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Pandey M, Xess I, Sachdev J, Yadav U, Singh G, Pradhan D, Xess AB, Rana B, Dar L, Bakhshi S, Seth R, Mahapatra M, Jyotsna VP, Jain AK, Kumar R, Agarwal R, Mani P. Development of a Sensitive and Specific Novel qPCR Assay for Simultaneous Detection and Differentiation of Mucormycosis and Aspergillosis by Melting Curve Analysis. FRONTIERS IN FUNGAL BIOLOGY 2022; 2:800898. [PMID: 37744098 PMCID: PMC10512281 DOI: 10.3389/ffunb.2021.800898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/17/2021] [Indexed: 09/26/2023]
Abstract
Molecular diagnostic assays can expedite the diagnosis of fungal infections, and subsequently help in early interventions and appropriate management of patients. The aim of this study was to develop a single set of primers for a real-time quantitative polymerase chain reaction (qPCR) assay to detect and identify commonly reported, clinically relevant molds i.e., Aspergillus spp, Mucorales and Fusarium spp., up to genus level by melting curve analysis. This assay was evaluated in whole blood from patients with suspected invasive aspergillosis (IA), and in tissue biopsy, bronchoalveolar lavage (BAL) fluid and other site-specific samples from patients with suspected invasive mucormycosis (IM). The limit of detection (LoD) was determined as 10 copies/μl for all three molds. The mean coefficient of variation (CV) across all sets of intra- and inter-assay data was 0.63% (ranging from 0.42 to 1.56%), showing high reproducibility of the assay. Sensitivity and specificity of the assay were 93.3 and 97.1% respectively for diagnosis of IA, and 99.29 and 83.84% respectively for diagnosis of IM. Fusarium was not detected in any of the clinical samples included and the few laboratory confirmed cases of fusariosis did not meet the inclusion criteria of the study. Hence no ROC curve or cutoff value could be generated for the same. This newly developed qPCR assay therefore appears to be a promising tool in detection of IA and IM.
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Affiliation(s)
- Mragnayani Pandey
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Immaculata Xess
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Janya Sachdev
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Usha Yadav
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Gagandeep Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Dibyabhaba Pradhan
- ICMR Computational Genomics Centre Informatics, Systems & Research Management Division Indian Council of Medical Research, All India Institute of Medical Sciences, New Delhi, India
| | - Ashit Bhushan Xess
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Bhaskar Rana
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Lalit Dar
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sameer Bakhshi
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Rachna Seth
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Manoranjan Mahapatra
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Viveka P. Jyotsna
- Department of Endocrinology, All India Institute of Medical Sciences, New Delhi, India
| | - Arun Kumar Jain
- Departments of Environmental Toxicology and Bioinformatics, ICMR-National Institute of Pathology Sri Ramachari Bhawan, Safdarjang Hospital Campus, New Delhi, India
| | - Rakesh Kumar
- Department of Otorhinolaryngology, All India Institute of Medical Sciences, New Delhi, India
| | - Reshu Agarwal
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Prashant Mani
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
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Bahadori T, Didehdar M, Khansarinezhad B, Shokohi T. Identification of opportunistic and nonopportunistic Exophiala species using high resolution melting analysis. Med Mycol 2021; 58:938-945. [PMID: 31977020 DOI: 10.1093/mmy/myz136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/02/2019] [Accepted: 12/20/2019] [Indexed: 01/13/2023] Open
Abstract
Exophiala is a genus comprising several species of opportunistic black yeasts. Exophiala species identification by morphological, physiological, and biochemical characteristics is challenging because of the low degree of phenotypic differences between species and its polyphyletic nature. We aimed to develop a high-resolution melting (HRM) assay based on the internal transcribed spacer (ITS) region to differentiate between pairs of clinical and environmental Exophiala species. HRM primers were designed based on the conserved ITS region of five Exophiala species (E. dermatitidis, E. phaeomuriformis, E. heteromorpha, E. xenobiotica, and E. crusticola). Environmental and clinical Exophiala isolates representing these five species (n = 109) were analyzed. The HRM assay was optimized using clinical and environmental reference isolates (n = 22), and then the results were compared with those obtained with nonreference isolates of Exophiala (n = 87) using two designed primer sets. The designed HRM assay was based on the normalized melting peak approach and two primer sets, and successfully distinguished between the five Exophiala species. The HRM1 primer set provided sufficient resolution, with a melting temperature (Tm) difference of approximately 2.5°C among the analyzed species and of approximately 1°C between E. dermatitidis and E. phaeomuriformis. HRM typing results were in agreement with those of ITS-sequence typing (100% sensitivity and specificity). The developed HRM assay can be used to ascertain the identity of Exophiala species, which may differ in clinical significance, with high accuracy. Its application to identify species directly in clinical samples and/or environmental niches may be possible in the future.
