Detección y caracterización de cepas Escherichia coli enteropatógena (EPEC) aisladas de la cavidad nasal de cerdos potencialmente sanos

Introducción: Escherichia coli enteropatógena (EPEC) es un importante patógeno, implicado enprocesos diarreicos asociados a infecciones extraintestinales tanto en clínica humana como enveterinaria. Las cepas EPEC poseen el gen eae (codificante de intimina) y carecen de stx (toxinashiga), y pueden ser EPEC típicas/atípicas en función de la presencia/ausencia del gen bfp. Elobjetivo de este estudio fue analizar la frecuencia de E. coli y EPEC en muestras nasales de cerdospotencialmente sanos, así como la relación genética y los perfiles de sensibilidad a antibióticos delos aislados EPEC. Materiales y métodos: Se analizaron muestras nasales de 40 cerdos de cuatrogranjas de Aragón (10 cerdos/granja) y fueron procesadas para el estudio de la microbiota nasalmediante el cultivo de bacterias Gram positivas y negativas. Se aislaron cepas de E. coli en agarsangre y se determinó a) la sensibilidad a antibióticos (CLSI, 2022); b) presencia del gen eae y bfppor PCR y el genotipo de resistencia a antibióticos de los aislados EPEC. Resultados: Se detectóla presencia de E. coli en 17/40 cerdos analizados (42.5%) y 25 aislados fueron recuperados. Lapresencia de EPEC se reflejó en 7/40 cerdos (17.5%) de 2/4 granjas, con 10 aislados EPEC. Los 10aislados eae-positivos fueron atípicos y presentaron un fenotipo de multi-resistencia (incluyendoresistencia a ampicilina, cloranfenicol, gentamicina, tetraciclina, y trimetoprim/sulfametoxazol) conlos genes blaTEM/tet(B)/floR/cmlA/sul1/sul2/sul3. Diversos linajes genéticos fueron detectados entrelos aislados eae-positivos. Conclusión: En la cavidad nasal de los cerdos se detecta con frecuenciaE. coli portador de genes de resistencia y virulencia de alto impacto clínico, las cuales pueden sertransferidas al hombre por la cadena alimentaria o por contacto con los animales. Aunque E. colies una bacteria comensal del tracto gastrointestinal, el estilo de vida de los animales favorece latransferencia al entono nasal

Nasotracheal enterococcal carriage and resistomes: detection of optrA-, poxtA- and cfrD-carrying strains in migratory birds, livestock, pets, and in-contact humans in Spain

This study determined the carriage rates and antimicrobial resistance (AMR) genes of enterococci from nasotracheal samples of three healthy animal species and in-contact humans. Nasal samples were collected from 27 dog-owning households (34 dogs, 41 humans) and 4 pig-farms (40 pigs, 10 pig-farmers), and they were processed for enterococci recovery (MALDI-TOF–MS identification). Also, a collection of 144 enterococci previously recovered of tracheal/nasal samples from 87 white stork nestlings were characterized. The AMR phenotypes were determined in all enterococci and AMR genes were studied by PCR/sequencing. MultiLocus-Sequence-Typing was performed for selected isolates. About 72.5% and 60% of the pigs and pig-farmers, and 29.4% and 4.9%, of healthy dogs and owners were enterococci nasal carriers, respectively. In storks, 43.5% of tracheal and 69.2% of nasal samples had enterococci carriages. Enterococci carrying multidrug-resistance phenotype was identified in 72.5%/40.0%/50.0%/23.5%/1.1% of pigs/pig-farmers/dogs/dogs’ owners/storks, respectively. Of special relevance was the detection of linezolid-resistant enterococci (LRE) in (a) 33.3% of pigs (E. faecalis-carrying optrA and/or cfrD of ST59, ST330 or ST474 lineages; E. casseliflavus-carrying optrA and cfrD); (b) 10% of pig farmers (E. faecalis-ST330-carrying optrA); (c) 2.9% of dogs (E. faecalis-ST585-carrying optrA); and (d) 1.7% of storks (E. faecium-ST1736-carrying poxtA). The fexA gene was found in all optrA-positive E. faecalis and E. casseliflavus isolates, while fexB was detected in the poxtA-positive E. faecium isolate. The enterococci diversity and AMR rates from the four hosts reflect differences in antimicrobial selection pressure. The detection of LRE carrying acquired and transferable genes in all the hosts emphasizes the need to monitor LRE using a One-Health approach

