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We developed a genomic surveillance program for real-time monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) in Uruguay. We report on a PCR method for SARS-CoV-2 VOCs, the surveillance workflow, and multiple independent introductions and community transmission of the SARS-CoV-2 P.1 VOC in Uruguay.
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COVID-19 , SARS-CoV-2 , Genômica , Humanos , Uruguai/epidemiologiaRESUMO
Here we report a case of septic arthritis associated with a genetically divergent Francisella philomiragia strain in a patient with chronic rheumatoid arthritis and Adult-onset Still's disease (AOSD) in Maldonado, Uruguay. In this study mass spectrometry together with whole-genome sequencing using Oxford Nanopore technology allowed for the correct identification of the etiologic agent.
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Parasite M17 leucine aminopeptidases (LAPs) have been associated with critical roles in different key functions such as the nutrition, migration, and invasion of the natural host. Native or recombinant LAP used as a vaccine antigen has proved effective to elicit protection against Fasciola hepatica infection in sheep, pointing to potential vaccine candidates against fascioliasis in ruminant species. Previously, the FhLAP1, abundantly secreted in vitro by the mature adult parasite was used as a vaccine antigen obtaining promising protection results against F. hepatica challenge in small ruminants. Here, we report the biochemical characterization of a second recombinant LAP (FhLAP2) associated with the juvenile stage of F. hepatica. FhLAP2 showed aminopeptidase activity using different synthetic substrates, including leucine, arginine, and methionine and was increased in the presence of Mn+ 2 and Mg+ 2. The activity was inhibited by bestatin, 1,10-phenanthroline, and EDTA, specific inhibitors of aminopeptidase and/or metalloproteases. Finally, the recombinant FhLAP2 functional form was tested in combination with Freund's incomplete adjuvant in an immunization trial in mice followed by an experimental challenge with F. hepatica metacercariae. The immunization with FhLAP2/FIA resulted in a significant reduction of parasite recovery compared to control groups. The immunized group elicited total specific IgG and subclasses IgG1 and IgG2 antibody responses. This study highlights the potential of a new candidate vaccine formulation with potential applications in natural ruminant hosts, especially those targeting the juvenile stage.
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Fasciola hepatica , Fasciolíase , Doenças dos Ovinos , Vacinas , Ovinos , Camundongos , Animais , Fasciolíase/prevenção & controle , Fasciolíase/veterinária , Leucil Aminopeptidase/química , Leucina , Anticorpos Anti-Helmínticos , Doenças dos Ovinos/parasitologiaRESUMO
Most biologically relevant and diagnostic mutations in the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genome have been identified in the S gene through global genomic surveillance efforts. However, large-scale whole-genome sequencing (WGS) is still challenging in developing countries due to higher costs, reagent delays and limited infrastructure. Consequently, only a small fraction of SARS-CoV-2 samples are characterized through WGS in these regions. Here, we present a complete workflow consisting of a fast library preparation protocol based on tiled amplification of the S gene, followed by a PCR barcoding step and sequencing using Nanopore platforms. This protocol facilitates fast and cost-effective identification of main variants of concern and mutational surveillance of the S gene. By applying this protocol, report time and overall costs for SARS-CoV-2 variant detection could be reduced, contributing to improved genomic surveillance programmes, particularly in low-income regions.
