1
|
Aboul-Ella H, Hamed R, Abo-Elyazeed H. Recent trends in rapid diagnostic techniques for dermatophytosis. Int J Vet Sci Med 2020; 8:115-123. [PMID: 33426048 PMCID: PMC7751388 DOI: 10.1080/23144599.2020.1850204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/24/2020] [Accepted: 11/09/2020] [Indexed: 11/04/2022] Open
Abstract
Dermatophytosis is a common contagious disease of both humans and animals. It is caused by a group of filamentous fungi known as dermatophytes, including several genera and various species. An accurate diagnosis of dermatophytes as a causative agent of a skin lesion requires up to one month of conventional laboratory diagnostics. The conventional gold standard diagnostic method is a direct microscopic examination followed by 3 to 4 weeks of Sabouraud's dextrose agar (SDA) culturing, and it may require further post-culturing identification through biochemical tests or microculture technique application. The laborious, exhaustive, and time-consuming gold standard method was a real challenge facing all dermatologists to achieve a rapid, accurate dermatophytosis diagnosis. Various studies developed more rapid, accurate, reliable, sensitive, and specific diagnostic tools. All developed techniques showed more rapidity than the classical method but variable specificities and sensitivities. An extensive bibliography is included and discussed through this review, showing recent variable dermatophytes diagnostic categories with an illustration of weaknesses, strengths, and prospects.
Collapse
Affiliation(s)
- Hassan Aboul-Ella
- Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, GizaEgypt
| | - Rafik Hamed
- Bacteriology Biotechnology Diagnostics Department, Institute for Evaluation of Veterinary Biologics (CLEVB), Agricultural Research Center (ARC), Cairo, Egypt
| | - Heidy Abo-Elyazeed
- Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, GizaEgypt
| |
Collapse
|
2
|
Identification of pathogens causing invasive fungal rhinosinusitis in surgical biopsies using polymerase chain reaction. J Laryngol Otol 2020; 134:632-635. [PMID: 32686637 DOI: 10.1017/s0022215120001395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND Invasive fungal rhinosinusitis is associated with high morbidity and mortality. Rapid pathogen identification is mandatory, but fresh tissue is not always available. A polymerase chain reaction method was designed in order to detect fungi in formalin-fixed paraffin-embedded samples. This was applied to a retrospective series of tissue biopsies from Thai patients with invasive fungal rhinosinusitis. METHODS Tissue blocks from 64 cases yielded adequate DNA. Three sequential polymerase chain reaction were performed: ZP3 (housekeeping gene) and panfungal polymerase chain reactions, and a differentiating polymerase chain reaction based on the 5.8s ribosomal RNA and internal transcribed spacer 2 regions. The polymerase chain reaction products were then sequenced. RESULTS Polymerase chain reaction identified a fungal pathogen in 20 of 64 cases (31 per cent). Aspergillus species was the most common cause of invasive fungal rhinosinusitis (nine cases). Other causes included candida (n = 4), cladosporium (n = 4), mucor (n = 1), alternaria (n = 1) and dendryphiella (n = 1) species. CONCLUSION Polymerase chain reaction can provide rapid identification of fungal pathogens in paraffin-embedded tissue, enabling prompt treatment of invasive fungal rhinosinusitis.
Collapse
|
3
|
A 16-year retrospective study on fungal prevalence and diversity in patients with cystic fibrosis: Candida dubliniensis was associated with a decline in lung function. Int J Infect Dis 2020; 96:663-670. [PMID: 32450290 DOI: 10.1016/j.ijid.2020.05.063] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 01/13/2023] Open
Abstract
OBJECTIVES To study the prevalence of fungal species in cystic fibrosis (CF) patients over a 16 years period. To examine the impact of Candida albicans (C. albicans), Candida dubliniensis (C. dubliniensis) and Aspergillus fumigatus (A. fumigatus) on lung function. METHODS Observational single-center cohort study (2000-2015) including 133 CF patients (ages 6-66 years). Linear mixed models with autoregressive covariance matrix were used. RESULTS The most common fungus was C. albicans (prevalence 62%) followed by A. fumigatus (22%) and C. dubliniensis (11%). In the initial year of detection, there was no impact of C. albicans, C. dubliniensis or A. fumigatus on lung function. However, one and two years after detection of C. dubliniensis a reduction in percent predicted forced expiratory volume in the first second (ppFEV1) was observed of 3.8% (p = 0.022) and 4.1% (p = 0.017), respectively, compared with CF patients without these findings. Furthermore, patients with positive cultures for any of these fungal species for three consecutive years exhibited a decline in lung function: C. dubliniensis, 7.6% reduction in ppFEV1 (p = 0.001); A. fumigatus, 4.9% (p = 0.007); C. albicans, 2.6% (p = 0.014). The results were adjusted for age, CFTR genotype, chronic and intermittent P. aeruginosa colonization, and numbers of intravenous antibiotic treatments per year. Persistence of C. dubliniensis for three consecutive years was positively correlated to age and erythrocyte sedimentation rate (ESR) (both p = 0.001). CONCLUSIONS Cystic fibrosis patients who were cultured positive for C. dubliniensis, C. albicans or A. fumigatus in sputum exhibited a decline in ppFEV1 over time. The effect was most pronounced for C. dubliniensis.
Collapse
|
4
|
Evaluation of Fluorescent Capillary Electrophoresis for Rapid Identification of Candida Fungal Infections. J Clin Microbiol 2016; 54:1295-303. [PMID: 26935732 DOI: 10.1128/jcm.00118-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 02/19/2016] [Indexed: 12/13/2022] Open
Abstract
Early diagnosis of fungal infection is critical for initiating antifungal therapy and reducing the high mortality rate in immunocompromised patients. In this study, we focused on rapid and sensitive identification of clinically important Candida species, utilizing the variability in the length of the ITS2 rRNA gene and fluorescent capillary electrophoresis (f-ITS2-PCR-CE). The method was developed and optimized on 29 various Candida reference strains from which 26 Candida species were clearly identified, while Candida guilliermondii, C. fermentati, and C. carpophila, which are closely related, could not be distinguished. The method was subsequently validated on 143 blinded monofungal clinical isolates (comprising 26 species) and was able to identify 88% of species unambiguously. This indicated a higher resolution power than the classical phenotypic approach which correctly identified 73%. Finally, the culture-independent potential of this technique was addressed by the analysis of 55 retrospective DNA samples extracted directly from clinical material. The method showed 100% sensitivity and specificity compared to those of the combined results of cultivation and panfungal PCR followed by sequencing used as a gold standard. In conclusion, this newly developed f-ITS2-PCR-CE analytical approach was shown to be a fast, sensitive, and highly reproducible tool for both culture-dependent and culture-independent identification of clinically important Candida strains, including species of the "psilosis" complex.
Collapse
|
5
|
Gobeil-Richard M, Tremblay DM, Beaulieu C, Van der Heyden H, Carisse O. A pyrosequencing-based method to quantify genetic substitutions associated with resistance to succinate dehydrogenase inhibitor fungicides in Botrytis spp. populations. PEST MANAGEMENT SCIENCE 2016; 72:566-573. [PMID: 25900263 DOI: 10.1002/ps.4026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 04/14/2015] [Accepted: 04/16/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND The genetic underlying resistance mechanisms in the population of the phytopathogenic fungus Botrytis cinerea are well documented. Specifically, several genetic substitutions associated with succinate dehydrogenase inhibitor (SDHI)-based fungicide resistance have been identified in the succinate dehydrogenase gene. The objective of the present work was to develop a molecular tool for accurate quantification of these genetic substitutions within Botrytis populations. A test using the PyroMark Q24 instrument was designed to detect and quantify five genetic substitutions associated with SDHI resistance. RESULTS The technique is based on sequencing by synthesis, and it generated quantitative and accurate data with a limit of quantification of a minimum of 500 spores. There was a linear relationship between the known and estimated percentages of spores with the targeted genetic substitutions and wild-type strains at ratios of 0-100%, with a 20% increment. CONCLUSION With the pyrosequencing assay developed in this study, a large number of Botrytis spp. individuals can be characterised in a timely fashion with greater accuracy than by commonly used methods. Hence, pyrosequencing-based methods will be useful for improving our understanding of fungicide resistance, detecting the arrival of new genetic substitutions, monitoring shifts in fungal populations and assessing the effectiveness of antiresistance strategies, and for routine monitoring of fungicide resistance.
