Highlights of infectious agents in tissue.

The evolution of the diagnosis of infectious diseases began with the observation of the morphological characteristics of organisms such as ascaris and whipworms, followed by the use of the microscope and haematoxylin and eosin stains, which allowed recognition of microscopic characteristics undetectable with the naked eye, such as the viral cytopathic changes of herpes and the presence of fungi. Patterns of acute and chronic granulomatous inflammation were also observed; these were not specific to the exact aetiology of the disease, which led to the introduction of special methenamine stains for fungi and Ziehl-Neelsen for fungi and mycobacteria. Later, the use of immunohistochemistry was introduced, which acknowledged the use of antibodies to classify microorganisms and detect cases that were either difficult to interpret or in the midst of severe inflammatory processes. Currently, the use of molecular biology has made it possible to reach diagnoses that would have been very difficult to obtain through traditional methods; these techniques show key specific characteristics and facilitate the diagnosis of various infectious pathologies. These new techniques are based on the detection of antigens and nucleic acids of microorganisms, an important advance in the diagnosis of infectious diseases.

Infection risks related to aesthetic procedures: microbial profile and professional perception about infection prevention measures / Riscos de infecção relacionados a procedimentos estéticos: perfil microbiano e percepção profissional sobre medidas de prevenção de infecção / Riesgos de infección relacionados con los procedimientos estéticos: perfil microbiano y percepción profesional sobre las medidas de prevención de infecciones

Background and Objectives: This study aimed to identify the presence of microorganisms in the aesthetic environment and assess professionals' knowledge about relevant infection prevention measures, considering the importance of the issue and the lack of study in the area. Methods: A total of 100 clinics that perform minimally invasive aesthetic procedures in Porto Alegre (RS), Brazil, were visited. Procedures such as botulin-toxin, dermal fillers, collagen biostimulators, thread lift, chemical peels and laser hair removal were considered. A questionnaire about infection prevention measures were answered by 50 professionals. Also, 100 samples were collected from the environment for bacterial identification and antimicrobial susceptibility testing. Results: There was an infection prevention protocol in 40% of clinics, in which 95% of respondents had complete college education. Periodic professional training regarding infection control measures were performed in 72% of clinics. An autoclave was used for sterilization of materials and instruments in 66% of clinics. From the samples collected, 85% showed bacterial growth by microbiological methods. Coagulase-negative Staphylococci was the most prevalent genera found, and 16% of them were resistant to both cefoxitin, erythromycin, and clindamycin. Four isolates were positive for mecA by PCR. Conclusion: The presence of well-trained professionals is critical in aesthetic clinics so that biosafety and infection prevention measures are taken.(AU)

Justificativa e Objetivos: Este estudo teve como objetivo identificar a presença de microrganismos no ambiente estético e avaliar o conhecimento dos profissionais sobre medidas relevantes de prevenção de infecções, considerando a importância do tema e a falta de estudos nesta área. Métodos: Foram visitadas 100 clínicas que realizam procedimentos estéticos minimamente invasivos em Porto Alegre (RS), Brasil. Foram considerados procedimentos injetáveis como aplicação de toxina botulínica, preenchedores faciais, microagulhamento, bioestimuladores de colágeno, fios de sustentação, peelings químicos e depilação a laser. Um questionário sobre medidas de prevenção de infecção foi respondido por 50 profissionais. Além disso, 100 amostras foram coletadas do ambiente para identificação bacteriana e teste de sensibilidade aos antimicrobianos. Resultados: Existia protocolo de prevenção de infecção em 40% dos ambulatórios, no qual 95% dos profissionais entrevistados possuíam ensino superior completo. Treinamento profissional periódico sobre medidas de controle de infecção foi realizado em 72% dos ambulatórios. Autoclave foi utilizada para esterilização de materiais e instrumentais em 66% das clínicas. Das amostras coletadas, 85% apresentaram crescimento bacteriano nas culturas microbiológicas. Staphylococci coagulase-negativo foi o gênero mais prevalente encontrado; e 16% deles eram resistentes à cefoxitina, eritromicina e clindamicina. Quatro isolados foram positivos para mecA por PCR. Conclusão: A presença de profissionais devidamente treinados é fundamental nas clínicas de estética, para que medidas de biossegurança e prevenção de infecções sejam tomadas.(AU)