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COVID-19 , Nanoporos , Humanos , SARS-CoV-2/genética , Análise Custo-Benefício , COVID-19/diagnósticoRESUMO
Understanding transmission routes of SARS-CoV-2 is crucial to establish effective interventions in healthcare institutions. Although the role of surface contamination in SARS-CoV-2 transmission has been controversial, fomites have been proposed as a contributing factor. Longitudinal studies about SARS-CoV-2 surface contamination in hospitals with different infrastructure (presence or absence of negative pressure systems) are needed to improve our understanding of their effectiveness on patient healthcare and to advance our knowledge about the viral spread. We performed a one-year longitudinal study to evaluate surface contamination with SARS-CoV-2 RNA in reference hospitals. These hospitals have to admit all COVID-19 patients from public health services that require hospitalization. Surfaces samples were molecular tested for SARS-CoV-2 RNA presence considering three factors: the dirtiness by measuring organic material, the circulation of a high transmissibility variant, and the presence or absence of negative pressure systems in hospitalized patients' rooms. Our results show that: (i) There is no correlation between the amount of organic material dirtiness and SARS-CoV-2 RNA detected on surfaces; (ii) SARS-CoV-2 high transmissible Gamma variant introduction significantly increased surface contamination; (iii) the hospital with negative pressure systems was associated with lower levels of SARS-CoV-2 surface contamination and, iv) most environmental samples recovered from contaminated surfaces were assigned as non-infectious. This study provides data gathered for one year about the surface contamination with SARS-CoV-2 RNA sampling hospital settings. Our results suggest that spatial dynamics of SARS-CoV-2 RNA contamination varies according with the type of SARS-CoV-2 genetic variant and the presence of negative pressure systems. In addition, we showed that there is no correlation between the amount of organic material dirtiness and the quantity of viral RNA detected in hospital settings. Our findings suggest that SARS CoV-2 RNA surface contamination monitoring might be useful for the understanding of SARS-CoV-2 dissemination with impact on hospital management and public health policies. This is of special relevance for the Latin-American region where ICU rooms with negative pressure are insufficient.
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Coronavirus disease 2019 (COVID-19), an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, can have a wide range of clinical manifestations, ranging from asymptomatic disease to potentially life-threatening complications. Convalescent plasma therapy has been proposed as an effective alternative for the treatment of severe cases. The aim of this study was to follow a two-time renal transplant patient with severe COVID-19 treated with convalescent plasma over time from an immunologic and virologic perspective. A 42-year-old female patient, who was a two-time kidney transplant recipient, was hospitalized with COVID-19. Due to worsening respiratory symptoms, she was admitted to the intensive care unit, where she received two doses of convalescent plasma. We analyzed the dynamics of viral load in nasopharyngeal swab, saliva, and tracheal aspirate samples, before and after convalescent plasma transfusion. The levels of pro-inflammatory cytokines and antibody titers were also measured in serum samples. A significant decrease in viral load was observed after treatment in the saliva and nasopharyngeal swab samples, and a slight decrease was observed in tracheal aspirate samples. In addition, we found evidence of an increase in antibody titers after transfusion, accompanied by a decrease in the levels of several cytokines responsible for cytokine storm.
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OBJECTIVES: The emergence and spread of carbapenem resistant clones is of major concern for global health. This study aimed to characterize the first detected Klebsiella pneumoniae ST15 harboring the epidemic carbapenemase OXA-48 in South America. METHODS: During a routine colonization screening with carbapenem-resistant bacteria, one K. pneumoniae strain (CGHM01) was isolated from the urine of a hospitalized patient suffering from a neurodegenerative disease in Uruguay. We used long-read whole-genome sequencing and a phylogenomic approach to characterize the emergence of K. pneumoniae CGHM01. RESULTS: K. pneumoniae CGHM01 is a multi-drug resistant strain carrying an IncL/M plasmid that encodes the carbapenemase gene blaOXA-48 within the Tn1999.2 transposon. Also, it carries an IncR plasmid harboring a class I integron with an array of antibiotic resistance genes including the extended-spectrum beta-lactamase blaCTX-M-15. Two copies of blaCTX-M-15 were also inserted in different positions of the chromosome. CGHM01 belongs to a ST15 sublineage that likely originated in continental Spain around 2012. CONCLUSIONS: The asymptomatic carriage of this strain in the urinary tract warns of difficulties for detection and reporting of emerging carbapenem-resistant clones in new geographic areas where these are not endemic.
