Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome.

Arms races between mobile genetic elements and prokaryotic hosts are major drivers of ecological and evolutionary change in microbial communities. Prokaryotic defense systems such as CRISPR-Cas have the potential to regulate microbiome composition by modifying the interactions among bacteria, plasmids, and phages. Here, we used longitudinal metagenomic data from 130 healthy and diseased individuals to study how the interplay of genetic parasites and CRISPR-Cas immunity reflects on the dynamics and composition of the human gut microbiome. Based on the coordinated study of 80 000 CRISPR-Cas loci and their targets, we show that CRISPR-Cas immunity effectively modulates bacteriophage abundances in the gut. Acquisition of CRISPR-Cas immunity typically leads to a decrease in the abundance of lytic phages but does not necessarily cause their complete disappearance. Much smaller effects are observed for lysogenic phages and plasmids. Conversely, phage-CRISPR interactions shape bacterial microdiversity by producing weak selective sweeps that benefit immune host lineages. We also show that distal (and chronologically older) regions of CRISPR arrays are enriched in spacers that are potentially functional and target crass-like phages and local prophages. This suggests that exposure to reactivated prophages and other endemic viruses is a major selective pressure in the gut microbiome that drives the maintenance of long-lasting immune memory.

RapidAIM 2.0: a high-throughput assay to study functional response of human gut microbiome to xenobiotics.

Aim: Our gut microbiome has its own functionalities which can be modulated by various xenobiotic and biotic components. The development and application of a high-throughput functional screening approach of individual gut microbiomes accelerates drug discovery and our understanding of microbiome-drug interactions. We previously developed the rapid assay of individual microbiome (RapidAIM), which combined an optimized culturing model with metaproteomics to study gut microbiome responses to xenobiotics. In this study, we aim to incorporate automation and multiplexing techniques into RapidAIM to develop a high-throughput protocol. Methods: To develop a 2.0 version of RapidAIM, we automated the protein analysis protocol, and introduced a tandem mass tag (TMT) multiplexing technique. To demonstrate the typical outcome of the protocol, we used RapidAIM 2.0 to evaluate the effect of prebiotic kestose on ex vivo individual human gut microbiomes biobanked with five different workflows. Results: We describe the protocol of RapidAIM 2.0 with extensive details on stool sample collection, biobanking, in vitro culturing and stimulation, sample processing, metaproteomics measurement, and data analysis. The analysis depth of 5,014 ± 142 protein groups per multiplexed sample was achieved. A test on five biobanking methods using RapidAIM 2.0 showed the minimal effect of sample processing on live microbiota functional responses to kestose. Conclusions: Depth and reproducibility of RapidAIM 2.0 are comparable to previous manual label-free metaproteomic analyses. In the meantime, the protocol realizes culturing and sample preparation of 320 samples in six days, opening the door to extensively understanding the effects of xenobiotic and biotic factors on our internal ecology.

Elevated complement C3 and increased CD8 and type 1 helper lymphocyte T populations in patients with post-COVID-19 condition.

BACKGROUND: Biological markers associated to post-COVID-19 condition (PCC) have not been clearly identified. METHODS: Eighty-two patients attending our post-COVID-19 outpatient clinic were recruited and classified as fully recovered (40.2%) or presenting with PCC (59.8%). Clinical and radiological data, laboratory markers, cytokines, and lymphocyte populations were analyzed. RESULTS: Median number of days after hospitalization was 78.5 [p25-p75: 60-93] days. PCC was significantly more frequent in women, in patients with a previously critical COVID-19, and in those with two or more comorbidities. No differences were found in lymphocyte counts, ferritin, C-reactive protein, D-dimer or sCD25, IL-1ß, IL-1Ra, IL-6, CXCL8, IL-17A, IL-18, IL-22, IFN-γ, TNF-α, and IL-10 cytokines levels. PCC patients showed significantly higher levels of complement factor C3 than fully recovered patients: median C3 128 mg/dL [p25-p75:107-135] vs 111 mg/dL [p25-p75: 100-125] (p =.005), respectively. In the flow cytometry assessment of peripheral blood lymphocyte subpopulations, PCC patients showed significantly increased CD8 populations compared to fully recovered patients: median CD8: 529 [p25-p75: 384-683] vs 370/mm3 [p25-p75:280-523], p =.007. When type 1, 2, 17/22, and 17.1 helper and follicular T lymphocyte subpopulations were analyzed, the frequency of Th1 was significantly higher in PCC patients compared to fully recovered patients (30% vs 38.5%, p =.028). CONCLUSION: Patients with a post-COVID-19 condition showed significantly increased immunological parameters of inflammation (complement factor C3 and CD8 and Th1 T lymphocyte populations) compared to fully recovered patients. These parameters could be used as biological markers of this condition.

