conducted with 16 HIV-infected ethnic Chinese individuals with and without symptoms of oropharyngeal candidiasis to evaluate the genotype distribution of oral C. albicans isolates during HIV disease progression. Oral-rinse samples were obtained from all individuals and up to five C. albicans colonies were selected for each visit, over a 12 month period of multiple visits. After identification of isolates using standard mycological criteria, the genetic similarities of yeast isolates within and between sequential clones of C. albicans were assessed by DNA fingerprinting through random amplification of polymorphic DNA (RAPD). The results of RAPD gel profiles and the lineage of each isolate were further analysed using commercially available software. RAPD studies revealed the prevalence of up to 14 different genotypes per individual during the study period, with multiple genotypes isolated simultaneously from a single oral rinse. Computer analysis of RAPD profiles revealed that yeasts isolated over sequential visits from symptomatic individuals demonstrated a striking level of relatedness compared with isolates from asymptomatic individuals. Genetically identical C. albicans strains also formed 'loosely' connected subclusters that overlapped multiple visits, implying genetic 'shuffling' in these isolates during disease progression. These data point to varying evolutionary genetic trends in C. albicans associated with symptomatic oral candidiasis and asymptomatic carriage in HIV disease.
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Affiliation(s)
- Y H Samaranayake
- Oral Bio-sciences, Faculty of Dentistry, University of Hong Kong, Hong Kong 2Department of Biochemistry, Chinese University, Hong Kong
| | - L P Samaranayake
- Oral Bio-sciences, Faculty of Dentistry, University of Hong Kong, Hong Kong 2Department of Biochemistry, Chinese University, Hong Kong
| | - R S Dassanayake
- Oral Bio-sciences, Faculty of Dentistry, University of Hong Kong, Hong Kong 2Department of Biochemistry, Chinese University, Hong Kong
| | - J Y Y Yau
- Oral Bio-sciences, Faculty of Dentistry, University of Hong Kong, Hong Kong 2Department of Biochemistry, Chinese University, Hong Kong
| | - W K Tsang
- Oral Bio-sciences, Faculty of Dentistry, University of Hong Kong, Hong Kong 2Department of Biochemistry, Chinese University, Hong Kong
| | - B P K Cheung
- Oral Bio-sciences, Faculty of Dentistry, University of Hong Kong, Hong Kong 2Department of Biochemistry, Chinese University, Hong Kong
| | - K W S Yeung
- Oral Bio-sciences, Faculty of Dentistry, University of Hong Kong, Hong Kong 2Department of Biochemistry, Chinese University, Hong Kong
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White PL, Shetty A, Barnes RA. Detection of seven Candida species using the Light-Cycler system. J Med Microbiol 2003; 52:229-238. [PMID: 12621088 DOI: 10.1099/jmm.0.05049-0] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Due to the limitations of classical methods for the detection of systemic fungal infections and the high mortality rates associated with these infections, it has become essential to develop a quick, sensitive and specific detection assay. By using the Idaho Technologies Light-Cycler system, a qualitative real-time PCR system has been developed for the detection of the leading causes of systemic infection within the genus Candida. The sensitivity of the assay was comparable to previously described PCR methods (1-5 c.f.u. ml(-1)) and, by the use of a single Candida probe, it was able to detect, but not differentiate between, seven species of Candida (Candida albicans, Candida dubliniensis, Candida glabrata, Candida kefyr, Candida krusei, Candida parapsilosis and Candida tropicalis). Single-round amplification on the Light-Cycler allowed rapid turn-around of clinical samples (within one working day) and it was shown to be more sensitive than classical procedures, exposing 39 possible systemic infections that were not detected by blood culture.
