Analysis of 16S-23S intergenic spacer regions of the rRNA operons in Edwardsiella ictaluri and Edwardsiella tarda isolates from fish

Differentiation Among Rodentibacter Species Based on 16S-23S rRNA Internal Transcribed Spacer Analysis

The internal transcribed spacer (ITS) regions of Rodentibacter pneumotropicus, R. heylii, R. rarus, R. ratti, and R. heidelbergensis and of a Rodentibacter- related β-hemolytic Pasteurellaceae taxon isolated from laboratory rodents were studied for their feasibility to discriminate among these species. The 6 species analyzed showed species-specific ITS patterns that were shared by the type strains and clinical isolates and that allowed their identification. Nevertheless, differentiating between the ITS band patterns of R. pneumotropicus and R. ratti is visually challenging. In all species tested, sequence analysis of the ITS fragments revealed a larger ITS^ile+ala, which contained the genes for tRNA^Ile(GAU) and tRNA ^Ala(UGC), and a smaller ITS^glu with the tRNA^Glu(UUC) gene. The ITS sequences varied among the 6 species evaluated, displaying identity levels ranging from 62% to 86% for ITS^ile+ala and 68% to 90% for ITS^glu. Overall, ITS amplification proved to be a reliable method to differentiate among these important Pasteurellaceae species of laboratory rodents. Moreover, the ITS sequence variations recorded here might facilitate the design of probes for specific identification of these species. The ability to diagnose these organisms to the species level could increase our understanding of their clinical significance.

Comparative proteomic study of Edwardsiella tarda strains with different degrees of virulence

Edwardsiella tarda is an enteric opportunistic pathogen that causes a great loss in aquaculture. This species has been described as a phenotypical homogeneous group; in contrast, serological studies and molecular typing revealed a wide heterogeneity. In this work, a proteomic study of differential expression of a virulent isolate from turbot cultured in the Norwest of Spain in comparison with an avirulent collection strain was performed in order to recognize proteins involved in virulence. One hundred and three proteins that presented different abundance were successfully identified and classified into 11 functional categories according to their biological processes: amino acid, carbohydrate and lipid metabolism, tricarboxylic cycle, stress response and protein fate, protein synthesis, biogenesis of cellular components, cell rescue defence and virulence, cell membrane and transport, signal transduction and purine and pyrimidine metabolism. Twenty three protein spots detected only in turbot isolate were identified. It was shown that the same proteins appeared in different spots in the two isolates. Mass spectra obtained by MALDITOF/TOF of some of these proteins and DNA sequencing explained the changes as a result of different amino acid sequences. Several proteins related with the virulence of E. tarda (FliC, ArnA or FeSODI) were only detected in the turbot European isolate. This article is part of a Special Issue entitled: HUPO 2014.

Genotypic characterization of Escherichia coli O157:H7 isolates from different sources in the North-West Province, South Africa, using enterobacterial repetitive intergenic consensus PCR analysis

In many developing countries, proper hygiene is not strictly implemented when animals are slaughtered and meat products become contaminated. Contaminated meat may contain Escherichia coli (E. coli) O157:H7 that could cause diseases in humans if these food products are consumed undercooked. In the present study, a total of 94 confirmed E. coli O157:H7 isolates were subjected to the enterobacterial repetitive intergenic consensus (ERIC) polymerase chain reaction (PCR) typing to generate genetic fingerprints. The ERIC fragments were resolved by electrophoresis on 2% (w/v) agarose gels. The presence, absence and intensity of band data were obtained, exported to Microsoft Excel (Microsoft Office 2003) and used to generate a data matrix. The unweighted pair group method with arithmetic mean (UPGMA) and complete linkage algorithms were used to analyze the percentage of similarity and matrix data. Relationships between the various profiles and/or lanes were expressed as dendrograms. Data from groups of related lanes were compiled and reported on cluster tables. ERIC fragments ranged from one to 15 per isolate, and their sizes varied from 0.25 to 0.771 kb. A large proportion of the isolates produced an ERIC banding pattern with three duplets ranging in sizes from 0.408 to 0.628 kb. Eight major clusters (I-VIII) were identified. Overall, the remarkable similarities (72% to 91%) between the ERIC profiles for the isolate from animal species and their corresponding food products indicated some form of contamination, which may not exclude those at the level of the abattoirs. These results reveal that ERIC PCR analysis can be reliable in comparing the genetic profiles of E. coli O157:H7 from different sources in the North-West Province of South Africa.