Advantages and Short-Term Outcomes of Laparoscopic-Assisted Renal Surgery in Elderly Patients.

OBJECTIVE: To compare the perioperative results of adult and elderly patients undergoing laparoscopic renal surgery. METHODOLOGY: Retrospective, analytical study. 448 who underwent kidney surgery for benign or malignant pathologies between 2011-2019 were included in the General Hospital of Mexico "Dr. Eduardo Liceaga". They were categorized into two groups: Group 1 <60 years and Group 2 >60 years. Descriptive statistics and bivariate analysis were performed, the calculations were performed with 95% reliability and a value of p (<0.05). RESULTS: In the group over 60 years of age, the following was found: Age: 67.1 years (60-83). IMC 28.3 kg/m2 (19-48.7). Intra and postsurgical outcomes: intraoperative bleeding = 184.4cc (5-1700). Surgical Time = 112.6min (30-240). Days of hospital stay = 2 (1-7). Complications in 2.6% (Clavien-Dindo: I = 2; II = 1), no conversion was required in any patient. There were no statistically significant differences with group 1, an exception for intraoperative bleeding. CONCLUSIONS: Our study is a pioneer in Latin America in the evaluation of the geriatric population and outcomes with laparoscopic surgery and we recommend that renal procedures with a laparoscopic approach should be considered as the best strategy in the management of benign or malignant renal pathology in geriatric patients.

Increased mRNA Levels of ADAM17, IFITM3, and IFNE in Peripheral Blood Cells Are Present in Patients with Obesity and May Predict Severe COVID-19 Evolution.

Gene expression patterns in blood cells from SARS-CoV-2 infected individuals with different clinical phenotypes and body mass index (BMI) could help to identify possible early prognosis factors for COVID-19. We recruited patients with COVID-19 admitted in Hospital Universitari Son Espases (HUSE) between March 2020 and November 2021, and control subjects. Peripheral blood cells (PBCs) and plasma samples were obtained on hospital admission. Gene expression of candidate transcriptomic biomarkers in PBCs were compared based on the patients' clinical status (mild, severe and critical) and BMI range (normal weight, overweight, and obesity). mRNA levels of ADAM17, IFITM3, IL6, CXCL10, CXCL11, IFNG and TYK2 were increased in PBCs of COVID-19 patients (n = 73) compared with controls (n = 47), independently of sex. Increased expression of IFNE was observed in the male patients only. PBC mRNA levels of ADAM17, IFITM3, CXCL11, and CCR2 were higher in those patients that experienced a more serious evolution during hospitalization. ADAM17, IFITM3, IL6 and IFNE were more highly expressed in PBCs of patients with obesity. Interestingly, the expression pattern of ADAM17, IFITM3 and IFNE in PBCs was related to both the severity of COVID-19 evolution and obesity status, especially in the male patients. In conclusion, gene expression in PBCs can be useful for the prognosis of COVID-19 evolution.

UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions.

Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. Within the last few years, a burst of research has led to the discovery of novel prokaryotic RTs with diverse antiviral properties, such as DRTs (Defense-associated RTs), which belong to the so-called group of unknown RTs (UG) and are closely related to the Abortive Infection system (Abi) RTs. In this work, we performed a systematic analysis of UG and Abi RTs, increasing the number of UG/Abi members up to 42 highly diverse groups, most of which are predicted to be functionally associated with other gene(s) or domain(s). Based on this information, we classified these systems into three major classes. In addition, we reveal that most of these groups are associated with defense functions and/or mobile genetic elements, and demonstrate the antiphage role of four novel groups. Besides, we highlight the presence of one of these systems in novel families of human gut viruses infecting members of the Bacteroidetes and Firmicutes phyla. This work lays the foundation for a comprehensive and unified understanding of these highly diverse RTs with enormous biotechnological potential.