Application of biological variation - a review

Ovaj rad sadrži opsežan pregled sastavnica biološke varijacije (BV), tj. intraindividualne (nasumična fluktuacija analita oko osnovne vrijednosti svakog pojedinca) i interindividualne (ukupna varijacija od osnovnih vrijednosti različitih osoba) varijacije, zatim ukratko objašnjava procjenu veličine intraindividualne i interindividualne BV u zdravih i oboljelih ispitanika, podrobno obrađuje osam složenijih primjena procjena BV, te govori o zanimljivim detaljima koji izazivaju najviše rasprava. Cilj rada je raspraviti kako pomoću današnje tehnologije doći do specifikacija kvalitete dobivenih na temelju BV u zdravih pojedinaca te u kojim se slučajevima koristiti podacima od oboljelih ispitanika. Konačno, u radu se promiče daljnji razvoj primjene BV, poput upozoravanja liječnika o promjenama u bolesnikovu stanju.This paper introduces an extensive revision of the types of components of biological variation (BV), i.e. intraindividual (random fluctuation of analytes around the setting point of each individual) and interindividual (overall variation from the different person\u27s setting point), briefly explains estimation of the magnitude of within- and between subject BV in healthy and non-healthy subjects, details the eight common applications of BV estimates and discusses the most debated points of interests. The aim is to discuss how quality specifications derived from BV determined in healthy individuals are attainable with current technology and in what cases data from non-healthy subjects should be used. Finally, the paper promotes further development of BV application, such as notifying doctors about changes in patient status

Application of biological variation - a review

Ovaj rad sadrži opsežan pregled sastavnica biološke varijacije (BV), tj. intraindividualne (nasumična fluktuacija analita oko osnovne vrijednosti svakog pojedinca) i interindividualne (ukupna varijacija od osnovnih vrijednosti različitih osoba) varijacije, zatim ukratko objašnjava procjenu veličine intraindividualne i interindividualne BV u zdravih i oboljelih ispitanika, podrobno obrađuje osam složenijih primjena procjena BV, te govori o zanimljivim detaljima koji izazivaju najviše rasprava. Cilj rada je raspraviti kako pomoću današnje tehnologije doći do specifikacija kvalitete dobivenih na temelju BV u zdravih pojedinaca te u kojim se slučajevima koristiti podacima od oboljelih ispitanika. Konačno, u radu se promiče daljnji razvoj primjene BV, poput upozoravanja liječnika o promjenama u bolesnikovu stanju.This paper introduces an extensive revision of the types of components of biological variation (BV), i.e. intraindividual (random fluctuation of analytes around the setting point of each individual) and interindividual (overall variation from the different person\u27s setting point), briefly explains estimation of the magnitude of within- and between subject BV in healthy and non-healthy subjects, details the eight common applications of BV estimates and discusses the most debated points of interests. The aim is to discuss how quality specifications derived from BV determined in healthy individuals are attainable with current technology and in what cases data from non-healthy subjects should be used. Finally, the paper promotes further development of BV application, such as notifying doctors about changes in patient status

