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Salinas L, Cárdenas P, Graham JP, Trueba G. IS 26 drives the dissemination of bla CTX-M genes in an Ecuadorian community. Microbiol Spectr 2024; 12:e0250423. [PMID: 38088550 PMCID: PMC10783052 DOI: 10.1128/spectrum.02504-23] [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: 06/15/2023] [Accepted: 11/06/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE The horizontal gene transfer events are the major contributors to the current spread of CTX-M-encoding genes, the most common extended-spectrum β-lactamase (ESBL), and many clinically crucial antimicrobial resistance (AMR) genes. This study presents evidence of the critical role of IS26 transposable element for the mobility of bla CTX-M gene among Escherichia coli isolates from children and domestic animals in the community. We suggest that the nucleotide sequences of IS26-bla CTX-M could be used to study bla CTX-M transmission between humans, domestic animals, and the environment, because understanding of the dissemination patterns of AMR genes is critical to implement effective measures to slow down the dissemination of these clinically important genes.
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Affiliation(s)
- Liseth Salinas
- Universidad San Francisco de Quito, Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Quito, Pichincha, Ecuador
| | - Paúl Cárdenas
- Universidad San Francisco de Quito, Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Quito, Pichincha, Ecuador
| | - Jay P. Graham
- Environmental Health Sciences Division, University of California, Berkeley, California, USA
| | - Gabriel Trueba
- Universidad San Francisco de Quito, Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Quito, Pichincha, Ecuador
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2
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Andrade-Molina DA, Morey-León GA, Muñoz-Mawyin KE, Cruz-Fatuly FF, Fernández-Cadena JC, Cárdenas P. First sequenced cases of Omicron BA.2 sublineage in Ecuador. Virus Res 2023; 334:199169. [PMID: 37406934 PMCID: PMC10410591 DOI: 10.1016/j.virusres.2023.199169] [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: 04/09/2022] [Revised: 07/01/2023] [Accepted: 07/02/2023] [Indexed: 07/07/2023]
Abstract
The largest wave of infection with SARS-CoV-2 virus in Ecuador was observed in mid-December 2021 and early January 2022, driven by B.1.1.529/BA (Omicron) variant. During the second half of March, an increase in the number of daily cases was observed and coincided with the emergence of the BA.2 variant, which we describe in the present study. The first sequenced five cases of SARS-CoV-2 21L/BA.2 in Ecuador were identified using variant specific genotyping by qPCR and confirmed by whole genome sequencing (WGS). The first sequenced Ecuadorian BA.2 isolate was obtained from a person with international travel history who became symptomatic 3 days after travelling, whereas in the other cases no travel history was recorded.
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Affiliation(s)
- D A Andrade-Molina
- Omics Sciences Laboratory, Faculty of Health Sciences, Universidad Espíritu Santo, Samborondón, Ecuador.
| | - G A Morey-León
- Faculty of Health Sciences, Universidad de Guayaquil, Guayaquil, Ecuador
| | - K E Muñoz-Mawyin
- Omics Sciences Laboratory, Faculty of Health Sciences, Universidad Espíritu Santo, Samborondón, Ecuador
| | - F F Cruz-Fatuly
- Omics Sciences Laboratory, Faculty of Health Sciences, Universidad Espíritu Santo, Samborondón, Ecuador
| | | | - P Cárdenas
- Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
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3
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Morton JT, Jin DM, Mills RH, Shao Y, Rahman G, McDonald D, Zhu Q, Balaban M, Jiang Y, Cantrell K, Gonzalez A, Carmel J, Frankiensztajn LM, Martin-Brevet S, Berding K, Needham BD, Zurita MF, David M, Averina OV, Kovtun AS, Noto A, Mussap M, Wang M, Frank DN, Li E, Zhou W, Fanos V, Danilenko VN, Wall DP, Cárdenas P, Baldeón ME, Jacquemont S, Koren O, Elliott E, Xavier RJ, Mazmanian SK, Knight R, Gilbert JA, Donovan SM, Lawley TD, Carpenter B, Bonneau R, Taroncher-Oldenburg G. Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles. Nat Neurosci 2023:10.1038/s41593-023-01361-0. [PMID: 37365313 DOI: 10.1038/s41593-023-01361-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/13/2023] [Indexed: 06/28/2023]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by heterogeneous cognitive, behavioral and communication impairments. Disruption of the gut-brain axis (GBA) has been implicated in ASD although with limited reproducibility across studies. In this study, we developed a Bayesian differential ranking algorithm to identify ASD-associated molecular and taxa profiles across 10 cross-sectional microbiome datasets and 15 other datasets, including dietary patterns, metabolomics, cytokine profiles and human brain gene expression profiles. We found a functional architecture along the GBA that correlates with heterogeneity of ASD phenotypes, and it is characterized by ASD-associated amino acid, carbohydrate and lipid profiles predominantly encoded by microbial species in the genera Prevotella, Bifidobacterium, Desulfovibrio and Bacteroides and correlates with brain gene expression changes, restrictive dietary patterns and pro-inflammatory cytokine profiles. The functional architecture revealed in age-matched and sex-matched cohorts is not present in sibling-matched cohorts. We also show a strong association between temporal changes in microbiome composition and ASD phenotypes. In summary, we propose a framework to leverage multi-omic datasets from well-defined cohorts and investigate how the GBA influences ASD.
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Affiliation(s)
- James T Morton
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
- Biostatistics & Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Dong-Min Jin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | | | - Yan Shao
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Gibraan Rahman
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Metin Balaban
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Yueyu Jiang
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Kalen Cantrell
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Antonio Gonzalez
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Julie Carmel
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | | | - Sandra Martin-Brevet
- Laboratory for Research in Neuroimaging, Centre for Research in Neurosciences, Department of Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Kirsten Berding
- Division of Nutritional Sciences, University of Illinois, Urbana, IL, USA
| | - Brittany D Needham
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - María Fernanda Zurita
- Microbiology Institute and Health Science College, Universidad San Francisco de Quito, Quito, Ecuador
| | - Maude David
- Departments of Microbiology & Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA
| | - Olga V Averina
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Alexey S Kovtun
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Antonio Noto
- Department of Biomedical Sciences, School of Medicine, University of Cagliari, Cagliari, Italy
| | - Michele Mussap
- Laboratory Medicine, Department of Surgical Sciences, School of Medicine, University of Cagliari, Cagliari, Italy
| | - Mingbang Wang
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China
- Microbiome Therapy Center, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, China
| | - Daniel N Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ellen Li
- Department of Medicine, Division of Gastroenterology and Hepatology, Stony Brook University, Stony Brook, NY, USA
| | - Wenhao Zhou
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China
| | - Vassilios Fanos
- Neonatal Intensive Care Unit and Neonatal Pathology, Department of Surgical Sciences, School of Medicine, University of Cagliari, Cagliari, Italy
| | - Valery N Danilenko
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Dennis P Wall
- Pediatrics (Systems Medicine), Biomedical Data Science, and Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Paúl Cárdenas
- Institute of Microbiology, COCIBA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Manuel E Baldeón
- Facultad de Ciencias Médicas, de la Salud y la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
| | - Sébastien Jacquemont
- Sainte Justine Hospital Research Center, Montréal, QC, Canada
- Department of Pediatrics, Université de Montréal, Montréal, QC, Canada
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Evan Elliott
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar Ilan University, Ramat Gan, Israel
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Sarkis K Mazmanian
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Jack A Gilbert
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Sharon M Donovan
- Division of Nutritional Sciences, University of Illinois, Urbana, IL, USA
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Bob Carpenter
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
- Prescient Design, a Genentech Accelerator, New York, NY, USA
| | - Gaspar Taroncher-Oldenburg
- Gaspar Taroncher Consulting, Philadelphia, PA, USA.