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Affiliation(s)
- P Lewis White
- Department of Medical Microbiology and PHLS, University Hospital Wales, Heath Park, Cardiff CF14 4XN, UK
| | - Anjali Shetty
- Department of Medical Microbiology and PHLS, University Hospital Wales, Heath Park, Cardiff CF14 4XN, UK
| | - Rosemary A Barnes
- Department of Medical Microbiology and PHLS, University Hospital Wales, Heath Park, Cardiff CF14 4XN, UK
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31
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Sampaio P, Gusmão L, Alves C, Pina-Vaz C, Amorim A, Pais C. Highly polymorphic microsatellite for identification of Candida albicans strains. J Clin Microbiol 2003; 41:552-7. [PMID: 12574245 PMCID: PMC149659 DOI: 10.1128/jcm.41.2.552-557.2003] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The polymorphism of a new microsatellite locus (CAI) was investigated in a total of 114 Candida albicans strains, including 73 independent clinical isolates, multiple isolates from the same patient, isolates from several episodes of recurrent vulvovaginal infections, and two reference strains. PCR genotyping was performed automatically, using a fluorescence-labeled primer, and in the 73 independent isolates, 26 alleles and 44 different genotypes were identified, resulting in a discriminatory power of 0.97. CAI was revealed to be species specific and showed a low mutation rate, since no amplification product was obtained when testing other pathogenic Candida species and no genotype differences were observed when testing over 300 generations. When applying this microsatellite to the identification of strains isolated from recurrent vulvovaginal infections in eight patients, it was found that 13 out of 15 episodes were due to the same strain. When multiple isolates, obtained from the same patient and plated simultaneously, were typed for CAI, the same genotype was found in each case, confirming that the infecting population was clonal. Moreover, the same genotype appeared in isolates from the rectum and the vagina, revealing that the former could be a reservoir of potentially pathogenic strains. This new microsatellite proves to be a valuable tool to differentiate C. albicans strains. Furthermore, when compared to other molecular genotyping techniques, CAI proved to be very simple, highly efficient, and reproducible, being suitable for low-quantity and very-degraded samples and for application in large-scale epidemiological studies.
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Affiliation(s)
- Paula Sampaio
- Centro de Ciências do Ambiente, Departamento de Biologia, Universidade do Minho, 4710-057 Braga, Portugal
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32
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Vargas KG, Joly S. Carriage frequency, intensity of carriage, and strains of oral yeast species vary in the progression to oral candidiasis in human immunodeficiency virus-positive individuals. J Clin Microbiol 2002; 40:341-50. [PMID: 11825940 PMCID: PMC153371 DOI: 10.1128/jcm.40.2.341-350.2002] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2001] [Revised: 09/24/2001] [Accepted: 11/07/2001] [Indexed: 11/20/2022] Open
Abstract
Candida samples were taken over a period of 2 years from 54 human immunodeficiency virus (HIV)-positive asymptomatic subjects to evaluate changes in yeast carriage, intensity of carriage, and genotype over time. Overall, we found that HIV-positive patients with CD4(+)-cell counts of between 200 and 400/microl had significantly more yeast colonization than healthy control subjects. Of the 54 patients, 11 developed thrush. We found that intensity of carriage in these 11 patients increased significantly in the progression from asymptomatic yeast carrier to an episode of oral thrush. Also, the most common yeast species isolated was Candida albicans; however, we did see a number of patients harboring multiple species at the same time. Using the C. albicans-specific probe Ca3, we found that 54% (n = 6) of the 11 patients who developed thrush maintained genetically similar strains throughout the study period, with minor genetic variations in all patients except one. Forty-six percent of these patients had either multiple strains throughout the study period (n = 2), strain replacement (n = 1), or species replacement (n = 2). Of the patients who had multiple strains, one (I4) was infected by two different strains of Candida dubliniensis distinguished by a recently developed species-specific probe. These results suggest that commensal strains colonizing HIV-positive individuals can undergo alterations prior to producing an episode of thrush.
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Affiliation(s)
- Kaaren G Vargas
- College of Dentistry, The University of Iowa, Iowa City, Iowa 52242, USA.
