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Comparison of in vitro activities of newer triazoles and classic antifungal agents against dermatophyte species isolated from Iranian University Hospitals: a multi-central study. Ann Clin Microbiol Antimicrob 2023; 22:15. [PMID: 36805670 PMCID: PMC9940349 DOI: 10.1186/s12941-023-00564-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Dermatophytes have the ability to invade the keratin layer of humans and cause infections. The aims of this study were the accurate identification of dermatophytes by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism method and sequencing and comparison between the in vitro activities of newer and established antifungal agents against them. METHODS Clinical specimens of patients from five Iranian university laboratories were entered in this study. Samples were cultured on sabouraud dextrose agar medium. For molecular identification, extracted DNAs were amplified by the universal fungal primers ITS1 and ITS4, and digested with MvaI enzymes. The antifungal susceptibility test for each isolate to terbinafine, griseofulvin, caspofungin, fluconazole, itraconazole, luliconazole, and isavuconazole was performed, according to the microdilution CLSI M38-A2 and CLSI M61 standard methods. RESULTS Two hundred and seven fungi species similar to dermatophytes were isolated of which 198 (95.6%) were dermatophytes by molecular assay. The most commonly isolated were Trichophyton mentagrophytes (76/198), followed by Trichophyton interdigitale (57/198), Trichophyton rubrum (34/198), Trichophyton tonsurans (12/198), Microsporum canis (10/198), Trichophyton simii (3/198), Epidermophyton floccosum (3/198), Trichophyton violaceum (2/198), and Trichophyton benhamiae (1/198). The GM MIC and MIC90 values for all the isolates were as follows: terbinafine (0.091 and 1 μg/ml), griseofulvin (1.01 and 4 μg/ml), caspofungin (0.06 and 4 μg/ml), fluconazole (16.52 and 32 μg/ml), itraconazole (0.861 and 8 μg/ml), isavuconazole (0.074 and 2 μg/ml), and luliconazole (0.018 and 0.25 μg/ml). CONCLUSION Trichophyton mentagrophytes, Trichophyton interdigitale, and Trichophyton rubrum were the most common fungal species isolated from the patients. luliconazole, terbinafine, and isavuconazole in vitro were revealed to be the most effective antifungal agents against all dermatophyte isolates.
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Eghtedar Nejad E, Ghasemi Nejad Almani P, Mohammadi MA, Salari S. Molecular identification of Candida isolates by Real-time PCR-high-resolution melting analysis and investigation of the genetic diversity of Candida species. J Clin Lab Anal 2020; 34:e23444. [PMID: 32656934 PMCID: PMC7595915 DOI: 10.1002/jcla.23444] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Candida species are considered as the cause of one of the most important opportunistic fungal diseases. Accurate identification of Candida species is important because of antifungal susceptibility patterns are different among these species, so proper identification helps in the selection of antifungal drugs for the prevention and treatment. Phenotypic methods for identification of Candida species, which are widely used in clinical microbiology laboratories, have some limitations. Real-time PCR followed by the high-resolution melting analysis (HRMA) is a novel approach for the rapid recognition of pathogenic fungi. Molecular phylogeny is essential for obtaining a better understanding of the evolution of the genus Candida and the identification of the relative degree of the Candida species. The purpose of this study was molecular identification of Candida isolates by Real-time PCR-high-resolution melting analysis and investigation of the genetic diversity of Candida species. METHODS Two hundred and thirty-two Candida isolates including 111 Candida isolates obtained from 96 HIV/AIDS patients and 121 Candida isolates obtained from 98 non-HIV persons were identified by real-time PCR and high-resolution melting curve analysis. To evaluate genetic diversity and relationships among Candida species, PCR products of nine clinical Candida isolates, as a representative of each kind of species, were randomly selected for DNA sequence analysis. RESULTS In HIV/AIDS patients, six species of Candida spp. were identified as follows: C albicans (n = 64; 57.7%), C glabrata (n = 31; 27.92%), C parapsilosis (n = 9; 8.1%), C tropicalis (n = 4; 3.6%), C krusei (n = 2; 1.8%), and C kefyr (n = 1; 0.90%). In non-HIV persons, we identified eight species of Candida including C albicans (n = 46; 38.33%) followed by C glabrata and C krusei (each one, n = 18; 15%), C tropicalis (n = 13; 10.83%), C lusitaniae (n = 12; 5.17%), C parapsilosis (n = 10; 4.31%), and C kefyr and C guillermondii (each one, n = 2; 1.66%). Also, the phylogenetic analysis showed the presence of two main clades and six separate subclades. Accordingly, about 88.9% of the isolates were located in clade I and 11.10% of the studied isolates were in clade II. CONCLUSIONS Real-time PCR followed by high-resolution melting analysis (HRMA) is known as a reliable, fast, and simple approach for detection and accurate identification of Candida species, especially in clinical samples.
