Multiplex-PCR for simultaneous detection of 3 bacterial fish pathogens, Flavobacterium columnare, Edwardsiella ictaluri, and Aeromonas hydrophila

A multiplex PCR (m-PCR) method was developed for simultaneous detection of 3 important fish pathogens in warm water aquaculture. The m-PCR to amplify target DNA fragments from Flavobacterium columnare (504 bp), Edwardsiella ictaluri (407 bp) and Aeromonas hydrophila (209 bp) was optimized by adjustment of reaction buffers and a touchdown protocol. The lower detection limit for each of the 3 bacteria was 20 pg of nucleic acid template from each bacteria per m-PCR reaction mixture. The sensitivity threshold for detection of the 3 bacteria in tissues ranged between 3.4 x 10(2) and 2.5 x 10(5) cells g(-1) of tissue (channel catfish Ictalurus punctatus Rafinesque). The diagnostic sensitivity and specificity of the m-PCR was evaluated with 10 representative isolates of each of the 3 bacteria and 11 other Gram-negative and 2 Gram-positive bacteria that are taxonomically related or ubiquitous in the aquatic environment. Except for a single species (A. salmonicida subsp. salmonicida), each set of primers specifically amplified the target DNA of the cognate species of bacteria. m-PCR was compared with bacteriological culture for identification of bacteria in experimentally infected fish. The m-PCR appears promising for the rapid, sensitive and simultaneous detection of Flavobacterium columnare, E. ictaluri and A. hydrophila in infected fish compared to the time-consuming traditional bacteriological culture techniques.     

Proteome analysis of Edwardsiella ictaluri

Edwardsiella ictaluri is a facultative intracellular Gram‐negative bacterium causing enteric septicemia of catfish (ESC), the most prevalent disease affecting farm‐raised channel catfish in the United States. Despite its economic importance, studies addressing high‐throughput proteomics were not possible because of lack of comprehensive protein database. Here, we report the first high‐throughput proteomics analysis of E. ictaluri using 2‐D LC ESI MS/MS and 2‐DE MALDI TOF/TOF MS. Proteins identified in this study and predicted from the whole E. ictaluri genome were clustered into functional groups using clusters of orthologous groups (COG), and their subcellular locations were predicted. Possible functional relationships among proteins were determined using pathway analysis. The total number of unique E. ictaluri proteins identified using both 2‐D LC and 2‐DE approaches was 788, of which 15.48% (122) were identified by both methods while 78.43% (618) and 6.09% (48) were unique in 2‐D LC and 2‐DE, respectively. COG groupings and subcellular localizations were quite similar between our data set and proteins predicted from the whole genome. Twelve pathways were significantly represented in our dataset (p <0.05). Results from this study provided experimental evidence for many proteins that were predicted from the E. ictaluri genome annotation, and they should accelerate future functional and comparative studies aimed at understanding virulence mechanisms of this important pathogen.     

Transmission and detection of Flavobacterium columnare in channel catfish Ictalurus punctatus

A specific and rapid PCR detection method for Flavobacterium columnare based on the 16S-23S rDNA intergenic spacer region (ISR) of the ribosomal RNA operon has been developed. The ISR of 30 F. columnare strains and other Flavobacterium species was amplified using universal primers and sequenced. Once F. columnare specific sequences within the ISR were recognized, specific PCR primers were designed against them (FCISRFL and FCISRR1). The primers were sensitive and able to detect as low as 7 colony forming units from pure culture by PCR. The new PCR detection method was applied to experimentally infected channel catfish. Two different experiments in which channel catfish fingerlings were infected by intramuscular injection or by immersion bath showed the advantage of the PCR method over standard culture techniques. F. columnare was detected by PCR in both tank water and catfish tissue samples with a higher frequency and in less time than standard microbiological methods. Furthermore, PCR detection confirmed that F. columnare can be transmitted horizontally indirectly through the water column without fish-to-fish contact. The newly developed PCR detection method for F. columnare was more sensitive and rapid than standard culture on bacteriological media for detection of F. columnare in channel catfish tissues and in tank water.     

Freezing induces biased results in the molecular detection of Flavobacterium columnare

Specific PCR detection and electron microscopy of Flavobacterium columnare revealed the risk of false-negative results in molecular detection of this fish pathogen. Freezing and thawing destroyed the cells so that DNA was for the most part undetectable by PCR. The detection of bacteria was also weakened after prolonged enrichment cultivation of samples from infected fish.     