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Botterel F, Desterke C, Costa C, Bretagne S. Analysis of microsatellite markers of Candida albicans used for rapid typing. J Clin Microbiol 2001; 39:4076-81. [PMID: 11682532 PMCID: PMC88489 DOI: 10.1128/jcm.39.11.4076-4081.2001] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To obtain a rapid genotyping method of Candida albicans, three polymorphic microsatellite markers were investigated by multiplex PCR. The three loci, called CDC3, EF3, and HIS3, were chosen because they are on different chromosomes so as to improve the chances of finding polymorphisms. One set of primers was designed for each locus, and one primer of each set was dye-labeled to read PCR signals by using an automatic sequencer. Amplifications were performed directly from the colonies harvested on the agar plate without a sophisticated DNA extraction step. At total of 27 reference strains and 73 clinical independent isolates were tested. The numbers of allelic associations were 10, 22, and 25 for the loci CDC3, EF3, and HIS3, respectively. The combined discriminatory power of the three microsatellites markers was 0.97. The markers were stable after 25 subcultures, and the amplifications were specific for C. albicans. An initial study of 17 clinical isolate pairs, including blood culture and peripheral sites, showed a similar genotype for 15 of them, confirming that candidemia usually originates from the colonizing isolate. Therefore, microsatellite marker analysis with multiplex PCR and automated procedures has a high throughput and should be suitable for large epidemiologic studies of C. albicans.
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Affiliation(s)
- F Botterel
- Laboratoire de Parasitologie-Mycologie, Hôpital H. Mondor et Université Paris XII, 94010 Créteil, France
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Chen YC, Eisner JD, Kattar MM, Rassoulian-Barrett SL, Lafe K, Bui U, Limaye AP, Cookson BT. Polymorphic internal transcribed spacer region 1 DNA sequences identify medically important yeasts. J Clin Microbiol 2001; 39:4042-51. [PMID: 11682528 PMCID: PMC88485 DOI: 10.1128/jcm.39.11.4042-4051.2001] [Citation(s) in RCA: 180] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Species-specific polymorphisms in the noncoding internal transcribed spacer 2 (ITS2) region of the rRNA operon provide accurate identification of clinically significant yeasts. In this study, we tested the hypothesis that ITS1 noncoding regions contain diagnostically useful alleles. The length of ITS1 region PCR products amplified from 40 species (106 clinical strains, 5 reference strains, and 30 type strains) was rapidly determined with single-base precision by automated capillary electrophoresis. Polymorphisms in the PCR product length permitted 19 species to be distinguished by ITS1 alone, compared with 16 species distinguished by using only ITS2. However, combination of both ITS alleles permitted identification of 30 species (98% of clinical isolates). The remaining 10 species with PCR products of similar sizes contained unique ITS alleles distinguishable by restriction enzyme analysis. DNA sequence analysis of amplified ITS1 region DNA from 79 isolates revealed species-specific ITS1 alleles for each of the 40 pathogenic species examined. This provided identification of unusual clinical isolates, and 53 diagnostic ITS1 sequences were deposited in GenBank. Phylogenetic analyses based on ITS sequences showed a similar overall topology to 26S rRNA gene-based trees. However, different species with identical 26S sequences contained distinct ITS alleles that provided species identification with strong statistical support. Together, these data indicate that the analysis of ITS polymorphisms can reliably identify 40 species of clinically significant yeasts and that the capacity for identifying potentially new pathogenic species by using this database holds significant promise.
