Antibiotic Resistance in Bacteria

This study identifies antimicrobial resistance genes in raw milk samples, showing their potential to transfer resistance to human gut bacteria.

The paper develops a transfer learning model, TRAC, for antibiotic resistance class prediction and introduces a curated dataset to benchmark existing tools.

The paper analyzes 64,628 bacterial genomes to identify the reservoir and origin of mcr gene variants, finding widespread presence in environmental bacteria, particularly in water sources.

The paper analyzes global E. coli ST131 genomes to trace the evolution and spread of antibiotic-resistant subclones, identifying a C2 lineage that displaced a C1 strain in an Irish LTCF.

The paper integrates whole-genome sequencing into the Philippines' antimicrobial resistance surveillance program to better understand and track carbapenem resistance in key bacterial species.

This study sequenced 176 Pseudomonas aeruginosa isolates from the Philippines to characterize their genomic diversity, antimicrobial resistance mechanisms, and clonal spread.

This study maps major bacterial antibiotic resistance genes in Australian fecal samples using shotgun metagenomics and targeted sequencing, finding higher ARG abundance in human and dog samples than in ducks.

The paper analyzes optrA-carrying Enterococcus faecalis genomes to identify common genetic features and a chromosomal hotspot for optrA acquisition across diverse hosts and regions.

The paper reports the first whole-genome analysis of multidrug-resistant E. coli isolates from bloodstream infections in India, identifying key resistance and virulence gene profiles.

The paper investigates the phylogenetic relationships and global distribution of blaKPC-2 and blaNDM-1 genes in carbapenem-resistant Klebsiella pneumoniae using NGS data.

The paper develops a metagenomic metric to predict antibiotic resistance in Enterobacterales infections using pooled human faecal samples from LMICs and high-income settings.

ARG-miner is a crowdsourcing-based platform for curating antibiotic resistance genes, achieving high accuracy and efficiency compared to manual curation.

This study compares DNA and RNA nanopore sequencing for detecting drug resistance in XDR K. pneumoniae, finding RNA sequencing identifies more resistance genes and shows strong correlation with qRT-PCR.

The paper uses three whole genome sequencing technologies to analyze a carbapenemase-producing Enterobacter hormaechei outbreak, identifying transmission dynamics and plasmid context.

VAMPr predicts antibiotic resistance using genomic data by analyzing variant associations and building machine learning models.

This study identifies a novel tigecycline resistance gene tet(X14) in Empedobacter stercoris and shows its co-occurrence with tet(X2) on a genome island.

This paper analyzes antimicrobial resistance assay data to identify biases and contradictions in training data for machine learning models.

The paper uses population genomics to analyze 4,071 E. coli ST131 isolates, revealing population structure, evolutionary relationships, and dynamics of AMR genes across three main clades and their subclades.

The paper analyzes metagenomic time-series data to track the spread of antibiotic resistance genes through bacterial chromosomes, plasmids, and phages during antibiotic therapy.

This study analyzes the genomic epidemiology of a blaKPC carbapenemase outbreak in Enterobacterales in the UK, revealing genetic plasticity and plasmid dynamics across multiple species and lineages.

The paper uses genomic analysis to assess MDRO transmission within and across hospitals, finding high transmission rates for vanA VRE and linking genomic data with epidemiologic data to evaluate infection control.

This study analyzes the population structure, virulence, and antimicrobial resistance of Klebsiella aerogenes using genomic data from 97 isolates.

The paper analyzes the pangenome and population structure of Enterobacter bugandensis, identifying antimicrobial resistance genes and iron acquisition strategies across different phylogroups.

The paper predicts antibiotic resistance in Elizabethkingia using pan-genomic analysis and machine learning, achieving high F1 scores for clindamycin and vancomycin resistance.

The paper analyzes quinolone resistance in Haemophilus influenzae strains from 2012-2017, finding increasing BLNAR prevalence and specific mutations in GyrA associated with resistance to moxifloxacin.

This study uses long-read sequencing to assemble E. coli ST131 genomes, revealing diverse plasmid and chromosomal contexts of antibiotic resistance genes.

The paper finds a correlation between antibiotic resistance and virulence genes in human gut and environmental microbiomes, with stronger correlations in less antibiotic-exposed populations.

This study reports whole-genome sequencing and antimicrobial resistance analysis of Klebsiella pneumoniae isolates from the Caribbean, revealing carbapenem resistance and hypervirulent strains.

The paper integrates whole-genome sequencing and culture-based antibiotic resistance data from 11,087 clinical isolates to identify gene-drug resistance associations and create a resource for research.

The paper uses whole-genome sequencing to investigate a hospital outbreak of carbapenem-resistant Klebsiella aerogenes, identifying genetic factors contributing to resistance and virulence.