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Affiliation(s)
- Esmaeel Eghtedar Nejad
- Pathobiology and Medical Diagnosis Laboratory, Mehregan Hospital, Kerman, Iran.,Department of Medical Parasitology and Mycology, Kerman University of Medical Sciences, Kerman, Iran
| | - Pooya Ghasemi Nejad Almani
- HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran.,Students Research Committee, Kerman University of Medical Sciences, Kerman, Iran.,Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Ali Mohammadi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Samira Salari
- Department of Medical Parasitology and Mycology, Kerman University of Medical Sciences, Kerman, Iran.,HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran.,Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran
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Nawar NN, Behiry IK, Yousef RHA, Emara MA. Application of High-Resolution Melting PCR to Detect the Genomic Fungal ITS 2 Region. Lab Med 2020; 51:66-73. [PMID: 31198973 DOI: 10.1093/labmed/lmz034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Invasive fungal infections (IFIs) are a main cause of morbidity and mortality. High-resolution melting polymerase chain reaction (HRM PCR) is promising for the identification of fungal species via the detection of internal transcribed spacer 2 (ITS2). OBJECTIVES To assess the sensitivity and specificity of HRM PCR in diagnosing IFIs, compared with blood culture. METHODS Our study included 100 patients who were suspected of having IFIs; we analyzed their specimens via blood culture and HRM PCR. RESULTS Blood culture results were positive in 57 cases and negative in 43 cases. HRM PCR results were positive in 14 cases and negative in 86 cases. The 14 cases with positive results included 4 with Candida tropicalis, 4 with Candida glabrata, and 6 with Candida krusei. HRM PCR sensitivity was 24.6%, specificity was 100%, positive predictive value (PPV) was 100%, and negative predictive value (NPV) was 50%. CONCLUSIONS HRM PCR is specific but not sensitive. Blood culture is more sensitive and cannot be replaced by HRM PCR.
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Affiliation(s)
- Nada N Nawar
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Egypt
| | - Iman K Behiry
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Egypt
| | - Reham H A Yousef
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Egypt
| | - Mohamed A Emara
- El Shiekh Zayed Specialized Hospital, Ministry of Health, Cairo, Egypt
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Koo SH, Teoh YL, Koh WL, Ochi H, Tan SK, Sim DMF, Jiang B, Tan AL, Tan TY, Lim SPR. Development and validation of a real-time multiplex PCR assay for the detection of dermatophytes and Fusarium spp. J Med Microbiol 2019; 68:1641-1648. [PMID: 31526456 DOI: 10.1099/jmm.0.001082] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Introduction: Onychomycosis is a debilitating, difficult-to-treat nail fungal infection with increasing prevalence worldwide. The main etiological agents are dermatophytes, which are common causative pathogens in superficial fungal mycoses. Conventional detection methods such as fungal culture have low sensitivity and specificity and are time-consuming.Aim: The main objective of this study was to design, develop and validate a real-time probe-based multiplex qPCR assay for the detection of dermatophytes and Fusarium species.Methodology: The performance characteristics of the qPCR assays were evaluated. The multiplex qPCR assays targeted four genes (assay 1: pan-dermatophytes/Fusarium spp.; assay 2: Trichophyton rubrum/Microsporum spp.). Analytical validation was accomplished using 150 fungal isolates and clinical validation was done on 204 nail specimens. The performance parameters were compared against the gold standard (fungal culture) and expanded gold standard (culture in conjunction with sequencing).Results: Both the single-plex and multiplex qPCR assays performed well especially when compared against the expanded gold standard. Among the 204 tested nail specimens, the culture method showed that 125 (61.3 %) were infected with at least one organism, of which 40 yielded positive results for dermatophytes and Fusarium spp. These target organisms detected include 20 dermatophytes and 22 Fusarium spp. The developed qPCR assays demonstrated excellent limit of detection, efficiency, coefficient of determination, analytical and clinical sensitivity and specificity.Conclusion: The multiplex qPCR assays were reliable for the diagnosis of onychomycosis, with shorter turn-around time as compared to culture method. This aids in the planning of treatment strategies to achieve optimal therapeutic outcome.
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Affiliation(s)
- Seok Hwee Koo
- Clinical Trials and Research Unit, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Yee Leng Teoh
- Department of Dermatology, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Wei Liang Koh
- Department of Dermatology, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Harumi Ochi
- Department of Dermatology, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Sher Kye Tan
- School of Chemical and Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Singapore
| | - Diana Miao Fang Sim
- Department of Laboratory Medicine, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Boran Jiang
- Department of Laboratory Medicine, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Ai Ling Tan
- Department of Microbiology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - Thean Yen Tan
- Department of Laboratory Medicine, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
| | - Su Ping Regina Lim
- Department of Dermatology, Changi General Hospital, 2 Simei Street 3, Singapore 529889, Singapore
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5
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Leal C, Silva G, Silva G, Silva L, Pinheiro Júnior J, Mota R. Padronização de uma PCR para diagnóstico molecular de Microsporum canis em amostras de pelos e crostas de cães e gatos. ARQ BRAS MED VET ZOO 2019. [DOI: 10.1590/1678-4162-9809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
RESUMO Objetivou-se neste estudo padronizar um protocolo de reação em cadeia da polimerase (PCR) para detecção de Microsporum canis em amostras de pelos e/ou crostas de cães e gatos. Foram selecionadas 48 amostras previamente identificadas por meio de cultura. Destas, 23 foram positivas para dermatófitos no cultivo. Padronizou-se a PCR a partir de primers desenhados para o alvo M. canis. Sessenta e um por cento (14/23) das amostras positivas para dermatófitos foram identificadas como M. canis em cultura. Desse total, 71,4% (10/14) apresentaram um fragmento de 218pb compatível com o esperado para a espécie fúngica alvo dessa reação. Observou-se uma sensibilidade de 71,4% e especificidade de 100% na PCR, além de uma boa concordância entre essas técnicas de diagnóstico (Kappa: 0,78; P<0,0001). O protocolo utilizado neste estudo apresentou alta especificidade na detecção de M. canis diretamente de amostras de pelos e/ou crostas de cães e gatos, viabilizando um diagnóstico mais rápido e específico, podendo esse protocolo ser empregado como um método confirmatório para agilizar a detecção de M. canis.
