A5013394238- Antibiotic Resistance in Bacteria
- Genomics and Phylogenetic Studies
- Antimicrobial Resistance in Staphylococcus
- Bacterial Identification and Susceptibility Testing
- Gut microbiota and health
- Bacteriophages and microbial interactions
- Pharmaceutical and Antibiotic Environmental Impacts
- Probiotics and Fermented Foods
- Microbial Community Ecology and Physiology
- Escherichia coli research studies
- Vibrio bacteria research studies
- Bacterial biofilms and quorum sensing
- Child Nutrition and Water Access
- Evolution and Genetic Dynamics
- Infections and bacterial resistance
- Microbial infections and disease research
- Bacterial Genetics and Biotechnology
- Mycobacterium research and diagnosis
- Enterobacteriaceae and Cronobacter Research
- Clostridium difficile and Clostridium perfringens research
- Plant Pathogenic Bacteria Studies
- Cell Image Analysis Techniques
- Origins and Evolution of Life
- RNA modifications and cancer
- Plant and Biological Electrophysiology Studies
Instituto Ramón y Cajal de Investigación Sanitaria
2016-2025
Instituto Cajal
2016-2025
Centre for Biomedical Network Research on Rare Diseases
2017-2025
Instituto de Salud Carlos III
2025
Hospital Universitario Ramón y Cajal
2014-2024
Medical Research Network
2023-2024
Centro de Investigación Biomédica en Red
2021-2024
Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública
2014-2021
Consejo Superior de Investigaciones Científicas
2014-2018
Universidad de Cantabria
2010-2017
Third-generation cephalosporins are a class of β-lactam antibiotics that often used for the treatment human infections caused by Gram-negative bacteria, especially Escherichia coli. Worryingly, incidence third-generation cephalosporin-resistant E. coli is increasing worldwide. Recent studies have suggested these strains, and their antibiotic resistance genes, can spread from food-producing animals, via food-chain, to humans. However, traditional typing methods, which may not provided...
Bacterial whole genome sequence (WGS) methods are rapidly overtaking classical analysis. Many bacterial sequencing projects focus on mobilome changes, since macroevolutionary events, such as the acquisition or loss of mobile genetic elements, mainly plasmids, play essential roles in adaptive evolution. Existing WGS analysis protocols do not assort contigs between plasmids and main chromosome, thus hampering full plasmid sequences. We developed a method (called constellation networks PLACNET)...
Antimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of “resistomes” (the ensemble genes encoding antimicrobial in given microbiome) disparate microbial ecosystems. However, low sensitivity specificity available metagenomic methods preclude detection minority populations (often present below their threshold) and/or identification allelic variants that differ resulting phenotype. Here, we describe novel strategy combines targeted...
Abstract Summary PLACNET is a graph-based tool for reconstruction of plasmids from next generation sequence pair-end datasets. graphs contain two types nodes (assembled contigs and reference genomes) edges (scaffold links homology to references). Manual pruning the necessary requirement in PLACNET, but this difficult users without solid bioinformatic background. PLACNETw, webtool based on provides an interactive graphic interface, automates BLAST searches, extracts relevant information...
Abstract Enterococcus faecalis is a commensal and nosocomial pathogen, which also ubiquitous in animals insects, representing classical generalist microorganism. Here, we study E. isolates ranging from the pre-antibiotic era 1936 up to 2018, covering large set of host species including wild birds, mammals, healthy humans, hospitalised patients. We sequence bacterial genomes using short- long-read techniques, identify multiple extant hospital-associated lineages, with last common ancestors...
Abstract Changes in the microbiota have been linked to persistent inflammation during treated HIV infection. In this pilot double-blind study, we study 30 HIV-infected subjects on antiretroviral therapy (ART) with a CD4/CD8 ratio < 1 randomized either weekly fecal capsules or placebo for 8 weeks. Stool donors were rationally selected based their signatures. We report that transplantation (FMT) is safe, not related severe adverse events, and attenuates HIV-associated dysbiosis. FMT elicits...