Fluconazole-resistant Candida parapsilosis clonally related genotypes: first report proving the presence of endemic isolates harbouring the Y132F ERG11 gene substitution in Spain.

OBJECTIVES: We report here for the first time the presence of Candida parapsilosis isolates harbouring the Y132F ERG11 gene substitution in patients admitted to a Spanish hospital. METHODS: We studied the available (n = 104) C parapsilosis isolates from patients admitted to the Son Espases reference hospital in the Balearic Islands from 1 April 2019 to 30 November 2020. Isolates were sourced from 70 patients: catheter (n = 41), blood cultures (n = 37), lower respiratory tract (n = 15), intra-abdominal (n = 8), and other samples (n = 3). Isolates were genotyped and tested for antifungal susceptibilities to amphotericin B, triazoles, anidulafungin, and micafungin using EUCAST E.Def 7.3.2. The ERG11 gene was sequenced in fluconazole-resistant isolates. RESULTS: Among the 104 isolates, fluconazole and voriconazole resistance was found in 87 (84%) and 30 (29%) isolates, respectively; all isolates were fully susceptible to echinocandins and amphotericin B. All fluconazole-resistant isolates harboured the Y132F substitution in the ERG11 gene and were grouped into 11 clonally related genotypes. A genotype accounted for 70% (61/87) of fluconazole-resistant isolates. Genotypes involving the fluconazole-resistant isolates were different from those found in the remaining fluconazole-susceptible genotypes. Fifty-six patients harboured fluconazole-resistant genotypes, and 35 of the 56 had candidaemia (48%), abdominal candidiasis (17%), or other forms of candidiasis (35%). Only 20% of the study patients infected by fluconazole-resistant genotypes had a history of azole use. DISCUSSION: Fluconazole resistance in C parapsilosis isolates from patients admitted to this reference hospital is not attributable to prior azole use, but rather to the presence of a group of fluconazole-resistant C parapsilosis genotypes that have become endemic.

Hyperinflammatory State and Low T1 Adaptive Immune Response in Severe and Critical Acute COVID-19 Patients.

Background: A better understanding of COVID-19 immunopathology is needed to identify the most vulnerable patients and improve treatment options. Objective: We aimed to identify immune system cell populations, cytokines, and inflammatory markers related to severity in COVID-19. Methods: 139 hospitalized patients with COVID-19-58 mild/moderate and 81 severe/critical-and 74 recovered patients were included in a prospective longitudinal study. Clinical data and blood samples were obtained on admission for laboratory markers, cytokines, and lymphocyte subsets study. In the recovered patients, lymphocyte subsets were analyzed 8-12 weeks after discharge. Results: A National Early Warning Score 2 >2 (OR:41.4; CI:10.38-167.0), ferritin >583 pg/mL (OR:16.3; CI: 3.88-69.9), neutrophil/lymphocyte ratio >3 (OR: 3.5; CI: 1.08-12.0), sIL-2rα (sCD25) >512 pg/mL (OR: 3.3; CI: 1.48-7.9), IL-1Ra >94 pg/mL (OR: 3.2; IC: 1.4-7.3), and IL-18 >125 pg/mL (OR: 2.4; CI: 1.1-5.0) were associated with severe/critical COVID-19 in the multivariate models used. Lower absolute values of CD3, CD4, CD8, and CD19 lymphocytes together with higher frequencies of NK cells, a CD4 and CD8 activated (CD38+HLA-DR+) memory T cell and effector memory CD45RA+ (EMRA) phenotype, and lower T regulatory cell frequencies were found in severe/critical patients relative to mild/moderate and recovered COVID-19 patients. A significant reduction in Th1, Tfh1, and Tc1 with higher Th2, Tfh2, Tc2, and plasma cell frequencies was found in the most severe cases. Conclusion: A characteristic hyperinflammatory state with significantly elevated neutrophil/lymphocyte ratio and ferritin, IL-1Ra, sIL-2rα, and IL-18 levels together with a "low T1 lymphocyte signature" was found in severe/critical COVID-19 patients.