Edwardsiella comparative phylogenomics reveal the new intra/inter-species taxonomic relationships, virulence evolution and niche adaptation mechanisms

Edwardsiella bacteria are leading fish pathogens causing huge losses to aquaculture industries worldwide. E. tarda is a broad-host range pathogen that infects more than 20 species of fish and other animals including humans while E. ictaluri is host-adapted to channel catfish causing enteric septicemia of catfish (ESC). Thus, these two species consist of a useful comparative system for studying the intricacies of pathogen evolution. Here we present for the first time the phylogenomic comparisons of 8 genomes of E. tarda and E. ictaluri isolates. Genome-based phylogenetic analysis revealed that E. tarda could be separate into two kinds of genotypes (genotype I, EdwGI and genotype II, EdwGII) based on the sequence similarity. E. tarda strains of EdwGI were clustered together with the E. ictaluri lineage and showed low sequence conservation to E. tarda strains of EdwGII. Multilocus sequence analysis (MLSA) of 48 distinct Edwardsiella strains also supports the new taxonomic relationship of the lineages. We identified the type III and VI secretion systems (T3SS and T6SS) as well as iron scavenging related genes that fulfilled the criteria of a key evolutionary factor likely facilitating the virulence evolution and adaptation to a broad range of hosts in EdwGI E. tarda. The surface structure-related genes may underlie the adaptive evolution of E. ictaluri in the host specification processes. Virulence and competition assays of the null mutants of the representative genes experimentally confirmed their contributive roles in the evolution/niche adaptive processes. We also reconstructed the hypothetical evolutionary pathway to highlight the virulence evolution and niche adaptation mechanisms of Edwardsiella. This study may facilitate the development of diagnostics, vaccines, and therapeutics for this under-studied pathogen.

Enhanced susceptibility of channel catfish to the bacterium Edwardsiella ictaluri after parasitism by Ichthyophthirius multifiliis

Bacterium Edwardsiella ictaluri and parasite Ichthyophthirius multifiliis (Ich) are two common pathogens of cultured fish. The objective of this study was to evaluate the susceptibility of channel catfish Ictalurus punctatus to E. ictaluri and determine bacterial loads in different fish organs after parasitism by Ich. Fish received the following treatments: (1) infected by I. multifiliis at 5000 theronts/fish and exposed to E. ictaluri; (2) infected by I. multifiliis alone; (3) exposed to E. ictaluri alone; and (4) non-infected control. E. ictaluri in fish organs were quantified by quantitative real-time polymerase chain reaction and reported as genome equivalents per mg of tissue (GEs/mg). The results demonstrated that the Ich-parasitized catfish showed significantly (P<0.05) higher mortality (91.7%) when exposed to E. ictaluri than non-parasitized fish (10%). The bacterial loads in fish infected by 5000 theronts/fish ranged from 6497 to 163,898 GEs/mg which was between 40 and 2000 fold higher than non-parasitized fish (49-141 GEs/mg). Ich infection enhanced the susceptibility of channel catfish to bacterial invasion and increased fish mortality.

Evaluation of an in vitro cell assay to select attenuated bacterial mutants of Aeromonas hydrophila and Edwardsiella tarda to channel catfish

AIMS

To evaluate the feasibility of using an in vitro cell assay to select attenuated bacterial mutants.

METHODS AND RESULTS

Using catfish gill cells G1B, the feasibility of using an in vitro assay instead of in vivo virulence assay using live fish to select attenuated bacterial mutants was evaluated in this study. Pearson correlation analysis between in vitro virulence to G1B cells and in vivo virulence of Aeromonas hydrophila and Edwardsiella tarda revealed that there was a significant correlation between the two (r = -0.768, P value = 3.7 × 10(-16)).

CONCLUSIONS

The in vitro cell assay might be initially used to screen large quantities of bacteria to select attenuated mutants of catfish pathogens.

SIGNIFICANCE AND IMPACT OF THE STUDY

The in vitro cell assay using catfish gill cells to identify attenuated mutants of catfish pathogens will reduce cost involved in the in vivo virulence assay that requires many fish and aquariums.

