Antibiotic Resistance in Bacteria

MOBFinder classifies plasmid metagenomic fragments into MOB categories using natural language models, achieving higher accuracy than existing tools.

MACI identifies drug classes of antibiotic resistance genes from metagenomic data using machine learning, achieving high precision and recall for multidrug resistant classes.

This study identifies a carbapenem-resistant Pseudomonas aeruginosa strain co-harboring blaKPC-2 and blaVIM-2 genes, revealing their genetic environment and plasmid-mediated transmission.

The paper analyzes WGS data of E. coli isolates to show that blaTEM gene amplification correlates with resistance to AMC and TZP but not SAM, highlighting the need for comprehensive analysis of genetic determinants in BL/BLI resistance.

The paper identifies a Tn7-like transposon carrying blaIMP-1 in carbapenem-resistant Pseudomonas aeruginosa strains and describes its genetic structure and potential role in intrahospital dissemination.

This study identifies the target pathway of a novel antimicrobial compound and discovers synergies with existing antibiotics using genome-wide screening in Gram-negative bacteria.

This study investigates genomic, functional, and metabolic adaptations of Enterobacter bugandensis isolated from the ISS, revealing resistance mechanisms and microbial interactions that contribute to its persistence in space.

The paper identifies four chromosomally clustered class-C β-lactamases (blaAmpH1/2/3/4) in Mycobacterium tuberculosis responsible for cephalosporin hydrolysis, while these genes are pseudogenes in M. leprae.

This paper introduces plasmidEC and gplas2 to accurately predict and reconstruct antibiotic resistance plasmids in E. coli using short-read sequencing data, outperforming existing methods.

The paper develops an interpretable model to predict antimicrobial resistance in Escherichia coli from livestock and companion animals using genomic and phenotypic data.

This study identifies genetic and structural mechanisms of colistin resistance in Klebsiella pneumoniae, showing mutations and insertion sequences disrupt lipid A modification and regulatory networks.

The paper analyzes the resistome, virulome, and mobilome of Klebsiella aerogenes using 561 genomes, identifying resistance mechanisms, virulence factors, and plasmid content across global isolates.

The paper uses machine learning to predict antimicrobial resistance phenotypes from genomic data across 28 bacterial genera, identifying 528 species-specific genomic pathways to resistance.

The paper identifies known and novel antimicrobial resistance genes across 12 species using pangenomics, gene annotation, and machine learning, finding gene transfer is mostly species-specific and demonstrating improved methods for AMR gene discovery.

This study characterizes an outbreak of XDR CRAB belonging to the IC2 clone in a Brazilian hospital, highlighting its resistance profile and potential spread during the COVID-19 pandemic.

This study characterizes the genomic features of a pandrug-resistant Klebsiella pneumoniae isolate from Brazil, identifying multiple resistance mechanisms contributing to its multidrug resistance profile.

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.

The study assesses AMR gene reservoirs in human, animal, and environmental samples from a Kathmandu temporary settlement using metagenomics and network analysis.

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

The paper reports nanopore sequencing of a K. pneumoniae isolate from Pakistan, identifying antibiotic resistance genes and contributing to the pan-genome of antibiotic-resistant strains.

This study compares antibiotic resistance gene profiles in Bangladeshi gut microbiomes to global samples, finding higher ARG abundance in Bangladeshi cohorts.

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

This study characterizes the genetic diversity and carbapenem resistance mechanisms in Acinetobacter baumannii isolates from Nigerian hospitals using whole-genome sequencing, revealing high prevalence of blaNDM-1 and transposon-mediated dissemination of resistance genes.

This study characterizes multidrug-resistant ESBL-producing K. pneumoniae isolates from a DRC hospital, identifying genetic diversity and resistance patterns.

The paper investigates how the amphiphilic peptide Mastoparan-B inhibits the AdeB efflux pump in A. baumannii, reducing adeB gene expression and restoring antibiotic susceptibility.

The paper identifies a subclass of the IS1202 family of bacterial insertion sequences that specifically target XerCD recombination sites, revealing their role in mobile genetic elements.

The paper introduces a computational pipeline for consistent plasmid typing using long-read sequencing data, enabling classification of novel and known plasmid types.

This study identifies three combinatorial mutations associated with colistin resistance in mcr-negative Shewanella algae using comparative genomics.