A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

BMC Microbiology

Research Article

Tarmo Ketola¹  Roghaieh Ashrafi¹  Lotta-Riina Sundberg¹  Nina Pekkala²  Katja Pulkkinen² 

[1] Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyvaskyla, P.O. Box 35, FI-40014, Jyväskylän yliopisto, Finland;Department of Biological and Environmental Science, University of Jyvaskyla, P.O. Box 35, FI-40014, Jyväskylän yliopisto, Finland;

关键词: Flavobacterium columnare;    MLST/MLSA scheme;    ClonalFrame;    Recombination rate;    Clonality;   

DOI  :  10.1186/s12866-015-0576-4

 received in 2015-05-06, accepted in 2015-10-16,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundColumnaris disease caused by Flavobacterium columnare is a serious problem in aquaculture, annually causing large economic losses around the world. Despite considerable research, the molecular epidemiology of F. columnare remains poorly understood.MethodsWe investigated the population structure and spatiotemporal changes in the genetic diversity of F. columnare population in Finland by using a multilocus sequence typing (MLST) and analysis (MLSA) based on DNA sequence variation within six housekeeping genes. A total of 83 strains of F. columnare were collected from eight different areas located across the country between 2003 and 2012.ResultsPartial sequencing of six housekeeping genes (trpB, tuf, atpA, rpoD, gyrB and dnaK) revealed eight sequence types and a moderate level of genetic diversity (H = 0.460). Phylogenetic analysis of the concatenated protein-encoding gene sequence data (ca. 3,509 nucleotides) formed two lineages, which could be further divided into five clusters. All analysed F. columnare strains appeared to have a genetic origin distinct from that of another important fish pathogen form the genus Flavobacterium, F. psychrophilum. Although the value of the index of association between alleles, 0.292 (P < 0.001), supports some degree of clonality for this species in Finland, recombination has introduced molecular diversity to the population almost three times more than mutation.ConclusionThe results suggest that Finnish F. columnare strains have an epidemic population structure followed by clonal expansion of successful genotypes. Our study with reproducible methodology and comparable results establishes a robust framework for the discrimination and phylogenetic analysis of F. columnare isolates, which will help to improve our understanding about geographic distribution and epidemiology of columnaris disease.

【 授权许可】

CC BY   
© Ashrafi et al. 2015