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Lara-Hernandez F, Cortez J, Garcia-Sorribes S, Blesa S, Olivares MD, Alic AS, Garcia-Garcia AB, Chaves FJ, Ivorra C. EOSAL-CNV for Easy and Rapid Detection of CNVs by Fragment Analysis : EOSAL: A Fast and Reliable New Method for CNV Detection. Methods Mol Biol 2023; 2621:241-253. [PMID: 37041448 DOI: 10.1007/978-1-0716-2950-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Copy number variations (CNVs) are a type of genetic variation involving from 50 base pairs (bps) to millions of bps and, in a general point of view, can include alterations of complete chromosomes. As CNVs mean the gain or loss of DNA sequences, their detection requires specific techniques and analysis. We have developed Easy One-Step Amplification and Labeling for CNV Detection (EOSAL-CNV) by fragment analysis in a DNA sequencer. The procedure is based on a single PCR reaction for amplification and labeling of all fragments included. The protocol includes specific primers for the amplification of the regions of interest with a tail in each of the primers (one for forward and another for the reverse primers) together with primers for tail amplification. One of the primers for tail amplification is labeled with a fluorophore, allowing the amplification and labeling in the same reaction. Combination of several tail pairs and labels allows the detection of DNA fragment by different fluorophores and increases the number of fragments that can be analyzed in one reaction. PCR products can be analyzed without any purification on a DNA sequencer for fragment detection and quantification. Finally, simple and easy calculations allow the detection of fragments with deletions or extra copies. The use of EOSAL-CNV allows simplifying and reducing costs in sample analysis for CNV detection.
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Affiliation(s)
| | - Jessica Cortez
- I+D+I Department, Sequencing Multiplex SL Serra, Valencia, Spain
| | | | - Sebastian Blesa
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, Valencia, Spain
| | | | - Andy S Alic
- I+D+I Department, Sequencing Multiplex SL Serra, Valencia, Spain
| | - Ana-Barbara Garcia-Garcia
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, Valencia, Spain.
- CIBERDEM, ISCIII, Madrid, Spain.
| | - F Javier Chaves
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, Valencia, Spain
- I+D+I Department, Sequencing Multiplex SL Serra, Valencia, Spain
- CIBERDEM, ISCIII, Madrid, Spain
| | - Carmen Ivorra
- I+D+I Department, Sequencing Multiplex SL Serra, Valencia, Spain
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Soares IMN, Polonio JC, Zequi JAC, Golias HC. Molecular techniques for the taxonomy of Aedes Meigen, 1818 (Culicidae: Aedini): A review of studies from 2010 to 2021. Acta Trop 2022; 236:106694. [PMID: 36122762 DOI: 10.1016/j.actatropica.2022.106694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/23/2022] [Accepted: 09/15/2022] [Indexed: 11/19/2022]
Abstract
The original description of Aedes Meigen in 1818, written in Latin, was very brief and included a single species, Aedes cinereus. In the last two decades the genus Aedes (Meigen, 1818) has undergone several revisions and reclassifications, with the current proposal being described by Wilkerson in 2015. However, the available keys for morphological identification are still not sufficient to differentiate cryptic species, damaged species, or those with confusing taxonomy. The current study aims to identify and describe the main taxonomic proposals and molecular methodologies available for the identification of the genus Aedes published between the years 2010 and 2021. The main molecular techniques used to identify the genus in the last 10 years, are: Multiplex PCR, DNA barcoding, nuclear and mitochondrial markers, environmental DNA, and bacterial microbiome analysis. This review highlights that there are catalogued data for only a few species of the genus Aedes, being restricted to medically important taxa such as Aedes albopictus and Aedes aegypti. The integrative taxonomy approach is a possibility to reconcile morphological and molecular data to improve species delimitation, contributing to future revisions of the genus.
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Affiliation(s)
| | - Julio Cesar Polonio
- Department of Cell Biology, Genetics and Biotechnology, State University of Maringá (UEM), Brazil
| | | | - Halison Correia Golias
- Department of Cell Biology, Genetics and Biotechnology, State University of Maringá (UEM), Brazil; Department of Humanities, Microbiology Laboratory, Federal Technological University of Paraná (UTFPR), Marcilio Dias Street, 635, Apucarana, Paraná, Brazil.
