Concordance analysis between different methodologies used for identification of oral isolates of Candida species

Introducción: La clasificación a nivel de especies de las levaduras del género Candida de origen clínico es fundamental para el diagnóstico y la instauración de un adecuado tratamiento para el paciente. Se realizó un estudio de concordancia de cinco metodologías usadas para la identificación de aislamientos orales de Candida spp en Colombia. Métodos: Sesenta y siete aislamientos de Candida spp fueron identificados a nivel de especie utilizando; API® 20 C AUX‚ Vitek® 2 Compact, MALDI TOF (Vitek® MS y Microflex®) y una prueba molecular, PCR Panfungal y secuenciación. Un análisis del costo comercial y tiempo de procesamiento de las muestras por cada método fue realizado mediante el análisis gráfico de ambas variables. Resultados: La PCR Panfungal y secuenciación diferenció 12 especies de Candida ‚ los métodos Vitek® MS y Microflex® identificaron 9 especies y los métodos API® 20 C AUX y Vitek® 2 Compact identificaron 8 especies. El análisis de Kappa ponderado (wK) demostró una concordancia alta entre los métodos PCR Panfungal y secuenciación‚ Vitek® MS‚ Microflex® y API® 20 C AUX‚ concordancias agrupadas en las categorías buena y muy buena (wK 0.62-0.93); los Kp que involucraron el método Vitek® 2 Compact presentaron concordancias moderadas o buenas frente a los otros métodos (wK 0.56-0.73). Las metodologías basadas en MALDI TOF MS requirieron 4 minutos para generar un resultado y el método Microflex® fue el método que en nuestro medio presentó el menor precio de venta del servicio. Conclusión: Los métodos evaluados presentaron una alta concordancia en sus resultados‚ siendo más alta para los métodos moleculares y las metodologías basadas en MALDI TOF MS; estas últimas son metodologías más rápidas, económicas y precisas, las cuales se presentan como alternativas prometedoras para la identificación rutinaria de especies de levaduras del género Candida.Q3Q3Artículo original160-167Background: The yeasts species determination is fundamental not only for an accurate diagnosis but also for establishing a suitable patient treatment. We performed a concordance study of five methodologies for the species identification of oral isolates of Candida in Colombia. Methods: Sixty-seven Candida isolates were tested by; API® 20C-AUX, Vitek®2 Compact, Vitek®MS, Microflex® and a molecular test (panfungal PCR and sequencing). The commercial cost and processing time of the samples was done by graphical analysis. Results: Panfungal PCR differentiated 12 species of Candida, Vitek®MS and Microflex® methods identified 9 species, and API® 20C-AUX and Vitek®2 Compact methods identified 8 species each. Weighted Kappa (wK) showed a high agreement between Panfungal PCR, Vitek®MS, Microflex® and API® 20C-AUX (wK 0.62-0.93). The wK that involved the Vitek®2 Compact method presented moderate or good concordances compared with the other methods (wK 0.56-0.73). Methodologies based on MALDI TOF MS required 4 minutes to generate results and the Microflex® method had the lowest selling price. Conclusion: The methods evaluated showed high concordance in their results, being higher for the molecular methods and the methodologies based on MALDI TOF. The latter are faster and cheaper, presenting as promising alternatives for the routine identification of yeast species of the genus Candida

Senda Darwin Biological Station: Long-term ecological research at the interface between science and society

