11 results on '"Jon Sicilia"'
Search Results
2. Insights into the Complexity of a Dormant Mycobacterium tuberculosis Cluster Once Transmission Is Resumed
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Fermin Acosta, Miguel Martínez-Lirola, Pedro J. Sola-Campoy, Jon Sicilia, Teresa Guerra-Galán, Sandra R. Maus, Patricia Muñoz, Laura Pérez-Lago, and Darío García de Viedma
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tuberculosis ,cluster ,transmission ,reactivation ,within-host diversity ,clonal complexity ,Microbiology ,QR1-502 - Abstract
ABSTRACT Genotyping tools help identify the complexity in Mycobacterium tuberculosis transmission clusters. We carried out a thorough analysis of the epidemiological and bacteriological complexity of a cluster in Almería, Spain. The cluster, initially associated with Moroccan migrants and with no secondary cases identified in 4 years, then reappeared in Spanish-born individuals. In one case, two Mycobacterium tuberculosis clonal variants were identified. We reanalyzed the cluster, supported by the characterization of multiple cultured isolates and respiratory specimens, whole-genome sequencing, and epidemiological case interviews. Our findings showed that the cluster, which was initially thought to have restarted activity with just a single case harboring a small degree of within-host diversity, was in fact currently growing due to coincidental reactivation of past exposures, with clonal diversity transmitted throughout the cluster. In one case, within-host diversity was amplified, probably due to prolonged diagnostic delay. IMPORTANCE The precise study of the dynamics of tuberculosis transmission in socio-epidemiologically complex scenarios may require more thorough analysis than the standard molecular epidemiology strategies. Our study illustrates the epidemiological and bacteriological complexity present in a transmission cluster in a challenging epidemiological setting with a high proportion of migrant cases. The combination of whole-genome sequencing, refined and refocused epidemiological interviews, and in-depth analysis of the bacterial composition of sputa and cultured isolates was crucial in order to correctly reinterpret the true nature of this cluster. Our global approach allowed us to reinterpret correctly the unnoticed epidemiological and bacteriological complexity involved in the Mycobacterium tuberculosis transmission event under study, which had been overlooked by the usual molecular epidemiology approaches.
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- 2022
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3. Complete Analysis of the Epidemiological Scenario around a SARS-CoV-2 Reinfection: Previous Infection Events and Subsequent Transmission
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Laura Pérez Lago, Leire Pérez Latorre, Marta Herranz, Francisco Tejerina, Pedro J. Sola-Campoy, Jon Sicilia, Julia Suárez-González, Cristina Andrés-Zayas, Alvaro Chiner-Oms, Santiago Jiménez-Serrano, Neris García-González, Iñaki Comas, Fernando González-Candelas, Carolina Martínez-Laperche, Pilar Catalán, Patricia Muñoz, and Darío García de Viedma
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Microbiology ,QR1-502 - Abstract
We present the first complete analysis of the epidemiological scenario around a reinfection by SARS-CoV-2, more severe than the first episode, including three cases preceding the reinfection, the reinfected case per se
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- 2021
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4. Variable selection for nonlinear dimensionality reduction of biological datasets through bootstrapping of correlation networks.
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David G. Aragones, Miguel Palomino-Segura, Jon Sicilia, Georgiana Crainiciuc, Iván Ballesteros, Fátima Sánchez-Cabo, Andrés Hidalgo, and Gabriel Fernández Calvo
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- 2024
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5. Strategies of neutrophil diversification
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Miguel Palomino-Segura, Jon Sicilia, Iván Ballesteros, and Andrés Hidalgo
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Immunology ,Immunology and Allergy - Published
- 2023
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6. ACME: Automatic feature extraction for cell migration examination through intravital microscopy imaging.