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Affiliation(s)
- C.A.S. Leal
- Universidade Federal Rural de Pernambuco, Brazil
| | - G.G. Silva
- Universidade Federal Rural de Pernambuco, Brazil
| | - G.M. Silva
- Universidade Federal Rural de Pernambuco, Brazil
| | | | | | - R.A. Mota
- Universidade Federal Rural de Pernambuco, Brazil
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Álvarez-Mosquera I, Hernáez S, Sánchez J, Suárez MD, Cisterna R. Diagnosis of Superficial Mycoses by a Rapid and Effective PCR Method from Samples of Scales, Nails and Hair. Mycopathologia 2018; 183:777-783. [PMID: 30094709 DOI: 10.1007/s11046-018-0290-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/28/2018] [Indexed: 11/26/2022]
Abstract
Superficial mycoses are the most frequently diagnosed affections of the stratum corneum of the skin, nails and hair. It is generally caused by the presence of yeasts and dermatophytes. Onychomycosis is the most common infection with an incidence of 80-90% in Europe generally produced by Trichophyton rubrum. The aim of this study is to compare the traditional diagnostic techniques of superficial mycoses with a homemade and wide-spectrum fungal polymerase chain reaction (PCR) technique that amplifies a specific region of the 18S ribosomal RNA (rRNA) directly from samples of scales, nails and hair. A total of 626 clinical samples (obtained in the Basurto University Hospital, Bilbao, Spain) were analysed by traditional culture, microscopy and PCR. DNA extraction was carried out by using an extraction buffer and bovine serum, and amplification of samples and performance of the PCR were checked by conventional agarose gel electrophoresis with subsequent sequencing of amplified samples. A total of 211 samples (34%) resulted in positive diagnosis with at least one of the two applied methods: culture (21%) and PCR (22%). Despite the low percentage of identification achieved by the sequencing technique (40%), the value contributed by the amplification of the 18S region of the rRNA was considered important in the identification as it showed a high predictive values for both positive and negative diagnoses (90.9% and 94.6%, respectively). The proposed PCR method has been confirmed as a complementary, rapid, and effective method in the diagnosis of superficial mycoses. Additionally, it reduces the time to obtain satisfactory results from 4 weeks to 7 h.
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Affiliation(s)
- Irene Álvarez-Mosquera
- Immunology, Microbiology and Parasitology Department, School of Medicine, University of Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Bizkaia, Spain.
| | - Silvia Hernáez
- Clinical Microbiology and Infection Control Department, Basurto University Hospital, Avda.Montevideo 18, 48013, Bilbao, Bizkaia, Spain
| | - Juan Sánchez
- Clinical Microbiology and Infection Control Department, Basurto University Hospital, Avda.Montevideo 18, 48013, Bilbao, Bizkaia, Spain
| | - Maria Dolores Suárez
- Clinical Microbiology and Infection Control Department, Basurto University Hospital, Avda.Montevideo 18, 48013, Bilbao, Bizkaia, Spain
| | - Ramón Cisterna
- Clinical Microbiology and Infection Control Department, Basurto University Hospital, Avda.Montevideo 18, 48013, Bilbao, Bizkaia, Spain
- Immunology, Microbiology and Parasitology Department, School of Medicine, University of Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Bizkaia, Spain
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7
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Jakobsen TH, Eickhardt SR, Gheorghe AG, Stenqvist C, Sønderholm M, Stavnsberg C, Jensen PØ, Odgaard A, Whiteley M, Moser C, Hvolris J, Hougen HP, Bjarnsholt T. Implants induce a new niche for microbiomes. APMIS 2018; 126:685-692. [PMID: 29962006 DOI: 10.1111/apm.12862] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/23/2018] [Indexed: 11/30/2022]
Abstract
Although much work is being done to develop new treatments, research and knowledge regarding factors underlying implant-related microbial colonization leading to infection are less comprehensive. Presence of microorganisms in and around implants clinically characterized as uninfected remains unknown. The objective of this study was to detect and identify bacteria and fungi on implants from various groups of patients with no prior indications of implant related infections. Patient samples (implants and tissue) were collected from five different hospitals in the Capital region of Denmark. By in-depth microbiological detection methods, we examined the prevalence of bacteria and fungi on 106 clinically uninfected implants from four patient groups (aseptic loosening, healed fractures, craniofacial complications and recently deceased). Of 106 clinically uninfected implants and 39 negative controls investigated, 66% were colonized by bacteria and 40% were colonized by fungi (p < 0.0001 compared to negative controls). A large number of microbes were found to colonize the implants, however, the most prevalent microbes present were not common aetiological agents of implant infections. The findings indicate that implants provide a distinct niche for microbial colonization. These data have broad implications for medical implant recipients, as well as for supporting the idea that the presence of foreign objects in the body alters the human microbiome by providing new colonization niches.
