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Díez Rodríguez GR, Figueredo Lago JE, Armas Cayarga A, González González YJ, García de la Rosa I, Collazo Mesa T, López Reyes I, Batista Lozada Y, Rodríguez Calá FR, García Sánchez JB. A novel high-resolution melting analysis strategy for detecting cystic fibrosis-causing variants. Lab Med 2024; 55:185-197. [PMID: 37417450 DOI: 10.1093/labmed/lmad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023] Open
Abstract
Cystic fibrosis (CF), an autosomal recessive disease, is caused by variants in both alleles of the CF transmembrane conductance regulator (CFTR) gene. A new assay based on allele-specific polymerase chain reaction and high-resolution melting analysis was developed for the detection of 18 CF-causing CFTR variants previously identified in Cuba and Latin America. The assay is also useful for zygosity determination of mutated alleles and includes internal controls. The reaction mixtures were normalized and evaluated using blood samples collected on filter paper. The evaluation of analytical parameters demonstrated the specificity and sensitivity of the method to detect the included CFTR variants. Internal and external validations yielded a 100% agreement between the new assay and the used reference tests. This assay can complement CF newborn screening not only in Cuba but also in Latin America.
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Affiliation(s)
| | | | | | | | | | - Teresa Collazo Mesa
- National Center of Medical Genetics, Medical University of Havana, Playa, Havana, Cuba
| | - Ixchel López Reyes
- National Center of Medical Genetics, Medical University of Havana, Playa, Havana, Cuba
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Perini M, Batisti Biffignandi G, Di Carlo D, Pasala AR, Piazza A, Panelli S, Zuccotti GV, Comandatore F. MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data. BMC Bioinformatics 2021; 22:76. [PMID: 33602119 PMCID: PMC7891011 DOI: 10.1186/s12859-021-04020-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/11/2021] [Indexed: 11/18/2022] Open
Abstract
Background The rapid identification of pathogen clones is pivotal for effective epidemiological control strategies in hospital settings. High Resolution Melting (HRM) is a molecular biology technique suitable for fast and inexpensive pathogen typing protocols. Unfortunately, the mathematical/informatics skills required to analyse HRM data for pathogen typing likely limit the application of this promising technique in hospital settings. Results MeltingPlot is the first tool specifically designed for epidemiological investigations using HRM data, easing the application of HRM typing to large real-time surveillance and rapid outbreak reconstructions. MeltingPlot implements a graph-based algorithm designed to discriminate pathogen clones on the basis of HRM data, producing portable typing results. The tool also merges typing information with isolates and patients metadata to create graphical and tabular outputs useful in epidemiological investigations and it runs in a few seconds even with hundreds of isolates. Availability: https://skynet.unimi.it/index.php/tools/meltingplot/. Conclusions The analysis and result interpretation of HRM typing protocols can be not trivial and this likely limited its application in hospital settings. MeltingPlot is a web tool designed to help the user to reconstruct epidemiological events by combining HRM-based clustering methods and the isolate/patient metadata. The tool can be used for the implementation of HRM based real time large scale surveillance programs in hospital settings.
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Affiliation(s)
- Matteo Perini
- Department of Biomedical and Clinical Sciences "L. Sacco", Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Gherard Batisti Biffignandi
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, 27100, Italia
| | - Domenico Di Carlo
- Department of Biomedical and Clinical Sciences "L. Sacco", Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Ajay Ratan Pasala
- Department of Biomedical and Clinical Sciences "L. Sacco", Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Aurora Piazza
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, 27100, Italia
| | - Simona Panelli
- Department of Biomedical and Clinical Sciences "L. Sacco", Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Gian Vincenzo Zuccotti
- Department of Biomedical and Clinical Sciences "L. Sacco", Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy.,Department of Pediatrics, Children's Hospital Vittore Buzzi, Università Di Milano, Milan, Italy
| | - Francesco Comandatore
- Department of Biomedical and Clinical Sciences "L. Sacco", Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy.
