Although C. difficile is still predominantly considered as a nosocomial pathogen there has been an increase in a number of community associated infections. Since C. difficile is ubiquitous and can be isolated from nearly any environment, one of the possibilities for community acquisition could be exposure in domestic environment. The aim of this study was to evaluate the presence of C. difficile spores on shoes, slippers and on dog paws and to explore the importance of these surfaces as vectors for dissemination of C. difficile in domestic environment. Overall, C. difficile was present in 14 (70%) of 20 households and in 31 of 90 (34.4%) collected samples. Shoes and slippers had the highest positivity rates, 19/44 (43.2%) and 6/21 (28.6%), respectively, followed by dog paws 6/25 (24.0%). Thirteen C. difficile PCR-ribotypes were identified with half of the isolates belonging to ribotype 014/020, which is the predominant type circulating in human population and is also commonly found in the environment (e.g. soil and water) in Slovenia. In three households identical PCR ribotype was found on dog paws, shoes and slippers. To understand the fine-scale genetic relatedness of these isolates we sequenced the genomes. Low level of single nucleotide variant (SNV) differences between isolates from the same households, consistent with a recent transmission from a common source, was obtained for isolates of PCR ribotype 014/020 but not for PCR ribotype 010. Our results suggest that shoe soles and dog paws could serve for dissemination of C. difficile spores between households and environment and could contribute to community relevant sources for C. difficile infection in humans.
The aim of this study was to investigate potential LA-MRSA transmission between animal and humans in rural settings. 14 farms in Slovenia were selected o the basis of a framer (initial patient) with confirmed LA-MRSA infectiona and regular animal contacts. The epidemiological link with hospital-related LA-MRSA isolates were included to investigate possible nosocomial transmission. On five farms, LA-MRSA was discovered both in animals and humans. A total, 49 LA-MRSA isolates of different origins underwent whole-genome sequencing, antimicrobial susceptibility testing and spa typing. No transmission pairs between animals and initial patients were discovered. However, several isolates originating from farm animals and other hosehold members formed clusters with pairwise distance of ( 14 single nucleotide polymorphisms (SNPs), indicating recent transmission events.????
Two strains of classical swine fever virus (CSFV) (SRB/CSFV/1264/2005 and SRB/CSFV/6168/2006), producing serious clinical signs of disease and high mortality during outbreaks in 2005 and 2006 in Serbia, were isolated on porcine kidney cells and their complete genomes were determined by next generation sequencing. The first complete genome characterization of Serbian CSFV strains provides new data of the evolution of CSFV from Balkan region and enables the further detailed phylogenetic studies among the various strains.
The complete genome of Lake Sinai virus 3 (LSV3) was sequenced by the Ion Torrent Next Generation Sequencing technology (NGS) from an archive sample of honeybees collected in 2010. This strain M92/2010 is the first complete genome sequence of LSV lineage 3. From October 2016 to December 2017, 56 honeybee samples from 32 different locations and 41 bumblebee samples from 5 different locations were collected. These samples were tested using a specific reverse transcriptase polymerase chain reaction (RT-PCR) method; 75.92% of honeybee samples and 17.07% of bumblebee samples were detected as being LSV positive with the RT-PCR method. Phylogenetic comparison of 557 base pair long RNA dependent RNA polymerase (RdRp) genome region of selected 23 positive samples of honeybees and 3 positive bumblebee samples identified three different LSV lineages: LSV1, LSV2 and LSV3. The LSV3 lineage was confirmed for the first time in Slovenia in 2010, and the same strain was later detected in several locations within the country.
Bovine viral diarrhea virus (BVDV) subtypes 1f and 1d were first time isolated in Slovenia in 1999 and detected later in a majority of BVDV infected cattle herds. Here, we report the first nearly complete genome sequences of noncythopathogenic BVDV-1f strain SLO/1170/2000 and cythopathogenic BVDV-1d strain SLO/2416/2002 isolated in Slovenia. The nearly genomes of BVDV SLO/1170/2000 and SLO/2416/2002 strains comprise of 12,259 and 12,241 nt with a G+C content of 46.8% and 45.1%, respectively. The single ORF consist in both isolates of 3,898 aa and showed 87.7% aa similarity to each other. Compared to the available complete sequences of BVDV in GenBank with NCBI blastn, strain SLO/1170/2000 displayed only 80.13% nucleotide similarity to strain SLO/2407/2006 (KX577637) from Slovenia belonging to the subgenotype BVDV-1e, while SLO/2416/2002 had 90.40% nucleotide similarity with BVDV-1d strain BJ1308 from China.