Slovenci vodilni v prepoznavanju bioterorističnih agensov s sekvenciranjem naslednje generacije

lukam — Fri, 04 Jan 2019 11:15:45 +0000

Slovenians Lead in Identifying Bioterrorist Agents Through Next-Generation Sequencing lukam Mon, 04/06/2020 - 20:46 Institute of Microbiology and Parasitology Diagnostics

With a view to reviewing the current state of countries’ preparedness for the detection of bioterrorist agents using the NGS method – specifically, using for whole-genome sequencing (WGS) method - the United States organisation ‘Secretary-General's Mechanism for Investigation of Alleged Use of Chemical , Biological or Toxin Weapons' (UNSGM)’, in collaboration with the 'Danish Technical University' (DTU), organised an inter-laboratory control in 2018. It invited numerous reference laboratories around the world to participate.

Bioterrorism is a threat to national and international security. Classic methods for determining and identifying such agents (e.g. culture assays, PCR) may be rapid and reliable, however, they are targeted and, as a rule, do not allow the identification of specific genetic changes responsible for the level of isolate virulence. With the advent of next-generation sequencing (NGS), it is possible to gain insight into the entire genetic material of the studied microorganisms or samples, allowing the species (strain) to be identified and genetic changes (e.g. a dedicated virulence record) to be determined.

The NGS method, however, presents a unique challenge due to the demanding bioinformatics processing of the large amount of sequenced data obtained.

Since the Institute of Microbiology and Parasitology of the Faculty of Veterinary Medicine has a contract with the Ministry of Defence of the Republic of Slovenia for providing professional advice and taking measures in the event of a biological weapons attack, the Laboratory for Molecular Bacteriology also participated in the aforementioned inter-laboratory control.

The aim of the inter-laboratory control was to identify microbial species, thus determining potential deliberate genetic changes (entering or deleting records for virulence factors) and assessing the laboratory's ability to assess biological risk. In a fictionalised (but realistic) scenario for inter-laboratory control, a suspected worker in a microbiology lab left 36 unmarked samples - potential bioterrorist agents. Their genomic sequences were available. What kind is it? Is this species a bioterrorist agent? Was the isolate in the sample genetically modified (GMO) by the suspect and thus affect its virulence?

The participating laboratories had to answer the above questions within one month of receiving the genomic sequences, based completely on their own ideas, and, in doing so, to use any bioinformatic tools and their own professional judgment for this purpose. The test involved public health, veterinary and general microbiology laboratories and laboratories specialising in biological defence. The participating institutions were located globally. Some countries collaborated with several laboratories. A total of 60 laboratories participated. The Institute of Microbiology and Parasitology at the Faculty of Veterinary Medicine, the University of Ljubljana (Bojan Papić, Darja Kušar, Jana Avberšek) performed best among the participating laboratories, with a success rate of 94.3%. Laboratories from China, Norway, Germany, Sweden, Portugal, the United Kingdom, Switzerland, USA, France, Singapore, Belgium, Italy and Australia also performed well with success rates of 82.3% to 91.4%. Most of the participating institutions (44/60) had less than an 80% success rate. The results show that Slovenia is very well prepared for the potential identification of bioterrorist agents using NGS. The overall poor performance of the participating institutions is also worrying and indicates the need to train staff in the field of bioterrorism and NGS bio-information processing.

Obvestilo o pojavu virusa Zahodnega Nila in Usutu virusa pri pticah

lukam — Fri, 04 Jan 2019 10:49:37 +0000

Notice About Outbreak of West Nile Disease and Usutu Virus in Birds lukam Mon, 04/06/2020 - 20:44 Institute of Microbiology and Parasitology Current

The Laboratory for Infectious Diseases of Poultry and Birds of the National Veterinary Institute has confirmed West Nile Virus (WNV) infection in hooded crows (Corvus cornix) and the Usutu virus in common blackbirds (Turdus merula). All the birds that tested positive were found in Ljubljana.

West Nile virus and Usutu virus are flaviviruses belonging to the serological group of Japanese encephalitis. Wild birds are natural hosts and the main carriers of the virus are mosquitoes, mainly from the Culex spp. genus, which are also found in Slovenia.

Some species of birds (e.g. crows, geese, birds of prey) are highly susceptible to the disease caused by WNV and die from a serious systemic disease. Signs of the disease can manifest in the form of nervous disorders (cramps, coordination problems) and death. Among mammals, horses are particularly sensitive and, after being infected with the WNV virus, they can fall ill showing signs of encephalitis or encephalomyelitis. The disease can be present with or without a fever, and it progresses progressively leading to paralysis, coma and death. In Europe, however, an increasing number of cases have been reported in humans.

Usutu virus infections can be particularly dangerous for some species of birds, such as blackbirds and some owls; the infection can cause them to die. It was first discovered in South Africa in 1959 in mosquitoes. Outbreaks of this disease in birds in Europe were reported as early as 2001 and 2002 in Austria, 2005 in Hungary, 2006 in Italy, Switzerland and Spain; 2011 in Germany and the Czech Republic, 2012 in Belgium, 2015 in France, 2016 in the Netherlands, Belgium, France and Germany, 2017 in Austria and 2018 in Germany.

According to available data, no clinical cases of this disease have yet been reported in other animal species, although the virus was isolated from the brains of two dead bats in Germany. However, there are known to be individual cases of infection in humans.

Useful links:

Priporočilo za ravnanje v primeru najdbe poginjene prostoživeče ptice

http://www.uvhvvr.gov.si/si/delovna_podrocja/zdravje_zivali/bolezni/

http://www.nijz.si/sl/spremljanje-virusa-zahodnega-nila

Inštitut za perutnino, ptice, male sesalce in plazilce, Veterinarska fakulteta Ljubljana

Inštitut za mikrobiologijo in parazitologijo

Slovenci vodilni v prepoznavanju bioterorističnih agensov s sekvenciranjem naslednje generacije

Obvestilo o pojavu virusa Zahodnega Nila in Usutu virusa pri pticah