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Arif AA, An-Nizamiya AD, Putri C, Nashrurrokhman M, Husna N, Hadisusanto S, Handayani NSN. Comparison Between Three Molecular Diagnostics for the Identification of Heterozygous Hemoglobin E. Pak J Biol Sci 2020; 23:17-26. [PMID: 31930879 DOI: 10.3923/pjbs.2020.17.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVES Hemoglobin E is a variant hemoglobin caused due to the base substitution G→A at codon 26 in the β-globin-coding gene that is followed by the alteration of glutamic acid (GAG) to lysine (AAG). Various types of molecular analysis methods such as tetra-primer amplification refractory mutation system (T-ARMS-PCR), Tm-shift real-time polymerase chain reaction (Tm-shift qPCR) and high-resolution melting analysis (HRMA) are commonly used to detect several mutations in the β-globin-coding gene. This study was conducted to compare the detection result of Cd 26 (G→A) mutation in the β-globin-coding gene of heterozygous HbE between the above-mentioned methods. MATERIALS AND METHODS DNA samples were isolated from blood archive of heterozygous HbE and analyzed for the detection of the mutation using HRMA and Tm-shift on a real-time PCR instrument, whereas T-ARMS analysis was performed on a conventional PCR equipment. High resolution melt v3.1 software and Bio-Rad CFX Manager software were used to analyze the result of HRMA and Tm-shift qPCR, whereas the T-ARMS-PCR result was analyzed by observing the number and size of DNA bands on gel electrophoresis. RESULTS Among 21 samples, the Cd 26 mutation was detected in numbers 18, 19 and 21 by HRMA, Tm-shift qPCR and T-ARMS-PCR. DNA Sequencing confirmed Cd 26 mutation on 5 ambiguous samples and revealed two homozygous mutation. CONCLUSION The Cd 26 (G→A) mutation was detected in proportions 100, 91 and 86% by T-ARMS-PCR, Tm-shift qPCR and HRMA, respectively.
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Hidayati NI, Wijayanti N, Handayani NSN. Detection of HBB:c.92+5G>C and HBB:c.108delC mutations in β-thalassemia carriers using high-resolution melting analysis. Mol Biol Rep 2020; 47:5665-5671. [PMID: 32638316 DOI: 10.1007/s11033-020-05625-x] [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: 02/26/2020] [Accepted: 06/26/2020] [Indexed: 11/27/2022]
Abstract
The HBB:c.92+5G>C [known as IVSI-5 (GC)] and HBB:c.108delC [known as Cd 35 (del C)] are the β-globin gene mutations that commonly found in Indonesia. Detection of the mutation in the β-thalassemia carriers can be useful to prevent an increase in the number of β-thalassemia patients. High-Resolution Melting Analysis (HRMA) is the method that can detect the mutation rapidly. The aim of this study was to detect HBB:c.92+5G>C and HBB:c.108delC mutations of the β-thalassemia carriers using HRMA. DNA was isolated from blood archive of ten hematologically proved β-thalassemia carriers. Detection of mutations was carried out by HRMA and then confirmed by sequencing. HRMA was performed by using two pairs of specific primers. One pair of primer targeted the region of HBB:c.92+5G>C and the other targeted the region of HBB:c.108delC. The results of detection of mutation using HRMA then were confirmed by sequencing. A specific primer pair covering the region of HBB:c.92+5G>C to HBB:c.108delC were used for sequencing. The results of HRMA showed that the HBB:c.92+5G>C and HBB:c.108delC mutations found in 50% and 30% samples, respectively. The HRMA results can be confirmed by sequencing in all samples. It can be concluded that HRMA can be used to detect HBB:c.92+5G>C heterozygote and HBB:c.108delC heterozygote mutations.
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Affiliation(s)
- Nurdiyah Ika Hidayati
- Laboratory of Animal Physiology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Nastiti Wijayanti
- Laboratory of Animal Physiology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Niken Satuti Nur Handayani
- Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia.