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Miguel Molina-Moreno, Iván González-Díaz 0001, Jon Sicilia, Georgiana Crainiciuc, Miguel Palomino-Segura, Andrés Hidalgo, and Fernando Díaz-de-María
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- 2022
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7. Different dynamics of mean SARS‐CoV‐2 RT‐PCR Ct values between the first and second COVID‐19 waves in the Madrid population
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Cristina Rodríguez-Grande, Sergio Buenestado-Serrano, Luis Alcalá, Javier Adán-Jiménez, Sandra Rodríguez-Maus, Fermín Acosta, Patricia Muñoz, Laura Pérez-Lago, Jon Sicilia, Darío García de Viedma, Marta Herranz, and Pilar Catalán
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medicine.medical_specialty ,2019-20 coronavirus outbreak ,RT‐PCR ,Coronavirus disease 2019 (COVID-19) ,040301 veterinary sciences ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Population ,Gastroenterology ,SARS‐CoV‐2 ,0403 veterinary science ,03 medical and health sciences ,COVID‐19 ,Internal medicine ,medicine ,Animals ,Serologic Tests ,education ,first wave ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,Cycle threshold ,General Veterinary ,General Immunology and Microbiology ,Reverse Transcriptase Polymerase Chain Reaction ,SARS-CoV-2 ,business.industry ,COVID-19 ,dynamics ,04 agricultural and veterinary sciences ,General Medicine ,Viral Load ,second wave ,Real-time polymerase chain reaction ,Rapid Communications ,business ,Cts ,Viral load ,Rapid Communication - Abstract
SARS‐CoV‐2 RT‐PCR cycle threshold values from 18,803 cases (2 March–4 October) in Madrid define three stages: (i) initial ten weeks with sustained reduction in viral load (Ct: 23.4–32.3), (ii) stability with low viral loads (Ct: 31.9–35.5) in the next nine weeks and (iii) sudden increase with progressive higher viral loads until reaching stability at high levels in the next twelve weeks, coinciding with an increased percentage of positive cases and reduced median age. These data indicate differential virological/epidemiological patterns between the first and second COVID‐19 waves in Madrid.
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- 2021
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8. Recurrences of multidrug-resistant tuberculosis: Strains involved, within-host diversity, and fine-tuned allocation of reinfections
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Noemí Yokobori, Mario José Matteo, Laura Pérez-Lago, Iñaki Comas, Viviana Ritacco, Marta Herranz, Beatriz López, Sandra R Maus, Jon Sicilia, Roxana Paul, Sandra Fajardo, Norberto Simboli, Patricia Muñoz, Johana Monteserin, Darío García de Viedma, Álvaro Chiner-Oms, Fermín Acosta, Instituto de Salud Carlos III, European Research Council, Agencia Nacional de Promoción Científica y Tecnológica (Argentina), Comas, Iñaki, and Chiner-Oms, Álvaro
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Tuberculosis ,Argentina ,Biology ,Microbiology ,Persistence (computer science) ,Tuberculosis, Multidrug-Resistant ,MDR ,medicine ,Animals ,SNP ,Recurrences ,Clonal variants ,Diversity ,General Veterinary ,General Immunology and Microbiology ,Molecular epidemiology ,Strain (chemistry) ,Host (biology) ,Mycobacterium tuberculosis ,General Medicine ,medicine.disease ,Multiple drug resistance ,Reinfection ,WGS - Abstract
34 páginas, 13 figuras, Recurrent tuberculosis occurs due to exogenous reinfection or reactivation/persistence. We analysed 90 sequential MDR Mtb isolates obtained in Argentina from 27 patients with previously diagnosed MDR-TB that recurred in 2018 (1-10 years, 2-10 isolates per patient). Three long-term predominant strains were responsible for 63% of all MDR-TB recurrences. Most of the remaining patients were infected by strains different from each other. Reactivation/persistence of the same strain caused all but one recurrence, which was due to a reinfection with a predominant strain. One of the prevalent strains showed marked stability in the recurrences, while in another strain higher SNP-based diversity was observed. Comparisons of intra- versus inter-patient SNP distances identified two possible reinfections with closely related variants circulating in the community. Our results show a complex scenario of MDR-TB infections in settings with predominant MDR Mtb strains., This work was supported by the ERANet-LAC (TRANS-TB-TRANS Project ELAC2015/T08-0664), the ISCIII (AC16/00057, 15/01554, 16/01449, 18/00599, 19/00331 and contract number MS15/00075) and the ANPCyT (grant number PICT-2016-3219). The authors are grateful to Dainora Jaloveckas (cienciatraducida.com) for editing and proofreading assistance.
