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Chrenkova V, Vadkertiova R, Vlachova K, Babjuk M, Lischke R, Bebrova E, Hubacek P. Candida sojae: First report of a human infection. J Mycol Med 2022; 32:101309. [PMID: 35870417 DOI: 10.1016/j.mycmed.2022.101309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Vanda Chrenkova
- Department of Medical Microbiology, Charles University 2nd Faculty of Medicine and Motol University Hospital, V Úvalu 84, 15006 Prague 5, Czech Republic.
| | - Renata Vadkertiova
- Culture Collection of Yeasts, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia.
| | - Katerina Vlachova
- Department of Urology, Charles University 2nd Faculty of Medicine and Motol University Hospital, V Úvalu 84, 15006 Prague 5, Czech Republic
| | - Marek Babjuk
- Department of Urology, Charles University 2nd Faculty of Medicine and Motol University Hospital, V Úvalu 84, 15006 Prague 5, Czech Republic
| | - Robert Lischke
- 3rd Department of Surgery, Charles University 1st Faculty of Medicine and Motol University Hospital, V Úvalu 84, 15006 Prague 5, Czech Republic
| | - Eliska Bebrova
- Department of Medical Microbiology, Charles University 2nd Faculty of Medicine and Motol University Hospital, V Úvalu 84, 15006 Prague 5, Czech Republic
| | - Petr Hubacek
- Department of Medical Microbiology, Charles University 2nd Faculty of Medicine and Motol University Hospital, V Úvalu 84, 15006 Prague 5, Czech Republic; Department of Paediatric Haematology and Oncology, Charles University 2nd Faculty of Medicine and Motol University Hospital, V Úvalu 84, 15006 Prague 5, Czech Republic
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Bazalová O, Cihlář JZ, Dlouhá Z, Bár L, Dráb V, Kavková M. Rapid sourdough yeast identification using panfungal PCR combined with high resolution melting analysis. METHODS IN MICROBIOLOGY 2022; 199:106522. [PMID: 35716843 DOI: 10.1016/j.mimet.2022.106522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/10/2022] [Accepted: 06/10/2022] [Indexed: 10/18/2022]
Abstract
The microbial composition of the sourdough starter affects the sourdough bread properties. Therefore, it is crucial to find a tool for rapid, time-saving, and economical identification of the sourdough microbiota. We focused on the rapid identification of sourdough yeasts. We designed a panfungal real time-PCR targeting the ITS2 region (ITS-amplicon) and a fragment of D1/D2 region of 26S rRNA gene (U-amplicon) and used high resolution melting analysis (HRM) for subsequent species identification. The sensitivity and specificity of our method were tested on the reference yeast cultures. We obtained divergent melting peaks (Tm). The further analysis of melt curves suggests the possibility to discriminate yeasts on the genus- and some on species-specific level in the mixed sample. The applicability of this method in routine practice was evaluated on nine sourdough samples. Revealed melt curves of U-amplicons were predominantly characteristic of the sourdough. The evaluation of the Tm and the shape of the melt curve was used to assess the sourdough yeasts. Additionally, using the HRM-PCR method the contamination with the ergot fungus DNA was revealed. Our data showed HRM-PCR is a simple, rapid, and inexpensive tool useful in identifying sourdough yeasts.
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Affiliation(s)
- Olga Bazalová
- Dairy Research Institute, Ltd., Department Tábor, Ke Dvoru 12a, 160 00 Praha, Vokovice, Czech Republic.
| | - Jaromír Z Cihlář
- Dairy Research Institute, Ltd., Department Tábor, Ke Dvoru 12a, 160 00 Praha, Vokovice, Czech Republic; Milcom, a.s., Collection of Dairy Microorganisms - Laktoflora, Ke Dvoru 12a, 160 00 Praha, Vokovice, Czech Republic
| | - Zuzana Dlouhá
- Milcom, a.s., Collection of Dairy Microorganisms - Laktoflora, Ke Dvoru 12a, 160 00 Praha, Vokovice, Czech Republic
| | - Ladislav Bár
- Dairy Research Institute, Ltd., Department Tábor, Ke Dvoru 12a, 160 00 Praha, Vokovice, Czech Republic; Milcom, a.s., Collection of Dairy Microorganisms - Laktoflora, Ke Dvoru 12a, 160 00 Praha, Vokovice, Czech Republic
| | - Vladimír Dráb
- Dairy Research Institute, Ltd., Department Tábor, Ke Dvoru 12a, 160 00 Praha, Vokovice, Czech Republic; Milcom, a.s., Collection of Dairy Microorganisms - Laktoflora, Ke Dvoru 12a, 160 00 Praha, Vokovice, Czech Republic
| | - Miloslava Kavková
- Dairy Research Institute, Ltd., Department Tábor, Ke Dvoru 12a, 160 00 Praha, Vokovice, Czech Republic; Milcom, a.s., Collection of Dairy Microorganisms - Laktoflora, Ke Dvoru 12a, 160 00 Praha, Vokovice, Czech Republic
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3
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Hoang MTV, Irinyi L, Hu Y, Schwessinger B, Meyer W. Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections. Front Microbiol 2022; 12:708550. [PMID: 35069461 PMCID: PMC8770865 DOI: 10.3389/fmicb.2021.708550] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022] Open
Abstract
Identification of the causative infectious agent is essential in the management of infectious diseases, with the ideal diagnostic method being rapid, accurate, and informative, while remaining cost-effective. Traditional diagnostic techniques rely on culturing and cell propagation to isolate and identify the causative pathogen. These techniques are limited by the ability and the time required to grow or propagate an agent in vitro and the facts that identification based on morphological traits are non-specific, insensitive, and reliant on technical expertise. The evolution of next-generation sequencing has revolutionized genomic studies to generate more data at a cheaper cost. These are divided into short- and long-read sequencing technologies, depending on the length of reads generated during sequencing runs. Long-read sequencing also called third-generation sequencing emerged commercially through the instruments released by Pacific Biosciences and Oxford Nanopore Technologies, although