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Affiliation(s)
- Tanaz Bahadori
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mojtaba Didehdar
- Department of Medical Mycology and Parasitology, Arak University of Medical Sciences, Arak, Iran
| | - Behzad Khansarinezhad
- Department of Microbiology and Immunology, Arak University of Medical Sciences, Arak, Iran
| | - Tahereh Shokohi
- Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran.,Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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Comparison of High-resolution Melting Curve Analysis with Specific Target Gene Sequencing to Identify the Most Common Species of Aspergillus and Fusarium. Jundishapur J Microbiol 2021. [DOI: 10.5812/jjm.110205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Currently, it appears that new molecular-based methods could substitute microscopic and culture assessment for the first-line detection of microorganisms isolated from clinical specimens. However, it will remain the "continual strategy" until this technology is attuned to identifying all fungi that can be isolated from biological specimens. Objectives: The present study aimed to validate a high-resolution melting (HRM) technique to identify clinical filamentous fungi. Moreover, it was attempted to compare the results with those of the target gene’s polymerase chain reaction (PCR) sequencing. Methods: A total of 54 specimens of bronchoalveolar lavage (BAL), nail, ear discharge, blood culture, and cornea were collected from patients suspected of fungal infection. All Fusarium spp. and Aspergillus spp. were recognized based on Tef-α and beta-tubulin region sequencing, as well as PCR-HRM analysis. Results: The Tef-α sequence analysis revealed the most frequent spp. to be Fusarium solani followed by F. oxysporum (n = 3), F. caucasicum (n = 3), F. coeruleum (n = 3), F. falciforme (n = 1), F. proliferatum (n = 1), F. brevicatenulatum (n = 1), F. globosom (n = 1), and F. verticillioides (n = 1). Based on the beta-tubulin sequences, Aspergillus flavus (n = 10), A. fumigatus (n = 7), A. niger (n = 2), A. terreus (n = 1), and A. orezea (n = 1) were identified in this study. Furthermore, the dataset analysis of PCR-HRM revealed that 33 isolates belonging to Fusarium spp. were F. solani (n = 24), F. oxysporum (n = 3), F. proliferatum (n = 3), F. falciforme (n = 1), F. verticillioides (n = 1), and F. brevicatenulatum (n = 1). Moreover, isolates (n = 21) belonging to Aspergillus spp. included A. flavus (n = 11), A. fumigatus (n = 7), A. niger (n = 2), and A. terreus (n = 1). Conclusions: The sequencing method has a time-consuming and costly nature, and there exists conformity between the sequence results of the Tef-α/beta-tubulin regions and PCR-HRM. The PCR-HRM method is a reliable approach in the clinical laboratory to identify Aspergillus and Fusarium spp. However, some closely related spp. show no curve algorithm differences in PCR-HRM.
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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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Kronholm I, Ormsby T, McNaught KJ, Selker EU, Ketola T. Marked Neurospora crassa Strains for Competition Experiments and Bayesian Methods for Fitness Estimates. G3 (BETHESDA, MD.) 2020; 10:1261-1270. [PMID: 32001556 PMCID: PMC7144071 DOI: 10.1534/g3.119.400632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 01/27/2020] [Indexed: 01/17/2023]
Abstract
The filamentous fungus Neurospora crassa, a model microbial eukaryote, has a life cycle with many features that make it suitable for studying experimental evolution. However, it has lacked a general tool for estimating relative fitness of different strains in competition experiments. To remedy this need, we constructed N. crassa strains that contain a modified csr-1 locus and developed an assay for detecting the proportion of the marked strain using a post PCR high resolution melting assay. DNA extraction from spore samples can be performed on 96-well plates, followed by a PCR step, which allows many samples to be processed with ease. Furthermore, we suggest a Bayesian approach for estimating relative fitness from competition experiments that takes into account the uncertainty in measured strain proportions. We show that there is a fitness effect of the mating type locus, as mating type mat a has a higher competitive fitness than mat A The csr-1* marker also has a small fitness effect, but is still a suitable marker for competition experiments. As a proof of concept, we estimate the fitness effect of the qde-2 mutation, a gene in the RNA interference pathway, and show that its competitive fitness is lower than what would be expected from its mycelial growth rate alone.
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Affiliation(s)
- Ilkka Kronholm
- Department of Biological and Environmental Sciences, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | | | | | | | - Tarmo Ketola
- Department of Biological and Environmental Sciences, University of Jyväskylä, FI-40014 Jyväskylä, Finland
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Wen X, Chen Q, Yin H, Wu S, Wang X. Rapid identification of clinical common invasive fungi via a multi-channel real-time fluorescent polymerase chain reaction melting curve analysis. Medicine (Baltimore) 2020; 99:e19194. [PMID: 32049856 PMCID: PMC7035122 DOI: 10.1097/md.0000000000019194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/31/2019] [Accepted: 01/15/2020] [Indexed: 01/25/2023] Open
Abstract
The incidence of invasive fungal infections (IFIs) has recently increased, and early and accurate diagnosis of IFIs is important for the rational selection of antifungal drugs with high efficacy. We developed a method for rapid and accurate clinical diagnosis of IFIs and provide a reference for personalized drug treatment.We designed and screened fungal internal transcribed spacer regions with universal primers and designed 8 TaqMan detection probes to establish a multi-channel real-time fluorescent polymerase chain reaction (PCR) melting curve analysis (MCA) method. The sensitivity, specificity, and reproducibility of this method were investigated using standard fungal strains and clinical isolates. Candidemia was detected using the MCA method.The limit of detection and assay cut-off (melting temperature [Tm]) for Candida albicans were 0.05 pg/μL and 66.50 °C; Candida glabrata were 0.1 pg/μL and 66.25 °C; Candida tropicalis were 0.1 pg/μL and 60.15 °C; Candida krusei were 0.1 pg/μL and 72.15 °C; Candida parapsilosis were 0.2 pg/μL and 63.10 °C; Candida guilliermondii were 0.1 pg/μL and 61.84 °C; Cryptococcus neoformans were 0.1 pg/μL and 65.50 °C; Aspergillus flavus were 0.05 pg/μL and 71.50 °C; Aspergillus terreus, Aspergillus fumigatus, and Aspergillus niger were 0.05 pg/μL and 76.80 °C. Analytical specificity was evaluated using 13 clinical pathogens including Streptococcus pneumoniae, Staphylococcus aureus, and Haemophilus influenzae, etc. No false-positive results were obtained for any of these samples. The MCA method can detect and identify different candidemia simulations. The limit detection concentration of C albicans was 44 cfu/mL, C glabrata was 73 cfu/mL, C tropicalis was 29 cfu/mL, C parapsilosis was 21 cfu/mL, C krusei was 71 cfu/mL, and C guilliermondii was 53 cfu/mL.The multi-channel real-time fluorescence PCR melting curve analysis displayed high sensitivity and specificity in detecting various clinically invasive fungi. Furthermore, it simultaneously detected the genera Candida, Cryptococcus, and Aspergillus and identified Candida at the species level. Our method can facilitate early and accurate clinical diagnosis and personalized medication regimens.