- Simons Foundation Autism Research Initiative, Simons Foundation, New York, NY, USA.
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4
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Ortiz A, Cárdenas P, Peralta M, Rodríguez H, Ortiz J, Vazquez E. Central retinal artery occlusion as an ophthalmic complication after snakebite. Arch Soc Esp Oftalmol (Engl Ed) 2022; 97:587-592. [PMID: 36088246 DOI: 10.1016/j.oftale.2022.05.007] [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] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Snakebite causes 421.000-1.200.000 poisonings per year due to and hematotoxicity, neurotoxicity y vasculotoxicity. Ophthalmological manifestations secondary to snake bites are rare. If the snake belongs to the Viperidae family, the most frequent ophthalmologic manifestations are macular infarction, chronic open-angle glaucoma, and retinal or vitreous hemorrhage. Central retinal artery occlusion is an extremely rare ocular complication. We report the case of a 30-year-old patient, who consulted due to poor vision in her left eye weeks after suffering a snake bite (Bothrops atrox) in her left lower limb. The diagnosis was a central retinal artery occlusion in the left eye with abnormal findings in the ophthalmological physical examination and in complementary retinal and neuro-ophthalmological tests.
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Affiliation(s)
- A Ortiz
- Fundación Oftalmológica de Santander (FOSCAL), Floridablanca, Colombia; Clínica Oftalmológica Aljaorza, Machala, Ecuador.
| | - P Cárdenas
- Fundación Oftalmológica de Santander (FOSCAL), Floridablanca, Colombia
| | - M Peralta
- Fundación Oftalmológica de Santander (FOSCAL), Floridablanca, Colombia; Clínica Oftalmológica Aljaorza, Machala, Ecuador
| | - H Rodríguez
- Fundación Oftalmológica de Santander (FOSCAL), Floridablanca, Colombia
| | - J Ortiz
- Clínica Oftalmológica Aljaorza, Machala, Ecuador
| | - E Vazquez
- Clínica Oftalmológica Aljaorza, Machala, Ecuador
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5
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Guevara R, Prado-Vivar B, Márquez S, Muñoz EB, Carvajal M, Guadalupe JJ, Becerra-Wong M, Proaño S, Bayas-Rea R, Coloma J, Grunauer M, Trueba G, Rojas-Silva P, Barragán V, Cárdenas P. Occurrence of SARS-CoV-2 reinfections at regular intervals in Ecuador. Front Cell Infect Microbiol 2022; 12:951383. [PMID: 36164552 PMCID: PMC9507970 DOI: 10.3389/fcimb.2022.951383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
SARS-CoV-2 reinfection is defined as a new infection with a different virus variant in an individual who has already recovered from a previous episode of COVID-19. The first case of reinfection in the world was described in August 2020, since then, reinfections have increased over time and their incidence has fluctuated with specific SARS-CoV-2 variant waves. Initially, reinfections were estimated to represent less than 1% of total COVID-19 infections. With the advent of the Omicron variant, reinfections became more frequent, representing up to 10% of cases (based on data from developed countries). The frequency of reinfections in Latin America has been scarcely reported. The current study shows that in Ecuador, the frequency of reinfections has increased 10-fold following the introduction of Omicron, after 22 months of surveillance in a single center of COVID-19 diagnostics. Suspected reinfections were identified retrospectively from a database of RT-qPCR-positive patients. Cases were confirmed by sequencing viral genomes from the first and second infections using the ONT MinION platform. Monthly surveillance showed that the main incidence peaks of reinfections were reached within four to five months, coinciding with the increase of COVID-19 cases in the country, suggesting that the emergence of reinfections is related to higher exposure to the virus during outbreaks. This study performed the longest monitoring of SARS-CoV-2 reinfections, showing an occurrence at regular intervals of 4-5 months and confirming a greater propensity of Omicron to cause reinfections.
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Affiliation(s)
- Rommel Guevara
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Belén Prado-Vivar
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Sully Márquez
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Erika B. Muñoz
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Mateo Carvajal
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Juan José Guadalupe
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Mónica Becerra-Wong
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Stefanie Proaño
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Rosa Bayas-Rea
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Josefina Coloma
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, CA, United States
| | - Michelle Grunauer
- Escuela de Medicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Patricio Rojas-Silva
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Verónica Barragán
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Paúl Cárdenas
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- *Correspondence: Paúl Cárdenas,
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6
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Mejía L, Prado B, Cárdenas P, Trueba G, González-Candelas F. The impact of genetic recombination on pathogenic Leptospira. Infect Genet Evol 2022; 102:105313. [PMID: 35688386 DOI: 10.1016/j.meegid.2022.105313] [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] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/28/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Leptospirosis is the most common zoonosis worldwide, and is increasingly common in poor urban communities, where there is inadequate sewage disposal and abundance of domestic and peridomestic animals. There are many risk factors associated with the disease, such as contaminated water exposure, close contact with animals, floods, recreational activities related to water, wet agriculture. The symptoms of leptospirosis are common to other infectious diseases and, if not treated, it can lead to meningitis, liver failure, kidney damage and death. Leptospirosis is caused by 38 pathogenic species of Leptospira, which are divided in almost 30 serogroups and more than 300 serovars. The serological classification (serogroups and serovars) is based on the expression of distinct lipopolysaccharide (LPS) antigens. These antigens are also associated to protective immunity; antibodies against a serovar protect from any member of the same serovar. Serologic and phylogenetic analyses are not congruent probably due to genetic recombination of LPS genes among different leptospiral species. To analyze the importance of recombination in leptospiral evolution, we performed a gene-by-gene tree topology comparison on closed genomes available in public databases at two levels: among core genomes of pathogenic species (34 recombinant among 1213 core genes), and among core genomes of L. interrogans isolates (178/798). We found that most recombinant genes code for proteins involved in translation, ribosomal structure and biogenesis, but also for cell wall, membrane and envelope biogenesis. Besides, our final results showed that half of LPS genes are recombinant (18/36). This is relevant because serovar classification and vaccine development are based on these epitopes. The frequent recombination of LPS-associated genes suggests that natural selection is promoting the survival of recombinant lineages. These results may help understanding the factors that make Leptospira a successful pathogen.
