Genomes of the most dangerous epidemic bacteria have a virulence repertoire characterized by fewer genes but more toxin-antitoxin modules
Authors: Didier Raoult
Kalliopi Georgiades
Journal: PloS one (2011)
Discipline: Multidisciplinary
Keywords: Comparative genomics; Virulence capacity; Pathogenic bacteria; Genome specificities; Pandemic bacteria
Affiliations: Unité de Recherche en Maladies Infectieuses Tropicales Emergentes, CNRS-IRD UMR 6236, Faculté de la Médecine, Université de la Méditerranée, Marseille, France.

Abstract:  Background: We conducted a comparative genomic study based on a neutral approach to identify genome specificities associated with the virulence capacity of pathogenic bacteria. We also determined whether virulence is dictated by rules, or if it is the result of individual evolutionary histories. We systematically compared the genomes of the 12 most dangerous pandemic bacteria for humans ("bad bugs") to their closest non-epidemic related species ("controls"). Methodology/principal findings: We found several significantly different features in the "bad bugs", one of which was a smaller genome that likely resulted from a degraded recombination and repair system. The 10 Cluster of Orthologous Group (COG) functional categories revealed a significantly smaller number of genes in the "bad bugs", which lacked mostly transcription, signal transduction mechanisms, cell motility, energy production and conversion, and metabolic and regulatory functions. A few genes were identified as virulence factors, including secretion system proteins. Five "bad bugs" showed a greater number of poly (A) tails compared to the controls, whereas an elevated number of poly (A) tails was found to be strongly correlated to a low GC% content. The "bad bugs" had fewer tandem repeat sequences compared to controls. Moreover, the results obtained from a principal component analysis (PCA) showed that the "bad bugs" had surprisingly more toxin-antitoxin modules than did the controls. Conclusions/significance: We conclude that pathogenic capacity is not the result of "virulence factors" but is the outcome of a virulent gene repertoire resulting from reduced genome repertoires. Toxin-antitoxin systems could participate in the virulence repertoire, but they may have developed independently of selfish evolution. 

Retracted: No

PubPeer comments:
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 Dear Capillacea, Thank you for pointing out our mistake. This is a mistake made when putting these pictures on a canvas for the first time. We are very sorry for the error. We already contacted the editors and sent the original data for the correction. This will make us pay more attention to the next article submission. Thank you again. Sincerely, Wang Baofeng , 
 Dear Capillacea, Thanks for your pointing out our mistake. This mistake was made during the first time putting these pictures together in one canvas. The picture in the third column of the first row was omitted owing to my carelessness. We have already contacted the editors and sent the original data for the correction and waiting for the reply to deal with this problem. Thank you again. Best regards, Cheng Fanglling Chengf , 
 Dear Capillacea, Thanks for your pointing out our mistake. This mistake was made during the first time putting these pictures together in one canvas. The picture in the third column of the first row was omitted owing to my carelessness. We have already contacted the editors and sent the original data for the correction and waiting for the reply to deal with this problem. Thank you again. Best regards, Cheng Fangling ,