Studenterprojekter på SSI

Echinococcus multilocularis (EM) is a tapeworm of the family Taeniidae. The parasite is endemic in red foxes in Denmark and the causal agent of alveolar echinococcosis in animal and human intermediate hosts.

As part of the project “Zoonotic parasites in foxes from Dennark” faecal samples from red foxes are screened by molecular methods to detect DNA of Echinococcus multilocularis. The DNA-extraction used is based on a magnetic-capture technique specific for EM. The method is, in combination with real-time PCR, quite sensitive, however, it is time consuming and expensive. Therefore, we would like to compare this method with our automated DNA-extraction platform at place at Statens Serum Institut (SSI), which is easier, faster and cheaper. Furthermore, the automated platform is not specific for EM, and therefore allows for the DNA to be used for a broader range of analyses including screening for other pathogens of interest.

The project will involve DNA-extraction of faecal samples and an introduction to molecular methods. Depending on the available time and the interest of the student(s) further analyses can be included.

The project will take place at SSI and can be carried out in English, Danish or other Scandinavian languages.

Contact: Rebecca Berg (rebe@ssi.dk) 

The nematode genus Trichinella can cause the disease trichinellosis in humans and animals. Adult worms live and reproduce in the intestines of the host. The released larvae then migrate to the muscles of the host, where they encyst inside the muscle cells. Larvae are transmitted to a new host through ingestion of infective larvae encysted in muscle tissue.

Trichinellosis is notifiable in suids and equids in Denmark, but has not been reported since 1930, though millions of swine are analysed each year.

The reference method for the detection of Trichinella-larvae is artificial digestion by the magnetic stirrer method, the aim of which is to release larvae from the muscle sample and then detect them by microscopy. However, the quality/handling of the muscle samples may affect the sensitivity and the quality of the digestion. For example, multiple freeze-thaw cycles are known to reduce the digestibility.

The aim of the project is to test modifications to the reference method to enhance the final product of the digestion and, hereby, the sensitivity of the method when using non-optimal sample material.

The project will involve training in the magnetic stirrer method and microscopy. Digestions will be performed on muscle samples spiked with a known number of larvae.

The project will take place at SSI and can be carried out in English, Danish or other Scandinavian languages.

Contact: Rebecca Berg (rebe@ssi.dk) 

The Arctic is getting warmer at an increasing rate, and the derived environmental changes are affecting the ecosystems markedly. In addition to changes in the vegetation, the expected change in precipitation in combination with increased melt-off from the ice caps will likely alter the hydrologic systems in areas of Greenland. Furthermore, temperatures may exceed the thermal tolerance of some arctic species. All these changes may lead to a potential change in pathogen transmission pathways and pathogen diversity.

Barren ground caribou (Rangifer tarandus groenlandicus) is one of the only ungulates native to Greenland. Populations are found on most of the west coast of Greenland and is in some areas mixed with reindeer (R. t. tarandus) introduced to Greenland from Norway. Caribou is commonly hunted for subsistence.

Due to the ecosystem changes and the importance of caribou as a food source, knowledge of their pathogen exposure is important in regard to population health as well as food safety. Therefore, the aim of the project is to provide further knowledge on the prevalence of selected zoonotic parasites within Greenland caribou.

Samples used in this study are collected by the Greenland Institute of Natural Resources and will be a collaboration between them, University of Copenhagen and Statens Serum Institut (SSI).

The project will take place at SSI and can be carried out in English, Danish or other Scandinavian languages.

Contact: Rebecca Berg (rebe@ssi.dk) 

Helminth infections are a major production- and animal welfare issue in grazing small ruminants. Especially the helminth Haemonchus contortus, which has previously had a high occurrence in Danish goat herds, can cause severe disease with anemia, weightloss and even death. For some years now, anthelminthic resistance has also been observed in the species.