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Affiliation(s)
- Lorena Mejía
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Institute for Integrative Systems Biology, University of Valencia, Valencia, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain
| | - Belén Prado
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Paúl Cárdenas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador.
| | - Fernando González-Candelas
- Institute for Integrative Systems Biology, University of Valencia, Valencia, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; CIBER (Centro de Investigación Biomédica en Red) in Epidemiology and Public Health, Valencia, Spain.
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7
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Fernandez-Cadena JC, Carvajal M, Muñoz E, Prado-Vivar B, Marquez S, Proaño S, Bayas R, Guadalupe JJ, Becerra-Wong M, Gutierrez B, Morey-Leon G, Trueba G, Grunauer M, Barragán V, Rojas-Silva P, Andrade-Molina D, Cárdenas P. First case of within-host co-infection of different SARS-CoV-2 variants in Ecuador. New Microbes New Infect 2022; 48:101001. [PMID: 35818397 PMCID: PMC9259011 DOI: 10.1016/j.nmni.2022.101001] [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: 01/29/2022] [Accepted: 06/24/2022] [Indexed: 11/28/2022] Open
Abstract
Background COVID-19 infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause mild symptoms to severe illness and death. Co-infections of SARS-CoV-2 with other respiratory viruses have been described. However, two SARS-CoV-2 lineage co-infection have been rarely reported. Methodology A genotyping analysis and two different types of whole genome sequencing were performed (Illumina MiniSeq and ONT MinION). When examining the phylogenetic analysis in NextClade and Pangolin webservers, and considering the genotyping findings, conflicting results were obtained. Results The raw data of the sequencing was analyzed, and nucleotide variants were identified between different reads of the virus genome. B.1 and P.1 lineages were identified within the same sample. Conclusions We concluded that this is a co-infection case with two SARS-CoV-2 lineages, the first one reported in Ecuador.
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Affiliation(s)
| | - M Carvajal
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - E Muñoz
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - B Prado-Vivar
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - S Marquez
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - S Proaño
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - R Bayas
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - J J Guadalupe
- Universidad San Francisco de Quito, COCIBA, Laboratorio de Biotecnología Vegetal, Ecuador
| | - M Becerra-Wong
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - B Gutierrez
- Universidad San Francisco de Quito, COCIBA, Laboratorio de Biotecnología Vegetal, Ecuador.,Departament of Zoology, University of Oxford, UK
| | | | - G Trueba
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - M Grunauer
- Universidad San Francisco de Quito, COCSA, Escuela de Medicina, Ecuador.,Unidad de Cuidados Intensivos, Hospital de los Valles, Quito, Ecuador
| | - V Barragán
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | - P Rojas-Silva
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
| | | | - P Cárdenas
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Ecuador
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8
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Uriu K, Cárdenas P, Muñoz E, Barragan V, Kosugi Y, Shirakawa K, Takaori-Kondo A, Sato K. Characterization of the immune resistance of SARS-CoV-2 Mu variant and the robust immunity induced by Mu infection. J Infect Dis 2022; 226:1200-1203. [PMID: 35176774 PMCID: PMC8903444 DOI: 10.1093/infdis/jiac053] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/15/2022] [Indexed: 11/14/2022] Open
Abstract
We have recently revealed that the SARS-CoV-2 Mu variant shows a pronounced resistance to antibodies elicited by natural SARS-CoV-2 infection and vaccination. However, it remains unclear which mutations determine the resistance of SARS-CoV-2 Mu to antiviral sera. Also, it is unclear how SARS-CoV-2 Mu infection induces antiviral immunity. Here we reveal that the two mutations in the SARS-CoV-2 Mu spike protein, YY144-145TSN and E484K, are responsible for the resistance to COVID-19 convalescent sera during early 2020 and vaccine sera. Notably, the convalescent sera of SARS-CoV-2 Mu-infected individuals are broadly antiviral against Mu as well as other SARS-CoV-2 variants of concern/interest.
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Affiliation(s)
- Keiya Uriu
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Paúl Cárdenas
- Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - Erika Muñoz
- Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - Veronica Barragan
- Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - Yusuke Kosugi
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,CREST, Japan Science and Technology Agency, Saitama, Japan
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9
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Mitman SL, Amato HK, Saraiva-Garcia C, Loayza F, Salinas L, Kurowski K, Marusinec R, Paredes D, Cárdenas P, Trueba G, Graham JP. Risk factors for third-generation cephalosporin-resistant and extended-spectrum β-lactamase-producing Escherichia coli carriage in domestic animals of semirural parishes east of Quito, Ecuador. PLOS Glob Public Health 2022; 2:e0000206. [PMID: 36962308 PMCID: PMC10021719 DOI: 10.1371/journal.pgph.0000206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/19/2022] [Indexed: 12/27/2022]
Abstract
Extended-spectrum β-lactamase (ESBL)-producing and other antimicrobial resistant (AR) Escherichia coli threaten human and animal health worldwide. This study examined risk factors for domestic animal colonization with ceftriaxone-resistant (CR) and ESBL-producing E. coli in semirural parishes east of Quito, Ecuador, where small-scale food animal production is common. Survey data regarding household characteristics, animal care, and antimicrobial use were collected from 304 households over three sampling cycles, and 1195 environmental animal fecal samples were assessed for E. coli presence and antimicrobial susceptibility. Multivariable regression analyses were used to assess potential risk factors for CR and ESBL-producing E. coli carriage. Overall, CR and ESBL-producing E. coli were detected in 56% and 10% of all fecal samples, respectively. The odds of CR E. coli carriage were greater among dogs at households that lived within a 5 km radius of more than 5 commercial food animal facilities (OR 1.72, 95% CI 1.15-2.58) and lower among dogs living at households that used antimicrobials for their animal(s) based on veterinary/pharmacy recommendation (OR 0.18, 95% CI 0.04-0.96). Increased odds of canine ESBL-producing E. coli carriage were associated with recent antimicrobial use in any household animal (OR 2.69, 95% CI 1.02-7.10) and purchase of antimicrobials from pet food stores (OR 6.83, 95% CI 1.32-35.35). Food animals at households that owned more than 3 species (OR 0.64, 95% CI 0.42-0.97), that used antimicrobials for growth promotion (OR 0.41, 95% CI 0.19-0.89), and that obtained antimicrobials from pet food stores (OR 0.47, 95% CI 0.25-0.89) had decreased odds of CR E. coli carriage, while food animals at households with more than 5 people (OR 2.22, 95% CI 1.23-3.99) and located within 1 km of a commercial food animal facility (OR 2.57, 95% CI 1.08-6.12) had increased odds of ESBL-producing E. coli carriage. Together, these results highlight the complexity of antimicrobial resistance among domestic animals in this setting.