Collapse
Affiliation(s)
- Mélanie Gobeil-Richard
- Biology Department, University of Sherbrooke, Sherbrooke, Quebec, Canada
- Horticulture Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, Quebec, Canada
| | - David-Mathieu Tremblay
- Horticulture Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, Quebec, Canada
| | - Carole Beaulieu
- Biology Department, University of Sherbrooke, Sherbrooke, Quebec, Canada
| | | | - Odile Carisse
- Horticulture Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, Quebec, Canada
| |
Collapse
|
6
|
Fraser M, Brown Z, Houldsworth M, Borman AM, Johnson EM. Rapid identification of 6328 isolates of pathogenic yeasts using MALDI-ToF MS and a simplified, rapid extraction procedure that is compatible with the Bruker Biotyper platform and database. Med Mycol 2015; 54:80-8. [PMID: 26591008 DOI: 10.1093/mmy/myv085] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 08/11/2015] [Indexed: 12/31/2022] Open
Abstract
Rapid and accurate identification of yeast isolates from clinical samples is essential, given their innately variable antifungal susceptibility profiles, and the proposal of species-specific antifungal susceptibility interpretive breakpoints. Here we have evaluated the utility of MALDI-ToF MS analysis for the identification of clinical isolates of pathogenic yeasts. A simplified, rapid extraction method, developed in our laboratory, was applied to 6343 isolates encompassing 71 different yeast species, which were then subjected to MALDI-ToF MS analysis using a Bruker Microflex and the resulting spectra were assessed using the supplied Bruker database. In total, 6328/6343 (99.8%) of isolates were correctly identified by MALDI-ToF MS. Our simplified extraction protocol allowed the correct identification of 93.6% of isolates, without the need for laborious full extraction, and a further 394 (6.2%) of isolates could be identified after full extraction. Clinically relevant identifications with both extraction methods were achieved using the supplied Bruker database and did not require the generation of bespoke, in-house databases created using profiles obtained with the adapted extraction method. In fact, the mean LogScores obtained using our method were as robust as those obtained using the recommended, published full extraction procedures. However, an in-house database can provide a useful additional identification tool for unusual or rarely encountered organisms. Finally, the proposed methodology allowed the correct identification of over 75% of isolates directly from the initial cultures referred to our laboratory, without the requirement for additional sub-culture on standardised mycological media.
Collapse
Affiliation(s)
- Mark Fraser
- UK National Mycology Reference Laboratory, Public Health England, Bristol, United Kingdom
| | - Zoe Brown
- UK National Mycology Reference Laboratory, Public Health England, Bristol, United Kingdom
| | - Marian Houldsworth
- UK National Mycology Reference Laboratory, Public Health England, Bristol, United Kingdom
| | - Andrew M Borman
- UK National Mycology Reference Laboratory, Public Health England, Bristol, United Kingdom
| | - Elizabeth M Johnson
- UK National Mycology Reference Laboratory, Public Health England, Bristol, United Kingdom
| |
Collapse
|
7
|
Nemcova E, Cernochova M, Ruzicka F, Malisova B, Freiberger T, Nemec P. Rapid identification of medically important Candida isolates using high resolution melting analysis. PLoS One 2015; 10:e0116940. [PMID: 25689781 PMCID: PMC4331273 DOI: 10.1371/journal.pone.0116940] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/17/2014] [Indexed: 11/18/2022] Open
Abstract
An increasing trend in non albicans infections and various susceptibility patterns to antifungal agents implies a requirement for the quick and reliable identification of a number of medically important Candida species. Real-time PCR followed by high resolution melting analysis (HRMA) was developed, tested on 25 reference Candida collection strains and validated on an additional 143 clinical isolates in this study. All reference strains and clinical isolates inconclusive when using phenotypic methods and/or HRMA were analysed using ITS2 sequencing. Considering reference and clinical strains together, 23 out of 27 Candida species could be clearly distinguished by HRMA, while the remaining 4 species were grouped in 2 pairs, when applying the mean Tm ± 3 SD values, the shape of the derivative melting curve (dMelt curve) and, in some cases, the normalized and temperature—shifted difference plot against C. krusei. HRMA as a simple, rapid and inexpensive tool was shown to be useful in identifying a wide spectrum of clinically important Candida species. It may complement the current clinical diagnostic approach based on commercially available biochemical kits.
Collapse
Affiliation(s)
- Eva Nemcova
- Centre for Cardiovascular Surgery and Transplantation Brno, Brno, Czech Republic
- International Clinical Research Centre, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Michaela Cernochova
- Centre for Cardiovascular Surgery and Transplantation Brno, Brno, Czech Republic
- Molecular Immunology and Microbiology, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Filip Ruzicka
- Department of Microbiology, Faculty of Medicine, Masaryk University and St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Barbora Malisova
- Centre for Cardiovascular Surgery and Transplantation Brno, Brno, Czech Republic
- Molecular Immunology and Microbiology, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tomas Freiberger
- Molecular Immunology and Microbiology, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- * E-mail: (TF); (PN)
| | - Petr Nemec
- Centre for Cardiovascular Surgery and Transplantation Brno, Brno, Czech Republic
- International Clinical Research Centre, St. Anne's University Hospital Brno, Brno, Czech Republic
- * E-mail: (TF); (PN)
| |
Collapse
|
8
|
Feasibility of mini-sequencing schemes based on nucleotide polymorphisms for microbial identification and population analyses. Appl Microbiol Biotechnol 2015; 99:2513-21. [DOI: 10.1007/s00253-015-6427-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 11/26/2022]
|
9
|
Abstract
One late afternoon in the beginning of January 1986, bicycling from the lab over the hill to the small village of Fulbourn, the idea for an alternative DNA sequencing technique came to my mind. The basic concept was to follow the activity of DNA polymerase during nucleotide incorporation into a DNA strand by analyzing the pyrophosphate released during the process. Today, the technique is used in multidisciplinary fields in academic, clinical, and industrial settings all over the word. This technique can be used for both single-base sequencing and whole-genome sequencing, depending on the format used.In this chapter, I give my personal account of the development of Pyrosequencing(®)-beginning on a winter day in 1986, when I first envisioned the method-until today, nearly 30 years later.
Collapse
Affiliation(s)
- Pål Nyrén
- Department of Biotechnology, Royal Institute of Technology, Roslagstullsbacken 21, AlbaNova, SE-106 91, Stockholm, Sweden,
| |
Collapse
|
10
|
Loonen AJM, Wolffs PFG, Bruggeman CA, van den Brule AJC. Developments for improved diagnosis of bacterial bloodstream infections. Eur J Clin Microbiol Infect Dis 2014; 33:1687-702. [PMID: 24848132 DOI: 10.1007/s10096-014-2153-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 04/30/2014] [Indexed: 12/26/2022]
Abstract
Bloodstream infections (BSIs) are associated with high mortality and increased healthcare costs. Optimal management of BSI depends on several factors including recognition of the disease, laboratory tests and treatment. Rapid and accurate identification of the etiologic agent is crucial to be able to initiate pathogen specific antibiotic therapy and decrease mortality rates. Furthermore, appropriate treatment might slow down the emergence of antibiotic resistant strains. Culture-based methods are still considered to be the "gold standard" for the detection and identification of pathogens causing BSI. Positive blood cultures are used for Gram-staining. Subsequently, positive blood culture material is subcultured on solid media, and (semi-automated) biochemical testing is performed for species identification. Finally, a complete antibiotic susceptibility profile can be provided based on cultured colonies, which allows the start of pathogen-tailored antibiotic therapy. This conventional workflow is extremely time-consuming and can take up to several days. Furthermore, fastidious and slow-growing microorganisms, as well as antibiotic pre-treated samples can lead to false-negative results. The main aim of this review is to present different strategies to improve the conventional laboratory diagnostic steps for BSI. These approaches include protein-based (MALDI-TOF mass spectrometry) and nucleic acid-based (polymerase chain reaction [PCR]) identification from subculture, blood cultures, and whole blood to decrease time to results. Pathogen enrichment and DNA isolation methods, to enable optimal pathogen DNA recovery from whole blood, are described. In addition, the use of biomarkers as patient pre-selection tools for molecular assays are discussed.