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Affiliation(s)
- Tim H Jakobsen
- Costerton Biofilm Center, Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Steffen R Eickhardt
- Costerton Biofilm Center, Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Alexandra G Gheorghe
- Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Majken Sønderholm
- Costerton Biofilm Center, Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Stavnsberg
- Costerton Biofilm Center, Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Peter Ø Jensen
- Costerton Biofilm Center, Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Anders Odgaard
- Department of Orthopedic Surgery, Copenhagen University Hospital Herlev - Gentofte, Copenhagen, Denmark
| | - Marvin Whiteley
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Claus Moser
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Jesper Hvolris
- Department of Orthopedic surgery, Bispebjerg Hospital, Copenhagen, Denmark
| | - Hans Petter Hougen
- Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
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8
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Hazlianda C, Muis K, Lubis I. A Comparative Study of Polymerase Chain Reaction-Restriction Fragment Length Polymorphism and Fungal Culture for the Evaluation of Fungal Species in Patients with Tinea Cruris. Open Access Maced J Med Sci 2017; 5:844-847. [PMID: 29362607 PMCID: PMC5771283 DOI: 10.3889/oamjms.2017.197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/20/2017] [Accepted: 10/21/2017] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND: Tinea cruris is the second most common dermatophytosis in the world and the most common in Indonesia. The conventional laboratory tests for dermatophyte infection are slow and less specific. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) is a PCR method with the addition of enzyme after amplification, therefore enabling for more specific results. AIM: This study aimed to find whether the PCR-RFLP test could yield the same fungal species result as a fungal culture. METHODS: The specimens were skin scrapings from thirty-one patients suspected tinea cruris. The tools and materials that were used were Sabaroud’s dextrose agar media, primer ITS 1 and ITS 4 and MvaI. RESULTS: The equation percentage of the test result species between PCR-RFLP and fungal culture was 50% of 12 subjects whose the test results were both positive from the fungal culture and PCR-RFLP. The percentage of the test result with fungal culture the fungal species were found, but in the PCR-RFLP test which the fungal species was not found, the percentage was 50% of 12 subjects which the test results were both positive as fungi from the culture and PCR-RFLP test. CONCLUSIONS: The species from PCR-RFLP examination was the same with the fungal culture.
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Affiliation(s)
- Cut Hazlianda
- Universitas Sumatera Utara, Fakultas Kedokteran, Dermatology and Venereology, Medan, Indonesia
| | - Kamaliah Muis
- Universitas Sumatera Utara, Fakultas Kedokteran, Dermatology and Venereology, Medan, Indonesia
| | - Isma Lubis
- Universitas Sumatera Utara, Fakultas Kedokteran, Dermatology and Venereology, Medan, Indonesia
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Štornik A, Skok B, Trček J. Comparison of Cultivable Acetic Acid Bacterial Microbiota in Organic and Conventional Apple Cider Vinegar. Food Technol Biotechnol 2016; 54:113-119. [PMID: 27904401 DOI: 10.17113/ftb.54.01.16.4082] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Organic apple cider vinegar is produced from apples that go through very restricted treatment in orchard. During the first stage of the process, the sugars from apples are fermented by yeasts to cider. The produced ethanol is used as a substrate by acetic acid bacteria in a second separated bioprocess. In both, the organic and conventional apple cider vinegars the ethanol oxidation to acetic acid is initiated by native microbiota that survived alcohol fermentation. We compared the cultivable acetic acid bacterial microbiota in the production of organic and conventional apple cider vinegars from a smoothly running oxidation cycle of a submerged industrial process. In this way we isolated and characterized 96 bacteria from organic and 72 bacteria from conventional apple cider vinegar. Using the restriction analysis of the PCR-amplified 16S-23S rRNA gene ITS regions, we identified four different HaeIII and five different HpaII restriction profiles for bacterial isolates from organic apple cider vinegar. Each type of restriction profile was further analyzed by sequence analysis of the 16S-23S rRNA gene ITS regions, resulting in identification of the following species: Acetobacter pasteurianus (71.90%), Acetobacter ghanensis (12.50%), Komagataeibacter oboediens (9.35%) and Komagataeibacter saccharivorans (6.25%). Using the same analytical approach in conventional apple cider vinegar, we identified only two different HaeIII and two different HpaII restriction profiles of the 16S‒23S rRNA gene ITS regions, which belong to the species Acetobacter pasteurianus (66.70%) and Komagataeibacter oboediens (33.30%). Yeasts that are able to resist 30 g/L of acetic acid were isolated from the acetic acid production phase and further identified by sequence analysis of the ITS1-5.8S rDNA‒ITS2 region as Candida ethanolica, Pichia membranifaciens and Saccharomycodes ludwigii. This study has shown for the first time that the bacterial microbiota for the industrial production of organic apple cider vinegar is clearly more heterogeneous than the bacterial microbiota for the industrial production of conventional apple cider vinegar. Further chemical analysis should reveal if a difference in microbiota composition influences the quality of different types of apple cider vinegar.
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Affiliation(s)
- Aleksandra Štornik
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor,
Koroška cesta 160, SI-2000 Maribor, Slovenia
| | - Barbara Skok
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor,
Koroška cesta 160, SI-2000 Maribor, Slovenia
| | - Janja Trček
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor,
Koroška cesta 160, SI-2000 Maribor, Slovenia; Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17,
SI-2000 Maribor, Slovenia
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10
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Lo CI, Fall B, Sambe-Ba B, Diawara S, Gueye MW, Mediannikov O, Sokhna C, Faye N, Diemé Y, Wade B, Raoult D, Fenollar F. MALDI-TOF Mass Spectrometry: A Powerful Tool for Clinical Microbiology at Hôpital Principal de Dakar, Senegal (West Africa). PLoS One 2015; 10:e0145889. [PMID: 26716681 PMCID: PMC4696746 DOI: 10.1371/journal.pone.0145889] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 12/09/2015] [Indexed: 12/26/2022] Open
Abstract
Our team in Europe has developed the routine clinical laboratory identification of microorganisms by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). To evaluate the utility of MALDI-TOF MS in tropical Africa in collaboration with local teams, we installed an apparatus in the Hôpital Principal de Dakar (Senegal), performed routine identification of isolates, and confirmed or completed their identification in France. In the case of discordance or a lack of identification, molecular biology was performed. Overall, 153/191 (80.1%) and 174/191 (91.1%) isolates yielded an accurate and concordant identification for the species and genus, respectively, with the 2 different MALDI-TOF MSs in Dakar and Marseille. The 10 most common bacteria, representing 94.2% of all bacteria routinely identified in the laboratory in Dakar (Escherichia coli, Klebsiella pneumoniae, Streptococcus agalactiae, Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus haemolyticus, Enterobacter cloacae, Enterococcus faecalis, and Staphylococcus epidermidis) were accurately identified with the MALDI-TOF MS in Dakar. The most frequent misidentification in Dakar was at the species level for Achromobacter xylosoxidans, which was inaccurately identified as Achromobacter denitrificans, and the bacteria absent from the database, such as Exiguobacterium aurientacum or Kytococcus schroeteri, could not be identified. A few difficulties were observed with MALDI-TOF MS for Bacillus sp. or oral streptococci. 16S rRNA sequencing identified a novel bacterium, “Necropsobacter massiliensis.” The robust identification of microorganisms by MALDI-TOF MS in Dakar and Marseille demonstrates that MALDI-TOF MS can be used as a first-line tool in clinical microbiology laboratories in tropical countries.
