Prevalence of Astroviruses in Different Animal Species in Poland

Astroviruses (AstVs) are small RNA viruses characterized by a high mutation rate, the ability to recombine, and interspecies transmission, which allows them to infect a multitude of hosts including humans, companion animals, and farmed animals as well as wildlife. AstVs are stable in the environment, and their transmission is usually through the fecal-oral route or via contaminated water and food. Although direct zoonotic transmission was not confirmed, interspecies transmission events have occurred or have been indicated to occur in the past between wild and domestic animals and humans. They cause large economic losses, mainly in the poultry sector, due to gastroenteritis and mortality. In young children, they are the second most common cause of diarrhea. This study involved 166 intestine samples and pools of spleen, lymph node, and kidney samples collected from 352 wild animals, 52 pigs, and 31 companion animals. Astroviruses were detected in the intestine samples and were separately detected in pools of tissue samples prepared for individual animals using a heminested RT-PCR protocol. Amplicons were subjected to Sanger sequencing, and a phylogenetic analysis of 320 nt RNA-dependent RNA polymerase (RdRp) fragments referring to known nt sequences of astroviruses was performed. Astroviral RNA was detected in the intestine samples and/or tissue pools of red foxes (nine positive intestines and six positive tissue pools), rats (two positive intestines and three positive tissue pools), a cat (one AstV detected in an intestine sample), pigs (eight positive tissue pools), and wild boars (two positive pools of spleens, kidneys, and lymph nodes). No astroviral RNA was detected in wild mustelids, dogs, or other small wild animals including rodents. A phylogenetic analysis revealed that the astroviruses detected during this study were mostly host-specific, such as porcine, canine, and rat astroviruses that were highly homologous to the sequences of reference strains. In one of two wild boars, an AstV distinct to porcine species was found with the highest nt identity to Avastroviruses, i.e., turkey astroviruses, which suggests potential cross-species transmission of the virus, as previously described. Here, we present the first detection of astroviruses in the population of wild animals, companion animals, and pigs in Poland, confirming that astroviruses are frequent pathogens circulating in animals in the field. Our study also suggests potential cross-species transmission of Avaastrovirus to wild boars; however, further molecular characterization is needed.

African Swine Fever: Transmission, Spread, and Control through Biosecurity and Disinfection, Including Polish Trends

African swine fever is a contagious disease, affecting pigs and wild boars, which poses a major threat to the pig industry worldwide and, therefore, to the agricultural economies of many countries. Despite intensive studies, an effective vaccine against the disease has not yet been developed. Since 2007, ASFV has been circulating in Eastern and Central Europe, covering an increasingly large area. As of 2018, the disease is additionally spreading at an unprecedented scale in Southeast Asia, nearly ruining China's pig-producing sector and generating economic losses of approximately USD 111.2 billion in 2019. ASFV's high resistance to environmental conditions, together with the lack of an approved vaccine, plays a key role in the spread of the disease. Therefore, the biosecurity and disinfection of pig farms are the only effective tools through which to prevent ASFV from entering the farms. The selection of a disinfectant, with research-proven efficacy and proper use, taking into account environmental conditions, exposure time, pH range, and temperature, plays a crucial role in the disinfection process. Despite the significant importance of ASF epizootics, little information is available on the effectiveness of different disinfectants against ASFV. In this review, we have compiled the current knowledge on the transmission, spread, and control of ASF using the principles of biosecurity, with particular attention to disinfection, including a perspective based on Polish experience with ASF control.

Phylogenetic analysis of Shewanella spp. isolated from fish

Different species of Shewanella spp. widely inhabit freshwater and marine environments. Some of them are opportunistic fish pathogens. The application of high-throughput sequencing enabled the characterization and taxonomic reclassification of many Shewanella spp. species. Still, some strains collected from fish need to be better recognized. The aim of the present study was to classify and determine the phylogenetic relationships of Shewanella spp. collected from fish. The complete genomes of 94 strains of Shewanella spp. from different fish species were sequenced using Illumina platform (MiSeq). The 16S rRNA gene, genomic features and whole-genome relationships of those bacteria were comprehensively analysed in comparison to reference strains. Whole-genome analysis showed that the tested Shewanella spp. strains were clustered into six groups similar to reference strains of S. xiamenensis, S. oneidensis, S. glacialipiscicola, S. hafniensis, S. baltica and S. oncorhynchi. Our study indicates that the whole-genome sequence analysis enabled taxonomic classification and assessment of the diversity of the Shewanella spp. strains, as opposed to recently the gold standard method of 16S rRNA amplicon sequencing. The high genetic diversity and low similarity to the reference genome of S. oneidensis indicate that the group of strains may be a subspecies or even new species. Furthermore, we showed that the most frequent Shewanella spp. species occurring in freshwater fish in our study is the recently described species S. oncorhynchi.