Justificación y Objetivos: Este estudio tuvo como objetivo identificar la presencia de microorganismos en el entorno estético y evaluar el conocimiento de los profesionales sobre las medidas de prevención de infecciones relevantes, considerando la importancia del tema y la falta de estudios en esta área. Métodos: Se visitaron 100 clínicas que realizan procedimientos estéticos mínimamente invasivos en Porto Alegre (RS), Brasil. Se consideraron procedimientos invasivos, como la aplicación de toxina botulínica, rellenos faciales, microagujas, bioestimuladores de colágeno, hilos de soporte, peelings químicos y depilación láser. Un cuestionario sobre medidas de prevención de infecciones fue respondido por 50 profesionales. Además, se recolectaron 100 muestras del medio ambiente para la identificación bacteriana y las pruebas de susceptibilidad a los antimicrobianos. Resultados: Existía un protocolo de prevención de infecciones en el 40% de las clínicas, en el que el 95% de los profesionales encuestados tenía educación universitaria completa. En el 72% de las clínicas se realizó capacitación profesional periódica sobre medidas de control de infecciones. Se utilizó un autoclave para la esterilización de materiales e instrumentos en el 66% de las clínicas. De las muestras recolectadas, el 85% mostró crecimiento bacteriano por métodos de cultivo microbiologicos. El Staphylococci coagulasa negativo fue el género más prevalente encontrado, y el 16% de ellos eran resistentes tanto a cefoxitina, eritromicina y clindamicina. Cuatro aislamientos fueron positivos para mecA por PCR. Conclusión: La presencia de profesionales debidamente capacitados es fundamental en las clínicas de estética, para la toma medidas de bioseguridad y prevención de infecciones.(AU)

Enteric pathogens induce tissue tolerance and prevent neuronal loss from subsequent infections.

The enteric nervous system (ENS) controls several intestinal functions including motility and nutrient handling, which can be disrupted by infection-induced neuropathies or neuronal cell death. We investigated possible tolerance mechanisms preventing neuronal loss and disruption in gut motility after pathogen exposure. We found that following enteric infections, muscularis macrophages (MMs) acquire a tissue-protective phenotype that prevents neuronal loss, dysmotility, and maintains energy balance during subsequent challenge with unrelated pathogens. Bacteria-induced neuroprotection relied on activation of gut-projecting sympathetic neurons and signaling via ß2-adrenergic receptors (ß2AR) on MMs. In contrast, helminth-mediated neuroprotection was dependent on T cells and systemic production of interleukin (IL)-4 and IL-13 by eosinophils, which induced arginase-expressing MMs that prevented neuronal loss from an unrelated infection located in a different intestinal region. Collectively, these data suggest that distinct enteric pathogens trigger a state of disease or tissue tolerance that preserves ENS number and functionality.

Editor's Choice - Validation of the Management of Aortic Graft Infection Collaboration (MAGIC) Criteria for the Diagnosis of Vascular Graft/Endograft Infection: Results from the Prospective Vascular Graft Cohort Study.

OBJECTIVE: The timely management of vascular graft/endograft infection (VGEI) is crucial to a favourable outcome, yet can be challenging as there is no validated gold standard diagnostic test. Recently, a new case definition has been proposed by the Management of Aortic Graft Infection Collaboration (MAGIC) to close the diagnostic gap. The aim of this study was to validate the MAGIC criteria as a suggested diagnostic standard for the diagnosis of suspected VGEI in the prospective Vascular Graft Cohort study (VASGRA). METHODS: VASGRA is an open, prospective, observational cohort study. Prospective participants in VASGRA between 2013 and 2019 were included (257 patients; 137 with VGEI). The accuracy of the MAGIC criteria for a diagnosis of VGEI was evaluated retrospectively by calculating the sensitivity and specificity vs. the consensually adjudicated VASGRA infection status. RESULTS: The VASGRA cohort categorised 137 (53.3%) patients as "diseased" and 120 patients as "not diseased"; using the MAGIC criteria, 183/257 (71.2%) patients were considered to be "diseased". Thus, for the MAGIC criteria, a sensitivity of 99% (95% confidence interval [CI] 96-100) and a specificity of 61% (95% CI 52-70) were calculated. Considering suspected VGEI according to the MAGIC criteria as "not diseased" achieved congruent assessments of the VASGRA team and the MAGIC criteria, with a sensitivity of 93% and a specificity of 93%. The accuracy of the MAGIC criteria for the different graft locations were also compared. If the suspected VGEIs were assigned to the "not diseased" group, VGEIs of the thoracic aorta seemed to have a poorer sensitivity (86%; 95% CI 73-95) than the other graft locations. CONCLUSION: The current MAGIC criteria offer good sensitivity and specificity in the context of true infections but a reduced specificity for a possible VGEI.