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Affiliation(s)
- Cheikh I. Lo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | | | | | | | | | - Oleg Mediannikov
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Cheikh Sokhna
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Ngor Faye
- Université Cheikh Anta Diop, Dakar, Senegal
| | - Yaya Diemé
- Hôpital Principal de Dakar, Dakar, Senegal
| | | | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Florence Fenollar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
- * E-mail:
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A novel, multiplex, real-time PCR-based approach for the detection of the commonly occurring pathogenic fungi and bacteria. BMC Microbiol 2013; 13:300. [PMID: 24364823 PMCID: PMC3879189 DOI: 10.1186/1471-2180-13-300] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 12/13/2013] [Indexed: 12/22/2022] Open
Abstract
Background Polymerase chain reaction (PCR)-based techniques are widely used to identify fungal and bacterial infections. There have been numerous reports of different, new, real-time PCR-based pathogen identification methods although the clinical practicability of such techniques is not yet fully clarified. The present study focuses on a novel, multiplex, real-time PCR-based pathogen identification system developed for rapid differentiation of the commonly occurring bacterial and fungal causative pathogens of bloodstream infections. Results A multiplex, real-time PCR approach is introduced for the detection and differentiation of fungi, Gram-positive (G+) and Gram-negative (G-) bacteria. The Gram classification is performed with the specific fluorescence resonance energy transfer (FRET) probes recommended for LightCycler capillary real-time PCR. The novelty of our system is the use of a non-specific SYBR Green dye instead of labelled anchor probes or primers, to excite the acceptor dyes on the FRET probes. In conjunction with this, the use of an intercalating dye allows the detection of fungal amplicons. With the novel pathogen detection system, fungi, G + and G- bacteria in the same reaction tube can be differentiated within an hour after the DNA preparation via the melting temperatures of the amplicons and probes in the same tube. Conclusions This modified FRET technique is specific and more rapid than the gold-standard culture-based methods. The fact that fungi, G + and G- bacteria were successfully identified in the same tube within an hour after the DNA preparation permits rapid and early evidence-based management of bloodstream infections in clinical practice.
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Winter I, Uhrlaß S, Krüger C, Herrmann J, Bezold G, Winter A, Barth S, Simon J, Gräser Y, Nenoff P. Molekularbiologischer Direktnachweis von Dermatophyten im klinischen Material bei Verdacht auf Onychomykose und Tinea pedis. Hautarzt 2013; 64:283-9. [DOI: 10.1007/s00105-013-2562-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Rothmund G, Sattler EC, Kaestle R, Fischer C, Haas CJ, Starz H, Welzel J. Confocal laser scanning microscopy as a new valuable tool in the diagnosis of onychomycosis - comparison of six diagnostic methods. Mycoses 2012; 56:47-55. [PMID: 22524550 DOI: 10.1111/j.1439-0507.2012.02198.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Onychomycosis is common and can mimic several different nail disorders. Accurate diagnosis is essential to choose the optimum antifungal therapy. The aim of this study was to evaluate the use of confocal laser scanning microscopy (CLSM) and optical coherence tomography (OCT) as new non-invasive diagnostic tools in onychomycosis and to compare them with the established techniques. In a prospective trial, 50 patients with suspected onychomycosis and 10 controls were examined by CLSM and OCT. Parallel KOH preparation, culture, PAS-staining and PCR were performed. PCR showed the highest sensitivity, followed by CLSM, PAS and KOH preparation. OCT offered the second best sensitivity but displayed the lowest specificity. CLSM and KOH preparation showed a high specificity and CLSM offered the best positive predictive value, similar to KOH preparation and OCT. Fungal culture showed the lowest sensitivity and the worst negative predictive value, yet culture and PCR are the only techniques able to identify genus and species. In summary, CLSM was comparable to PAS staining and superior to KOH preparation. Due to the low specificity we assess OCT not as appropriate. In the differentiation of species PCR outplays the fungal culture in terms of time and sensitivity.
