Classification of Dairy Farms According to Intensification of Production Based on a New Management Model

This study took place between 2011 and 2015 in order to classify dairy farms according to the scope of production intensification, based on a new management model. The study lasted five years, and it covered 90 local farms in Jimaguayú-Camagüey, and comprised 450 cases. The information was collected through interviews to farmers in their working places. Production intensification indicators were chosen for classification. Principal Component Analysis was used, which resulted in three new dimensions: areas, diversity and supplies. Finally, the sample was classified by k means clustering analysis, depending on every dimension and production intensification. Concerning the areas, the mid and mid-high categories prevailed. The opposite was observed in diversification and supplies, where the two former engulfed most cases, with low and mid values for their indicators

Rapid and accurate detection of the SARS-CoV-2 omicron variant with a CRISPR-Cas12a reaction in the RT-qPCR Pot

Gene sequencing in back of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the current approach for discriminating infections produced by different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in the clinic. However, sequencing is often a time-consuming step, which hinders the deployment of a very fast response during a pandemic. Here, we propose to run a CRISPR-Cas12a reaction after completing the RT-qPCR and in the very same pot to detect with high specificity genetic marks characterizing variants of concern. A crRNA was appropriately designed to detect the S gene of the SARS-CoV-2 Omicron BA.1 variant. A significant response with >20-fold dynamic range was obtained for the Omicron BA.1 S gene, while the Delta S gene did not produce any detectable signal. The sensitivity of the method was analyzed with a series of diluted samples and different Cas12a nucleases. A correlation between the RT-qPCR CT values and the CRISPR-Cas12a reaction signals was observed. Variant discrimination with the CRISPR-Cas12a reaction was possible in some minutes with high accuracy from patient samples. In conclusion, CRISPR-Cas systems seem ready to be exploited in the clinic to boost personalized diagnoses and accelerate epidemiological surveillance in a cost-effective way.Work supported by Generalitat Valenciana (GVA-COVID19/2021/036), Ministerio de Ciencia e Innovación (PDC2022−133941-I00; cofunded by NextGenerationEU), CRUE and Banco Santander (Fondo Supera Covid-19), CSIC PTI Salud Global (NextGenerationEU Fund, regulation 2020/2094), and IDIVAL (INNVAL21/13)

Clasificación de fincas lecheras según dimensiones de la intensificación productiva en un nuevo modelo de gestión.

El trabajo se desarrolló entre 2011 al 2015 con el objetivo clasificar fincas lecheras según dimensiones de la intensificación productiva en  un nuevo modelo de gestión. Fueron seleccionadas 90 fincas de la región Jimaguayú-Camagüey, quedando conformada la muestra por 450 casos, pertenecientes a cinco años de estudio. La información se obtuvo a través de entrevistas a los productores en las áreas de trabajo. Para la clasificación fueron seleccionados indicadores de intensificación productiva; se aplicó el análisis de componente principal, con lo que se obtuvieron tres nuevas dimensiones, denominadas áreas, diversidad e insumos; finalmente fue clasificada la muestra mediante un análisis de conglomerados k-means clustering, en correspondencia con cada dimensión de la intensificación produ c-tiva. En relación a las áreas se observó un predominio para las categorías de media y media-alta, no así en la diversi-ficación y los insumos, donde las dos primeras agruparon la mayor cantidad de casos, con valores bajos y medios, para los indicadores que la forman.Classification of Dairy Farms According to Dimensions of Production Intensification Based on a New Management Model.ABSTRACTThis study took place between 2011 and 2015 in order to classify dairy farms according to the scope of production intensification based on a new management model. The study  lasted five years, and  comprised 90  local farms in Jimaguayú-Camagüey, which included a sample of 450 cases. The information was collected through interviews to farmers in their working places. Production intensification indicators were chosen for classification. Principal Com-ponent Analysis was used, which resulted in three new dimensions, named areas, diversity and supplies. Finally, the sample was classified by k means clustering conglomerate analysis, depending on every dimension and production intensification. Regarding the areas, the mid and mid-high categories were observed to prevail. The opposite was ob-served in diversification and supplies, where the two former  engulfed  most cases, with low and mid values for their indicators

Induction of SARS-CoV-2-Specific IgG and IgA in Serum and Milk with Different SARS-CoV-2 Vaccines in Breastfeeding Women: A Cross-Sectional Study in Northern Spain

