Fecal Microbiota of Toxigenic Clostridioides difficile-Associated Diarrhea

Clostridioides difficile infection (CDI) is currently one of the most important causes of infectious diarrhea in developed countries and the main cause in healthcare settings. Here, we characterized the gut microbiota from the feces of 57 patients with diarrhea from nosocomial and community-acquired CDI. We performed an ecological analysis by high-throughput sequencing of the V3-V4 region of 16S rRNA amplicons and evaluated the association of the various ecological profiles with CDI risk factors. Among all samples Bacteroidaceae 31.01%, Enterobacteriaceae 9.82%, Lachnospiraceae 9.33%, Tannerellaceae 6,16%, and Ruminococcaceae 5.64%, were the most abundant families. A reduced abundance of Bacteroides was associated with a poor CDI prognosis, with severe diarrhea and a high incidence of recurrence. This reduction was associated with a weakened host immune system and previous aggressive antibiotherapy. Peptostreptococcaceae family was 1.56% overall and within the family the only identified member was the genus Clostridioides, positively correlated with the presence of Akkermansia that may be predictive of the presence of a CDI. Finally, a relevant aspect that must be considered in clinical practice is the misdiagnosis of CDI, as patients with a stool sample that tests positive for C. difficile are usually diagnosed with CDI and subsequently treated as such. However, co-infection with other pathogenic agents often plays an important role in the development of diarrhea, and must be considered when prescribing antibiotic treatment

Occurrence of Hepatitis E Virus in Pigs and Pork Cuts and Organs at the Time of Slaughter, Spain, 2017

Zoonotic hepatitis E, mainly caused by hepatitis E virus (HEV) genotype (gt) 3, is a foodborne disease that has emerged in Europe in recent decades. The main animal reservoir for genotype 3 is domestic pigs. Pig liver and liver derivates are considered the major risk products, and studies focused on the presence of HEV in pig muscles are scarce. The objective of the present study was to evaluate the presence of HEV in different organs and tissues of 45 apparently healthy pigs from nine Spanish slaughterhouses (50% national production) that could enter into the food supply chain. Anti-HEV antibodies were evaluated in serum by an ELISA test. Ten samples from each animal were analyzed for the presence of HEV RNA by reverse transcription realtime PCR (RT-qPCR). The overall seroprevalence obtained was 73.3% (33/45). From the 450 samples analyzed, a total of 26 RT-qPCR positive samples were identified in the liver (7/45), feces (6/45), kidney (5/45), heart (4/45), serum (3/45), and diaphragm (1/45). This is the first report on detection of HEV RNA in kidney and heart samples of naturally infected pigs. HEV RNA detection was negative for rib, bacon, lean ham, and loin samples. These findings indicate that pig meat could be considered as a low risk material for foodborne HEV infection.Fil: García, Nerea. Universidad Complutense de Madrid; EspañaFil: Hernández, Marta. Universidad de Burgos; EspañaFil: Gutierrez Boada, Maialen. Universidad de Burgos; EspañaFil: Valero, Antonio. Universidad de Córdoba; EspañaFil: Navarro, Alejandro. Universidad Complutense de Madrid; EspañaFil: Muñoz Chimeno, Milagros. Universidad Carlos III de Madrid. Instituto de Salud; EspañaFil: Fernández Manzano, Alvaro. Universidad Complutense de Madrid; EspañaFil: Escobar, Franco Matias. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Martínez, Irene. Universidad Complutense de Madrid; EspañaFil: Bárcena, Carmen. Universidad Complutense de Madrid; EspañaFil: González, Sergio. Universidad Complutense de Madrid; EspañaFil: Avellón, Ana. Universidad Carlos III de Madrid. Instituto de Salud; EspañaFil: Eiros, Jose M.. Hospital Universitario Rio Hortega; EspañaFil: Fongaro, Gislaine. Universidade Federal de Santa Catarina; BrasilFil: Domínguez, Lucas. Universidad Complutense de Madrid; EspañaFil: Goyache, Joaquín. Universidad Complutense de Madrid; EspañaFil: Rodríguez Lázaro, David. Universidad de Burgos; Españ

Th1 and Th17 hypercytokinemia as early host response signature in severe pandemic influenza