Haemonchus contortus is a nematode in the strongyle family, and even though fecal flotation can be of diagnostic aid, accurate species differentiation based on egg morphology is not possible. Different diagnostic tools have been suggested for species differentiation, and molecular methods has proven to have a high sensitivity, but there is currently no commercially available diagnostics in Denmark.

Accurate diagnosis is of paramount importance with regards to helminth control and treatment of infection. SSI suggests a student project involving the test of different diagnostic tools with the possibility of surveying the occurrence of Haemonchus contortus in small ruminants in Denmark. The project is suited for students in veterinary medicine, animal health, biology etc.

The project will take place at SSI and can be carried out in English, Danish or other Scandinavian languages.

Contact: Rebecca Berg (rebe@ssi.dk)

Influenza A virus er et virus der inficerer en lang række værter, heriblandt mennesker, svin og fugle. Indimellem kan influenza A virus springe fra dyr til mennesker og omvendt og kan derfor optræde som et zoonotisk virus. Influenza A virus har historisk set givet anledning til nogle af de største og mest udbredte pandemier i verden. For at forstå hvornår og hvordan et influenza A virus kan springe mellem dyr og mennesker eller give anledning til en ny pandemi, er det vigtigt at have gode metoder til at undersøge virussets genomer. I dette projekt vil formålet være at videreudvikle en simpel og hurtig metode til at fuldgenomsekventere alle influenza A virus, der kan optræde hos dyr og mennesker. Projektet vil give kendskab til metoderne PCR og hurtig sekventering ved brug af moderne teknologi, samt viden om influenza A virus og dets genetiske karakteristika.

Projektet foregår på SSI.

Kontakt: Ramona Trebbien (ratr@ssi.dk)

I de seneste år har der været udbrud med højpatogen fugleinfluenza i Europa og mange andre steder i verden. Den genetiske diversitet har været tiltagende fra sæson til sæson. Virus subtypes og genotypes på basis af virus genomsekvenser og fylogenetisk analyse. I sæsonen 2021/2022 var der udbrud i Europa med mindst 5 forskellige subtyper og 33 forskellige genotyper af højpatogen H5 fugleinfluenza. Projektet vil tage udgangspunkt i de danske virusfund og tilsigte udvikling af en metode til inddeling i genotyper samt mutations analyse med fokus på værtsspecificitet og zoonotisk (smitte fra dyr til mennesker) potentiale. Projektet vil give kendskab til metoderne PCR, moderne sekvensteknologi og influenzavirus bioinformatik, samt viden om influenza A virus og dets genetiske karakteristika.

Projektet foregår på SSI og KU.

Kontakt: Charlotte Hjulsager (ckhj@ssi.dk) og Yuan Liang (yuan.liang@sund.ku.dk)

Fugleinfluenzavirus med subtyperne H5 og H7 kan optræde i lavpatogen eller højpatogen form. Når der opstår mistanke om fugleinfluenza i en fjerkræbesætning udtager Fødevarestyrelsen prøver til diagnostisk undersøgelse på SSI. Såfremt der påvises influenza A virus i prøverne med subtyperne H5 og H7, afgøres patogeniciteten ved sekventering af den del af HA-genet der koder for HA proteinets kløvningssite. Patogeniciteten er en afgørende del af diagnostikken og afgørende for, hvorledes myndighederne skal følge op på en bekræftet mistanke om fugleinfluenza. Projektet går ud på at afprøve Nanopore sekventering til erstatning eller supplement til den nuværende analyse der foretages med Sanger sekventering. Projektet vil give kendskab til metoderne PCR, moderne sekvensteknologi og influenzavirus bioinformatik, samt viden om influenza A virus og dets genetiske karakteristika.

Projektet foregår på SSI.

