Reduced set of virulence genes allows high accuracy prediction of bacterial pathogenicity in humans.

Although there have been great advances in understanding bacterial pathogenesis, there is still a lack of integrative information about what makes a bacterium a human pathogen. The advent of high-throughput sequencing technologies has dramatically increased the amount of completed bacterial genomes,...

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Autores principales:	Gregorio Iraola, Gustavo Vazquez, Lucía Spangenberg, Hugo Naya
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/bbaa3439c0594f829769ceb90f5de4eb
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spelling	oai:doaj.org-article:bbaa3439c0594f829769ceb90f5de4eb2021-11-18T07:09:30ZReduced set of virulence genes allows high accuracy prediction of bacterial pathogenicity in humans.1932-620310.1371/journal.pone.0042144https://doaj.org/article/bbaa3439c0594f829769ceb90f5de4eb2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22916122/?tool=EBIhttps://doaj.org/toc/1932-6203Although there have been great advances in understanding bacterial pathogenesis, there is still a lack of integrative information about what makes a bacterium a human pathogen. The advent of high-throughput sequencing technologies has dramatically increased the amount of completed bacterial genomes, for both known human pathogenic and non-pathogenic strains; this information is now available to investigate genetic features that determine pathogenic phenotypes in bacteria. In this work we determined presence/absence patterns of 814 different virulence-related genes among more than 600 finished bacterial genomes from both human pathogenic and non-pathogenic strains, belonging to different taxonomic groups (i.e: Actinobacteria, Gammaproteobacteria, Firmicutes, etc.). An accuracy of 95% using a cross-fold validation scheme with in-fold feature selection is obtained when classifying human pathogens and non-pathogens. A reduced subset of highly informative genes (120) is presented and applied to an external validation set. The statistical model was implemented in the BacFier v1.0 software (freely available at http : ==bacfier:googlecode:com=files=Bacfier v1 0:zip), that displays not only the prediction (pathogen/non-pathogen) and an associated probability for pathogenicity, but also the presence/absence vector for the analyzed genes, so it is possible to decipher the subset of virulence genes responsible for the classification on the analyzed genome. Furthermore, we discuss the biological relevance for bacterial pathogenesis of the core set of genes, corresponding to eight functional categories, all with evident and documented association with the phenotypes of interest. Also, we analyze which functional categories of virulence genes were more distinctive for pathogenicity in each taxonomic group, which seems to be a completely new kind of information and could lead to important evolutionary conclusions.Gregorio IraolaGustavo VazquezLucía SpangenbergHugo NayaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 8, p e42144 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Gregorio Iraola Gustavo Vazquez Lucía Spangenberg Hugo Naya Reduced set of virulence genes allows high accuracy prediction of bacterial pathogenicity in humans.
description	Although there have been great advances in understanding bacterial pathogenesis, there is still a lack of integrative information about what makes a bacterium a human pathogen. The advent of high-throughput sequencing technologies has dramatically increased the amount of completed bacterial genomes, for both known human pathogenic and non-pathogenic strains; this information is now available to investigate genetic features that determine pathogenic phenotypes in bacteria. In this work we determined presence/absence patterns of 814 different virulence-related genes among more than 600 finished bacterial genomes from both human pathogenic and non-pathogenic strains, belonging to different taxonomic groups (i.e: Actinobacteria, Gammaproteobacteria, Firmicutes, etc.). An accuracy of 95% using a cross-fold validation scheme with in-fold feature selection is obtained when classifying human pathogens and non-pathogens. A reduced subset of highly informative genes (120) is presented and applied to an external validation set. The statistical model was implemented in the BacFier v1.0 software (freely available at http : ==bacfier:googlecode:com=files=Bacfier v1 0:zip), that displays not only the prediction (pathogen/non-pathogen) and an associated probability for pathogenicity, but also the presence/absence vector for the analyzed genes, so it is possible to decipher the subset of virulence genes responsible for the classification on the analyzed genome. Furthermore, we discuss the biological relevance for bacterial pathogenesis of the core set of genes, corresponding to eight functional categories, all with evident and documented association with the phenotypes of interest. Also, we analyze which functional categories of virulence genes were more distinctive for pathogenicity in each taxonomic group, which seems to be a completely new kind of information and could lead to important evolutionary conclusions.
format	article
author	Gregorio Iraola Gustavo Vazquez Lucía Spangenberg Hugo Naya
author_facet	Gregorio Iraola Gustavo Vazquez Lucía Spangenberg Hugo Naya
author_sort	Gregorio Iraola
title	Reduced set of virulence genes allows high accuracy prediction of bacterial pathogenicity in humans.
title_short	Reduced set of virulence genes allows high accuracy prediction of bacterial pathogenicity in humans.
title_full	Reduced set of virulence genes allows high accuracy prediction of bacterial pathogenicity in humans.
title_fullStr	Reduced set of virulence genes allows high accuracy prediction of bacterial pathogenicity in humans.
title_full_unstemmed	Reduced set of virulence genes allows high accuracy prediction of bacterial pathogenicity in humans.
title_sort	reduced set of virulence genes allows high accuracy prediction of bacterial pathogenicity in humans.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/bbaa3439c0594f829769ceb90f5de4eb
work_keys_str_mv	AT gregorioiraola reducedsetofvirulencegenesallowshighaccuracypredictionofbacterialpathogenicityinhumans AT gustavovazquez reducedsetofvirulencegenesallowshighaccuracypredictionofbacterialpathogenicityinhumans AT luciaspangenberg reducedsetofvirulencegenesallowshighaccuracypredictionofbacterialpathogenicityinhumans AT hugonaya reducedsetofvirulencegenesallowshighaccuracypredictionofbacterialpathogenicityinhumans
_version_	1718423877438144512

Reduced set of virulence genes allows high accuracy prediction of bacterial pathogenicity in humans.

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