Journal Article

Genetic and phenotypic diversity of Flavobacterium psychrophilum isolates from Czech salmonid fish farms

Cejkova, Darina, Palikova, Miroslava, Schwarzerova, Jana, Vaibarova, Vera, Nejezchlebova, Julie, Kralova, Stanislava, Cizek, Alois

2024

Overview

Background The salmonid pathogen Flavobacterium psychrophilum poses a significant economic threat to global aquaculture, yet our understanding of its genetic and phenotypic diversity remains incomplete across much of its geographic range. In this study, we characterise the genetic and phenotypic diversity of 70 isolates collected from rainbow trout ( Oncorhynchus mykiss ) and brown trout ( Salmo trutta m. fario ) from fish farms in the Czech Republic between 2012 and 2019 to compare their genomic content with all draft or complete genomes present in the NCBI database ( n  = 187). Results The Czech isolates underwent comprehensive evaluation, including multiplex PCR-based serotyping, genetic analysis, antimicrobial resistance testing, and assessment of selected virulence factors. Multiplex PCR serotyping revealed 43 isolates as Type 1, 23 as Type 2, with sporadic cases of Types 3 and 4. Multi-locus sequence typing unveiled 12 sequence types (ST), including seven newly described ones. Notably, 24 isolates were identified as ST329, a novel sequence type, while 22 were classified as the globally-distributed ST2. Phylogenetic analysis demonstrated clonal distribution of ST329 in the Czech Republic, with these isolates lacking a phage sequence in their genomes. Antimicrobial susceptibility testing revealed a high proportion of isolates classified as non-wild type with reduced susceptibility to oxolinic acid, oxytetracycline, flumequine, and enrofloxacin, while most isolates were classified as wild type for florfenicol, sulfamethoxazole-trimethoprim, and erythromycin. However, 31 isolates classified as wild type for florfenicol exhibited minimum inhibitory concentrations at the susceptibility breakpoint. Conclusion The prevalence of the Czech F. psychrophilum serotypes has evolved over time, likely influenced by the introduction of new isolates through international trade. Thus, it is crucial to monitor F. psychrophilum clones within and across countries using advanced methods such as MLST, serotyping, and genome sequencing. Given the open nature of the pan-genome, further sequencing of strains promises exciting discoveries in F. psychrophilum genomics.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Analysis / Animals / Anti-Bacterial Agents - pharmacology / Antibiotics / Antimicrobial resistance / Antimicrobial susceptibility / Aquaculture / Aquaculture industry / Bacterial infections / Biofilms / Biological diversity / Biological Microscopy / Biomedical and Life Sciences / Causes of / Czech Republic / Disease / Disease susceptibility / Distribution / DNA sequencing / Drug resistance in microorganisms / Drug Resistance, Bacterial - genetics / Enrofloxacin / Epidemiology / Erythromycin / Farmed rainbow-trout / Fish / Fish Diseases - microbiology / Fish farms / Fish production / Fish-culture / Flavobacteriaceae Infections - microbiology / Flavobacteriaceae Infections - veterinary / Flavobacterium - classification / Flavobacterium - drug effects / Flavobacterium - genetics / Flavobacterium - isolation & purification / Flavobacterium psychrophilum / Florfenicol / Flumequine / Gene sequencing / Genetic analysis / Genetic aspects / Genetic diversity / Genetic Variation / Genome, Bacterial - genetics / Genomes / Genomics / Glycerol / Gram-negative bacteria / Health aspects / Identification and classification / International economic relations / International trade / Life Sciences / Mariculture / Microbial Sensitivity Tests / Microbiological research / Microbiology / Motility / Multilocus Sequence Typing / Multiplexing / Mycology / Nucleotide sequencing / Oncorhynchus mykiss / Oncorhynchus mykiss - microbiology / Oxolinic acid / Oxytetracycline / Parasitology / Pathogens / Phenotype / Phenotypic variations / Phylogeny / Resistance factors / Risk factors / Salmon / Seafood industry / Serotypes / Serotyping / Sulfamethoxazole / Trimethoprim / Trout / Trout - microbiology / Veterinarians / Virology / Virulence factors / Virulence Factors - genetics / Whole genome sequencing / Yeast