ArticleScientific reports2023
Genotypic resistance determined by whole genome sequencing versus phenotypic resistance in 234 Escherichia coli isolates.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed, 42 citations in OpenAlex.
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- Bacterial heteroresistance mechanisms, dynamics, and emerging diagnostic approaches.Bioscience reports · 2026Review
- Machine Learning-Based Prediction of Antimicrobial Resistance inDiagnostics (Basel, Switzerland) · 2026Article
- Genomic diversity and high-risk lineages in clinical Escherichia coli from Mexico.Archives of microbiology · 2026Article
- New genotyping method for Escherichia coli using RSXC repeat polymorphism and gene-neighborhood architecture.BMC genomics · 2026Article
- Sheep-associated Escherichia coli in Albania show high genomic similarity to European ovine lineages and a conserved core resistome.FEMS microbiology letters · 2026Article
- A Pilot Study ofDiagnostics (Basel, Switzerland) · 2026Article
- Genotypic and phenotypic strategies to detect antibiotic resistance in foodborne pathogens along the food processing chain.Current research in food science · 2026Review
- Genome-wide investigation of outbreak-associatedFrontiers in microbiology · 2026Article
- Phenotype-genotype discordance in antimicrobial resistance profiles of Gram-negative uropathogens recovered from catheter-associated urinary tract infections in Egypt.The Journal of antimicrobial chemotherapy · 2025Article
- Antimicrobial resistance patterns of Campylobacter jejuni isolated from retail raw chicken meat in Jordan.Poultry science · 2025Article
- Phenotypic and genotypic relationships between Shigella species and Escherichia coli O37:H10 isolates in Addis Ababa, Ethiopia.BMC research notes · 2025Article
- Comprehensive analysis of extensive drug-resistantMicrobiology spectrum · 2025Article
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- Genomic insights into extended-spectrumJournal of medical microbiology · 2025Article
- Comparison of commercial next-generation sequencing assays to conventional culture methods for bacterial identification and antimicrobial susceptibility of samples obtained from clinical cases of canine superficial bacterial folliculitis.Veterinary dermatology · 2025Article
- An explainable machine learning pipeline for prediction of antimicrobial resistance inBioinformatics advances · 2025Article
- Phylogenetic analysisOpen veterinary journal · 2024Article
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole genome sequencing (WGS) enables detailed characterization of bacteria at single nucleotide resolution. It provides data about acquired resistance genes and mutations leading to resistance. Although WGS is becoming an essential tool to predict resistance patterns accurately, comparing genotype to phenotype with WGS is still in its infancy. Additional data and validation are needed. In this retrospective study, we analysed 234 E. coli isolates from positive blood cultures using WGS as well as microdilution for 11 clinically relevant antibiotics, to compare the two techniques. We performed whole genome sequencing analyses on 234 blood culture isolates (genotype) to detect acquired antibiotic resistance. Minimal inhibitory concentrations (MIC) for E. coli were performed for amoxicillin, cefepime, cefotaxime, ceftazidime, meropenem, amoxicillin/clavulanic acid, piperacillin/tazobactam, amikacin, gentamicin, tobramycin, and ciprofloxacin, using the ISO 20776-1 standard broth microdilution method as recommended by EUCAST (phenotype). We then compared the two methods for statistical 'agreement'. A perfect (100%) categorical agreement between genotype and phenotype was observed for gentamicin and meropenem. However, no resistance to meropenem was observed. A high categorical agreement (> 95%) was observed for amoxicillin, cefepime, cefotaxime, ceftazidime, amikacin, and tobramycin. A categorical agreement lower than 95% was observed for amoxicillin/clavulanic acid, piperacillin/tazobactam, and ciprofloxacin. Most discrepancies occurred in isolates with MICs within ± 1 doubling dilution of the breakpoint and 22.73% of the major errors were samples that tested phenotypically susceptible at higher antibiotic exposure and were therefore considered as 'not resistant'. This study shows that WGS can be used as a valuable tool to predict phenotypic resistance against most of the clinically relevant antibiotics used for the treatment of E. coli bloodstream infections.
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