Bioinformatics analysis of mutations in SARSCoV- 2 and clinical phenotypes

1 p.-1 fig.-8 tab.Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), initially reported in Wuhan (China) hasspread worldwide. Like other viruses, SARS-CoV-2 accumulates mutations with each cycle of replication by continuously evolving a viral strain with one or more single nucleotide variants (SNVs). However, SNVs that cause severe COVID-19 or lead to immune escape or vaccine failure are not well understood. We aim to identify SNVs associated with severe clinical phenotypes.Methods: In this study, 27429 whole-genome aligned consensus sequences of SARS-CoV-2 were collected from genomic epidemiology of SARS-CoV-2 project in Spain (SeqCOVID) [1]. These samples were obtained from patients who required hospitalization and/or intensive care unit admission (ICU), excluding those registered in the first pandemic wave.Besides, 248 SARS-CoV-2 genomes were isolated from COVID-19 hospitalized patients from Gregorio Marañon General University Hospital (GMH) of which 142 were fully vaccinated. Bioinformatics tools using R and Python programming languages were developed and implemented comparing those to SARS-CoV-2 Wuhan-Hu-1 (reference genome).Results: Using a selection threshold mutational frequency 10%, 27 SNVs were expected to have association with hospitalization and ICU risk. The reference haplotype differing at the SNV coding for lysine at the residue 203 (N:R203K) was found to have negative association with COVID-19 hospitalization risk (p = 5.37 x 10-04). Similarly, a negative association was observed when the residue at 501 is replaced by tyrosine (S:N501Y) (p = 1.33 x 10-02). The application of a Chi-square test suggested that SNV-haplotypes coding for mutants residues such as (S:A222V, N:A220V, ORF10:V30L) and (ORF1a:T1001I, ORF1a:I2230T, S:N501Y, S:T716S, S:S982A, ORF8:Q27*, N:R203K, N:S235F) have negative associations with COVID-19 hospitalization risk (p = 6.58 x 10-07 and p = 2.27 x 10-16, respectively) and COVID-19 ICU risk (p = 1.15 x 10-02 and p = 2.51 x 10-02, respectively). Focusing on the SNV-haplotype coding the mutations (S:A222V, N:A220V, N:D377Y, ORF10:V30L) were observed to increase the risk of COVID-19 hospitalization (p = 2.71 x 10-04). Results from SARS-CoV-2 genomes analysis from GMH showed 63 coding SNVs which met the established threshold value. Applying a Chi-square test, the SNV-haplotype carrying coding variants for mutant residues in 5 ORF proteins and surface and membrane glycoprotein and nucleocapsid phosphoprotein was significantly associated with vaccine failure in hospitalized COVID-19 patients (p = 7.91 x 10-04).Conclusions: SNV-haplotypes carrying variants lead to non-synonymous mutations located along SARS-CoV-2 wholeproteome may influence COVID-19 severity and vaccine failure suggesting a functional role in the clinical outcome for COVID-19 patients.This research work was funded by the European Commission-NextGenerationEU (Regulation EU 2020/2094), through CSIC’s Global Health Platform (PTI Salud Global)Peer reviewe

XLI Jornadas de teatro clásico

Jornadas organizadas por el Instituto Almagro de teatro clásico, dedicadas a la figura de Agustín Moreto

Evolutionary genomics of SARS-CoV-2: keys for viral success

Resumen del trabajo presentado al 44º Congreso de la Sociedad Española de Bioquímica y Biología Molecular, celebrado en Málaga del 6 al 9 de septiembre de 2022.Peer reviewe

Genomic surveillance and impact of SARS-CoV-2 mutations

Resumen del póster presentado a las II Jornadas Científicas PTI + Salud Global, celebradas los días 5 y 6 de octubre de 2022 en el Auditorio Santiago Grisolía de Valencia (España).Peer reviewe

Congenital extrahepatic portosystemic shunts (Abernethy malformation): An international observational study

Congenital extrahepatic portosystemic shunt (CEPS) or Abernethy malformation is a rare condition in which splanchnic venous blood bypasses the liver draining directly into systemic circulation through a congenital shunt. Patients may develop hepatic encephalopathy (HE), pulmonary hypertension (PaHT), or liver tumors, among other complications. However, the actual incidence of such complications is unknown, mainly because of the lack of a protocolized approach to these patients. This study characterizes the clinical manifestations and outcome of a large cohort of CEPS patients with the aim of proposing a guide for their management. This is an observational, multicenter, international study. Sixty-six patients were included; median age at the end of follow-up was 30 years. Nineteen patients (28%) presented HE. Ten-, 20-, and 30-year HE incidence rates were 13%, 24%, and 28%, respectively. No clinical factors predicted HE. Twenty-five patients had benign nodular lesions. Ten patients developed adenomas (median age, 18 years), and another 8 developed HCC (median age, 39 years). Of 10 patients with dyspnea, PaHT was diagnosed in 8 and hepatopulmonary syndrome in 2. Pulmonary complications were only screened for in 19 asymptomatic patients, and PaHT was identified in 2. Six patients underwent liver transplantation for hepatocellular carcinoma or adenoma. Shunt closure was performed in 15 patients with improvement/stability/cure of CEPS manifestations. Conclusion: CEPS patients may develop severe complications. Screening for asymptomatic complications and close surveillance is needed. Shunt closure should be considered both as a therapeutic and prophylactic approach