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Infecções por Klebsiella , Doenças Neurodegenerativas , Carbapenêmicos , Humanos , Infecções por Klebsiella/epidemiologia , Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/genética , Testes de Sensibilidade Microbiana , beta-Lactamases/genéticaRESUMO
BACKGROUND: The microbial community composition of urban environments is primarily determined by human activity. The use of metagenomics to explore how microbial communities are shaped in a city provides a novel input that can improve decisions on public health measures, architectural design, and urban resilience. Of note, the sewage system in a city acts as a complex reservoir of bacteria, pharmaceuticals, and antimicrobial resistant (AMR) genes that can be an important source of epidemiological information. Hospital effluents are rich in patient-derived bacteria and can thus readily become a birthplace and hotspot reservoir for antibiotic resistant pathogens which are eventually incorporated into the environment. Yet, the scope to which nosocomial outbreaks impact the urban environment is still poorly understood. RESULTS: In this work, we extensively show that different urban waters from creeks, beaches, sewage spillways and collector pipes enclose discrete microbial communities that are characterized by a differential degree of contamination and admixture with human-derived bacteria. The abundance of human bacteria correlates with the abundance of AMR genes in the environment, with beta-lactamases being the top-contributing class to distinguish low vs. highly-impacted urban environments. Indeed, the abundance of beta-lactamase resistance and carbapenem resistance determinants in the urban environment significantly increased in a 1-year period. This was in line with a pronounced increase of nosocomial carbapenem-resistant infections reported during the same period that was mainly driven by an outbreak-causing, carbapenemase-producing Klebsiella pneumoniae (KPC) ST-11 strain. Genome-resolved metagenomics of urban waters before and after this outbreak, coupled with high-resolution whole-genome sequencing, confirmed the dissemination of the ST-11 strain and a novel KPC megaplasmid from the hospital to the urban environment. City-wide analysis showed that geospatial dissemination of the KPC megaplasmid in the urban environment inversely depended on the sewage system infrastructure. CONCLUSIONS: We show how urban metagenomics and outbreak genomic surveillance can be coupled to generate relevant information for infection control, antibiotic stewardship, and pathogen epidemiology. Our results highlight the need to better characterize and understand how human-derived bacteria and antimicrobial resistance disseminate in the urban environment to incorporate this information in the development of effluent treatment infrastructure and public health policies. Video Abstract.
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Infecção Hospitalar , Microbiota , Humanos , Antibacterianos/farmacologia , Esgotos , Farmacorresistência Bacteriana/genética , Microbiota/genética , Hospitais , CarbapenêmicosRESUMO
Uruguay is one of the few countries in the Americas that successfully contained the coronavirus disease 19 (COVID-19) epidemic during the first half of 2020. Nevertheless, the intensive human mobility across the dry border with Brazil is a major challenge for public health authorities. We aimed to investigate the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains detected in Uruguayan localities bordering Brazil as well as to measure the viral flux across this â¼1,100 km uninterrupted dry frontier. Using complete SARS-CoV-2 genomes from the Uruguayan-Brazilian bordering region and phylogeographic analyses, we inferred the virus dissemination frequency between Brazil and Uruguay and characterized local outbreak dynamics during the first months (May-July) of the pandemic. Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 Brazilian lineages B.1.1.28 and B.1.1.33 into Uruguayan localities at the bordering region. The most probable sources of viral strains introduced to Uruguay were the Southeast Brazilian region and the state of Rio Grande do Sul. Some of the viral strains introduced in Uruguayan border localities between early May and mid-July were able to locally spread and originated the first outbreaks detected outside the metropolitan region. The viral lineages responsible for Uruguayan urban outbreaks were defined by a set of between four and 11 mutations (synonymous and non-synonymous) with respect to the ancestral B.1.1.28 and B.1.1.33 viruses that arose in Brazil, supporting the notion of a rapid genetic differentiation between SARS-CoV-2 subpopulations spreading in South America. Although Uruguayan borders have remained essentially closed to non-Uruguayan citizens, the inevitable flow of people across the dry border with Brazil allowed the repeated entry of the virus into Uruguay and the subsequent emergence of local outbreaks in Uruguayan border localities. Implementation of coordinated bi-national surveillance systems is crucial to achieve an efficient control of the SARS-CoV-2 spread across this kind of highly permeable borderland regions around the world.
