Figure 4 - uploaded by Snorre Gulla
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Electropherogram visualizing stutter and split peaks. In this case, both occur simultaneously, which is not always the case. The longer and taller peak, representing the YR1070 VNTR locus, can be readily distinguished. The display is magnified and shows only blue dye peaks. Please click here to view a larger version of this figure.
Source publication
Yersinia ruckeri is an important pathogen of farmed salmonids worldwide, but simple tools suitable for epizootiological investigations (infection tracing, etc.) of this bacterium have been lacking. A Multi-Locus Variable-number tandem-repeat Analysis (MLVA) assay was therefore developed as an easily accessible and unambiguous tool for high-resoluti...
Context in source publication
Context 1
... peaks and stutter peaks, both well-known artefacts in CE based MLVA typing 17 , may be observed in electropherograms during size calling (Figure 4). While stutter peaks should be disregarded, the longer peak should consistently be selected for downstream applications in the case of split peaks separated by a single base pair. ...
Citations
... It has also been proven that applying appropriate sequences (e.g., 16S-23S, ITS) in capillary gel electrophoresis is useful for bacteria and yeast identification [2,3]. Therefore, capillary gel electrophoresis has already been applied to a number of research studies dedicated to particular microbial investigation and differentiation, including viruses [4,5], bacteria [6][7][8][9][10] and fungi [11]. Other application aspects are especially dedicated to foodborne pathogen detection [8,[12][13][14][15] and their typing [16][17][18][19][20]. ...
Clostridioides difficile is a complex of anaerobic bacteria responsible for the epidemics of post-antibiotic diarrhea as one of the examples of CDI (Clostridioides difficile infection). As many as 70% of cases concern hospitalized patients, particularly those in intensive care units. Ribotyping is one of the most common methods for differentiating bacterial strains. The purpose of this work was to show the effectiveness of the gel electrophoresis-based PCR ribotyping method and the Webribo database for typing C. difficile isolates, including the hypervirulent 027 ribotype. DNA samples extracted from 69 C. difficile strains with previously marked genotypes were included in this study. PCR was performed using 16S–23S primers, and capillary gel electrophoresis was performed on the Applied Biosystem 3130xl Genetic Analyzer. The Webribo database was applied for ribotype assignment. Out of 69 samples, 48 belonged to already known ribotypes, 13 represented new ribotypes and 8 was indicated as similar to the existing ones, having some differences. Capillary gel electrophoresis-based PCR is an effective method for the differentiation of C. difficile ribotypes and can be recognized as a very useful tool in epidemiological studies, while the Webribo database is a useful and an accessible database for a quick analysis of C. difficile ribotypes.
... SDS phenotype was assessed on TSA agar plates with 1% SDS prepared according to Furones, Gilpin & Munn [33], with colonies surrounded by crystalline deposits after 48h incubation at 22˚C interpreted as a positive result. MLVA typing was performed according to Gulla, Mohammad & Colquhoun [76] or data derived from previous work [12,18]. Serotypes were derived from previously published data or typed using in-house polyclonal rabbit antisera for Yersinia ruckeri O1, O2 and O5 with the slide agglutination technique. ...
While both virulent and putatively avirulent Yersinia ruckeri strains exist in aquaculture environments, the relationship between the distribution of virulence-associated factors and de facto pathogenicity in fish remains poorly understood. Pan-genome analysis of 18 complete genomes, representing established virulent and putatively avirulent lineages of Y. ruckeri, revealed the presence of a number of accessory genetic determinants. Further investigation of 68 draft genome assemblies revealed that the distribution of certain putative virulence factors correlated well with virulence and host-specificity. The inverse-autotransporter invasin locus yrIlm was, however, the only gene present in all virulent strains, while absent in lineages regarded as avirulent. Strains known to be associated with significant mortalities in salmonid aquaculture display a combination of serotype O1-LPS and yrIlm, with the well-documented highly virulent lineages, represented by MLVA clonal complexes 1 and 2, displaying duplication of the yrIlm locus. Duplication of the yrIlm locus was further found to have evolved over time in clonal complex 1, where some modern, highly virulent isolates display up to three copies.
... The cells grow fairly rapidly in a wide temperature range from 22 • C to 37 • C, but best between 22 • C and 25 • C. Y. ruckeri can be identified using serological and molecular diagnostic tests [20,[23][24][25][26][27][28][29][30][31][32][33][34][35][36]. Recently, a multi-locus variable-number tandem-repeat analysis has been developed as a fast and efficient method for high-resolution genotyping of Y. ruckeri isolates [37]. Y. ruckeri strains are biochemically uniform regardless of geographical location. ...
Yersinia ruckeri is the causative agent of enteric redmouth disease, a bacterial infection of marine and freshwater fish. The disease mainly affects salmonids, and outbreaks have significant economic impact on fish farms all over the world. Vaccination routines are in place against the major serotypes of Y. ruckeri but are not effective in all cases. Despite the economic importance of enteric redmouth disease, a detailed molecular understanding of the disease is lacking. A considerable number of mostly omics-based studies have been performed in recent years to identify genes related to Y. ruckeri virulence. This review summarizes the knowledge on Y. ruckeri virulence factors. Understanding the molecular pathogenicity of Y. ruckeri will aid in developing more efficient vaccines and antimicrobial compounds directed against enteric redmouth disease.
Yersinia ruckeri is the causative agent for enteric redmouth disease of salmonids. Although the bacterium (NBRC102019) was isolated from the sediment of a river before 2007 in Japan, the disease first occurred in a different region in March 2015 in a chum salmon Oncorhynchus keta hatchery. In the present study, we characterized the isolate from the river sediment and 9 isolates from the disease outbreak. The serotype of NBRC102019 was classified as O-6, whereas the serotypes of the 9 isolates from the outbreak were all O-7. Multilocus sequence typing revealed that the 9 isolates from the outbreak belong to the same genotype and that the genotype of NBRC102019 was distinct from that of the 9 isolates. In challenge tests using chum salmon with one of the isolates from the outbreak and NBRC102019, substantial mortality was observed (the average cumulative mortality of the duplicated test was 43.3%) with the outbreak isolate but not with NBRC102019, although both of these isolates did not cause any deaths in rainbow trout O. mykiss. These results suggest that the Y. ruckeri that caused the outbreak in chum salmon belongs to a distinct lineage from that of the bacterium isolated from the river sediment.
Non‐motile strains of Yersinia ruckeri, known as Y. ruckeri biotype 2, now dominate amongst clinical isolates retrieved from rainbow trout internationally. Due to an acute increase in the number of yersiniosis cases in Norway in recent years, followed by introduction of widespread intraperitoneal vaccination against the disease, an investigation on the prevalence of Y. ruckeri biotype 2 in Norwegian aquaculture was conducted. We biotyped 263 Y. ruckeri isolates recovered from diseased salmonids in Norway between 1985 and 2020. A total of seven biotype 2 isolates were identified, four of which were collected between 1985 and 1987, and three of which belong to the current epizootic clone, isolated from two different sea‐farms in 2017. Whole‐genome sequencing revealed single non‐synonymous nucleotide polymorphisms in the flagellar genes flhC in isolates from the 1980s, and in fliP in isolates from 2017. In both variants, motility was restored both by complementation with wild‐type alleles in trans and via spontaneous mutation‐driven reversion following prolonged incubation on motility agar. While biotype 2 strains do not yet seem to have become broadly established in Norwegian aquaculture, the seven isolates described here serve to document a further two independent cases of Y. ruckeri biotype 2 emergence in salmonid aquaculture.
