An empirical test of the estimation of historical effective population size using Drosophila melanogaster

The availability of a large number of high-density markers (SNPs) allows the estimation of historical effective population size (Ne) from linkage disequilibrium between loci. A recent refinement of methods to estimate historical Ne from the recent past has been shown to be rather accurate with simulation data. The method has also been applied to real data for numerous species. However, the simulation data cannot encompass all the complexities of real genomes, and the performance of any estimation method with real data is always uncertain, as the true demography of the populations is not known. Here, we carried out an experimental design with Drosophila melanogaster to test the method with real data following a known demographic history. We used a population maintained in the laboratory with a constant census size of about 2800 individuals and subjected the population to a drastic decline to a size of 100 individuals. After a few generations, the population was expanded back to the previous size and after a few further generations again expanded to twice the initial size. Estimates of historical Ne were obtained with the software GONE both for autosomal and X chromosomes from samples of 17 individuals sequenced for the whole genome. Estimates of the historical effective size were able to infer the patterns of changes that occurred in the populations showing generally good performance of the method. We discuss the limitations of the method and the application of the software carried out so farMinisterio de Ciencia, Innovación y Universidades | Ref. PID2020-114426GB- C21Ministerio de Educación, Cultura y Deporte | Ref. FPU16/02299Ministerio de Ciencia, Innovación y Universidades | Ref. FPU18/04642Universidade de Vigo/CISUG | Ref. Financiamiento de acceso abiertoCRUE-CSIC | Ref. Financiamiento de acceso abiertoXunta de Galicia | Ref. ED431C 2020-0

Long-term exhaustion of the inbreeding load in Drosophila melanogaster

Inbreeding depression, the decline in fitness of inbred individuals, is a ubiquitous phenomenon of great relevance in evolutionary biology and in the fields of animal and plant breeding and conservation. Inbreeding depression is due to the expression of recessive deleterious alleles that are concealed in heterozygous state in noninbred individuals, the so-called inbreeding load. Genetic purging reduces inbreeding depression by removing these alleles when expressed in homozygosis due to inbreeding. It is generally thought that fast inbreeding (such as that generated by full-sib mating lines) removes only highly deleterious recessive alleles, while slow inbreeding can also remove mildly deleterious ones. However, a question remains regarding which proportion of the inbreeding load can be removed by purging under slow inbreeding in moderately large populations. We report results of two long-term slow inbreeding Drosophila experiments (125–234 generations), each using a large population and a number of derived lines with effective sizes about 1000 and 50, respectively. The inbreeding load was virtually exhausted after more than one hundred generations in large populations and between a few tens and over one hundred generations in the lines. This result is not expected from genetic drift alone, and is in agreement with the theoretical purging predictions. Computer simulations suggest that these results are consistent with a model of relatively few deleterious mutations of large homozygous effects and partially recessive gene actionAgencia Estatal de Investigación (AEI) | Ref. PGC2018-095810-B-I00Agencia Estatal de Investigación (AEI) | Ref. PID2020-114426GB-C21Xunta de Galicia | Ref. ED431C 2020-0

Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation

Natural selection often produces parallel phenotypic changes in response to a similar adaptive challenge. However, the extent to which parallel gene expression differences and genomic divergence underlie parallel phenotypic traits and whether they are decoupled or not remains largely unexplored. We performed a population genomic study of parallel ecological adaptation among replicate ecotype pairs of the rough periwinkle (Littorina saxatilis) at a regional geographical scale (NW Spain). We show that genomic changes underlying parallel phenotypic divergence followed a complex pattern of both repeatable differences and of differences unique to specific ecotype pairs, in which parallel changes in expression or sequence are restricted to a limited set of genes. Yet, the majority of divergent genes were divergent either for gene expression or coding sequence, but not for both simultaneously. Overall, our findings suggest that divergent selection significantly contributed to the process of parallel molecular differentiation among ecotype pairs, and that changes in expression and gene sequence underlying phenotypic divergence could, at least to a certain extent, be considered decoupled processesMinisterio de Economía y Competitividad | Ref. BFU2013- 44635-PMinisterio de Economía y Competitividad | Ref. CGL2016-75482-PMinisterio de Economía y Competitividad | Ref. CGL2016-75904-C2-1Xunta de Galicia | Ref. ED431C 2016-037Xunta de Galicia | Ref. INCITE09 310 006 PRSwedish Research Councils VR | Ref. Linnaeus grant Formas 217-2008-171