Tight Junctions as a Key for Pathogens Invasion in Intestinal Epithelial Cells.

Tight junctions play a major role in maintaining the integrity and impermeability of the intestinal barrier. As such, they act as an ideal target for pathogens to promote their translocation through the intestinal mucosa and invade their host. Different strategies are used by pathogens, aimed at directly destabilizing the junctional network or modulating the different signaling pathways involved in the modulation of these junctions. After a brief presentation of the organization and modulation of tight junctions, we provide the state of the art of the molecular mechanisms leading to permeability breakdown of the gut barrier as a consequence of tight junctions' attack by pathogens, including bacteria, viruses, fungi, and parasites.

Infections in hematopoietic stem cell transplant patients admitted to Hematology intensive care unit: a single-center study.

OBJECTIVE: The aim of this study was to investigate the data of HSCT patients who were admitted to our Hematology ICU due to infections or infectious complications. MATERIALS AND METHODS: HSCT patients who were admitted to our Hematology ICU between 01 January 2014 and 01 September 2017 were analyzed retrospectively. RESULTS: 62 HSCT patients were included in this study. The median age was 55.5 years and 58% of the patients were allogeneic HSCT patients. Major underlying hematologic disorders were multiple myeloma (29%) and lymphoma (27.4%). The most common reasons for ICU admission were sepsis/septic shock (61.3%) and acute respiratory failure (54.8%). Overall ICU mortality rate was 45.2%. However, a lot of factors were related with ICU mortality of HSCT patients in univariate analysis, only APACHE II score was found to be an independent risk factor for ICU mortality. While there was infection in 58 patients at ICU admission, new infections developed in 38 patients during ICU stay. The most common new infection was pneumonia/VAP, while the most frequently isolated bacteria were Acinetobacter baumannii. Length of ICU stay, sepsis/septic shock as a reason for ICU admission and the presence of urinary catheter at ICU admission were determined factors for ICU-acquired infections. There was no difference between autologous and allogeneic stem cell transplant patients in terms of ICU morbidities and mortality. However, pneumonia/VAP developed in the ICU was higher in autologous HSCT patients, while bloodstream/catheter-related bloodstream infection was higher in allogeneic HSCT patients. CONCLUSION: It was concluded that early or late post-HSCT infections and related complications (sepsis, organ failure, etc.) constituted a major part of the reasons for ICU admission, ICU mortality and ICU morbidities.

In vitro three-dimensional organotypic culture models of the oral mucosa.

Three-dimensional, organotypic models of the oral mucosa have been developed to study a wide variety of phenomena occurring in the oral cavity. Although a number of models have been developed in academic research labs, only a few models have been commercialized. Models from academic groups offer a broader range of phenotypes while the commercial models are more focused on the oral and gingival mucosa. The commercialized models are manufactured under highly controlled conditions and meet the requirements of quality standards, which leads to high levels of reproducibility. These in vitro models have been used to evaluate the irritancy of oral care products such as toothpastes, mouthwashes, and mucoadhesives. The effects of cigarette smoke on oral cavity tissues have been studied and compared to those of e-cigarettes. Oral tissue models have facilitated investigation of the mechanisms of oral mucositis and oral candidiasis and have been used to examine transbuccal drug delivery rates and the absorption of nanoparticles. Infection studies have investigated the effects of HIV-1 along with the effects of commensal and pathogenic bacteria. More recently, a differentiated oral tissue model has been shown to express the ACE2 receptor, which is known to be important for the receptor-mediated entry of the SARS-CoV-2 coronavirus into human cells and tissues. Hence, oral mucosal models may find application in determining whether viral infection of the oral mucosa is possible and whether such infection has implications vis-a-vis the current COVID-19 pandemic. As is apparent, these models are used in a broad variety of applications and often offer advantages versus animal models in terms of reproducibility, avoiding species extrapolation, and the ethical concerns related to human and animal experimentation. The goals of this paper are to review commercially available models of the human buccal and gingival mucosa and highlight their use to gain a better understanding of a broad range of phenomena affecting tissues in the oral cavity.