Breastfeeding mothers were excluded from the clinical trials conducted for vaccines against SARS-CoV-2. Since the start of the vaccination, some doubts have arisen regarding its compatibility with breastfeeding. The aim of this study was to analyse the presence of anti-SARS-CoV-2 antibodies in breast milk and serum (IgG and IgA) of vaccinated breastfeeding women. The main variables of the observational study were: adverse related events after vaccination and determination of the presence of IgG and IgA isotypes antibodies in serum and in breast milk of vaccinated women against the SARS-CoV-2 antigens. Results: 110 breastfeeding mothers were included; 70 women (63.6%) were vaccinated with two doses of BNT162b2, 20 women (18.2%) with two doses of mRNA-1273, and 20 women (18.2%) with a single dose of ChAdOx1-S. Regarding adverse reactions and vaccine safety, 38 women had no adverse reactions; 20 (18.2%) had general malaise or adenopathies; 10 (9.1%) had a headache; and 7 (6.4%) had fever. When analysing IgG antibodies, significantly higher levels of antibodies were found in serum and breast milk from mothers vaccinated with BNT162b2 or mRNA-1273 vs. ChAdOx1-S (p < 0.001 and p = 0.001, respectively). Analysing IgA antibodies, significant differences were found when comparing mean values in serum from mothers vaccinated with BNT162b2 or mRNA-1273 vs. ChAdOx1-S (0.12, 0.16, and 0.02, respectively; p < 0.001) and breast milk of mothers vaccinated when comparing BNT16b2 vs. ChAdOx1-S. All vaccinated breastfeeding mothers had serum anti-S1 IgG antibodies in response to vaccination against SARS-CoV-2, regardless of the commercial vaccine administered. Conclusions: the anti-SARS-CoV-2 vaccines were well tolerated by the mothers and the breastfed infant. In addition, breastfeeding mothers offer their infants IgA and IgG isotype antibodies directed against SARS-CoV-2 protein S in breast milk

Automatic classification of Candida species using Raman spectroscopy and machine learning

One of the problems that most affect hospitals is infections by pathogenic microorganisms. Rapid identification and adequate, timely treatment can avoid fatal consequences and the development of antibiotic resistance, so it is crucial to use fast, reliable, and not too laborious techniques to obtain quick results. Raman spectroscopy has proven to be a powerful tool for molecular analysis, meeting these requirements better than traditional techniques. In this work, we have used Raman spectroscopy combined with machine learning algorithms to explore the automatic identification of eleven species of the genus Candida, the most common cause of fungal infections worldwide. The Raman spectra were obtained from more than 220 different measurements of dried drops from pure cultures of each Candida species using a Raman Confocal Microscope with a 532 nm laser excitation source. After developing a spectral preprocessing methodology, a study of the quality and variability of the measured spectra at the isolate and species level, and the spectral features contributing to inter-class variations, showed the potential to discriminate between those pathogenic yeasts. Several machine learning and deep learning algorithms were trained using hyperparameter optimization techniques to find the best possible classifier for this spectral data, in terms of accuracy and lowest possible overfitting. We found that a one-dimensional Convolutional Neural Network (1-D CNN) could achieve above 80 % overall accuracy for the eleven classes spectral dataset, with good generalization capabilities.This work was supported by the R + D projects INNVAL19/17 (funded by Instituto de Investigación Valdecilla-IDIVAL), PID2019-107270RB-C21 (funded by MCIN/ AEI /10.13039/501100011033) and by Plan Nacional de I + D + and Instituto de Salud Carlos III (ISCIII), Subdirección General de Redes y Centros de Investigación Cooperativa, Ministerio de Ciencia, Innovación y Universidades, Spanish Network for Research in Infectious Diseases (REIPI RD16/0016/0007), CIBERINFEC (CB21/13/00068), CIBER-BBN (BBNGC1601), cofinanced by European Development Regional Fund “A way to achieve Europe”. A. A. O.-S was financially supported by the Miguel Servet II program (ISCIII-CPII17-00011)

Epitopes for Multivalent Vaccines Against Listeria, Mycobacterium and Streptococcus spp: A Novel Role for Glyceraldehyde-3-Phosphate Dehydrogenase

