ArticleThe Journal of antimicrobial chemotherapy2025
Phenotype-genotype discordance in antimicrobial resistance profiles of Gram-negative uropathogens recovered from catheter-associated urinary tract infections in Egypt.
Article in The Journal of antimicrobial chemotherapy, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Antibiotic-Specific Genotype-Phenotype Concordance and Cross-Database Interoperability in PublicInternational journal of molecular sciences · 2026Article
- Molecular epidemiology and antimicrobial resistance of extended-spectrum beta-lactamases-producingJAC-antimicrobial resistance · 2026Article
- The Resistance Landscape of Uropathogens in a Romanian Tertiary Center: A 13-Month Single-Center Study with Focus onMicroorganisms · 2026Article
- Co-occurrence of biofilm formation, acid tolerance, and antibiotic resistance in environmental Escherichia coli associated with lettuce.BMC microbiology · 2026Article
- Whole-genome sequencing reveals high-risk ESBL and carbapenemase-producing Enterobacterales on maternity ward surfaces in Cameroon.Scientific reports · 2026Article
- Complete genome sequence and description of Escherichia coli isolated from fresh vegetables in Baghdad, Iraq.Journal, genetic engineering & biotechnology · 2026Article
- Global survey of extraintestinal pathogenic Escherichia coli identifies stable serogroup-virulence-resistance linkages.Genome medicine · 2026Article
- Longitudinal genomic insights into resistance and virulence dynamics of Klebsiella pneumoniae clinical isolates from Pakistan.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Genotype-Phenotype Links Between Aminoglycoside-Modifying Enzymes and Aminoglycoside MICs in Aminoglycoside-ResistantMicroorganisms · 2026Article
- Sheep-associated Escherichia coli in Albania show high genomic similarity to European ovine lineages and a conserved core resistome.FEMS microbiology letters · 2026Article
- Editorial: Next-generation technologies for antibiotic susceptibility testing.Frontiers in microbiology · 2026Article
- Phenotypic and genome-based characterization ofFrontiers in microbiology · 2026Article
- Analysis of Multi-Antimicrobial Resistance Patterns in U.S. Foodborne Pathogens (2015-2025) Using Data from the NCBI Pathogen Isolates Browser.Pathogens (Basel, Switzerland) · 2025Article
- Prevalence of ESBL-ProducingPathogens (Basel, Switzerland) · 2025Article
- Applications of Genome Sequencing in Infectious Diseases: From Pathogen Identification to Precision Medicine.Pharmaceuticals (Basel, Switzerland) · 2025Review
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5 authors.
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Abstract
objectivesCatheter-associated urinary tract infections (CAUTIs) are among the most common healthcare-associated infections in low- and middle-income countries (LMICs), but there are few resistome data available for relevant uropathogens. The goal of this study was to characterize the antimicrobial resistance (AMR) phenotypes and genotypes of a large collection of Gram-negative bacteria recovered from CAUTIs in a hospital in Mansoura, Egypt.
methodsPhenotypic AMR profiles and whole-genome sequence data were generated for 132 isolates. Resistomes were predicted using ResFinder, CARD and AMRFinder. Similarity of uropathogen genomic data was determined using sourmash (kmer signatures). Escherichia coli genomic data were subject to a pangenome analysis using Panaroo.
resultsSixty-seven E. coli (Phylogroup B2; 53.7%, 36/67), 14 Pseudomonas aeruginosa, 11 Klebsiella pneumoniae, 9 Proteus mirabilis, 8 Providencia spp., 5 Enterobacter hormaechei and 18 rare CAUTI-associated isolates were identified. Several (22/132) isolates were multidrug-resistant, while almost half (62/132) were extensively drug-resistant. Phenotype-genotype discordance was found to be an important consideration in resistome studies in Egypt, with a total concordance of 91% (1115/1225), 85.7% (1273/1485) and 80.5% (1196/1485) for ResFinder, CARD and AMRFinder, respectively. Pseudomonas, at the species level, exhibited the greatest discordance. At the antimicrobial level, meropenem was subject to greatest discordance. New AMR variants were found for Egypt for Pseudomonas (blaOXA-486, blaOXA-488, blaOXA-905, blaIMP-43, blaPDC-35, blaPDC-45, blaPDC-201) and E. coli (blaTEM-176, blaTEM-190).
conclusionsThis study shows that there is phenotype-genotype discordance in AMR profiling among CAUTI isolates, highlighting the need for comprehensive approaches in resistome studies. We also show the genomic diversity of Gram-negative uropathogens contributing to disease burden in a little-studied LMIC setting.
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