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Affiliation(s)
- Xiaozi Wen
- Department of The Fourth Clinical Medical College affiliated to Zhejiang Chinese Medical University
| | - Qiong Chen
- Department of Clinical Laboratory, Hangzhou First People's Hospital affiliated to Zhejiang Chinese Medical University
| | - Huali Yin
- Department of Research and Development, Hangzhou Qianji Biological Technology Co., Ltd., Hangzhou, China
| | - Shenghai Wu
- Department of Clinical Laboratory, Hangzhou First People's Hospital affiliated to Zhejiang Chinese Medical University
| | - Xianjun Wang
- Department of Clinical Laboratory, Hangzhou First People's Hospital affiliated to Zhejiang Chinese Medical University
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Evaluation of a Novel Mitochondrial Pan-Mucorales Marker for the Detection, Identification, Quantification, and Growth Stage Determination of Mucormycetes. J Fungi (Basel) 2019; 5:jof5040098. [PMID: 31614610 PMCID: PMC6958370 DOI: 10.3390/jof5040098] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 02/06/2023] Open
Abstract
Mucormycosis infections are infrequent yet aggressive and serious fungal infections. Early diagnosis of mucormycosis and its discrimination from other fungal infections is required for targeted treatment and more favorable patient outcomes. The majority of the molecular assays use 18 S rDNA. In the current study, we aimed to explore the potential of the mitochondrial rnl (encoding for large-subunit-ribosomal-RNA) gene as a novel molecular marker suitable for research and diagnostics. Rnl was evaluated as a marker for: (1) the Mucorales family, (2) species identification (Rhizopus arrhizus, R. microsporus, Mucor circinelloides, and Lichtheimia species complexes), (3) growth stage, and (4) quantification. Sensitivity, specificity, discriminatory power, the limit of detection (LoD), and cross-reactivity were evaluated. Assays were tested using pure cultures, spiked clinical samples, murine organs, and human paraffin-embedded-tissue (FFPE) samples. Mitochondrial markers were found to be superior to nuclear markers for degraded samples. Rnl outperformed the UMD universal® (Molyzm) marker in FFPE (71.5% positive samples versus 50%). Spiked blood samples highlighted the potential of rnl as a pan-Mucorales screening test. Fungal burden was reproducibly quantified in murine organs using standard curves. Identification of pure cultures gave a perfect (100%) correlation with the detected internal transcribed spacer (ITS) sequence. In conclusion, mitochondrial genes, such as rnl, provide an alternative to the nuclear 18 S rDNA genes and deserve further evaluation.
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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: 55] [Impact Index Per Article: 11.0] [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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Nganthavee V, Phutthasakda W, Atipas K, Tanpong S, Pungprasert T, Dhirachaikulpanich D, Krithin S, Tanglitanon S, Jutidamronphang W, Owattanapanich W, Chayakulkeeree M, Phikulsod P. High incidence of invasive fungal infection during acute myeloid leukemia treatment in a resource-limited country: clinical risk factors and treatment outcomes. Support Care Cancer 2019; 27:3613-3622. [PMID: 31165931 DOI: 10.1007/s00520-019-04720-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/26/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND Invasive fungal infection (IFI) causes high morbidity and mortality during acute myeloid leukemia (AML) treatment. Interventions to prevent fungal infection, including air filtration systems and antifungal prophylaxis, may improve outcomes in this group of patients. However, they are expensive and therefore inapplicable in resource-limited countries. The benefit of antifungal therapy is also dependent on the local epidemiology. That led us to conduct the study to evaluate the characteristics and impact of IFI in AML patients without prophylaxis in our setting. METHODS Clinical data from patients with AML who have been treated with chemotherapy without antifungal prophylaxis were retrieved during a 5-year period at Thailand's hematology referral center. Incidence and risk factors of IFI and outcomes of patients were evaluated. RESULTS Among 292 chemotherapy courses, there were 65 (22.3%) episodes of IFI. Of those, 10 (15.4%) were proven, 19 (29.2%) were probable, and 36 (55.4%) were categorized as being possible IFI. Molds were the most commonly observed causative pathogens (93.1%). The incidence of probable/proven IFI was highest during first induction (20.5%), followed by second induction (6.1%), and consolidation (2.7%). A long duration of neutropenia, old age, and low serum albumin were the strongest predictors of IFI. Compared with patients who had no IFI, patients with probable/proven IFI had a longer length of hospital stay and higher in-hospital mortality. Patients with proven IFI had a significantly worse outcome at 1 year. CONCLUSIONS These results suggest the change in health policy to implement IFI preventive measures to improve outcomes of AML treatment.
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Affiliation(s)
- Variya Nganthavee
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Woraphun Phutthasakda
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kawita Atipas
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sirikul Tanpong
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Teeramet Pungprasert
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Saran Krithin
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Supang Tanglitanon
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Weerapat Owattanapanich
- Division of Hematology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Wanglang Road, Bangkoknoi, Bangkok, 10700, Thailand
| | - Methee Chayakulkeeree
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ployploen Phikulsod
- Division of Hematology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Wanglang Road, Bangkoknoi, Bangkok, 10700, Thailand.
