Antibiotic Resistance in Bacteria

The paper uses bacterial Hi-C to study horizontal gene transfer of mobile antibiotic resistance genes in gut microbiomes, finding distinct HGT networks between individuals and increased dispersal in neutropenic patients.

The paper uses Nanopore sequencing to track antibiotic resistance plasmid evolution and transfer between bacterial species in a hospital setting, identifying plasmid fusion and gene rearrangements.

This study characterizes the genome of a multidrug-resistant Pseudomonas aeruginosa strain, identifying genomic features and resistance mechanisms.

The paper analyzes IncF plasmid diversity across environmental and livestock settings using network community analysis, revealing niche-driven partitioning and core gene-defined communities.

The paper models the structure of MefA/E protein in Streptococcus pneumoniae using in silico methods and finds it resembles MFS proteins with 13 transmembrane helices in a V-shaped conformation.

The paper detects the frequency of the bla OXA-48 gene in Pseudomonas aeruginosa clinical isolates from Sudan, finding a higher prevalence in carbapenem-resistant strains.

This study analyzes the whole-genome sequence of a pan-drug resistant Acinetobacter baumannii isolate from Uganda to identify chromosomal and mobile genetic element-mediated antibiotic resistance mechanisms.

The paper characterizes a large antibiotic-resistant plasmid in ST131 E. coli using long-read hybrid assembly, identifying the blaCTX-M-27 gene and associated genetic elements.

The paper evaluates targeted sampling strategies for detecting novel antibiotic resistance variants in Neisseria gonorrhoeae, finding that pathogen-based approaches are more efficient than patient-based ones.

The paper characterizes ESBL-producing E. coli and K. pneumoniae isolates from animal samples in Assam, India, reporting prevalence, resistance patterns, and resistance gene profiles.

The paper develops an online platform to search and analyze antibiotic resistance gene distribution in metagenomic and bacterial genome databases.

Reads2Resistome is a high-throughput whole-genome sequencing pipeline that assembles and annotates bacterial genomes to characterize the resistome using long or short reads.

The paper reports the first detection of the tigecycline resistance gene tet(X6) on a plasmid in a livestock-associated Acinetobacter towneri isolate.

This study characterizes the genomic context of blaNDM-1 in E. coli ST101 isolates using long-read sequencing, revealing two clades with distinct resistance profiles and plasmid-mediated blaNDM-1 carriage mechanisms.

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.