Fingerprinting of Flavobacterium psychrophilum isolates by ribotyping and plasmid profiling

Chakroun, C.; Grimont, Francine; Urdaci, Maria C.; Bernardet, Jean‐François

doi:10.3354/dao033167

Cited by 53 publications

(56 citation statements)

References 12 publications

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“…They reported a particularly strong association between one genotype and ayu Plecoglossus altivelis from Japan. Chakroun et al (1997Chakroun et al ( , 1998 used ribotyping or randomly amplified polymorphic (RAPD) DNA methods to compare strains of F. psychrophilum isolated from different countries and fish species and reported associations between ribotypes and hosts and between RAPD profiles and hosts (particularly isolates of trout origin). We caution that host-associations may be evident in a given data set, but because these analyses are based on clinical isolates rather than on a random sample from the population of all F. psychrophilum strains, the conclusions are tentative at best (Borucki et al 2003).…”

Section: Discussionmentioning

confidence: 99%

“…Genetic variation has been assessed between strains using ribotyping, plasmid profiles, randomly amplified polymorphic DNA (RAPD), and PCR-RFLP of specific gene fragments (Chakroun et al 1997, Chakroun et al 1998, Madetoja et al 2001, Izumi et al 2003. Studies of outbreak strains from Danish trout farms suggest dominance by a single ribotype , Madetoja et al 2002, but other studies show greater genetic variation across geographic scales (Chakroun et al 1997, Madetoja et al 2000.…”

Section: Introductionmentioning

confidence: 99%

“…Studies of outbreak strains from Danish trout farms suggest dominance by a single ribotype , Madetoja et al 2002, but other studies show greater genetic variation across geographic scales (Chakroun et al 1997, Madetoja et al 2000. Izumi et al (2003) and Chakroun et al (1998) published evidence for host-species associations between different strains of Flavobacterium psychrophilum. In a recent study, Soule et al (2005) used comparative genomic hybridizations with DNA microarrays and demonstrated that 34 geographically diverse strains of F. psychrophilum could be classified into 2 distinct genetic lineages that correlate well with either trout or salmon origin.…”

mentioning

confidence: 99%

“…Not all strains of F. psychrophilum are capable of causing the same degree of disease (Holt 1987, Madetoja et al 2002, LaFrentz et al 2003 and they can be antigenically diverse (Evensen & Lorenzen 1996, Crump et al 2001, Madetoja et al 2002. Immunization with killed cells of one strain does not necessarily convey protective immunity from infection by other strains (Holt et al 1989, Obach & Laurencin 1991.Genetic variation has been assessed between strains using ribotyping, plasmid profiles, randomly amplified polymorphic DNA (RAPD), and PCR-RFLP of specific gene fragments (Chakroun et al 1997, Chakroun et al 1998, Madetoja et al 2001, Izumi et al 2003. Studies of outbreak strains from Danish trout farms suggest dominance by a single ribotype , Madetoja et al 2002, but other studies show greater genetic variation across geographic scales (Chakroun et al 1997, Madetoja et al 2000.…”

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Polymorphisms in 16S rRNA genes of Flavobacterium psychrophilum correlate with elastin hydrolysis and tetracycline resistance

Soule¹,

LaFrentz²,

Cain³

et al. 2005

Dis. Aquat. Org.

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Flavobacterium psychrophilum is the etiological agent of bacterial coldwater disease, which causes significant problems to aquaculture worldwide. A recent study (Soule M, Cain K, LaFrentz S, Call DR [2005] Infect Immun 73:3799-3802) identified two 16S rRNA gene sequence variants (6 base differences) within the variable stem-loop region 3 for F. psychrophilum strains ATCC 49418 and CSF 259-93. That study also hypothesized that F. psychrophilum is composed of at least 2 distinct genetic lineages (I and II) described by a microarray-based comparative genomics study. In the present study, we augmented an existing 16S rDNA microarray to detect both 16S rRNA sequence variants from F. psychrophilum. Subsequent microarray experiments showed that CSF 259-93 hybridized as expected, but ATCC 49418 was positive for both sequence variants. We then developed a PCR-restriction fragment length polymorphism (RFLP) assay (MnlI and MaeIII) to distinguish between the 2 sequences. Gel isolation of PCR-RFLP products, cloning, and sequencing confirmed that ATCC 49418 harbors both 16S rRNA sequences. Microarray experiments showed that 11 of 14 strains from genetic Lineage I harbor both the CSF 259-93 and ATCC 49418 16S rRNA sequence variants, whereas all 15 Lineage II strains were only positive for the CSF 259-93 sequence (p < 0.0001). Elastin hydrolysis and tetracycline resistance were most closely associated with the latter strains (p < 0.0001 and p = 0.024, respectively). These data support the hypothesis that F. psychrophilum is composed of at least 2 distinct genetic lineages that are closely associated with host origin. KEY WORDS: 16S rRNA · Flavobacterium psychrophilum · Bacterial coldwater disease · Elastin hydrolysis · Microarray hybridization · Tetracycline resistance Resale or republication not permitted without written consent of the publisherDis Aquat Org 65: [209][210][211][212][213][214][215][216] 2005 In general, Flavobacterium psychrophilum strains are biochemically homogeneous, with the exception of some variation in the presence or absence of caseinases, gelatinases, and elastases (Bertolini et al. 1994, Lorenzen et al. 1997, Madetoja et al. 2001. Not all strains of F. psychrophilum are capable of causing the same degree of disease (Holt 1987, Madetoja et al. 2002, LaFrentz et al. 2003 and they can be antigenically diverse (Evensen & Lorenzen 1996, Crump et al. 2001, Madetoja et al. 2002. Immunization with killed cells of one strain does not necessarily convey protective immunity from infection by other strains (Holt et al. 1989, Obach & Laurencin 1991.Genetic variation has been assessed between strains using ribotyping, plasmid profiles, randomly amplified polymorphic DNA (RAPD), and PCR-RFLP of specific gene fragments (Chakroun et al. 1997, Chakroun et al. 1998, Madetoja et al. 2001, Izumi et al. 2003. Studies of outbreak strains from Danish trout farms suggest dominance by a single ribotype , Madetoja et al. 2002, but other studies show greater genetic variation across geographic scales (Chakroun et a...