Indexación: Web of Science; Scielo.La Estación Biológica Senda Darwin (EBSD) constituye un centro de investigación inmerso en el paisaje rural del norte de la Isla de Chiloé (42º S), donde fragmentos del bosque siempreverde original coexisten con praderas de uso ganadero, turberas de Sphagnum, matorrales sucesionales, plantaciones de Eucalyptus y otras formaciones de origen antropogénico. Desde 1994 hemos realizado estudios de largo plazo centrados en algunas especies de plantas (e.g., Pilgerodendron uviferum D. Don) y animales (e.g., Aphrastura spinicauda Gmelin, Dromiciops gliroides [Thomas]) catalogados como amenazados o escasamente conocidos y en ecosistemas nativos de importancia regional y global (e.g., turberas de Sphagnum, bosque Valdiviano y Nordpatagónico). Las investigaciones han considerado las respuestas de las especies y de los ecosistemas frente al cambio antropogénico del paisaje y cambio climático, así como los efectos de diferentes formas de manejo. Este escenario es semejante al de otras regiones de Chile y Latinoamérica lo que da generalidad a nuestros resultados y modelos. En este período, investigadores asociados a la EBSD han producido más de un centenar de publicaciones en revistas nacionales e internacionales y 30 tesis de pre y postgrado. Entendiendo el papel clave de los seres humanos en los procesos ecológicos de la zona rural, la EBSD ha desarrollado un programa de educación ecológica y vinculación del avance científico con la sociedad local y nacional. La integración de la EBSD a la naciente red de Sitios de Estudios Socio-Ecológicos de Largo Plazo en Chile consolidará y fortalecerá la investigación básica y aplicada que realizamos para proyectarla hacia la siguiente década.Senda Darwin Biological Station (SDBS) is a field research center immersed in the rural landscape of northern Chiloé island (42º S), where remnant patches of the original evergreen forests coexist with open pastures, secondary successional shrublands, Sphagnum bogs, Eucalyptus plantations and other anthropogenic cover types, constituting an agricultural frontier similar to other regions in Chile and Latin America. Since 1994, we have conducted long-term research on selected species of plants (e.g., Pilgerodendron uviferum) and animals (e.g., Aphrastura spinicauda, Dromiciops glirioides) that are considered threatened, poorly known or important for their ecological functions in local ecosystems, and on ecosystems of regional and global relevance (e.g., Sphagnum bogs, North Patagonian and Valdivian rain forests). Research has assessed the responses of species and ecosystems to anthropogenic land-use change, climate change, and the impact of management. During this period, more than 100 scientific publications in national and international journals, and 30 theses (graduate and undergraduate) have been produced by scientists and students associated with SDBS. Because of our understanding of the key role that humans play in ecological processes at this agricultural frontier, since the establishment of SDBS we have been committed to creative research on the communication of science to society and ecological education. The integration of SDBS to the nascent Chilean network of long-term socio-ecological research will consolidate and strengthen basic and applied research to project our work into the next decade.http://ref.scielo.org/vbm4r

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality

Autoantibodies against type I IFNs in patients with critical influenza pneumonia

In an international cohort of 279 patients with hypoxemic influenza pneumonia, we identified 13 patients (4.6%) with autoantibodies neutralizing IFN-alpha and/or -omega, which were previously reported to underlie 15% cases of life-threatening COVID-19 pneumonia and one third of severe adverse reactions to live-attenuated yellow fever vaccine. Autoantibodies neutralizing type I interferons (IFNs) can underlie critical COVID-19 pneumonia and yellow fever vaccine disease. We report here on 13 patients harboring autoantibodies neutralizing IFN-alpha 2 alone (five patients) or with IFN-omega (eight patients) from a cohort of 279 patients (4.7%) aged 6-73 yr with critical influenza pneumonia. Nine and four patients had antibodies neutralizing high and low concentrations, respectively, of IFN-alpha 2, and six and two patients had antibodies neutralizing high and low concentrations, respectively, of IFN-omega. The patients' autoantibodies increased influenza A virus replication in both A549 cells and reconstituted human airway epithelia. The prevalence of these antibodies was significantly higher than that in the general population for patients 70 yr of age (3.1 vs. 4.4%, P = 0.68). The risk of critical influenza was highest in patients with antibodies neutralizing high concentrations of both IFN-alpha 2 and IFN-omega (OR = 11.7, P = 1.3 x 10(-5)), especially those <70 yr old (OR = 139.9, P = 3.1 x 10(-10)). We also identified 10 patients in additional influenza patient cohorts. Autoantibodies neutralizing type I IFNs account for similar to 5% of cases of life-threatening influenza pneumonia in patients <70 yr old

Lack of adequate seed supply is a major bottleneck for effective ecosystem restoration in Chile: friendly amendment to Bannister et al. (2018)

We argue that the need for a quality seed supply chain is a major bottleneck for the restoration of Chile's native ecosystems, thus supplementing the list of bottlenecks proposed by Bannister et al. in 2018. Specifically, there is a need for defining seed transfer zones, developing standards and capacities for properly collecting and storing seeds, reducing information gaps on seed physiology and longevity, and implementing an efficient seed supply chain with certification of seed origin and quality. Without such capacities, countries are unlikely to meet their restoration commitments. Although we focus on bottlenecks in Chile, the issues we raise are relevant to other countries and thus the global agenda for ecological restoration