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Shi M, Li X, Feng J, Jia S, Xiao X, Chen C, Fransisca C, Xi L, Zhang J. High-resolution melting analysis assay for identification of Fonsecaea species. J Clin Lab Anal 2017; 32. [PMID: 28543666 DOI: 10.1002/jcla.22257] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/17/2017] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Chromoblastomycosis (CBM) is a chronic fungal disease. In China, the principle etiologic agent was a group of dematiaceous fungi, including Fonsecaea monophora, Fonsecaea nubica, and Cladophialophora carrionii. Although the Fonsecaea species have similar morphology, their pathogenicity is quite different. This study aims to establish a new solution for early identification of Fonsecaea species because of their distinctive potential infection risk. METHODS Five reference strains and 35 clinical isolates from patients with CBM, preserved in our laboratory, were used in this study. The universal primer ITS1 and ITS2 were chosen to amplify the highly conserved regions of rDNA. High-resolution melting (HRM) analysis was performed using the LIGHTCYCLER® 96 System. All the amplicons were verified by direct sequencing and the sequence were aligned with those in GenBank by BLAST analysis. RESULTS We successfully differentiated the five strains according to their different Tm values and curve shapes. The 35 clinical isolates from patients were identified as 24 strains for F. monophora and 11 strains for F. nubica, which is consistent with the DNA sequencing results. CONCLUSION It is the first time to use HRM analysis for identification of Fonsecaea species. Since the CBM etiologic agent in South China is mainly F. monophora and F. nubica, this strategy is sufficient to be applied in the clinical examination with high accuracy, speed, and throughput.
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Affiliation(s)
- Minglan Shi
- Department of Dermatology and Venerology, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiqing Li
- Department of Dermatology and Venerology, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiao Feng
- Department of Dermatology and Venerology, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shulin Jia
- Department of Dermatology, Guangdong Province Hospital of Chinese Medicine, Guangzhou, China
| | - Xing Xiao
- Department of Dermatology and Venerology, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chunmei Chen
- Department of Dermatology and Venerology, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Cindy Fransisca
- Department of Dermatology and Venerology, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Liyan Xi
- Department of Dermatology and Venerology, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Junmin Zhang
- Department of Dermatology and Venerology, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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Xiong C, Hu ZG, Tu Y, Liu HG, Wang P, Zhao MM, SHIi YH, Wu L, Sun W, Chen SL. ITS2 barcoding DNA region combined with high resolution melting (HRM) analysis of Hyoscyami Semen, the mature seed of Hyoscyamus niger. Chin J Nat Med 2017; 14:898-903. [PMID: 28262116 DOI: 10.1016/s1875-5364(17)30014-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Indexed: 10/20/2022]
Abstract
Hyoscyami Semen, the mature dried seed of Hyoscyamus niger L., has long been used as a traditional Chinese medicine to treat human diseases. Hyoscyami Semen is found in local markets in China. In markets, sellers and buyers commonly inadvertently mix the seeds of H. niger with the seeds of related species such as Hygrophila salicifolia (Vahl) Nees, Astragalus complanatus R. Br., Cuscuta australis R. Br., Cuscuta chinensis Lam., and Impatiens balsamina L. because of their similar morphologies or similar names. Thus, developing a reliable method for discriminating H. niger seeds from its adulterants is necessary to reduce confusion and ensure the safe use of Hyoscyami Semen. The present study was designed to evaluate the efficiency of high-resolution melting analysis combined with DNA barcoding (Bar-HRM) with internal transcribed spacer 2 to discriminate H. niger. Our results show that Bar-HRM successfully identified the adulterants and detected the proportion of H. niger DNA extract within an admixture. In particular, HRM detected H. niger DNA extract in A. complanatus DNA extract at concentrations as low as 1%. In conclusion, the Bar-HRM method developed in the present study for authenticating H. niger is rapid and cost-effective. It can be used in the future to guarantee the purity of Hyoscyami Semen for the clinical use.
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Affiliation(s)
- Chao Xiong
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China; Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zhi-Gang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China; Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yuan Tu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China; Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Traditional Chinese Medicine Resources Research Center, Tianjin Tasly Pharmaceutical Co., Ltd., Tianjin 300402, China
| | - He-Gang Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Ping Wang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Ming-Ming Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yu-Hua SHIi
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Lan Wu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China; Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Shi-Lin Chen
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China; Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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12
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Lu S, Mirchevska G, Phatak SS, Li D, Luka J, Calderone RA, Fonzi WA. Dynamic time warping assessment of high-resolution melt curves provides a robust metric for fungal identification. PLoS One 2017; 12:e0173320. [PMID: 28264030 PMCID: PMC5338801 DOI: 10.1371/journal.pone.0173320] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/17/2017] [Indexed: 12/16/2022] Open
Abstract
Fungal infections are a global problem imposing considerable disease burden. One of the unmet needs in addressing these infections is rapid, sensitive diagnostics. A promising molecular diagnostic approach is high-resolution melt analysis (HRM). However, there has been little effort in leveraging HRM data for automated, objective identification of fungal species. The purpose of these studies was to assess the utility of distance methods developed for comparison of time series data to classify HRM curves as a means of fungal species identification. Dynamic time warping (DTW), first introduced in the context of speech recognition to identify temporal distortion of similar sounds, is an elastic distance measure that has been successfully applied to a wide range of time series data. Comparison of HRM curves of the rDNA internal transcribed spacer (ITS) region from 51 strains of 18 fungal species using DTW distances allowed accurate classification and clustering of all 51 strains. The utility of DTW distances for species identification was demonstrated by matching HRM curves from 243 previously identified clinical isolates against a database of curves from standard reference strains. The results revealed a number of prior misclassifications, discriminated species that are not resolved by routine phenotypic tests, and accurately identified all 243 test strains. In addition to DTW, several other distance functions, Edit Distance on Real sequence (EDR) and Shape-based Distance (SBD), showed promise. It is concluded that DTW-based distances provide a useful metric for the automated identification of fungi based on HRM curves of the ITS region and that this provides the foundation for a robust and automatable method applicable to the clinical setting.