relying on different sequencing chemistries, with the first one being more accurate both platforms can generate ultra-long sequence reads. Long-read sequencing is capable of entirely spanning previously established genomic identification regions or potentially small whole genomes, drastically improving the accuracy of the identification of pathogens directly from clinical samples. Long-read sequencing may also provide additional important clinical information, such as antimicrobial resistance profiles and epidemiological data from a single sequencing run. While initial applications of long-read sequencing in clinical diagnosis showed that it could be a promising diagnostic technique, it also has highlighted the need for further optimization. In this review, we show the potential long-read sequencing has in clinical diagnosis of fungal infections and discuss the pros and cons of its implementation.
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Affiliation(s)
- Minh Thuy Vi Hoang
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
| | - Yiheng Hu
- Research School of Biology, Australia National University, Canberra, ACT, Australia
| | | | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
- Westmead Hospital (Research and Education Network), Westmead, NSW, Australia
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5
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Liu K, Wu M, Lin X, Lonan P, Chen S, Wu Y, Lai X, Yu L, Zhou X, Li G. Molecular analysis of edible bird's nest and rapid authentication of Aerodramus fuciphagus from its subspecies by PCR-RFLP based on the cytb gene. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:2710-2717. [PMID: 32930302 DOI: 10.1039/c9ay02548k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Edible bird's nest (EBN), for its great nutritional value, is widely used around the world, especially in China and Singapore. EBNs of different origins and types may vary in price and quality. Nowadays, birds' nests are difficult to identify morphologically, except for some whole bird's nests of which origins can be roughly identified. In this study, forty-two samples were collected from different regions for sequencing analysis and phylogenetic classification to initially determine their origins. Two stable enzyme digestion sites were found in the analysis of restriction maps of the species. Then, a quick and specific PCR-RFLP method was established to identify the EBN samples' origins. The genetic identification results indicated that the forty-two samples were from five origins. With the Af/g-486bp-F/R primer and restriction enzyme Taq I, Aerodramus fuciphagus (A. fuciphagus) was efficiently differentiated from the other species. Furthermore, the cytb-592bp-F/R primer and the BamH I enzyme were found to be useful in distinguishing Aerodramus fuciphagus (A. fuciphagus) from its subspecies (Aerodramus germani, A. germani). The PCR-RFLP method provides a potential tool for the rapid discrimination of A. fuciphagus at the species and even the subspecies levels to ensure the quality of the EBN products.
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Affiliation(s)
- Kunfeng Liu
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Maoyong Wu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xuemei Lin
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Piyanuch Lonan
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Sitai Chen
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Yina Wu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiaoping Lai
- Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Liangwen Yu
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Xiaoming Zhou
- College of Life Science, South China Normal University, Guangzhou 510631, China.
| | - Geng Li
- Laboratory Animal Center, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
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Cai S, Xu J, Shao Y, Gong J, Zhao F, He L, Shan X. Rapid identification of the Candida glabrata species complex by high-resolution melting curve analysis. J Clin Lab Anal 2020; 34:e23226. [PMID: 32048348 PMCID: PMC7307358 DOI: 10.1002/jcla.23226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/13/2019] [Accepted: 01/07/2020] [Indexed: 02/02/2023] Open
Abstract
Background Candida glabrata is a common pathogen that causes invasive candidiasis. Among non‐albicans Candida infections, C glabrata infections are associated with the highest fatality rates. Candida glabrata sensu stricto, Candida nivariensis, and Candida bracarensis have been identified and together form the C glabrata species complex. It is difficult to detect the two rare species by traditional laboratory methods. This study established a method for the rapid identification of members of the C glabrata species complex based on high‐resolution melting curve (HRM) analysis and evaluated its practical application. Methods The internal transcribed spacer (ITS) region was used as target gene region to design specific primers. HRM analysis was performed with three subspecies of the C glabrata species complex and negative controls to test its specificity and sensitivity. To evaluate its practical application, the HRM technique was tested with clinical isolates, and the results were compared with the DNA sequencing results. Results Differences were detected among the melting profiles of the members of the C glabrata species complex. The negative controls were not amplified, indicating the high specificity of the method. The minimum detection limits of C glabrata sensu stricto, C nivariensis, and C bracarensis were approximately 1 × 101 copies/µL or less. The results of the HRM analysis of the clinical isolates were consistent with the DNA sequencing results. Conclusions The HRM method is sensitive and can be used to rapidly identify the members of the C glabrata species complex. The method can allow early and targeted treatment of patients with invasive candidiasis.