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Affiliation(s)
- Siena L Mitman
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
- Division of Environmental Sciences, University of California, Berkeley School of Public Health, Berkeley, California, United States of America
| | - Heather K Amato
- Division of Environmental Sciences, University of California, Berkeley School of Public Health, Berkeley, California, United States of America
| | - Carlos Saraiva-Garcia
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Fernanda Loayza
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Liseth Salinas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Kathleen Kurowski
- Division of Infectious Diseases and Vaccinology, University of California, Berkeley School of Public Health, Berkeley, California, United States of America
| | - Rachel Marusinec
- Division of Infectious Diseases and Vaccinology, University of California, Berkeley School of Public Health, Berkeley, California, United States of America
| | - Diana Paredes
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Paúl Cárdenas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jay P Graham
- Division of Environmental Sciences, University of California, Berkeley School of Public Health, Berkeley, California, United States of America
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10
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Egas D, Guadalupe JJ, Prado-Vivar B, Becerra-Wong M, Márquez S, Castillo S, Latta J, Rodriguez F, Escorza G, Trueba G, Grunauer M, Barragán V, Rojas-Silva P, Cárdenas P. SARS-CoV-2 detection and sequencing in heart tissue associated with myocarditis and persistent arrhythmia: A case report. IDCases 2021; 25:e01187. [PMID: 34136351 PMCID: PMC8192838 DOI: 10.1016/j.idcr.2021.e01187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 06/10/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND SARS-CoV-2 uses the human cell receptor angiotensin-converting enzyme (ACE2). ACE2 is widely present in the cardiovascular system including the myocardium and the conduction system. COVID-19 patients that present severe symptoms have been reported to have complications involving myocardial injuries caused by the virus. Here we report the detection of SARS-CoV-2 by whole genome sequencing in the endocardium of a patient with severe bradycardia. CASE PRESENTATION We report a case of a 34-year-old male patient with COVID-19 tested by PCR, he started with gastrointestinal symptoms, however, he quickly deteriorated his hemodynamic state by means of myocarditis and bradycardia. After performing an endocardium biopsy, it was possible to identify the presence of SARS-CoV-2 in the heart tissue and to sequence its whole genome using the ARTIC-Network protocol and a modified tissue RNA extraction method. The patient's outcome was improved after a permanent pacemaker was implanted. CONCLUSIONS It was possible to identify a SARS-CoV-2 clade 20A in the endocardium of the reported patient.
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Affiliation(s)
- Diego Egas
- Hospital Quito N° 1 de la Policía Nacional, Quito, Ecuador
| | - Juan José Guadalupe
- Universidad San Francisco de Quito, COCIBA, Laboratorio de Biotecnología Vegetal, Quito, Ecuador
| | - Belén Prado-Vivar
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Quito, Ecuador
- Universidad San Francisco de Quito, Centro de Bioinformática, Quito, Ecuador
| | - Mónica Becerra-Wong
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Quito, Ecuador
| | - Sully Márquez
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Quito, Ecuador
| | | | - Johanna Latta
- Hospital Quito N° 1 de la Policía Nacional, Quito, Ecuador
| | | | | | - Gabriel Trueba
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Quito, Ecuador
| | - Michelle Grunauer
- Universidad San Francisco de Quito, Escuela de Medicina, Quito, Ecuador
| | - Verónica Barragán
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Quito, Ecuador
| | - Patricio Rojas-Silva
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Quito, Ecuador
| | - Paúl Cárdenas
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología, Quito, Ecuador
- Universidad San Francisco de Quito, Centro de Bioinformática, Quito, Ecuador
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11
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Prado-Vivar B, Becerra-Wong M, Guadalupe JJ, Márquez S, Gutierrez B, Rojas-Silva P, Grunauer M, Trueba G, Barragán V, Cárdenas P. A case of SARS-CoV-2 reinfection in Ecuador. Lancet Infect Dis 2021; 21:e142. [PMID: 33242475 PMCID: PMC7833993 DOI: 10.1016/s1473-3099(20)30910-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023]
Affiliation(s)
- Belén Prado-Vivar
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador; Colegio de Ciencias Biológicas y Ambientales, and Centro de Bioinformática, Universidad San Francisco de Quito, Quito, Ecuador
| | - Mónica Becerra-Wong
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Juan José Guadalupe
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito, Quito, Ecuador
| | - Sully Márquez
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Bernardo Gutierrez
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito, Quito, Ecuador; Department of Zoology, University of Oxford, Oxford, UK
| | | | - Michelle Grunauer
- Escuela de Medicina, Universidad San Francisco de Quito, Quito, Ecuador
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Verónica Barragán
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Paúl Cárdenas
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador; Colegio de Ciencias Biológicas y Ambientales, and Centro de Bioinformática, Universidad San Francisco de Quito, Quito, Ecuador.
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12
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Gutierrez B, Márquez S, Prado-Vivar B, Becerra-Wong M, Guadalupe JJ, da Silva Candido D, Fernandez-Cadena JC, Morey-Leon G, Armas-Gonzalez R, Andrade-Molina DM, Bruno A, de Mora D, Olmedo M, Portugal D, Gonzalez M, Orlando A, Drexler JF, Moreira-Soto A, Sander AL, Brünink S, Kühne A, Patiño L, Carrazco-Montalvo A, Mestanza O, Zurita J, Sevillano G, du Plessis L, McCrone JT, Coloma J, Trueba G, Barragán V, Rojas-Silva P, Grunauer M, Kraemer MU, Faria NR, Escalera-Zamudio M, Pybus OG, Cárdenas P. Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador. medRxiv 2021:2021.03.31.21254685. [PMID: 33851177 PMCID: PMC8043474 DOI: 10.1101/2021.03.31.21254685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Characterisation of SARS-CoV-2 genetic diversity through space and time can reveal trends in virus importation and domestic circulation, and permit the exploration of questions regarding the early transmission dynamics. Here we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the COVID-19 pandemic. We generate and analyse 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylgeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions (NPIs), with differential degrees of persistence and national dissemination.