The glycolytic enzyme and bacterial virulence factor of Listeria monocytogenes, the glyceraldehyde-3-phosphate dehydrogenase (GAPDH, Lmo2459), ADP-ribosylated the small GTPase, Rab5a, and blocked phagosome maturation. This inhibitory activity localized within the NAD binding domain of GAPDH at the N-terminal 1?22 peptides, also conferred listeriosis protection when used in dendritic cell-based vaccines. In this study, we explore GAPDH of Listeria, Mycobacterium, and Streptococcus spp. taxonomic groups to search for epitopes that confer broad protection against pathogenic strains of these bacteria. GAPDH multivalent epitopes are selected if they induce inhibitory actions and wide-ranging immune responses. Proteomic isolation of GAPDH from dendritic cells infected with Listeria, Mycobacterium, or Streptococcus confirmed similar enzymatic, Rab5a inhibitory and immune stimulation abilities. We identified by bioinformatics and functional analyses GAPDH N-terminal 1?22 peptides from Listeria, Mycobacterium, and Streptococcus that shared 95% sequence homology, enzymatic activity, and B and T cell immune domains. Sera obtained from patients or mice infected with hypervirulent pathogenic Listeria, Mycobacterium, or Streptococcus presented high levels of anti-GAPDH 1?22 antibodies and Th2 cytokines. Monocyte derived dendritic cells from healthy donors loaded with GAPDH 1?22 peptides from Listeria, Mycobacterium, or Streptococcus showed activation patterns that correspond to cross-immunity abilities. In summary, GAPDH 1?22 peptides appeared as putative candidates to include in multivalent dendritic based vaccine platforms for Listeria, Mycobacterium, or Streptococcus

Repetition of microbiological tests in suspect of SARS-CoV-2 infection: utility of a score based on clinical probability

Objective: The diagnosis of SARS-CoV-2 infection presents some limitations. RT-PCR in nasopharyngeal swabs is considered the gold standard for the diagnosis, although it can have false negative results. We aimed to analyze the accuracy of repeating nasopharyngeal swabs based on different clinical probabilities. Methods: Retrospective observational study of the first patients admitted to a two COVID Internal Medicine wards at the University Hospital Marqués de Valdecilla, Santander, from March to April 2020. RT-PCR targering E, N, RdRP and ORFab1 genes and antibody tests detecting IgG. Results: A total of 145 hospitalized patients with suspected SARS-Cov2 infection were admitted and in 98 (67.5%) diagnosis was confirmed. The independent predictive variables for SARS-CoV-2 infection were: epidemiological contact, clinical presentation as pneumonia, absence of pneumonia in the last year, onset of symptoms > 7 days, two or more of the following symptoms -dyspnea, cough or fever- and serum lactate dehydrogenase levels >350 U/L (p<0.05). A score based on these variables yielded an AUC-ROC of 0.89 (CI95%, 0.831-0.946; p<0.001). The accuracy of the first nasopharyngeal swabs was 54.9%. Repeating nasopharyngeal swabs two or three times allows to detect an additional 16% of positive cases. The overall accuracy of successive RT-PCR tests in patients with low pre-test probability was <5%. Conclusions: We have defined a pre-test probability score based on epidemiological and clinical data with a high accuracy for diagnosis of SARS-CoV-2. Repeating nasopharyngeal swabs avoids sampling errors, but only in medium of high probability pre-test clinical scenarios

COVID-19 mRNA Based Vaccine Immune-Response Assessment in Nursing Home Residents for Public Health Decision

Nursing home residents (NHR) have been targeted as a vaccination priority due to their higher risk of worse outcome after COVID-19 infection. The mRNA-based vaccine BTN2b2 was first approved in Europe for NHRs. The assessment of the specific vaccine immune response (both humoral and cellular) at long term in NHRs has not been addressed yet. A representative sample of 624 NHR subjects in Northern region of Spain was studied to assess immune response against full vaccination with BTN2b2. The anti-S1 antibody levels and specific T cells were measured at two and six months after vaccination. 24.4% of NHR had a previous infection prior to vaccination. The remaining NHR were included in the full vaccination assessment group (FVA). After two months, a 94.9% of the FVA presented anti-S1 antibodies, whereas those seronegative without specific cellular response were 2.54%. At long-term, the frequency of NHR within the FVA group with anti-S1 antibodies at six months were 88.12% and the seronegative subjects without specific cellular response was 8.07%. The cellular immune assays complement the humoral test in the immune vaccine response assessment. Therefore, the cellular immune assessment in NHRs allows for the fine tuning of those seronegative subjects with potential competent immune responses against the vaccine

Factores que influyen en la duración de la vida reproductiva útil en rebaños bovinos de la provincia de Camagüey, Cuba

