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Aguilar-Martinez SL, Sandoval-Peña GA, Molina-Mora JA, Tsukayama-Cisneros P, Díaz-Vélez C, Aguilar-Gamboa FR, Bonilla-Aldana DK, Rodriguez-Morales AJ. Genomic and Phylogenetic Characterisation of SARS-CoV-2 Genomes Isolated in Patients from Lambayeque Region, Peru. Trop Med Infect Dis 2024; 9:46. [PMID: 38393135 PMCID: PMC10892787 DOI: 10.3390/tropicalmed9020046] [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: 11/22/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
OBJECTIVE this study aims to identify and characterise genomic and phylogenetically isolated SARS-CoV-2 viral isolates in patients from Lambayeque, Peru. METHODS Nasopharyngeal swabs were taken from patients from the Almanzor Aguinaga Asenjo Hospital, Chiclayo, Lambayeque, Peru, which had been considered mild, moderate, and severe cases of COVID-19. Patients had to have tested positive for COVID-19, using a positive RT-PCR for SARS-CoV-2. Subsequently, the SARS-CoV-2 complete viral genome sequencing was carried out using Illumina MiSeq®. The sequences obtained from the sequence were analysed in Nextclade V1.10.0 to assign the corresponding clades, identify mutations in the SARS-CoV-2 genes and perform quality control of the sequences obtained. All sequences were aligned using MAFFT v7.471. The SARS-CoV-2 isolate Wuhan NC 045512.2 was used as a reference sequence to analyse mutations at the amino acid level. The construction of the phylogenetic tree model was achieved with IQ-TREE v1.6.12. RESULTS It was determined that during the period from December 2020 to January 2021, the lineages s C.14, C.33, B.1.1.485, B.1.1, B.1.1.1, and B.1.111 circulated, with lineage C.14 being the most predominant at 76.7% (n = 23/30). These lineages were classified in clade 20D mainly and also within clades 20B and 20A. On the contrary, the variants found in the second batch of samples of the period from September to October 2021 were Delta (72.7%), Gamma (13.6%), Mu (4.6%), and Lambda (9.1%), distributed between clades 20J, 21G, 21H, 21J, and 21I. CONCLUSIONS This study reveals updated information on the viral genomics of SARS-CoV-2 in the Lambayeque region, Peru, which is crucial to understanding the origins and dispersion of the virus and provides information on viral pathogenicity, transmission and epidemiology.
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Affiliation(s)
- Sergio Luis Aguilar-Martinez
- Grupo de Investigación en Bioinformática y Biología Estructural, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - Gustavo Adolfo Sandoval-Peña
- Grupo de Investigación en Bioinformática y Biología Estructural, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - José Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San Jose 11501-2060, Costa Rica
| | | | - Cristian Díaz-Vélez
- Facultad de Medicina, Universidad Privada Antenor Orrego, Trujillo 13008, Peru
| | - Franklin Rómulo Aguilar-Gamboa
- Grupo de Investigación en Inmunología y Virología del Norte, Laboratorio de Inmunología y Virología, Hospital Regional Lambayeque, Lambayeque 14011, Peru
| | | | - Alfonso J Rodriguez-Morales
- Faculty of Health Sciences, Universidad Científica del Sur, Lima 15307, Peru
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut P.O. Box 13-5053, Lebanon
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2
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Mesén-Porras S, Rojas-Céspedes A, Molina-Mora JA, Vega-Baudrit J, Siles F, Quiros S, Mora-Rodríguez R. Sphingolipid-Based Synergistic Interactions to Enhance Chemosensitivity in Lung Cancer Cells. Cells 2023; 12:2588. [PMID: 37998323 PMCID: PMC10670127 DOI: 10.3390/cells12222588] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/13/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