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Antunes AM, Nunes Stival JG, Targueta CP, de Campos Telles MP, Soares TN. A Pipeline for the Development of Microsatellite Markers using Next Generation Sequencing Data. Curr Genomics 2022; 23:175-181. [PMID: 36777003 PMCID: PMC9878831 DOI: 10.2174/1389202923666220428101350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Accepted: 02/14/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Also known as Simple Sequence Repetitions (SSRs), microsatellites are profoundly informative molecular markers and powerful tools in genetics and ecology studies on plants. Objective: This research presents a workflow for developing microsatellite markers using genome skimming. Methods: The pipeline was proposed in several stages that must be performed sequentially: obtaining DNA sequences, identifying microsatellite regions, designing primers, and selecting candidate microsatellite regions to develop the markers. Our pipeline efficiency was analyzed using Illumina sequencing data from the non-model tree species Pterodon emarginatus Vog. Results: The pipeline revealed 4,382 microsatellite regions and drew 7,411 pairs of primers for P. emarginatus. However, a much larger number of microsatellite regions with the potential to develop markers were discovered from our pipeline. We selected 50 microsatellite regions with high potential for developing markers and organized 29 microsatellite regions in sets for multiplex PCR. Conclusion: The proposed pipeline is a powerful tool for fast and efficient development of microsatellite markers on a large scale in several species, especially nonmodel plant species.
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Affiliation(s)
- Adriana Maria Antunes
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Programa de Pós Graduação em Genética e Melhoramento de Plantas, Escola de Agronomia, Universidade Federal de Goias, Goiânia, Goiás, Brasil;,Address correspondence to this author at the Department of Genetics, Institute of Biological Sciences, Goias Federal University, Goiânia, Brazil; Tel/Fax: +55 62 981660987; E-mail:
| | - Júlio Gabriel Nunes Stival
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil
| | - Cíntia Pelegrineti Targueta
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil
| | - Mariana Pires de Campos Telles
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brasil
| | - Thannya Nascimentos Soares
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Programa de Pós Graduação em Genética e Melhoramento de Plantas, Escola de Agronomia, Universidade Federal de Goias, Goiânia, Goiás, Brasil
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Deoclécio da Silva LM, do Prado FD, Hashimoto DT, Senhorini JA, Foresti F, Porto-Foresti F. Use of Molecular Genetic Methods to Reduce the Risk of Incorrect Identification of Fish Strains in Brazilian Aquaculture. Front Genet 2021; 12:720736. [PMID: 34956306 PMCID: PMC8695485 DOI: 10.3389/fgene.2021.720736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
The identification of fish species using traditional methods is generally based only on morphological characteristics and these methods are currently under review. This kind of identification of hybrid fishes solely based on their morphologies may be unreliable, especially when the samples include juveniles and post-F1 lineage fishes. Therefore, in the present study, we used molecular markers to accurately identify the fish species of economic interest that are used as materials in the projects developed in research institutions. We evaluated six lots of fishes sampled from different research centers, containing a total of 84 specimens acquired from private fish farms that were considered to be the representatives of pure species. Genetic analyses of all the specimens revealed that, globally, 22 samples (26.2%) were interspecific hybrids, while 20 (90.9%) samples were surprisingly characterized as post-F1 hybrids. This result confirms that hybrids are sold in markets without adequate labeling and also indicates the lack of proper control of the commercialization and management of stocks and products in fish farms. In addition, we determined that molecular diagnosis was an extremely effective and necessary method to test the reliability of biological materials currently used in scientific research.
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Affiliation(s)
- Luana Maria Deoclécio da Silva
- Laboratório de Genética de Peixes, Faculdade de Ciências, Departmento de Ciências Biológicas, Universidade Estadual Paulista, Bauru, Brazil
| | - Fernanda Dotti do Prado
- Laboratório de Genética de Peixes, Faculdade de Ciências, Departmento de Ciências Biológicas, Universidade Estadual Paulista, Bauru, Brazil
| | - Diogo Teruo Hashimoto
- Laboratório de Genética em Aquicultura e Conservação, Centro de Aquicultura, Universidade Estadual Paulista, Jaboticabal, Brazil
| | - José Augusto Senhorini
- Centro Nacional de Pesquisa e Conservação da Biota Aquática Continental (CEPTA-ICMBIO), Pirassununga, Brazil
| | - Fausto Foresti
- Laboratório de Biologia e Genética de Peixes, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Fabio Porto-Foresti
- Laboratório de Genética de Peixes, Faculdade de Ciências, Departmento de Ciências Biológicas, Universidade Estadual Paulista, Bauru, Brazil
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Neder VE, Amadio AF, Calvinho LF. Detection by multiplex PCR of Mycoplasma species associated with dairy cattle in Argentina. Rev Argent Microbiol 2021; 54:158-161. [PMID: 34489142 DOI: 10.1016/j.ram.2021.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 04/20/2021] [Accepted: 07/04/2021] [Indexed: 11/28/2022] Open
Abstract
There is scarce information about the frequency and epidemiological and clinical features associated with the presence of Mycoplasma spp. in Argentine dairy herds. The objectives of this study were to develop a multiplex PCR for identifying M.bovis and M.canadense and to describe the frequency of Mycoplasma spp. isolated from clinical samples submitted to a diagnostic laboratory. Of a total of 1548 samples from intramammary infections, bulk tank milk and biological fluids, 38 Mycoplasma isolates were obtained. M. bovis, M. canadense, M.californicum and M.leachii were detected by using two multiplex PCRs, confirming their presence in clinical conditions in dairy cattle. The techniques used in the present study can be useful to broaden the knowledge about Mycoplasma infections in cattle, since the search for these organisms is not usually included in routine diagnoses.
