Antibiotic Resistance in Bacteria

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.

This paper introduces deepARG, a deep learning method for predicting antibiotic resistance genes from metagenomic data, achieving high precision and recall over traditional methods.

This study develops an XGBoost-based machine learning model to predict minimum inhibitory concentrations for 20 antibiotics in Klebsiella pneumoniae using whole genome sequencing data, achieving 92% overall accuracy.

This study combines real-time genomic and epidemiological analysis to identify and manage KPC-producing Enterobacteriaceae outbreaks, revealing transmission networks and informing infection control.

This study analyzes the genomic features of 141 commensal E. coli from healthy pigs, identifying antimicrobial resistance genes, class 1 integrons, and IS26 elements associated with zoonotic potential.

MetaCherchant analyzes metagenomic data to reconstruct the genomic environment of antibiotic resistance genes, revealing potential transmission mechanisms in gut microbiota.

ARIBA rapidly identifies antimicrobial resistance genes and SNPs from sequencing reads, outperforming existing tools on bacterial datasets.

This study reconstructs genomes of drug-resistant bacteria from human faeces using metagenomic sequencing and self-organising maps, demonstrating the potential for culture-independent pathogen analysis.

The paper identifies 134 distinct Klebsiella capsule synthesis loci from whole-genome data, introduces a novel software tool for locus identification, and proposes a standardized nomenclature.