Collapse
Affiliation(s)
- A J M Loonen
- Laboratory for Molecular Diagnostics, Department of Medical Microbiology and Pathology, Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
| | | | | | | |
Collapse
|
11
|
Caboche S, Audebert C, Hot D. High-Throughput Sequencing, a VersatileWeapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology. Pathogens 2014; 3:258-79. [PMID: 25437800 PMCID: PMC4243446 DOI: 10.3390/pathogens3020258] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 02/28/2014] [Accepted: 03/20/2014] [Indexed: 12/19/2022] Open
Abstract
The recent progresses of high-throughput sequencing (HTS) technologies enable easy and cost-reduced access to whole genome sequencing (WGS) or re-sequencing. HTS associated with adapted, automatic and fast bioinformatics solutions for sequencing applications promises an accurate and timely identification and characterization of pathogenic agents. Many studies have demonstrated that data obtained from HTS analysis have allowed genome-based diagnosis, which has been consistent with phenotypic observations. These proofs of concept are probably the first steps toward the future of clinical microbiology. From concept to routine use, many parameters need to be considered to promote HTS as a powerful tool to help physicians and clinicians in microbiological investigations. This review highlights the milestones to be completed toward this purpose.
Collapse
Affiliation(s)
- Ségolène Caboche
- FRE 3642 Molecular and Cellular Medecine, CNRS, Institut Pasteur de Lille and University Lille Nord de France, Lille 59019, France.
| | | | - David Hot
- FRE 3642 Molecular and Cellular Medecine, CNRS, Institut Pasteur de Lille and University Lille Nord de France, Lille 59019, France.
| |
Collapse
|
12
|
Preuner S, Lion T. Towards molecular diagnostics of invasive fungal infections. Expert Rev Mol Diagn 2014; 9:397-9. [DOI: 10.1586/erm.09.27] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
13
|
Candida identification: a journey from conventional to molecular methods in medical mycology. World J Microbiol Biotechnol 2014; 30:1437-51. [PMID: 24379160 DOI: 10.1007/s11274-013-1574-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 12/02/2013] [Indexed: 12/17/2022]
Abstract
The incidence of Candida infections have increased substantially in recent years due to aggressive use of immunosuppressants among patients. Use of broad-spectrum antibiotics and intravascular catheters in the intensive care unit have also attributed with high risks of candidiasis among immunocompromised patients. Among Candida species, C. albicans accounts for the majority of superficial and systemic infections, usually associated with high morbidity and mortality often caused due to increase in antimicrobial resistance and restricted number of antifungal drugs. Therefore, early detection of candidemia and correct identification of Candida species are indispensable pre-requisites for appropriate therapeutic intervention. Since blood culture based methods lack sensitivity, and species-specific identification by conventional method is time-consuming and often leads to misdiagnosis within closely related species, hence, molecular methods may provide alternative for accurate and rapid identification of Candida species. Although, several molecular approaches have been developed for accurate identification of Candida species but the internal transcribed spacer 1 and 2 (ITS1 and ITS2) regions of the rRNA gene are being used extensively in a variety of formats. Of note, ITS sequencing and PCR-RFLP analysis of ITS region seems to be promising as a rapid, easy, and cost-effective method for identification of Candida species. Here, we review a number of existing techniques ranging from conventional to molecular approaches currently in use for the identification of Candida species. Further, advantages and limitations of these methods are also discussed with respect to their discriminatory power, reproducibility, and ease of performance.
Collapse
|
14
|
Preuner S, Lion T. Species-specific identification of a wide range of clinically relevant fungal pathogens by the Luminex(®) xMAP technology. Methods Mol Biol 2013; 968:119-39. [PMID: 23296890 DOI: 10.1007/978-1-62703-257-5_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Invasive fungal infections (IFI) are a common cause of life-threatening events in immunocompromised patients. Early detection and identification of the fungal pathogen is an important prerequisite for timely onset of the most appropriate treatment. Methods based on fungal culture are often too slow to be clinically useful. Other approaches to the identification of fungal species, including molecular techniques, are often restricted to a small number of the most commonly occurring pathogens and are therefore of limited use in the clinical setting. The development of assays for the detection and identification of a broad-range of clinically relevant fungal species is therefore an urgently needed step towards optimized diagnostics of IFI.The Luminex(®) xMAP technology offers a platform for the establishment of multiplex assays permitting high-throughput analysis of up to 100 different target molecules in a single test. Here we describe a Luminex(®)-based multiplex assay permitting rapid detection and identification of 10 fungal genera and 29 different species, including both commonly occurring and emerging fungal pathogens.
Collapse
Affiliation(s)
- S Preuner
- Children's Cancer Research Institute (CCRI), Labdia Labordiagnostik, Vienna, Austria
| | | |
Collapse
|
15
|
Kim JY, Hahn HJ, Choe YB, Lee YW, Ahn KJ, Moon KC. Molecular biological identification of malassezia yeasts using pyrosequencing. Ann Dermatol 2013; 25:73-9. [PMID: 23467187 PMCID: PMC3582932 DOI: 10.5021/ad.2013.25.1.73] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 05/03/2012] [Accepted: 05/04/2012] [Indexed: 11/29/2022] Open
Abstract
Background A Pyrosequencing assay has been used in identification of fungal species such as Candida or Aspergillus and diagnosis of pathogenic bacteria such as Helicobacter pylori but there has been no report on successful isolation and identification of Malassezia yeasts using the pyrosequencing method. Objective Examine the applicability and plausibility of the pyrosequencing method in identification of the Malassezia species. Methods At internal transcribed spacer (ITS) sites 1 and 2, three primers were developed using Pyrosequencing Assay Design Software (Biotage AB). Pyrosequencing was performed on 11 standard strains and 83 genomic DNA samples obtained from 66 healthy controls aged from 1 to 80. Results The eleven Malassezia standard species and 83 genomic DNA samples were successfully identified using the pyrosequencing assay. Conclusion The pyrosequencing method is a new tool for analysis of Malassezia yeasts, and its precision and rapidity suggests its clinical applicability.
Collapse
Affiliation(s)
- Ji Young Kim
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea
| | | | | | | | | | | |
Collapse
|
16
|
Hume ME, Hernandez CA, Barbosa NA, Sakomura NK, Dowd SE, Oviedo-Rondón EO. Molecular Identification and Characterization of Ileal and Cecal Fungus Communities in Broilers Given Probiotics, Specific Essential Oil Blends, and Under MixedEimeriaInfection. Foodborne Pathog Dis 2012; 9:853-60. [DOI: 10.1089/fpd.2011.1093] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Michael E. Hume
- Food and Feed Safety Research Unit (FFSRU), Southern Plains Agricultural Research Center (SPARC), Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), College Station, Texas
| | - Charles A. Hernandez
- Food and Feed Safety Research Unit (FFSRU), Southern Plains Agricultural Research Center (SPARC), Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), College Station, Texas
| | - Nei A. Barbosa
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Jaboticabal, Brazil
- Department of Poultry Science, North Carolina State University, Raleigh, North Carolina
| | - Nilva K. Sakomura
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Jaboticabal, Brazil
| | - Scott E. Dowd
- Research and Testing Laboratories, Medical Biofilm Research Institute, Lubbock, Texas
| | | |
Collapse
|
17
|
Javed F, Tenenbaum HC, Nogueira-Filho G, Nooh N, Taiyeb Ali TB, Samaranayake LP, Al-Hezaimi K. Oral Candida carriage and species prevalence amongst habitual gutka-chewers and non-chewers. Int Wound J 2012; 11:79-84. [PMID: 22883719 DOI: 10.1111/j.1742-481x.2012.01070.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Oral Candida colonisation is higher in tobacco smokers as compared to non-smokers; however, it remains unknown whether smokeless tobacco chewers are susceptible to increased oral Candida colonisation. The aim was to determine the oral Candida carriage and species prevalence amongst habitual gutka-chewers and non-chewers in a cohort from Karachi, Pakistan. Forty-five gutka-chewers and 45 non-chewers were included. Information regarding age, sex, duration of gutka-chewing habit, daily frequency of gutka consumption, duration of holding gutka in the mouth, daily frequency of tooth-brushing and tongue brushing was collected using a questionnaire. Oral yeast samples were collected by scraping the dorsum of the tongue and bilateral buccal mucosa with a sterile cotton swab. Identification of yeast species was performed using standard techniques. Tongue lesions were identified and recorded. Unstimulated whole salivary flow rate (UWSFR) was also measured. There was no significant difference in the mean age, UWSFR and oral Candida carriage among gutka-chewers and non-chewers. Individuals were chewing gutka since 4·4 years and were consuming five gutka sachets daily. Candida albicans (C. albicans) was the most common yeast species isolated from 57·8% gutka-chewers and 64.4% non-chewers. In 24.4% gutka-chewers and 22·2% non-chewers, two candidal strains (C. albicans and Candida tropicalis) were isolated. In conclusion, the present results indicated no significant difference in oral Candida carriage in habitual gutka-chewers and non-chewers.