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Affiliation(s)
- G Rothmund
- Department of Dermatology and Allergology, General Hospital Augsburg, Augsburg, Germany
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Telleria O, Ezpeleta G, Herrero O, Miranda-Zapico I, Quindós G, Cisterna R. Validation of the PCR–dHPLC method for rapid identification of Candida glabrata phylogenetically related species in different biological matrices. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 893-894:150-6. [DOI: 10.1016/j.jchromb.2012.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 02/27/2012] [Accepted: 03/04/2012] [Indexed: 01/31/2023]
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Higashi Y, Miyoshi H, Takeda K, Saruwatari H, Kubo H, Sakaguchi I, Iwata M, Uchida Y, Tada K, Miyamoto M, Wakamoto H, Takasaki S, Ishida H, Noriki S, Kanekura T. Evaluation of a newly-developed immunochromatography strip test for diagnosing dermatophytosis. Int J Dermatol 2012; 51:406-9. [DOI: 10.1111/j.1365-4632.2011.05046.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Beifuss B, Bezold G, Gottlöber P, Borelli C, Wagener J, Schaller M, Korting HC. Direct detection of five common dermatophyte species in clinical samples using a rapid and sensitive 24-h PCR-ELISA technique open to protocol transfer. Mycoses 2011; 54:137-45. [PMID: 19793206 DOI: 10.1111/j.1439-0507.2009.01771.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Identification of dermatophytes is usually based on morphological characteristics determined by time-consuming microscopic and cultural examinations. An effective PCR-ELISA method has been developed for rapid detection of dermatophyte species directly from clinical specimens within 24 h. Isolated genomic DNA of skin scrapings and nail samples from patients with suspected dermatophyte infections is amplified with species-specific digoxigenin-labelled primers targeting the topoisomerase II gene. The subsequent ELISA procedure with biotin-labelled probes allows a sensitive and specific identification of the five common dermatophytes -Trichophyton rubrum, T. interdigitale, T. violaceum, Microsporum canis and Epidermophyton floccosum. PCR-ELISA, based on the new polyphasic species concept, was assessed using 204 microscopy-positive samples in two university mycological laboratories in Munich and Tübingen, and 316 consecutive specimens - regardless of mycological findings - in a dermatological practice laboratory in Neu-Ulm. One of the five dermatophytes was confirmed by PCR-ELISA in 163 of 204 (79.9%) of the clinical samples from the university hospitals found positive using microscopy. Culture was positive for dermatophytes in 59.8% of the same cases. A significant difference between these two methods could be demonstrated using the McNemar test (P < 0.005). Analysis of specimens from Neu-Ulm confirmed the results in a dermatological practice laboratory as 25.0% of the specimens had positive PCR results, whereas only 7.3% were positive according to culture. Direct DNA isolation from clinical specimens and the PCR-ELISA method employed in this study provide a rapid, reproducible and sensitive tool for detection and discrimination of five major dermatophytes at species level, independent of morphological and biochemical characteristics.
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Affiliation(s)
- Barbara Beifuss
- Department of Dermatology and Allergology, Ludwig Maximilians University of Munich, Munich, Germany
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Wisselink G, van Zanten E, Kooistra-Smid A. Trapped in keratin; a comparison of dermatophyte detection in nail, skin and hair samples directly from clinical samples using culture and real-time PCR. J Microbiol Methods 2011; 85:62-6. [DOI: 10.1016/j.mimet.2011.01.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 01/13/2011] [Accepted: 01/15/2011] [Indexed: 11/25/2022]
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Brasch J, Beck-Jendroschek V, Gläser R. Fast and sensitive detection of Trichophyton rubrum in superficial tinea and onychomycosis by use of a direct polymerase chain reaction assay. Mycoses 2010; 54:e313-7. [DOI: 10.1111/j.1439-0507.2010.01904.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lau A, Chen S, Sleiman S, Sorrell T. Current status and future perspectives on molecular and serological methods in diagnostic mycology. Future Microbiol 2009; 4:1185-222. [DOI: 10.2217/fmb.09.70] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Invasive fungal infections are an important cause of infectious morbidity. Nonculture-based methods are increasingly used for rapid, accurate diagnosis to improve patient outcomes. New and existing DNA amplification platforms have high sensitivity and specificity for direct detection and identification of fungi in clinical specimens. Since laboratories are increasingly reliant on DNA sequencing for fungal identification, measures to improve sequence interpretation should support validation of reference isolates and quality control in public gene repositories. Novel technologies (e.g., isothermal and PNA FISH methods), platforms enabling high-throughput analyses (e.g., DNA microarrays and Luminex® xMAP™) and/or commercial PCR assays warrant further evaluation for routine diagnostic use. Notwithstanding the advantages of molecular tests, serological assays remain clinically useful for patient management. The serum Aspergillus galactomannan test has been incorporated into diagnostic algorithms of invasive aspergillosis. Both the galactomannan and the serum β-D-glucan test have value for diagnosing infection and monitoring therapeutic response.
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Affiliation(s)
- Anna Lau
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia
| | - Sharon Chen
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia and Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Sue Sleiman
- Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Tania Sorrell
- Centre for Infectious Diseases & Microbiology, Westmead Hospital, Darcy and Hawkesbury Roads, Westmead, NSW 2145, Australia
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Ebihara M, Makimura K, Sato K, Abe S, Tsuboi R. Molecular detection of dermatophytes and nondermatophytes in onychomycosis by nested polymerase chain reaction based on 28S ribosomal RNA gene sequences. Br J Dermatol 2009; 161:1038-44. [PMID: 19566663 DOI: 10.1111/j.1365-2133.2009.09249.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Onychomycosis is often caused by dermatophytes, but the role of nondermatophytes is underestimated due to the difficulty of identifying them by conventional direct microscopy and culture. OBJECTIVES This study aims to detect nondermatophytes, as well as dermatophytes, in the nail samples of patients with onychomycosis using a polymerase chain reaction (PCR)-based culture-independent method. MATERIALS AND METHODS The nested PCR assay targeting the sequence of the 28S ribosomal RNA gene was used to amplify fungal DNAs from 50 microscopy-positive nail specimens. Newly designed primer sets for dermatophyte universal, Trichophyton rubrum, T. mentagrophytes, Aspergillus spp., Scopulariopsis brevicaulis, Fusarium solani, F. oxysporum, F. verticillioides, Candida albicans and C. tropicalis were used after confirmation of their specificity. RESULTS Forty-seven cases (94%) were positive for fungal DNA, among which dermatophytes were detected in 39 cases (83.0%): T. rubrum in 35 cases (74.5%) and T. mentagrophytes in eight cases (17.0%). Surprisingly, nondermatophytes were detected in 18 cases (38.3%), both dermatophytes and nondermatophytes in 10 cases (21.3%) and nondermatophytes alone in eight cases (17.0%). Aspergillus spp. alone was observed in five cases (10.6%). CONCLUSIONS This study indicates that most of the affected nail plates of patients with onychomycosis were positive for specific fungal DNAs, and suggests that nondermatophytes detected at high rates may be involved in the pathogenesis of onychomycosis.