Efficacy and Safety of Sarilumab in patients with COVID19 Pneumonia: A Randomized, Phase III Clinical Trial (SARTRE Study).

INTRODUCTION: SARS-CoV-2 pneumonia is often associated with hyper-inflammation. The cytokine-storm-like is one of the targets of current therapies for coronavirus disease 2019 (COVID-19). High Interleukin-6 (IL6) blood levels have been identified in severe COVID-19 disease, but there are still uncertainties regarding the actual role of anti-IL6 antagonists in COVID-19 management. Our hypothesis was that the use of sarilumab plus corticosteroids at an early stage of the hyper-inflammatory syndrome would be beneficial and prevent progression to acute respiratory distress syndrome (ARDS). METHODS: We randomly assigned (in a 1:1 ratio) COVID-19 pneumonia hospitalized patients under standard oxygen therapy and laboratory evidence of hyper-inflammation to receive sarilumab plus usual care (experimental group) or usual care alone (control group). Corticosteroids were given to all patients at a 1 mg/kg/day of methylprednisolone for at least 3 days. The primary outcome was the proportion of patients progressing to severe respiratory failure (defined as a score in the Brescia-COVID19 scale ≥ 3) up to day 15. RESULTS: A total of 201 patients underwent randomization: 99 patients in the sarilumab group and 102 patients in the control group. The rate of patients progressing to severe respiratory failure (Brescia-COVID scale score ≥ 3) up to day 15 was 16.16% in the Sarilumab group versus 15.69% in the control group (RR 1.03; 95% CI 0.48-2.20). No relevant safety issues were identified. CONCLUSIONS: In hospitalized patients with Covid-19 pneumonia, who were under standard oxygen therapy and who presented analytical inflammatory parameters, an early therapeutic intervention with sarilumab plus standard of care (including corticosteroids) was not shown to be more effective than current standard of care alone. The study was registered at EudraCT with number: 2020-002037-15.

Predictive Immunological, Virological, and Routine Laboratory Markers for Critical COVID-19 on Admission.

BACKGROUND: Early identification of COVID-19 patients at risk of critical illness is a challenging endeavor for clinicians. We aimed to establish immunological, virological, and routine laboratory markers, which, in combination with clinical information, may allow identifying such patients. METHODS: Blood tests to measure neutrophil/lymphocyte ratio (NLR) and levels of ferritin, CRP, D-dimer, complement components (C3 and C4), cytokines, and lymphocyte subsets, as well as SARS-Cov-2 RT-PCR tests, were performed in COVID-19-confirmed cases within 48 hours of admission. RT-PCR cycle threshold (Ct) values from oropharyngeal or nasopharyngeal swabs were determined on the day of admission. Symptom severity was categorized as mild (grade 1), severe (grade 2), or critical (grade 3). RESULTS: Of 120 patients who were included, 49 had mild, 32 severe, and 39 critical COVID-19. Levels of ferritin >370 ng/mL (OR 16.4, 95% CI 5.3-50.8), D-dimer >440 ng/mL (OR 5.45, 95% CI 2.36-12.61), CRP >7.65 mg/dL (OR 11.54, 95% CI 4.3-30.8), NLR >3.77 (OR 13.4, 95% CI 4.3-41.1), IL-6 >142.5 pg/mL (OR 8.76, 95% CI 3.56-21.54), IL-10 >10.8 pg/mL (OR 16.45, 95% CI 5.32-50.81), sIL-2rα (sCD25) >804.5 pg/mL (OR 14.06, 95% CI 4.56-43.28), IL-1Ra >88.4 pg/mL (OR 4.54, 95% CI 2.03-10.17), and IL-18 >144 pg/mL (OR 17.85, 95% CI 6.54-48.78) were associated with critical COVID-19 in the univariate age-adjusted analysis. This association was confirmed in the multivariate age-adjusted analysis only for ferritin, CRP, NLR, IL-10, sIL-2rα, and IL-18. T, B, and NK cells were significantly decreased in critical patients. SARS-CoV-2 was not detected in blood except in 3 patients who had indeterminate results. RT-PCR Ct values from oropharyngeal or nasopharyngeal swabs on admission were not related to symptom severity. CONCLUSION: Ferritin, D-dimer, CRP, NLR, cytokine (IL-18 and IL-10), and cytokine receptor (IL-6, IL1-Ra, and sCD25) test results combined with clinical data can contribute to the early identification of critical COVID-19 patients.

