MSDeepAMR: antimicrobial resistance prediction based on deep neural networks and transfer learning.

Introduction: Antimicrobial resistance (AMR) is a global health problem that requires early and effective treatments to prevent the indiscriminate use of antimicrobial drugs and the outcome of infections. Mass Spectrometry (MS), and more particularly MALDI-TOF, have been widely adopted by routine clinical microbiology laboratories to identify bacterial species and detect AMR. The analysis of AMR with deep learning is still recent, and most models depend on filters and preprocessing techniques manually applied on spectra. Methods: This study propose a deep neural network, MSDeepAMR, to learn from raw mass spectra to predict AMR. MSDeepAMR model was implemented for Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus under different antibiotic resistance profiles. Additionally, a transfer learning test was performed to study the benefits of adapting the previously trained models to external data. Results: MSDeepAMR models showed a good classification performance to detect antibiotic resistance. The AUROC of the model was above 0.83 in most cases studied, improving the results of previous investigations by over 10%. The adapted models improved the AUROC by up to 20% when compared to a model trained only with external data. Discussion: This study demonstrate the potential of the MSDeepAMR model to predict antibiotic resistance and their use on external MS data. This allow the extrapolation of the MSDeepAMR model to de used in different laboratories that need to study AMR and do not have the capacity for an extensive sample collection.

Cryo-EM Map Anisotropy Can Be Attenuated by Map Post-Processing and a New Method for Its Estimation.

One of the most important challenges in cryogenic electron microscopy (cryo-EM) is the substantial number of samples that exhibit preferred orientations, which leads to an uneven coverage of the projection sphere. As a result, the overall quality of the reconstructed maps can be severely affected, as manifested by the presence of anisotropy in the map resolution. Several methods have been proposed to measure the directional resolution of maps in tandem with experimental protocols to address the problem of preferential orientations in cryo-EM. Following these works, in this manuscript we identified one potential limitation that may affect most of the existing methods and we proposed an alternative approach to evaluate the presence of preferential orientations in cryo-EM reconstructions. In addition, we also showed that some of the most recently proposed cryo-EM map post-processing algorithms can attenuate map anisotropy, thus offering alternative visualization opportunities for cases affected by moderate levels of preferential orientations.

Hyperspectral Microscopy Technology to Detect Syrups Adulteration of Endemic Guindo Santo and Quillay Honey Using Machine-Learning Tools.

Honey adulteration is a common practice that affects food quality and sale prices, and certifying the origin of the honey using non-destructive methods is critical. Guindo Santo and Quillay are fundamental for the honey production of Biobío and the Ñuble region in Chile. Furthermore, Guindo Santo only exists in this area of the world. Therefore, certifying honey of this species is crucial for beekeeper communities-mostly natives-to give them advantages and competitiveness in the global market. To solve this necessity, we present a system for detecting adulterated endemic honey that combines different artificial intelligence networks with a confocal optical microscope and a tunable optical filter for hyperspectral data acquisition. Honey samples artificially adulterated with syrups at concentrations undetectable to the naked eye were used for validating different artificial intelligence models. Comparing Linear discriminant analysis (LDA), Support vector machine (SVM), and Neural Network (NN), we reach the best average accuracy value with SVM of 93% for all classes in both kinds of honey. We hope these results will be the starting point of a method for honey certification in Chile in an automated way and with high precision.

Microencapsulation of Piscirickettsia salmonis Antigens for Fish Oral Immunization: Optimization and Stability Studies.

The development of fish oral vaccines is of great interest to the aquaculture industry due to the possibility of rapid vaccination of a large number of animals at reduced cost. In a previous study, we evaluated the effect of alginate-encapsulated Piscirickettsia salmonis antigens (AEPSA) incorporated in feed, effectively enhancing the immune response in Atlantic salmon (Salmo salar). In this study, we seek to characterize AEPSA produced by ionic gelation using an aerodynamically assisted jetting (AAJ) system, to optimize microencapsulation efficiency (EE%), to assess microparticle stability against environmental (pH, salinity and temperature) and gastrointestinal conditions, and to evaluate microparticle incorporation in fish feed pellets through micro-CT-scanning. The AAJ system was effective in obtaining small microparticles (d < 20 µm) with a high EE% (97.92%). Environmental conditions (pH, salinity and temperature) generated instability in the microparticles, triggering protein release. 62.42% of the protein content was delivered at the intestinal level after in vitro digestion. Finally, micro-CT-scanning images confirmed microparticle incorporation in fish feed pellets. In conclusion, the AAJ system is effective at encapsulating P. salmonis antigens in alginate with a high EE% and a size small enough to be incorporated in fish feed and produce an oral vaccine.

Determination of the Dissolution/Permeation and Apparent Solubility for Microencapsulated Emamectin Benzoate Using In Vitro and Ex Vivo Salmo salar Intestine Membranes.