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Uruguay controlled the viral dissemination during the first nine months of the SARS-CoV-2 pandemic. Unfortunately, towards the end of 2020, the number of daily new cases exponentially increased. Herein, we analyzed the country-wide genetic diversity of SARS-CoV-2 between November 2020 and April 2021. We identified that the most prevalent viral variant during the first epidemic wave in Uruguay (December 2020-February 2021) was a B.1.1.28 sublineage carrying Spike mutations Q675H + Q677H, now designated as P.6, followed by lineages P.2 and P.7. P.6 probably arose around November 2020, in Montevideo, Uruguay's capital department, and rapidly spread to other departments, with evidence of further local transmission clusters; it also spread sporadically to the USA and Spain. The more efficient dissemination of lineage P.6 with respect to P.2 and P.7 and the presence of mutations (Q675H and Q677H) in the proximity of the key cleavage site at the S1/S2 boundary suggest that P.6 may be more transmissible than other lineages co-circulating in Uruguay. Although P.6 was replaced by the variant of concern (VOC) P.1 as the predominant lineage in Uruguay since April 2021, the monitoring of the concurrent emergence of Q675H + Q677H in VOCs should be of worldwide interest.
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COVID-19/virologia , SARS-CoV-2/genética , Glicoproteína da Espícula de Coronavírus/genética , COVID-19/transmissão , Genoma Viral , Humanos , Mutação , Filogeografia , Estudos Retrospectivos , SARS-CoV-2/patogenicidade , UruguaiRESUMO
Liver fluke Fasciola hepatica remains an important agent of foodborne trematode disease producing great economic losses due to its negative effect on productivity of grazing livestock in temperate areas. The prevailing control strategies based on antihelminthic drugs are not long term sustainable due to widespread resistance. Hence, vaccination appears as an attractive option to pursue for parasite eradication.
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Fasciola hepatica/imunologia , Fasciolíase/imunologia , Vacinas/imunologia , Animais , Anti-Helmínticos/farmacologia , Antígenos de Helmintos/imunologia , Bovinos , Doenças dos Bovinos/tratamento farmacológico , Doenças dos Bovinos/imunologia , Doenças dos Bovinos/parasitologia , Fasciola hepatica/efeitos dos fármacos , Fasciolíase/tratamento farmacológico , Fasciolíase/parasitologia , Gado/imunologia , Vacinação/métodosRESUMO
Many studies have shown that the degree of organization and repetitiveness of an antigen correlates with its efficiency to induce a B-cell response and production of neutralizing antibodies. Here we describe the design of a chimeric protein based on the hexamer form of the highly immunogenic Fasciola hepatica leucine aminopeptidase as a carrier system of small peptides with potential use as a multiepitope vaccine.