Tumor heterogeneity leads to drug resistance in cancer treatment with the crucial role of sphingolipids in cell fate and stress signaling. We analyzed sphingolipid metabolism and autophagic flux to study chemotherapeutic interactions on the A549 lung cancer model. Loaded cells with fluorescent sphingomyelin analog (BODIPY) and mCherry-EGFP-LC3B were used to track autophagic flux and assess cytotoxicity when cells are exposed to chemotherapy (epirubicin, cisplatin, and paclitaxel) together with sphingolipid pathway inhibitors and autophagy modulators. Our cell model approach employed fluorescent sphingolipid biosensors and a Gaussian Mixture Model of cell heterogeneity profiles to map the influence of chemotherapy on the sphingolipid pathway and infer potential synergistic interactions. Results showed significant synergy, especially when combining epirubicin with autophagy inducers (rapamycin and Torin), reducing cell viability. Cisplatin also synergized with a ceramidase inhibitor. However, paclitaxel often led to antagonistic effects. Our mapping model suggests that combining chemotherapies with autophagy inducers increases vesicle formation, possibly linked to ceramide accumulation, triggering cell death. However, the in silico model proposed ceramide accumulation in autophagosomes, and kinetic analysis provided evidence of sphingolipid colocalization in autophagosomes. Further research is needed to identify specific sphingolipids accumulating in autophagosomes. These findings offer insights into potential strategies for overcoming chemotherapy resistance by targeting the sphingolipid pathway.
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Affiliation(s)
- Susana Mesén-Porras
- Research Center on Tropical Diseases (CIET), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (S.M.-P.); (A.R.-C.); (J.A.M.-M.); (S.Q.)
- Research Center on Surgery and Cancer (CICICA), Campus Rodrigo Facio, University of Costa Rica, San José 11501-2060, Costa Rica;
- Master Program in Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica
- National Laboratory of Nanotechnology (LANOTEC), National Center of High Technology (CeNAT), Pavas, San José 1174-1200, Costa Rica;
| | - Andrea Rojas-Céspedes
- Research Center on Tropical Diseases (CIET), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (S.M.-P.); (A.R.-C.); (J.A.M.-M.); (S.Q.)
| | - José Arturo Molina-Mora
- Research Center on Tropical Diseases (CIET), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (S.M.-P.); (A.R.-C.); (J.A.M.-M.); (S.Q.)
| | - José Vega-Baudrit
- National Laboratory of Nanotechnology (LANOTEC), National Center of High Technology (CeNAT), Pavas, San José 1174-1200, Costa Rica;
| | - Francisco Siles
- Research Center on Surgery and Cancer (CICICA), Campus Rodrigo Facio, University of Costa Rica, San José 11501-2060, Costa Rica;
- Pattern Recognition and Intelligent Systems Laboratory (PRIS-Lab), Department and Postgraduate Studies in Electrical Engineering, University of Costa Rica, San José 11501-2060, Costa Rica
| | - Steve Quiros
- Research Center on Tropical Diseases (CIET), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (S.M.-P.); (A.R.-C.); (J.A.M.-M.); (S.Q.)
- Research Center on Surgery and Cancer (CICICA), Campus Rodrigo Facio, University of Costa Rica, San José 11501-2060, Costa Rica;
| | - Rodrigo Mora-Rodríguez
- Research Center on Tropical Diseases (CIET), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (S.M.-P.); (A.R.-C.); (J.A.M.-M.); (S.Q.)