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Affiliation(s)
- Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, UK
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Sully Márquez
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Belén Prado-Vivar
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Mónica Becerra-Wong
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Juan José Guadalupe
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Juan Carlos Fernandez-Cadena
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón, Ecuador
| | - Gabriel Morey-Leon
- Faculty of Medical Sciences, Universidad de Guayaquil, Guayaquil, Ecuador
| | - Rubén Armas-Gonzalez
- Faculty of Sciences, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Derly Madeleiny Andrade-Molina
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón, Ecuador
| | - Alfredo Bruno
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
- Universidad Agraria del Ecuador
| | - Domenica de Mora
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Maritza Olmedo
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Denisse Portugal
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Manuel Gonzalez
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Andres Moreira-Soto
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Anna-Lena Sander
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Sebastian Brünink
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Arne Kühne
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Leandro Patiño
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | | | - Orson Mestanza
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Jeannete Zurita
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - Gabriela Sevillano
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | | | - John T. McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Josefina Coloma
- School of Public Health, University of California, Berkeley, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Verónica Barragán
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Michelle Grunauer
- Escuela de Medicina, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Nuno R. Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | | | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
| | - Paúl Cárdenas
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
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13
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Márquez S, Prado-Vivar B, Guadalupe JJ, Becerra-Wong M, Gutierrez B, Fernández-Cadena JC, Andrade-Molina D, Morey-Leon G, Moncayo M, Guevara R, Coloma J, Trueba G, Grunauer M, Barragán V, Rojas-Silva P, Cárdenas P. SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis. medRxiv 2021:2021.03.19.21253620. [PMID: 33791722 PMCID: PMC8010754 DOI: 10.1101/2021.03.19.21253620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
SARS-CoV-2, the etiological agent of COVID-19, was first described in Wuhan, China in December 2019 and has now spread globally. Ecuador was the second country in South America to confirm cases and Guayaquil was one of the first cities in the world to experience high mortality due to COVID-19. The aim of this study was to describe the lineages circulating throughout the country and to compare the mutations in local variants, to the reference strain. In this work we used the MinION platform (Oxford Nanopore Technologies) to sequence the whole SARS-CoV-2 genomes of 119 patients from all provinces of Ecuador, using the ARTIC network protocols. Our data from lineage assignment of the one hundred and nineteen whole genomes revealed twenty different lineages. All genomes presented differences in the S gene compared to the Wuhan reference strain, being the D614G amino acid replacement the most common change. The B.1.1.119 lineage was the most frequent and was found in several locations in the Coast and Andean region. Three sequences were assigned to the new B.1.1.7 lineage. Our work is an important contribution to the understanding of the epidemiology of SARS-CoV-2 in Ecuador and South America.
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Affiliation(s)
- Sully Márquez
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología
| | - Belén Prado-Vivar
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología
- Universidad San Francisco de Quito, Centro de Bioinformática
| | - Juan José Guadalupe
- Universidad San Francisco de Quito, COCIBA, Laboratorio de Biotecnología Vegetal
| | | | - Bernardo Gutierrez
- Universidad San Francisco de Quito, COCIBA, Laboratorio de Biotecnología Vegetal
- Departament of Zoology, University of Oxford
| | | | | | | | | | - Miguel Moncayo
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología
| | - Rommel Guevara
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología
| | | | - Gabriel Trueba
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología
| | - Michelle Grunauer
- Universidad San Francisco de Quito, COCSA, Escuela de Medicina
- Unidad de Cuidados Intensivos, Hospital de los Valles, Quito
| | - Verónica Barragán
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología
| | | | - Paúl Cárdenas
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología
- Universidad San Francisco de Quito, Centro de Bioinformática
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14
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Salinas L, Loayza F, Cárdenas P, Saraiva C, Johnson TJ, Amato H, Graham JP, Trueba G. Environmental Spread of Extended Spectrum Beta-Lactamase (ESBL) Producing Escherichia coli and ESBL Genes among Children and Domestic Animals in Ecuador. Environ Health Perspect 2021; 129:27007. [PMID: 33617318 PMCID: PMC7899495 DOI: 10.1289/ehp7729] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/30/2021] [Accepted: 02/01/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND There is a significant gap in our understanding of the sources of multidrug-resistant bacteria and resistance genes in community settings where human-animal interfaces exist. OBJECTIVES This study characterized the relationship of third-generation cephalosporin-resistant Escherichia coli (3GCR-EC) isolated from animal feces in the environment and child feces based on phenotypic antimicrobial resistance (AMR) and whole genome sequencing (WGS). METHODS We examined 3GCR-EC isolated from environmental fecal samples of domestic animals and child fecal samples in Ecuador. We analyzed phenotypic and genotypic AMR, as well as clonal relationships (CRs) based on pairwise single-nucleotide polymorphisms (SNPs) analysis of 3GCR-EC core genomes. CRs were defined as isolates with fewer than 100 different SNPs. RESULTS A total of 264 3GCR-EC isolates from children (n=21), dogs (n=20), and chickens (n=18) living in the same region of Quito, Ecuador, were identified. We detected 16 CRs total, which were found between 7 children and 5 domestic animals (5 CRs) and between 19 domestic animals (11 CRs). We observed that several clonally related 3GCR-EC isolates had acquired different plasmids and AMR genes. Most CRs were observed in different homes (n=14) at relatively large distances. Isolates from children and domestic animals shared the same blaCTX-M allelic variants, and the most prevalent were blaCTX-M-55 and blaCTX-M-65, which were found in isolates from children, dogs, and chickens. DISCUSSION This study provides evidence of highly dynamic horizontal transfer of AMR genes and mobile genetic elements (MGEs) in the E. coli community and shows that some 3GCR-EC and (extended-spectrum β-lactamase) ESBL genes may have moved relatively large distances among domestic animals and children in semirural communities near Quito, Ecuador. Child-animal contact and the presence of domestic animal feces in the environment potentially serve as important sources of drug-resistant bacteria and ESBL genes. https://doi.org/10.1289/EHP7729.
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Affiliation(s)
- Liseth Salinas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Fernanda Loayza
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Paúl Cárdenas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Carlos Saraiva
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
- Mid Central Research & Outreach Center, Willmar, Minnesota, USA
| | - Heather Amato
- Environmental Health Sciences Division, University of California, Berkeley, California, USA
| | - Jay P. Graham
- Environmental Health Sciences Division, University of California, Berkeley, California, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
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15
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Gutierrez B, Márquez S, Prado-Vivar B, Becerra-Wong M, Guadalupe JJ, Candido DDS, Fernandez-Cadena JC, Morey-Leon G, Armas-Gonzalez R, Andrade-Molina DM, Bruno A, De Mora D, Olmedo M, Portugal D, Gonzalez M, Orlando A, Drexler JF, Moreira-Soto A, Sander AL, Brünink S, Kühne A, Patiño L, Carrazco-Montalvo A, Mestanza O, Zurita J, Sevillano G, Du Plessis L, McCrone JT, Coloma J, Trueba G, Barragán V, Rojas-Silva P, Grunauer M, Kraemer MUG, Faria NR, Escalera-Zamudio M, Pybus OG, Cárdenas P. Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador. Virus Evol 2021; 7:veab051. [PMID: 34527281 PMCID: PMC8244811 DOI: 10.1093/ve/veab051] [Citation(s) in RCA: 3] [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: 04/01/2021] [Revised: 05/12/2021] [Accepted: 06/03/2021] [Indexed: 12/23/2022] Open
Abstract
Characterisation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic diversity through space and time can reveal trends in virus importation and domestic circulation and permit the exploration of questions regarding the early transmission dynamics. Here, we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the coronavirus-19 pandemic. We generated and analysed 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylogeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions, with differential degrees of persistence and national dissemination.