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- 2022
9. Behavioral immune landscapes of inflammation
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Georgiana Crainiciuc, Miguel Palomino-Segura, Miguel Molina-Moreno, Jon Sicilia, David G. Aragones, Jackson Liang Yao Li, Rodrigo Madurga, José M. Adrover, Alejandra Aroca-Crevillén, Sandra Martin-Salamanca, Alfonso Serrano del Valle, Sandra D. Castillo, Heidi C. E. Welch, Oliver Soehnlein, Mariona Graupera, Fátima Sánchez-Cabo, Alexander Zarbock, Thomas E. Smithgall, Mauro Di Pilato, Thorsten R. Mempel, Pierre-Louis Tharaux, Santiago F. González, Angel Ayuso-Sacido, Lai Guan Ng, Gabriel F. Calvo, Iván González-Díaz, Fernando Díaz-de-María, Andrés Hidalgo, Ministerio de Ciencia e Innovación (España), Fundación La Caixa, Transatlantic Network of Excellence, Fondation Leducq, Unión Europea. Comisión Europea, Federation of European Biochemical Societies, European Molecular Biology Organization, Fundación ProCNIC, and Marie Curie
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Inflammation ,Proteomics ,Mice ,Multidisciplinary ,src-Family Kinases ,Neutrophils ,Proto-Oncogene Proteins ,Leukocytes ,Animals ,Endothelium ,Cell Shape ,Article - Abstract
Transcriptional and proteomic profiling of individual cells have revolutionized interpretation of biological phenomena by providing cellular landscapes of healthy and diseased tissues1,2. These approaches, however, do not describe dynamic scenarios in which cells continuously change their biochemical properties and downstream 'behavioural' outputs3-5. Here we used 4D live imaging to record tens to hundreds of morpho-kinetic parameters describing the dynamics of individual leukocytes at sites of active inflammation. By analysing more than 100,000 reconstructions of cell shapes and tracks over time, we obtained behavioural descriptors of individual cells and used these high-dimensional datasets to build behavioural landscapes. These landscapes recognized leukocyte identities in the inflamed skin and trachea, and uncovered a continuum of neutrophil states inside blood vessels, including a large, sessile state that was embraced by the underlying endothelium and associated with pathogenic inflammation. Behavioural screening in 24 mouse mutants identified the kinase Fgr as a driver of this pathogenic state, and interference with Fgr protected mice from inflammatory injury. Thus, behavioural landscapes report distinct properties of dynamic environments at high cellular resolution. This study was supported by RTI2018-095497-B-I00 from Ministerio de Ciencia e Innovación (MCIN), HR17_00527 from Fundación La Caixa, Transatlantic Network of Excellence (TNE-18CVD04) from the Leducq Foundation, and FET-OPEN (no. 861878) from the European Commission to A.H. M.P-S. is supported by a Federation of European Biochemical Societies and the EMBO ALTF (no. 1142-2020) long-term fellowships. J.S. is supported by a fellowship (PRE2019-089130) from MICINN and A.A.-C. is supported by fellowship CF/BQ/ DR19/11740022 from La Caixa Foundation. J.L.Y.L. was supported by A*STAR and a Juan de la Cierva JCI-2017-33136 Fellowship from MICINN. S.D.C. is a recipient of a Marie Sklodowska-Curie fellowship (749731). M.G. is supported by SAF2017-89116R-P from MCIN and HR18_00120 from la Fundación La Caixa. T.R.M. is supported by grant NIH AI163223, L.G.N. is supported by SIgN core funding from A*STAR, and G.F.C. is supported by MCIN/ AEI/10.13039/501100011033 (grant PID2019-110895RB-I00) and by Junta de Comunidades de Castilla-La Mancha (SBPLY/19/180501/000211). F.S.-C. is supported by MCIN (grant RTI2018- 102084-B-I00), O.S. is supported by the Leducq Foundation (TNE-18CVD04), F.D.-d.-M. is supported by MCIN (TEC2017-84395-P), and T.E.S. is supported by the National Cancer Institute, NIH grant CA233576. The CNIC is supported by the MCIN and the Pro-CNIC Foundation. Sí