Abstract Introduction Human host immune response following infection with the new variant of A/H1N1 pandemic influenza virus (nvH1N1) is poorly understood. We utilize here systemic cytokine and antibody levels in evaluating differences in early immune response in both mild and severe patients infected with nvH1N1. Methods We profiled 29 cytokines and chemokines and evaluated the haemagglutination inhibition activity as quantitative and qualitative measurements of host immune responses in serum obtained during the first five days after symptoms onset, in two cohorts of nvH1N1 infected patients. Severe patients required hospitalization (n = 20), due to respiratory insufficiency (10 of them were admitted to the intensive care unit), while mild patients had exclusively flu-like symptoms (n = 15). A group of healthy donors was included as control (n = 15). Differences in levels of mediators between groups were assessed by using the non parametric U-Mann Whitney test. Association between variables was determined by calculating the Spearman correlation coefficient. Viral load was performed in serum by using real-time PCR targeting the neuraminidase gene. Results Increased levels of innate-immunity mediators (IP-10, MCP-1, MIP-1β), and the absence of anti-nvH1N1 antibodies, characterized the early response to nvH1N1 infection in both hospitalized and mild patients. High systemic levels of type-II interferon (IFN-γ) and also of a group of mediators involved in the development of T-helper 17 (IL-8, IL-9, IL-17, IL-6) and T-helper 1 (TNF-α, IL-15, IL-12p70) responses were exclusively found in hospitalized patients. IL-15, IL-12p70, IL-6 constituted a hallmark of critical illness in our study. A significant inverse association was found between IL-6, IL-8 and PaO2 in critical patients. Conclusions While infection with the nvH1N1 induces a typical innate response in both mild and severe patients, severe disease with respiratory involvement is characterized by early secretion of Th17 and Th1 cytokines usually associated with cell mediated immunity but also commonly linked to the pathogenesis of autoimmune/inflammatory diseases. The exact role of Th1 and Th17 mediators in the evolution of nvH1N1 mild and severe disease merits further investigation as to the detrimental or beneficial role these cytokines play in severe illness

Trends in the prevalence and distribution of HTLV-1 and HTLV-2 infections in Spain

<p>Abstract</p> <p>Background</p> <p>Although most HTLV infections in Spain have been found in native intravenous drug users carrying HTLV-2, the large immigration flows from Latin America and Sub-Saharan Africa in recent years may have changed the prevalence and distribution of HTLV-1 and HTLV-2 infections, and hypothetically open the opportunity for introducing HTLV-3 or HTLV-4 in Spain. To assess the current seroprevalence of HTLV infection in Spain a national multicenter, cross-sectional, study was conducted in June 2009.</p> <p>Results</p> <p>A total of 6,460 consecutive outpatients attending 16 hospitals were examined. Overall, 12% were immigrants, and their main origin was Latin America (4.9%), Africa (3.6%) and other European countries (2.8%). Nine individuals were seroreactive for HTLV antibodies (overall prevalence, 0.14%). Evidence of HTLV-1 infection was confirmed by Western blot in 4 subjects (prevalence 0.06%) while HTLV-2 infection was found in 5 (prevalence 0.08%). Infection with HTLV types 1, 2, 3 and 4 was discarded by Western blot and specific PCR assays in another two specimens initially reactive in the enzyme immunoassay. All but one HTLV-1 cases were Latin-Americans while all persons with HTLV-2 infection were native Spaniards.</p> <p>Conclusions</p> <p>The overall prevalence of HTLV infections in Spain remains low, with no evidence of HTLV-3 or HTLV-4 infections so far.</p

Direct association between pharyngeal viral secretion and host cytokine response in severe pandemic influenza

<p>Abstract</p> <p>Background</p> <p>Severe disease caused by 2009 pandemic influenza A/H1N1virus is characterized by the presence of hypercytokinemia. The origin of the exacerbated cytokine response is unclear. As observed previously, uncontrolled influenza virus replication could strongly influence cytokine production. The objective of the present study was to evaluate the relationship between host cytokine responses and viral levels in pandemic influenza critically ill patients.</p> <p>Methods</p> <p>Twenty three patients admitted to the ICU with primary viral pneumonia were included in this study. A quantitative PCR based method targeting the M1 influenza gene was developed to quantify pharyngeal viral load. In addition, by using a multiplex based assay, we systematically evaluated host cytokine responses to the viral infection at admission to the ICU. Correlation studies between cytokine levels and viral load were done by calculating the Spearman correlation coefficient.</p> <p>Results</p> <p>Fifteen patients needed of intubation and ventilation, while eight did not need of mechanical ventilation during ICU hospitalization. Viral load in pharyngeal swabs was 300 fold higher in the group of patients with the worst respiratory condition at admission to the ICU. Pharyngeal viral load directly correlated with plasma levels of the pro-inflammatory cytokines IL-6, IL-12p70, IFN-γ, the chemotactic factors MIP-1β, GM-CSF, the angiogenic mediator VEGF and also of the immuno-modulatory cytokine IL-1ra (p < 0.05). Correlation studies demonstrated also the existence of a significant positive association between the levels of these mediators, evidencing that they are simultaneously regulated in response to the virus.</p> <p>Conclusions</p> <p>Severe respiratory disease caused by the 2009 pandemic influenza virus is characterized by the existence of a direct association between viral replication and host cytokine response, revealing a potential pathogenic link with the severe disease caused by other influenza subtypes such as H5N1.</p