Intercistronic heterogeneity of the 16S-23S rRNA spacer region among Pseudomonas strains isolated from subterranean seeds of hog peanut (Amphicarpa bracteata)

Intercistronic heterogeneity of the 16S-23S rRNA internal transcribed spacer regions (ITS1) was investigated in 29 strains of fluorescent pseudomonads isolated from subterranean seeds of Amphicarpa bracteata (hog peanut). PCR amplification of the ITS1 region generated one or two products from the strains. Sequence analysis of the amplified fragments revealed an ITS1 fragment of about 517 bp that contained genes for tRNA(Ile) and tRNA(Ala) in all 29 strains; an additional smaller ITS1 of 279 bp without tRNA features was detected in 15 of the strains. The length difference appeared to be due to deletions of several nucleotide blocks between the 70 bp and 359 bp positions of the alignment. The end of the deletions in the variant ITS1 type coincided with the start of antiterminator box A, which is homologous to box A of other bacteria. Phylogenetic analyses using the neighbour-joining algorithm revealed two major phylogenetic clusters, one for each of the ITS1 types. Using a single specific primer set and the DNA-intercalating dye SYBR Green I for real-time PCR and melting-curve analysis produced highly informative curves with one or two recognizable melting peaks that readily distinguished between the two ITS1 types in pure cultures. The assay was used to confirm the presence of the variant ITS1 type in the Pseudomonas community in total DNA from root-zone soil and seed coats of hog peanut. Heterogeneity of the ITS1 region between species has potential for studying molecular systematics and population genetics of the genus Pseudomonas, but the presence of non-identical rRNA operons within a genome may pose problems.

Characterization of the rrn operons in the channel catfish pathogen Edwardsiella ictaluri

AIMS

To advance diagnostics and phylogenetics of Edwardsiella ictaluri by sequencing and characterizing its rrn operons.

METHODS AND RESULTS

The Edw. ictaluri rrn operons were identified from a 5-7 kbp insert lambda library and from Edw. ictaluri fosmid clones. We present the complete sequences and analysis of all eight Edw. ictaluri rrn operons and unique regions located upstream and downstream. Two rrn operons were located in tandem with 169 bp separating them, which is apparently a conserved feature between Edw. ictaluri and Edwardsiella tarda. I-CeuI enzyme digestion of Edw. ictaluri genomic DNA and analysis by pulsed field gel electrophoresis indicated that rrn operon number and chromosomal locations are conserved within the species Edw. ictaluri.

CONCLUSIONS

The rrn operons of Edw. ictaluri have similar structure and flanking regions compared with other members of the family Enterobacteriaceae; however, the presence of eight copies of the rrn operon makes Edw. ictaluri unique within the family.

SIGNIFICANCE AND IMPACT OF THE STUDY

This research clarifies previous phylogenetic analyses of Edw. ictaluri and provides support for the Edw. ictaluri genome sequencing project. In addition, we identified a unique feature of two rrn operons that shows potential for the development of a diagnostic PCR method.

Identification and characterization of an intervening sequence within the 23S ribosomal RNA genes of Edwardsiella ictaluri

Comparison of the 23S rRNA gene sequences of Edwardsiella tarda and Edw. ictaluri confirmed a close phylogenetic relationship between these two fish pathogen species and a distant relation with the 'core' members of the Enterobacteriaceae family. Analysis of the rrl gene for 23S rRNA in Edw. ictaluri revealed the presence of an intervening sequence (IVS) in helix-45. This new 98bp IVS shared 97% nucleotide identity with Salmonella typhimurium helix-45 IVS. Edw. ictaluri helix-45 IVS was present in all Edw. ictaluri strains analyzed and in at least six rrl operons within each cell. Fragmentation of 23S rRNA due to IVS excision by RNase III was observed by methylene blue staining of ribosomal RNA extracted from Edw. ictaluri isolates. This is the first report of an IVS in the 23S rRNA gene of the genus Edwardsiella.

Genotyping of Edwardsiella tarda isolated from freshwater fish culture system

The applicability of PCR-RFLP of 16S rDNA and conventional phenotypic methods for differentiation of Edwardsiella tarda associated in freshwater fish culture system was studied. In this study, by conventional biochemical tests and antibiotic resistant patterns 2 and 14 groups were obtained. But these methods failed to discriminate the isolates habitat wise. However, PCR-RFLP of 16S rDNA was found to be specific to detect habitat-specific isolates. All the fish isolates belonging to particular genotypes were found only in fish, not in water or sediment. Some of the genotypes were exclusively present in water and sediment. This study indicates the prevalence of site-specific genotypes in freshwater ecosystems. Molecular method is found to be superior to discriminate the E. tarda habitat wise to conventional typing methods.