Antimicrobial susceptibility of Edwardsiella ictaluri

Edwardsiella ictaluri isolates collected over the past 7 yr from outbreaks of disease in fish occurring in different geographic areas were screened against 37 antimicrobial agents. Edwardsiella ictaluri were found to be susceptible to most agents active against gram negative bacteria such as aminoglycosides, cephalosporins, the "newer" penicillins, quinolones, tetracyclines, chloramphenicol, nitrofurantoin, and potentiated sulfonamides. Resistance was observed against colistin, sulfonamides, and several agents regarded as effective for gram positive bacteria. There was no evidence of unusual antimicrobial resistance associated with E. ictaluri or of developing resistance.     

Biochemical characteristics of Edwardsiella ictaluri

A total of 119 isolates of Edwardsiella ictaluri collected over the last 7 years from several states were biochemically characterized. Although not very reactive biochemically, this bacterium shows a high degree of homogeneity. Differences were found only in the production of gas from formate or from glucose at 37 degrees C and in the production of hydrogen sulfide as detected by lead acetate paper. Analysis of E. ictaluri by year of geographic area indicated that some differences existed, but no clear-cut biotypic variations were found. All isolates studied were capable of degrading chondroitin sulfate, a major component of cartilage, which may be an important virulence factor in the formation of the hole-in-the-head lesion characteristic of infected fish.     

The fish pathogen Flavobacterium columnare represents four distinct species: Flavobacterium columnare,Flavobacterium covae sp. nov., Flavobacterium davisii sp. nov. and Flavobacterium oreochromis sp. nov., and emended description of Flavobacterium columnare

Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish and four discrete genetic groups exist within the species, suggesting that the species designation requires revision. The present study determined the taxonomic status of the four genetic groups of F. columnare using polyphasic and phylogenomic approaches and included five representative isolates from each genetic group (including type strain ATCC 23463^T; genetic group 1). 16S rRNA gene sequence analysis revealed genetic group 2 isolate AL-02-36^T, genetic group 3 isolate 90-106^T, and genetic group 4 isolate Costa Rica 04-02-TN^T shared less than <98.8 % sequence identity to F. columnare ATCC 23463^T. Phylogenetic analyses of 16S rRNA and gyrB genes using different methodologies demonstrated the four genetic groups formed well-supported and distinct clades within the genus Flavobacterium. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (GGDC) values between F. columnare ATCC 23463^T, genetic group 2 isolate AL-02-36^T, genetic group 3 isolate 90-106^T, and genetic group 4 isolate Costa Rica 04-02-TN^T were less than 90.84% and 42.7%, respectively. Biochemical and physiological characteristics were similar among the four genetic groups; however, quantitative differences in fatty acid profiles were detected and MALDI-TOF analyses demonstrated numerous distinguishing peaks unique to each genetic group. Chemotaxonomic, MALDI-TOF characterization and ANI/GGDC calculations afforded differentiation between the genetic groups, indicating each group is a discrete species. Herein, the names F. covae sp. nov. (AL-02-36^T), F. davisii sp. nov. (90-106^T), and F. oreochromis sp. nov. (Costa Rica 04-02-TN^T) are proposed to represent genetic groups 2, 3, and 4, respectively.     

Biochemical characteristics of Edwardsiella ictaluri.

A total of 119 isolates of Edwardsiella ictaluri collected over the last 7 years from several states were biochemically characterized. Although not very reactive biochemically, this bacterium shows a high degree of homogeneity. Differences were found only in the production of gas from formate or from glucose at 37 degrees C and in the production of hydrogen sulfide as detected by lead acetate paper. Analysis of E. ictaluri by year of geographic area indicated that some differences existed, but no clear-cut biotypic variations were found. All isolates studied were capable of degrading chondroitin sulfate, a major component of cartilage, which may be an important virulence factor in the formation of the hole-in-the-head lesion characteristic of infected fish.     

Development of bioluminescent Edwardsiella ictaluri for noninvasive disease monitoring

Edwardsiella ictaluri is a facultative intracellular bacterium that causes enteric septicemia of catfish (ESC). In this study, we aimed to develop bioluminescent E. ictaluri that can be monitored by noninvasive bioluminescence imaging (BLI). To accomplish this, the luxCDABE operon of Photorhabdus luminescens was cloned downstream of the lacZ promoter in the broad host range plasmid pBBR1MCS4. Edwardsiella ictaluri strain 93-146 transformed with the new plasmid, pAKlux1, was highly bioluminescent. pAKlux1 was stably maintained in E. ictaluri without any apparent effect on growth or native plasmid stability. To assess the usefulness of the bioluminescent strain in disease studies, catfish were infected with 93-146 pAKlux1 by intraperitoneal injection and by bath immersion, and in vivo bacterial dissemination was observed using BLI. This study demonstrated that bioluminescent E. ictaluri can be used for real-time monitoring of ESC in live fish, which should enable observation of pathogen attachment sites and tissue predilections.     