Parsing the Role of PPARs in Macrophage Processes.

Cells are richly equipped with nuclear receptors, which act as ligand-regulated transcription factors. Peroxisome proliferator activated receptors (PPARs), members of the nuclear receptor family, have been extensively studied for their roles in development, differentiation, and homeostatic processes. In the recent past, there has been substantial interest in understanding and defining the functions of PPARs and their agonists in regulating innate and adaptive immune responses as well as their pharmacologic potential in combating acute and chronic inflammatory disease. In this review, we focus on emerging evidence of the potential roles of the PPAR subtypes in macrophage biology. We also discuss the roles of dual and pan PPAR agonists as modulators of immune cell function, microbial infection, and inflammatory diseases.

Microbiological evaluation of resection margins of the infected diabetic foot ulcer.

AIM: To evaluate the impact of surgical debridement on the microbiology of resection margins of an infected diabetic foot ulcer and to compare the use of marginal sampling as a guide for antimicrobial therapy. METHODS: Forty consecutive participants were studied. Tissue samples from infected diabetic foot ulcers were obtained at first contact by podiatrists. After surgical debridement to macroscopically healthy tissue, multiple samples were obtained from the margins of the residuum and also from excised non-viable tissue. Debridement was done by a single surgeon. Bacterial species were classified according to pathogenic potential a priori into Red Group-Definite pathogen causing infection, Yellow Group-Likely to be causing infection if present in more than one specimen and Green Group -Commensals, not causing infection. RESULTS: There was a relative reduction of 49% (p = 0.002) in bacteria in the most pathogenic (red) group, and 59% (p = 0.002) in the yellow group in podiatry samples compared with resection specimen. Positive cultures from margins of the residuum were observed in 75% of cases. There was a relative reduction of 67% (p = 0.0001) in bacteria in the red and 48% (p = 0.06) in the yellow group in marginal samples from the residuum compared with podiatry samples. CONCLUSIONS: After surgical debridement to healthy tissue, positive cultures from marginal tissue samples provided vital information on the presence of pathogenic bacteria. This allowed antibiotics to be individualised post-surgical debridement.

Clinical importance of "occult-bacterial translocation" in patients undergoing highly invasive gastrointestinal surgery: A review.

In the clinical setting, mild bacteremia cannot be detected by conventional culture methods, only by a highly sensitive bacterial detection system. One of the major causes of mild bacteremia is bacterial translocation (BT) induced by a dysregulated intestinal microenvironment and increased intestinal epithelial permeability. This condition is called "occult-bacterial translocation (O-BT)"; however, the concept of O-BT is not yet fully recognized. In our previous studies, done using a highly sensitive bacterial detection system such as bacterium-specific ribosomal RNA-targeted reverse transcriptase quantitative polymerase chain reaction (RT-qPCR), O-BT was commonly observed in patients who underwent highly invasive surgery. We collected blood and mesenteric lymph node (MLN) samples from patients undergoing esophagectomy for esophageal cancer, before and after they were subjected to surgical stress. The detection rate of bacteria in these samples increased from approximately 20% before surgical stress to more than 50% after surgical stress. Moreover, positivity for bacteria in the blood or MLN samples was associated with the incidence of postoperative infectious complications (POICs). Using the RT-qPCR system, it is possible to detect the specific bacteria that cause O-BT immediately after surgery. This may allow us to select the exact antibiotic that targets possible pathogenic bacteria of POICs.