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Affiliation(s)
- Sha Lu
- Dermatology Department, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Gordana Mirchevska
- Institute for Microbiology and Parasitology, University Sts Cyril and Methodius, Skopje, Macedonia
| | - Sayali S. Phatak
- Department of Microbiology & Immunology, Georgetown University, Washington, DC, United States of America
| | - Dongmei Li
- Department of Microbiology & Immunology, Georgetown University, Washington, DC, United States of America
| | - Janos Luka
- Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States of America
| | - Richard A. Calderone
- Department of Microbiology & Immunology, Georgetown University, Washington, DC, United States of America
| | - William A. Fonzi
- Department of Microbiology & Immunology, Georgetown University, Washington, DC, United States of America
- * E-mail:
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13
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New Panfungal Real-Time PCR Assay for Diagnosis of Invasive Fungal Infections. J Clin Microbiol 2016; 54:2910-2918. [PMID: 27629898 DOI: 10.1128/jcm.01580-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/08/2016] [Indexed: 11/20/2022] Open
Abstract
The diagnosis of invasive fungal infections (IFIs) is usually based on the isolation of the fungus in culture and histopathological techniques. However, these methods have many limitations often delaying the definitive diagnosis. In recent years, molecular diagnostics methods have emerged as a suitable alternative for IFI diagnosis. When there is not a clear suspicion of the fungus involved in the IFI, panfungal real-time PCR assays have been used, allowing amplification of any fungal DNA. However, this approach requires subsequent amplicon sequencing to identify the fungal species involved, increasing response time. In this work, a new panfungal real-time PCR assay using the combination of an intercalating dye and sequence-specific probes was developed. After DNA amplification, a melting curve analysis was also performed. The technique was standardized by using 11 different fungal species and validated in 60 clinical samples from patients with proven and probable IFI. A melting curve database was constructed by collecting those melting curves obtained from fungal species included in the standardization assay. Results showed high reproducibility (coefficient of variation [CV] < 5%; r > 0.95) and specificity (100%). The overall sensitivity of the technique was 83.3%, with the group of fungi involved in the infection detected in 77.8% of the positive samples with IFIs covered by molecular beacon probes. Moreover, sequencing was avoided in 67.8% of these "probe-positive" results, enabling report of a positive result in 24 h. This technique is fast, sensitive, and specific and promises to be useful for improving early diagnosis of IFIs.
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14
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Didehdar M, Khansarinejad B, Amirrajab N, Shokohi T. Development of a high-resolution melting analysis assay for rapid and high-throughput identification of clinically important dermatophyte species. Mycoses 2016; 59:442-9. [PMID: 26991756 DOI: 10.1111/myc.12492] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 01/12/2016] [Accepted: 02/02/2016] [Indexed: 11/27/2022]
Abstract
Accurate identification of dermatophyte species is important both for epidemiological studies and for implementing antifungal treatment strategies. Although nucleic acid amplification-based assays have several advantages over conventional mycological methods, a major disadvantage is their high cost. The aim of this study was to develop a rapid and accurate real-time PCR-based high-resolution melting (HRM) assay for differentiation of the most common dermatophyte species. The oligonucleotide primers were designed to amplify highly conserved regions of the dermatophyte ribosomal DNA. Analysis of a panel containing potentially interfering fungi demonstrated no cross reactivity with the assay. To evaluate the performance characteristics of the method, a total of 250 clinical isolates were tested in comparison with the long-established PCR-RFLP method and the results were reassessed using DNA sequencing, as the reference standard method. The assay is able to type dermatophytes using normalised melting peak, difference plot analysis or electrophoresis on agarose gel methods. The results showed that, in comparison to PCR-RFLP, the developed HRM assay was able to differentiate at least 10 common dermatophytes species with a higher speed, throughput and accuracy. These results indicate that the HRM assay will be a useful sensitive, high throughput and cost-effective method for differentiating the most common dermatophyte species.
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Affiliation(s)
- M Didehdar
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran.,Department of Medical Mycology and Parasitology, Arak University of Medical Sciences, Arak, Iran
| | - B Khansarinejad
- Molecular and Medicine Research Center, Arak University of Medical Sciences, Arak, Iran
| | - N Amirrajab
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran.,Department of Laboratory Sciences and Tropical Medicine Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - T Shokohi
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran
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15
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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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16
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Duyvejonck H, Cools P, Decruyenaere J, Roelens K, Noens L, Vermeulen S, Claeys G, Decat E, Van Mechelen E, Vaneechoutte M. Validation of High Resolution Melting Analysis (HRM) of the Amplified ITS2 Region for the Detection and Identification of Yeasts from Clinical Samples: Comparison with Culture and MALDI-TOF Based Identification. PLoS One 2015; 10:e0132149. [PMID: 26295947 PMCID: PMC4546670 DOI: 10.1371/journal.pone.0132149] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 06/10/2015] [Indexed: 11/18/2022] Open
Abstract
AIM Candida species are known as opportunistic pathogens, and a possible cause of invasive infections. Because of their species-specific antimycotic resistance patterns, reliable techniques for their detection, quantification and identification are needed. We validated a DNA amplification method for direct detection of Candida spp. from clinical samples, namely the ITS2-High Resolution Melting Analysis (direct method), by comparing it with a culture and MALDI-TOF Mass Spectrometry based method (indirect method) to establish the presence of Candida species in three different types of clinical samples. MATERIALS AND METHODS A total of 347 clinical samples, i.e. throat swabs, rectal swabs and vaginal swabs, were collected from the gynaecology/obstetrics, intensive care and haematology wards at the Ghent University Hospital, Belgium. For the direct method, ITS2-HRM was preceded by NucliSENS easyMAG DNA extraction, directly on the clinical samples. For the indirect method, clinical samples were cultured on Candida ID and individual colonies were identified by MALDI-TOF. RESULTS For 83.9% of the samples there was complete concordance between both techniques, i.e. the same Candida species were detected in 31.1% of the samples or no Candida species were detected in 52.8% of the samples. In 16.1% of the clinical samples, discrepant results were obtained, of which only 6.01% were considered as major discrepancies. Discrepancies occurred mostly when overall numbers of Candida cells in the samples were low and/or when multiple species were present in the sample. DISCUSSION Most of the discrepancies could be decided in the advantage of the direct method. This is due to samples in which no yeast could be cultured whereas low amounts could be detected by the direct method and to samples in which high quantities of Candida robusta according to ITS2-HRM were missed by culture on Candida ID agar. It remains to be decided whether the diagnostic advantages of the direct method compensate for its disadvantages.