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Affiliation(s)
- Verónica E Neder
- Instituto de Investigación de la Cadena Láctea (INTA-CONCET), Estación Experimental Agropecuaria Rafaela, Instituto Nacional de Tecnología Agropecuaria, Rafaela, Santa Fe, Argentina
| | - Ariel F Amadio
- Instituto de Investigación de la Cadena Láctea (INTA-CONCET), Estación Experimental Agropecuaria Rafaela, Instituto Nacional de Tecnología Agropecuaria, Rafaela, Santa Fe, Argentina
| | - Luis F Calvinho
- Instituto de Investigación de la Cadena Láctea (INTA-CONCET), Estación Experimental Agropecuaria Rafaela, Instituto Nacional de Tecnología Agropecuaria, Rafaela, Santa Fe, Argentina; Facultad de Ciencias Veterinarias, Universidad Nacional del Litoral, Esperanza, Santa Fe, Argentina.
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Picard L, Maakaroun-Vermesse Z, Hoarau C, Castelnau P, Périvier M. Pediatric neurolisteriosis: A diagnosis to consider even in the absence of immunodeficiency. Arch Pediatr 2019; 26:171-173. [PMID: 30885606 DOI: 10.1016/j.arcped.2019.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 12/31/2018] [Accepted: 02/09/2019] [Indexed: 11/29/2022]
Abstract
Neurolisteriosis is known to affect vulnerable groups, for example neonates or children with immunodeficiency. This is a key point of the current clinical guidelines regarding pediatric meningitis. We report a rare case of neurolisteriosis in an immunocompetent infant, without the typical signs of listeriosis, which led to a delay in administering the appropriate antibiotherapy. This case illustrates the clinical heterogeneity of neurolisteriosis and the relevance of appropriate polymerase chain reaction (PCR) tests when the clinical presentation differs from the current guidelines. This case also reminds us that raw or unpasteurized milk-based food products pose a risk even in immunocompetent infants or children.
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Affiliation(s)
- L Picard
- Service de Neuropédiatrie et handicaps de l'enfant, hôpital pédiatrique Gatien de Clocheville, Centre Hospitalier Régional Universitaire de Tours, 49, boulevard Béranger, 37044 Tours, France
| | - Z Maakaroun-Vermesse
- Service de médecine interne et de maladies infectieuses, hôpital Bretonneau, Centre Hospitalier Régional Universitaire de Tours, 2, boulevard Tonnellé, 37000 Tours, France
| | - C Hoarau
- Unité transversale d'allergologie et immunologie clinique, hôpital Bretonneau, Centre Hospitalier Régional Universitaire de Tours, 2, boulevard Tonnellé, 37000 Tours, France
| | - P Castelnau
- Service de Neuropédiatrie et handicaps de l'enfant, hôpital pédiatrique Gatien de Clocheville, Centre Hospitalier Régional Universitaire de Tours, 49, boulevard Béranger, 37044 Tours, France; Inserm, UMR 1253, iBrain, Université de Tours, 37000 Tours, France
| | - M Périvier
- Service de Neuropédiatrie et handicaps de l'enfant, hôpital pédiatrique Gatien de Clocheville, Centre Hospitalier Régional Universitaire de Tours, 49, boulevard Béranger, 37044 Tours, France; Inserm, UMR 1253, iBrain, Université de Tours, 37000 Tours, France.