Collapse
Affiliation(s)
- Fawad Javed
- 3D Imaging and Biomechanical Lab., College of Applied Medical Sciences, King Saud University, Riyadh, Saudi ArabiaDepartment of Periodontics and Community Dentistry, King Saud University, Riyadh, Saudi ArabiaDepartment of Periodontology, Faculty of Dentistry, University of Toronto, Ontario, CanadaDepartment of Preventive Dentistry, Faculty of Dentistry, University of Toronto, Ontario, CanadaDepartment of Oral and Maxillofacial Surgery, College of Dentistry, King Saud University, Riyadh, Saudi ArabiaDepartment of Oral Pathology and Oral Medicine and Periodontology, Faculty of Dentistry, University of Malaya, Kuala Lumpur, MalaysiaOral Biosciences, Faculty of Dentistry, Prince Philip Dental Hospital, University of Hong Kong, Hong Kong
| | | | | | | | | | | | | |
Collapse
|
18
|
Dollive S, Peterfreund GL, Sherrill-Mix S, Bittinger K, Sinha R, Hoffmann C, Nabel CS, Hill DA, Artis D, Bachman MA, Custers-Allen R, Grunberg S, Wu GD, Lewis JD, Bushman FD. A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples. Genome Biol 2012; 13:R60. [PMID: 22759449 PMCID: PMC4053730 DOI: 10.1186/gb-2012-13-7-r60] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 07/03/2012] [Indexed: 11/23/2022] Open
Abstract
Eukaryotic microorganisms are important but understudied components of the human microbiome. Here we present a pipeline for analysis of deep sequencing data on single cell eukaryotes. We designed a new 18S rRNA gene-specific PCR primer set and compared a published rRNA gene internal transcribed spacer (ITS) gene primer set. Amplicons were tested against 24 specimens from defined eukaryotes and eight well-characterized human stool samples. A software pipeline https://sourceforge.net/projects/brocc/ was developed for taxonomic attribution, validated against simulated data, and tested on pyrosequence data. This study provides a well-characterized tool kit for sequence-based enumeration of eukaryotic organisms in human microbiome samples.
Collapse
|
19
|
Ahmad S, Khan Z. Invasive candidiasis: A review of nonculture-based laboratory diagnostic methods. Indian J Med Microbiol 2012; 30:264-9. [DOI: 10.4103/0255-0857.99482] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
20
|
Shokralla S, Zhou X, Janzen DH, Hallwachs W, Landry JF, Jacobus LM, Hajibabaei M. Pyrosequencing for mini-barcoding of fresh and old museum specimens. PLoS One 2011; 6:e21252. [PMID: 21818256 PMCID: PMC3144868 DOI: 10.1371/journal.pone.0021252] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 05/25/2011] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding is an effective approach for species identification and for discovery of new and/or cryptic species. Sanger sequencing technology is the method of choice for obtaining standard 650 bp cytochrome c oxidase subunit I (COI) barcodes. However, DNA degradation/fragmentation makes it difficult to obtain a full-length barcode from old specimens. Mini-barcodes of 130 bp from the standard barcode region have been shown to be effective for accurate identification in many animal groups and may be readily obtained from museum samples. Here we demonstrate the application of an alternative sequencing technology, the four-enzymes single-specimen pyrosequencing, in rapid, cost-effective mini-barcode analysis. We were able to generate sequences of up to 100 bp from mini-barcode fragments of COI in 135 fresh and 50 old Lepidoptera specimens (ranging from 53–97 year-old). The sequences obtained using pyrosequencing were of high quality and we were able to robustly match all the tested pyro-sequenced samples to their respective Sanger-sequenced standard barcode sequences, where available. Simplicity of the protocol and instrumentation coupled with higher speed and lower cost per sequence than Sanger sequencing makes this approach potentially useful in efforts to link standard barcode sequences from unidentified specimens to known museum specimens with only short DNA fragments.
Collapse
Affiliation(s)
- Shadi Shokralla
- Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.
| | | | | | | | | | | | | |
Collapse
|
21
|
Pannanusorn S, Elings MA, Römling U, Fernandez V. Pyrosequencing of a hypervariable region in the internal transcribed spacer 2 to identify clinical yeast isolates. Mycoses 2011; 55:172-80. [PMID: 21736632 DOI: 10.1111/j.1439-0507.2011.02064.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The incidence of invasive fungal infection has increased significantly. A majority of the infections is caused by yeast. Clinically important yeast show species-specific differences in susceptibility to antifungal agents therefore rapid and accurate identification of the pathogen is essential. We aimed to validate pyrosequencing of 40 nucleotides in the internal transcribed spacer 2 (ITS2) for species identification of yeast. Amplification of ITS2 and pyrosequencing of targeted region were performed in 940 clinical isolates of yeast. A local database containing the 40 nucleotide ITS2 sequences of 33 species of medically important yeast was generated using published sequences of type strains. The sequencing results were searched against the local database using the BLAST algorithm to identify the species of yeast. The length of sequences obtained from pyrosequencing averaged between 40-61 nucleotides. Pyrosequencing identified 940 clinical isolates of yeast down to 14 species level, whereby 931 isolates belonged to genus Candida (11 species), four of Saccharomyces cerevisiae, three of Malassezia pachydermatis and two of Rhodotorula mucilaginosa. In addition, intraspecies specific sequence variations in Candida albicans and Candida glabrata were detected. Pyrosequencing of 40 nucleotides in ITS2 is reliable for species identification of yeast. This methodology can contribute to the high quality management of patients with fungal infections.
Collapse
Affiliation(s)
- Srisuda Pannanusorn
- Department of Parasitology, Mycology and Environmental Microbiology, Swedish Institute for Infectious Disease Control, Solna, Sweden.
| | | | | | | |
Collapse
|
22
|
Rapid identification of yeasts from positive blood culture bottles by pyrosequencing. Eur J Clin Microbiol Infect Dis 2010; 30:21-4. [PMID: 20803046 DOI: 10.1007/s10096-010-1045-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Accepted: 08/10/2010] [Indexed: 10/19/2022]
Abstract
We have developed a rapid protocol for the identification of Candida species from positive blood cultures by combining a simple method for nucleic acid extraction and preparation using microbial storage cardboards with polymerase chain reaction (PCR) and pyrosequencing of a small region of the 18 S rRNA gene. The protocol is robust and easy to implement and can be performed in 4 h. The method was tested against a collection of clinical blood cultures. Agreement of sequence identifications with standard microbiological methods was 100%.