Cortisol Metabolism in Carp Macrophages: A Role for Macrophage-Derived Cortisol in M1/M2 Polarization.

Macrophages are crucial not only for initiation of inflammation and pathogen eradication (classically polarized M1 macrophages), but also for inflammation inhibition and tissue regeneration (alternatively polarized M2 macrophages). Their polarization toward the M1 population occurs under the influence of interferon-γ + lipopolysaccharide (IFN-γ + LPS), while alternatively polarized M2 macrophages evolve upon, e.g., interlukin 4 (IL-4) or cortisol stimulation. This in vitro study focused on a possible role for macrophage-derived cortisol in M1/M2 polarization in common carp. We studied the expression of molecules involved in cortisol synthesis/conversion from and to cortisone like 11ß-hydroxysteroid dehydrogenase type 2 and 3. (11ß-HSD2 and 3) and 11ß-hydroxylase (CYP11b), as well as the expression of glucocorticoid receptors (GRs) and proliferator-activated receptor gamma (PPARγ) in M1 and M2 macrophages. Lastly, we analyzed how inhibition of these molecules affect macrophage polarization. In M1 cells, upregulation of gene expression of GRs and 11ß-HSD3 was found, while, in M2 macrophages, expression of 11ß-hsd2 was upregulated. Moreover, blocking of cortisol synthesis/conversion and GRs or PPARγ induced changes in expression of anti-inflammatory interleukin 10 (IL-10). Consequently, our data show that carp monocytes/macrophages can convert cortisol. The results strongly suggest that cortisol, via intracrine interaction with GRs, is important for IL-10-dependent control of the activity of macrophages and for the regulation of M1/M2 polarization to finally determine the outcome of an infection.

Recognizing and Managing Complications in Laser Resurfacing, Chemical Peels, and Dermabrasion.

Skin resurfacing techniques allow improvement of skin texture and color. This includes the effacement of wrinkles, signs of photoaging, and the softening of scars. Laser resurfacing, chemical peels, and dermabrasion are associated with overlapping risks of complications. The most common of these include infection, hypopigmentation, hyperpigmentation, and scarring. Patient evaluation helps provide treatment that gives the maximal benefit with a minimization of risks. This includes understanding the extent of each patient's issues (Glogau scale) and Fitzpatrick type. A thorough knowledge of potential risks will reduce their incidence and optimize early recognition and treatment of these complications when they do occur.

Infection prophylaxis patterns following pediatric autologous hematopoietic stem cell transplantation: A survey of Pediatric Transplant and Cell Therapy Consortium centers.

No standardized guidelines exist for infectious prophylaxis following pediatric auto-HSCT. We hypothesized significant variation in clinical practice. Thirty-three Pediatric Transplant and Cell Therapy Consortium centers completed a survey to assess institutional management. The majority utilize viral (91%) and fungal prophylaxis (94%), but duration varies. Bacterial prophylaxis during neutropenia is instituted by 42%. Our study demonstrates marked practice variability in infectious prophylaxis across centers. Additional research is needed to address patterns of infectious complications and to develop meaningful clinical practice guidelines for pediatric auto-HSCT.

Going Beyond Antibiotics: Natural Plant Extracts as an Emergent Strategy to Combat Biofilm-Associated Infections.

Biofilms are a collective of multiple types of bacteria that develop on a variety of surfaces. Biofilm development results in heightened resistance to antibiotics. Quorum sensing plays an important role in biofilm development as it is one of the common communication mechanisms within cells, which balances and stabilizes the environment, when the amount of bacteria increases. Because of the important implications of the roles biofilms play in infectious diseases, it is crucial to investigate natural antibacterial agents that are able to regulate biofilm formation and development. Various studies have suggested that natural plant products have the potential to suppress bacterial growth and exhibit chemopreventive traits in the modulation of biofilm development. In this review, we discuss and collate potential antibiofilm drugs and biological molecules from natural sources, along with their underlying mechanisms of action. In addition, we also discuss the antibiofilm drugs that are currently under clinical trials and highlight their potential future uses.

Cyst infection in autosomal dominant polycystic kidney disease: our experience at Toranomon Hospital and future issues.