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Affiliation(s)
- Shuqian Cai
- Department of Clinical Laboratory, Jinhua Municipal Central Hospital, Zhejiang, China.,State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Juan Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,School of Public Health, Wuhan University of Science and Technology, Hubei, China
| | - Yakun Shao
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Jie Gong
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fei Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lihua He
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaoyun Shan
- Department of Clinical Laboratory, Jinhua Municipal Central Hospital, Zhejiang, China
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Saffioti C, Mesini A, Bandettini R, Castagnola E. Diagnosis of invasive fungal disease in children: a narrative review. Expert Rev Anti Infect Ther 2019; 17:895-909. [PMID: 31694414 DOI: 10.1080/14787210.2019.1690455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Invasive fungal diseases (IFD) represent important causes of morbidity and mortality in pediatrics. Early diagnosis and treatment of IFD is associated with better outcome and this entails the need to use fast and highly sensitive and specific methods that can support clinicians in the management of IFD.Areas covered: A narrative review was performed on conventional diagnostic methods such as culture, microscopy and histopathology are still gold standard but are burdened by a lack of sensitivity and specificity; on the other hand, imaging and noninvasive antigen-based such as beta-D-glucan, galactomannan and molecular biomarkers are the most convenient nonculture methods for diagnosis and monitoring effects of therapy. Aim of the present review is to summarize what is available in these fields at end of the second decade of the third millennium and look for future perspectives.Expert opinion: Promising and useful diagnostic methods have been applied in infectious disease diagnosis in clinical practice or in designing platforms. Unfortunately, most of them are not standardized or validated in pediatric population. However, clinicians should be aware of all innovative diagnostic tools to use in combination with conventional diagnostic methods for a better management of pathology and patient.
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Affiliation(s)
- Carolina Saffioti
- Department of Infectious Diseases, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Alessio Mesini
- Department of Infectious Diseases, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Roberto Bandettini
- Department of laboratory Medicine, Microbiology Service, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Elio Castagnola
- Department of Infectious Diseases, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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Diba K, Jangi F, Makhdoomi K, Moshiri N, Mansouri F. Aspergillus diversity in the environments of nosocomial infection cases at a university hospital. J Med Life 2019; 12:128-132. [PMID: 31406513 PMCID: PMC6685303 DOI: 10.25122/jml-2018-0057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aspergillus species (sp.) that causes opportunistic infections have been increasingly found in human mainly immunosuppressive patients around the world every year. The main objective was to use a rapid and cheap molecular method for monitoring Aspergillus infections and epidemiological approaches. In order to identity Aspergilli species (spp.), a number of molecular methods including restriction fragment length polymorphism (RFLP) have been employed in accordance with ribosomal RNA amplification. The focus of this study — a group of hospitalized patients with clinical and subclinical signs of infection. All of the collected clinical specimens were transported to the medical mycology lab and examined for Aspergillus identification. The environmental specimens were collected from air and surfaces inspected for the Aspergillus within the hospital sources. At first, growth characteristics and microscopic features on mycological media for the identification of Aspergillus sp. were performed. For the confirmation of Aspergillus isolates which similarly found in clinical and environmental sources, molecular method polymerase chain reaction/restriction fragment length polymorphism was carried out. From the mentioned specimens, 102 fungal isolates included Candida spp., Aspergillus spp. and other fungi. Aspergillus flavus (47%), Aspergillus fumigatus (29.4%) and Aspergillus niger (23.5%) all were found as the most common clinical isolates. In addition, Aspergillus isolates from environmental were Aspergillus niger (43.7%), Aspergillus flavus (41.7%), Aspergillus fumigatus (14.6%). Therefore, polymerase chain reaction-restriction fragment length polymorphism with a single restriction enzyme can be very useful in the identification of Aspergillus spp., because of its facility in use, speed, robust, and high sensitivity of diagnosis.
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Affiliation(s)
- Kambiz Diba
- Department of Medical Mycology and Parasitology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran.,Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Farzaneh Jangi
- Imam Khomeini Hospital, Urmia University of Medical Sciences, Urmia, Iran
| | - Khadijeh Makhdoomi
- Imam Khomeini Hospital, Urmia University of Medical Sciences, Urmia, Iran
| | - Naser Moshiri
- Imam Khomeini Hospital, Urmia University of Medical Sciences, Urmia, Iran
| | - Fatemeh Mansouri
- Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran.,Department of Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
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Gabaldón T. Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. FEMS Microbiol Rev 2019; 43:517-547. [PMID: 31158289 PMCID: PMC8038933 DOI: 10.1093/femsre/fuz015] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/31/2019] [Indexed: 12/29/2022] Open
Abstract
The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.