- Research Center on Surgery and Cancer (CICICA), Campus Rodrigo Facio, University of Costa Rica, San José 11501-2060, Costa Rica;
- Master Program in Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica
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3
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Badilla-Vargas L, Pereira R, Molina-Mora JA, Alape-Girón A, Flores-Díaz M. Clostridium perfringens phospholipase C, an archetypal bacterial virulence factor, induces the formation of extracellular traps by human neutrophils. Front Cell Infect Microbiol 2023; 13:1278718. [PMID: 37965263 PMCID: PMC10641792 DOI: 10.3389/fcimb.2023.1278718] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/09/2023] [Indexed: 11/16/2023] Open
Abstract
Neutrophil extracellular traps (NETs) are networks of DNA and various microbicidal proteins released to kill invading microorganisms and prevent their dissemination. However, a NETs excess is detrimental to the host and involved in the pathogenesis of various inflammatory and immunothrombotic diseases. Clostridium perfringens is a widely distributed pathogen associated with several animal and human diseases, that produces many exotoxins, including the phospholipase C (CpPLC), the main virulence factor in gas gangrene. During this disease, CpPLC generates the formation of neutrophil/platelet aggregates within the vasculature, favoring an anaerobic environment for C. perfringens growth. This work demonstrates that CpPLC induces NETosis in human neutrophils. Antibodies against CpPLC completely abrogate the NETosis-inducing activity of recombinant CpPLC and C. perfringens secretome. CpPLC induces suicidal NETosis through a mechanism that requires calcium release from inositol trisphosphate receptor (IP3) sensitive stores, activation of protein kinase C (PKC), and the mitogen-activated protein kinase/extracellular signal-regulated kinase (MEK/ERK) pathways, as well as the production of reactive oxygen species (ROS) by the metabolism of arachidonic acid. Proteomic analysis of the C. perfringens secretome identified 40 proteins, including a DNAse and two 5´-nucleotidases homologous to virulence factors that could be relevant in evading NETs. We suggested that in gas gangrene this pathogen benefits from having access to the metabolic resources of the tissue injured by a dysregulated intravascular NETosis and then escapes and spreads to deeper tissues. Understanding the role of NETs in gas gangrene could help develop novel therapeutic strategies to reduce mortality, improve muscle regeneration, and prevent deleterious patient outcomes.
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Affiliation(s)
- Lisa Badilla-Vargas
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica
| | - Reynaldo Pereira
- Centro Nacional de alta Tecnología, Consejo Nacional de Rectores (CONARE), San José, Costa Rica
| | - José Arturo Molina-Mora
- Centro de investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Alberto Alape-Girón
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica
| | - Marietta Flores-Díaz
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
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Li J, Wang H, Zhu J, Yang Q, Luan Y, Shi L, Molina-Mora JA, Zheng Y. De novo assembly of a chromosome-level reference genome of the ornamental butterfly Sericinus montelus based on nanopore sequencing and Hi-C analysis. Front Genet 2023; 14:1107353. [PMID: 36968580 PMCID: PMC10030965 DOI: 10.3389/fgene.2023.1107353] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/27/2023] [Indexed: 03/29/2023] Open
Abstract
Sericinus montelus (Lepidoptera, Papilionidae, Parnassiinae) is a high-value ornamental swallowtail butterfly species widely distributed in Northern and Central China, Japan, Korea, and Russia. The larval stage of this species feeds exclusively on Aristolochia plants. The Aristolochia species is well known for its high levels of aristolochic acids (AAs), which have been found to be carcinogenic for numerous animals. The swallowtail butterfly is among the few that can feed on these toxic host plants. However, the genetic adaptation of S. montelus to confer new abilities for AA tolerance has not yet been well explored, largely due to the limited genomic resources of this species. This study aimed to present a chromosome-level reference genome for S. montelus using the Oxford Nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C technology. The final assembly was composed of 581.44 Mb with an expected genome size of 619.27 Mb. Further, 99.98% of the bases could be anchored onto 30 chromosomes. The N50 of contigs and scaffolds was 5.74 and 19.12 Mb, respectively. Approximately 48.86% of the assembled genome was suggested to be repeat elements, and 13,720 protein-coding genes were predicted in the current assembly. The phylogenetic analysis indicated that S. montelus diverged from the common ancestor of swallowtails about 58.57-80.46 million years ago. Compared with related species, S. montelus showed a significant expansion of P450 gene family members, and positive selections on eloa, heatr1, and aph1a resulted in the AA tolerance for S. montelus larva. The de novo assembly of a high-quality reference genome for S. montelus provided a fundamental genomic tool for future research on evolution, genome genetics, and toxicology of the swallowtail butterflies.