Whole Genome Sequencing and Comparative Genomic Analysis of Chlamydia gallinacea Field Strains Isolated from Poultry in Poland

Chlamydia gallinacea is an intracellular bacterium belonging to the Chlamydiaceae family. Poultry is considered to be the major reservoir of this agent, which has worldwide distribution and a particularly consistent worldwide occurrence in chicken flocks. The bacterium has been linked to respiratory disease in humans but without definitive confirmation; nevertheless, while it has not been proved to be the cause of human respiratory disease, a recent report from Italy verified its bird-to-human transmission. This aspect being significant for public health, more research is needed to gain insight into the infection biology of C. gallinacea. In this study, the genomes of eleven novel C. gallinacea field strains from different regions of Poland were analyzed comparatively. It was confirmed that C. gallinacea strains are closely related, with at least 99.46% sequence identity. They possess a conservative genome structure involving the plasticity zone with a complete cytotoxin, the type three secretion system, inclusion membrane proteins, polymorphic membrane proteins, hctA and hctB histone-like proteins, and the chlamydial protease-like activating factor exoenzyme, as well as plasmids. Genetic diversity seems to be restricted. However, some genetic loci, such as ompA and multi-locus sequence typing target genes, are diverse enough to enable high-resolution genotyping and epidemiological tracing.

Perfluoroalkyl substances in Baltic fish - the risk to consumers

Perfluoroalkyl substances (PFASs) were investigated in five Baltic fish species (sprat, herring, salmon, trout, and cod). Each species' median lower bound (LB) concentration of ∑14 PFASs was as follows: in sprat it was 3.54 µg/kg wet weight (w.w.), in cod 2.15 µg/kg w.w., in salmon 2.10 µg/kg w.w., in trout 2.03 µg/kg w.w. and in herring 1.74 µg/kg w.w.. Regarding the species' median LB of ∑4 PFASs (perfluorooctane sulfonic acid (PFOS), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), and perfluorohexane sulfonic acid (PFHxS)), sprat was the most contaminated with 2.90 µg/kg w.w. and herring was the least with 1.17 µg/kg w.w.. Among all PFASs, PFOS was found in the highest concentrations (range 0.04-9.16 µg/kg w.w.) and the percentage share in the total concentration of ∑14 PFASs was between 56 and 73%. The average proportion of linear PFOS (L-PFOS) in the total PFOS (branched and linear) was the highest in salmon at 89% and trout at 87%, and in the other three species it ranged from 75 to 80%. Different consumption scenarios were assumed and the intake of PFASs was calculated for children and adults. Dietary intake via fish consumption was 3.20-25.13 ng/kg of body weight (b.w.) for children and 1.68-8.30 ng/kg b.w. for adults. Baltic fish caught along Polish coastal areas are a significant source of PFASs, especially for children.

Virucidal Activity of Plant Extracts against African Swine Fever Virus

African swine fever is one of the most dangerous and fatal swine diseases, described for the first time roughly a hundred years ago. Even now, there is neither a commercially approved vaccine nor treatment available. The only way to hinder further spread of the disease is by culling the affected herds and applying prevention based mainly on proper biosecurity. Due to growing awareness of the potential ASF threat among pig producers, disinfection processes are considered as one of the most important preventive measures. Currently, a variety of chemical compounds are applied for the disinfection of pig farms. Meanwhile, these chemicals may pose a potential risk, due to their toxic, irritant or corrosive effect. The aim of this study was to determine whether any plant-based natural compounds may show a virucidal effect against ASFV, and simultaneously be depleted of some of the side-effects typical for chemical compounds. Ideally, natural virucidal compounds should be safe for both humans and animals, biodegradable, easily available and inexpensive. Fourteen plant extracts were selected and screened for their virucidal effect against ASFV, using the suspension test inspired by the PN-EN 14675:2015 European Standard procedure. The results of our study showed that most of the tested plant extracts were ineffective against ASFV. Some extracts suspended in a hydroglycolic medium exhibited high virus titre reduction, but it was confirmed that the effect resulted from medium composition. However, a 1.05% peppermint extract showed high effectiveness against ASFV, reducing the virus titre by ≥4 log10, thus demonstrating that natural compounds used as virucidal agents could potentially be used in disinfection procedures, being both effective and harmless to humans and animals.