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Affiliation(s)
- Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- ICREA, Pg Lluís Companys 23, 08010 Barcelona, Spain
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Detection and identification of fungi in bronchoalveolar lavage fluid from immunocompromised patients using panfungal PCR. Folia Microbiol (Praha) 2018; 64:421-428. [PMID: 30535753 DOI: 10.1007/s12223-018-00669-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/29/2018] [Indexed: 01/24/2023]
Abstract
Rapid diagnostics of fungal pneumonia and initiation of appropriate therapy are still challenging. In this study, we used two panfungal assays to test bronchoalveolar lavage fluid (BALF) samples to prove their ability to confirm invasive fungal disease diagnosis and identify causative agents. Two methods targeting different fungal rDNA regions were used, and the obtained PCR products were sequenced directly or after cloning. In total, 106 BALF samples from 104 patients were tested. After sequencing, we obtained 578 sequences. Four hundred thirty-seven sequences were excluded from further analysis due to duplication (n = 335) or similarity with sequences detected in the extraction control sample (n = 102); 141 unique sequences were analyzed. Altogether, 23/141 (16%) of the fungi detected belonged to pathogenic species, and 63/141 (45%) were identified as various yeasts; a variety of environmental or very rare fungal human pathogens represented 29/141 (21%) of the total and 26/141 (18%) were described as uncultured fungus. Panfungal PCR detected fungal species that would be missed by specific methods in only one case (probable cryptococcosis). Panfungal PCR followed by sequencing has limited use for testing BALF samples due to frequent commensal or environmental fungal species pickup.
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Meyer W, Irinyi L, Hoang MTV, Robert V, Garcia-Hermoso D, Desnos-Ollivier M, Yurayart C, Tsang CC, Lee CY, Woo PCY, Pchelin IM, Uhrlaß S, Nenoff P, Chindamporn A, Chen S, Hebert PDN, Sorrell TC. Database establishment for the secondary fungal DNA barcode translational elongation factor 1α ( TEF1α) 1. Genome 2018; 62:160-169. [PMID: 30465691 DOI: 10.1139/gen-2018-0083] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
With new or emerging fungal infections, human and animal fungal pathogens are a growing threat worldwide. Current diagnostic tools are slow, non-specific at the species and subspecies levels, and require specific morphological expertise to accurately identify pathogens from pure cultures. DNA barcodes are easily amplified, universal, short species-specific DNA sequences, which enable rapid identification by comparison with a well-curated reference sequence collection. The primary fungal DNA barcode, ITS region, was introduced in 2012 and is now routinely used in diagnostic laboratories. However, the ITS region only accurately identifies around 75% of all medically relevant fungal species, which has prompted the development of a secondary barcode to increase the resolution power and suitability of DNA barcoding for fungal disease diagnostics. The translational elongation factor 1α (TEF1α) was selected in 2015 as a secondary fungal DNA barcode, but it has not been implemented into practice, due to the absence of a reference database. Here, we have established a quality-controlled reference database for the secondary barcode that together with the ISHAM-ITS database, forms the ISHAM barcode database, available online at http://its.mycologylab.org/ . We encourage the mycology community for active contributions.
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Affiliation(s)
- Wieland Meyer
- a Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney School of Medicine, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Laszlo Irinyi
- a Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney School of Medicine, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Minh Thuy Vi Hoang
- a Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney School of Medicine, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Vincent Robert
- b Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Dea Garcia-Hermoso
- c Institut Pasteur, National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Molecular Mycology Unit, CNRS UMR2000, Paris, France
| | - Marie Desnos-Ollivier
- c Institut Pasteur, National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Molecular Mycology Unit, CNRS UMR2000, Paris, France
| | - Chompoonek Yurayart
- d Mycology Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,e Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Chi-Ching Tsang
- f Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Chun-Yi Lee
- f Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Patrick C Y Woo
- f Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Ivan Mikhailovich Pchelin
- g Laboratory of Molecular Genetic Microbiology, Kashkin Research Institute of Medical Mycology, I.I. Mechnikov North-Western State Medical University, St Petersburg, Russia
| | - Silke Uhrlaß
- h Laboratory of Medical Microbiology, Partnership Dr. C. Krueger & Prof. Dr. P. Nenoff, Roetha OT Moelbis, Germany
| | - Pietro Nenoff
- h Laboratory of Medical Microbiology, Partnership Dr. C. Krueger & Prof. Dr. P. Nenoff, Roetha OT Moelbis, Germany
| | - Ariya Chindamporn
- d Mycology Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sharon Chen
- a Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney School of Medicine, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Westmead, NSW, Australia.,i Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, Westmead Hospital, Westmead, NSW, Australia
| | - Paul D N Hebert
- j Department of Integrative Biology and Director of the Biodiversity Institute of Ontario at the University of Guelph, Guelph, ON, Canada
| | - Tania C Sorrell
- a Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney School of Medicine, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Westmead, NSW, Australia
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Lehrnbecher T, Robinson PD, Fisher BT, Castagnola E, Groll AH, Steinbach WJ, Zaoutis TE, Negeri ZF, Beyene J, Phillips B, Sung L. Galactomannan, β-D-Glucan, and Polymerase Chain Reaction-Based Assays for the Diagnosis of Invasive Fungal Disease in Pediatric Cancer and Hematopoietic Stem Cell Transplantation: A Systematic Review and Meta-Analysis. Clin Infect Dis 2016; 63:1340-1348. [PMID: 27567122 DOI: 10.1093/cid/ciw592] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/19/2016] [Indexed: 12/22/2022] Open
Abstract
We systematically reviewed and analyzed the available data for galactomannan (GM), β-D-glucan (BG), and polymerase chain reaction (PCR)-based assays to detect invasive fungal disease (IFD) in patients with pediatric cancer or undergoing hematopoietic stem cell transplantation when used as screening tools during immunosuppression or as diagnostic tests in patients presenting with symptoms such as fever during neutropenia (FN). Of 1532 studies screened, 25 studies reported on GM (n = 19), BG (n = 3), and PCR (n = 11). All fungal biomarkers demonstrated highly variable sensitivity, specificity, and positive predictive values, and these were generally poor in both clinical settings. GM negative predictive values were high, ranging from 85% to 100% for screening and 70% to 100% in the diagnostic setting, but failure to identify non-Aspergillus molds limits its usefulness. Future work could focus on the usefulness of combinations of fungal biomarkers in pediatric cancer and HSCT.