Significance P II , a signal transduction protein involved in nitrogen control bacteria and plants, NtcA, the transcriptional regulator of cyanobacteria, can form complexes with interacting X (PipX). We demonstrate by combination genetic, transcriptomic, multivariate analyses that PipX is much wider interaction network affecting assimilation, translation, photosynthesis. Two groups genes differentially regulated pipX provided further insights into function NtcA–PipX an improved definition...
Linezolid-resistant Enterococcus faecalis (LREfs) carrying optrA are increasingly reported globally from multiple sources, but we lack a comprehensive analysis of human and animal optrA-LREfs strains. To assess if is dispersed in isolates with varied genetic backgrounds or common features, investigated the phylogenetic structure, content [antimicrobial resistance (AMR), virulence, prophages, plasmidome] optrA-containing platforms 27 publicly available optrA-positive E. genomes different...
ABSTRACT Multidrug-resistant Enterococcus faecium strains represent a major concern due to their ability thrive in diverse environments and cause life-threatening infections. While antimicrobial resistance virulence mechanisms have been extensively studied, the contribution of bacteriocins E. ’s adaptability remains poorly explored. , within Bacillota phylum, is prominent bacteriocin producer. Here, we developed tailored database 76 (217 sequences, including 40 novel bacteriocins) applied it...
ABSTRACT Serratia marcescens is an opportunistic pathogen historically associated with sudden outbreaks in intensive care units (ICUs) and the spread of carbapenem-resistant genes. However, ecology S. populations hospital ecosystem remains largely unknown. We combined epidemiological information 1,432 spp. isolates collected from sinks a large ICU that underwent demographic operational changes (2019–2021) 99 non-redundant outbreak/non-outbreak same (2003–2019) 165 genomic data. These genomes...
Abstract The three main processes shaping the evolutionary ecology of antibiotic resistance (AbR) involve emergence, invasion and occupation by antibiotic‐resistant genes significant environments for human health. process emergence in complex bacterial populations is a high‐frequency, continuous swarming ephemeral combinatory genetic epigenetic explorations inside cells among cells, communities, expanding different (migration), creating stochastic variation required progress. Invasion refers...
Klebsiella pneumoniae sequence type 14 (ST14) and ST15 caused outbreaks of CTX-M-15 and/or carbapenemase producers worldwide, but their phylogeny global dynamics remain unclear. We clarified the evolution K. clonal group (CG14) CG15 by analyzing capsular locus (KL), resistome, virulome, plasmidome public genomes (n = 481) de novo sequences 9) representing main sublineages circulating in Portugal. CG14 evolved independently within 6 subclades defined according to KL accessory genome. The 65)...
AcCNET (Accessory genome Constellation Network) is a Perl application that aims to compare accessory genomes of large number genomic units, both at qualitative and quantitative levels. Using the proteomes extracted from analysed genomes, creates bipartite network compatible with standard analysis platforms. allows merging phylogenetic functional information about concerned thus improving capability current methods analysis. The opens new perspective explore pangenome bacterial species,...
<ns4:p>Next-Generation Sequencing (NGS) technologies are expected to play a crucial role in the surveillance of infectious diseases, with their unprecedented capabilities for characterisation genetic information underlying virulence and antimicrobial resistance (AMR) properties microorganisms. In implementation any novel technology regulatory purposes, important considerations such as harmonisation, validation quality assurance need be addressed. NGS pose unique challenges these regards,...
is present in multiple hosts and environmental compartments as a normal inhabitant, temporary or persistent colonizer, pathogen. Transmission of
This is a longitudinal study comprising 649 Escherichia coli isolates representing all 7,165 E. bloodstream infection (BSI) episodes recorded in hospital (1996 to 2016). Strain analysis included clonal identification (phylogenetic groups/subgroups, STc131 subclades, pulsed-field gel electrophoresis [PFGE], and whole-genome sequencing [WGS]), antibiotic susceptibility (13 antibiotics), virulence-associated genes (VAGs; 29 genes). The incidence of BSI increased from 1996 2016 (5.5 10.8...
Extrachromosomal elements of bacterial cells such as plasmids are notorious for their importance in evolution and adaptation to changing ecology. However, high-resolution population-wide analysis has only become accessible recently with the advent scalable long-read sequencing technology. Current typing methods classification remain limited scope which motivated us develop a computationally efficient approach simultaneously recognize novel types classify into previously identified groups....