In this work, two microencapsulation techniques were used to protect and improve the absorption of emamectin benzoate (EB), which is an antiparasitic drug used to control Caligus rogercresseyi. EB has a low aqueous solubility, which affects its absorption in the intestine of Salmo salar. Microparticles were produced by spray drying and ionic gelation, using Soluplus® (EB−SOL) and sodium alginate (EB−ALG) as polymers, respectively. Studies were conducted on dissolution/permeation, apparent permeability (Papp), apparent solubility (Sapp), and absorption using synthetic and biological membranes. Based on these results, the amount of EB in the microparticles needed to achieve a therapeutic dose was estimated. The EB−ALG microparticles outperformed both EB−SOL and free EB, for all parameters analyzed. The results show values of 0.45 mg/mL (80.2%) for dissolution/permeation, a Papp of 6.2 mg/mL in RS−L, an absorption of 7.3% in RS, and a Sapp of 53.1% in EM medium. The EB−ALG microparticles decrease the therapeutic dose necessary to control the parasite, with values of 3.0−2 mg/mL and 1.1−2 mg/mL for EB in EM and RS, respectively. The Korsmeyer−Peppas kinetic model was the best model to fit the EB−ALG and EB−SOL dissolution/permeation experiments. In addition, some of our experimental results using synthetic membranes are similar to those obtained with biological membranes, which suggests that, for some parameters, it is possible to replace biological membranes with synthetic membranes. The encapsulation of EB by ionic gelation shows it is a promising formulation to increase the absorption of the poorly soluble drug. In contrast, the spray-dried microparticles produced using Soluplus® result in even less dissolution/permeation than free EB, so the technique cannot be used to improve the solubility of EB.

Distributional homogeneity and penetration depth assessment of antibiotic added by surface coating to pellets with mid Infrared imaging and multivariate curve resolution.

Fourier Transform Mid Infrared with Attenuated Total Reflection Imaging (FTIR-ATR imaging) and Multivariate Curve Resolution with Alternating Least Squares (MCR-ALS) were used in a multiblock fashion to study the presence, distribution and penetration depth of very low concentrations of florfenicol (FF) in a complex matrix like feed pellets for salmonids. Images from the surface, at 150 µm deep and 200 µm deep from the surface were analyzed to certify the penetration power of FF added by surface coating methodology. Besides, the unique homogeneity index was calculated in order to evaluate the distributional homogeneity of each component. The results demonstrated the reliability of MCR-ALS in studying the distributional homogeneity of FF. It was demonstrated that FF remains mostly on the surface of the pellets with almost no penetration. The rest of the components of the pellets (oil, protein and carbohydrates) were also analyzed. These three nutrients are distributed on the three layers analyzed with a relatively homogeneous location, being carbohydrates (%H = 51 ± 3) the component with the best homogeneous distribution, unlike protein (%H = 45 ± 5), and oil (%H = 40 ± 7). This is the first publication where the penetration of an antibiotic, added with surface-coating to feed pellets, was analyzed with FTIR-ATR imaging and multivariate analysis, showing the contribution these analytical tools can make to the medicated feed industry.

"Limiting access to iron decreases infection of Atlantic salmon SHK-1 cells with bacterium Piscirickettsia salmonis".

BACKGROUND: Vertebrate hosts limit the availability of iron to microbial pathogens in order to nutritionally starve the invaders. The impact of iron deficiency induced by the iron chelator deferoxamine mesylate (DFO) was investigated in Atlantic salmon SHK-1 cells infected with the facultative intracellular bacterium Piscirickettsia salmonis. RESULTS: Effects of the DFO treatment and P. salmonis on SHK-1 cells were gaged by assessing cytopathic effects, bacterial load and activity, and gene expression profiles of eight immune biomarkers at 4- and 7-days post infection (dpi) in the control group, groups receiving single treatments (DFO or P. salmonis) and their combination. The chelator appears to be well-tolerated by host cells, while it had a negative impact on the number of bacterial cells and associated cytotoxicity. DFO alone had minor effects on gene expression of SHK-1 cells, including an early activation of IL-1ß at 4 dpi. In contrast to few moderate changes induced by single treatments (either infection or chelator), most genes had highest upregulation in the infected groups receiving DFO. The mildest induction of hepcidin-1 (antimicrobial peptide precursor and regulator of iron homeostasis) was observed in cells exposed to DFO alone, followed by P. salmonis infected cells while the addition of DFO to infected cells further increased the mRNA abundance of this gene. Transcripts encoding TNF-α (immune signaling) and iNOS (immune effector) showed sustained increase at both time points in this group while cathelicidin-1 (immune effector) and IL-8 (immune signaling) were upregulated at 7 dpi. The stimulation of protective gene responses seen in infected cultures supplemented with DFO coincided with the reduction of bacterial load and activity (judged by the expression of P. salmonis 16S rRNA), and damage to cultured host cells. CONCLUSION: The absence of immune gene activation under normal iron conditions suggests modulation of host responses by P. salmonis. The negative effect of iron deficiency on bacteria likely allowed host cells to respond in a more protective manner to the infection, further decreasing its progression. Presented findings encourage in vivo exploration of iron chelators as a promising strategy against piscirickettsiosis.

