ArticleScientific reports2023
Pipeline validation for the identification of antimicrobial-resistant genes in carbapenem-resistant Klebsiella pneumoniae.
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 11 papers.
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Who cites it
11 citing papers in PubMed.
- Molecular determinants of antimicrobial resistance inMicrobiology spectrum · 2026Article
- Pangenomic and genomic plasticity analyses of the genus Rickettsia.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Virulence-Associated Genomic Architecture of Canine Otitis Externa-DerivedVeterinary sciences · 2026Article
- In silico genomic analysis of resistome, virulome, and mobilome of β-lactamase-producing Klebsiella pneumoniae.Scientific reports · 2026Article
- A leakage-aware genomic prediction pipeline for meropenem resistance inBioinformatics advances · 2026Article
- Genomic insight into the antibiotic-resistant determinants ofFrontiers in microbiology · 2026Article
- Network analysis of antimicrobial resistance inNAR genomics and bioinformatics · 2025Article
- Genomic characterization of Microbacterium meiriae sp. nov., a novel bacterium isolated from the International Space Station.Scientific reports · 2025Article
- Leveraging illumina iSeq100 for whole genome sequencing of Salmonella Typhi for a resource-limited setting.Scientific reports · 2025Article
- Biodegradation of plastics and pesticides by soil bacteria in Bangladesh: Insights into antibiotic resistance and potential therapeutic targets.Journal, genetic engineering & biotechnology · 2025Article
- Plastispheres as reservoirs of antimicrobial resistance: Insights from metagenomic analyses across aquatic environments.PloS one · 2025Article
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8 authors.
Funding
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Abstract
Antimicrobial-resistant Klebsiella pneumoniae is a global threat to healthcare and an important cause of nosocomial infections. Antimicrobial resistance causes prolonged treatment periods, high mortality rates, and economic impacts. Whole Genome Sequencing (WGS) has been used in laboratory diagnosis, but there is limited evidence about pipeline validation to parse generated data. Thus, the present study aimed to validate a bioinformatics pipeline for the identification of antimicrobial resistance genes from carbapenem-resistant K. pneumoniae WGS. Sequences were obtained from a publicly available database, trimmed, de novo assembled, mapped to the K. pneumoniae reference genome, and annotated. Contigs were submitted to different tools for bacterial (Kraken2 and SpeciesFinder) and antimicrobial resistance gene identification (ResFinder and ABRicate). We analyzed 201 K. pneumoniae genomes. In the bacterial identification by Kraken2, all samples were correctly identified, and in SpeciesFinder, 92.54% were correctly identified as K. pneumoniae, 6.96% erroneously as Pseudomonas aeruginosa, and 0.5% erroneously as Citrobacter freundii. ResFinder found a greater number of antimicrobial resistance genes than ABRicate; however, many were identified more than once in the same sample. All tools presented 100% repeatability and reproducibility and > 75% performance in other metrics. Kraken2 was more assertive in recognizing bacterial species, and SpeciesFinder may need improvements.
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