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Affiliation(s)
- Y C Chen
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA
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Bartie KL, Williams DW, Wilson MJ, Potts AJ, Lewis MA. PCR fingerprinting of Candida albicans associated with chronic hyperplastic candidosis and other oral conditions. J Clin Microbiol 2001; 39:4066-75. [PMID: 11682531 PMCID: PMC88488 DOI: 10.1128/jcm.39.11.4066-4075.2001] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The purpose of this study was to genotype strains of Candida albicans to determine whether specific types were associated with chronic hyperplastic candidosis (CHC). A total of 67 candidal isolates from CHC patients (n = 17) and from patients with other oral conditions (n = 21) were genotyped by PCR fingerprinting employing two interrepeat primer combinations (1245 and 1246 primers or 1251 primer) and a single minisatellite-specific M13 primer. The most suitable primer for fingerprint analysis was found to be primer 1251, yielding well-resolved banding patterns. For the 67 isolates tested, PCR fingerprinting delineated 25 (1245 and 1246 primers), 27 (1251 primer), and 25 (M13 primer) profiles. The majority of C. albicans isolates from multiple sites within the mouth produced identical profiles (six out of nine subjects examined). For patients for whom a series of longitudinal isolates was available, strain persistence for up to 7 years was evident for five out of eight individuals, despite episodes of antifungal therapy. Computer-assisted comparison of the interrepeat PCR fingerprints identified seven distinct profiles that were shared among isolates from different individuals. However, no association was evident among isolates of C. albicans from specific clinical conditions. Eight isolates that were initially identified as C. albicans but having atypical PCR profiles were later confirmed as Candida dubliniensis. In conclusion, the genotypic data do not indicate clonal restriction of C. albicans with respect to CHC. Furthermore, these results have demonstrated that in the majority of individuals, colonizing populations of C. albicans are clonal in nature and exhibit strain persistence.
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Affiliation(s)
- K L Bartie
- Department of Oral Surgery, Medicine & Pathology, Dental School, Heath Park, Cardiff, CF14 4XY, United Kingdom
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Lasker BA, Elie CM, Lott TJ, Espinel-Ingroff A, Gallagher L, Kuykendall RJ, Kellum ME, Pruitt WR, Warnock DW, Rimland D, McNeil MM, Reiss E. Molecular epidemiology of Candida albicans strains isolated from the oropharynx of HIV-positive patients at successive clinic visits. Med Mycol 2001; 39:341-52. [PMID: 11556764 DOI: 10.1080/mmy.39.4.341.352] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Candida albicans strain diversity and fluconazole resistance were prospectively analyzed in oral strains from 29 adult human immunodeficiency virus (HIV)-positive patients followed for > 1 year who had five or more culture-positive clinic visits. Molecular typing consisted of genomic blots probed with the Ca3 repetitive element. Sixteen patients had one or more episodes of oropharyngeal candidiasis (OPC), 12 (75%) maintained the original genotype, whereas the remaining four patients had a succession of 2-3 genotypes. The original genotype, either alone or mixed with another strain or with non-C. albicans Candida spp., was recovered from oral lesions in 13 of 15 evaluable (86.7%) patients. C. dubliniensis was the infecting yeast in the remaining two patients. Different patterns of fluconazole resistance occurred in three OPC patients. One patient's infecting strain became less susceptible. A second patient was infected with a resistant genotype and a progressively more susceptible minor genotype variant. C. dubliniensis isolates from the third patient varied in susceptibility. Thirteen colonized patients who never developed OPC harbored a greater variety of C. albicans genotypes (2-6) than their infected counterparts (P = 0.35). OPC patients maintained their original endogenous C. albicans strains for prolonged periods, whether or not they demonstrated decreased in vitro susceptibility to fluconazole. The adaptation and maintenance of an endogenous C. albicans strain within its host may be linked to as yet uncharacterized factors.
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Affiliation(s)
- B A Lasker
- Mycotic Diseases Branch, Division of Bacterial and Mycotic Diseases, National Cancer for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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Shemer R, Weissman Z, Hashman N, Kornitzer D. A highly polymorphic degenerate microsatellite for molecular strain typing of Candida krusei. MICROBIOLOGY (READING, ENGLAND) 2001; 147:2021-2028. [PMID: 11495980 DOI: 10.1099/00221287-147-8-2021] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Simple sequence repeats, due to their high variability, are widely used for molecular epidemiology of pathogenic micro-organisms. However, their usefulness is restricted by their high instability and low information content. Here, a locus, CKTNR, in the fungal pathogen Candida krusei is described which displays considerable sequence, as well as length, heterogeneity. Alleles of this locus, which contains a degenerate trinucleotide repeat, appear to be stable. The CKTNR polymorphism could serve as the basis for a molecular typing system of C. krusei. Furthermore, analysis of the CKTNR allele distribution suggested that C. krusei reproduces mainly clonally.