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Affiliation(s)
- Hans Duyvejonck
- Laboratory Bacteriology Research, Department of Clinical Chemistry, Microbiology and Immunology, Faculty of Medicine and Health Sciences, University of Ghent, De Pintelaan 185, 9000, Ghent, Belgium
- Department of Biomedical Sciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium
| | - Piet Cools
- Laboratory Bacteriology Research, Department of Clinical Chemistry, Microbiology and Immunology, Faculty of Medicine and Health Sciences, University of Ghent, De Pintelaan 185, 9000, Ghent, Belgium
| | - Johan Decruyenaere
- Department of Intensive Care Medicine, Ghent University Hospital, De Pintelaan 185, 9000, Ghent, Belgium
| | - Kristien Roelens
- Department of Obstetrics and Gynaecology, Faculty of Medicine and Health Sciences, Ghent University Hospital, 9000, Ghent, Belgium
| | - Lucien Noens
- Department of Haematology and Blood Bank, Ghent University Hospital, 9000, Ghent, Belgium
| | - Stefan Vermeulen
- Department of Biomedical Sciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium
| | - Geert Claeys
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, 9000, Ghent, Belgium
| | - Ellen Decat
- Laboratory Bacteriology Research, Department of Clinical Chemistry, Microbiology and Immunology, Faculty of Medicine and Health Sciences, University of Ghent, De Pintelaan 185, 9000, Ghent, Belgium
| | - Els Van Mechelen
- Department of Biomedical Sciences, Faculty of Education, Health and Social Work, University College Ghent, Keramiekstraat 80, 9000, Ghent, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Clinical Chemistry, Microbiology and Immunology, Faculty of Medicine and Health Sciences, University of Ghent, De Pintelaan 185, 9000, Ghent, Belgium
- * E-mail:
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17
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Bineshian F, Yadegari MH, Sharifi Z, Akbari Eidgahi M, Nasr R. Identification of Candida Species Using MP65 Gene and Evaluation of the Candida albicans MP65 Gene Expression in BALB/C Mice. Jundishapur J Microbiol 2015; 8:e18984. [PMID: 26060567 PMCID: PMC4458353 DOI: 10.5812/jjm.8(5)2015.18984] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 10/22/2014] [Accepted: 11/04/2014] [Indexed: 01/11/2023] Open
Abstract
Background: Systemic candidiasis is a major public health concern. In particular, in immunocompromised people, such as patients with neutropenia, patients with Acquired Immune Deficiency Syndrome (AIDS) and cancer who are undergoing antiballistic chemotherapy or bone marrow transplants, and people with diabetes. Since the clinical signs and symptoms are nonspecific, early diagnosis is often difficult. The 65-kDa mannoprotein (MP65) gene of Candida albicans is appropriate for detection and identification of systemic candidiasis. This gene encodes a putative b-glucanase mannoprotein of 65 kDa, which plays a major role in the host-fungus relationship, morphogenesis and pathogenicity. Objectives: The current study aimed to identify different species of Candida (C. albicans, C. glabrata and C. parapsilosis) using the Polymerase Chain Reaction (PCR) technique and also to evaluate C. albicans MP65 gene expression in BALB/C mice. Materials and Methods: All yeast isolates were identified on cornmeal agar supplemented with tween-80, germ tube formation in serum, and assimilation of carbon sources in the API 20 C AUX yeast identification system. Polymerase Chain Reaction was performed on all samples using species-specific primers for the MP65 65 kDa gene. After RNA extraction, cDNA synthesis was performed by the Maxime RT Pre Mix kit. Candida albicans MP65 gene expression was evaluated by quantitative Real-Time (q Real-Time) and Real-Time (RT) PCR techniques. The 2-ΔΔCT method was used to analyze relative changes in gene expression of MP65. For statistical analysis, nonparametric Wilcoxon test was applied using the SPSS version 16 software. Results: Using biochemical methods, one hundred, six and one isolates of clinical samples were determined as C. albicans, C. glabrata and C. parapsilosis, respectively. Species-specific primers for PCR experiments were applied to clinical specimens, and in all cases a single expected band for C. albicans, C. glabrata and C. parapsilosis was obtained (475, 361 and 124 base pairs, respectively). All species isolated by culture methods (100% positivity) were evaluated with PCR using species-specific primers to identify Candida species. Relative expression of Mp65 genes increased significantly after C. albicans injection into the mice (P < 0.05). Conclusions: The results of the current study showed that the PCR method is reproducible for rapid identification of Candida species with specific primers. Mp65 gene expression of C. albicans after injection into the mice was 2.3 folds higher than before injection, with this difference being significant. These results indicated that increase of Mp65 gene expression might be an early stage of infection; however definitive conclusions require further studies.
