Pathological and immunohistochemical assessment of the impact of three different strains of swine enteric coronaviruses in the intestinal barrier.

Swine enteric coronaviruses, such as porcine epidemic diarrhea virus (PEDV) or transmissible gastroenteritis virus (TGEV), have risen concern for the porcine industry and research community due to the increase in their virulence, their potential recombination capacity and the emergence of new variants. This in vivo study aims to compare the impact of three different strains of swine enteric coronaviruses [(two G1b (S-INDEL) PEDV strains and a recombinant TGEV-PEDV or Swine enteric coronavirus (SeCoV)] in the intestine of 3-weeks-old infected piglets, focusing on the pathology and main components of the intestinal barrier, including the number of goblet cells, and the expression of IgA as well as FoxP3, a regulatory T cell marker. Severity of lesions was evidenced in the three infected groups and was highly correlated with the viral load in feces and the frequency of viral antigen-positive cells. Furthermore, higher cellular death together with an increase in the expression of the FoxP3 marker was detected in the duodenum and jejunum of infected animals at 3 days post-infection. Our results highlight a recruitment of FoxP3+ cells in the small intestine of infected animals which may represent a response to the tissue damage caused by viral replication and cell death. Further studies should be addressed to determine the potential role of these cells during swine enteric coronavirus infections.

Predictive factors of COVID-19 in patients with negative RT-qPCR / Factores predictivos del COVID-19 en pacientes con RT-qPCR negativa

OBJECTIVE: To evaluate the factors associated with false negatives in RT-qPCR in patients with mild-moderate symptoms of COVID-19. MATERIALS AND METHODS: This was a cross-sectional study that used a random sample of non-hospitalized patients from the primary care management division of the Healthcare Area of Leon (58 RT-qPCR-positive cases and 52 RT-qPCR-negative cases). Information regarding symptoms was collected and all patients were simultaneously tested using two rapid diagnostic tests - RDTs (Combined - cRDT and Differentiated - dRDT). The association between symptoms and SARS-CoV-2 infection was evaluated by non-conditional logistic regression, with estimation of Odds Ratio. RESULTS: A total of 110 subjects were studied, 52% of whom were women (mean age: 48.2±11.0 years). There were 42.3% of negative RT-qPCRs that were positive in some RDTs. Fever over 38°C (present in 35.5% of cases) and anosmia (present in 41.8%) were the symptoms most associated with SARS-CoV-2 infection, a relationship that remained statistically significant in patients with negative RT-qPCR and some positive RDT (aOR=6.64; 95%CI=1.33-33.13 and aOR=19.38; 95% CI=3.69-101.89, respectively). CONCLUSIONS: RT-qPCR is the technique of choice in the diagnosis of SARS-CoV-2 infection, but it is not exempt from false negatives. Our results show that patients who present mild or moderate symptoms with negative RT-qPCR, but with fever and/or anosmia, should be considered as suspicious cases and should be evaluated with other diagnostic methods

OBJETIVO: Evaluar los factores asociados con falsos negativos a RT-qPCR negativa y sintomatología leve o moderada de COVID-19. MATERIALES Y MÉTODOS: Estudio transversal. Se utilizó una muestra aleatoria de pacientes no hospitalizados de la Gerencia de Atención Primaria del Área de Salud de León (58 con RT-qPCR positiva y 52 con RT-qPCR negativa). Se recogió información sobre síntomas, y a todos se les realizaron simultáneamente dos pruebas de diagnóstico rápido (PDR): combinada (PRD-C) y diferenciada (PRD-D). La asociación de los síntomas con la infección por SARS-CoV-2 se evaluó mediante regresión logística no condicional, con el cálculo de odds ratio (OR). RESULTADOS: Se estudiaron un total de 110 personas, y el 52% de ellas fueron mujeres (edad media: 48,2±11,0años). El 42,3% de las RT-qPCR negativas dieron positivo en algún PDR. La fiebre de más de 38°C (presente en el 35,5% de los casos) y la anosmia (presente en el 41,2%) fueron los síntomas más asociados a la infección por SARS-CoV-2, relación que se mantuvo estadísticamente significativa en pacientes con RT-qPCR negativa y algún PDR positivo (ORa: 6,64; IC95%: 1,33-33,13, y ORa: 19,38; IC95%: 3,69-101,89, respectivamente). CONCLUSIONES: La RT-qPCR es la técnica de elección en el diagnóstico de la infección por SARS-CoV-2, pero no está exenta de falsos negativos. Nuestros resultados ponen de manifiesto que los pacientes que presentan síntomas leves o moderados con RT-qPCR negativa pero con fiebre y/o anosmia deben ser considerados casos sospechosos y deben ser valorados con otros métodos diagnósticos

Predictive factors of COVID-19 in patients with negative RT-qPCR.