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Affiliation(s)
- Revital Shemer
- Department of Molecular Microbiology, B. Rappaport Faculty of Medicine1, and Department of Clinical Microbiology2, Rambam Medical Center, Haifa 31096, Israel
| | - Ziva Weissman
- Department of Molecular Microbiology, B. Rappaport Faculty of Medicine1, and Department of Clinical Microbiology2, Rambam Medical Center, Haifa 31096, Israel
| | - Nehama Hashman
- Department of Molecular Microbiology, B. Rappaport Faculty of Medicine1, and Department of Clinical Microbiology2, Rambam Medical Center, Haifa 31096, Israel
| | - Daniel Kornitzer
- Department of Molecular Microbiology, B. Rappaport Faculty of Medicine1, and Department of Clinical Microbiology2, Rambam Medical Center, Haifa 31096, Israel
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Waltimo TM, Dassanayake RS, Ørstavik D, Haapasalo MP, Samaranayake LP. Phenotypes and randomly amplified polymorphic DNA profiles of Candida albicans isolates from root canal infections in a Finnish population. ORAL MICROBIOLOGY AND IMMUNOLOGY 2001; 16:106-12. [PMID: 11240864 DOI: 10.1034/j.1399-302x.2001.016002106.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A total of thirty-seven Candida albicans isolates from root canal infections in a Finnish population were subtyped using phenotypic and genotypic methods. A previously described biotyping method based on the presence of five different enzymes, assimilation of eleven different carbohydrates and boric acid sensitivity of the yeasts was used to determine the phenotype. Commercially available API ZYM and API 20 C test kits were used to determine the presence of enzymes and assimilation of carbohydrates. The sensitivity of the isolates to boric acid was tested by their ability to grow on yeast-nitrogen-agar with incorporated boric acid (1.8 mg. ml(-1)). Combination of the tests revealed a total of 14 different phenotypes. The majority of the isolates, 26 strains, were classifiable into three major phenotypes: 16 isolates (43.2%) belonged to phenotype A1R, six (16.2%) to A1S and four (10.8%) to B1S. The remaining 11 phenotypes represented only a single isolate each. The randomly amplified polymorphic DNA profiles were used to determine the genotypes. For this purpose two different primers, RSD6 and RSD12 were used to develop a combination randomly amplified polymorphic DNA profile for each isolate. Altogether 31 genotypes were noted among the 37 isolates, of which only three pairs of isolates presented with congruent phenotypic and genotypic profiles. The heterogeneity of both the phenotypic and randomly amplified polymorphic DNA profiles of C. albicans isolates from root canal infections is akin to previous reports from other oral and non-oral sources in different geographic locales.
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Affiliation(s)
- T M Waltimo
- NIOM, Scandinavian Institute of Dental Materials, Haslum, Norway
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Daniels W, Glover DD, Essmann M, Larsen B. Candidiasis during pregnancy may result from isogenic commensal strains. Infect Dis Obstet Gynecol 2001; 9:65-73. [PMID: 11495556 PMCID: PMC1784641 DOI: 10.1155/s1064744901000138] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE Our laboratory previously demonstrated that asymptomatic vaginal colonization during pregnancy is a factor predisposing patients to subsequent symptomatic vulvovaginal candidiasis. It is unknown whether symptoms result from strain replacement or a change in host relationship to the original colonizing strain. This study was undertaken to determine whether Candida albicans isolates from asymptomatic women could be responsible for subsequent symptomatic vaginitis. METHODS We retained isolates of C. albicans from women followed longitudinally through pregnancy, and identified six pairs of cultures from women who were colonized without symptoms and who later became symptomatic (average time 14 weeks). We used a random amplification of polymorphic DNA (RAPD) analysis to determine whether isolates from our study patients were genetically similar or dissimilar. RESULTS Analysis of these pairs of yeast strains by RAPD revealed that five of the six women had symptoms apparently due to the same yeast strain that was found initially as a commensal strain. To increase the power of these observations, we also performed RAPD analysis on six randomly selected yeast strains from other women in this study who had not become symptomatic to determine whether any of these unrelated strains matched strains from those women who became symptomatic. CONCLUSION Symptomatic yeast vaginitis is usually due to strains of C. albicans already carried in the lower genital tract, underscoring the need to understand regulation of growth and virulence of the organism in vivo.
