Improved Strategy for Molecular Characterization of African Swine Fever Viruses from Sardinia, Based on Analysis of p30, CD2V and I73R/I329L Variable Regions.

African swine fever virus (ASFV) is the aetiological agent of a highly lethal haemorrhagic disease affecting pigs that inflicts significant economic damage on the swine industry. ASF is present in many African countries, in several eastern and central European countries and in Sardinia (Italy). Sequence analyses of variable genomic regions have been extensively used for molecular epidemiological studies of ASFV isolates. Previous sequencing data of genes that codify for viral protein p54, p72 and the central variable region (CVR) within the B602L gene revealed that Sardinian isolates show a very low level of variability. To achieve a finer level of discrimination among such closely related viruses, in this study, we have chosen three different genome regions to investigate the within-genotype relationships and to provide a more accurate assessment of the origin of outbreaks. The analysis of p30 and I73R/I329L sequences obtained from ASFV collected in Sardinia over a 13-years period confirms a remarkable genetic stability in these regions. The sequence comparison of the protein encoded by the EP402R gene (CD2v), carried out on various strains from 1978 to 2014, revealed a temporal subdivision of Sardinian viruses into two subgroups: one group includes the historical isolates from 1978 to 1990, and the second one is comprised of the viruses collected from 1990 until 2014. These data, together with those obtained from CVR within the B602L gene analysis, demonstrated that the viruses circulating in Sardinia belong to p72 genotype I, but have undergone genetic variations in two different regions of the genome since 1990. We proposed the cytoplasmic region of CD2v protein as a new genetic marker that could be use to analyse ASFVs from different locations to track virus spread. Our study reaffirms the need to analyse other genome regions in order to improve the molecular characterization of ASFV.

Draft Genome Sequence of the Host-Restricted Salmonella enterica Serovar Abortusovis Strain SS44.

Salmonella enterica serovar Abortusovis is a pathogen strictly adapted to ovines, in which it causes abortion. To enhance our understanding of this pathogen, we assembled the first draft sequence of an S. Abortusovis genome (strain SS44). The obtained genomic data might facilitate the study of S. enterica evolution and host adaptation.

Compositional generative mapping for tree-structured data--part II: topographic projection model.

We introduce GTM-SD (Generative Topographic Mapping for Structured Data), which is the first compositional generative model for topographic mapping of tree-structured data. GTM-SD exploits a scalable bottom-up hidden-tree Markov model that was introduced in Part I of this paper to achieve a recursive topographic mapping of hierarchical information. The proposed model allows efficient exploitation of contextual information from shared substructures by a recursive upward propagation on the tree structure which distributes substructure information across the topographic map. Compared to its noncompositional generative counterpart, GTM-SD is shown to allow the topographic mapping of the full sample tree, which includes a projection onto the lattice of all the distinct subtrees rooted in each of its nodes. Experimental results show that the continuous projection space generated by the smooth topographic mapping of GTM-SD yields a finer grained discrimination of the sample structures with respect to the state-of-the-art recursive neural network approach.

SipA, SopA, SopB, SopD and SopE2 effector proteins of Salmonella enterica serovar Typhimurium are synthesized at late stages of infection in mice.

Salmonella pathogenicity island (SPI)-1 is essential for invasion of non-phagocytic cells, whereas SPI-2 is required for intracellular survival and proliferation in phagocytes. Some SPI-1 effectors, however, are induced upon invasion of both phagocytic and non-phagocytic cells, suggesting that they may also be required post-invasion. In the present work, the presence was analysed of SipA, SopA, SopB, SopD and SopE2 effector proteins of Salmonella enterica serovar Typhimurium in vitro and in vivo during murine salmonellosis. Tagged (3xFLAG) strains of S. enterica serovar Typhimurium were inoculated intraperitoneally or intragastrically to BALB/c mice and recovered from the spleen and mesenteric lymph nodes of moribund mice. Tagged proteins were detected by SDS-PAGE and immunoblotting with anti-FLAG antibodies. In vitro experiments showed that SPI-1 effector proteins SipA, SopA, SopB, SopD and SopE2 were secreted under SPI-1 conditions. Interestingly, it was found that S. enterica serovar Typhimurium continued to synthesize SipA, SopB, SopD and SopE2 in colonized organs for several days, regardless of the route of inoculation. Together, these results indicate that SPI-1 effector proteins may participate in the late stages of Salmonella infection in mice.

Salmonella enterica serovar-host specificity does not correlate with the magnitude of intestinal invasion in sheep.

The colonization of intestinal and systemic tissues by Salmonella enterica serovars with different host specificities was determined 7 days after inoculation of 1 to 2-month-old lambs. Following oral inoculation, S. enterica serovars Abortusovis, Dublin, and Gallinarum were recovered in comparable numbers from the intestinal mucosa, but serovar Gallinarum was recovered in lower numbers than the other serovars from systemic sites. The pattern of bacterial recovery from systemic sites following intravenous inoculation was similar. The magnitude of intestinal invasion was evaluated in ovine ligated ileal loops in vivo. Serovars Dublin and Gallinarum and the broad-host-range Salmonella serovar Typhimurium were recovered in comparable numbers from ileal mucosa 3 h after loop inoculation, whereas the recovery of serovar Abortusovis was approximately 10-fold lower. Microscopic analysis of intestinal mucosae infected with serovars Typhimurium and Dublin showed dramatic morphological changes and infiltration of inflammatory cells, whereas mucosae infected with serovars Abortusovis and Gallinarum were indistinguishable from uninfected mucosae. Together these data suggest that Salmonella serovar specificity in sheep correlates with bacterial persistence at systemic sites. Intestinal invasion and avoidance of the host's intestinal inflammatory response may contribute to but do not determine the specificity of serovar Abortosovis for sheep. Intestinal invasion by serovar Abortusovis was significantly reduced after mutation of invH but was not reduced following curing of the virulence plasmid, suggesting that the Salmonella pathogenicity island 1 influences but the virulence plasmid genes do not influence the ability of serovar Abortusovis to invade the intestinal mucosa in sheep.