Collapse
|
23
|
Rapid molecular identification of pathogenic yeasts by pyrosequencing analysis of 35 nucleotides of internal transcribed spacer 2. J Clin Microbiol 2010; 48:3648-53. [PMID: 20702674 DOI: 10.1128/jcm.01071-10] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid identification of yeast species isolates from clinical samples is particularly important given their innately variable antifungal susceptibility profiles. Here, we have evaluated the utility of pyrosequencing analysis of a portion of the internal transcribed spacer 2 region (ITS2) for identification of pathogenic yeasts. A total of 477 clinical isolates encompassing 43 different fungal species were subjected to pyrosequencing analysis in a strictly blinded study. The molecular identifications produced by pyrosequencing were compared with those obtained using conventional biochemical tests (AUXACOLOR2) and following PCR amplification and sequencing of the D1-D2 portion of the nuclear 28S large rRNA gene. More than 98% (469/477) of isolates encompassing 40 of the 43 fungal species tested were correctly identified by pyrosequencing of only 35 bp of ITS2. Moreover, BLAST searches of the public synchronized databases with the ITS2 pyrosequencing signature sequences revealed that there was only minimal sequence redundancy in the ITS2 under analysis. In all cases, the pyrosequencing signature sequences were unique to the yeast species (or species complex) under investigation. Finally, when pyrosequencing was combined with the Whatman FTA paper technology for the rapid extraction of fungal genomic DNA, molecular identification could be accomplished within 6 h from the time of starting from pure cultures.
Collapse
|
24
|
Agvald-Ohman C, Klingspor L, Hjelmqvist H, Edlund C. Invasive candidiasis in long-term patients at a multidisciplinary intensive care unit: Candida colonization index, risk factors, treatment and outcome. ACTA ACUST UNITED AC 2009; 40:145-53. [PMID: 17852926 DOI: 10.1080/00365540701534509] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The incidence of fungal infections in hospitalized patients has increased, and due to demographic changes and increasingly advanced medical methods, the intensive care units (ICU) have emerged as epicentres for fungal infections. The aim of the present study was to investigate Candida colonization pattern and colonization index (CI), in combination with other risk factors and its relation to invasive candida infection (ICI), in 59 consecutive patients with at least 7 d length of stay (LOS) at a multidisciplinary ICU. Surveillance samples were collected on d 7 and then weekly during the ICU stay. In addition, immunological status was monitored by measuring the histocompatibility leukocyte antigen-DR (HLA-DR). In the present study with a patient population burdened by several risk factors for ICI, 17% acquired an invasive infection. Overall ICU mortality was 30%. We could demonstrate that both a high colonization index and recent extensive gastroabdominal surgery were significantly correlated with ICI, while a decreased level of HLA-DR (< or = 70%) was not predictive for ICI in this high-risk population. The results indicate that ICU patients exposed to extensive gastroabdominal surgery would benefit from early antifungal prophylaxis.
Collapse
Affiliation(s)
- Christina Agvald-Ohman
- Department of Clinical Science, Intervention and Technology, Division of Anaesthesiology and Intensive Care, Karolinska University Hospital Huddinge, Karolinska Institutet, Stockholm, Sweden.
| | | | | | | |
Collapse
|
25
|
|
26
|
Javed F, Klingspor L, Sundin U, Altamash M, Klinge B, Engström PE. Periodontal conditions, oral Candida albicans and salivary proteins in type 2 diabetic subjects with emphasis on gender. BMC Oral Health 2009; 9:12. [PMID: 19435501 PMCID: PMC2698828 DOI: 10.1186/1472-6831-9-12] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 05/12/2009] [Indexed: 11/10/2022] Open
Abstract
Background The association between periodontal conditions, oral yeast colonisation and salivary proteins in subjects with type 2 diabetes (T2D) is not yet documented. The present study aimed to assess the relationship between these variables in type 2 diabetic subjects with reference to gender. Methods Fifty-eight type 2 diabetic subjects (23 males and 35 females) with random blood glucose level ≥ 11.1 mmol/L were investigated. Periodontal conditions (plaque index [PI], bleeding on probing [BOP], probing pocket depth [PD] (4 to 6 mm and ≥ 6 mm), oral yeasts, salivary immunoglobulin (Ig) A, IgG and total protein concentrations, and number of present teeth were determined. Results Periodontal conditions (PI [p < 0.00001], BOP [p < 0.01] and PD of 4 to 6 mm [p < 0.001], salivary IgG (μg)/mg protein (p < 0.001) and salivary total protein concentrations (p < 0.05) were higher in type 2 diabetic females with Candida albicans (C. albicans) colonisation compared to males in the same group. Type 2 diabetic females with C. albicans colonisation had more teeth compared to males in the same group (p < 0.0001). Conclusion Clinical and salivary parameters of periodontal inflammation (BOP and IgG (μg)/mg protein) were higher in type 2 diabetic females with oral C. albicans colonisation compared to males in the same group. Further studies are warranted to evaluate the association of gender with these variables in subjects with T2D.
Collapse
Affiliation(s)
- Fawad Javed
- Department of Dental Medicine, Division of Periodontology, Karolinska Institutet, Huddinge, Sweden.
| | | | | | | | | | | |
Collapse
|
27
|
Pyrosequencing analysis of 20 nucleotides of internal transcribed spacer 2 discriminates Candida parapsilosis, Candida metapsilosis, and Candida orthopsilosis. J Clin Microbiol 2009; 47:2307-10. [PMID: 19403763 DOI: 10.1128/jcm.00240-09] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two new cryptic sister species, Candida orthopsilosis and Candida metapsilosis, were recently identified by consistent DNA sequence differences among several genes within the genetically heterogeneous Candida parapsilosis complex. Here, we present data demonstrating that Pyrosequencing analysis of 20 nucleotides of internal transcribed spacer region 2 rapidly and robustly distinguishes between these three closely related Candida species.
Collapse
|
28
|
Utility of pyrosequencing in identifying bacteria directly from positive blood culture bottles. J Clin Microbiol 2008; 47:368-72. [PMID: 19091813 DOI: 10.1128/jcm.01991-08] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Growth in liquid media is the gold standard for detecting microorganisms associated with bloodstream infections. The Gram stain provides the first clue as to the etiology of infection, with phenotypic identification completed 1 or 2 days later. Providing more detailed information than the Gram stain can impart, and in less time than subculturing, would allow the use of more directed empirical therapy and, thus, reduce the patient's exposure to unnecessary or ineffective antibiotics sooner. The study had two objectives, as follows: (i) to identify new targets to improve our ability to differentiate among certain enteric gram-negative rods or among certain Streptococcus species and (ii) to determine whether real-time PCR and pyrosequencing could as accurately identify organisms directly from positive blood culture bottles as culture-based methods. Two hundred and fifty-five consecutive positive blood culture bottles were included. The results showed a high level of agreement between the two approaches; of the 270 bacteria isolated from the 255 blood culture bottles, results for pyrosequencing and culture-based identifications were concordant for 264/270 (97.8%) bacteria with three failed sequences, and three sequences without match. Additionally, compared to the universal 16S rRNA gene target, the new 23S rRNA gene targets greatly improved our ability to differentiate among certain enteric gram-negative rods or among certain Streptococcus species. In conclusion, combining real-time PCR and pyrosequencing provided valuable information beyond that derived from the initial Gram stain and in less time than phenotypic culture-based identification. This strategy, if implemented, could result in a more directed empirical therapy in patients and would promote responsible antibiotic stewardship.