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Affiliation(s)
- M Ebihara
- Department of Dermatology, Tokyo Medical University, Nishishinjuku, 6-1-1 Shinjuku-ku, Tokyo 160-0023, Japan
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Vollmer T, Störmer M, Kleesiek K, Dreier J. Evaluation of novel broad-range real-time PCR assay for rapid detection of human pathogenic fungi in various clinical specimens. J Clin Microbiol 2008; 46:1919-26. [PMID: 18385440 PMCID: PMC2446849 DOI: 10.1128/jcm.02178-07] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 01/02/2008] [Accepted: 03/23/2008] [Indexed: 11/20/2022] Open
Abstract
In the present study, a novel broad-range real-time PCR was developed for the rapid detection of human pathogenic fungi. The assay targets a part of the 28S large-subunit ribosomal RNA (rDNA) gene. We investigated its application for the most important human pathogenic fungal genera, including Aspergillus, Candida, Cryptococcus, Mucor, Penicillium, Pichia, Microsporum, Trichophyton, and Scopulariopsis. Species were identified in PCR-positive reactions by direct DNA sequencing. A noncompetitive internal control was applied to prevent false-negative results due to PCR inhibition. The minimum detection limit for the PCR was determined to be one 28S rDNA copy per PCR, and the 95% detection limit was calculated to 15 copies per PCR. To assess the clinical applicability of the PCR method, intensive-care patients with artificial respiration and patients with infective endocarditis were investigated. For this purpose, 76 tracheal secretion samples and 70 heart valve tissues were analyzed in parallel by real-time PCR and cultivation. No discrepancies in results were observed between PCR analysis and cultivation methods. Furthermore, the application of the PCR method was investigated for other clinical specimens, including cervical swabs, nail and horny skin scrapings, and serum, blood, and urine samples. The combination of a broad-range real-time PCR and direct sequencing facilitates rapid screening for fungal infection in various clinical specimens.
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Affiliation(s)
- Tanja Vollmer
- Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum Nordrhein-Westfalen, Universitätsklinik der Ruhr-Universität Bochum, Georgstrasse 11, 32545 Bad Oeynhausen, Germany
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Kanbe T. Molecular Approaches in the Diagnosis of Dermatophytosis. Mycopathologia 2008; 166:307-17. [DOI: 10.1007/s11046-008-9107-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [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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Arabatzis M, Bruijnesteijn van Coppenraet LES, Kuijper EJ, de Hoog GS, Lavrijsen APM, Templeton K, van der Raaij-Helmer EMH, Velegraki A, Gräser Y, Summerbell RC. Diagnosis of common dermatophyte infections by a novel multiplex real-time polymerase chain reaction detection/identification scheme. Br J Dermatol 2007; 157:681-9. [PMID: 17672875 DOI: 10.1111/j.1365-2133.2007.08100.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
BACKGROUND In the absence of a functional dermatophyte-specific polymerase chain reaction (PCR), current diagnosis of dermatophytoses, which constitute the commonest communicable diseases worldwide, relies on microscopy and culture. This combination of techniques is time-consuming and notoriously low in sensitivity. OBJECTIVES Recent dermatophyte gene sequence records were used to design a real-time PCR assay for detection and identification of dermatophytes in clinical specimens in less than 24 h. PATIENTS AND METHODS Two assays based on amplification of ribosomal internal transcribed spacer regions and on the use of probes specific to relevant species and species-complexes were designed, optimised and clinically evaluated. One assay was for detecting the Trichophyton mentagrophytes species complex plus T. tonsurans and T. violaceum. The second assayed for the T. rubrum species complex, Microsporum canis and M. audouinii. RESULTS The analytical sensitivity of both assays was 0.1 pg DNA per reaction, corresponding to 2.5-3.3 genomes per sample. The protocol was clinically evaluated over 6 months by testing 92 skin, nail and hair specimens from 67 patients with suspected dermatophytosis. Real-time PCR detected and correctly identified the causal agent in specimens from which T. rubrum, T. interdigitale, M. audouinii or T. violaceum grew in culture, and also identified a dermatophyte species in an additional seven specimens that were negative in microscopy and culture. CONCLUSIONS This highly sensitive assay also proved to have high positive and negative predictive values (95.7% and 100%), facilitating the accurate, rapid diagnosis conducive to targeted rather than empirical therapy for dermatophytoses.
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Affiliation(s)
- M Arabatzis
- Second Dermatology Clinic, A. Syngros Hospital, Medical School, University of Athens, Ionos Dragoumi 4, Athens 11621, Greece.