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- 2022
10. The first wave of the Spanish COVID-19 epidemic was associated with early introductions and fast spread of a dominating genetic variant
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Begoña Palop-Borrás, Mónica Parra Grande, Verónica González Galán, Alexander Tristancho, Maitane Aranzamendi Zaldumbide, Irene Pedrosa-Corral, Jon Sicilia, Sara Sanbonmatsu-Gámez, Fernando González-Candelas, Maria Angeles Marcos, María Dolores Tirado Balaguer, Irving Cancino-Muñoz, José María Navarro-Marí, Galo A. Goig, Mariana G. López, Nuria Rabella, David Navarro, Rosario Moreno-Muñoz, Inmaculada Gómez-Navarro, Jovita Fernández-Pinero, Vicente Martín, Llucia Martínez-Priego, Lorena Robles Fonseca, Neris García-González, José Luis López-Hontangas, Mireia Coscolla, José Luis del Pozo, Begoña Fuster Escrivá, Paula Ruiz-Hueso, Ángel Rodríguez-Villodres, Ana Milagro Beamonte, María Alma Bracho, Jordi Reina, Manuela Torres-Puente, María Pilar Bea-Escudero, Ignacio Torres, Marta Herranz, Antonio Rezusta, Elisa Martró, José J. Costa-Alcalde, Maria Rodriguez, Laura Pérez-Lago, Giuseppe D’Auria, Lidia Ruiz-Roldán, Paula Ruiz-Rodríguez, José Antonio Boga, Silvia Hernáez Crespo, Ana Carvajal, Gustavo Cilla Eguiluz, María de Toro, Juan Alberola, Darío García de Viedma, Iñaki Comas, Eliseo Albert, José A. Lepe, Griselda de Marco, Anna Not, Milagrosa Montes Ros, Inmaculada de Toro Peinado, Álvaro Chiner-Oms, Concepción Gimeno Cardona, Nieves Gonzalo Jimeno, Luis Piñeiro Vázquez, Andrés Canut, Santiago Serrano, María Carmen Pérez González, Antoni E. Bordoy, Sebastián Duchêne, Jose Maria Marimon, Antonio Oliver, Instituto de Salud Carlos III, Consejo Superior de Investigaciones Científicas (España), European Commission, European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), López, Mariana G., Chiner-Oms, Álvaro, Coscolla, Mireia, González-Candelas, Fernando, Comas, Iñaki, López, Mariana G. [0000-0002-2216-9232], Chiner-Oms, Álvaro [0000-0002-0463-0101], Coscolla, Mireia [0000-0003-0752-0538], González-Candelas, Fernando [0000-0002-0879-5798], and Comas, Iñaki [0000-0001-5504-9408]
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0303 health sciences ,03 medical and health sciences ,2019-20 coronavirus outbreak ,0302 clinical medicine ,Geography ,Coronavirus disease 2019 (COVID-19) ,Research council ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Genetic variants ,Library science ,030212 general & internal medicine ,030304 developmental biology ,3. Good health - Abstract
The COVID-19 pandemic has shaken the world since the beginning of 2020. Spain is among the European countries with the highest incidence of the disease during the first pandemic wave. We established a multidisciplinar consortium to monitor and study the evolution of the epidemic, with the aim of contributing to decision making and stopping rapid spreading across the country. We present the results for 2170 sequences from the first wave of the SARS-Cov-2 epidemic in Spain and representing 12% of diagnosed cases until 14th March. This effort allows us to document at least 500 initial introductions, between early February-March from multiple international sources. Importantly, we document the early raise of two dominant genetic variants in Spain (Spanish Epidemic Clades), named SEC7 and SEC8, likely amplified by superspreading events. In sharp contrast to other non-Asian countries those two variants were closely related to the initial variants of SARS-CoV-2 described in Asia and represented 40% of the genome sequences analyzed. The two dominant SECs were widely spread across the country compared to other genetic variants with SEC8 reaching a 60% prevalence just before the lockdown. Employing Bayesian phylodynamic analysis, we inferred a reduction in the effective reproductive number of