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Vandroux D, Allou N, Jabot J, Li Pat Yuen G, Brottet E, Roquebert B, Martinet O. Intensive care admission for Coronavirus OC43 respiratory tract infections. Med Mal Infect 2018; 48:141-144. [PMID: 29402475 PMCID: PMC7126704 DOI: 10.1016/j.medmal.2018.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/24/2017] [Accepted: 01/03/2018] [Indexed: 11/30/2022]
Abstract
Background Coronavirus OC43 infection causes severe pneumonia in patients presenting with comorbidities, but clinical signs alone do not allow for viral identification. Objectives To analyze acute manifestations of Coronavirus OC43 infections and outcomes of patients admitted to an intensive care unit (ICU). Patients and methods Retrospective and monocentric study performed during a Coronavirus OC43 outbreak. We used multiplex PCR to detect an OC43 outbreak in Reunion Island during the 2016 Southern Hemisphere's winter: seven admissions to the ICU. Results Mean age of patients was 71 [67;76] years, SAPS II was 42 [28;53], pneumonia severity index 159 [139;182] vs 73 [40.5;107] for patients in medical wards, and 43% required mechanical ventilation. Comorbidities were diabetes mellitus (87%), chronic respiratory failure (57%), and chronic renal failure (29%). One patient died from Haemophilus influenzae co-infection. Conclusion As for MERS Co-V infections, underlying comorbidities impacted the clinical outcomes of OC43 infections.
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Affiliation(s)
- D Vandroux
- Service de réanimation polyvalente, hôpital Félix-Guyon, CHU La-Réunion, allée des topazes, CS11021, 97400 Saint-Denis-de-La-Réunion, France; CHU La-Réunion, Inserm, CIC 1410, 97410 Saint-Pierre, France.
| | - N Allou
- Service de réanimation polyvalente, hôpital Félix-Guyon, CHU La-Réunion, allée des topazes, CS11021, 97400 Saint-Denis-de-La-Réunion, France
| | - J Jabot
- Service de réanimation polyvalente, hôpital Félix-Guyon, CHU La-Réunion, allée des topazes, CS11021, 97400 Saint-Denis-de-La-Réunion, France
| | - G Li Pat Yuen
- Laboratoire de biologie moléculaire, service de microbiologie, hôpital Félix-Guyon, CHU La-Réunion, allée des topazes, CS11021, 97400 Saint-Denis, Reunion
| | - E Brottet
- Santé publique France, CIRE océan indien, 2, bis avenue Georges-Brassens, CS 61002, 97443 Saint-Denis cedex 9, Reunion
| | - B Roquebert
- CHU La-Réunion, Inserm, CIC 1410, 97410 Saint-Pierre, France; Laboratoire de biologie moléculaire, service de microbiologie, hôpital Félix-Guyon, CHU La-Réunion, allée des topazes, CS11021, 97400 Saint-Denis, Reunion
| | - O Martinet
- Service de réanimation polyvalente, hôpital Félix-Guyon, CHU La-Réunion, allée des topazes, CS11021, 97400 Saint-Denis-de-La-Réunion, France
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Martín A, Pérez-Ayala A, Chaves F, Lora D, Orellana MÁ. Evaluation of the multiplex PCR Allplex-GI assay in the detection of bacterial pathogens in diarrheic stool samples. J Microbiol Methods 2017; 144:33-36. [PMID: 29100990 DOI: 10.1016/j.mimet.2017.10.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 02/04/2023]
Abstract
Rapid and accurate detection of the pathogens that cause gastrointestinal infection is important for appropriate therapy and proper infection control. This study assesses the performance of a new molecular assay for simultaneous detection of 13 different gastrointestinal bacteria in stool specimens. Using the Allplex GI-Bacteria (AGI-BI/AGI-BII) assay, a total of 394 stool samples were tested and the results were compared with culturing on selective differential followed by identification by mass spectroscopy. Discordant results were analyzed by a different multiplex PCR method, the Fast-Track Diagnostics Bacterial gastroenteritis (FTD-BG). The routine method (RM) detected 109 (27.7%) positive samples and the Allplex-GI assay, 261 (66.2%). Analysis of discordant results revealed that the molecular assay detected 44 pathogens that were not detected by the RM, including 23 Campylobacter spp., 11 Salmonella spp, 3 Y. enterocolitica, 2 EIEC/Shigella spp, 2 E. coli 0157, 2 C. difficile and 1 Aeromonas spp. Five cases not detected by the molecular method were detected by the RM (3 Aeromonas spp, 1 Salmonella spp and 1 Y. enterocolitica). For all targets, the percentages of sensitivity and specificity were >95%, except for Aeromonas spp., which were 81% and 99% respectively. This study suggests that Allplex-GI multiplex PCR is a sensitive and specific assay that enables a rapid and accurate diagnosis of bacterial gastrointestinal infections.