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Evangeli L, Ioannis S, Valentinos K, Antigony M, Elli I, Eleftheria H, Vasiliki G, Evangelos B. SLCO1B3 screening in colorectal cancer patients using High-Resolution Melting Analysis method and immunohistochemistry. Tumour Biol 2017; 39:1010428317691176. [PMID: 28349822 DOI: 10.1177/1010428317691176] [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] [Indexed: 01/19/2023] Open
Abstract
Personalized medicine has made some major advances in colorectal cancer, but new biomarkers still remain a hot issue as an emerging tool with potential prognostic and therapeutic potential. We investigated for SLCO1B3 gene alterations and protein expression in colorectal cancer, using the novel high-resolution melting analysis technique and immunohistochemistry. Formalin-fixed paraffin-embedded tumor samples from 30 colorectal cancer patients were used. The screening for gene alterations was done by high-resolution melting analysis for all exons of SLCO1B3 gene. Organic anion-transporting polypeptide 1B3 protein expression was assessed by immunohistochemistry using the monoclonal mouse MDQ antibody. High level of polymorphism was observed in the SLCO1B3 gene. We identified three previously reported polymorphisms in exons 7, 12, and 14, 699G>A, 1557A>G, and 1833G>A, respectively. In the exon 5, one variant seems to correspond to an as yet unknown SLCO family member. The immunohistochemical study revealed that organic anion-transporting polypeptide 1B3 was expressed in 27/30 samples. Of great interest, the three samples, which were immunohistochemically negative, all appeared to accommodate mutations which lead to either early stop codons or other conformations of the tertiary protein structures affecting the antibody-epitope binding. The results of this study are of much interest as high-resolution melting analysis proved to be a reliable and rapid genotyping/scanning method for mutation detection of SLCO1B3 gene.
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Affiliation(s)
- Lampri Evangeli
- 1 Cancer Biobank Center, University of Ioannina, Ioannina, Greece
| | - Sainis Ioannis
- 1 Cancer Biobank Center, University of Ioannina, Ioannina, Greece
| | - Kounnis Valentinos
- 1 Cancer Biobank Center, University of Ioannina, Ioannina, Greece.,2 Hypoxia and Angiogenesis Group, Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John, Radcliffe Hospital
| | - Mitselou Antigony
- 4 Department of Forensic Pathology, University of Ioannina, Ioannina, Greece
| | - Ioachim Elli
- 3 Department of Pathology, "G. Hatzikosta" General Hospital, Ioannina, Greece
| | - Hatzimichael Eleftheria
- 1 Cancer Biobank Center, University of Ioannina, Ioannina, Greece.,5 Department of Hematology, Medical School, University of Ioannina, Ioannina, Greece
| | - Galani Vasiliki
- 6 Departments of Embryology, Histology and Anatomy, University of Ioannina, Ioannina, Greece
| | - Briasoulis Evangelos
- 1 Cancer Biobank Center, University of Ioannina, Ioannina, Greece.,5 Department of Hematology, Medical School, University of Ioannina, Ioannina, Greece
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Hur D, Kim MS, Song M, Jung J, Park H. Detection of genetic variation using dual-labeled peptide nucleic acid (PNA) probe-based melting point analysis. Biol Proced Online 2015; 17:14. [PMID: 26539063 PMCID: PMC4632671 DOI: 10.1186/s12575-015-0027-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/27/2015] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Thermal denaturation of probe-target hybrid is highly reproducible, and which makes probe melting point analysis reliable in the detection of mutations, polymorphisms and epigenetic differences in DNA. To improve resolution of these detections, we used dual-labeled (quencher and fluorescence), full base of peptide nucleic acid (PNA) probe for fluorescence probe based melting point analysis. Because of their uncharged nature and peptide bond-linked backbone, PNA probes have more favorable hybridization properties, which make a large difference in the melting temperature between specific hybridization and partial hybridization. RESULTS Here, we have shown that full base dual-labeled PNA is apt material for fluorescence probe-based melting point analysis with large difference in the melting temperature between full specific hybridization and that of partial hybridization, including insertion and deletion. In case of narrowly distributed mutations, PNA probe effectively detects three mutations in a single reaction tube with three probes. Moreover, we successfully diagnose virus analogues with amplification and melting temperature signal. Lastly, Melting temperature of PNA oligomer can be easily adjusted just by adding gamma-modified PNA probe. CONCLUSIONS The PNA probes offer advantage of improved flexibility in probe design, which could be used in various applications in mutation detection among a wide range of spectrums.