Protocolo nacional de vigilancia, atención y control de cólera (2022)

El cólera es una de las enfermedades más antiguas de la humanidad, pero es hasta inicios del siglo XIX que se dispone de un mayor conocimiento de sus causas, formas de transmisión y tratamiento. El mecanismo de transmisión del Vibrio cholerae se da por medio de las heces de personas infectadas, por lo cual, la enfermedad se disemina rápidamente si no se cuenta con un manejo apropiado del agua potable, sistemas de alcantarillado sanitario y de tratamiento. La enfermedad se adquiere al ingerir agua o alimentos contaminados o mediante contacto de persona a persona. Aunque la enfermedad generalmente es benigna o incluso en un 75 % de los casos pueden cursar en forma asintomática, se reporta que un 5 % de las personas enfermas requieren atención urgente y un 2 % desarrollan formas graves. Con atención oportuna y rehidratación apropiada la tasa de letalidad es inferior al 1 %. En Costa Rica, los primeros casos de la epidemia de cólera de 1991 en América y Suramérica se detectaron en 1992, con un último caso en el año 1997. En 1998 la OMS declara una reemergencia por cólera en la región de las Américas y en los años 2010, 2017 y en octubre 2022 se han presentado brotes epidémicos de cólera en Haití. Ante la situación de riesgo por diseminación entre países de la región, Costa Rica procedió a activar los planes de preparación y respuesta, se intensificó el sistema de vigilancia y se actualizaron los lineamientos que se presentan en este protocolo. La promoción de prácticas apropiada de higiene mediante el lavado de manos y consumo de alimentos adecuadamente cocidos y lavados, así como la garantía de dotación de agua segura para consumo humano son condiciones esenciales para prevenir el cólera. Agradecemos a todos los profesionales y equipos de trabajo que brindaron información y valiosos aportes a la actualización de este protocolo. La puesta en práctica de los conceptos y procedimientos contenidos en este documento, son condiciones claves que permitirán prevenir, detectar, atender y controlar la enfermedad del cólera.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Instituto de Investigaciones en Salud (INISA

International Nosocomial Infection Control Consortium report, data summary of 50 countries for 2010-2015: Device-associated module

•We report INICC device-associated module data of 50 countries from 2010-2015.•We collected prospective data from 861,284 patients in 703 ICUs for 3,506,562 days.•DA-HAI rates and bacterial resistance were higher in the INICC ICUs than in CDC-NHSN's.•Device utilization ratio in the INICC ICUs was similar to CDC-NHSN's. Background: We report the results of International Nosocomial Infection Control Consortium (INICC) surveillance study from January 2010-December 2015 in 703 intensive care units (ICUs) in Latin America, Europe, Eastern Mediterranean, Southeast Asia, and Western Pacific. Methods: During the 6-year study period, using Centers for Disease Control and Prevention National Healthcare Safety Network (CDC-NHSN) definitions for device-associated health care-associated infection (DA-HAI), we collected prospective data from 861,284 patients hospitalized in INICC hospital ICUs for an aggregate of 3,506,562 days. Results: Although device use in INICC ICUs was similar to that reported from CDC-NHSN ICUs, DA-HAI rates were higher in the INICC ICUs: in the INICC medical-surgical ICUs, the pooled rate of central line-associated bloodstream infection, 4.1 per 1,000 central line-days, was nearly 5-fold higher than the 0.8 per 1,000 central line-days reported from comparable US ICUs, the overall rate of ventilator-associated pneumonia was also higher, 13.1 versus 0.9 per 1,000 ventilator-days, as was the rate of catheter-associated urinary tract infection, 5.07 versus 1.7 per 1,000 catheter-days. From blood cultures samples, frequencies of resistance of Pseudomonas isolates to amikacin (29.87% vs 10%) and to imipenem (44.3% vs 26.1%), and of Klebsiella pneumoniae isolates to ceftazidime (73.2% vs 28.8%) and to imipenem (43.27% vs 12.8%) were also higher in the INICC ICUs compared with CDC-NHSN ICUs. Conclusions: Although DA-HAIs in INICC ICU patients continue to be higher than the rates reported in CDC-NSHN ICUs representing the developed world, we have observed a significant trend toward the reduction of DA-HAI rates in INICC ICUs as shown in each international report. It is INICC's main goal to continue facilitating education, training, and basic and cost-effective tools and resources, such as standardized forms and an online platform, to tackle this problem effectively and systematically