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Savin C, Huck S, Rolland C, Benderdouche M, Faure O, Noacco G, Menotti J, Candolfi E, Pelloux H, Grillot R, Coupe S, Derouin F. Multicenter evaluation of a commercial PCR-enzyme-linked immunosorbent assay diagnostic kit (Onychodiag) for diagnosis of dermatophytic onychomycosis. J Clin Microbiol 2007; 45:1205-10. [PMID: 17287330 PMCID: PMC1865812 DOI: 10.1128/jcm.01418-06] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We prospectively evaluated a new PCR-enzyme-linked immunosorbent assay kit (Onychodiag; BioAdvance, France) for the diagnosis of dermatophytic onychomycosis by testing nail samples from 438 patients with suspected onychomycosis and from 108 healthy controls in three independent laboratories. In two laboratories, samples were collected by trained mycologists as close as possible to the lesions (proximal samples). In one laboratory, samples were collected by other physicians. All samples were processed by conventional mycological techniques and by Onychodiag, blindly to the mycological results. An additional distal sample, collected by clipping the nail plate, was obtained from 75 patients and tested with Onychodiag alone. In patients with culture-proven dermatophytic onychomycosis, the sensitivity of Onychodiag was 83.6% (87.9% including the gray zone) and ranged from 75 to 100% according to the laboratory and the sampling conditions. The specificity was 100% when healthy subjects were considered true negative controls. Onychodiag was positive on 68 patient samples that were sterile or yielded nondermatophyte species in culture. Based on the results of Onychodiag for mycologically proven positive samples and true-negative samples, these results were considered true positives, and the poor performance of mycology on these samples was attributed to inconvenient sampling conditions or to contaminants. When tested on distal samples, Onychodiag was positive in 49/53 (92%) cases of proven dermatophytic onychomycosis. Finally, with either proximal or distal samples, Onychodiag provided a diagnosis of dermatophytic onychomycosis within 24 to 48 h after sampling, and its sensitivity was close to that of mycological techniques applied to proximal samples.
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Affiliation(s)
- C Savin
- Bio Advance, Espace Villa Parc, l'érable, 1 avenue Marne et Gondoire, 77600 Bussy-Saint-Martin, France.
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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.
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Affiliation(s)
- S Arunmozhi Balajee
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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Arabatzis M, Xylouri E, Frangiadaki I, Tzimogianni A, Milioni A, Arsenis G, Velegraki A. Rapid detection of Arthroderma vanbreuseghemii in rabbit skin specimens by PCR?RFLP. Vet Dermatol 2006; 17:322-6. [PMID: 16961817 DOI: 10.1111/j.1365-3164.2006.00535.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Three commercial rabbit farms independently reported suspected dermatophyte infections during 2004. Cultures confirmed that the infection was caused by the zoophilic Tricophyton mentagrophytes, while mating studies and sequencing of the internal transcribed spacer (ITS)1/4 polymerase chain reaction products, directly amplified from skin lesions and from pure culture isolates, established its Arthroderma vanbreuseghemii lineage. Subsequently, the corresponding DdeI restriction profiles of the ITS1/4 PCR products matched one of the two published T. mentagrophytes complex profiles. Sequence analysis of the published ITS sequences predicted distinct DdeI restriction sites for Arthroderma benhamiae and A. vanbreuseghemii, while all DdeI-generated restriction fragment length polymorphisms of the rabbit isolates were identical to those of A. vanbreuseghemii. The proposed procedure can be used for rapid dermatophyte detection and presumptive T. mentagrophytes identification.
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Affiliation(s)
- Michael Arabatzis
- Mycology Laboratory, Department of Microbiology, Medical School, University of Athens, Athens, Greece.
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De Baere T, Van Keerberghen A, Van Hauwe P, De Beenhouwer H, Boel A, Verschraegen G, Claeys G, Vaneechoutte M. An interlaboratory comparison of ITS2-PCR for the identification of yeasts, using the ABI Prism 310 and CEQ8000 capillary electrophoresis systems. BMC Microbiol 2005; 5:14. [PMID: 15774019 PMCID: PMC1082908 DOI: 10.1186/1471-2180-5-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2004] [Accepted: 03/18/2005] [Indexed: 11/11/2022] Open
Abstract
Background Currently, most laboratories identify yeasts routinely on the basis of morphology and biochemical reactivity. This approach has quite often limited discriminatory power and may require long incubation periods. Due to the increase of fungal infections and due to specific antifungal resistence patterns for different species, accurate and rapid identification has become more important. Several molecular techniques have been described for fast and reliable identification of yeast isolates, but interlaboratory exchangeability of identification schemes of molecular techniques has hardly been studied. Here, we compared amplified ITS2 fragment length determination by an ABI Prism 310 (Applied Biosystems, Foster City, Ca.) capillary electrophoresis system with that obtained by a CEQ8000 (Beckman Coulter, Fullerton, Ca.) capillary electrophoresis system. Results Although ITS2 size estimations on both systems differed and separate libraries had to be constructed for each system, both approaches had the same discriminatory power with regard to the 44 reference strains, identical identifications were obtained for 39/ 40 clinical isolates in both laboratories and strains from 51 samples were correctly identified using CEQ8000, when compared to phenotypic identification. Conclusion Identification of yeasts with ITS2-PCR followed by fragment analysis can be carried out on different capillary electrophoresis systems with comparable discriminatory power.
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Affiliation(s)
- Thierry De Baere
- Department of Clinical Chemistry, Microbiology and Immunology, University Hospital Ghent, Belgium
| | | | - Peter Van Hauwe
- Laboratory Microbiology, Onze Lieve Vrouw Ziekenhuis, Aalst, Belgium
| | | | - An Boel
- Laboratory Microbiology, Onze Lieve Vrouw Ziekenhuis, Aalst, Belgium
| | - Gerda Verschraegen
- Department of Clinical Chemistry, Microbiology and Immunology, University Hospital Ghent, Belgium
| | - Geert Claeys
- Department of Clinical Chemistry, Microbiology and Immunology, University Hospital Ghent, Belgium
| | - Mario Vaneechoutte
- Department of Clinical Chemistry, Microbiology and Immunology, University Hospital Ghent, Belgium
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