Kontakt: Charlotte Hjulsager (ckhj@ssi.dk) og Lars E. Larsen (lael@sund.ku.dk)

African swine fever has become a major threat to the pig production industry across Europe and Asia. The disease is spread, in part, by transmission between wild boar and from wild boar to domestic pigs. During summer months, there is an increase in the number of outbreaks in domestic pigs and this may be linked to an increase in insect activity. It has been shown that blood-feeding insects can contain sufficient virus to enable mechanical transmission of the virus to domestic pigs. Thus, if blood-feeding insects take blood from ASFV-infected wild boar and then enter premises with domestic pigs then transfer of the virus may occur. It is important to be able to determine if blood-fed insects, captured within a pig stable, contain blood from wild boar or only from domestic pigs. In principle, it is possible to discriminate between blood from these two sub-species on the basis of sequence differences within the mitochondrial cytochrome b gene. The project will aim to establish an assay suitable for the discrimination of blood samples from domestic pigs and wild boar using PCR and DNA sequencing. It can then be tested on samples of blood fed insects.

This project will be performed in collaboration between KU and SSI.

Contact: Graham J. Belsham (grbe@sund.ku.dk) and Ann Sofie Olesen (asjo@ssi.dk)

There are 17 different species of bats present within Denmark. Different species have their own types of virus. There is evidence for a variety of different bat alphacoronaviruses (closely related to the porcine epidemic diarrhea virus) within these distinct bat populations. Using fecal samples from bats, it is possible to detect these different viruses, and the source of the samples, including the specific bat species, can be identified based on sequencing of PCR amplified fragments corresponding to the mitochondrial cytochrome b gene and also the mitochondrial 16S ribosomal RNA gene. A collection of bat samples obtained from passive surveillance is available and the specific bat species represented by these samples should be established using these assays.

This project will be performed in collaboration between KU and SSI.

Contact: Graham J. Belsham (grbe@sund.ku.dk) and Thomas Bruun Rasmussen (tbru@ssi.dk)

African swine fever (ASF) is a serious viral disease of domestic pigs and wild boar in Africa, which from one introduction to Georgia in 2007 has become widespread in Europe, Russia and Asia.

The virus causing ASF, African swine fever virus (ASFV), is quite resistant to inactivation, in particular within a protein-rich environment. Studies investigating the effect of a commonly used inactivating reagent in the laboratory, MPLB buffer, for the virus in various protein-rich materials are scarce or lacking. Substantial knowledge of the effect of MPLB buffer on ASFV is important to ensure proper inactivation of the virus within laboratory settings. The project will aim at testing the effect of MPLB buffer on ASFV in different sample materials (e.g. organs and blood). The project will include virus isolation in cell culture and qPCR for detection of viral DNA in sample materials.

This project will be performed in collaboration between KU and SSI.

Contact: Graham J. Belsham (grbe@sund.ku.dk) and Ann Sofie Olesen (asjo@ssi.dk)

Antibiotikaresistens findes i bakterier fra mennesker, dyr og miljøet og giver store udfordringer ved behandling. I Danmark bliver en stor andel af antibiotika brugt til behandling af dyr, herunder især svin. Danmark har siden 1995 haft fokus på overvågning af antibiotikaresistens i patogene bakterier fra mennesker og i zoonotiske og indikator-bakterier indsamlet i produktionsdyr, og siden 2015 er der også blevet indsamlet data om antibiotikaresistens i udvalgte patogene bakterier fra svin. I 2021 blev overvågningen i svin udvidet med andre patogene bakterier og suppleret med helgenom-sekventering.

I dette projekt vil den studerende skulle udføre fænotypisk resistensbestemmelse, identificere resistensgener og -mutationer i de sekventerede genomer, sammenligne fænotypiske og genotypiske fund og udføre bioinformatiske og fylogenetiske analyser af de enkelte bakteriearter med henblik på at undersøge, hvorvidt og hvordan antibiotikaresistens spreder sig i den danske svineproduktion og mellem svin og mennesker. Projektet udføres under Dansk Veterinær Konsortium, som består af eksperter fra Statens Serum Institut og Københavns Universitet, og sker i tæt samarbejde med Veterinært Laboratorium under Landbrug & Fødevarer, som står for dyrkning og isolering af bakterier i kliniske prøver fra svin.