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Affiliation(s)
- Farahnaz Bineshian
- Department of Mycology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, IR Iran
- Corresponding author: Farahnaz Bineshian, Department of Mycology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, IR Iran. Tel: + 98-2313354170, Fax: + 98-2313354161, E-mail:
| | | | - Zohre Sharifi
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, IR Iran
| | | | - Reza Nasr
- Department of Biotechnology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, IR Iran
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18
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Sobel JD, Akins RA. The Role of PCR in the Diagnosis of Candida Vulvovaginitis-a New Gold Standard? Curr Infect Dis Rep 2015; 17:488. [PMID: 26003471 DOI: 10.1007/s11908-015-0488-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PCR is recognized as a reliable technique for detection of all types of microorganisms. Being highly objective and reproducible also sensitive and specific, PCR is now widely used for sexually transmitted infection (STI) diagnosis. Potential, however, exists for detecting non-pathogens, and not identifying a pathogenic state decreases specificity or clinical significance. PCR Candida tests of vaginal specimens are now widely available and frequently used offering a modest to moderate increase in sensitivity and are likely to replace traditional culture and DNA homology testing. Nevertheless, there remain considerable gaps in our knowledge regarding the usefulness and applications of these expensive tests.
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Affiliation(s)
- J D Sobel
- Division of Infectious Diseases, Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI, USA,
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19
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Souza RA, Frazão MR, Almeida AMP, Falcão JP. Rapid and efficient differentiation of Yersinia species using high-resolution melting analysis. J Microbiol Methods 2015; 115:6-12. [PMID: 25980404 DOI: 10.1016/j.mimet.2015.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 11/18/2022]
Abstract
The primary goal of clinical microbiology is the accurate identification of the causative agent of the disease. Here, we describe a method for differentiation between Yersinia species using PCR-HRMA. The results revealed species-specific melting profiles. The herein developed assay can be used as an effective method to differentiate Yersinia species.
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Affiliation(s)
- Roberto A Souza
- Brazilian Reference Center on Yersinia spp. other than Y. pestis, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, Ribeirão Preto, SP, Brazil
| | - Miliane R Frazão
- Brazilian Reference Center on Yersinia spp. other than Y. pestis, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, Ribeirão Preto, SP, Brazil
| | - Alzira M P Almeida
- Brazilian Reference Service on Plague, Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz (CPqAM/FIOCRUZ), Recife, PE, Brazil
| | - Juliana P Falcão
- Brazilian Reference Center on Yersinia spp. other than Y. pestis, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, Ribeirão Preto, SP, Brazil.
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20
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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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21
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Identification of CandidaSpecies Using MP65 Gene and Evaluation of the Candida albicansMP65 Gene Expression in BALB/C Mice. Jundishapur J Microbiol 2014. [DOI: 10.5812/jjm.18984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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22
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Gago S, Alastruey-Izquierdo A, Marconi M, Buitrago MJ, Kerhornou A, Kersey PJ, Mellado E, Cuenca-Estrella M, Rodríguez-Tudela JL, Cuesta I. Ribosomic DNA intergenic spacer 1 region is useful when identifying Candida parapsilosis spp. complex based on high-resolution melting analysis. Med Mycol 2014; 52:472-81. [PMID: 24847037 DOI: 10.1093/mmy/myu009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The epidemiology of Candida parapsilosis and the closely related species C. orthopsilosis and C. metapsilosis has changed in recent years, justify the need to identify this complex at the species level. In this study we investigate the intergenic spacer 1 (IGS1) of the ribosomal DNA (rDNA) to evaluate the utility of this gene region as a phylogenetic molecular marker and the suitability of a high-resolution melting (HRM) strategy based on this region for identification of members of the C. parapsilosis spp. complex. We sequenced the IGS1 and the internal transcribed spacer (ITS) regions of the rDNA from 33 C. parapsilosis sensu lato strains. Although both regions are useful in identifying species, comparative sequence analysis showed that the diversity in the IGS1 region was higher than in the ITS sequences. We also developed an HRM analysis that reliably identifies C. parapsilosis spp. complex based on the amplification of 70 bp in the IGS1 region. All isolates were correctly identified with a confidence interval >98%. Our results demonstrate that HRM analysis based on the IGS1 region is a powerful tool for distinguishing C. parapsilosis from cryptic species.
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Affiliation(s)
- Sara Gago
- Mycology Service, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Ana Alastruey-Izquierdo
- Mycology Service, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain Spanish Network for Research on Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Marco Marconi
- Bioinformatic Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - María José Buitrago
- Mycology Service, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Arnaud Kerhornou
- Protein and Nucleotide Database (PANDA) Group, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul J Kersey
- Protein and Nucleotide Database (PANDA) Group, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Emilia Mellado
- Mycology Service, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Manuel Cuenca-Estrella
- Mycology Service, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Juan Luis Rodríguez-Tudela
- Mycology Service, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Isabel Cuesta
- Bioinformatic Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Alnuaimi A, Wiesenfeld D, O'Brien-Simpson N, Reynolds E, Peng B, McCullough M. The development and validation of a rapid genetic method for species identification and genotyping of medically important fungal pathogens using high-resolution melting curve analysis. Mol Oral Microbiol 2014; 29:117-30. [DOI: 10.1111/omi.12050] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2014] [Indexed: 11/26/2022]
Affiliation(s)
- A.D. Alnuaimi
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
| | - D. Wiesenfeld
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
- Head and Neck Oncology; The Royal Melbourne Hospital; Melbourne Vic. Australia
| | - N.M. O'Brien-Simpson
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
| | - E.C. Reynolds
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
| | - B. Peng
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
| | - M.J. McCullough
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
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24
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Molecular fingerprints to identify Candida species. BIOMED RESEARCH INTERNATIONAL 2013; 2013:923742. [PMID: 23844370 PMCID: PMC3703398 DOI: 10.1155/2013/923742] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/30/2013] [Accepted: 06/06/2013] [Indexed: 11/17/2022]
Abstract
A wide range of molecular techniques have been developed for genotyping Candida species. Among them, multilocus sequence typing (MLST) and microsatellite length polymorphisms (MLP) analysis have recently emerged. MLST relies on DNA sequences of internal regions of various independent housekeeping genes, while MLP identifies microsatellite instability. Both methods generate unambiguous and highly reproducible data. Here, we review the results achieved by using these two techniques and also provide a brief overview of a new method based on high-resolution DNA melting (HRM). This method identifies sequence differences by subtle deviations in sample melting profiles in the presence of saturating fluorescent DNA binding dyes.
