Biology subjects

Ripoll, A.

Publications and source records attributed to Ripoll, A..

3 recordsLinked to original sources

bioRxiv2026

Bacterial Mercury Resistance Reveals a Robust Species-Structured Human Antimicrobial Mobilome

Antimicrobial resistance (AMR) is increasingly recognized as an ecological and evolutionary phenomenon that extends beyond clinical environments. Despite the predominant focus on antibiotics, bacterial metal resistance genes are among the oldest and most widespread adaptive antimicrobial systems, yet their distribution within human-associated microbial communities remains poorly characterized. Here, we investigated the ecology of mercury (Hg) resistance in children from a birth cohort with relatively high Hg exposure. Fecal samples from 234 children aged 4-8 years were analyzed using culture-based screening, whole-genome sequencing, and comparative analyses of metal- and antibiotic-resistance determinants and associated mobile genetic elements (MGEs). Hg-resistance was detected in 79.7% of samples, with HgR Enterobacterales isolated from 57% of children. Hair mercury concentrations were not associated with carriage. Sequencing revealed a phylogenetically diverse collection dominated by Escherichia spp. (61%). Hg resistance was mediated by 79 mer operons primarily associated with Tn21, Tn1696, and Tn5053 families circulating on chromosomes and a highly diverse plasmidome. Both rare and globally distributed plasmids related to foodborne, animal, and clinical Enterobacterales were identified. Metal resistance determinants exhibited strong taxonomic structuring, with Escherichia enriched in iron-uptake systems and siderophores whereas non-Escherichia taxa carried multimetal resistance operons. These findings indicate that Hg-resistance is shaped by ecological interactions and MGEs, becoming partially decoupled from contemporary Hg-exposure and bacterial community composition. The human gut therefore serves as an important reservoir linking environmental metal resistance to the broader evolution of AMR and provides insight into the baseline resistome and plasmidome of human populations.

microbiology↗

bioRxiv2024

Hypermigration of macrophages through the concerted action of GRA effectors on NF-κB/p38 signaling and host chromatin accessibility potentiates Toxoplasma dissemination

Mononuclear phagocytes facilitate the dissemination of the obligate intracellular parasite Toxoplasma gondii. Here, we report how a set of secreted parasite effector proteins from dense granule organelles (GRA) orchestrates dendritic cell-like chemotactic and pro-inflammatory activation of parasitized macrophages. These effects enabled efficient dissemination of the type II T. gondii lineage, a highly prevalent genotype in humans. We identify novel functions for effectors GRA15 and GRA24 in promoting CCR7-mediated macrophage chemotaxis by acting on NF-{kappa}B and p38 MAPK signaling pathways, respectively, with contributions of GRA16/18 and counter-regulation by effector TEEGR. Further, GRA28 boosted chromatin accessibility and GRA15/24/NF-{kappa}B-dependent transcription at the Ccr7 gene locus in primary macrophages. In vivo, adoptively transferred macrophages infected with wild-type T. gondii outcompeted macrophages infected with a GRA15/24 double mutant in migrating to secondary organs in mice. The data show that T. gondii, rather than being passively shuttled, actively promotes its dissemination by inducing a finely regulated pro-migratory state in parasitized human and murine phagocytes via co-operating polymorphic GRA effectors. ImportanceIntracellular pathogens can hijack cellular functions of infected host cells to their advantage, for example, for intracellular survival and for dissemination. However, how microbes orchestrate the hijacking of complex cellular processes, such as host cell migration, remains poorly understood. As such, the common parasite Toxoplasma gondii actively invades immune cells of humans and other vertebrates and modifies their migratory properties. Here, we show that the concerted action of a number of secreted effector proteins from the parasite, principally GRA15 and GRA24, act on host cell signaling pathways to activate chemotaxis. Further, the protein effector GRA28 selectively acted on chromatin accessibility in the host cell nucleus to selectively boost host gene expression. The joint activities of effectors culminated in pro-migratory signaling within the infected phagocyte. We provide a molecular framework delineating how T. gondii can orchestrate a complex biological phenotype, such as the migratory activation of phagocytes to boost dissemination.

microbiology↗

bioRxiv2022

Demuxafy: Improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

Recent innovations in droplet-based single-cell RNA-sequencing (scRNA-seq) have provided the technology necessary to investigate biological questions at cellular resolution. With the ability to assay thousands of cells in a single capture, pooling cells from multiple individuals has become a common strategy. Droplets can subsequently be assigned to a specific individual by leveraging their inherent genetic differences, and numerous computational methods have been developed to address this problem. However, another challenge implicit with droplet-based scRNA-seq is the occurrence of doublets - droplets containing two or more cells. The inaccurate assignment of cells to individuals or failure to remove doublets contribute unwanted noise to the data and result in erroneous scientific conclusions. Therefore, it is essential to assign cells to individuals and remove doublets accurately. We present a new framework to improve individual singlet classification and doublet removal through a multi-method intersectional approach. We developed a framework to evaluate the enhancement in donor assignment and doublet removal through the consensus intersection of multiple demultiplexing and doublet detecting methods. The accuracy was assessed using scRNA-seq data of [~]1.4 million peripheral blood mononucleated cells from 1,034 unrelated individuals and [~]90,000 fibroblast cells from 81 unrelated individuals. We show that our approach significantly improves droplet assignment by separating singlets from doublets and classifying the correct individual compared to any single method. We show that the best combination of techniques varies under different biological and experimental conditions, and we present a framework to optimise cell assignment for a given experiment. We offer Demuxafy (https://demultiplexing-doublet-detecting-docs.readthedocs.io/en/latest/index.html) - a framework built-in Singularity to provide clear, consistent documentation of each method and additional tools to simplify and improve demultiplexing and doublet removal. Our results indicate that leveraging multiple demultiplexing and doublet detecting methods improves accuracy and, consequently, downstream analyses in multiplexed scRNA-seq experiments.

genomics↗