Genomic structure of bacteriophage 6H and its distribution as prophage inFlavobacterium psychrophilumstrains

Abstract

Flavobacterium psychrophilum is currently one of the most devastating fish pathogens worldwide causing considerable economic losses in salmonid aquaculture. Recently, attention has been drawn to the use of phages for controlling F. psychrophilum, and phages infecting the pathogen have been isolated. Here, we present the genome sequence of F. psychrophilum bacteriophage 6H and its distribution as prophage in F. psychrophilum isolates. The DNA sequence revealed a genome of 46 978 bp containing 63 predicted ORFs, of which 13% was assigned a putative function, including an integrase. Sequence analysis showed > 80% amino acid similarity to a specific region found in the virulent F. psychrophilum strain JIP02/86 (ATCC 49511), suggesting that a prophage similar to phage 6H was present in this strain. Screening for a collection of 49 F. psychrophilum strains isolated in Chile, Denmark, and USA for the presence of four phage 6H genes (integrase, tail tape protein and two hypothetical proteins) by PCR showed the presence of these prophage genes in 80% of the isolates. In conclusion, we hypothesize that bacteriophage 6H belongs to an abundant group of temperate phages which has lysogenized a large fraction of the global F. psychrophilum community.

Bacteriophage Resistance Mechanisms in the Fish Pathogen Flavobacterium psychrophilum: Linking Genomic Mutations to Changes in Bacterial Virulence Factors

“…Thus, even though the V3-5 resistant strain contained two spacers matching phage 6H sequences, the strain had gained sensitivity to this particular phage (28). Similarly, previous results have displayed that F. psychrophilum strain MH1, which has an identical CRISPR1 locus (unpublished results), is also sensitive to phage 6H (29). Moreover, the fact that an identical CRISPR locus was found in both the Danish F. psychrophilum strain 950106-1/1 and the previously sequenced strain JIPO2/86, isolated in France Ͼ10 years earlier (45), suggests that the CRISPR system in F. psychrophilum is not an active and dynamic system involved in phage resistance.…”

“…Studies on the effects of bacteriophages on F. psychrophilum populations have shown multiple phenotypic effects of phage exposure, including cross-resistance to some phages and loss of resistance to other phages (28), as well as the loss of a specific prophage (29) and metabolic changes (Christiansen et al, unpublished). Obviously, more knowledge about genetic properties in both phages and hosts determining susceptibility and host range properties is needed to understand the complex network of underlying genetic changes behind these phenotypic changes in F. psychrophilum following phage exposure.…”

“…A recent compilation of bacteriophage susceptibility patterns in a collection of F. psychrophilum isolates which obtained resistance after exposure to specific phages revealed both cross-resistance to and loss of resistance to other bacteriophages (28). The loss of resistance was associated with the loss of a specific 6H-type prophage (29), suggesting that prophages play a role in resistance to certain phages. However, the underlying genomic mechanisms of phage resistance and their phenotypic consequences in F. psychrophilum have not been investigated in detail.…”

Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512

“…Three incomplete regions are in the F. branchiophilum FL-15 genome, and one incomplete and one questionable region are in the F. johnsoniae UW101 genome. Only the F. psychrophilum JIP02/86 genome carries a complete phage region, which has been previously described (Castillo et al, 2014) and is absent in other Flavobacterium genomes (Wiens et al, 2014). F. indicum GPTSA100-9 genome does not carry any predicted bacteriophage regions.…”

Complete Genome Sequence of Flavobacterium psychrophilum Strain CSF259-93, Used To Select Rainbow Trout for Increased Genetic Resistance against Bacterial Cold Water Disease

“…There is a substitution of several lipopolysaccharide (LPS) biosynthesis genes (FPSM_02190 through FPSM_02194 and FPSM_02202). Finally, strain CSF259-93 lacks an integrated prophage that is found in the JIP02/86 genome (22). …”