A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0576-4) contains supplementary material, which is available to authorized users.

Coinfection outcome in an opportunistic pathogen depends on the inter-strain interactions

“…Flavobacterium columnare is a genetically homogeneous species [45], and according to the MLSA analysis, the genotypes C and E used in this study are closely related [46]. However, the genomic content outside the housekeeping genes often differs substantially between bacterial strains, suggesting genetic variability in these strains isolated originally from different fish farms in different years.…”

Intensive aquaculture selects for increased virulence and interference competition in bacteria

“…The MLSA method produces genetic clustering comparable with the ARISA method [25], and the two methods can be used interchangeably. The outlet water strains and one inlet water strain (B355) were genotyped in this study using ARISA, as described earlier [30,32] (see the electronic supplementary material for more details).…”

“…The strains collected in 2003 -2010 and the inlet water strains were genetically characterized in an earlier study using multilocus sequence analysis (MLSA) [25] and automated ribosomal intergenic spacer analysis (ARISA) [30]. The MLSA method produces genetic clustering comparable with the ARISA method [25], and the two methods can be used interchangeably.…”

New Zealand rickettsia‐like organism (NZ‐RLO) and Tenacibaculum maritimum: Distribution and phylogeny in farmed Chinook salmon (Oncorhynchus tshawytscha)

“…Housekeeping genes are selected due to their slow rate of evolution and variation; hence, mutations are more likely to be real. MLST has commonly been used to answer questions of relatedness and bacterial typing in many species including Flavobacterium columnare (Ashrafi, Pulkkinen, Sundberg, Pekkala, & Ketola, ), Neisseria meningitides (Maiden et al., ) and Tenacibaculum species (Habib et al., ).…”