J. Botelho

Timescales and genetic linkage explain the variable impact of defense systems on horizontal gene transfer

The paper examines how defense systems affect horizontal gene transfer (HGT) across different timescales and finds that CRISPR-Cas most often reduces MGE abundance and gene acquisition, but this effect is masked by recent co-transfer events.

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

The paper studies how CRISPR-Cas immunity in the human gut microbiome affects phage abundances and bacterial diversity using longitudinal metagenomic data.

Variation in the response to antibiotics and life-history across the major Pseudomonas aeruginosa clone type (mPact) panel

The paper evaluates antibiotic resistance and life-history traits across 20 Pseudomonas aeruginosa strains to identify adaptive strategies and inform new treatment approaches.

Defense systems are pervasive across chromosomally integrated mobile genetic elements and are inversely correlated to virulence and antimicrobial resistance

The paper catalogs over 13,000 chromosomally integrated mobile genetic elements across 34 phyla, finding defense systems inversely correlated with virulence and antimicrobial resistance.

Phylogroup-specific variation shapes the clustering of antimicrobial resistance genes and defence systems across regions of genome plasticity

This study examines phylogroup-specific evolutionary dynamics in Pseudomonas aeruginosa genomes, revealing distinct pangenome characteristics and distribution patterns of antimicrobial resistance genes and defence systems.

The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements

The paper analyzes MGEs in ESKAPE pathogens, showing their role in AMR spread and CRISPR-mediated conflicts among mobile elements.

Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically-relevant bacteria

This study identifies 66 carbapenemase-encoding genes (CEGs) located within integrative and conjugative elements (ICEs) across 182,663 bacterial genomes, highlighting ICEs as underappreciated contributors to carbapenem resistance.

ICEs are the main reservoirs of the ciprofloxacin-modifying crpP gene in Pseudomonas aeruginosa

This study identifies ICEs as the main vectors for the dissemination of the ciprofloxacin-modifying crpP gene in Pseudomonas aeruginosa.

Megaplasmids on the rise: combining sequencing approaches to fully resolve a carbapenemase-encoding plasmid in a proposed novel Pseudomonas species

The paper combines Nanopore and Illumina sequencing to fully assemble a carbapenemase-encoding megaplasmid from a putative novel Pseudomonas species.

A large self-transmissible plasmid from Nigeria confers resistance to multiple antibacterials without a carrying cost

Carbapenemases on the move: it’s good to be on ICE

This study identifies ICEs in Pseudomonas aeruginosa that carry carbapenemase-encoding genes, highlighting their role in antibiotic resistance spread.