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Affiliation(s)
- Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - Sully Márquez
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Belén Prado-Vivar
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Mónica Becerra-Wong
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Juan José Guadalupe
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | | | - Juan Carlos Fernandez-Cadena
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón 092301, Ecuador
| | - Gabriel Morey-Leon
- Faculty of Medical Sciences, Universidad de Guayaquil, Guayaquil 090613, Ecuador
| | - Rubén Armas-Gonzalez
- Faculty of Sciences, Escuela Superior Politécnica del Litoral, Guayaquil 090112, Ecuador
| | - Derly Madeleiny Andrade-Molina
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón 092301, Ecuador
| | - Alfredo Bruno
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Domenica De Mora
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Maritza Olmedo
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Denisse Portugal
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Manuel Gonzalez
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - 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 10117, Germany
| | - 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 10117, Germany
| | - Anna-Lena Sander
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Sebastian Brünink
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Arne Kühne
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Leandro Patiño
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | | | - Orson Mestanza
- Servicio de Genética, Instituto Nacional de Salud del Niño San Borja, Lima 15037, Perú
| | - Jeannete Zurita
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito 170143, Ecuador
| | - Gabriela Sevillano
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
| | - Louis Du Plessis
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JW, UK
| | - Josefina Coloma
- School of Public Health, University of California, Berkeley CA 94704, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Verónica Barragán
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Patricio Rojas-Silva
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Michelle Grunauer
- Escuela de Medicina, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | | | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - Paúl Cárdenas
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
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16
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Reyes J, Cárdenas P, Tamayo R, Villavicencio F, Aguilar A, Melano RG, Trueba G. Characterization of blaKPC-2-Harboring Klebsiella pneumoniae Isolates and Mobile Genetic Elements from Outbreaks in a Hospital in Ecuador. Microb Drug Resist 2020; 27:752-759. [PMID: 33217245 DOI: 10.1089/mdr.2019.0433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 11/13/2022] Open
Abstract
Aim: To investigate the mobile genetic elements harboring blaKPC gene in carbapenem-resistant Klebsiella pneumoniae recovered during a 6-month outbreak in a high-complexity hospital from Ecuador. Results: A total of 62 isolates belonging to ST258 pilv-I-positive (n = 45), ST25 serotype K2 (n = 8), ST348 (n = 6), ST42 (n = 1), ST196 (n = 1), and ST1758 (n = 1) were collected from intensive care unit (ICU), neurosurgery, burn unit, internal medicine, pneumology, and neurology. Pulsed-field gel electrophoresis analysis showed two major clusters of ST258 and ST25 related to bloodstream infections and pneumonia circulating in ICU. The PCR assay showed that in non-ST258 isolates, the blaKPC-2 gene were located on the Tn4401a transposon inserted in the transferable pKpQIL-like IncFIIK2 plasmid; the whole-genome sequencing of ST258 clone showed two plasmids, the blaKPC-2 gene was located on nonconjugative IncR plasmid, whereas the IncFIB/IncFII plasmid lacked ß-lactamase genes. We found an IncM plasmid in blaKPC-2-harboring Klebsiella pneumoniae ST1758 clone. Conclusions: These findings highlight the presence of pKpQIL-like plasmids in non-ST258 and nonconjugative plasmids in ST258 isolates causing hospital outbreaks.
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Affiliation(s)
- Jorge Reyes
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador.,Facultad de Ciencias Químicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Paúl Cárdenas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Rafael Tamayo
- Centro de Referencia Nacional de Resistencia a los antimicrobianos "LIP," Quito, Ecuador
| | - Fernando Villavicencio
- Centro de Referencia Nacional de Resistencia a los antimicrobianos "LIP," Quito, Ecuador
| | - Ana Aguilar
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador.,Escuela de Medicina, Colegio de Ciencias de la Salud (COCSA), Universidad San Francisco de Quito, Quito, Ecuador
| | - Roberto G Melano
- Public Health Ontario Laboratory, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
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17
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Márquez S, Prado-Vivar B, Guadalupe JJ, Gutierrez B, Jibaja M, Tobar M, Mora F, Gaviria J, García M, Espinosa F, Ligña E, Reyes J, Barragán V, Rojas-Silva P, Trueba G, Grunauer M, Cárdenas P. Genome sequencing of the first SARS-CoV-2 reported from patients with COVID-19 in Ecuador. medRxiv 2020:2020.06.11.20128330. [PMID: 32588004 PMCID: PMC7310664 DOI: 10.1101/2020.06.11.20128330] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
SARS-CoV-2, the etiological agent of COVID-19 was first described in Wuhan in December 2019 and has now spread globally. Ecuador was the second country in South America to report confirmed cases. The first case reported in Quito, the capital city of Ecuador, was a tourist who came from the Netherlands and presented symptoms on March 10th, 2020 (index case). In this work we used the MinION platform (Oxford Nanopore Technologies) to sequence the metagenome of the bronchoalveolar lavage (BAL) from this case reported, and subsequently we sequenced the whole genome of the index case and other three patients using the ARTIC network protocols. Our data from the metagenomic approach confirmed the presence of SARS-CoV-2 coexisting with pathogenic bacteria suggesting coinfection. Relevant bacteria found in the BAL metagenome were Streptococcus pneumoniae, Mycobacterium tuberculosis, Staphylococcus aureus and Chlamydia spp. Lineage assignment of the four whole genomes revealed three different origins. The variant HEE-01 was imported from the Netherlands and was assigned to B lineage, HGSQ-USFQ-018, belongs to the B.1 lineage showing nine nucleotide differences with the reference strain and grouped with sequences from the United Kingdom, and HGSQ-USFQ-007 and HGSQ-USFQ-010 belong to the B lineage and grouped with sequences from Scotland. All genomes show mutations in their genomes compared to the reference strain, which could be important to understand the virulence, severity and transmissibility of the virus. Our findings also suggest that there were at least three independent introductions of SARS-CoV-2 to Ecuador.
