Phylogeny of the Viral Hemorrhagic Septicemia Virus in European Aquaculture

<p>One of the most valuable aquaculture fish in Europe is the rainbow trout, Oncorhynchus mykiss, but the profitability of trout production is threatened by a highly lethal infectious disease, viral hemorrhagic septicemia (VHS), caused by the VHS virus (VHSV). For the past few decades, the subgenogroup Ia of VHSV has been the main cause of VHS outbreaks in European freshwater-farmed rainbow trout. Little is currently known, however, about the phylogenetic radiation of this Ia lineage into subordinate Ia clades and their subsequent geographical spread routes. We investigated this topic using the largest Ia-isolate dataset ever compiled, comprising 651 complete G gene sequences: 209 GenBank Ia isolates and 442 Ia isolates from this study. The sequences come from 11 European countries and cover the period 1971-2015. Based on this dataset, we documented the extensive spread of the Ia population and the strong mixing of Ia isolates, assumed to be the result of the Europe-wide trout trade. For example, the Ia lineage underwent a radiation into nine Ia clades, most of which are difficult to allocate to a specific geographic distribution. Furthermore, we found indications for two rapid, large-scale population growth events, and identified three polytomies among the Ia clades, both of which possibly indicate a rapid radiation. However, only about 4% of Ia haplotypes (out of 398) occur in more than one European country. This apparently conflicting finding regarding the Europe-wide spread and mixing of Ia isolates can be explained by the high mutation rate of VHSV. Accordingly, the mean period of occurrence of a single Ia haplotype was less than a full year, and we found a substitution rate of up to 7.813 × 10^-4 nucleotides per site per year. Finally, we documented significant differences between Germany and Denmark regarding their VHS epidemiology, apparently due to those countries' individual handling of VHS.</p

Bacterial diseases of tilapia, their zoonotic potential and risk of antimicrobial resistance

Tilapia culture is an important source of income and nutrition to many rural families. Since 2000, the production of tilapia increased and reached domestic and global markets. Major farmed species is Nile tilapia (Oreochromis niloticus), in earthen ponds and cage cultures. Intensification contributed to global tilapia disease outbreaks, with bacterial infections causing mortalities and morbidities, threatening sustainable production. At tilapia farms, high nutrient concentrations, water temperature and fish densities enhance bacterial growth including virulent bacterial clones and potential zoonotic bacteria. Global warming favours this. This review respectively provides a comprehensive overview of the most common and emerging bacterial pathogens, diseases, clinical presentations and diagnostics of tilapia, including bacteria and diseases with zoonotic potential. First, common bacterial disease outbreaks, including streptococcosis, motile Aeromonas septicaemia, francisellosis, columnaris disease and vibriosis are described. Then, information on emerging bacterial infections of concern for tilapia, like edwardsiellosis through Edwardsiella ictaluri and E. tarda, as well as Aeromonas schubertii is provided. Reports of infectious bacterial tilapia disease outbreaks from other bacteria, including Lactococcus garvieae, Aerococcus viridans, Pseudomonas spp., Mycobacterium marinum and Chlamydia spp., and others are reviewed. Furthermore, bacteria with zoonotic potential, like Streptococcus agalactiae ST283, S. iniae, Aeromonas sp., E. tarda, Vibrio vulnificus pathovar (pv) piscis and M. marinum are included in the review, to provide the most current overview of the disease risks affecting production and post-harvest stages. Additionally, the status and risks of antimicrobial resistance in bacteria from tilapia and other cultured fish through imprudent use of antibiotics, and its future at a global level are provided

Median-joining network based on the complete <i>G</i> gene sequence from 294 IHNV isolates (transition/transversion bias = 4).

<p>The country is indicated using a color code. The black triangles with the number 1 and 2 represent polytomy nodes (node 1 and 2). In accordance with a largely phylotemporal structure in the network, the black triangle with the number 1 (node 1) is surrounded by the oldest French isolate (X89213 from 1987, marked by an asterisk), Italian isolate (FJ711518 from 1987, marked by an asterisk), and the second eldest German isolate (LN897500 from 1993, marked by an asterisk). The <i>E</i> haplotypes are divided into two clades (the <i>E1</i> and <i>E2</i> clade). Isolate <i>M</i> is the outgroup in the network.</p

Consensus Maximum Likelihood tree and Median-joining network (transition/transversion bias = 4) of the <i>E</i> genogroup.

<p>The upper and the lower phylogeny show the phylogenetic relationship between <i>E</i> haplotypes of IHNV, based on the complete <i>G</i> gene sequence and were generated using 294 <i>E</i> isolates. The upper phylogeny is illustrated as a Consensus Maximum Likelihood tree (conflicting branching patterns are resolved by selecting the pattern seen in more than 50% of the trees). Numbers to the right of the branches represent the bootstrap support values obtained from 250 replicates. The lower phylogeny is illustrated as a Median-joining network. The subordinated lineages of clade <i>E</i>–<i>1</i> (<i>E–1–a</i> to <i>E–1–a–k</i>) and <i>E</i>–<i>2</i> (<i>E–2–a</i> to <i>E–1–c</i>) are indicated using a color code. Black triangles marked “1”or “2” represent nodes (node 1 and node 2) that correspond in the Median-joining network with a polytomy. Isolate <i>M</i> is the outgroup in each diagram.</p