Cyst infection is a frequent and serious complication of autosomal dominant polycystic kidney disease (ADPKD) that is often difficult to treat and can be fatal. However, much is still unknown about cyst infection. Positron emission tomography (PET) is generally recommended for detecting infected cysts, but it has the disadvantages of limited availability, high cost, and radiation exposure. We have devised magnetic resonance imaging (MRI) diagnostic criteria for cyst infection. Lipid-soluble antibiotics such as fluoroquinolones show good penetration into cysts and are recommended for cyst infection. However, we reported that fluoroquinolone-resistant microorganisms showed a high prevalence in cyst infection. We should, therefore, reconsider the empirical use of fluoroquinolones for ADPKD patients with cyst infection. We have suggested a new antibiotic strategy according to the severity of cyst infection. It may be important to consider the drug half-life in serum in addition to the drug susceptibility when selecting antibiotics Cyst drainage is necessary for some patients with refractory cyst infection; however, cyst drainage can be associated with severe adverse events. We suggest adaptation criteria for cyst drainage in patients with cyst infection in ADPKD. Most causative bacteria of cyst infection are enterobacteria, and hematogenous spread via bacterial translocation in the intestine is considered the main cause of cyst infection. Therefore, intestinal flora may be important for cyst infection. The role of the intestinal flora in cyst infection in ADPKD is unknown and should be explored in future research.

LRCH1 deficiency enhances LAT signalosome formation and CD8+ T cell responses against tumors and pathogens.

CD8+ T cells play pivotal roles in eradicating pathogens and tumor cells. T cell receptor (TCR) signaling is vital for the optimal activation of CD8+ T cells. Upon TCR engagement, the transmembrane adapter protein LAT (linker for activation of T cells) recruits other key signaling molecules and forms the "LAT signalosome" for downstream signal transduction. However, little is known about which functional partners could restrain the formation of the LAT signalosome and inhibit CD8+ cytotoxic T lymphocyte (CTL)-mediated cytotoxicity. Here we have demonstrated that LRCH1 (leucine-rich repeats and calponin homology domain containing 1) directly binds LAT, reduces LAT phosphorylation and interaction with GRB2, and also promotes the endocytosis of LAT. Lrch1-/- mice display better protection against influenza virus and Listeria infection, with enhanced CD8+ T cell proliferation and cytotoxicity. Adoptive transfer of Lrch1-/- CD8+ CTLs leads to increased B16-MO5 tumor clearance in vivo. Furthermore, knockout of LRCH1 in human chimeric antigen receptor (CAR) T cells that recognize the liver tumor-associated antigen glypican-3 could improve CAR T cell migration and proliferation in vitro. These findings suggest LRCH1 as a potential translational target to improve T cell immunotherapy against infection and tumors.

An overview of in silico vaccine design against different pathogens and cancer.

INTRODUCTION: Due to overcome the hardness of the vaccine design, computational vaccinology is emerging widely. Prediction of T cell and B cell epitopes, antigen processing analysis, antigenicity analysis, population coverage, conservancy analysis, allergenicity assessment, toxicity prediction, and protein-peptide docking are important steps in the process of designing and developing potent vaccines against various viruses and cancers. In order to perform all of the analyses, several bioinformatics tools and online web servers have been developed. Scientists must take the decision to apply more suitable and precise servers for each part based on their accuracy. AREAS COVERED: In this review, a wide-range list of different bioinformatics tools and online web servers has been provided. Moreover, some studies were proposed to show the importance of various bioinformatics tools for predicting and developing efficient vaccines against different pathogens including viruses, bacteria, parasites, and fungi as well as cancer. EXPERT OPINION: Immunoinformatics is the best way to find potential vaccine candidates against different pathogens. Thus, the selection of the most accurate tools is necessary to predict and develop potent preventive and therapeutic vaccines. To further evaluation of the computational and in silico vaccine design, in vitro/in vivo analyses are required to develop vaccine candidates.

[Pay attention to the diagnosis and treatment of intestinal infectious diarrhea after colorectal surgery].