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Affiliation(s)
- Sully Márquez
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología
| | - Belén Prado-Vivar
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología
- Universidad San Francisco de Quito, Centro de Bioinformática
| | - Juan José Guadalupe
- Universidad San Francisco de Quito, COCIBA, Laboratorio de Biotecnología Vegetal
| | - Bernardo Gutierrez
- Universidad San Francisco de Quito, COCIBA, Laboratorio de Biotecnología Vegetal
- Departament of Zoology, University of Oxford
| | - Manuel Jibaja
- Unidad de Cuidados Intensivos, Hospital Eugenio Espejo, Quito
| | - Milton Tobar
- Unidad de Cuidados Intensivos, Hospital Eugenio Espejo, Quito
| | | | | | | | | | | | - Jorge Reyes
- Hospital General Sur de Quito, IESS
- Universidad Central del Ecuador, Facultad Ciencias Químicas
| | - Verónica Barragán
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología
| | | | - Gabriel Trueba
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología
| | - Michelle Grunauer
- Universidad San Francisco de Quito, Escuela de Medicina, COCSA
- Unidad de Cuidados Intensivos, Hospital de los Valles, Quito
| | - Paúl Cárdenas
- Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología
- Universidad San Francisco de Quito, Centro de Bioinformática
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18
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Quiroga C, Cevallos V, Morales D, Baldeón ME, Cárdenas P, Rojas-Silva P, Ponce P. Molecular Identification of Leishmania spp. in Sand Flies (Diptera: Psychodidae, Phlebotominae) From Ecuador. J Med Entomol 2017; 54:1704-1711. [PMID: 28981860 PMCID: PMC5850347 DOI: 10.1093/jme/tjx122] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Indexed: 05/26/2023]
Abstract
The detection and identification of natural infections in sand flies by Leishmania protozoan species in endemic areas is a key factor in assessing the risk of leishmaniasis and in designing prevention and control measures for this infectious disease. In this study, we analyzed the Leishmania DNA using nuclear ribosomal internal transcript spacer (ITS) sequences. Parasite DNA was extracted from naturally infected, blood-fed sand flies collected in nine localities considered leishmaniasis-endemic foci in Ecuador. The species of parasites identified in sand flies were Leishmania major-like, Leishmania naiffi, Leishmania mexicana, Leishmania lainsoni, and “Leishmania sp. siamensis”. Sand fly specimens of Brumptomyia leopoldoi, Mycropigomyia cayennensis, Nyssomyia yuilli yuilli, Nyssomyia trapidoi, Pressatia triacantha, Pressatia dysponeta, Psychodopygus carrerai carrerai, Psychodopygus panamensis, and Trichophoromyia ubiquitalis were found positive for Leishmania parasite. These findings contribute to a better understanding of the epidemiology and transmission dynamics of the disease in high-risk areas of Ecuador.
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Affiliation(s)
- Cristina Quiroga
- Instituto Nacional de Investigación en Salud Pública, Centro Nacional de Referencia e Investigación en Vectores, Quito, Ecuador (; ; ; )
- Universidad de Las Américas, Centro de Investigación Traslacional, Quito, Ecuador (; ; )
| | - Varsovia Cevallos
- Instituto Nacional de Investigación en Salud Pública, Centro Nacional de Referencia e Investigación en Vectores, Quito, Ecuador (; ; ; )
| | - Diego Morales
- Instituto Nacional de Investigación en Salud Pública, Centro Nacional de Referencia e Investigación en Vectores, Quito, Ecuador (; ; ; )
| | - Manuel E Baldeón
- Universidad de Las Américas, Centro de Investigación Traslacional, Quito, Ecuador (; ; )
- Universidad Tecnológica Equinoccial, Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Quito, Ecuador
| | - Paúl Cárdenas
- Universidad de Las Américas, Centro de Investigación Traslacional, Quito, Ecuador (; ; )
- Universidad San Francisco de Quito, Instituto de Microbiología, Quito, Ecuador
| | - Patricio Rojas-Silva
- Universidad de Las Américas, Centro de Investigación Traslacional, Quito, Ecuador (; ; )
- Universidad Tecnológica Equinoccial, Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Quito, Ecuador
| | - Patricio Ponce
- Instituto Nacional de Investigación en Salud Pública, Centro Nacional de Referencia e Investigación en Vectores, Quito, Ecuador (; ; ; )
- Universidad Central del Ecuador, Instituto de Biomedicina, Facultad de Biología, Quito, Ecuador
- Yachay Tech University, School of Biological Sciences and Engineering. Urcuquí, Ecuador
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19
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Abstract
Systematics is nowadays facing new challenges with the introduction of new concepts and new techniques. Compared to most other phyla, phylogenetic relationships among sponges are still largely unresolved. In the past 10 years, the classical taxonomy has been completely overturned and a review of the state of the art appears necessary. The field of taxonomy remains a prominent discipline of sponge research and studies related to sponge systematics were in greater number in the Eighth World Sponge Conference (Girona, Spain, September 2010) than in any previous world sponge conferences. To understand the state of this rapidly growing field, this chapter proposes to review studies, mainly from the past decade, in sponge taxonomy, nomenclature and phylogeny. In a first part, we analyse the reasons of the current success of this field. In a second part, we establish the current sponge systematics theoretical framework, with the use of (1) cladistics, (2) different codes of nomenclature (PhyloCode vs. Linnaean system) and (3) integrative taxonomy. Sponges are infamous for their lack of characters. However, by listing and discussing in a third part all characters available to taxonomists, we show how diverse characters are and that new ones are being used and tested, while old ones should be revisited. We then review the systematics of the four main classes of sponges (Hexactinellida, Calcispongiae, Homoscleromorpha and Demospongiae), each time focusing on current issues and case studies. We present a review of the taxonomic changes since the publication of the Systema Porifera (2002), and point to problems a sponge taxonomist is still faced with nowadays. To conclude, we make a series of proposals for the future of sponge systematics. In the light of recent studies, we establish a series of taxonomic changes that the sponge community may be ready to accept. We also propose a series of sponge new names and definitions following the PhyloCode. The issue of phantom species (potential new species revealed by molecular studies) is raised, and we show how they could be dealt with. Finally, we present a general strategy to help us succeed in building a Porifera tree along with the corresponding revised Porifera classification.
