Antibiotic Resistance in Bacteria

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.

VERA simulates antibiotic resistance transmission between pathogens and gut microbiota, showing nonlinear dependencies and exponential disease spread with pathogen resistance.

The paper analyzes ESBL-producing Klebsiella strains to show dynamic resistance evolution and highlights that successful lineages are not necessarily the most resistant or virulent.

This paper validates Fourier Transform Infrared (FT-IR) spectroscopy as a cost-effective method for K-type characterization of Klebsiella pneumoniae, achieving resolution comparable to whole-genome sequencing.

This study analyzes the genomes of Enterococcus faecium strains to understand their adaptive evolution, identifying plasmids as key indicators of host specificity through population-wide genomic analysis.

The paper identifies two Klebsiella pneumoniae isolates with convergent virulence and multidrug resistance genes on a single plasmid, highlighting the risk of rapid emergence of hypervirulent multidrug-resistant strains.

This paper predicts antibiotic resistance in E. coli from whole genome sequences using machine learning, achieving high accuracy without prior knowledge of resistance mechanisms.

The paper investigates an Acinetobacter baumannii outbreak using cgMLST and identifies two transmission chains originating from colonized patients.

This study identifies 38 loci and 250 epistatic pairs affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings.

TETyper classifies transposable element variation and genetic contexts from whole-genome sequencing data, revealing high transposition diversity in KPC-associated Tn4401.

This study identifies and tracks virulence loci encoding siderophore synthesis in K. pneumoniae using genomic surveillance tools.

PlaScope improves plasmid detection in E. coli by combining Centrifuge with a curated database, achieving high recall, specificity, and accuracy compared to existing tools.

RM-seq detects and quantifies antibiotic resistance mutations in bacterial populations with high sensitivity and accuracy.

The paper uses targeted molecular dynamics simulations to explore the transport mechanism of substrates in the AcrB multidrug resistance pump and suggests ligand competition as a potential efflux inhibition strategy.

The paper identifies vitamin metabolizing genes in multidrug-resistant plasmids of superbugs and highlights their potential role in antibiotic resistance.

This study tracks the evolution of carbapenem resistance in Acinetobacter baumannii during a 45-day infection in a burn patient, identifying novel mutations in resistance genes and showing collateral resistance from exposure to other antibiotics.