Antibiotic Resistance in Bacteria

This study analyzes the evolutionary patterns of beta-lactamases (BLs) using phylogenetics and protein interactions, revealing distinct chromosomal and plasmid-encoded BL evolution and the mosaic role of VIM linking NDM and IMP.

The paper identifies a tigecycline-resistant E. coli strain carrying tet(x4) and NDM-5 genes from a Canadian patient.

This study uses whole genome sequencing to identify Enterobacter hormaechei as the most common bloodstream pathogen in Nigerian hospitals, revealing its diversity and potential outbreaks.

The paper reports genome sequences of ten multidrug-resistant Escherichia coli strains from Egyptian children with diarrhoea, identifying resistance genes and high-risk clones.

This study uses machine learning to identify minimal gene signatures predicting antibiotic resistance in Pseudomonas aeruginosa with high accuracy.

The paper identifies diverse beta-lactamases in Antarctic and Subantarctic soil microbiota using a structure-guided bioinformatic pipeline, revealing novel families and variants.

The paper shows that E. coli phylogeny influences blaTEM-1 expression and co-amoxiclav resistance through lineage-specific regulatory differences.

This study characterizes a new multidrug-resistant Acinetobacter baumannii isolate and evaluates the transcriptomic effects of a synthetic antimicrobial peptide in combination with meropenem.

The paper introduces BDXR, a tool for predicting antimicrobial resistance from whole genome sequencing, achieving high accuracy in the CAMDA 2025 challenge.

This study profiles antimicrobial resistance genes in bee microbiomes, finding higher diversity on plasmids in honey bees compared to bumble bees and different tetracycline resistance mechanisms.

The paper reports the first detailed analysis of AmpC β-lactamase distribution, diversity, and evolutionary characteristics in ESKAPE pathogens, highlighting their role in antibiotic resistance.

This study identifies consistent collateral sensitivity interactions between antibiotics in S. pneumoniae and develops a model to guide treatment strategies.

This study shows that β-lactam resistance in Haemophilus influenzae leads to fitness costs and collateral sensitivities, with unpredictable evolutionary outcomes.

This paper uses genomic data from 47k Klebsiella pneumoniae genomes to predict AMR evolutionary pathways across 102 countries, showing how resistance traits vary with geography and drug policy.

This study sequences AMR bacteria from U.S. travelers to identify regional resistance patterns and detect emerging threats.

This study uses whole-genome sequencing to characterize multidrug-resistant Escherichia coli from poultry in Nigeria, identifying chromosomal and plasmid-borne resistance genes and virulence factors.

CARD k-mers classifies antimicrobial resistance genes in metagenomic data by predicting taxonomy and genomic context, outperforming existing tools in accuracy and speed.

This study identifies fragment-based inhibitors of VatD, an enzyme responsible for streptogramin resistance, using X-ray crystallography to guide inhibitor development.

This study develops a deep learning model using FCGR and ResNet-18 to predict antimicrobial resistance in Salmonella and Staphylococcus aureus, achieving high accuracy for some antibiotics but not others.

The paper introduces AMRscope, a protein language model-based tool for predicting antimicrobial resistance likelihood from single mutations, showing strong performance across bacterial species and identifying new resistance candidates.

The paper develops a framework to analyze multivariate beta-lactam resistance in Streptococcus pneumoniae using MIC data from 3,628 isolates, revealing genetic mutations and lineage-specific resistance profiles.

This paper investigates the pleiotropic effects of the AcrAB efflux pump in Photorhabdus laumondii, showing it influences secondary metabolite biosynthesis, motility, and bioluminescence by exporting signaling molecules like stilbenes.

This study identifies ESBL-producing multidrug-resistant E. coli isolates from UTI patients, finding bla-CTX-M as the most prevalent ESBL gene.

This study compares phenotypic and genomic AMR profiles of Gram-negative uropathogens from CAUTIs in Egypt, finding significant phenotype-genotype discordance and reporting new AMR variants.

This study investigates antibiotic cycling regimens using collateral sensitivity, finding that backward collateral sensitivity can restore antibiotic susceptibility and improve treatment outcomes.

This study investigates why some blaNDM-1-positive Enterobacterales are susceptible to meropenem despite carrying the gene, finding lower gene copy numbers and expression correlate with reduced MIC values, supporting meropenem's efficacy in these cases.

This paper evaluates RASE, a neighbor typing method using long-read sequencing, for predicting sequence types and antimicrobial susceptibility of Klebsiella pneumoniae in real time.

This study analyzes historical microbial genomes to show that antibiotic resistance genes existed before antibiotics were introduced but became more frequent and mobile with antibiotic use.

This paper uses metagenomics to identify antimicrobial resistance genes in a UK veterinary hospital and compares them with phenotypic results from bacterial isolates.

This study uses whole-genome sequencing and pan-genome analysis of Bangladeshi diarrheal pathogens to identify core genes involved in pathogenesis and antibiotic resistance.