Experiencia de la plastia laparoscópica de uréter retrocavo en el Hospital General de México Dr. Eduardo Liceaga.

INTRODUCCIÓN: El uréter retrocavo es una anomalía congénita rara que requiere manejo quirúrgico. OBJETIVO: Reportar los resultados en el manejo laparoscópico para uréter retrocavo y hacer una revisión bibliográfica. MÉTODO: Estudio retrospectivo, descriptivo, transversal, en pacientes con diagnóstico de uréter retrocavo que fueron sometidos a plastia laparoscópica de uréter retrocavo. RESULTADOS: Cuatro pacientes sometidos a plastia laparoscópica por diagnóstico de uréter retrocavo, 1 hombre y 3 mujeres, con una media de edad de 40.7 años. La media del tiempo operatorio fue de 138.2 minutos. La pérdida de sangre cuantificada transoperatoria media fue de 23.7 ml. Ningún paciente presentó complicaciones transoperatorias ni posoperatorias. Los pacientes permanecieron hospitalizados hasta su egreso una media de 2.5 días. Todos los pacientes presentaron mejoría de su sintomatología. CONCLUSIONES: El uréter retrocavo es una condición rara y aún no existe un consenso sobre su diagnóstico, tratamiento y seguimiento. El manejo quirúrgico laparoscópico es una opción para el tratamiento de estos pacientes. INTRODUCTION: The retrocave ureter is a rare congenital anomaly that requires surgical management. OBJECTIVE: Report the results in laparoscopic management for retrocave ureter and literature review. METHOD: Retrospective, descriptive, cross-sectional study in patients with a diagnosis of retrocave ureter who were sometimes a laparoscopic retrocave ureter. RESULTS: Four patients sometimes underwent laparoscopic plasty for diagnosis of retrocave ureter, 1 man and 3 women, with a mean age of 40.7 years. The mean operative time was 138.2 minutes. The mean intraoperative quantified blood loss was 23.7 ml. No patient presented transoperative or postoperative complications. The patients remained hospitalized until their progress with an average of 2.5 days. All patients visualize improvement in their symptoms. CONCLUSION: The retrocave ureter is a rare condition and there is still no consensus on its diagnosis, treatment and follow-up. Laparoscopic surgical management is an option for the treatment of these patients.

Adrenal cyst: our experience in its laparoscopic management.

ANTECEDENTES: Los quistes suprarrenales son una afección rara. Su diagnóstico y su tratamiento son un desafío debido a la escasa información, lo que genera incertidumbre respecto al mejor manejo. CASOS CLÍNICOS: Presentamos tres casos de quistes suprarrenales que recibieron tratamiento de mínima invasión con cirugía laparoscópica, sin presentar complicaciones y con una evolución favorable. DISCUSIÓN: Las nuevas técnicas quirúrgicas de mínima invasión ofrecen una oportunidad terapéutica que permite preservar estructuras y obtener material necesario para su diagnóstico histopatológico, así como la resolución de la sintomatología. BACKGROUND: Adrenal cysts are a rare entity; their diagnosis and treatment are challenging due to the lack of information, generating uncertainty regarding the best management. CASE REPORTS: We present three cases of adrenal cysts that received minimally invasive treatment with laparoscopic surgery, without complications and with a favorable evolution. DISCUSSION: The new minimally invasive surgical techniques offer a therapeutic opportunity that allows preserving structures and obtaining the necessary material for histopathological diagnosis, as well as a resolution of the symptoms.

Epidemiological and clinical characteristics of community-acquired and nosocomial influenza cases and risk factors associated with complications: A four season analysis of all adult patients admitted in a tertiary hospital.