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Affiliation(s)
- Wayne Daniels
- Infectious Disease Research LaboratoryDes Moines University Osteopathic Medical Center3200 Grand AvenueDes MoinesIA50312USA
| | - Douglas D. Glover
- Infectious Disease Research LaboratoryDes Moines University Osteopathic Medical Center3200 Grand AvenueDes MoinesIA50312USA
| | - Michael Essmann
- Consortium on Reproductive and Developmental HealthRobert C. Byrd Health Sciences Center of the
West Virginia UniversityMorgantownWVUSA
| | - Bryan Larsen
- Infectious Disease Research LaboratoryDes Moines University Osteopathic Medical Center3200 Grand AvenueDes MoinesIA50312USA
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40
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Dalle F, Franco N, Lopez J, Vagner O, Caillot D, Chavanet P, Cuisenier B, Aho S, Lizard S, Bonnin A. Comparative genotyping of Candida albicans bloodstream and nonbloodstream isolates at a polymorphic microsatellite locus. J Clin Microbiol 2000; 38:4554-9. [PMID: 11101595 PMCID: PMC87636 DOI: 10.1128/jcm.38.12.4554-4559.2000] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular typing studies have shown that the predominant form of reproduction of Candida albicans is clonal and that, in a majority of situations, persistent or recurrent infections are due to a unique strain. Characterization of distinct subpopulations and correlation with clinical features may thus be important to understanding the pathogenesis of candidiasis. In a clonal model, a unique polymorphic marker may identify populations with different biological properties. We therefore compared 48 bloodstream isolates and 48 nonbloodstream matched strains of C. albicans at the elongation factor 3-encoding gene (CEF3) polymorphic microsatellite locus of C. albicans. Sizing of the alleles was performed by automated capillary electrophoresis. A new, 137-bp allele was characterized, and seven nondescribed combinations were observed, resulting in 15 and 11 distinct CEF3 profiles in bloodstream and control strains, respectively. Genotypes 126-135, 130-136, and 131-131 accounted for 60.4% of both bloodstream and control strains. Four bloodstream isolates but no control strains displayed the 135-135 combination. None of the other genotypes was present at an increased frequency in bloodstream isolates. Bloodstream and nonbloodstream strains of C. albicans thus have a heterogeneous structure at the CEF3 locus, with three major and multiple minor allelic combinations.