Collapse
|
29
|
Boyanton BL, Luna RA, Fasciano LR, Menne KG, Versalovic J. DNA pyrosequencing-based identification of pathogenic Candida species by using the internal transcribed spacer 2 region. Arch Pathol Lab Med 2008; 132:667-74. [PMID: 18384218 DOI: 10.5858/2008-132-667-dpiopc] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2007] [Indexed: 11/06/2022]
Abstract
CONTEXT The incidence of infections due to diverse Candida species is increasing, with correspondingly different antifungal susceptibility patterns. Routine yeast identification methods cause significant delays in appropriate patient management. OBJECTIVE A DNA pyrosequencing strategy was evaluated for identification of pathogenic Candida species associated with human infections. DESIGN Clinical (n = 51) and commercial (n = 9) Candida isolates were identified in a blinded, parallel study consisting of routine fungal cultures and biochemical analyses in comparison with DNA pyrosequencing. RESULTS DNA pyrosequencing yielded species-level identification of all 60 Candida isolates, and sequencing interpretations agreed in all cases with results of biochemical and morphologic testing. Different Candida species were identified, such as C. albicans, C. dubliniensis, C. glabrata, C. guilliermondii, C. krusei, C. lusitaniae, C. parapsilosis, and C. tropicalis. Automated and manual approaches to DNA sequence interpretation, each coupled with the Identifire identification software, demonstrated 100% agreement with respect to Candida species identification. Twenty-one isolates yielded intraspecies DNA sequence differences (90%-98% nucleic acid sequence identity) by automated interpretation. Sequence differences resulted from single-nucleotide polymorphisms or single-base additions/deletions, in addition to interpretative challenges in homopolymeric tracts. CONCLUSION DNA pyrosequencing coupled with automated DNA sequence alignment provides a practical approach for accurate and timely identification of Candida pathogens. Relatively rapid and facile genotypic studies by DNA pyrosequencing matched the effectiveness of extensive biochemical/morphologic studies for yeast identification.
Collapse
Affiliation(s)
- Bobby L Boyanton
- Department of Pathology, Baylor College of Medicine, Houston, USA.
| | | | | | | | | |
Collapse
|
30
|
Blakey GL, Luna RA, Versalovic J. Infectious diseases testing. ACTA ACUST UNITED AC 2008; Chapter 9:Unit 9.18. [PMID: 18428383 DOI: 10.1002/0471142905.hg0918s47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Molecular methods have been applied widely for the diagnosis of infectious diseases. Beginning with solution hybridization in the early 1990s, multiple methods for nucleic acid hybridization and amplification have been introduced into the laboratory for the identification and characterization of microbial pathogens. This unit contains examples of several basic approaches for microbial detection or characterization in the laboratory. Methods in this chapter include automated nucleic acid extraction, direct detection of microbial pathogens, and characterization of pathogens by DNA sequencing or typing. Any of these methods could be customized for the characterization of bacteria, fungi, parasites, or viruses.
Collapse
|
31
|
Evaluation of Pyrosequencing technology for the identification of clinically relevant non-dematiaceous yeasts and related species. Eur J Clin Microbiol Infect Dis 2008; 27:821-30. [PMID: 18421488 DOI: 10.1007/s10096-008-0510-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Accepted: 03/03/2008] [Indexed: 10/22/2022]
Abstract
Pyrosequencing was used to identify 133 isolates of clinically relevant non-dematiaceous yeasts. These included 97 ATCC strains (42 type strains), seven UAMH strains, and 29 clinical isolates. Isolates belonged to the following genera: Candida (18 species), Trichosporon (10), Cryptococcus (7), Malassezia (3), Rhodotorula (2), Geotrichum (1), Blastoschizomyces (1), and Kodamaea (1). Amplicons of a hyper-variable ITS region were obtained and analyzed using Pyrosequencing technology. The data were evaluated by a BLAST search against the GenBank database and correlated with data obtained by conventional cycle sequencing of the ITS1-5.8S-ITS2 region. Cycle sequencing identified 78.9% of the isolates to the species level. Pyrosequencing technology identified 69.1%. In 90.1% of all of the strains tested, the identification results of both sequencing methods were identical. Most Candida isolates can be identified to the species level by Pyrosequencing. Trichosporon species and some Cryptococcus species cannot be differentiated at the species level. Pyrosequencing can be used for the reliable identification of most commonly isolated non-dematiaceous yeasts, with a reduction of cost per identification compared to conventional sequencing.
Collapse
|
32
|
Das MK, Ehrlich KC, Cotty PJ. Use of pyrosequencing to quantify incidence of a specific Aspergillus flavus strain within complex fungal communities associated with commercial cotton crops. PHYTOPATHOLOGY 2008; 98:282-288. [PMID: 18944078 DOI: 10.1094/phyto-98-3-0282] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Atoxigenic strains of Aspergillus flavus have been used as aflatoxin management tools on over 50,000 hectares of commercial crops since 2000. To assess treatment efficacy, atoxigenic strain incidence is routinely monitored by vegetative compatibility analyses (VCA) that require culturing, generation of auxotrophs, and complementation with tester mutants. Two pyrosequencing assays (PA) that require no culturing were developed for monitoring incidences of atoxigenic strains on ginned cottonseed. The assays, which quantify frequencies of characteristic single nucleotide polymorphisms (SNPs) in the aflR and pksA genes, were validated against standard VCA on cottonseed collected from commercial gins in South Texas, Arizona, and Southern California where the atoxigenic strain AF36 is used to manage aflatoxin contamination. Cottonseed washings were subjected to both VCA and PA. PA was performed directly on DNA isolated from particulates pelleted from the wash water by centrifugation. Addition of CaCl(2) and diatomaceous earth prior to pelleting increased the amount of DNA isolated. Accuracy and reproducibility of the PA were contrasted with those for the VCA that has been used for over a decade. Correlation coefficients between VCA and PA indicated good correspondence between the results from the two assays (r = 0.91 for aflR assay and r = 0.80 for pksA assay). PAs were highly variable for samples with low incidences of A. flavus due to variability in the initial polymerase chain reaction step. This held for both DNA isolated from cottonseed washes and for mixtures of purified DNA. For samples yielding low quantities of A. flavus DNA, averaging of results from 4 to 5 replicates was required to achieve acceptable correlations with VCA. Pyrosequencing has the potential to become a powerful tool for monitoring atoxigenic strains within complex A. flavus communities without limitations imposed by traditional culturing methods.
Collapse
Affiliation(s)
- Modan K Das
- Agricultural Research Service, United States Department of Agriculture, Department of Plant Sciences, University of Arizona, Tucson 85721-0036, USA
| | | | | |
Collapse
|
33
|
Identification of enterovirus serotypes by pyrosequencing using multiple sequencing primers. J Virol Methods 2007; 148:260-4. [PMID: 18082902 DOI: 10.1016/j.jviromet.2007.10.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Revised: 09/24/2007] [Accepted: 10/10/2007] [Indexed: 10/22/2022]
Abstract
Human enteroviruses (HEV) are considered as one of the major causes of central nervous system infections in pediatrics. They are currently classified into five species involving more than 60 officially recognized serotypes. This study describes a rapid molecular method, based on pyrosequencing of a VP1 fragment, for the identification of enterovirus serotypes. In order to do so, 200 isolates and clinical specimens that were first grouped into 62 different HEV serotypes using neutralization test, were analyzed by pyrosequencing. All serotypes were identified using the proposed method. Most of the isolates previously untypeable by classical procedures, as well as mixed enterovirus infections containing viruses belonging to different species, could also be determined using pyrosequencing. The present results give support to pyrosequencing as an efficient method of HEV genotyping.
Collapse
|
34
|
Bergman A, Fernandez V, Holmström KO, Claesson BEB, Enroth H. Rapid identification of pathogenic yeast isolates by real-time PCR and two-dimensional melting-point analysis. Eur J Clin Microbiol Infect Dis 2007; 26:813-8. [PMID: 17680284 DOI: 10.1007/s10096-007-0369-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
There is a need in the clinical microbiological laboratory for rapid and reliable methods for the universal identification of fungal pathogens. Two different regions of the rDNA gene complex, the highly polymorphic ITS1 and ITS2, were amplified using primers targeting conserved regions of the 18S, 5.8S and 28S genes. After melting-point analysis of the amplified products, the T(m) of the two PCR-products were plotted into a spot diagram where all the 14 tested, clinically relevant yeasts separated with good resolution. Real-time amplification of two separate genes, melting-point analysis and two-dimensional plotting of T(m) data can be used as a broad-range method for the identification of clinical isolates of pathogenic yeast such as Candida and Cryptococcus spp.