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Fasciola hepatica/imunologia , Proteínas de Helminto/imunologia , Leucil Aminopeptidase/imunologia , Peptídeos/imunologia , Vacinas de Subunidades Antigênicas/imunologia , Sequência de Aminoácidos , Animais , Anticorpos Anti-Helmínticos/imunologia , Antígenos de Helmintos/imunologia , Linfócitos B/imunologia , Bovinos , Doenças dos Bovinos/imunologia , Doenças dos Bovinos/parasitologia , Epitopos de Linfócito B/imunologia , Fasciolíase/imunologia , Fasciolíase/parasitologiaRESUMO
BACKGROUND: Microbial communities present in environmental waters constitute a reservoir for antibiotic-resistant pathogens that impact human health. For this reason, a diverse variety of water environments are being analyzed using metagenomics to uncover public health threats. However, the composition of these communities along the coastal environment of a whole city, where sewage and beach waters are mixed, is poorly understood. RESULTS: We shotgun-sequenced 20 coastal areas from the city of Montevideo (capital of Uruguay) including beach and sewage water samples to characterize bacterial communities and their virulence and antibiotic resistance repertories. As expected, we found that sewage and beach environments present significantly different bacterial communities. This baseline allowed us to detect a higher prevalence and a more diverse repertory of virulence and antibiotic-resistant genes in sewage samples. Many of these genes come from well-known enterobacteria and represent carbapenemases and extended-spectrum betalactamases reported in hospital infections in Montevideo. Additionally, we were able to genotype the presence of both globally disseminated pathogenic clones and emerging antibiotic-resistant bacteria in sewage waters. CONCLUSIONS: Our study represents the first in using metagenomics to jointly analyze beaches and the sewage system from an entire city, allowing us to characterize antibiotic-resistant pathogens circulating in urban waters. The data generated in this initial study represent a baseline metagenomic exploration to guide future longitudinal (time-wise) studies, whose systematic implementation will provide useful epidemiological information to improve public health surveillance.
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Antibacterianos/farmacologia , Bactérias/classificação , Metagenômica/métodos , Esgotos/microbiologia , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/patogenicidade , Proteínas de Bactérias/genética , Praias , Estudos Transversais , Farmacorresistência Bacteriana , Humanos , Análise de Sequência de DNA , Uruguai , Microbiologia da ÁguaRESUMO
Metagenomics is providing a broad overview of bacterial functional diversity; however, culturing and biobanking are still essential for microbiology. Here, we present the Bacterial Biobank of the Urban Environment (BBUE), a sizable culture collection for long-term storage and characterization of the microbiota associated with urban environments relevant for public health.
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El avance en las terapias oncológicas trae consigo un aumento progresivo en la sobrevida de los niños con cáncer, lo que implica la necesidad de un abordaje integral en el cuidado de estos pacientes. En Chile no existen reportes formales sobre los efectos psicosociales en sobrevivientes de cáncer infantil. Con el fin de identificar el impacto psicosocial y calidad de vida, se realiza una revisión de literatura utilizando las bases de datos PubMed, Proquest Nursing Journals, EBM Reviews, Scielo y CINHAL. La búsqueda comprende textos completos de los últimos cinco años, en inglés y español. Se encuentran 91 artículos y se seleccionan 22 investigaciones cuantitativas y cualitativas. Los resultados muestran que el impacto psicosocial se manifiesta principalmente por baja autoestima e incertidumbre hacia el futuro, así como problemas de relaciones sociales en las áreas de empleo e independencia financiera, rendimiento académico y relaciones de pares y matrimonio las que se encuentran relacionadas con baja percepción en la calidad de vida. Por otra parte se observa mejor aceptación de sus limitaciones, adaptabilidad a las situaciones negativas y madurez psicológica. La experiencia de vivir con cáncer genera múltiples efectos en la vida de los niños sobrevivientes a nivel psicosocial. En Chile es fundamental que la enfermera, profesional encargada de la gestión del cuidado, realice seguimiento integral a los pacientes pediátricos desde el diagnóstico, promoviendo el autocuidado para mejorar su calidad de vida.
The advances in cancer therapies bring a progressive increase in survival of cancer among children, which implies the need for a more holistic approach of care for these patients. In Chile there are no formal reports about the psychosocial effects of childhood cancer survivors. To identify the psychosocial impact and quality of life, a literature review was done using databases: PubMed, Proquest Nursing Journals, EBM Reviews, Scielo and CINAHL. The search limits included: full texts of the last five years in English and Spanish. Ninety-one articles were found and 22 of them were selected using the criteria of having a quantitative or qualitative design. The results demostrate that the psychosocial impact is manifested mainly by low self-esteem and uncertainty toward the future, and problems of social relationships in areas such as employment, financial independence, academic performance and marriage, and relating to peers, which were related to low perceived quality of life. Also, greater acceptance of limitations, adaptability to negative situations and psychological maturity were identified. The experience of living with cancer produces multiple psychological effects in the lives of surviving children. In Chile, it is essential that the nurses in charge of child oncology care, management make a follow up of pediatric patients, beginning from the time of diagnosis, promoting self-care, and thereby improving quality of life.