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Affiliation(s)
- Deokhwe Hur
- />SeaSun Biomaterials, N517 Deadoek Campus, Pai Chai University, 11-3 Tekeuno 1-ro, Gwanpyeong-dong, Yuseong-gu, Deajeon 305-509 South Korea
| | - Myoung Sug Kim
- />Pathology Division, National Fisheries Research and Development Institute, Busan, 619-902 South Korea
| | - Minsik Song
- />SeaSun Biomaterials, N517 Deadoek Campus, Pai Chai University, 11-3 Tekeuno 1-ro, Gwanpyeong-dong, Yuseong-gu, Deajeon 305-509 South Korea
| | - Jinwook Jung
- />SeaSun Biomaterials, N517 Deadoek Campus, Pai Chai University, 11-3 Tekeuno 1-ro, Gwanpyeong-dong, Yuseong-gu, Deajeon 305-509 South Korea
| | - Heekyung Park
- />SeaSun Biomaterials, N517 Deadoek Campus, Pai Chai University, 11-3 Tekeuno 1-ro, Gwanpyeong-dong, Yuseong-gu, Deajeon 305-509 South Korea
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7
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Abstract
Torque teno viruses (TTVs) are recently discovered DNA viruses, with heterogeneous genomes, highly prevalent in populations worldwide. The species that infect humans are Torque teno virus (TTV), Torque teno midi virus (TTMDV) and Torque teno mini virus (TTMV). High-resolution melting analysis (HRMA) is a sensitive and effective method for genotyping and mutation scanning. Up to now, HRMA has not been utilized for detection of TTVs. The aim of this study was to asses if HRMA is suitable for detecting TTVs variants. DNA was extracted from the blood and saliva of 13 healthy subjects for method optimization. Additionally, saliva samples from 100 healthy individuals were collected for estimating the TTVs' prevalence. Viral DNA was amplified by heminested polymerase chain reaction (PCR). Second round amplicons were used for the HRMA. The samples were analyzed using two fluorescent dyes, SYBR (®) Green I and EvaGreen®. The prevalence values for TTV, TTMDV and TTMV were 71.0, 31.0 and 54.0%, respectively. The three major melting curve patterns corresponding to TTV, TTMDV and TTMV on HRMA can be easily distinguished regardless of kit used. Our results showed that HRMA is a rapid and efficient method of detecting human TTVs.
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8
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Balboni A, Dondi F, Prosperi S, Battilani M. Development of a SYBR Green real-time PCR assay with melting curve analysis for simultaneous detection and differentiation of canine adenovirus type 1 and type 2. J Virol Methods 2015; 222:34-40. [PMID: 26028428 DOI: 10.1016/j.jviromet.2015.05.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/11/2015] [Accepted: 05/21/2015] [Indexed: 11/29/2022]
Abstract
Canine adenovirus type 1 (CAdV-1) and canine adenovirus type 2 (CAdV-2) cause infectious canine hepatitis (ICH) and infectious tracheobronchitis (ITB) in dogs, respectively. Cases of ICH have been documented in recent years and recent surveys have demonstrated a wide percentage of asymptomatic CAdV-1 infection in the canine population. Since both CAdV types are detectable in the same biological matrices, and viral coinfection with CAdV-1 and CAdV-2 are reported with high frequency, it is urgent to have available a rapid, highly sensitive and specific assay for the diagnosis of CAdV infection and distinction between CAdV-1 and CAdV-2. In order to detect canine adenovirus in biological samples and to rapidly distinguish the two viral types, a SYBR Green real-time PCR assay was optimized to discriminate CAdV-1 and CAdV-2 via a melting curve analysis. The developed assay showed high sensitivity and reproducibility and was highly efficient and specific in discriminating the two CAdV types. This reliable and rapid technique may represent a simple, useful and economic option for simultaneous CAdV types detection, which would be feasible and attractive for all diagnostic laboratories, both for clinical purposes and for epidemiological investigations.
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Affiliation(s)
- Andrea Balboni
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia (BO), Italy
| | - Francesco Dondi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia (BO), Italy
| | - Santino Prosperi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia (BO), Italy
| | - Mara Battilani
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia (BO), Italy.