Colorectal surgery patients have severe intestinal flora disorders and antibiotic resistant bacteria due to the disease itself and preoperative treatment, as well as the influence of dietary structure and environmental factors. Perioperative anesthesia and operative stress can cause gastrointestinal motility disorders. In addition, the widespread use of prophylactic broad-spectrum antibiotics and antiacids aggravate intestinal flora disorders and induces severe postoperative infectious diarrhea, such as pseudomembranous enteritis and fatal enteritis. The clinical manifectation are severe infectious diarrhea with high fever and abdominal distension after surgery. The disease progresses rapidly. When the diagnosis and treatment are delayed, the patient can quickly develop shock and other serious complications such as anastomotic leakage, even die of multiple organ failure. Therefore, early diagnosis and treatment are crucial.

Aplicación de la secuenciación masiva y la bioinformática al diagnóstico microbiológico clínico / Bioinformatics of next generation sequencing in clinical microbiology diagnosis

Resumen La aparición de secuenciadores masivos que permiten leer en paralelo de millones a miles de millones de secuencias o fragmentos del ADN (reads) ha revolucionado la microbiología, la cual ha pasado de un ámbito exclusivamente laboratorial a uno computacional, con la aplicación ineludible de la bioinformática. La posibilidad de efectuar estudios de la microbiota, el microbioma y el metagenoma de una muestra clínica de manera rápida y a un coste reducido permite avanzar más rápidamente en el diagnóstico de enfermedades, en el conocimiento de la taxonomía y la epidemiología de los agentes involucrados, así como de su virulencia. También posibilita la realización de estudios de genómica comparada y el descubrimiento de genes o variantes de interés, lo que puede llevar a que enfermedades tradicionalmente consideradas como de carácter no microbiano sean asociadas a la presencia de microrganismos. En esta revisión se aclara la terminología usada en este campo, y se describen las principales tecnologías de secuenciación y su utilidad en el análisis microbiano. Asimismo, se señalan diversos programas de código libre, pipelines de análisis, bases de datos y plataformas web que permiten que la bioinformática se integre exitosamente al ámbito de la microbiología clínica y al estudio de las enfermedades infecciosas.

Abstract Massive parallel sequencing (High-Throughput Sequencing [HTS]) allows to read millions or billions of DNA sequences or fragments (reads) in parallel and is revolutionizing microbiology research, moving from laboratory methods to computed-assisted analyses, with the compelling use of Bioinformatics. The time and cost reduction in studies on the microbiota, microbiome and metagenome, allows to rapidly progress in diagnosis, taxonomy, epidemiology, comparative genomics, virulence, discovery of genes or variants of interest and the association of microorganisms with traditionally considered non-microbial diseases. In this review, the terminology, the sequencing technologies and their applications are described for microbial analysis using open-source bioinformatics software, analysis pipelines, databases and web platforms that allow a user-friendly bioinformatics approach affordable by the clinical microbiologist and infectious disease practitioners.

The ABC of Major Histocompatibility Complexes and T Cell Receptors in Health and Disease.

A seminal discovery of major histocompatibility complex (MHC) restriction in T cell recognition by Peter Doherty and Rolf Zinkernagel has led to 45 years of exciting research on the mechanisms governing peptide MHC (pMHC) recognition by T cell receptors (TCRs) and their importance in health and disease. T cells provide a significant level of protection against viral, bacterial, and parasitic infections, as well as tumors, hence, the generation of protective T cell responses is a primary goal for cell-mediated vaccines and immunotherapies. Understanding the mechanisms underlying generation of optimal high-avidity effector T cell responses, memory development, maintenance, and recall is of major importance for the rational design of preventative and therapeutic vaccines/immunotherapies. In this review, we summarize the lessons learned over the last four decades and outline our current understanding of the basis and consequences of pMHC/TCR interactions on T cell development and function, and TCR diversity and composition, driving better clinical outcomes and prevention of viral escape. We also discuss the current models of T cell memory formation and determinants of immunodominant T cell responses in animal models and humans. As TCR composition and diversity can affect both the protective capacity of T cells and protection against viral escape, defining the spectrum of TCR selection has implications for improving the functional efficacy of effector T cell responsiveness and memory formation.