A medium for the selective isolation of Edwardsiella ictaluri

A selective medium, called Edwardsiella ictaluri medium (EIM), has been formulated for the isolation of Edwardsiella ictaluri. The medium inhibits the growth of most gram-negative bacteria, except Proteus sp., Serratia marcescens and some isolates of Aeromonas hydrophila and Yersinia ruckeri. The bacteria that grow on the EIM are easily differentiated from E. ictaluri based on colony morphology. The EIM inhibits gram-positive bacteria with the exception of enterococci. The addition of fungizone to EIM suppressed the growth of most fungi. The EIM allows the evaluation of environmental reservoirs, levels of contamination and carrier states of E. ictaluri.     

Sequencing and analysis of the Edwardsiella ictaluri plasmids

To determine possible functions of the Edwardsiella ictaluri plasmids, pEI1 and pEI2, we analyzed the sequence of both plasmids. Plasmid pEI1 is 4807 bp, with 51% G + C, and 23 possible open reading frames of 40 amino acids or greater. Plasmid pEI2 is 5643 bp, with 51% G + C, and 24 possible reading frames. Database searches indicated that pEI1 contains an insertion element and a ROM analog. In addition, pEI1 possesses an open reading frame with strong homology to SlrP, SspH1, and SspH2 of Salmonella typhimurium and IpaH of Shigella flexnari, which have leucine-rich repeat regions and are components of type III secretory systems. pEI2 has a frame with weak homology to Spa15 of S. flexnari 5 and InvB of S. sonnei and S. typhimurium, which are also type III secretory system components, three origins of replication, a Rep analog, and a multimer resolution site.     

Plasmid and serological differences between Edwardsiella ictaluri strains.

Several studies have shown that isolates of Edwardsiella ictaluri obtained from infected channel catfish in the southeastern United States harbor two cryptic plasmids, designated pCL1 (5.7 kb) and pCL2 (4.9 kb). These isolates appear to be serologically homogeneous. To extend these studies, we focused our analyses on two isolates of nonictalurid origin. Plasmid analyses of a danio isolate showed that it harbored plasmids which were similar if not identical to pCL1 and pCL2. This strain was also serologically indistinguishable from those isolated from channel catfish. In contrast, a green knife fish (GNF) isolate harbored four plasmids with relative mobilities of 6.0, 5.7, 4.1, and 3.1 kb. Southern blot analyses indicated that only the 5.7- and 4.1-kb plasmids strongly hybridized under high-stringency conditions to probes specific for pCL1 and pCL2, respectively. The GNF isolate showed minimal reactivity when reacted with polyclonal antiserum prepared against a channel catfish isolate. However, polyclonal antiserum to the GNF isolate strongly reacted with the GNF isolate in both surface fluorescence and agglutination reactions. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analyses of cell lysates showed that the protein banding patterns of the strains compared were similar. However, Western blots of proteinase K-digested cell extracts showed that O antigen of the GNF isolate was antigenically distinct from the O antigen of the other isolates. These studies indicate that there are different serotypes of E. ictaluri and suggest that plasmid and serological analyses of future isolates of E. ictaluri can be used to determine whether structurally distinct strains are emerging in major channel catfish aquaculture areas.     

三种提取柱状黄杆菌基因组DNA方法的比较

采用酚氯仿抽提法、CTAB法和SDS-蛋白酶K法分别对鱼类病原菌柱状黄杆菌提取基因组DNA。使用超微量紫外分光光度计和琼脂糖凝胶电泳检测所提取的基因组DNA的产量和质量,并用PCR扩增对DNA进行了评价。结果显示,3种方法均可提取到柱状黄杆菌的基因组DNA,并能有效扩增细菌16S rDNA序列,但CTAB法提取的DNA产量和质量最高,CTAB法可以作为柱状黄杆菌DNA提取以开展分子生物学研究的首选方法。     

Activities of Wogonin Analogs and Other Flavones against Flavobacterium columnare