Kontakt: Lina Cavaco (cav@ssi.dk) og Jesper Larsen (jrl@ssi.dk) på SSI samt Peter Damborg (pedam@sund.ku.dk) på Københavns Universitet 

The purpose of this project is to set up a running Endopeptidase-MALDI-TOF MS-procedure for detection of clinical and veterinary relevant botulinum toxins, based on the procedure described by Perry et al. (2017). Botulinum neurotoxins (BoNTs) are toxins of considerable human health concern. There are currently described seven different types of BoNTs, named A to G. Human botulism is caused mainly by BoNT/A /B /E and occasionally /F, with BoNT/A being the most toxic followed by BoNT/B. Currently, the mouse bioassay is the reference detection method for monitoring the activity of BoNT in relation to human health cases; however, the assay is both laborious, expensive, and there are ethical issues due to the use of live animals. Setting up a MALDI-TOF based BoNT detection assay will both reduce the test time, laboratory costs and the use of live animals. By using the well characterized cosmetic BoNT A and B toxins as control toxins in evaluating the MALDI-TOF method, and the described research procedure for MALDI-TOF BoNT detection, it will be possible to establish a standard clinical laboratory protocol which can be used at SSI for detection of BoNT A and B toxin cases. It will further be possible to extend the protocols to include other BoNT toxins relevant for both humans and animals.

The project takes place at SSI.

Contact: Hans-Christian Slotsved (hcs@ssi.dk)  

Påvisning af antistoffer mod MKS virus benyttes bl.a. i bekæmpelsen af MKS udbrud, til fritestning og overvågning efter MKS udbrud, til fritestning før eksport og import, og til epidemiologisk opklaring i lande, hvor MKS forekommer endemisk (Afrika, Mellemøsten, Asien). MKS virus inddeles i syv serotyper (O, A, C, Asia 1, SAT 1, SAT 2, SAT 3), som kan differentieres serologisk ved ELISA og neutralisations tests. Projektet har til formål at karakterisere udviklingen af serotype-specifikke antistoffer i prøver fra eksperimentelt inficerede og re-inficerede dyr (kvæg og får), herunder kryds-reaktivitet mellem vores syv serotype-specifikke antistof ELISAer. Projektet vil inkludere laboratoriearbejde med ELISA og neutralisations tests, og forventes at føre til publikation sammen med allerede testede prøver.

Projektet er et samarbejde mellem KU og SSI.

Kontakt: Graham J. Belsham (grbe@sund.ku.dk) og Kirsten Tjørnehøj (kitj@ssi.dk)  

Som noget nyt blev der ved dekommissionering af de ældre høj-indesluttede bygninger på Lindholm Ø benyttet inaktivering ved opvarmning til 70 °C i 8 døgn. Bygningerne var en del af Danmarks veterinære beredskab for alvorlige virus-sygdomme i dyr, og havde i perioden 1926-2019 været benyttet til forskning i og diagnostik af bl.a. mund- og klovesyge virus (MKSV), afrikansk og klassisk svinepest virus (ASFV/CSFV), swine vesicular disease virus (SVDV) og rabiesvirus (RABV). Brugen af varmeinaktivering til dekommissionering var baseret på indledende studier af varmeinaktivering af MKSV, ASFV, CSFV og SVDV udført på Lindholm i 2019 (Kristensen et al., 2021). Resultaterne fra dette arbejde ønskes udvidet med undersøgelse af inaktivering af virus i forskellige medier og materialer, som ifølge litteraturen må forventes at beskytte virus mod nedbrydning.

Projektet vil inkludere fremstilling af virus præparationer til eksperimenterne, udførsel af eksperimenter og virus dyrkning, og resultaterne forventes publiceret.

Projektet er et samarbejde mellem KU og SSI.

Kontakt: Graham J. Belsham (grbe@sund.ku.dk) og Kirsten Tjørnehøj (kitj@ssi.dk)