VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center.

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.

PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions.

Since 2005, the Pathogen-Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to the identification and presentation of phenotype information on pathogenicity and effector genes and their host interactions. Specific gene alterations that did not alter the in host interaction phenotype are also presented. PHI-base is invaluable for comparative analyses and for the discovery of candidate targets in medically and agronomically important species for intervention. Version 4.12 (September 2021) contains 4387 references, and provides information on 8411 genes from 279 pathogens, tested on 228 hosts in 18, 190 interactions. This provides a 24% increase in gene content since Version 4.8 (September 2019). Bacterial and fungal pathogens represent the majority of the interaction data, with a 54:46 split of entries, whilst protists, protozoa, nematodes and insects represent 3.6% of entries. Host species consist of approximately 54% plants and 46% others of medical, veterinary and/or environmental importance. PHI-base data is disseminated to UniProtKB, FungiDB and Ensembl Genomes. PHI-base will migrate to a new gene-centric version (version 5.0) in early 2022. This major development is briefly described.

The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments.

Spironucleus salmonicida causes systemic infections in salmonid fish. It belongs to the group diplomonads, binucleated heterotrophic flagellates adapted to micro-aerobic environments. Recently we identified energy-producing hydrogenosomes in S. salmonicida. Here we present a genome analysis of the fish parasite with a focus on the comparison to the more studied diplomonad Giardia intestinalis. We annotated 8067 protein coding genes in the ∼12.9 Mbp S. salmonicida genome. Unlike G. intestinalis, promoter-like motifs were found upstream of genes which are correlated with gene expression, suggesting a more elaborate transcriptional regulation. S. salmonicida can utilise more carbohydrates as energy sources, has an extended amino acid and sulfur metabolism, and more enzymes involved in scavenging of reactive oxygen species compared to G. intestinalis. Both genomes have large families of cysteine-rich membrane proteins. A cluster analysis indicated large divergence of these families in the two diplomonads. Nevertheless, one of S. salmonicida cysteine-rich proteins was localised to the plasma membrane similar to G. intestinalis variant-surface proteins. We identified S. salmonicida homologs to cyst wall proteins and showed that one of these is functional when expressed in Giardia. This suggests that the fish parasite is transmitted as a cyst between hosts. The extended metabolic repertoire and more extensive gene regulation compared to G. intestinalis suggest that the fish parasite is more adapted to cope with environmental fluctuations. Our genome analyses indicate that S. salmonicida is a well-adapted pathogen that can colonize different sites in the host.

Risk factors and control of intestinal parasite infections in sled dogs in Poland.

Training and racing constitute serious challenges for working sled dogs. Attainment of the highest levels of stamina and speed are possible only by completely healthy dogs. Infections with nematodes as whipworm Trichuris sp. or hookworms Uncinaria/Ancylostoma can significantly reduce the fitness of working dogs leading to anemia or even to death. In the middle of the racing season, between December 2009 and April 2010, 108 individual fecal samples were collected from 25 sled dog kennels situated in different regions of Poland. Saturated salt flotation was performed for helminth egg detection. The immunofluorescent assay MeriFluor Cryptosporidium/Giardia and nested PCRs on 18S rRNA (Cryptosporidium spp.) and TPI gene (Giardia spp.) were carried out for detection of intestinal protozoa. Overall prevalence of 6 species of intestinal parasites was 68% in sled dogs (73/108). In 51 samples the eggs of a single species of helminth were detected (47%), two nematode species were detected in 13%, three species of nematodes were found in two dogs. The most prevalent helminths were the hookworms Uncinaria/Ancylostoma-identified in 36% of kennels, and in 34% of sled dogs. Toxocara eggs were detected in 36% of kennels, in 17% of dogs. Trichuris sp. eggs were found in 20% of kennels (5/25), in 13% of dogs. Cysts/oocysts of intestinal protozoa were detected in 31% of sled dogs. The most prevalent was Giardia spp. infection-in 54% of kennels [13/24], in 28% of dogs. Cryptosporidium spp. infections were identified in 37.5% of kennels [9/24], in 13% of dogs. Two sequenced Giardia isolates presented 100% homology with G. intestinalis Assemblage C isolate (AY228641.1), specific for dogs. A range of factors was shown to affect the prevalence of intestinal parasites in sled dogs. The highest prevalence of parasites was found among dogs from large kennels (housing >3 dogs), in dogs less than 2 years old, and in kennels, where prophylactic treatment was carried out 1-4 times a year. The present study has demonstrated a high prevalence of intestinal parasites in working sled dogs in Poland, including the zoonotic human pathogens Toxocara or Cryptosporidium.