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Affiliation(s)
- Thomas Lehrnbecher
- Division of Pediatric Hematology and Oncology, Hospital for Children and Adolescents, Johann Wolfgang Goethe University, Frankfurt, Germany
| | | | - Brian T Fisher
- Division of Pediatric Infectious Diseases, The Children's Hospital of Philadelphia, Pennsylvania
| | - Elio Castagnola
- Infectious Diseases Unit, Istituto Giannina Gaslini, Genova, Italy
| | - Andreas H Groll
- Infectious Disease Research Program, Center for Bone Marrow Transplantation, Department of Pediatric Hematology/Oncology, University Children's Hospital Muenster, Albert Schweitzer Campus 1, Germany
| | - William J Steinbach
- Division of Pediatric Infectious Diseases, Duke University Medical Center, Durham, North Carolina
| | - Theoklis E Zaoutis
- Division of Pediatric Infectious Diseases, The Children's Hospital of Philadelphia, Pennsylvania
| | | | - Joseph Beyene
- Department of Mathematics and Statistics
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Canada
| | - Bob Phillips
- Leeds General Infirmary, Leeds Teaching Hospitals, NHS Trust
- Centre for Reviews and Dissemination, University of York, United Kingdom
| | - Lillian Sung
- Division of Haematology/Oncology, Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada
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13
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Zhang J, Hung GC, Nagamine K, Li B, Tsai S, Lo SC. Development of Candida-Specific Real-Time PCR Assays for the Detection and Identification of Eight Medically Important Candida Species. Microbiol Insights 2016; 9:21-8. [PMID: 27103821 PMCID: PMC4836890 DOI: 10.4137/mbi.s38517] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/17/2016] [Accepted: 02/19/2016] [Indexed: 11/28/2022] Open
Abstract
Culture-based identification methods have been the gold standard for the diagnosis of fungal infection. Currently, molecular technologies such as real-time PCR assays with short turnaround time can provide desirable alternatives for the rapid detection of Candida microbes. However, most of the published PCR primer sets are not Candida specific and likely to amplify DNA from common environmental contaminants, such as Aspergillus microbes. In this study, we designed pan-Candida primer sets based on the ribosomal DNA-coding regions conserved within Candida but distinct from those of Aspergillus and Penicillium. We demonstrate that the final two selected pan-Candida primer sets would not amplify Aspergillus DNA and could be used to differentiate eight medically important Candida pathogens in real-time PCR assays based on their melting profiles, with a sensitivity of detection as low as 10 fg of Candida genomic DNA. Moreover, we further evaluated and selected species-specific primer sets covering Candida albicans, Candida glabrata, Candida tropicalis, and Candida dubliniensis and show that they had high sensitivity and specificity. These real-time PCR primer sets could potentially be assembled into a single PCR array for the rapid detection of Candida species in various clinical settings, such as corneal transplantation.
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Affiliation(s)
- Jing Zhang
- Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Guo-Chiuan Hung
- Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Kenjiro Nagamine
- Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA.; Department of Oral and Maxillofacial Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Bingjie Li
- Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Shien Tsai
- Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Shyh-Ching Lo
- Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA.; Senior Investigator, Medical Officer, Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
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14
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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.