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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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Koirala R, Taverniti V, Balzaretti S, Ricci G, Fortina MG, Guglielmetti S. Melting curve analysis of a groEL PCR fragment for the rapid genotyping of strains belonging to the Lactobacillus casei group of species. Microbiol Res 2015; 173:50-8. [PMID: 25801971 DOI: 10.1016/j.micres.2015.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 12/13/2014] [Accepted: 01/02/2015] [Indexed: 10/24/2022]
Abstract
Lactobacillus casei group (Lcs) consists of three phylogenetically closely related species (L. casei, L. paracasei, and L. rhamnosus), which are widely used in the dairy and probiotic industrial sectors. Strategies to easily and rapidly characterize Lcs are therefore of interest. To this aim, we developed a method according to a technique known as high resolution melting analysis (HRMa), which was applied to a 150 bp groEL gene fragment. The analysis was performed on 53 Lcs strains and 29 strains representatives of species that are commonly present in dairy and probiotic products and can be most probably co-isolated with Lcs strains. DNA amplification was obtained only from Lcs strains, demonstrating the specificity of the groEL primers designed in this study. The HRMa clustered Lcs strains in three groups that exactly corresponded to the species of the L. casei group. A following HRMa separated the 39 L. paracasei strains in two well distinct intraspecific groups, indicating the possible existence of at least two distinct genotypes inside the species. Nonetheless, the phenotypic characterization demonstrated that the genotypes do not correspond to the two L. paracasei subspecies, namely paracasei and tolerans. In conclusion, the melting curve analysis developed in this study is demonstrably a simple, labor-saving, and rapid strategy obtain the genotyping of a bacterial isolate and simultaneously potentially confirm its affiliation to the L. casei group of species. The application of this method to a larger collection of strains may validate the possibility to use the proposed HRMa protocol for the taxonomic discrimination of L. casei group of species. In general, this study suggests that HRMa can be a suitable technique for the genetic typization of Lactobacillus strains.
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Affiliation(s)
- Ranjan Koirala
- Nepal Academy of Science and Technology (NAST), Khumaltar, Lalitpur, Nepal; Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Valentina Taverniti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Division of Food Microbiology and Bioprocessing, Università degli Studi di Milano, Italy
| | - Silvia Balzaretti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Division of Food Microbiology and Bioprocessing, Università degli Studi di Milano, Italy
| | - Giovanni Ricci
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Division of Food Microbiology and Bioprocessing, Università degli Studi di Milano, Italy
| | - Maria Grazia Fortina
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Division of Food Microbiology and Bioprocessing, Università degli Studi di Milano, Italy
| | - Simone Guglielmetti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Division of Food Microbiology and Bioprocessing, Università degli Studi di Milano, Italy.
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Rapid detection and identification of nontuberculous mycobacterial pathogens in fish by using high-resolution melting analysis. Appl Environ Microbiol 2013; 79:7837-45. [PMID: 24123734 DOI: 10.1128/aem.00822-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterial infections in fish are commonly referred to as piscine mycobacteriosis, irrespectively of the specific identity of the causal organism. They usually cause a chronic disease and sometimes may result in high mortalities and severe economic losses. Nearly 20 species of Mycobacterium have been reported to infect fish. Among them, Mycobacterium marinum, M. fortuitum, and M. chelonae are generally considered the major agents responsible for fish mycobacteriosis. As no quick and inexpensive diagnostic test exists, we tested the potential of high-resolution melting analysis (HRMA) to rapidly identify and differentiate several Mycobacterium species involved in fish infections. By analyzing both the melting temperature and melting profile of the 16S-23S rRNA internal transcribed spacer (ITS), we were able to discriminate 12 different species simultaneously. Sensitivity tests conducted on purified M. marinum and M. fortuitum DNA revealed a limit of detection of 10 genome equivalents per reaction. The primers used in this procedure did not lead to any amplification signal with 16 control non-Mycobacterium species, thereby demonstrating their specificity for the genus Mycobacterium.
