Understanding the molecular virulence mechanisms of a bacterium which is pathogenic for fish

lcatto — 2007-10-19T09:45:00Z

An understanding of the molecular mechanisms which confer an aptitude for colonization, invasiveness, and reorientation of the physiology of a host constitutes a challenge of major importance, from academic, medical and agronomic points of view: these studies serve to guide the conception of new strategies for fighting pathogenic organisms.

The genus Flavobacterium includes a large diversity of species, principally isolated from aquatic environments. These species include notably three which are pathogenic for fish: F. psychrophilum, F. columnare and F. branchiophilum. The genome of the JIP 02/86 strain of the bacterium F. psychrophilum which is pathogenic for the salmonides has been already sequenced and analyzed (Duchaud E.)

Whereas F. columnare and F. psychrophilum are sometimes capable of causing branchial lesions in several species of fish, a third species, F. branchiophilum, is mainly responsible for gill disease (Kimura et al., and Wakabayashi H. et al.), a pathology which primarily affects salmonides. Since the first description of this bacterium in Japan, F. branchiophilum has been detected in numerous regions in which salmoniculture is practiced (USA, Hungary, Canada, Korea).

In contrast to F. psychrophilum and F. columnare, F. branchiophilum is considered to be a non-invasive bacterium. The branchial tropism is probably linked to proteolytic and hemagglutinating activities of extracellular products as well as to the adherence capacities of the bacterium, which affects the respiratory capacity of the colonized hosts (Wakabayashi, H., and Iwado, T.).

Whole genome shotgun

lcatto — 2007-10-19T09:51:57Z

The Infection and Immunity of Fish Team from the INRA in Jouy-en-Josas (France) has been studying pathogenic bacteria from the Flavobacterium genus since the first strains appeared in Europe in the 1960s. Their work has notably led to the complete revision of the genus (Bernardet, J-F, & Bowman), and the description of the Flavobacteriaceae family (Bernardet J-F, & Nakagawa,Y). They have developed methods for molecular typing, and standardized culture techniques and methods of experimental infection of the rainbow trout.

Genoscope is undertaking the sequencing of the complete genome of the bacterium, Flavobacterium branchiophilum, the pathogen responsible for gill disease, which primarily affects the salmonides.

The size of the genome of F. branchiophilum is estimated at 2.8 Mb. The genome will be sequenced by the shotgun method using two plasmid libraries with inserts of 5 kb and 10 kb, cloned respectively in multicopy plasmid pcdna2.1 and low copy number plasmid pCNS, and a fosmid library (40 kb inserts in pCC1Fos).

The sequencing of both ends of about 18,500 clones from the small insert plasmid library, 6,000 clones from the large insert plasmid library and 3,000 clones from the fosmid library should constitute a volume of 55,000 reads, corresponding to 12 genome equivalents.

The shotgun phase will be followed by an assembly step, and finishing of the sequence according to quality assurance criteria in effect at Genoscope.

Contacts: Valérie Barbe (Genoscope) - Eric Duchaud (INRA)

Site du Genoscope

Understanding the molecular virulence mechanisms of a bacterium which is pathogenic for fish

Whole genome shotgun