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15
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Svobodova L, Bednarova D, Ruzicka F, Chrenkova V, Dobias R, Mallatova N, Buchta V, Kocmanova I, Olisarova P, Stromerova N, Thongsri Y, Hamal P. High frequency of Candida fabianii among clinical isolates biochemically identified as Candida pelliculosa and Candida utilis. Mycoses 2016; 59:241-246. [PMID: 26763103 DOI: 10.1111/myc.12454] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 12/03/2015] [Accepted: 12/04/2015] [Indexed: 11/28/2022]
Abstract
Clinical yeast isolates belonging to Candida pelliculosa, Candida utilis and Candida fabianii are difficult to distinguish in a routine mycology laboratory using common biochemical tests. The aims of this study were to determine the prevalence of C. pelliculosa, C. utilis and C. fabianii in clinical samples and to compare their minimum inhibitory concentrations (MICs) to systemic antifungals. Two hundred and forty-eight clinical yeast isolates obtained from eight large hospitals in the Czech Republic were included in this study. Identification was performed biochemically using ID 32C kit and by MALDI-TOF MS. MICs were determined using colorimetric broth dilution Sensititre YeastOne panels. From a total number of 248 isolates, 175 were identified as C. pelliculosa and 73 as C. utilis using the biochemical kit. In contrast, MALDI-TOF MS identified 222 isolates as C. fabianii, 20 as C. pelliculosa and 6 as C. utilis. The highest mean MICs were found in C. fabianii and, regardless of the studied species, in isolates from blood cultures and central venous catheters. MALDI-TOF MS revealed C. fabianii to be most prevalent in clinical samples as compared with the other studied species. Higher MIC values in C. fabianii support the importance of correct identification of this species.
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Affiliation(s)
- L Svobodova
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Olomouc, Czech Republic
| | - D Bednarova
- Research & Development Department, GeneProof a.s., Brno, Czech Republic
| | - F Ruzicka
- Department of Microbiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - V Chrenkova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - R Dobias
- Laboratory of Clinical Mycology, Public Health Institute Ostrava, Ostrava, Czech Republic
| | - N Mallatova
- Laboratory of Parasitology and Mycology, Ceske Budejovice Hospital, Ceske Budejovice, Czech Republic
| | - V Buchta
- Department of Clinical Microbiology, Faculty of Medicine and University Hospital, Charles University, Hradec Kralove, Czech Republic
| | - I Kocmanova
- Department of Clinical Microbiology, University Hospital Brno, Brno, Czech Republic
| | - P Olisarova
- Mycology Laboratory, Clinical Microbiology and ATB Centre, Institute of Medical Biochemistry and Laboratory Diagnostics of the General University Hospital and of the First Faculty of Medicine of Charles University in Prague, Prague, Czech Republic
| | - N Stromerova
- State Veterinary Institute Olomouc, Olomouc, Czech Republic
| | - Y Thongsri
- Cellular and Molecular Immunology Research Unit (CMIRU), Department of Medical Technology, Faculty of Allied Health Science, Naresuan University, Phitsanulok, Thailand
| | - P Hamal
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Olomouc, Czech Republic
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16
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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.
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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)
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Diba K, Rahimirad M, Makhdoomi K, Eslamloo N. Aspergillus monitoring project in a large educational hospital using molecular assay. Afr J Infect Dis 2014; 8:1-4. [PMID: 24653809 DOI: 10.4314/ajid.v8i1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND It is important to find reliable and accessible methods for the diagnosis and identification of fungal species causing hospital acquired infections. Our main objective was using a rapid and accessible molecular method for the monitoring of Aspergillus infections and identification of causing agents in the level of species. MATERIAL AND METHODS The study subjects were primarily clinical specimens collected from suspected HAI patients with clinical symptoms after hospitalization. Also some environmental specimens were collected from air and instruments of health care facilities for the investigation of Aspergillus sources in a university hospital of UMSU, Urmia. All specimens were transported to Medical Mycology Center for the detection and identification of Aspergillus species using morphological methods. Also molecular method, PCR-RFLP using single restriction enzyme as a rapid and available method was performed to investigate environmental sources of Aspergillus infections. RESULTS Total of 110 clinical fungal isolates included Candida and Aspergillus species and some other opportunistic fungi. Among the clinical Aspergillus findings, Aspergillus flavus (47%), Aspergillus fumigatus (29.4%) and Aspergillus niger (23.6%) were the most frequent species respectively and also Aspergillus niger (43.7%), Aspergillus flavus (41.8%), Aspergillus fumigatus (14.7%) were isolated as the most frequent species from environmental sources. CONCLUSION Because of accessibility, speed and high sensitivity of diagnosis, the PCR-RFLP was very useful for the identification of medically important Aspergillus species and epidemiological approaches.