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Affiliation(s)
- Jingjing Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- Grandomics Biosciences Institute, Wuhan, China
| | - Haiyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | | | - Qi Yang
- Grandomics Biosciences Institute, Wuhan, China
| | - Yang Luan
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- Cancer Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - José Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- *Correspondence: José Arturo Molina-Mora, ; Yuanting Zheng,
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- *Correspondence: José Arturo Molina-Mora, ; Yuanting Zheng,
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Campos-Sánchez R, Flores-Cruz A, Molina-Mora JA, Mora R, Rodríguez C, Gatica A, Guzmán-Verri C. Avances de la bioinformática en Costa Rica: vista retrospectiva y perspectivas. REV BIOL TROP 2021. [DOI: 10.15517/rbt.v69i4.46873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Introducción: La disciplina científica de la bioinformática tiene aplicaciones innovadoras para las sociedades humanas. Costa Rica, pequeña en tamaño y población en comparación con otros países de América Latina, ha ido adoptando la disciplina de manera progresiva. Reconocer los avances puede ayudarnos a determinar hacia dónde queremos ir como país, así como también cómo podemos contribuir a la región latinoamericana. Objetivos: Este manuscrito revisa el impacto de la investigación bioinformática en Costa Rica, la aplicación de la ciencia, los desafíos y oportunidades en su desarrollo y su potencial contribución a la sociedad. Métodos: Evaluamos los avances en este campo de investigación, por lo que buscamos datos de publicaciones y repositorios de secuencias, así como información de actividades de capacitación, redes, infraestructura, páginas web y fuentes de financiamiento. Resultados: Observamos avances importantes desde el año 2010, incluyendo un aumento en oportunidades de entrenamiento y número de publicaciones, aportes significativos a las bases de datos de secuencias y conexiones por medio de redes. Sin embargo, ciertas áreas, como la masa crítica, el mapeo de grupos de investigación y la financiación requieren más atención. Conclusiones: Sugerimos que para beneficiarse de las aplicaciones de la bioinformática se deben fortalecer tres aspectos clave: la comunidad científica, la infraestructura de investigación y las oportunidades de financiamiento. La comunidad científica y sus patrocinadores deben promover la investigación basada en bioinformática, invertir en la formación de estudiantes de posgrado, aumentar la formación de profesionales, crear oportunidades laborales para carreras en bioinformática y promover colaboraciones internacionales a través de redes. El impacto de tal inversión sería el desarrollo de proyectos ambiciosos pero factibles y colaboraciones extendidas dentro de la región latinoamericana. Esto permitiría realizar contribuciones significativas para abordar los desafíos globales y la aplicación de nuevos enfoques de investigación, innovación y transferencia de conocimiento para el desarrollo de la economía, siempre considerando la ética de la investigación.
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6
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Moreira-Soto A, Arguedas M, Brenes H, Buján W, Corrales-Aguilar E, Díaz C, Echeverri A, Flores-Díaz M, Gómez A, Hernández A, Herrera M, León G, Macaya R, Kühne A, Molina-Mora JA, Mora J, Sanabria A, Sánchez A, Sánchez L, Segura Á, Segura E, Solano D, Soto C, Stynoski JL, Vargas M, Villalta M, Reusken CBEM, Drosten C, Gutiérrez JM, Alape-Girón A, Drexler JF. High Efficacy of Therapeutic Equine Hyperimmune Antibodies Against SARS-CoV-2 Variants of Concern. Front Med (Lausanne) 2021; 8:735853. [PMID: 34552949 PMCID: PMC8451950 DOI: 10.3389/fmed.2021.735853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 07/03/2021] [Accepted: 08/10/2021] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 variants of concern show reduced neutralization by vaccine-induced and therapeutic monoclonal antibodies; therefore, treatment alternatives are needed. We tested therapeutic equine polyclonal antibodies (pAbs) that are being assessed in clinical trials in Costa Rica against five globally circulating variants of concern: alpha, beta, epsilon, gamma and delta, using plaque reduction neutralization assays. We show that equine pAbs efficiently neutralize the variants of concern, with inhibitory concentrations in the range of 0.146–1.078 μg/mL, which correspond to extremely low concentrations when compared to pAbs doses used in clinical trials. Equine pAbs are an effective, broad coverage, low-cost and a scalable COVID-19 treatment.