these two SECs from around 2.5 to below 0.5 after the implementation of strict public-health interventions in mid March. The effects of lockdown on the genetic variants of the virus are reflected in the general replacement of preexisting SECs by a new variant at the beginning of the summer season. Our results reveal a significant difference in the genetic makeup of the epidemic in Spain and support the effectiveness of lockdown measures in controlling virus spread even for the most successful genetic variants. Finally, earlier control of SEC7 and particularly SEC8 might have reduced the incidence and impact of COVID-19 in our country., This work was funded by the Instituto de Salud Carlos III project COV20/00140, Spanish 593 National Research Council project CSIC-COV19-021 and ERC StG 638553 to IC, and BFU2017- 594 89594R to FGC. MC is supported by Ramón y Cajal program from Ministerio de Ciencia and 595 grants RTI2018-094399-A-I00 and SEJI/2019/011. 596 We gratefully acknowledge Hospital Universitari Vall d'Hebron, Instituto de Salud Carlos 597 III, IrsiCaixa AIDS Research Lab and all the international researchers and institutions that 598 submitted sequenced SARS-CoV-2 genomes to the GISAID’s EpiCov™ Database, as an 599 important part of our analyses have been made possible by the share of their work.
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- 2020
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11. A complete analysis of the epidemiological scenario around a SARS-CoV-2 reinfection: previous infection events and subsequent transmission
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Laura Pérez Lago, Leire Pérez Latorre, Marta Herranz, Francisco Tejerina, Pedro J Sola Campoy, Jon Sicilia, Julia Suárez González, Cristina Andrés Zayas, Alvaro Chiner Oms, Santiago Jiménez Serrano, Neris García González, Iñaki Comas, Fernando González Candelas, Carolina Martínez Laperche, Pilar Catalán, Patricia Muñoz, and Darío García de Viedma
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Rationale: The first descriptions of reinfection by SARS-CoV-2 have been recently reported. However, these studies focus exclusively on the reinfected case, without considering the epidemiological context of the event.Objectives: To perform a complete analysis of the sequential infections and transmission events around a SARS-CoV-2 reinfection, including the infection events preceding it, the exposure and subsequent transmissions.Methods: Our analysis was supported by host genetics, viral whole genome sequencing, phylogenomic viral population analysis, and refined epidemiological data obtained from interviews with the involved subjects.Results: The reinfection involved a 53-year-old woman with asthma (Case A), with a first COVID-19 episode in April-2020 and a much more severe second episode four months and a half later, with COVID-19 seroconversion in August, and requiring hospital admission. An extended genomic analysis allowed us to demonstrate that the strain involved in Case A´s reinfection was circulating in the epidemiological context of Case A and was also transmitted subsequently from Case A to her family context. The reinfection was also supported by a phylogenetic analysis, including 348 strains from Madrid, which revealed that the strain involved in the reinfection was circulating by the time Case A suffered the second episode, August/September-2020, but absent at the time range corresponding to Case A´s first episode.Conclusion: We present the first complete analysis of the epidemiological scenario around a reinfection by SARS-CoV-2, more severe than the first episode, including three cases preceding the reinfection, the reinfected case per se, and the subsequent transmission to another seven cases.
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- 2020
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