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Rapid and accurate identification of isolates of Candida species by melting peak and melting curve analysis of the internally transcribed spacer region 2 fragment (ITS2-MCA). Res Microbiol 2013; 164:110-7. [DOI: 10.1016/j.resmic.2012.10.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 10/15/2012] [Indexed: 11/23/2022]
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26
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Gago S, Lorenzo B, Gomez-Lopez A, Cuesta I, Cuenca-Estrella M, Buitrago MJ. Analysis of strain relatedness using high resolution melting in a case of recurrent candiduria. BMC Microbiol 2013; 13:13. [PMID: 23343107 PMCID: PMC3561232 DOI: 10.1186/1471-2180-13-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 01/18/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several genotyping protocols have been described to study Candida albicans strains with different sensitivity values. In this study we have analyzed the genetic relatedness and the antifungal susceptibility of several Candida albicans strains isolated from a patient who from suffered recurrent candiduria for a period of five years. Strains were genotyped using Microsatellite Length Polymorphism (MLP) with three microsatellite markers (HIS 3, EF 3 and CDC 3), and a new method based on high resolution melting (HRM) was developed to analyze the microsatellite region. This method was compared with the conventional technique that uses capillary electrophoresis. RESULTS MICs of the isolates showed the existence of fluconazole susceptible and resistant strains. An inter-colony test using single concentration (8 and 16 mg/l) of fluconazole revealed the coexistence of both fluconazole susceptible and resistant strains. Both genotyping analysis methods showed that all the patient's isolates had a clonal origin. HRM analysis method developed was able to accurately establish strain relatedness and presented a discriminatory power of 0.77. CONCLUSIONS Although HRM analysis method presented a lower discriminatory power compared to methods based on capillary electrophoresis, it provided a more cost-effective and suitable alternative for genotyping C. albicans in a clinical laboratory.
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Affiliation(s)
- Sara Gago
- Servicio de Micología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra Majadahonda-Pozuelo, Km 2, Majadahonda, Madrid, 28220, Spain
| | - Belen Lorenzo
- Servicio de Microbiología, Hospital Virgen de la Concha, Zamora, España
| | - Alicia Gomez-Lopez
- Servicio de Micología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra Majadahonda-Pozuelo, Km 2, Majadahonda, Madrid, 28220, Spain
| | - Isabel Cuesta
- Unidad de Bioinformática, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Manuel Cuenca-Estrella
- Servicio de Micología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra Majadahonda-Pozuelo, Km 2, Majadahonda, Madrid, 28220, Spain
| | - Maria J Buitrago
- Servicio de Micología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra Majadahonda-Pozuelo, Km 2, Majadahonda, Madrid, 28220, Spain
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27
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Lochlainn SÓ, Amoah S, Graham NS, Alamer K, Rios JJ, Kurup S, Stoute A, Hammond JP, Østergaard L, King GJ, White PJ, Broadley MR. High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes. PLANT METHODS 2011; 7:43. [PMID: 22152063 PMCID: PMC3251530 DOI: 10.1186/1746-4811-7-43] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 12/08/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND Targeted Induced Loci Lesions IN Genomes (TILLING) is increasingly being used to generate and identify mutations in target genes of crop genomes. TILLING populations of several thousand lines have been generated in a number of crop species including Brassica rapa. Genetic analysis of mutants identified by TILLING requires an efficient, high-throughput and cost effective genotyping method to track the mutations through numerous generations. High resolution melt (HRM) analysis has been used in a number of systems to identify single nucleotide polymorphisms (SNPs) and insertion/deletions (IN/DELs) enabling the genotyping of different types of samples. HRM is ideally suited to high-throughput genotyping of multiple TILLING mutants in complex crop genomes. To date it has been used to identify mutants and genotype single mutations. The aim of this study was to determine if HRM can facilitate downstream analysis of multiple mutant lines identified by TILLING in order to characterise allelic series of EMS induced mutations in target genes across a number of generations in complex crop genomes. RESULTS We demonstrate that HRM can be used to genotype allelic series of mutations in two genes, BraA.CAX1a and BraA.MET1.a in Brassica rapa. We analysed 12 mutations in BraA.CAX1.a and five in BraA.MET1.a over two generations including a back-cross to the wild-type. Using a commercially available HRM kit and the Lightscanner™ system we were able to detect mutations in heterozygous and homozygous states for both genes. CONCLUSIONS Using HRM genotyping on TILLING derived mutants, it is possible to generate an allelic series of mutations within multiple target genes rapidly. Lines suitable for phenotypic analysis can be isolated approximately 8-9 months (3 generations) from receiving M3 seed of Brassica rapa from the RevGenUK TILLING service.
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Affiliation(s)
- Seosamh Ó Lochlainn
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | | | - Neil S Graham
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Khalid Alamer
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Juan J Rios
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | | | | | - John P Hammond
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Lars Østergaard
- Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, UK
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, PO Box 157Lismore NSW 2480, Australia
| | - Phillip J White
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
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