Collapse
Affiliation(s)
- A Bergman
- Department of Clinical Microbiology, Capio Diagnostik AB, Kärnsjukhuset, Skövde, Sweden.
| | | | | | | | | |
Collapse
|
35
|
Ronaghi M, Shokralla S, Gharizadeh B. Pyrosequencing for discovery and analysis of DNA sequence variations. Pharmacogenomics 2007; 8:1437-41. [DOI: 10.2217/14622416.8.10.1437] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Since the invention of pyrosequencing, more than 500 articles have been published describing different applications of this technology, most notably for DNA structure variation and microbial detection. Technological advances have been made to enhance the robustness and accuracy of this technique as well as to reduce the cost and increase the throughput. This review intends to cover recent advances in this technology and discuss its application for low and high-throughput DNA variation studies.
Collapse
Affiliation(s)
- Mostafa Ronaghi
- Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, CA 94304, USA
| | - Shadi Shokralla
- Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, CA 94304, USA
| | - Baback Gharizadeh
- Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, CA 94304, USA
| |
Collapse
|
36
|
Abstract
The focus of this review is the evolution of biochemical phenotypic yeast identification methods with emphasis on conventional approaches, rapid screening tests, chromogenic agars, comprehensive commercial methods, and the eventual migration to genotypic methods. As systemic yeast infections can be devastating and resistance is common in certain species, accurate identification to the species level is paramount for successful therapy and appropriate patient care.
Collapse
Affiliation(s)
- D H Pincus
- bioMérieux, Inc., Hazelwood, Missouri 63042, USA.
| | | | | |
Collapse
|
37
|
Edvinsson B, Dardé ML, Pelloux H, Evengård B. Rapid genotyping of Toxoplasma gondii by pyrosequencing. Clin Microbiol Infect 2007; 13:424-9. [PMID: 17410643 DOI: 10.1111/j.1469-0691.2006.01661.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: 11/29/2022]
Abstract
Most human infections with the protozoan parasite Toxoplasma gondii are asymptomatic, but severe symptoms can occur in immunocompromised patients, in developing foetuses, and in ocular infections in immunocompetent individuals. The majority of T. gondii strains can be divided into three main lineages, denoted types I, II and III, which are known to cause different clinical presentations. Simple molecular methods with the capacity to discriminate rapidly among strains may help to predict the course of infection and influence the choice of treatment. In the present study, real-time PCR followed by pyrosequencing was used to discriminate among types I, II and III by analysis of two single nucleotide polymorphisms in the GRA6 gene. Twenty-one isolates of T. gondii characterised previously were analysed. Three different GRA6 alleles detected by the pyrosequencing technique identified types I, II and III isolates correctly, while four atypical isolates possessed either the GRA6 allele 1 or the GRA6 allele 3. Reproducibility was 100%, and typeability, when including atypical strains, was 81%. It was also possible to discriminate a mixture of two genotypes. The method was used to identify GRA6 type II in blood and lung tissue from an allogeneic transplant recipient with toxoplasmosis.
Collapse
Affiliation(s)
- B Edvinsson
- Karolinska Institutet, Department of Laboratory Medicine, Division of Clinical Bacteriology, Karolinska University Hospital Huddinge, Stockholm, Sweden.
| | | | | | | |
Collapse
|
38
|
Mashayekhi F, Ronaghi M. Analysis of read length limiting factors in Pyrosequencing chemistry. Anal Biochem 2007; 363:275-87. [PMID: 17343818 PMCID: PMC1978072 DOI: 10.1016/j.ab.2007.02.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Revised: 02/01/2007] [Accepted: 02/05/2007] [Indexed: 11/30/2022]
Abstract
Pyrosequencing is a bioluminometric DNA sequencing technique that measures the release of pyrophosphate during DNA synthesis. The amount of pyrophosphate is proportionally converted into visible light by a cascade of enzymatic reactions. Pyrosequencing has heretofore been used for generating short sequence reads (1-100 nucleotides) because certain factors limit the system's ability to perform longer reads accurately. In this study, we have characterized the main read length limiting factors in both three-enzyme and four-enzyme Pyrosequencing systems. A new simulation model was developed to simulate the read length of both systems based on the inhibitory factors in the chemical equations governing each enzymatic cascade. Our results indicate that nonsynchronized extension limits the obtained read length, albeit to a different extent for each system. In the four-enzyme system, nonsynchronized extension due mainly to a decrease in apyrase's efficiency in degrading excess nucleotides proves to be the main limiting factor of read length. Replacing apyrase with a washing step for removal of excess nucleotide proves to be essential in improving the read length of Pyrosequencing. The main limiting factor of the three-enzyme system is shown to be loss of DNA fragments during the washing step. If this loss is minimized to 0.1% per washing cycle, the read length of Pyrosequencing would be well beyond 300 bases.
Collapse
Affiliation(s)
| | - Mostafa Ronaghi
- CORRESPONDING AUTHOR: Mostafa Ronaghi, 855 California Ave, Palo Alto, CA 94304, , Phone: (650) 812-1971, Fax: (650) 812-1975
| |
Collapse
|
39
|
Balajee SA, Sigler L, Brandt ME. DNA and the classical way: Identification of medically important molds in the 21st century. Med Mycol 2007; 45:475-90. [PMID: 17710617 DOI: 10.1080/13693780701449425] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The advent of the 21st century has seen significant advances in the methods and practices used for identification of medically important molds in the clinical microbiology laboratory. Historically, molds have been identified by using observations of colonial and microscopic morphology, along with tables, keys and textbook descriptions. This approach still has value for the identification of many fungal organisms, but requires expertise and can be problematic in determining a species identification that is timely and useful in the management of high-risk patients. For the increasing number of isolates that are uncommon, atypical, or unusual, DNA-based identification methods are being increasingly employed in many clinical laboratories. These methods include the commercially available GenProbe assay, methods based on the polymerase chain reaction such as single-step PCR, RAPD-PCR, rep-PCR, nested PCR, PCR-RFLP, PCR-EIA, and more recent microarray-based, Luminex technology-based, and real-time PCR-based methods. Great variation in assay complexity, targets, and detection methods can be found, and many of these methods have not been widely used or rigorously validated. The increasing availability of DNA sequencing chemistry has made comparative DNA sequence analysis an attractive alternative tool for fungal identification. DNA sequencing methodology can be purchased commercially or developed in-house; such methods display varying degrees of usefulness depending on the breadth and reliability of the databases used for comparison. The future success of sequencing-based approaches will depend on the choice of DNA target, the reliability of the result, and the availability of a validated sequence database for query and comparison. Future studies will be required to determine sequence homology breakpoints and to assess the accuracy of molecular-based species identification in various groups of medically important filamentous fungi. At this time, a polyphasic approach to identification that combines morphologic and molecular methods will ensure the greatest success in the management of patients with fungal infections.
Collapse
Affiliation(s)
- S Arunmozhi Balajee
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | | | | |
Collapse
|
40
|
Balajee SA, Marr KA. Phenotypic and genotypic identification of human pathogenic aspergilli. Future Microbiol 2006; 1:435-45. [PMID: 17661634 DOI: 10.2217/17460913.1.4.435] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Human pathogenic aspergilli are identified in the clinical diagnostic laboratory predominantly by macro- and micro-morphology. Such phenotypic characteristics are largely subjective and unstable, as they are influenced by environmental factors, including media and temperature of incubation. Recent advances in molecular biology have impacted the field of mycology; multiple studies have noted new genetically distinct species that are not easily distinguished by phenotypic characteristics. Strengths of molecular typing methods include objectivity and the ability to identify nonsporulating or slowly growing fungi. As such, molecular methods provide powerful tools for the study of the epidemiology, evolution and population biology of fungal pathogens. This review focuses on current and future methods of identifying aspergilli, and implications regarding Aspergillus species/strain identification.