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Affiliation(s)
- F Dalle
- Laboratoire de Parasitologie et Mycologie, and Laboratoire de Génétique Moléculaire, Centre George François Leclerc, Dijon, France
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Deak T, Chen J, Beuchat LR. Molecular characterization of Yarrowia lipolytica and Candida zeylanoides isolated from poultry. Appl Environ Microbiol 2000; 66:4340-4. [PMID: 11010879 PMCID: PMC92305 DOI: 10.1128/aem.66.10.4340-4344.2000] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yeast isolates from raw and processed poultry products were characterized using PCR amplification of the internally transcribed spacer (ITS) 5.8S ribosomal DNA region (ITS-PCR), restriction analysis of amplified products, randomly amplified polymorphic DNA (RAPD) analysis, and pulsed-field gel electrophoresis (PFGE). ITS-PCR resulted in single fragments of 350 and 650 bp, respectively, from eight strains of Yarrowia lipolytica and seven strains of Candida zeylanoides. Digestion of amplicons with HinfI and HaeIII produced two fragments of 200 and 150 bp from Y. lipolytica and three fragments of 350, 150, and 100 bp from C. zeylanoides, respectively. Although these fragments showed species-specific patterns and confirmed species identification, characterization did not enable intraspecies typing. Contour-clamped heterogeneous electric field PFGE separated chromosomal DNA of Y. lipolytica into three to five bands, most larger than 2 Mbp, whereas six to eight bands in the range of 750 to 2,200 bp were obtained from C. zeylanoides. Karyotypes of both yeasts showed different polymorphic patterns among strains. RAPD analysis, using enterobacterial repetitive intergenic sequences as primers, discriminated between strains within the same species. Cluster analysis of patterns formed groups that correlated with the source of isolation. For ITS-PCR, extraction of DNA by boiling yeast cells was successfully used.
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Affiliation(s)
- T Deak
- Center for Food Safety and Quality Enhancement, University of Georgia, Griffin, Georgia 30223-1797, USA
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Abstract
DNA fingerprinting methods have evolved as major tools in fungal epidemiology. However, no single method has emerged as the method of choice, and some methods perform better than others at different levels of resolution. In this review, requirements for an effective DNA fingerprinting method are proposed and procedures are described for testing the efficacy of a method. In light of the proposed requirements, the most common methods now being used to DNA fingerprint the infectious fungi are described and assessed. These methods include restriction fragment length polymorphisms (RFLP), RFLP with hybridization probes, randomly amplified polymorphic DNA and other PCR-based methods, electrophoretic karyotyping, and sequencing-based methods. Procedures for computing similarity coefficients, generating phylogenetic trees, and testing the stability of clusters are then described. To facilitate the analysis of DNA fingerprinting data, computer-assisted methods are described. Finally, the problems inherent in the collection of test and control isolates are considered, and DNA fingerprinting studies of strain maintenance during persistent or recurrent infections, microevolution in infecting strains, and the origin of nosocomial infections are assessed in light of the preceding discussion of the ins and outs of DNA fingerprinting. The intent of this review is to generate an awareness of the need to verify the efficacy of each DNA fingerprinting method for the level of genetic relatedness necessary to answer the epidemiological question posed, to use quantitative methods to analyze DNA fingerprint data, to use computer-assisted DNA fingerprint analysis systems to analyze data, and to file data in a form that can be used in the future for retrospective and comparative studies.
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Abstract
DNA fingerprinting methods have evolved as major tools in fungal epidemiology. However, no single method has emerged as the method of choice, and some methods perform better than others at different levels of resolution. In this review, requirements for an effective DNA fingerprinting method are proposed and procedures are described for testing the efficacy of a method. In light of the proposed requirements, the most common methods now being used to DNA fingerprint the infectious fungi are described and assessed. These methods include restriction fragment length polymorphisms (RFLP), RFLP with hybridization probes, randomly amplified polymorphic DNA and other PCR-based methods, electrophoretic karyotyping, and sequencing-based methods. Procedures for computing similarity coefficients, generating phylogenetic trees, and testing the stability of clusters are then described. To facilitate the analysis of DNA fingerprinting data, computer-assisted methods are described. Finally, the problems inherent in the collection of test and control isolates are considered, and DNA fingerprinting studies of strain maintenance during persistent or recurrent infections, microevolution in infecting strains, and the origin of nosocomial infections are assessed in light of the preceding discussion of the ins and outs of DNA fingerprinting. The intent of this review is to generate an awareness of the need to verify the efficacy of each DNA fingerprinting method for the level of genetic relatedness necessary to answer the epidemiological question posed, to use quantitative methods to analyze DNA fingerprint data, to use computer-assisted DNA fingerprint analysis systems to analyze data, and to file data in a form that can be used in the future for retrospective and comparative studies.