Ultrastructure and molecular diagnosis of Spironucleus salmonis (Diplomonadida) from rainbow trout Oncorhynchus mykiss in Germany.

Diplomonad flagellates infect a wide range of fish hosts in aquaculture and in the wild in North America, Asia and Europe. Intestinal diplomonad infection in juvenile farmed trout can be associated with morbidity and mortality, and in Germany, diplomonads in trout are commonly reported, and yet are poorly characterised. We therefore undertook a comprehensive study of diplomonads from German rainbow trout Oncorhynchus mykiss, using scanning and transmission electron microscopy, and sequencing of the small subunit (ssu) rRNA gene. The diplomonad was identified as Spironucleus salmonis, formerly reported from Germany as Hexamita salmonis. Our new surface morphology studies showed that the cell surface was unadorned and a caudal projection was present. Transmission electron microscopy facilitated new observations of functional morphology, including vacuoles discharging from the body surface, and multi-lobed apices of the nuclei. We suggest the lobes form, via hydrostatic pressure on the nucleoplasm, in response to the beat of the anterior-medial flagella. The lobes serve to intertwine the nuclei, providing stability in the region of the cell exposed to internal mechanical stress. The ssu rRNA gene sequence clearly distinguished S. salmonis from S. barkhanus, S. salmonicida, and S. vortens from fish, and can be used for identification purposes. A 1405 bp sequence of the ssu rRNA gene from S. salmonis was obtained and included in a phylogenetic analysis of a selection of closely related diplomonads, showing that S. salmonis was recovered as sister taxon to S. vortens.

Fluid absorption in the small intestine of healthy game birds and those infected with Spironucleus spp.

Absorption of fluid by the small intestine of 4-week-old to 12-week-old farmed pheasants and partridges has been studied using an inverted sac technique. The mean rate of absorption was 54 +/- 4 (mean +/- standard error of the mean) microl/g dry tissue/min in pheasants and 49 +/- 3 microl/g dry tissue/min in partridges. Use of inhibitors and ion substitution suggested transepithelial transport driven by baso-lateral Na+/K+ pumps, in combination with mucosal Na+-coupled transporters, including Cl(-)-coupled transporters. Absorption was more than halved to 17 +/- 2 microl/g dry tissue/min (P < 0.001) in birds that were very heavily infected with Spironucleus spp. in their small intestine and showing a syndrome of diarrhoea, depression and loss of weight to severe emaciation. Birds carrying light to moderate levels of infection with Spironucleus had very variable rates of absorption that were statistically similar to the controls. Doubling the glucose concentration in the buffer to 40 mM significantly enhanced absorption.

Intracellular infection with Spironucleus barkhanus (Diplomonadida: Hexamitidae) in farmed Arctic char Salvelinus alpinus.

A case of intracellular systemic infection with the diplomonad flagellate Spironucleus barkhanus in farmed Arctic char Salvelinus alpinus is described. The parasites were widely disseminated throughout the vasculature and in most organs. Aggregates of the parasites were seen within well-defined structures regarded as host cells in capillaries and sinusoids of the liver, spleen and head kidney. Intracellular infection with Spironucleus spp. has never previously been reported. The prevalence of infection and mortality in the affected farm was low. In contrast to systemic spironucleosis in farmed Atlantic salmon, and despite huge numbers of flagellates in the vasculature, the tissues of the organs were remarkably unaffected. The relatively few gross and histopathological lesions may indicate that Arctic char are more tolerant to this parasite than Atlantic salmon.

Spironucleus vortens, a possible cause of hole-in-the-head disease in cichlids.

Hole-in-the-head disease is recorded in 11 discus Symphysodon discus Heckel, 1840 and 1 angelfish Pterophyllum scalare Lichtenstein, 1823 obtained from local aquarists within the Southwest of the UK. Spironucleus vortens Poynton et al. 1995, was isolated from the kidney, liver, spleen and head lesions of discus showing severe signs of the disease and from the intestines of all fish. The hexamitid was also recorded from the head lesions of the angelfish. The identity of these flagellates was confirmed as S. vortens on the basis of topographical features seen with the aid of SEM. A modified in vitro culture method was successfully developed for the detection, isolation and long-term maintenance of S. vortens. The flagellate was sub-cultured at 3 to 5 d intervals, new media being supplemented with fresh liver from Oreochromis niloticus (Linnaeus, 1757) free from infection. The results are discussed in relation to S. vortens as the causative agent for hole-in-the-head disease following systemic infection via the digestive tract.