Collapse
Affiliation(s)
- S Arunmozhi Balajee
- Centers for Disease Control and Prevention, Mycotic Diseases Branch, Atlanta, GA 30333, USA.
| | | |
Collapse
|
41
|
Gharizadeh B, Akhras M, Nourizad N, Ghaderi M, Yasuda K, Nyrén P, Pourmand N. Methodological improvements of pyrosequencing technology. J Biotechnol 2006; 124:504-11. [PMID: 16530870 PMCID: PMC2933062 DOI: 10.1016/j.jbiotec.2006.01.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Revised: 01/06/2006] [Accepted: 01/16/2006] [Indexed: 11/25/2022]
Abstract
Pyrosequencing technology is a rather novel DNA sequencing method based on the sequencing-by-synthesis principle. This bioluminometric, real-time DNA sequencing technique employs a cascade of four enzymatic reactions producing sequence peak signals. The method has been proven highly suitable for single nucleotide polymorphism analysis and sequencing of short stretches of DNA. Although the pyrosequencing procedure is relatively straightforward, users may face challenges due to varying parameters in PCR and sequencing primer design, sample preparation and nucleotide dispensation; such challenges are labor and cost intensive. In this study, these issues have been addressed to increase signal quality and assure sequence accuracy.
Collapse
Affiliation(s)
- Baback Gharizadeh
- Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, CA 94304, USA
| | - Michael Akhras
- Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, CA 94304, USA
- Department of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Nader Nourizad
- Department of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Mehran Ghaderi
- Division of Biomedicine, Department of Caring Sciences, Örebro, University, Örebro, Sweden
| | - Kenji Yasuda
- Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, CA 94304, USA
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Pål Nyrén
- Department of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Nader Pourmand
- Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, CA 94304, USA
- Corresponding author. Tel.: +1 650 812 2002; fax: +1 650 812 1975. (N. Pourmand)
| |
Collapse
|
42
|
Salk JJ, Sanchez JA, Pierce KE, Rice JE, Soares KC, Wangh LJ. Direct amplification of single-stranded DNA for pyrosequencing using linear-after-the-exponential (LATE)-PCR. Anal Biochem 2006; 353:124-32. [PMID: 16540077 PMCID: PMC1533996 DOI: 10.1016/j.ab.2006.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2006] [Revised: 02/06/2006] [Accepted: 02/07/2006] [Indexed: 12/21/2022]
Abstract
Pyrosequencing is a highly effective method for quantitatively genotyping short genetic sequences, but it currently is hampered by a labor-intensive sample preparation process designed to isolate single-stranded DNA from double-stranded products generated by conventional PCR. Here linear-after-the-exponential (LATE)-PCR is introduced as an efficient and potentially automatable method of directly amplifying single-stranded DNA for pyrosequencing, thereby eliminating the need for solid-phase sample preparation and reducing the risk of laboratory contamination. These improvements are illustrated for single-nucleotide polymorphism genotyping applications, including an integrated single-cell-through-sequencing assay to detect a mutation at the globin IVS 110 site that frequently is responsible for beta-thalassemia.
Collapse
Affiliation(s)
- Jesse J Salk
- Department of Biology, Brandeis University, Waltham, MA 02454, USA.
| | | | | | | | | | | |
Collapse
|
43
|
Saunte DM, Klingspor L, Jalal S, Arnau J, Arendrup MC. Four cases of Candida albicans infections with isolates developing pink colonies on CHROMagar Candida plates. Mycoses 2005; 48:378-81. [PMID: 16262872 DOI: 10.1111/j.1439-0507.2005.01146.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Candida albicans, the most commonly isolated yeast species, is typically identified by its green colony-colour on CHROMagar Candida plates. We here report four cases of Candida albicans infections, in which the initial identification was non-albicans isolates due to a clear pink colour of the colonies on CHROMagar Candida plates. However, classical phenotypic criteria, biochemical assimilation pattern and molecular characterisation identified all four isolates as C. albicans isolates.
Collapse
Affiliation(s)
- D M Saunte
- Unit of Mycology and Parasitology, Department for Bacteriology, Mycology and Parasitology, Statens Serum Institute, Copenhagen, Denmark.
| | | | | | | | | |
Collapse
|
44
|
Gharizadeh B, Eriksson J, Nourizad N, Nordström T, Nyrén P. Improvements in Pyrosequencing technology by employing Sequenase polymerase. Anal Biochem 2005; 330:272-80. [PMID: 15203333 DOI: 10.1016/j.ab.2004.03.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2004] [Indexed: 11/24/2022]
Abstract
Pyrosequencing is a DNA sequencing technique based on the bioluminometric detection of inorganic pyrophosphate, which is released when nucleotides are incorporated into a target DNA. Since the technique is based on an enzymatic cascade, the choice of enzymes is a critical factor for efficient performance of the sequencing reaction. In this study we have analyzed the performance of an alternative DNA polymerase, Sequenase, on the sequencing performance of the Pyrosequencing technology. Compared to the Klenow fragment of DNA polymerase I, Sequenase could read through homopolymeric regions with more than five T bases. In addition, Sequenase reduces remarkably interference from primer-dimers and loop structures that give rise to false sequence signals. By using Sequenase, synchronized extensions and longer reads can be obtained on challenging templates, thereby opening new avenues for applications of Pyrosequencing technology.
Collapse
Affiliation(s)
- Baback Gharizadeh
- Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, CA 94304, USA
| | | | | | | | | |
Collapse
|
45
|
Sullivan A, Fianu-Jonasson A, Landgren BM, Nord CE. Ecological effects of perorally administered pivmecillinam on the normal vaginal microflora. Antimicrob Agents Chemother 2005; 49:170-5. [PMID: 15616292 PMCID: PMC538917 DOI: 10.1128/aac.49.1.170-175.2005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Revised: 09/10/2004] [Accepted: 09/16/2004] [Indexed: 11/20/2022] Open
Abstract
The knowledge of the effects of antimicrobial agents on the normal vaginal microflora is limited. The objective of the present study was to study the ecological impact of pivmecillinam on the normal vaginal microflora. In 20 healthy women, the estimated day of ovulation was determined during three subsequent menstrual cycles. Microbiological and clinical examinations were performed on the estimated day of ovulation and on day 3 in all cycles and also on day 7 after ovulation in cycles 1 and 2. Anaerobic and facultative anaerobic gram-positive rods, mainly species of lactobacilli and actinomycetes, dominated the microflora. One woman was colonized on the third day of administration with a resistant Escherichia coli strain, and Candida albicans was detected in one woman on days 3 and 7 in cycle 2. No other major changes in the normal microflora occurred during the study. Administration of pivmecillinam had a minor ecological impact on the normal vaginal microflora.
Collapse
Affiliation(s)
- Asa Sullivan
- Division of Clinical Bacteriology, F82, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | | | | | | |
Collapse
|
46
|
Plachý R, Hamal P, Raclavský V. McRAPD as a new approach to rapid and accurate identification of pathogenic yeasts. J Microbiol Methods 2005; 60:107-13. [PMID: 15567230 DOI: 10.1016/j.mimet.2004.09.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2004] [Revised: 08/28/2004] [Accepted: 09/07/2004] [Indexed: 11/19/2022]
Abstract
Despite advances in antifungal prophylaxis and therapy, morbidity and mortality incurred by yeasts remain a significant burden. As pathogenic yeast species vary in their susceptibilities to antifungal agents, clinical microbiology laboratories face an important challenge to identify them rapidly and accurately. Although a vast array of phenotyping and genotyping methods has been developed, these are either unable to cover the whole spectrum of potential yeast pathogens or can do this only in a rather costly or laborious way. Random amplified polymorphic DNA (RAPD) fingerprinting was repeatedly demonstrated to be a convenient tool for species identification in pathogenic yeasts. However, its wider acceptance has been limited mainly due to special expertise and software needed for analysis and comparison of the resulting banding patterns. Based on a pilot study, we demonstrate here that a simple and rapid melting curve analysis of RAPD products can provide data for identification of five of the most medically important Candida species. We have termed this new approach melting curve of random amplified polymorphic DNA (McRAPD) to emphasize its rapidity and potential for automation, highly desirable features for a routine laboratory test.
Collapse
Affiliation(s)
- Radek Plachý
- Department of Microbiology, Faculty of Medicine, Palacký University, Hnvotínská 3, CZ-775 15 Olomouc, Czech Republic
| | | | | |
Collapse
|