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Affiliation(s)
- Andres Moreira-Soto
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Mauricio Arguedas
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Hebleen Brenes
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Ministry of Health, Tres Ríos, Costa Rica
| | - Willem Buján
- School of Medicine, Universidad de Costa Rica, San Jose, Costa Rica.,Caja Costarricense del Seguro Social, San Jose, Costa Rica
| | - Eugenia Corrales-Aguilar
- Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Cecilia Díaz
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica.,School of Medicine, Universidad de Costa Rica, San Jose, Costa Rica
| | - Ann Echeverri
- Caja Costarricense del Seguro Social, San Jose, Costa Rica
| | - Marietta Flores-Díaz
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Aarón Gómez
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Andrés Hernández
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - María Herrera
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Guillermo León
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Román Macaya
- Caja Costarricense del Seguro Social, San Jose, Costa Rica
| | - Arne Kühne
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - José Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Javier Mora
- Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | | | - Andrés Sánchez
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Laura Sánchez
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Álvaro Segura
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Eduardo Segura
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Daniela Solano
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Claudio Soto
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Ministry of Health, Tres Ríos, Costa Rica
| | - Jennifer L Stynoski
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Mariángela Vargas
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Mauren Villalta
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Chantal B E M Reusken
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - José María Gutiérrez
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica
| | - Alberto Alape-Girón
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica.,School of Medicine, Universidad de Costa Rica, San Jose, Costa Rica
| | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Centre for Infection Research (DZIF), Associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
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7
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Alape-Girón A, Moreira-Soto A, Arguedas M, Brenes H, Buján W, Corrales-Aguilar E, Díaz C, Echeverri A, Flores-Díaz M, Gómez A, Hernández A, Herrera M, León G, Macaya R, Molina-Mora JA, Mora J, Narayanan A, Sanabria A, Sánchez A, Sánchez L, Segura Á, Segura E, Solano D, Soto C, Stynoski JL, Vargas M, Villalta M, Drexler JF, Gutiérrez JM. Heterologous Hyperimmune Polyclonal Antibodies Against SARS-CoV-2: A Broad Coverage, Affordable, and Scalable Potential Immunotherapy for COVID-19. Front Med (Lausanne) 2021; 8:743325. [PMID: 34552950 PMCID: PMC8450768 DOI: 10.3389/fmed.2021.743325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alberto Alape-Girón
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
- School of Medicine University of Costa Rica, San Pedro, Costa Rica
| | - Andrés Moreira-Soto
- Institute of Virology, Charité Medical University of Berlin, Berlin, Germany
| | - Mauricio Arguedas
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - Hebleen Brenes
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Ministry of Health, Cartago, Costa Rica
| | - Willem Buján
- School of Medicine University of Costa Rica, San Pedro, Costa Rica
- Caja Costarricense del Seguro Social, San Jose, Costa Rica
| | - Eugenia Corrales-Aguilar
- Research Center for Tropical Diseases, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - Cecilia Díaz
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
- School of Medicine University of Costa Rica, San Pedro, Costa Rica
| | - Ann Echeverri
- Caja Costarricense del Seguro Social, San Jose, Costa Rica
| | - Marietta Flores-Díaz
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - Aarón Gómez
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - Andrés Hernández
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - María Herrera
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - Guillermo León
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - Román Macaya
- Caja Costarricense del Seguro Social, San Jose, Costa Rica
| | - José Arturo Molina-Mora
- Research Center for Tropical Diseases, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - Javier Mora
