The bacterial pangenome as a new tool for analysing pathogenic bacteria

L Rouli; V Merhej; P-E Fournier; D Raoult

doi:10.1016/j.nmni.2015.06.005

The bacterial pangenome as a new tool for analysing pathogenic bacteria

New Microbes New Infect. 2015 Jun 26:7:72-85. doi: 10.1016/j.nmni.2015.06.005. eCollection 2015 Sep.

Authors

L Rouli¹, V Merhej¹, P-E Fournier¹, D Raoult¹

Affiliation

¹ Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France.

Abstract

The bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. Thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and the accessory genome, offering a large panel of uses. In this review, we have presented the analysis methods, the pangenome composition and its application as a study of lifestyle. We have also shown that the pangenome may be used as a new tool for redefining the pathogenic species. We applied this to the Escherichia coli and Shigella species, which have been a subject of controversy regarding their taxonomic and pathogenic position.

Keywords: Bacteria; bioinformatics tools; comparative genomics; pangenome; pathogenic species.