In our on‐going pursuit to discover natural products and natural product‐based compounds to control the bacterial species Flavobacterium columnare, which causes columnaris disease in channel catfish (Ictalurus punctatus), we synthesized flavone and chalcone analogs, and evaluated these compounds, along with flavonoids from natural sources, for their antibacterial activities against two isolates of F. columnare (ALM‐00‐173 and BioMed) using a rapid bioassay. The flavonoids chrysin ( 1a ), 5,7‐dihydroxy‐4′‐methoxyflavone ( 11 ), isorhamnetin ( 26 ), luteolin ( 27 ), and biochanin A ( 29 ), and chalcone derivative 8b showed strong antibacterial activities against F. columnare ALM‐00‐173 based on minimum inhibition concentration (MIC) results. Flavonoids 1a, 8, 11, 13 (5,4′‐dihydroxy‐7‐methoxyflavone), 26 , and 29 exhibited strong antibacterial activities against F. columnare BioMed based upon MIC results. The 24‐h 50% inhibition concentration (IC₅₀) results revealed that 27 and 29 were the most active compounds against F. columnare ALM‐00‐173 (IC₅₀ of 7.5 and 8.5 mg/l, resp.), while 26 and 29 were the most toxic compound against F. columnare BioMed (IC₅₀ of 9.2 and 3.5 mg/l, resp.). These IC₅₀ results were lower than those obtained for wogonin against F. columnare ALM‐00‐173 and F. columnare BioMed (28.4 and 5.4 mg/l, resp.). However, based on MIC results, none of the compounds evaluated in this study were as active as wogonin (MIC 0.3 mg/l for each F. columnare isolate). Further modification of the wogonin structure to enhance antibacterial is of interest.     

Phage specificity of the freshwater fish pathogen Flavobacterium columnare

Flavobacteria and their phages were isolated from Finnish freshwaters and fish farms. Emphasis was placed on finding phages infecting the fish pathogen Flavobacterium columnare for use as phage therapy agents. The host ranges of the flavobacterial phages varied, phages infecting F. columnare being more host specific than the other phages.     

Genetic fingerprinting of Flavobacterium columnare isolates from cultured fish

AIMS: To evaluate the intraspecific diversity of the fish pathogen Flavobacterium columnare. METHODS AND RESULTS: Genetic variability among Fl. columnare isolates was characterized using restriction fragment length polymorphism analysis of the 16S rDNA gene, intergenic spacer region (ISR) sequencing, and amplified fragment length polymorphism (AFLP) fingerprinting. Thirty Fl. columnare cultures isolated from different fish species and geographical origins as well as reference strains were included in the study. Fifteen isolates belonged to genomovar I while eleven were ascribed to genomovar II. Analysis of the ISR sequence confirmed the genetic differences between both genomovars but revealed a higher diversity among genomovar I isolates. The maximum resolution was provided by AFLP fingerprinting, as up to 22 AFLP profiles could be defined within the species. CONCLUSIONS: We confirmed the division of Fl. columnare isolates from cultured fish into different genogroups. We showed that both genomovars I and II are present in channel catfish from the US. We described a unique genetic group represented by four Fl. columnare isolates from tilapia in Brazil which appears to be related to both genomovars. We were able to further subdivide the species by analysing the ISR. Finally, the use of AFLP allowed us to fingerprint the species at clone level without losing the higher genetic hierarchy of genomovar division. SIGNIFICANCE AND IMPACT OF THE STUDY: This paper reports on an extensive assessment of the use of molecular tools for the study of the epidemiology of the fish pathogen Fl. columnare.     

Development of a Defined Minimal Medium for the Growth of Edwardsiella ictaluri

In this report, a complete defined medium and a minimally defined medium are described for Edwardsiella ictaluri. The complete defined medium consists of 46 individual components, including a basal salt solution, glucose, magnesium sulfate, iron sulfate, six trace metals, four nucleotides, 10 vitamins, and 19 amino acids. This medium supports growth in broth and on solid media. Optimal growth at 30(deg)C was obtained at pH 7.0, and at an osmolality of 390 mosmol/kg of H(inf2)O, with a glucose concentration of 4 g/liter. The defined minimal medium reduces the 46 components of the complete medium to eight essential components, including the basal salt solution, glucose, magnesium sulfate, pantothenic acid, and niacinamide. In addition, specific amino acids that depend on the specific requirements of the individual strains of E. ictaluri are added.     

Genome sequence of the fish pathogen Flavobacterium columnare ATCC 49512

Flavobacterium columnare is a Gram-negative, rod-shaped, motile, and highly prevalent fish pathogen causing columnaris disease in freshwater fish worldwide. Here, we present the complete genome sequence of F. columnare strain ATCC 49512.