Antibiotic Resistance in Bacteria

This paper introduces a cumulative cgMLST approach to improve discrimination of nested phylogenetic groups by adding conserved loci, showing increased allelic distances and utility for epidemiological analysis.

PhyloMLST, a Python command-line tool, groups MLST sequence types into clonal complexes and international clones, optionally using a phylogeny to remove spuriously chained 'straggly' assignments.

This study evolves uropathogenic E. coli to fosfomycin resistance in a 3D bladder microtissue model and validates mutations in clinical isolates.

The paper develops a framework to assess antibiotic resistance and virulence risks in pathogens, finding that resistance can increase virulence through genetic changes.

ALPAR automates AMR data analysis from genomic data processing to ML model training and GWAS, offering a reproducible pipeline for single-reference AMR studies.

This paper identifies BMM_1567, a peptide that enhances aminoglycoside activity against multidrug-resistant Gram-negative bacteria by inhibiting resistance enzymes.

The paper identifies a novel mcr-13.1 gene in E. coli from grassland, showing its presence on an IncFIB plasmid and its resistance to colistin.

Survey of 46,185 A. baumannii assemblies and NCBI entries added 168 novel capsule loci, expanding the Kaptive typing database to 409 K loci with 1010 annotated protein clusters.

The paper characterizes multidrug-resistant bacteria and plasmids in hospital plumbing and finds shared strains between environmental and clinical sources.

This study identifies heteroresistance in Enterococcus faecalis against three antibiotics, showing that it is mainly caused by chromosomal mutations and mobile genetic elements.

This study characterizes four Est-type macrolide esterases, revealing structural and functional insights into their substrate specificity and resistance mechanisms.

The paper investigates how intra- and extracellular β-lactamase activity contributes to collective β-lactam survival in E. coli under cefotaxime stress.

This study identifies new TIME-COMP-like structures containing antibiotic resistance genes in Enterobacteriaceae genomes, highlighting the role of TIMEs in ARG mobilization.

The paper introduces amR, an R package suite for predicting antimicrobial resistance in bacterial pathogens using genome data and interpretable machine learning models.

This study explores how NDM-1 evolves under different therapeutic pressures to predict resistance to emerging β-lactam-based therapies.

This study shows that AZT resistance in bacterial mating partners affects plasmid transfer efficiency, revealing that resistance reshapes physiological compatibility between partners.

This study examines how iron uptake systems affect cefiderocol activity in E. coli, showing that the fec operon increases resistance and is linked to virulence.

This study identifies mechanisms of cefiderocol resistance in Pseudomonas aeruginosa clinical strains, showing that acquired β-lactamases and siderophore transport defects are major contributors.

This study shows that anaerobic conditions increase plasmid transfer rates in Escherichia coli strains, revealing oxygen blind spots in conventional conjugation assays.

This study evaluates ML pipelines for AMR prediction using genomic data, identifying key factors affecting performance and supporting tree-based models.

This study shows that transporting bacterial DNA at ambient temperature from Uganda to the UK allows high-quality whole-genome sequencing, revealing AMR patterns and misidentification issues in Gram-negative bacteria from cancer patients.

This study identifies genetic loci beyond OXA-23 associated with carbapenem resistance in Acinetobacter baumannii using a bacterial genome-wide association study framework.

This study shows 3-BP covalently inhibits NDM-1 and NDM-5 MBLs, restoring carbapenem activity against resistant bacterial strains.

The paper analyzes antibiotic-resistant E. coli from cattle and sheep farms to identify clonal dissemination pathways and assess the impact of antibiotic withdrawal on resistance patterns.

This study shows that NDM-7 carbapenemase is exported to outer membrane vesicles in Klebsiella pneumoniae, enabling extracellular antibiotic degradation and conferring resistance to imipenem and cefiderocol.

Sarand extracts AMR gene contexts from metagenomic assembly graphs, improving precision and sensitivity over existing methods.

The paper identifies essential genes in Acinetobacter baumannii that support efflux pump overproducer fitness during ciprofloxacin treatment, revealing roles in outer membrane integrity and pH homeostasis.

This study analyzes plasmid dynamics in CRKp clones to show lineage-specific resistance-virulence convergence through distinct plasmid configurations.

This study profiles antibiotic resistance and virulence genes in the gut microbiota of black soldier fly larvae, identifying potential risks associated with their use in sustainable agriculture.