Antibiotic Resistance in Bacteria

The paper compares two NGS platforms and four databases for AMR gene analysis, finding CARD identifies the most genes and results are comparable across platforms.

This study characterizes antibiotic resistance in Danish Klebsiella pneumoniae isolates, finding differences in AMR profiles and virulence compared to global strains.

The paper identifies cargo genes of Tn7-like transposons, revealing their role in transferring diverse genes including MGEs, defense systems, and antibiotic resistance genes.

The paper investigates a suspected MDR K. pneumoniae outbreak using whole-genome sequencing to identify strain types and resistance genes.

Kaptive 2.0 updates capsule and LPS locus typing for Klebsiella pneumoniae by adding novel sequences and improving O2 antigen prediction, enabling better surveillance and control strategies.

The paper analyzes probiotic samples to identify antimicrobial resistance genes and their potential for horizontal gene transfer.

This paper identifies a specific biomarker for Acinetobacter baumannii Global Clone 1 using machine learning and PCR, highlighting its potential for early diagnosis and antibiotic stewardship.

This study uses whole-genome sequencing to analyze carbapenem-resistant Acinetobacter baumannii isolates in the Philippines, identifying resistance mechanisms and transmission patterns.

The paper introduces Pathogenwatch, a web tool for genomic surveillance of Klebsiella, showing it identifies drug-resistant clones and vaccine candidate O-types in genomes from low- and middle-income countries.

This study uses whole genome sequencing to analyze antimicrobial-resistant Klebsiella isolates from Nigeria, identifying known and novel lineages, including multidrug-resistant ESBL producers.

This study analyzes CRKP isolates in Colombia using WGS, identifying high-risk clones and carbapenemase genes, emphasizing the need for WGS-based surveillance.

Whole genome sequencing identified three previously unrecognized Klebsiella pneumoniae outbreaks in neonatal intensive care units in the Philippines, revealing an epidemic plasmid associated with carbapenem resistance.

Flanker clusters gene flanking sequences to identify mobile genetic element patterns associated with antimicrobial resistance genes.

This study characterizes the genomic diversity of carbapenem-resistant Klebsiella pneumoniae isolates from India, identifying high-risk clones and resistance mechanisms.

The paper uses whole genome sequencing to analyze carbapenem-resistant Acinetobacter baumannii isolates from Indian hospitals, identifying novel sequence types and clonal complexes associated with carbapenemase resistance.

This paper introduces ONN4ARG, an ontology-aware deep learning method for antibiotic resistance gene discovery, identifying 120,726 candidate ARGs, including novel ones not in public databases.

This study identifies the global distribution and transmission dynamics of tet(X) genes, revealing Riemerella anatipestifer as a potential ancestral source and Bacteroidaceae as a hidden reservoir for mobile tigecycline resistance.

This study benchmarks six plasmid prediction tools for E. coli short-read data, finding that none reliably reconstruct all plasmids, especially those carrying antibiotic resistance genes.

The paper shows that specific protein-membrane interactions enhance the export of metallo-β-lactamases into outer membrane vesicles in Gram-negative bacteria.

The paper investigates the role of insertion sequences in antibiotic resistance gene mobilization and phenotype modification in Enterococcus isolates from a patient with prolonged bacteremia.

The paper identifies and characterizes putative colistin resistance genes (MCR) in the human gut microbiome using bioinformatics analysis of metagenome assembled genomes.

The paper analyzes ESBL-Ec from swine microbiomes in Cameroon and South Africa to assess their resistance and pathogenic potential using whole genome sequencing.

This paper develops a machine learning model to predict ceftazidime-resistant bacterial strains from beta-lactamase amino acid sequences, achieving AUROC of 0.80 on training data.

This study evaluates the performance of short-read sequencing for detecting antimicrobial resistance genes in genomes and metagenomes, finding that assembly-based methods require 15X coverage for reliable detection.

The paper identifies mutations in bdcA and valS associated with quinolone resistance in wastewater E. coli using genome-wide association analysis.

This study analyzes ceftriaxone-resistant Salmonella Typhi isolates from India, finding that resistance arises from plasmid acquisition, with IncX3 and IncN plasmids contributing to sporadic resistance while IncY plasmids are associated with outbreaks in Pakistan.

The paper analyzes whole genome sequences of Shigella isolates from Malawi to identify fluoroquinolone resistance determinants.

The paper sequenced N. gonorrhoeae isolates from the Philippines to assess antimicrobial resistance and genetic diversity, finding high resistance to penicillin, ciprofloxacin, and tetracycline and genetic diversity within global lineage A.

The paper analyzes CRAB isolates from ICU surfaces to study their phylogenetic relationships and transmission patterns, finding a dominant global clone and evidence of outbreaks.