FastANI, Mash and Dashing equally differentiate between Klebsiella species

Bacteria of the genus Klebsiella are among the most important multi-drug resistant human pathogens, though they have been isolated from a variety of environments. The importance and ubiquity of these organisms call for quick and accurate methods for their classification. Average Nucleotide Identity...

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Published in:PeerJ (San Francisco, CA) Vol. 10; p. e13784
Main Authors: Hernández-Salmerón, Julie E., Moreno-Hagelsieb, Gabriel
Format: Journal Article
Language:English
Published: United States PeerJ, Inc 21.07.2022
PeerJ Inc
Subjects:
Antibiotics
Bacteria
Bioinformatics
Computational Biology
Datasets
Deoxyribonucleic acid
DNA
Drug resistance
FastANI
Genome comparison
Genome, Bacterial - genetics
Genomes
Genomics
Hierarchical clustering
Humans
Klebsiella
Klebsiella - genetics
Microbiology
Multidrug resistance
Nucleotide sequence
Sketching algorithms
Species
Klebsiella
Sketching algorithms
FastANI
Hierarchical clustering
Genome comparison
ISSN:2167-8359, 2167-8359
Online Access:Get full text
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Summary:Bacteria of the genus Klebsiella are among the most important multi-drug resistant human pathogens, though they have been isolated from a variety of environments. The importance and ubiquity of these organisms call for quick and accurate methods for their classification. Average Nucleotide Identity (ANI) is becoming a standard for species delimitation based on whole genome sequence comparison. However, much faster genome comparison tools have been appearing in the literature. In this study we tested the quality of different approaches for genome-based species delineation against ANI. To this end, we compared 1,189 Klebsiella genomes using measures calculated with Mash, Dashing, and DNA compositional signatures, all of which run in a fraction of the time required to obtain ANI. Receiver Operating Characteristic (ROC) curve analyses showed equal quality in species discrimination for ANI, Mash and Dashing, with Area Under the Curve (AUC) values above 0.99, followed by DNA signatures (AUC: 0.96). Accordingly, groups obtained at optimized cutoffs largely agree with species designation, with ANI, Mash and Dashing producing 15 species-level groups. DNA signatures broke the dataset into more than 30 groups. Testing Mash to map species after adding draft genomes to the dataset also showed excellent results (AUC above 0.99), producing a total of 26 Klebsiella species-level groups. The ecological niches of Klebsiella strains were found to neither be related to species delimitation, nor to protein functional content, suggesting that a single Klebsiella species can have a wide repertoire of ecological functions.
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ISSN:2167-8359
2167-8359
DOI:10.7717/peerj.13784