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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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Autores principales: Hernández-Salmerón, Julie E., Moreno-Hagelsieb, Gabriel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9308963/
https://www.ncbi.nlm.nih.gov/pubmed/35891643
http://dx.doi.org/10.7717/peerj.13784
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author Hernández-Salmerón, Julie E.
Moreno-Hagelsieb, Gabriel
author_facet Hernández-Salmerón, Julie E.
Moreno-Hagelsieb, Gabriel
author_sort Hernández-Salmerón, Julie E.
collection PubMed
description 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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spelling pubmed-93089632022-07-25 FastANI, Mash and Dashing equally differentiate between Klebsiella species Hernández-Salmerón, Julie E. Moreno-Hagelsieb, Gabriel PeerJ Bioinformatics 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. PeerJ Inc. 2022-07-21 /pmc/articles/PMC9308963/ /pubmed/35891643 http://dx.doi.org/10.7717/peerj.13784 Text en © 2022 Hernández-Salmerón and Moreno-Hagelsieb https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Hernández-Salmerón, Julie E.
Moreno-Hagelsieb, Gabriel
FastANI, Mash and Dashing equally differentiate between Klebsiella species
title FastANI, Mash and Dashing equally differentiate between Klebsiella species
title_full FastANI, Mash and Dashing equally differentiate between Klebsiella species
title_fullStr FastANI, Mash and Dashing equally differentiate between Klebsiella species
title_full_unstemmed FastANI, Mash and Dashing equally differentiate between Klebsiella species
title_short FastANI, Mash and Dashing equally differentiate between Klebsiella species
title_sort fastani, mash and dashing equally differentiate between klebsiella species
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9308963/
https://www.ncbi.nlm.nih.gov/pubmed/35891643
http://dx.doi.org/10.7717/peerj.13784
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