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Polymorphisms in 16S rRNA genes of Flavobacterium psychrophilum correlate with elastin hydrolysis and tetracycline resistance

Soule¹,

LaFrentz²,

Cain³

et al. 2005

Dis. Aquat. Org.

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“…The 50 F. psychrophilum strains used in this study were isolated from all over the world over a period of more than 20 (11,12).…”

Section: Methodsmentioning

confidence: 99%

Population Structure of the Fish-Pathogenic Bacterium Flavobacterium psychrophilum

Nicolas

Mondot

Achaz

et al. 2008

Appl Environ Microbiol

195

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Flavobacterium psychrophilum is currently one of the main bacterial pathogens hampering the productivity of salmonid farming worldwide, and its control mainly relies on antibiotic treatments. To better understand the population structure of this bacterium and its mode of evolution, we have examined the nucleotide polymorphisms at 11 protein-coding loci of the core genome in a set of 50 isolates. These isolates were selected to represent the broadest possible diversity, originating from 10 different host fish species and four continents. The nucleotide diversity between pairs of sequences amounted to fewer than four differences per kilobase on average, corresponding to a particularly low level of diversity, possibly indicative of a small effective-population size. The recombination rate, however, seemed remarkably high, and as a consequence, most of the isolates harbored unique combinations of alleles (33 distinct sequence types were resolved). The analysis also showed the existence of several clonal complexes with worldwide geographic distribution but marked association with particular fish species. Such an association could reflect preferential routes of transmission and/or adaptive niche specialization. The analysis provided no clues that the initial range of the bacterium was originally limited to North America. Instead, the historical record of the expansion of the pathogen may reflect the spread of a few clonal complexes. As a resource for future epidemiological surveys, a multilocus sequence typing website based on seven highly informative loci is available.

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Flavobacterium

Bernardet

Bowman

2015

Bergey's Manual of Systematics of Archaea and Bacteria

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Fla.vo.bac.te'ri.um. L. adj. flavus yellow; L. neut. n. bacterium a rod or staff and, in biology, a bacterium (so called because the first ones observed were rod‐shaped); N.L. neut. n. Flavobacterium a yellow bacterium. Bacteroidetes / Flavobacteriia / Flavobacteriales / Flavobacteriaceae / Flavobacterium Straight or slightly curved, single rods with rounded or slightly tapered ends typically about 0.3–0.5 µm in diameter and variable in length, often 2–5 µm; shorter (1 µm) or filamentous (10–40 µm) cells and pleomorphism also occur. The longer rods are flexible. Do not form endospores. Several species produce spherical degenerative forms (spheroplasts) in stationary growth phase. Nonmotile or motile by gliding. Flagella have not been reported. Colonies are pale to bright yellow due to the production of nondiffusible, nonfluorescent carotenoid or flexirubin types of pigments or both . Gram‐stain‐negative. Chemoorganotrophic. Most species are obligately aerobic, having a strictly respiratory type of metabolism with oxygen as the terminal electron acceptor. A few species may also grow weakly under microaerobic to anaerobic conditions. About half of the species are able to reduce nitrate to nitrite, but only one species is able to carry out complete denitrification . The optimum growth temperature range is 20–30°C for most temperate species and 15–20°C for most cold‐living species. Most species grow readily on nutrient and tryptic soy agars; no growth factors are required. Most species also grow on media containing up to 2–4% NaCl. Usually positive for catalase and oxidase . About half of the species are able to oxidize carbohydrates. Esculin and starch are hydrolyzed by most species, but agar and carboxymethylcellulose are hydrolyzed by only a few species. Strong proteolytic activity occurs. Menaquinone MK‐6 is the only or predominant respiratory quinone. Predominant cellular fatty acids are C 15:0 , C 15:0 iso, C 15:0 iso 3‐OH, C 15:0 anteiso, C 15:1 ω6 c , C 15:1 iso G , C 16:0 iso 3‐OH, and C 17:0 iso 3‐OH, as well as C 15:0 iso 2‐OH and/or C 16:1 ω7 c and/or C 16:1 ω7 t . Sphingophospholipids are absent in all tested species. Homospermidine is the major polyamine in all tested species. Occur in soil and in freshwater, marine, or saline environments in warm, temperate, or polar locations. Three species are pathogenic for freshwater fish and three others have occasionally been isolated from diseased freshwater fish. DNA G + C content ( mol %): 30–41. Type species : Flavobacterium aquatile (Frankland and Frankland 1889) Bergey, Harrison, Breed, Hammer and Huntoon 1923, 100 ( Bacillus aquatilis Frankland and Frankland 1889, 381) (not Flavobacterium antarcticum as erroneously printed in Bernardet and Bowman, 2006).

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Fingerprinting of Flavobacterium psychrophilum isolates by ribotyping and plasmid profiling

Cited by 53 publications

References 12 publications

Polymorphisms in 16S rRNA genes of Flavobacterium psychrophilum correlate with elastin hydrolysis and tetracycline resistance

Polymorphisms in 16S rRNA genes of Flavobacterium psychrophilum correlate with elastin hydrolysis and tetracycline resistance

Population Structure of the Fish-Pathogenic Bacterium Flavobacterium psychrophilum

Flavobacterium

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