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Affiliation(s)
- K Diba
- Cellular and Molecular Research Center, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Mh Rahimirad
- Department of Lung Diseases, Imam educational hospital, Urmia University of Medical Sciences, Urmia, Iran ( )
| | - Kh Makhdoomi
- Department of Nephrology, Imam educational hospital, Urmia University of Medical Sciences, Urmia, Iran ( )
| | - Nf Eslamloo
- Department of foreign languages, Urmia University of Medical Sciences, Urmia, Iran. ( )
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18
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Vykydalová M, Horká M, Růžička F, Duša F, Moravcová D, Kahle V, Šlais K. Combination of micropreparative solution isoelectric focusing and high-performance liquid chromatography for differentiation of biofilm-positive and biofilm-negative Candida parapsilosis group from vascular catheter. Anal Chim Acta 2014; 812:243-9. [DOI: 10.1016/j.aca.2013.12.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 12/16/2013] [Accepted: 12/25/2013] [Indexed: 10/25/2022]
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19
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Toskova M, Palousova D, Kocmanova I, Pavlovsky Z, Timilsina S, Lengerova M, Mayer J, Racil Z. Invasive mould disease involving the gastrointestinal tract caused by Neosartorya pseudofischeri in a haematological patient. Mycoses 2013; 56:385-8. [PMID: 23356572 DOI: 10.1111/myc.12038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martina Toskova
- Department of Internal Medicine-Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
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20
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Kourkoumpetis TK, Fuchs BB, Coleman JJ, Desalermos A, Mylonakis E. Polymerase chain reaction-based assays for the diagnosis of invasive fungal infections. Clin Infect Dis 2012; 54:1322-31. [PMID: 22362884 DOI: 10.1093/cid/cis132] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Currently accepted fungal diagnostic techniques, such as culture, biopsy, and serology, lack rapidity and efficiency. Newer diagnostic methods, such as polymerase chain reaction (PCR)-based assays, have the potential to improve fungal diagnostics in a faster, more sensitive, and specific manner. Preliminary data indicate that, when PCR-based fungal diagnostic assays guide antifungal therapy, they may lower patient mortality and decrease unnecessary antifungal treatment, improving treatment-associated costs and avoiding toxicity. Moreover, newer PCR techniques can identify antifungal resistance DNA loci, but the clinical correlation between those loci and clinical failure has to be studied further. In addition, future studies need to focus on the implementation of PCR techniques in clinical decision making and on combining them with other diagnostic tests. A consensus on the standardization of PCR techniques, along with validation from large prospective studies, is necessary to allow widespread adoption of these assays.
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Affiliation(s)
- Themistoklis K Kourkoumpetis
- Department of Medicine, Infectious Disease Division, Massachusetts General Hospital, Harvard Medical School, Boston 02214, USA
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21
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An insight into the distribution, genetic diversity, and mycotoxin production of Aspergillus section Flavi in soils of pistachio orchards. Folia Microbiol (Praha) 2011; 57:27-36. [DOI: 10.1007/s12223-011-0090-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2011] [Accepted: 11/23/2011] [Indexed: 10/14/2022]
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22
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A survey on distribution and toxigenicity of Aspergillus flavus from indoor and outdoor hospital environments. Folia Microbiol (Praha) 2011; 56:527-34. [DOI: 10.1007/s12223-011-0078-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2011] [Accepted: 10/13/2011] [Indexed: 10/15/2022]
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23
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Bacterial and fungal microflora in surgically removed lung cancer samples. J Cardiothorac Surg 2011; 6:137. [PMID: 21999143 PMCID: PMC3212932 DOI: 10.1186/1749-8090-6-137] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 10/14/2011] [Indexed: 11/26/2022] Open
Abstract
Background Clinical and experimental data suggest an association between the presence of bacterial and/or fungal infection and the development of different types of cancer, independently of chemotherapy-induced leukopenia. This has also been postulated for the development of lung cancer, however the prevalence and the exact species of the bacteria and fungi implicated, have not yet been described. Aim To determine the presence of bacterial and fungal microflora in surgically extracted samples of patients with lung cancer. Materials and methods In this single-center prospective, observational study, tissue samples were surgically extracted from 32 consecutive patients with lung cancer, and reverse-transcription polymerase chain reaction (RT-PCR) was used to identify the presence of bacteria and fungi strains. Results The analysis of the electrophoresis data pointed out diversity between the samples and the strains that were identified. Mycoplasma strains were identified in all samples. Strains that appeared more often were Staphylococcus epidermidis, Streptococcus mitis and Bacillus strains, followed in descending frequency by Chlamydia, Candida, Listeria, and Haemophilus influenza. In individual patients Legionella pneumophila and Candida tropicalis were detected. Conclusions A diversity of pathogens could be identified in surgically extracted tissue samples of patients with lung cancer, with mycoplasma strains being present in all samples. These results point to an etiologic role for chronic infection in lung carcinogenesis. Confirmation of these observations and additional studies are needed to further characterize the etiologic role of inflammation in lung carcinogenesis.
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24
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Molecular Approaches to the Diagnosis of Sepsis. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Horká M, Růžička F, Kubesová A, Němcová E, Šlais K. Separation of phenotypically indistinguishable Candida species, C. orthopsilosis, C. metapsilosis and C. parapsilosis, by capillary electromigration techniques. J Chromatogr A 2011; 1218:3900-7. [DOI: 10.1016/j.chroma.2011.04.057] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 04/19/2011] [Accepted: 04/20/2011] [Indexed: 12/19/2022]
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26
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PCR diagnosis of invasive candidiasis: systematic review and meta-analysis. J Clin Microbiol 2010; 49:665-70. [PMID: 21106797 DOI: 10.1128/jcm.01602-10] [Citation(s) in RCA: 255] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Invasive candidiasis (IC) is a significant cause of morbidity and mortality. Diagnosis relies on culture-based methods, which lack sensitivity and delay diagnosis. We conducted a systematic review assessing the diagnostic accuracy of PCR-based methods to detect Candida spp. directly in blood samples. We searched electronic databases for prospective or retrospective cohort and case-control studies. Two reviewers abstracted data independently. Meta-analysis was performed using a hierarchical logistic regression model. Random-effects metaregression was performed to assess the effects of study methods and infection characteristics on sensitivity or specificity values. We included 54 studies with 4,694 patients, 963 of whom had proven/probable or possible IC. Perfect (100%) sensitivity and specificity for PCR in whole-blood samples was observed when patients with cases had candidemia and controls were healthy people. When PCR was performed to evaluate patients with suspected invasive candidiasis, the pooled sensitivity for the diagnosis of candidemia was 0.95 (confidence interval, 0.88 to 0.98) and the pooled specificity was 0.92 (0.88 to 0.95). A specificity of >90% was maintained in several analyses considering different control groups. The use of whole-blood samples, rRNA, or P450 gene targets and a PCR detection limit of ≤ 10 CFU/ml were associated with improved test performance. PCR positivity rates among patients with proven or probable IC were 85% (78 to 91%), while blood cultures were positive for 38% (29 to 46%). We conclude that direct PCR using blood samples had good sensitivity and specificity for the diagnosis of IC and offers an attractive method for early diagnosis of specific Candida spp. Its effects on clinical outcomes should be investigated.