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Navrátilová L, Safářová D, Raclavský V. Usefulness of PCR-HRMA in identification of non-fermentative Gram-negative rods recovered from patients suffering from cystic fibrosis or chronic obstructive pulmonary disease. Folia Microbiol (Praha) 2013; 59:17-21. [PMID: 23761199 DOI: 10.1007/s12223-013-0263-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 05/30/2013] [Indexed: 12/19/2022]
Abstract
Adequate treatment of microbial infections requires rapid and accurate identification of the etiological agent. In routine diagnostics, identification of bacteria conventionally relies on phenotypic testing, which can be hindered by phenotypic variations. Therefore, genotyping techniques should perform faster and more accurately. Recently, the technique of high-resolution melting analysis (HRMA) of PCR amplicons promises to provide a convenient and economic tool of genotypic identification. In our study, we performed prospective routine testing of a PCR-HRMA system that was recently published in a proof-of-the-principle study. The system was evaluated by analysing 275 clinical isolates of bacteria acquired from 65 patients suffering from cystic fibrosis or chronic obstructive pulmonary disease. Our results show that its routine use may result in partial worsening of its discriminatory power; however, it still outmatched conventional phenotyping in the group of non-fermentative Gram-negative rods. Moreover, when supplemented by rapid, simple and economic oxidase test, it can be even simplified for more economic performance.
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Affiliation(s)
- Lucie Navrátilová
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
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Morinha F, Travassos P, Seixas F, Santos N, Sargo R, Sousa L, Magalhães P, Cabral JA, Bastos E. High-resolution melting analysis for bird sexing: a successful approach to molecular sex identification using different biological samples. Mol Ecol Resour 2013; 13:473-83. [PMID: 23433263 DOI: 10.1111/1755-0998.12081] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 01/10/2013] [Accepted: 01/10/2013] [Indexed: 12/19/2022]
Abstract
High-resolution melting (HRM) analysis is a very attractive and flexible advanced post-PCR method with high sensitivity/specificity for simple, fast and cost-effective genotyping based on the detection of specific melting profiles of PCR products. Next generation real-time PCR systems, along with improved saturating DNA-binding dyes, enable the direct acquisition of HRM data after quantitative PCR. Melting behaviour is particularly influenced by the length, nucleotide sequence and GC content of the amplicons. This method is expanding rapidly in several research areas such as human genetics, reproductive biology, microbiology and ecology/conservation of wild populations. Here we have developed a successful HRM protocol for avian sex identification based on the amplification of sex-specific CHD1 fragments. The melting curve patterns allowed efficient sexual differentiation of 111 samples analysed (plucked feathers, muscle tissues, blood and oral cavity epithelial cells) of 14 bird species. In addition, we sequenced the amplified regions of the CHD1 gene and demonstrated the usefulness of this strategy for the genotype discrimination of various amplicons (CHD1Z and CHD1W), which have small size differences, ranging from 2 bp to 44 bp. The established methodology clearly revealed the advantages (e.g. closed-tube system, high sensitivity and rapidity) of a simple HRM assay for accurate sex differentiation of the species under study. The requirements, strengths and limitations of the method are addressed to provide a simple guide for its application in the field of molecular sexing of birds. The high sensitivity and resolution relative to previous real-time PCR methods makes HRM analysis an excellent approach for improving advanced molecular methods for bird sexing.
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Affiliation(s)
- Francisco Morinha
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes e Alto Douro (IBB/CGB-UTAD), Quinta de Prados, Vila Real, 5001-801, Portugal.
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Gabriel EM, Douarre PE, Fitzgibbon S, Clair J, Lucey B, Coffey A, O'Mahony JM. High-resolution melting analysis for rapid detection of linezolid resistance (mediated by G2576T mutation) in Staphylococcus epidermidis. J Microbiol Methods 2012; 90:134-6. [PMID: 22561095 DOI: 10.1016/j.mimet.2012.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 04/05/2012] [Accepted: 04/08/2012] [Indexed: 10/28/2022]
Abstract
We describe a novel HRM-PCR (high-resolution melting) assay capable of the accurate identification of the G2576T point mutation in domain V of the 23S rRNA genes attributed to linezolid resistance in Staphylococcus epidermidis. This rapid method demonstrated 100% correlation with the previously established NheI restriction digest assay.
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Hamal P, Hanzen J, Horn F, Trtkova J, Ruskova L, Vecerova R, Ruzicka F, Vollekova A, Raclavsky V. Usefulness of McRAPD for typing and importance of biofilm production in a case of nosocomial ventriculoperitoneal shunt infection caused by Candida lusitaniae. Folia Microbiol (Praha) 2011; 56:407-14. [DOI: 10.1007/s12223-011-0063-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 08/14/2011] [Indexed: 11/29/2022]
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