218 cows from five different races or crosses were sampled to characterize female bovine reproductive span. Animals were dis- tributed into seven herds out of three livestock centers in Camagüey province. Interval from reproduction cycle beginning to pregnancy by insemination to reproductive span (period between the beginning and the end of the reproduction cycle) was esti- mated. The analysis was carried out through a general lineal pattern, which showed lower values for total number of deliveries, age at the end of the reproduction cycle, interval from reproduction cycle beginning to pregnancy, and age at first calving. Aver- age reproductive span was too short (6,50 ± 0,26 years) due to cattle herd (P&lt;0,05), race or cross (P&lt;0,001), age at the beginning of the reproduction cycle (P&lt;0,001), total number of deliveries (P&lt;0,001), and age at first calving (P&lt;0,001). Holstein x Zebu crossbreeding improved reproductive span compared to purebred cattle and ¾ Zebu x ¼ Charolaise crossing. According to these results, herd handling must be improved and genotype for each place must be properly selected to make possible a decrease in age at the beginning of the reproduction cycle and at first calving, and therefore an increase in the total number of calvings.Con el objetivo de contribuir a caracterizar la duración de la vida reproductiva de la hembra bovina y sus implicaciones, fueron seleccionadas 218 vacas de 5 razas o cruces distribuidas en 7 rebaños pertenecientes a 3 empresas pecuarias de la provincia de Camagüey. Se calcularon el intervalo entre la incorporación a la reproducción y la inseminación fecundante (intervalo incorpora- ción-gestación) y la vida reproductiva útil (período comprendido entre la incorporación a la reproducción y el desecho). Se utilizó el modelo general lineal (G.M.L.) que reflejó valores deficientes para el total de partos, la edad de desecho, el intervalo incorpora- ción-gestación y la edad al primer parto. La vida reproductiva promedio de la muestra fue sumamente corta (6,50 ± 0,26 años) y estuvo influida por el rebaño (P&lt;0,05),&nbsp; &nbsp;la raza o cruce (P&lt;0,001),&nbsp; &nbsp;la edad a la incorporación&nbsp;&nbsp; (P&lt;0,001), el total de partos (P&lt;0,001) y la edad al primer parto (P&lt;0,001). &nbsp;El mestizaje del ganado Holstein con el Cebú mejoró la duración de la vida reproductiva al compararlo con las razas puras &nbsp;y el cruce ¾ Cebú x ¼ Charolaise. &nbsp;De acuerdo con los resultados obtenidos se requiere mejorar el manejo en los rebaños, lo que conjugado con la selección del genotipo adecuado a cada lugar pudiera &nbsp;permitir &nbsp;la reducción de &nbsp;las &nbsp;edades a la incorporación y al primer parto e incrementar el total de partos

Molecular characterization of multidrug resistant Enterobacterales strains isolated from liver and kidney transplant recipients in Spain

The objective of this study was to analyse the mechanisms of resistance to carbapenems and other extended-spectrum-?-lactams and to determine the genetic relatedness of multidrug-resistant Enterobacterales (MDR-E) causing colonization or infection in solid-organ transplantation (SOT) recipients. Prospective cohort study in kidney (n= 142), liver (n= 98) or kidney/pancreas (n= 7) transplant recipients between 2014 and 2018 in seven Spanish hospitals. We included 531 MDR-E isolates from rectal swabs obtained before transplantation and weekly for 4?6 weeks after the procedure and 10 MDR-E from clinical samples related to an infection. Overall, 46.2% Escherichia coli, 35.3% Klebsiella pneumoniae, 6.5% Enterobacter cloacae, 6.3% Citrobacter freundii and 5.7% other species were isolated. The number of patients with MDR-E colonization post-transplantation (176; 71.3%) was 2.5-fold the number of patients colonized pre-transplantation (71; 28.7%). Extended spectrum ?-lactamases (ESBLs) and carbapenemases were detected in 78.0% and 21.1% of MDR-E isolates respectively. In nine of the 247 (3.6%) transplant patients, the microorganism causing an infection was the same strain previously cultured from surveillance rectal swabs. In our study we have observed a low rate of MDR-E infection in colonized patients 4?6 weeks post-transplantation. E. coli producing blaCTX-M-G1 and K. pneumoniae harbouring blaOXA-48 alone or with blaCTX-M-G1 were the most prevalent MDR-E colonization strains in SOT recipients.Acknowledgements The authors thank Mª Jesús Lecea and Laura Álvarez for technical assistance. Tis research was supported by ‘Plan Nacional de I+D+i and Instituto de Salud Carlos III (Fondo de Investigaciones Sanitarias 13/01191), Subdirección General de Redes y Centros de Investigación Cooperativa, Ministerio de Ciencia, Innovación y Universidades, and the Spanish Network for Research in Infectious Diseases (REIPI RD16/0016/0007, RD16/0016/0010, RD16/0016/0012, RD16/0016/0011, RD16/0016/0008, RD16/0016/0002). Te study was co-fnanced by the European Development Regional Fund “A way to achieve Europe” and the Operative Program Intelligent Growth 2014‐2020