- Research Center for Tropical Diseases, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - Aarthi Narayanan
- National Center for Biodefense and Infectious Diseases, College of Science, George Mason University, Fairfax, VA, United States
| | | | - Andrés Sánchez
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - Laura Sánchez
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - Álvaro Segura
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - Eduardo Segura
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - Daniela Solano
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - Claudio Soto
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Ministry of Health, Cartago, Costa Rica
| | - Jennifer L. Stynoski
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - Mariángela Vargas
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - Mauren Villalta
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
| | - Jan Felix Drexler
- Institute of Virology, Charité Medical University of Berlin, Berlin, Germany
| | - José María Gutiérrez
- Instituto Clodomiro Picado, School of Microbiology, University of Costa Rica, San Pedro, Costa Rica
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Molina-Mora JA, Campos-Sánchez R, Rodríguez C, Shi L, García F. High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers. Sci Rep 2020; 10:1392. [PMID: 31996747 PMCID: PMC6989561 DOI: 10.1038/s41598-020-58319-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/06/2020] [Indexed: 12/14/2022] Open
Abstract
Genotyping methods and genome sequencing are indispensable to reveal genomic structure of bacterial species displaying high level of genome plasticity. However, reconstruction of genome or assembly is not straightforward due to data complexity, including repeats, mobile and accessory genetic elements of bacterial genomes. Moreover, since the solution to this problem is strongly influenced by sequencing technology, bioinformatics pipelines, and selection criteria to assess assemblers, there is no systematic way to select a priori the optimal assembler and parameter settings. To assembly the genome of Pseudomonas aeruginosa strain AG1 (PaeAG1), short reads (Illumina) and long reads (Oxford Nanopore) sequencing data were used in 13 different non-hybrid and hybrid approaches. PaeAG1 is a multiresistant high-risk sequence type 111 (ST-111) clone that was isolated from a Costa Rican hospital and it was the first report of an isolate of P. aeruginosa carrying both blaVIM-2 and blaIMP-18 genes encoding for metallo-β-lactamases (MBL) enzymes. To assess the assemblies, multiple metrics regard to contiguity, correctness and completeness (3C criterion, as we define here) were used for benchmarking the 13 approaches and select a definitive assembly. In addition, annotation was done to identify genes (coding and RNA regions) and to describe the genomic content of PaeAG1. Whereas long reads and hybrid approaches showed better performances in terms of contiguity, higher correctness and completeness metrics were obtained for short read only and hybrid approaches. A manually curated and polished hybrid assembly gave rise to a single circular sequence with 100% of core genes and known regions identified, >98% of reads mapped back, no gaps, and uniform coverage. The strategy followed to obtain this high-quality 3C assembly is detailed in the manuscript and we provide readers with an all-in-one script to replicate our results or to apply it to other troublesome cases. The final 3C assembly revealed that the PaeAG1 genome has 7,190,208 bp, a 65.7% GC content and 6,709 genes (6,620 coding sequences), many of which are included in multiple mobile genomic elements, such as 57 genomic islands, six prophages, and two complete integrons with blaVIM-2 and blaIMP-18 MBL genes. Up to 250 and 60 of the predicted genes are anticipated to play a role in virulence (adherence, quorum sensing and secretion) or antibiotic resistance (β-lactamases, efflux pumps, etc). Altogether, the assembly and annotation of the PaeAG1 genome provide new perspectives to continue studying the genomic diversity and gene content of this important human pathogen.
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Affiliation(s)
- José Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica.
| | - Rebeca Campos-Sánchez
- Centro de Investigación en Biología Celular y Molecular, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - César Rodríguez
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Leming Shi
- Human Phenome Institute of Fudan University, Shanghai, China
| | - Fernando García
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
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