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27
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Characterization of molds isolated from smoked paprika by PCR-RFLP and micellar electrokinetic capillary electrophoresis. Food Microbiol 2009; 26:776-82. [DOI: 10.1016/j.fm.2009.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Revised: 04/28/2009] [Accepted: 05/04/2009] [Indexed: 11/22/2022]
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28
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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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Can fungal biomarkers be used to improve antifungal therapy in the intensive care unit? CURRENT FUNGAL INFECTION REPORTS 2009. [DOI: 10.1007/s12281-009-0019-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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30
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Use of variability of the fungal ITS2 intergenic region for the identification of medically important yeast species. Biologia (Bratisl) 2009. [DOI: 10.2478/s11756-009-0120-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Harun A, Perdomo H, Gilgado F, Chen SCA, Cano J, Guarro J, Meyer W. Genotyping ofScedosporiumspecies: a review of molecular approaches. Med Mycol 2009; 47:406-14. [DOI: 10.1080/13693780802510240] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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32
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Identification of fungal species by fragment length analysis of the internally transcribed spacer 2 region. Eur J Clin Microbiol Infect Dis 2008; 28:613-22. [DOI: 10.1007/s10096-008-0683-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 11/29/2008] [Indexed: 11/26/2022]
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33
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Keynan Y, Sprecher H, Weber G. Acremonium Vertebral Osteomyelitis: Molecular Diagnosis and Response to Voriconazole. Clin Infect Dis 2007; 45:e5-6. [PMID: 17554690 DOI: 10.1086/518700] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Accepted: 03/14/2007] [Indexed: 11/03/2022] Open
Abstract
We present a case of Acremonium vertebral osteomyelitis that relapsed despite surgical debridement and prolonged treatment with liposomal amphotericin B, but which responded to voriconazole therapy. The report highlights the role of molecular diagnosis of rare fungal osteomyelitis. The patient was successfully treated with voriconazole.
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Affiliation(s)
- Yoav Keynan
- Department of Medicine, Infectious Diseases Unit, Carmel Medical Center, Haifa, Israel.
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Trtkova J, Raclavsky V. MOLECULAR-GENETIC APPROACHES TO IDENTIFICATION AND TYPING OF PATHOGENIC CANDIDA YEASTS. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2006; 150:51-61. [PMID: 16936901 DOI: 10.5507/bp.2006.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Currently, invasive candidal infections represent an increasing cause of morbidity and mortality in seriously ill hospitalised patients. Because the accurate diagnosis of candidiasis remains difficult, a fast and reliable assay for characterization of fungal pathogens is critical for the early initiation of adequate antifungal therapy and/or for introduction of preventive measures. As novel molecular genetic techniques are continuously introduced, their role in the management of infectious diseases has also been growing. Today, molecular strategies complement conventional methods and provide more accurate and detailed insight. It can be expected that future technical development will improve their potential furthermore. In this article, we provide a critical review on the value and limitations of molecular tools in pathogenic Candida species identification and strain typing regarding their sensitivity, discriminatory power, reproducibility, cost and ease of performance.
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Affiliation(s)
- Jitka Trtkova
- Department of Biology, Faculty of Medicine, Palacký University, Hnevotínská 3, Olomouc, Czech Republic.
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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.
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Affiliation(s)
- Radek Plachý
- Department of Microbiology, Faculty of Medicine, Palacký University, Hnvotínská 3, CZ-775 15 Olomouc, Czech Republic
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Anguita-Alonso P, Patel R. Molecular Methods in the Diagnosis of Endocarditis. Curr Infect Dis Rep 2004; 6:270-275. [PMID: 15265454 DOI: 10.1007/s11908-004-0047-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Advances in molecular microbiologic diagnostics have yielded new tools to diagnose infective endocarditis. These tools can detect microorganisms that are difficult to grow or are uncultivable, because of prior antimicrobial therapy or because of innate characteristics of the microorganisms. This paper reviews molecular microbiologic diagnostic techniques and their role in the diagnosis of infective endocarditis.
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Affiliation(s)
- Paloma Anguita-Alonso
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA.
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