OBJECTIVE: To evaluate the factors associated with false negatives in RT-qPCR in patients with mild-moderate symptoms of COVID-19. MATERIALS AND METHODS: This was a cross-sectional study that used a random sample of non-hospitalized patients from the primary care management division of the Healthcare Area of Leon (58 RT-qPCR-positive cases and 52 RT-qPCR-negative cases). Information regarding symptoms was collected and all patients were simultaneously tested using two rapid diagnostic tests - RDTs (Combined - cRDT and Differentiated - dRDT). The association between symptoms and SARS-CoV-2 infection was evaluated by non-conditional logistic regression, with estimation of Odds Ratio. RESULTS: A total of 110 subjects were studied, 52% of whom were women (mean age: 48.2±11.0 years). There were 42.3% of negative RT-qPCRs that were positive in some RDTs. Fever over 38°C (present in 35.5% of cases) and anosmia (present in 41.8%) were the symptoms most associated with SARS-CoV-2 infection, a relationship that remained statistically significant in patients with negative RT-qPCR and some positive RDT (aOR=6.64; 95%CI=1.33-33.13 and aOR=19.38; 95% CI=3.69-101.89, respectively). CONCLUSIONS: RT-qPCR is the technique of choice in the diagnosis of SARS-CoV-2 infection, but it is not exempt from false negatives. Our results show that patients who present mild or moderate symptoms with negative RT-qPCR, but with fever and/or anosmia, should be considered as suspicious cases and should be evaluated with other diagnostic methods.

Comprehensive analysis of pig feces metabolome by chromatographic techniques coupled to mass spectrometry in high resolution mode: Influence of sample preparation on the identification coverage.

Pig feces is an interesting biological sample to be implemented in metabolomics experiments by virtue of the information that can be deduced from the interaction between host and microbiome. However, pig fecal samples have received scant attention, especially in untargeted metabolomic studies. In this research, an analytical strategy was planned to maximize the identification coverage of metabolites found in pig fecal samples. For this purpose, two complementary platforms such as LC-QTOF MS/MS and GC-TOF/MS were used. Concerning sample preparation six extractant solvents with different polarity grade were tested to evaluate the extraction performance and, in the particular case of GC-MS, two derivatization protocols were compared. A total number of 303 compounds by combination of all the extractants and analytical platforms were tentatively identified. The main identified families were amino acids, fatty acids and derivatives, carbohydrates and carboxylic acids. For GC-TOF/MS analysis, the recommended extractant is methanol, while methoxymation was required in the derivatization protocol since this step allows detecting the α-keto acids, which are direct markers of the microbiome status. Concerning LC-QTOF MS/MS analysis, a dual extraction approach with methanol (MeOH) or MeOH/water and ethyl acetate is proposed to enhance the detection of polar and non-polar metabolites.

Salmonella in breeding pigs: Shedding pattern, transmission of infection and the role of environmental contamination in Irish commercial farrow-to-finish herds.

This study aimed to provide new insights into the epidemiology of Salmonella in pig production, focusing on potential shedding patterns in breeding pigs throughout a full production cycle and the risk of transmission of infection from the sow to her offspring. A longitudinal study was conducted on five farrow-to-finish commercial pig farms. In each herd, shedding of Salmonella in faeces was monitored in breeders through service, gestation and lactation. Swabs of the farrowing room floor and pools of faeces from piglets were collected on two occasions during lactation. Environmental pen swabs were also taken in the weaning and finisher houses. Salmonella isolates were serotyped, tested for antimicrobial resistance (AMR) and typed by Multiple-Locus Variable number tandem repeat Analysis (MLVA). Shedding by breeding pigs was low in all stages of the production cycle; 5% of sows shed at service, the production stage with highest risk of shedding (p < .01), 1.6% shed during gestation and 2.5% after farrowing. Salmonella was detected in 4% of piglet faecal pools in the second week post-farrowing and 5% in the fourth week. Serotyping and AMR profiles of Salmonella isolates revealed that strains in sows and gilts were mostly different from strains isolated in weaner and finisher facilities. MLVA typing confirmed that the source of infection in piglets was in most instances the contaminated environment rather than their dam. Based on the typing results, it appears that sows do not pose a major risk in the maintenance and transmission of Salmonella to their progeny but instead the contaminated pen environment is more significant in the perpetuation of the organism on farm.

Investigation of in-feed organic acids as a low cost strategy to combat Salmonella in grower pigs.