Molecular Characterization of <i>Serratia marcescens</i> Strain Isolated from Yellow Mealworms, <i>Tenebrio molitor</i>, in The Netherlands

Insect culture has developed rapidly worldwide; it faces important security and safety control issues, including animal infections and disease development. In the Netherlands, in 2021, a ~30% mortality of mealworms, Tenebrio molitor, occurred at one farm, where over-humid sites in the substrate were observed. Bacterial cultures from both the external and internal partsof fry and larger mealworms were identified by MALDI-TOF to predominantly Serratia marcescens, Staphylococcus xylosus and Staphylococus saprofyticus. Due to the important role of S. marcescens as a potential zoonotic bacterium, we performed a molecular characterization of the isolated strain. Genomic analysis showed a multidrug-resistant S. marcescens isolate carrying a tet (41), aac (6′)-Ic, and blaSST-1 chromosomal class C beta-lactamase-resistantgenes, all located on the chromosome. Additionally, several virulence genes were identified. The phylogenetic tree revealed that the S. marcescens strain from this study was similar to other S. marcescens strains from different ecological niches. Although the entomopathogenic activity was not confirmed, this case demonstrates that T. molitor can act as a reservoir and as an alternative path for exposing clinically important antibiotic-resistant bacteria that can affect animals and humans. It underlines the need to keep management factors optimal, before insects and their products enter the feed and food chain

Complete genome sequence of a common midwife toad virus-like ranavirus associated with mass mortalities in wild amphibians in the Netherlands

A ranavirus associated with mass mortalities in wild water frogs (Pelophylax spp.) and other amphibians in the Netherlands since 2010 was isolated, and its complete genome sequence was determined. The virus has a genome of 107,772 bp and shows 96.5% sequence identity with the common midwife toad virus from Spain

Complete Genome Sequence of Frog virus 3, Isolated from a Strawberry Poison Frog (Oophaga pumilio) Imported from Nicaragua into the Netherlands

Frog virus 3 was isolated from a strawberry poison frog (Oophaga pumilio) imported from Nicaragua via Germany to the Netherlands, and its complete genome sequence was determined. Frog virus 3 isolate Op/2015/Netherlands/UU3150324001 is 107,183 bp long and has a nucleotide similarity of 98.26% to the reference Frog virus 3 isolate

Ranavirus genotypes in the Netherlands and their potential association with virulence in water frogs (Pelophylax spp.)

Ranaviruses are pathogenic viruses for poikilothermic vertebrates worldwide. The identification of a common midwife toad virus (CMTV) associated with massive die-offs in water frogs (Pelophylax spp.) in the Netherlands has increased awareness for emerging viruses in amphibians in the country. Complete genome sequencing of 13 ranavirus isolates collected from ten different sites in the period 2011-2016 revealed three CMTV groups present in distinct geographical areas in the Netherlands. Phylogenetic analysis showed that emerging viruses from the northern part of the Netherlands belonged to CMTV-NL group I. Group II and III viruses were derived from the animals located in the center-east and south of the country, and shared a more recent common ancestor to CMTV-amphibian associated ranaviruses reported in China, Italy, Denmark, and Switzerland. Field monitoring revealed differences in water frog host abundance at sites where distinct ranavirus groups occur; with ranavirus-associated deaths, host counts decreasing progressively, and few juveniles found in the north where CMTV-NL group I occurs but not in the south with CMTV-NL group III. Investigation of tandem repeats of coding genes gave no conclusive information about phylo-geographical clustering, while genetic analysis of the genomes revealed truncations in 17 genes across CMTV-NL groups II and III compared to group I. Further studies are needed to elucidate the contribution of these genes as well as environmental variables to explain the observed differences in host abundance

Complete genome sequence of a common midwife toad virus-like ranavirus associated with mass mortalities in wild amphibians in the Netherlands

A ranavirus associated with mass mortalities in wild water frogs (Pelophylax spp.) and other amphibians in the Netherlands since 2010 was isolated, and its complete genome sequence was determined. The virus has a genome of 107,772 bp and shows 96.5% sequence identity with the common midwife toad virus from Spain

Mismatch distributions and Bayesian skyline plot of 5<i>i</i> sequences.

<p>The mismatch distribution is based on the complete <i>G</i> gene sequence and is calculated separately for the following: 152 <i>5i</i> sequences from Denmark, Germany, and the United Kingdom, collected between 2000 and 2011; and 137 Danish <i>5i</i> sequences from 2000 to 2009. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0164475#pone.0164475.t001" target="_blank">Table 1</a> lists the respective values of the raggedness index (r), nucleotide diversity (PI), Tajima’s D, and Fu’s Fs of each dataset. The Bayesian skyline plot shows changes of the 5<i>i</i> population size between 2000 and 2009. The plot was generated using 137 Danish 5<i>i</i> sequences (complete <i>G</i> gene sequence). X axis: time in years, Y axis: population size. The middle solid line is the median estimate, and the area between the blue lines shows the 95% highest probability density (HPD).</p