Senda Darwin Biological Station: Long-term ecological research at the interface between science and society Estación Biológica Senda Darwin: Investigación ecológica de largo plazo en la interfase ciencia-sociedad

Senda Darwin Biological Station (SDBS) is a field research center immersed in the rural landscape of northern Chiloé island (42° S), where remnant patches of the original evergreen forests coexist with open pastures, secondary successional shrublands, Sphagnum bogs, Eucalyptus plantations and other anthropogenic cover types, constituting an agricultural frontier similar to other regions in Chile and Latin America. Since 1994, we have conducted long-term research on selected species of plants (e.g., Pilgerodendron uviferum) and animals (e.g., Aphrastura spinicauda, Dromiciops glirioides) that are considered threatened, poorly known or important for their ecological functions in local ecosystems, and on ecosystems of regional and global relevance (e.g., Sphagnum bogs, North Patagonian and Valdivian rain forests). Research has assessed the responses of species and ecosystems to anthropogenic land-use change, climate change, and the impact of management. During this period, more than 100

Estación Biológica Senda Darwin: Investigación ecológica de largo plazo en la interfase ciencia-sociedad Senda Darwin Biological Station: Long-term ecological research at the interface between science and society

La Estación Biológica Senda Darwin (EBSD) constituye un centro de investigación inmerso en el paisaje rural del norte de la Isla de Chiloé (42º S), donde fragmentos del bosque siempreverde original coexisten con praderas de uso ganadero, turberas de Sphagnum, matorrales sucesionales, plantaciones de Eucalyptus y otras formaciones de origen antropogénico. Desde 1994 hemos realizado estudios de largo plazo centrados en algunas especies de plantas (e.g., Pilgerodendron uviferum D. Don) y animales (e.g., Aphrastura spinicauda Gmelin, Dromiciops gliroides [Thomas]) catalogados como amenazados o escasamente conocidos y en ecosistemas nativos de importancia regional y global (e.g., turberas de Sphagnum, bosque Valdiviano y Nordpatagónico). Las investigaciones han considerado las respuestas de las especies y de los ecosistemas frente al cambio antropogénico del paisaje y cambio climático, así como los efectos de diferentes formas de manejo. Este escenario es semejante al de otras regiones de Chile y Latinoamérica lo que da generalidad a nuestros resultados y modelos. En este período, investigadores asociados a la EBSD han producido más de un centenar de publicaciones en revistas nacionales e internacionales y 30 tesis de pre y postgrado. Entendiendo el papel clave de los seres humanos en los procesos ecológicos de la zona rural, la EBSD ha desarrollado un programa de educación ecológica y vinculación del avance científico con la sociedad local y nacional. La integración de la EBSD a la naciente red de Sitios de Estudios Socio-Ecológicos de Largo Plazo en Chile consolidará y fortalecerá la investigación básica y aplicada que realizamos para proyectarla hacia la siguiente década.Senda Darwin Biological Station (SDBS) is a field research center immersed in the rural landscape of northern Chiloé island (42º S), where remnant patches of the original evergreen forests coexist with open pastures, secondary successional shrublands, Sphagnum bogs, Eucalyptus plantations and other anthropogenic cover types, constituting an agricultural frontier similar to other regions in Chile and Latin America. Since 1994, we have conducted long-term research on selected species of plants (e.g., Pilgerodendron uviferum) and animals (e.g., Aphrastura spinicauda, Dromiciops glirioides) that are considered threatened, poorly known or important for their ecological functions in local ecosystems, and on ecosystems of regional and global relevance (e.g., Sphagnum bogs, North Patagonian and Valdivian rain forests). Research has assessed the responses of species and ecosystems to anthropogenic land-use change, climate change, and the impact of management. During this period, more than 100 scientific publications in national and international journals, and 30 theses (graduate and undergraduate) have been produced by scientists and students associated with SDBS. Because of our understanding of the key role that humans play in ecological processes at this agricultural frontier, since the establishment of SDBS we have been committed to creative research on the communication of science to society and ecological education. The integration of SDBS to the nascent Chilean network of long-term socio-ecological research will consolidate and strengthen basic and applied research to project our work into the next decade