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality

TORMES: an automated pipeline for whole bacterial genome analysis

El progreso de las tecnologías de secuenciación de alto rendimiento (HTS) y la reducción de los costes de secuenciación son tales que la secuenciación del genoma completo (WGS) ha sustituido a muchos ensayos y procedimientos tradicionales de laboratorio. La explotación del volumen de datos producidos por las plataformas de HTS requiere importantes conocimientos informáticos, lo que constituye el principal cuello de botella para la implantación de la WGS como técnica rutinaria de laboratorio. La forma de presentar la ingente cantidad de resultados a investigadores y clínicos sin conocimientos especializados en secuenciación genómica es también un problema importante. Nuestro trabajo como especialistas en técnicas de laboratorio tuvo que evolucionar hacia el aprendizaje bioinformático así que tras realizar el diploma en la universidad sevillana Pablo Olavide fuimos capaces de desarrollar el pipeline TORMES, en honor al río salmantino, un pipeline de fácil uso para el análisis WGS de bacterias de cualquier origen generadas por HTS en plataformas Illumina. Permite realizar un análisis genómico completo de un conjunto de bacterias (sin importar el número, especie u origen) partiendo directamente de los datos sin tratar procedentes de la plataforma de secuenciación. TORMES es de código libre y requiere seguir unas instrucciones sencillas para su instalación y uso, lo que lo convierte en una herramienta idónea para los usuarios sin conocimientos avanzados en bioinformática. TORMES está diseñado para usuarios no bioinformáticos, y automatiza los pasos necesarios para el análisis WGS directamente a partir de los datos de la secuencia en bruto: filtrado de la calidad de la secuencia, ensamblaje de novo, ordenación del genoma borrador frente a una referencia, anotación del genoma, tipado de secuencias multilocus (MLST), búsqueda de resistencia a antibióticos y genes de virulencia, y comparaciones de pangenomas. Una vez finalizado el análisis, TORMES genera un informe interactivo de tipo web que puede abrirse en cualquier navegador y ser compartido y revisado por los investigadores de forma sencilla. TORMES puede ejecutarse mediante comandos muy sencillos y representa una forma rápida y fácil de realizar análisis WGS

Infrequent isolation of extensively drug-resistant (XDR) Klebsiella pneumoniae resistant to colistin in Spain

Entre las Enterobacteriaceae se detecta con frecuencia una corresistencia al carbapenem con otras clases de antimicrobianos (por ejemplo, fluoroquinolonas o aminoglucósidos), lo que a menudo limita las opciones terapéuticas a antibióticos de último recurso como la colistina o la tigeciclina [1]. Tras la reintroducción de la colistina a mediados de los años noventa para combatir las infecciones causadas por bacterias Gram negativas productoras de carbapenemasas, la resistencia a las polimixinas, sobre todo en la Klebsiella pneumoniae resistente a los carbapenemasas, ha ido aumentando de forma constante en todo el mundo y constituye ahora un importante motivo de preocupación en Europa [2]. Del mismo modo, también se han notificado casos de corresistencia a otros antibióticos de último recurso, como la tigeciclina [3]. Nuestro objetivo fue investigar los fenotipos de resistencia a los antimicrobianos entre K. pneumoniae resistentes a carbapenemes aislados en 2016 en un hospital terciario de España y caracterizar aquellos que eran extremadamente resistentes a los fármacos (XDR). Se recogieron un total de 814 aislados de K. pneumoniae en el Hospital Universitario Río Hortega (Valladolid, Castilla y León, España) en 2016 durante la vigilancia interna (vigilancia epidemiológica rutinaria de frotis faríngeos y rectales, así como de aspirados traqueales en unidades de cuidados intensivos, y análisis microbiológico de muestras infecciosas clínicas), de los cuales 67 aislados se confirmaron como productores de OXA-48 mediante Xpert® Carba-R (Cepheid, Sunnyvale, CA). De los 67 aislados, 5 (7,5%) eran productores de β-lactamasas de espectro extendido (BLEE) y eran resistentes a la colistina y las quinolonas, y 4 aislados (6,0%) también eran resistentes a la tigeciclina (Tabla 1). Curiosamente, cuatro de los cinco aislados XDR se recogieron en un estrecho margen de tiempo de una semana en mayo de 2016