Antibiotic Resistance in Bacteria

This study identifies essential genes for Klebsiella pneumoniae growth in human urine and serum using transposon mutagenesis, highlighting potential antimicrobial targets.

This study shows that vancomycin inhibits Pseudomonas aeruginosa growth under nutrient limitation and identifies resistance mechanisms linked to LPS biosynthesis and CpxSR signaling.

The paper investigates maternal transmission of ESBL-E in Cambodian infants using whole genome sequencing of mother-neonate pairs, finding evidence of bacterial transmission but not plasmid transfer.

This study analyzes ARG diversity and mobility in kefir and yoghurt bacteria using metagenomic data, finding significant ARG presence associated with mobile genetic elements.

The paper investigates plasmid sharing among Enterobacterales in human infections, livestock, wastewater, and waterways in Oxfordshire, finding shared plasmid backbones and rapid accessory gene changes across niches.

KARGVA identifies antibiotic resistance gene variants from metagenomics data with high accuracy and efficiency, outperforming existing tools in detecting ARGVs.

The paper shows that ecological factors, not antibiotic use, mainly determine the global spread of aminoglycoside resistance genes.

This paper develops a whole-cell E. coli biosensor to quantify β-lactamase inhibition in a cellular context and evaluates existing inhibitors.

The study detects antimicrobial resistance genes in the gut microbiome of healthy individuals in Kolkata, highlighting the need for antimicrobial stewardship.

The paper identifies antimicrobial resistance genes in canine saliva that could transfer to humans, posing a risk for antimicrobial resistance spread.

The paper assesses plasmid-host compatibility by analyzing protein-protein interactions across 4,363 bacterial hosts, identifying species with high interaction rates with specific plasmids like pOXA-48.

The paper updates the A. baumannii K locus reference sequence database to include 145 new KL sequences, improving CPS typing accuracy from whole genome sequence data.

This study profiles resistance determinants, virulence factors, and mobile genetic elements in 1273 Enterococcus faecium genomes from UK and Canada, showing habitat-associated gene and MGE patterns and a workflow for AMR surveillance.

The paper characterizes the ecological and evolutionary dynamics of gut microbiomes colonized by carbapenemase-producing Enterobacteriaceae (CPE) using longitudinal metagenomics and whole genome sequencing.

The paper identifies a plasmid (Plasmid A) that transmitted four times into different Klebsiella lineages, causing 50% of ESBL episodes and persisting for 3-6 years, contributing to 21% of ESBL+ infections.

The paper uses a deep learning model to identify antimicrobial resistance genes in ISS microbiome data, revealing resistance patterns in specific bacterial species.

The paper compares sequencing and assembly methods' impact on plasmid and chromosomal phylogenies and horizontal gene transfer inference in E. coli.

This study shows that β-lactamases from different Ambler classes confer cefiderocol resistance and can evolve to increase resistance through mutations.

The paper characterizes plasmids in clinical bacterial isolates from a Tanzanian hospital, finding high plasmid prevalence and co-occurrence of resistance and virulence genes.

The paper identifies two mutations in TEM beta-lactamase that shift drug specificity through salt bridges, validated by simulations and experiments.

This paper identifies evolutionarily stable gene clusters in Acinetobacter species that reveal genetic features associated with pathogenicity and host interaction.

This paper develops a random forest model to predict plasmid hosts, achieving 0.662 and 0.867 Matthews correlation coefficients at species and order levels, respectively.

The paper develops a method to trace horizontal gene transfer and persistence of carbapenem resistance genes across bacterial species using genomic data from clinical isolates.

IntegronFinder 2.0 identifies and analyzes integrons in bacterial genomes, revealing a large diversity of integrons and antibiotic resistance genes in Klebsiella pneumoniae.

This paper investigates Arg717 substitutions in Escherichia coli AcrB, finding they increase resistance to macrolides and fluoroquinolones while decreasing resistance to novobiocin and cloxacillin.

HAM-ART improves metagenomics by linking AMR genes to host chromosomes and plasmids, showing differences in AMR gene distribution between pig farms with varying antibiotic use.

The paper evaluates AMR prediction methods using HTS data from clinical isolates, finding high variance in performance and highlighting issues with sampling bias and uncharacterized AMR genes.

This paper analyzes the genomic evolution of Klebsiella pneumoniae clonal group 147, identifying its global spread and resistance mechanisms through comparative genomics and phylogenetic analysis.

The paper introduces Acinetobase, a database that compiles Acinetobacter strains and their associated phenotypic and genetic data to address the heterogeneity of A. baumannii.

The paper identifies cargo genes of Tn7-like transposons, revealing their role in transferring diverse genes including MGEs, defense systems, and antibiotic resistance genes.