BACKGROUND: Information on the characteristics of patients with nosocomial influenza and associated complications is scarce. This study compared epidemiological and clinical characteristics of patients admitted with hospital-acquired influenza (HAI) to those with community-acquired influenza (CAI) and analyzed risk factors associated with complications. METHODS: This retrospective, observational study included all adult patients with confirmed influenza virus infection admitted to Son Espases University Hospital during the influenza season in Spain (October to May) from 2012-2013 to 2015-2016. Symptom onset before admission was included as CAI, and 2 days after admission or within 48 hours after previous discharge were considered as HAI. RESULTS: Overall, 666 patients with laboratory-confirmed influenza were included; 590 (88.6%) and 76 (11.4%) had CAI and HAI, respectively. Baseline characteristics and vaccination rates were similar in both groups. Patients with HAI had significantly fewer symptoms, less radiological alterations, and earlier microbiological diagnosis than those with CAI. Eighty-five (14.4%) and 20 (27.6%) CAI and HAI patients, respectively, experienced at least one complication, including septic shock, admission to the intensive care unit, mechanical ventilation or evolution to death (any one, P = .003). Univariate and multivariate binary logistic regression was performed to assess independent risk factors associated with the occurrence of complications: nosocomial infection, diabetes, oseltamivir treatment, having received no vaccination, microbiological delay, dyspnea, and the state of confusion were the most important significant factors. CONCLUSIONS: Our study shows the need to implement microbiological diagnostic measures in the first 48 hours to reduce HAI frequency and associated complications.

Prevalencia de Blues (depresión puerperal inmediata) en el Hospital Regional San Vicente de Paul / Prevalencia de Blues (inmediate puerperal depression) in the Regional Hospital San Vicente of Paúl

Dentro de los trastornos afectivos del postparto la depresión es el Trastorno mas frecuente, y se puede presentar desde unas pocas horas de iniciado el puerperio hasta los 6 meses posteriores al parto. A estos trastornos depresivos se los ha dividido en tres categorías: El Blues (depresión azul), la Depresión Mayor y Psicosis postparto. El primero es un trastorno muy frecuente, cuya etiología aun no está suficientemente aclarada, sin embargo se piensa que factores biológicos, psicológicos y sociales especiales, pueden conjugarse en la génesis de este trastorno. Nosotros realizamos un estudio proyectivo descriptivo en la ciudad de Ibarra, en el servicio de Ginecoobstetricia, del Hospital Regional "San Vicente de Paul" en 108 mujeres que cursaban el cuarto día postparto y que reunían los criterios de inclusión propuestos en el protocolo de investigación. Para su evaluación clínica tomamos como marco de referencia los criterios diagnósticos de investigación para Trastorno Depresivo del Manual Diagnóstico y Estadístico de la Asociación Norteamericana de Psiquiatría, tercera edición revisada (DSM III-R). Se encontró una prevalencia de Blues total del 38.9 por ciento, y por niveles: Leve 20.4 por ciento, moderada 14.8 por ciento y severa 3.7 por ciento. Se determinó el riesgo relativo para Blues entre las variables planteadas y se encontró en orden descendente de importancia los siguientes factores de riesgo: Bajo nivel de instrucción, desempleadas o dedicadas a las tareas del hoga, Mayores de 35 años, Procedentes de área rural, Presencia de estrés psicosocial durante el embarazo, Mujeres solteras o sin relación estable de pareja...

Aspectos psiquiátricos del sueño / Psychiatric aspects of the dream

Revisa los aspectos más importantes relacionados con el sueño, su desarrollo ontogénico, fisiología, neuranatomía y pautas diagnósticas. Se realizó un estudio de prevalencia de insomnio por hospitalización en 50 pacientes que llenaron un formulario básico construido en base a los criterios diagnósticos del DSMIII-R para insomnio, Se encontró que un 55,5xcto de pacientes hospitalizados presentó insomnio debido a la hospitalización, el tipo de insomnio mas reportado fue el Intermedio. Se encontró que a mayor edad hay mayor riesgo para insomnio. Los hombres presentan más insomnio por hospitalización que las mujeres. La falta de sueño reparador fue una queja común a todos los pacientes que refirieron insomnio. Los pacientes con antecedentes de insomnio crónico tenían una prevalencia mayor de ronquido durante la noche. A pesar del alto porcentaje de pacientes con insomnio crónico, es muy bajo el porcentaje de personas que buscan ayuda profesional y prefieren automedicarse.