A novel genotyping technique for distinguishing between Flavobacterium psychrophilum isolates virulent and avirulent to ayu, Plecoglossus altivelis altivelis (Temminck & Schlegel)

Abstract

We developed a simple genotyping method for Flavobacterium psychrophilum for analysing two single nucleotide polymorphisms (SNPs) in the gyrA gene and to distinguish between isolates that are virulent and avirulent to ayu, Plecoglossus altivelis altivelis (Temminck & Schlegel). The genotyping method is an on/off switch assay and is based on the polymerase chain reaction technique with phosphorothioated primers. We classified 232 isolates from four families of fish (i.e. Plecoglossidae, Osmeridae, Cyprinidae and Salmonidae) into four genotypes (G-C, A-T, A-C and G-T). The G-C type isolates exhibited strong pathogenicity to ayu, whereas the A-T and G-T types did not show any pathogenicity to this species. The A-C type exhibited no or weak pathogenicity to ayu. These results indicate that genotyping F. psychrophilum isolates with two SNPs from gyrA can clearly distinguish between isolates potentially harmful to ayu (G-C type) and those that are potentially not harmful or less harmful (A-C, A-T and G-T type). The on/off switch assay provides a quick, simple, and very powerful DNA genotyping technique for F. psychrophilum isolates.

Population structure of the fish pathogen Flavobacterium psychrophilum at whole-country and model river levels in Japan

“…Strains in these three CC showed various levels of virulence against ayu in bath infection challenges and strains from CC-ST48/CC-ST56 generally seem more virulent than those from CC-ST52 [14]. Of note, CC-ST56 also infects cyprinids in Japan and [14] reported that ST-51 isolates from cyprinids cause mortality in ayu by bath infection challenge, providing experimental support for the possibility of transfer between carp and ayu in CC-ST56.…”

“…The actual host range of F. psychrophilum is, however, not limited to salmonids [12], although the infection is apparently less severe in non-salmonids [13]. In Japan, F. psychrophilum has been reported on a number of local non-salmonid wild fish species [14-16]. …”

“…Correlations between bacterial genotype and host fish have been observed in several studies on field isolates [14,17-20] and we recently reported that ayu could be experimentally infected in bath infection challenges by isolates collected from ayu but not from coho salmon or rainbow trout [14]. However mimicking the conditions of natural infections is generally difficult for F. psychrophilum [21-24] and field studies that would provide a deeper knowledge of the distribution of the genotypes in terms of geographical area and host fish species are essential.…”

Draft Genome Sequence of Flavobacterium psychrophilum Strain KTEN-1510 with Genotype A/G-C, Isolated from an Ayu (Plecoglossus altivelis altivelis ) in the Kagami River, Kochi, Japan

“…Type A was detected only in isolates from ayu. Fujiwara-Nagata et al (10) identified four genotypes (G-C, A-T, A-C, and G-T) among 232 isolates using single-nucleotide polymorphism (SNP) analysis of the DNA gyrase subunit A ( gyrA ) gene. Type G-C showed strong pathogenicity to ayu, whereas the other three were not or only weakly pathogenic.…”

Draft Genome Sequence of Flavobacterium psychrophilum Strain SSADA-1411, Isolated from an Ayu (Plecoglossus altivelis altivelis) Migrating Downriver To Spawn in the Shimanto River, Kochi, Japan

“…Also, some isolates from ayu harbor a 2.8-, 3.4-, or 4.1-kbp plasmid (6). Four genotypes—type G-C, type A-T, type A-C, and type G-T—are classified based on genotyping by single nucleotide polymorphism analysis of the DNA gyrase subunit A gene (7). Type G-C shows strong pathogenicity to ayu, whereas the other three exhibit no or weak pathogenicity.…”