Open Access Research article

An easy, simple inexpensive test for the specific detection of Pectobacterium carotovorum subsp. carotovorum based on sequence analysis of the pmrA gene

Mohamed Kettani-Halabi13, Meriam Terta1, Mohamed Amdan1, El Mostafa El Fahime2, François Bouteau3 and Moulay Mustapha Ennaji1*

Author Affiliations

1 Laboratoire de Virologie, Microbiologie et Qualité /Eco Toxicologie et Biodiversité, Université Hassan II Mohammedia – Casablanca, Faculté des Sciences et Techniques - Mohammedia - FSTM, BP 146, Mohammedia 20650, Maroc

2 UATRS – CNRST, Angle Allal Fassi / FAR, Hay Riad 10 000, Rabat, Maroc

3 Université Paris Diderot, Sorbonne Paris Cité, LEM Institut de Biologie des Plantes, 91405 Orsay, France

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BMC Microbiology 2013, 13:176  doi:10.1186/1471-2180-13-176

Published: 29 July 2013



The species Pectobacterium carotovorum includes a diverse subspecies of bacteria that cause disease on a wide variety of plants. In Morocco, approximately 95% of the P. carotovorum isolates from potato plants with tuber soft rot are P. carotovorum subsp. carotovorum. However, identification of this pathogen is not always related to visual disease symptoms. This is especially true when different pathogen cause similar diseases on potato, citing as an example, P. carotovorum, P. atrosepticum and P. wasabiae. Numerous conventional methods were used to characterize Pectobacterium spp., including biochemical assays, specific PCR-based tests, and construction of phylogenetic trees by using gene sequences. In this study, an alternative method is presented using a gene linked to pathogenicity, in order to allow accuracy at subspecies level. The pmrA gene (response regulator) has been used for identification and analysis of the relationships among twenty nine Pectobacterium carotovorum subsp. carotovorum and other Pectobacterium subspecies.


Phylogenetic analyses of pmrA sequences compared to ERIC-PCR and 16S rDNA sequencing, demonstrated that there is considerable genetic diversity in P. carotovorum subsp. carotovorum strains, which can be divided into two distinct groups within the same clade.


pmrA sequence analysis is likely to be a reliable tool to identify the subspecies Pectobacterium carotovorum subsp. carotovorum and estimate their genetic diversity.

pmrA gene; Pectobacterium carotovorum; Potato tuber; Soft rot disease; Genetic diversity; Phylogenetic analysis