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Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine
A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex
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Conflicts of Interest
Identified Weaknesses
Rating Explanation
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Paper Summary
Paperzilla title
Kleborate-ing Klebsiella: A New Tool for Genomic Surveillance
This paper introduces Kleborate, a new bioinformatics tool for analyzing Klebsiella pneumoniae genomes. Kleborate rapidly identifies species, AMR genes, virulence factors, and other key features, providing valuable information for genomic surveillance and epidemiological studies. The tool was applied to public genome datasets, revealing trends in AMR, virulence, and the convergence of these traits.
Possible Conflicts of Interest
None identified
Identified Weaknesses
Sampling Bias
The study relies heavily on publicly available genome data, which may not accurately represent the true diversity of Klebsiella pneumoniae in different populations or environments. This introduces potential bias in the analysis and limits the generalizability of the findings.
Genotype-Phenotype Correlation
While Kleborate provides valuable information on genotypes associated with AMR and virulence, it does not predict phenotypes. This is a significant limitation because the relationship between genotype and phenotype is not always straightforward, especially for complex traits like antibiotic resistance.
Score Validation
The virulence and resistance scores, while useful for summarizing genotypic information, are not validated measures of clinical risk. The clinical significance of different combinations of virulence and resistance determinants requires further investigation.
Rating Explanation
This paper describes a well-designed and useful tool for Klebsiella pneumoniae genomic surveillance. The software addresses a critical need in the field and has already been widely adopted by researchers. The methodology is sound and the analysis is comprehensive. While some limitations exist regarding sampling bias and the interpretation of genotypic data, the overall contribution is significant and warrants a strong rating.
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Topic Hierarchy
File Information
Original Title:
A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex
File Name:
s41467-021-24448-3.pdf
[download]
File Size:
3.01 MB
Uploaded:
July 14, 2025 at 10:52 AM
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