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Affiliation(s)
- P Cárdenas
- Département Milieux et Peuplements Aquatiques, Muséum National d'Histoire Naturelle, UMR 7208 "BOrEA", Paris, France
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20
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Bustamante M, Carvajal C, Gottlieb B, Contreras JE, Uribe M, Melkonian E, Cárdenas P, Amadori A, Parra JA. [A new instrument for the evaluation of the medical profession. Use of the OSCE method]. Rev Med Chil 2000; 128:1039-44. [PMID: 11349493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
BACKGROUND Objective structured clinical examination has advantages over traditional oral examination of medical student. However, it is not routinely used in Chile. AIM To describe the objective structured clinical examination system and report the results of its first use with Chilean medical students. MATERIAL AND METHODS Thirteen interns ware evaluated at the end of their surgical rotation, using the objective structured clinical examination. Thirteen stations were structured for this examination: one for history taking, two for physical examination, four for problem solving and knowledge, one for radiological interpretation, one for instrumental recognition, one for skills and one for text comprehension. There were a total of 88 questions. RESULTS All students exceeded 60% of requirements. Mean approval score was 73%. The higher score was 80% and the lower 61%. Ten students had a score over 70%. The method was well accepted by teachers and students. CONCLUSIONS This first local experience with the objective structured clinical examination was successful.
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Affiliation(s)
- M Bustamante
- Departamento de Cirugía, Campus Oriente, Facultad de Medicina, Universidad de Chile
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21
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Chacín J, Cárdenas P, Lobo P, Hernández I. Secretory and metabolic effects of ethanol in the isolated amphibian gastric mucosa. Gastroenterology 1991; 100:1288-95. [PMID: 1901555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The effects of pure ethanol and some alcoholic beverages on acid secretion and metabolism were examined in the isolated toad gastric mucosa. Pure ethanol applied to the luminal side or to the submucosal side at low concentrations (2%-10%) was a potent stimulant of acid secretion, whereas high concentrations (greater than or equal to 20%) were inhibitory. Cimetidine and calcium-free solutions did not abolish the secretory effect of ethanol. Beer and wine, but not rum and whisky, caused a significant stimulation of acid secretion. Respiration was progressively increased by ethanol at concentrations between 2% and 20%. This effect was not affected by cimetidine or by SCH 28080, an inhibitor of the gastric hydrogen-potassium-stimulated adenosine triphosphatase. Ethanol (10%) significantly increased by 46% the tissue lactate-pyruvate ratio. The oxidations of glucose, butyrate, and acetate were progressively reduced by low concentrations of ethanol (5% and 10%). The results indicate that (a) low concentrations of ethanol and alcoholic beverages with low ethanol content are direct stimulants of acid secretion and (b) the secretory and metabolic effects of low concentrations of ethanol seem to be mediated via its oxidation.
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Affiliation(s)
- J Chacín
- Laboratorio de Investigaciones Gastrointestinales, Facultad de Medicina, Universidad del Zulia, Maracaibo, Venezuela
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22
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Cárdenas P, Riveros B, Martínez V. [Chronic active hepatitis induced by nitrofurantoin]. Rev Med Chil 1988; 116:1172-6. [PMID: 3267901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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23
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Chacín J, Cárdenas P, Lobo P, Subero O. Role of calcium in secretory and metabolic effects of substrates in the gastric mucosa. Am J Physiol 1986; 251:G161-8. [PMID: 3090895 DOI: 10.1152/ajpgi.1986.251.2.g161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The role of extracellular Ca2+ in the effects and oxidation of metabolic substrates was investigated in the isolated toad gastric mucosa. In the presence of lipoate, the stimulating effect of 10 mM glucose on spontaneous acid secretion was significantly reduced by 76% in Ca2+-free solutions. The inhibition was overcome by addition of 5 mM Ca2+. The increment in respiration induced by glucose was also blocked in the absence of external Ca2+. The effect of 10 mM pyruvate on acid secretion was inhibited by 37% in Ca2+-free solutions. The secretory responses induced by 10 mM butyrate and 10 mM octanoate were not significantly affected by Ca2+-free solutions. The rates of oxidation of [14C]-glucose and [14C]pyruvate were significantly reduced by incubating in Ca2+-free solutions containing 0.1 mM of EGTA. When O2 uptake and glucose oxidation were measured simultaneously in the same preparation, the increment in the rate of glucose oxidation accounted for by 43% of the total increase of respiration observed in the presence of Ca2+. The rates of oxidation of [14C]butyrate and [14C]acetate were not significantly affected by Ca2+-free solutions. The rate of oxidation of [14C]glucose exhibited saturation kinetics versus concentration and was lower in the absence of external Ca2+ under a range of glucose concentrations. Similar results were observed when the experiments were performed in the absence of external potassium to block the acid secretory process. Ca2+ stimulated the rate of glucose oxidation in a dose-dependent manner. The kinetics of 45Ca2+ efflux and 45Ca2+ uptake were not significantly affected by glucose and butyrate.(ABSTRACT TRUNCATED AT 250 WORDS)
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24
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Abstract
The substrate-level energy dependence of acid secretion was investigated in the human gastric mucosa in vitro using biopsy specimens obtained during fiberoptic gastroscopy in symptomatic patients. The oxygen consumption and the accumulation of aminopyrine were used as indexes of secretory activity. Basal and histamine-stimulated oxygen uptake by fundic biopsy specimens were not affected by medications (pethidine and diazepam) administered during gastroscopy. Under substrate-depleted conditions, the oxygen consumption and the aminopyrine accumulation of fundic mucosa were not significantly increased by histamine. Stimulation of functional activities by gastric secretagogues was observed only in the presence of exogenous substrates. The ability of various substrates to support acid formation in the presence of gastric secretagogues was evaluated. Carbohydrates were found to be effective substrates in supporting the functional responses of the tissue, with glucose being the most effective. Propionate, butyrate, beta-hydroxybutyrate, and octanoate were ineffective as substrates. Glucose by itself, but not butyrate, significantly increased oxygen uptake and aminopyrine accumulation. The results suggest that the human gastric mucosa, in vitro, has an absolute requirement for metabolic substrates to support secretory responses and that carbohydrates seem to be the preferential substrates.
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25
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Chacín J, Cárdenas P. Inhibition by cimetidine of the secretory and respiratory responses induced by theophylline and cyclic AMP in the amphibian gastric mucosa. Comp Biochem Physiol C Comp Pharmacol Toxicol 1983; 74:195-9. [PMID: 6132765 DOI: 10.1016/0742-8413(83)90174-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
1. The effects of cimetidine, a histamine H2-receptor antagonist, on acid secretory and respiratory responses induced by histamine, theophylline and dibutyryl cyclic AMP were investigated in the in vitro toad gastric mucosa. 2. Histamine- and theophylline-stimulated acid secretion was competitively inhibited by cimetidine. A significant but lesser degree of inhibition was observed on oxygen uptake. 3. Cimetidine significantly inhibited acid secretion and oxygen uptake stimulated by dibutyryl cyclic AMP. 4. The results may suggest that cimetidine may have an additional action beyond the point of cyclic AMP in the oxyntic cells.
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