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Affiliation(s)
- D R Soll
- Department of Biological Sciences, University of Iowa, Iowa City, IA 52242, USA.
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Xu J, Ramos AR, Vilgalys R, Mitchell TG. Clonal and spontaneous origins of fluconazole resistance in Candida albicans. J Clin Microbiol 2000; 38:1214-20. [PMID: 10699025 PMCID: PMC86380 DOI: 10.1128/jcm.38.3.1214-1220.2000] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genotypes and susceptibilities to fluconazole of 78 strains of the human pathogenic yeast Candida albicans were compared. The strains comprised two sets of samples from Durham, N.C.: one from patients infected with the human immunodeficiency virus (HIV) and the other from healthy volunteers. For each strain, the MIC of fluconazole was determined by the standard National Committee for Clinical Laboratory Standards protocol. Genotypes were determined by PCR fingerprinting with five separate primers. The analysis revealed little evidence for genotypic clustering according to HIV status or body site. However, a small group of fluconazole-resistant strains isolated from patients infected with HIV formed a distinct cluster. In addition, two fluconazole-resistant strains were isolated from individuals who never took fluconazole, one from a patient infected with HIV and the other from a healthy person. The results suggest both clonal and spontaneous origins of fluconazole resistance in C. albicans.
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Affiliation(s)
- J Xu
- Department of Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA.
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Richard GF, Hennequin C, Thierry A, Dujon B. Trinucleotide repeats and other microsatellites in yeasts. Res Microbiol 1999; 150:589-602. [PMID: 10672999 DOI: 10.1016/s0923-2508(99)00131-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Microsatellites are direct tandem DNA repeats found in all genomes. A particular class of microsatellites, called trinucleotide repeats, is responsible for a number of neurological disorders in humans. We review here our current state of knowledge on trinucleotide repeat instability, and discuss the molecular mechanisms that may be involved in trinucleotide repeat expansions leading to fatal diseases in humans. We also present original data on microsatellite distribution in several microbial genomes, and on the use of microsatellites as physical markers to accurately and easily genotype yeast strains.
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Affiliation(s)
- G F Richard
- Unité de génétique moléculaire des levures, URA1300 CNRS, UFR927, université Pierre et Marie Curie, Institut Pasteur, Paris, France
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Davis CL, Field D, Metzgar D, Saiz R, Morin PA, Smith IL, Spector SA, Wills C. Numerous length polymorphisms at short tandem repeats in human cytomegalovirus. J Virol 1999; 73:6265-70. [PMID: 10400717 PMCID: PMC112704 DOI: 10.1128/jvi.73.8.6265-6270.1999] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/1999] [Accepted: 04/12/1999] [Indexed: 11/20/2022] Open
Abstract
We show the presence of numerous short tandem repeats in the human cytomegalovirus (HCMV) genome and assess their usefulness as molecular markers. The genome is shown to contain at least 24 microsatellite regions that exhibit length polymorphisms. Insertion-deletion polymorphisms at these short tandem repeats are common (80% of repeats examined are polymorphic among two laboratory strains and 10 clinical isolates). This is the first report of widespread microsatellite length polymorphism in a viral genome. Some regions are highly polymorphic: one was revealed by DNA sequencing to contain length variants at five closely linked sites, which combined resulted in 10 variants for this region among the 12 strains and isolates examined. This study not only provides a new molecular marker system for this virus but also extends our understanding of microsatellite polymorphism in two important ways. First, variable-length repeats in HCMV can be considerably shorter than polymorphic repeats previously found in other organisms. Second, highly variable microsatellite repeats are not confined to prokaryotes and eukaryotes, as previously assumed. This variation provides a useful marker system for distinguishing viral isolates, and similar markers are also likely to be found in other large-genome DNA viruses.
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Affiliation(s)
- C L Davis
- Department of Biology, University of California, San Diego, La Jolla, California 92093-0116, USA.
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