Salmonella carriage in pigs is a significant food safety issue. Dietary supplementation with organic acids has previously been shown to reduce shedding and transmission of Salmonella. Therefore, this study aimed to examine the effect of three commercially available organic acid-based products on Salmonella levels in grower pigs, using a model of experimental infection that closely mimics natural exposure to the organism. Seven week old trial pigs (n=40) with a mean weight of 14.7kg were placed in one of four pens with 10 pigs/pen. Pens had previously been contaminated with Salmonella Typhimurium 4,[5],12;i;- via seeder pigs. Trial pigs received one of four diets for 28days: 1, control diet; 2, sodium butyrate supplemented diet; 3, benzoic acid supplemented diet and 4, formic-citric acid supplemented diet. A further 10 pigs were placed in a Salmonella-free pen receiving the control diet. Pigs were weighed and blood sampled on days 0 and 28. Faeces was collected on day 0, 2, 3, 5, 7, 14, 21 and 28 and examined for Salmonella. On day 28, 5 pigs/group were euthanised and ileocaecal lymph nodes (ILN) and caecal contents sampled for culture. The remaining 5 pigs/pen were then fed the control diet and faeces were collected on days 35 and 42. On day 42 pigs were euthanised and ILN and caecal contents tested for Salmonella levels. The trial was repeated once. Within the first two days of exposure to the contaminated environment, 96% (77/80) of pigs became infected. Most pigs shed Salmonella at levels of between 100-103 CFU/g faeces for at least 7days post-exposure. A significant reduction in Salmonella faecal concentration was observed after supplementation with sodium butyrate (p=0.001) and a formic citric acid blend (p<0.0001). Average daily weight gain (ADWG) was significantly increased in all groups fed the supplemented feed when compared to the positive control group. The use of sodium butyrate or a blend of formic and citric acid in feed could be considered a cost-effective control measure to reduce Salmonella faecal shedding and improve ADWG in Salmonella infected herds.

Antibacterial activity and mode of action of a commercial citrus fruit extract.

AIMS: This study addresses the antibacterial activity and mechanism of action of BIOLL(+®), a commercial extract obtained from citrus fruits. METHODS AND RESULTS: Strong activities with minimum inhibitory concentrations (MIC) ranging from 10 ppm (for some Brachyspira hyodysenteriae strains) to 80 ppm (for various Salmonella enterica and Escherichia coli strains) were observed. Membrane integrity tests and Fourier transform infrared (FT-IR) spectroscopic analyses were performed to shed light on the effects caused on molecular structure and composition. Physical effects, with formation of pores and leakage of intracellular components, and chemical effects, which were dependent on the bacterial species, were evident on cellular envelopes. Whereas for S. enterica and E. coli, changes were focused on the carboxylic group of membrane fatty acids, for B. hyodysenteriae, the main effects were found in polysaccharides and carbohydrates of the cell wall. CONCLUSIONS: The great antibacterial activity shown by BIOLL(+®) and its proposed dual physico-chemical mode of action, with species-specific cellular targets, show its attractiveness as an alternative to antibiotics. SIGNIFICANCE AND IMPACT OF THE STUDY: Antibiotic resistance is becoming a serious problem. Our study characterizes a novel antimicrobial extract, which could represent an alternative to antibiotics for treatment or prevention of bacterial infectious diseases.

Predicción de la estructura secundaria de proteínas usando Máquinas de soporte Vectorial / Protein secondary structure prediction using support vector machines

Entre los métodos computacionales utilizados para la predicción de la estructura secundaria de proteí­nas, se destaca el uso de máquinas de soporte vectorial. Este trabajo de investigación presenta la predicción de la estructura secundaria de proteínas desde su secuencia primaria de aminoácidos usando Máquinas de Soporte Vectorial. Como entradas, en la metodologí­a propuesta, se utilizan características de los diferentes motivos estructurales o cadenas de texto asociadas a la estructura primaria que representa la estructura secundaria, tales como el R-grupo y la probabilidad de que el aminoácido en la posición central adopte una determinada estructura secundaria. Para la extracción de características se utiliza un método de codificación de secuencias en el que cada símbolo en la estructura primaria se relaciona con cada sí­mbolo en la estructura secundaria. El uso de este método de codificación permite reducir la dimensionalidad de los datos de miles de características a sólo 220 de estas. Los resultados obtenidos son comparables a los registrados en la literatura, teniendo cerca de un 70% de precisión. Además, se logra reducir los costos computacionales en la construcción de los clasificadores debido a que este trabajo modela el problema de multi-clasificación como un grupo de clasificadores binarios.

Among the computational methods used for predicting secondary structure proteins highlights the use of support vector machines. This research shows the predicted secondary structure of protein from its primary amino acid sequence using Support Vector Machines. As inputs, in the proposed methodology, features are used from different structural motifs or text strings associated with the primary structure which represents the secondary structure, such as R-group and the probability that the amino acid at position adopts a central particular secondary structure. For feature extraction method is used coding of sequences in which each symbol in the primary structure is associated with each symbol in the secondary structure. The use of this encoding method reduces the dimensionality of the data of thousands of characteristics only 220 of these. The results obtained are comparable to those reported in the literature, taking about 70% accuracy. Furthermore, it is possible to reduce computational cost in the construction of classifiers because this work models the problem of multi classification as a group of binary classifiers.