Protein-Based Vaccine Protect Against Piscirickettsia salmonis in Atlantic Salmon (Salmo salar).

An effective and economical vaccine against the Piscirickettsia salmonis pathogen is needed for sustainable salmon farming and to reduce disease-related economic losses. Consequently, the aquaculture industry urgently needs to investigate efficient prophylactic measures. Three protein-based vaccine prototypes against Piscirickettsia salmonis were prepared from a highly pathogenic Chilean isolate. Only one vaccine effectively protected Atlantic salmon (Salmo salar), in correlation with the induction of Piscirickettsia-specific IgM antibodies and a high induction of transcripts encoding pro-inflammatory cytokines (i.e., Il-1ß and TNF-α). In addition, we studied the proteome fraction protein of P. salmonis strain Austral-005 using multidimensional protein identification technology. The analyzes identified 87 proteins of different subcellular origins, such as the cytoplasmic and membrane compartment, where many of them have virulence functions. The other two prototypes activated only the innate immune responses, but did not protect Salmo salar against P. salmonis. These results suggest that the knowledge of the formulation of vaccines based on P. salmonis proteins is useful as an effective therapy, this demonstrates the importance of the different research tools to improve the study of the different immune responses, resistance to diseases in the Atlantic salmon. We suggest that this vaccine can help prevent widespread infection by P. salmonis, in addition to being able to be used as a booster after a primary vaccine to maintain high levels of circulating protective antibodies, greatly helping to reduce the economic losses caused by the pathogen.

Assessing the Immune Response of Atlantic Salmon (Salmo salar) after the Oral Intake of Alginate-Encapsulated Piscirickettsia salmonis Antigens.

Salmon rickettsial septicaemia (SRS) is the infectious disease that produces the highest losses in the Chilean salmon industry. As a new strategy for the control of SRS outbreaks, in this study we evaluated the effect of alginate-encapsulated Piscirickettsia salmonis antigens (AEPSA) incorporated in the feed as an oral vaccine to induce the immune response in Atlantic salmon (Salmo salar). Fish were distributed into three vaccination groups (injectable, oral high dose, oral low dose). Feed intake and fish growth were recorded during the trial. The P. salmonis-specific IgM levels in blood plasma were measured by ELISA. Alginate microparticles containing the antigen were effectively incorporated in fish feed to produce the oral vaccine. Incorporation of AEPSA did not affect the palatability of the feed or the fish appetite. Furthermore, the oral vaccine did not have a negative effect on fish growth. Finally, the oral vaccine (high and low dose) produced an acquired immune response (IgM) similar to the injectable vaccine, generating a statistically significant increase in the IgM levels at 840-degree days for both experimental groups. These findings suggest that AEPSA incorporated in the feed can be an effective alternative to boost the immune response in Atlantic salmon (S. salar).

Evaluation of the microscopic distribution of florfenicol in feed pellets for salmon by Fourier Transform infrared imaging and multivariate analysis.

Fourier Transform infrared imaging and multivariate analysis were used to identify, at the microscopic level, the presence of florfenicol (FF), a heavily-used antibiotic in the salmon industry, supplied to fishes in feed pellets for the treatment of salmonid rickettsial septicemia (SRS). The FF distribution was evaluated using Principal Component Analysis (PCA) and Augmented Multivariate Curve Resolution with Alternating Least Squares (augmented MCR-ALS) on the spectra obtained from images with pixel sizes of 6.25 µm × 6.25 µm and 1.56 µm × 1.56 µm, in different zones of feed pellets. Since the concentration of the drug was 3.44 mg FF/g pellet, this is the first report showing the powerful ability of the used of spectroscopic techniques and multivariate analysis, especially the augmented MCR-ALS, to describe the FF distribution in both the surface and inner parts of feed pellets at low concentration, in a complex matrix and at the microscopic level. The results allow monitoring the incorporation of the drug into the feed pellets.

Angioplastia coronaria transluminal percutánea

En el presente artículo mostramos una revisión de la Angioplastia Coronaria Transluminal Percutanea (ACTP), la cual es una técnica invasiva no quirúrgica utilizada en el tratamiento de las obstrucciones arteroescleróticas de las arterias coronarias. Esta técnica representa hoy en día una alternativa eficaz, al menos en el 40% de los pacientes candidatos a cirugía de puente aorto-coronario en los Estados Unidos. Haremos especial énfasis en las indicaciones y contraindicaciones del procedimiento, así como una breve descripción de la técnica en sí y su mecanismo de acción