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Affiliation(s)
- Ariadna Martín
- Servicio de Microbiología, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Ana Pérez-Ayala
- Servicio de Microbiología, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Fernando Chaves
- Servicio de Microbiología, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - David Lora
- Clinical Research Unit, IMAS12-CIBERESP, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - M Ángeles Orellana
- Servicio de Microbiología, Hospital Universitario 12 de Octubre, Madrid, Spain.
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van der Ploeg CA, Rogé AD, Bordagorría XL, de Urquiza MT, Castillo ABC, Bruno SB. Design of Two Multiplex PCR Assays for Serotyping Shigella flexneri. Foodborne Pathog Dis 2017; 15:33-38. [PMID: 29016188 DOI: 10.1089/fpd.2017.2328] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Shigella flexneri is a major health problem in developing countries. There are 19 serotypes recognized based on O-antigen structure and its typing is important for epidemiological purposes. However, the diversity of serotypes and the difficulties presented by phenotypic serotyping, for example, unavailable antisera for less common antigens, require the implementation of molecular techniques. In this study, we developed two multiplex PCR assays targeting the O-antigen synthesis genes and the O-antigen modification genes, for the rapid identification of S. flexneri serotypes 1/7, 2, 4, 5, and 6 (PCR A) and serotype 7 and group antigenic factors (3,4; 6; 7,8; E1037) (PCR B). A total of 73 S. flexneri strains representing 18 serotypes, except serotype 1d, were used in the study. Specific amplification patterns were obtained for each of the different serotypes. All strains tested had concordant results with phenotypic and genotypic serotyping; therefore, its implementation in the microbiology clinical laboratory will significantly improve S. flexneri serotyping.
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Affiliation(s)
- Claudia A van der Ploeg
- Servicio Antígenos y Antisueros, Instituto Nacional de Producción de Biológicos (INPB) , ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Ariel D Rogé
- Servicio Antígenos y Antisueros, Instituto Nacional de Producción de Biológicos (INPB) , ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Ximena L Bordagorría
- Servicio Antígenos y Antisueros, Instituto Nacional de Producción de Biológicos (INPB) , ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Maria T de Urquiza
- Servicio Antígenos y Antisueros, Instituto Nacional de Producción de Biológicos (INPB) , ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Ana B Celi Castillo
- Servicio Antígenos y Antisueros, Instituto Nacional de Producción de Biológicos (INPB) , ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Susana B Bruno
- Servicio Antígenos y Antisueros, Instituto Nacional de Producción de Biológicos (INPB) , ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
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Fernández G, Martró E, González V, Saludes V, Bascuñana E, Marcó C, Rivaya B, López E, Coll P, Matas L, Ausina V. Usefulness of a novel multiplex real-time PCR assay for the diagnosis of sexually-transmitted infections. Enferm Infecc Microbiol Clin 2016; 34:471-6. [PMID: 26706392 DOI: 10.1016/j.eimc.2015.10.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Sexually transmitted infections (STI) are currently on the increase worldwide. New molecular tools have been developed in the past few years in order to improve their diagnosis. An evaluation was carried out using a new commercially available real-time PCR assay, Anyplex™ II STI-7 (Seegene, Seoul, Korea), which detects seven major pathogens in a single reaction - Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, Mycoplasma hominis, Mycoplasma genitalium, Ureaplasma urealyticum, and Ureaplasma parvum - and compared with conventional methods performed in our laboratory. MATERIALS AND METHODS Two different populations were included, and 267 specimens from different sites of infection (urines, endocervical swabs, rectal swabs, vaginal swabs, urethral swabs and one inguinal adenopathy) were processed for both methods. RESULTS The parameters of clinical performance were calculated for C. trachomatis, N. gonorrhoeae, and T. vaginalis, and the assay achieved sensitivities (SE) from 93.94% to 100%, and specificities (SP) from 96.55% to 100%, with negative predictive values (NPV) from 93.33% to 98.85%, and positive predictive values (PPV) from 96.88% to 100%, with a very good agreement (kappa index from 0.88 to 1). CONCLUSIONS Anyplex™ II STI-7 is a good tool for the reliable diagnosis of STI. Its ease of use and processing allows it to be incorporated into the day to day laboratory work.
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