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Humanos , Criança , Enfermagem Pediátrica/métodos , Qualidade de Vida/psicologia , Autocuidado , Sobreviventes de Câncer/psicologia , Transtornos de Estresse Pós-Traumáticos , Psico-Oncologia , Neoplasias/terapiaRESUMO
Antecedentes: La tuberculosis (TB) es una enfermedad infecciosa responsable de ocho millones de casos y tres millones de muertos cada año. De acuerdo a la Organización Mundial de la Salud, el conocimiento y la actitud del personal médico sobre la enfermedad se ubica como un elemento importante para el correcto desarrollo de los programas de lucha contra la TB, con especial énfasis en países de economías emergentes. Es por lo anterior que el objetivo del este trabajo es evaluar los conocimientos y actitudes en personal médico de Veracruz, México. Metodología: Se encuestó a una muestra representativa de médicos que laboran en una institución pública, identificando edad, género, especialidad médica y antigüedad. El conocimiento de TB se consideró en cinco apartados (enfermedad, diagnóstico, tratamiento, prevención y normativo), que integrados mostraron el conocimiento global; se compararon las variables del médico y el conocimiento mediante pruebas t y x ². Resultados: De los 220 médicos encuestados, solo 38 (17%) obtuvieron una evaluación global adecuada; por apartados, 142 (65%) mostraron conocimiento adecuado en prevención y 40 (18%) en enfermedad. No se observaron diferencias entre los niveles de conocimiento y las variables analizadas. El 70% de los médicos refieren a la TB como un tema poco importante en el total de sus actividades, e identificamos que el enfoque que se da a la enfermedad esté orientado hacia la prevención. Conclusión: Se observó un bajo conocimiento global; sin embargo, se ubicaron los apartados que deberían ser reforzados para generar un mejor entendimiento y en consecuencia un cambio de actitud hacia la enfermedad. [Aguilar-Nájera MJ, Cortés-Salazar CS, Zenteno-Cuevas R. Conocimiento y actitudes sobre tuberculosis en personal médico de Veracruz, México. MedUNAB 2008; 11: 213-217].
Background: Tuberculosis (TB) is an infectious disease responsible of 8 millions of cases and 3 millions of deaths each year. According to the World Health Organization, the knowledge and attitude of the medical staff about the disease is considered a very important element for the correct development of the fight programs against TB, with special emphasis in emerging countries. The main goal of this work is to evaluate the knowledge and attitudes of medical staff from Veracruz, Mexico. Methods: A representative sample of physicians that works in a public institution were survey, identifying age, gender, medical specialty and years of service. TB knowledge was evaluated by 5 issues (disease, diagnosis, treatment, prevention, and normative), that integrated show the global knowledge. The variables from the physicians and knowledge were compared by t and X² test. Results: From 220 surveyed physicians, only 38 (17%) obtain an adequated global evaluation; by issues, 142 (65%) show an adequate knowledge in prevention, and only 40 (18%) in disease. No differences were observed between the knowledge level and the variables analyzed. Beside 70% of the doctors mention that the TB is an aspect with minimal transcendence in all their activities; additionally, we found their focus to TB is more oriented to prevention. Conclusion: We identified the issues of TB that need to be reinforced in order to induce in the doctors a better understanding of illness and, in consequence, a change of attitude toward TB. [Aguilar-Nájera MJ, Cortés-Salazar CS, Zenteno-Cuevas R. Knowledge and attitudes about tuberculosis in medical staff from Veracruz, Mexico. MedUNAB 2008; 11:213-217].