Project description:Salmonella enterica variants exhibit diverse host adaptation, outcome of infection, and associated risk to humans. Analysis of 6,335 Salmonella isolates recovered from integrated human-animal surveillance in Emilia Romagna region, Northern Italy, (human population ca 4,500,000), from 2012 to 2017 showed that Salmonella enterica serovar Derby constitutes a swine associated serovar in this epidemiological context while representing also a significant causative agent of human infections. Comparison of the distribution of subtypes of Salmonella Derby from human and swine identified isolates with a distinct PFGE profile that were significantly less isolated in human infections than in swine infections compared to all other subtypes. Here we show that isolates with this PFGE profile form a distinct phylogenetic sub-clade within Salmonella Derby and exhibit a marked reduction in invasion and replication in human epithelial cells but a relatively small reduction in swine epithelial cells, in line with the epidemiological evidence. A single missense mutation in hilD, that encodes the master-regulator of the Salmonella Pathogenicity Island 1 (SPI-1), was identified in this lineage of Salmonella Derby. Since SPI-1 encodes for a primary system of Salmonella invasion into epithelial cells, we investigated the role of the observed mutation in detail. We demonstrated that the missense mutation results in a loss of function of HilD that accounts for the reduced invasion and replication in human epithelial cells while showing a relatively small impact on the interaction with swine cells. This finding is suggestive of a mechanism of invasion alternative to SPI-1 in the Salmonella-swine combination
2020-12-16 | GSE142220 | GEO
Project description:Mycobacterium tuberculosis variant caprae in Lombardy and Emilia Romagna regions, Italy
Project description:Miseq Whole Genome Sequencing of Micobacterium Avium Paratuberculosis clone isolated in Emilia Romagna (Italy) within a single herd
Project description:Focus of this project is to evaluate the possible financial benefit resulting from an optimization of surgical outcomes throughout a collaborative and systematic auditing activity.The primary objective of this analysis is to assess the employed resources by National Health System related to surgical activities for primary colorectal cancer during a collaborative and systematic auditing activity in 8 Surgical Units of Emilia-Romagna
Project description:Whole-genome sequencing and Phylogeographic analysis of Salmonella enterica serovar Napoli strains isolated from human cases occurred in Lombardy and Emilia-Romagna, Northern Italy
Project description:We performed shallow whole genome sequencing (WGS) on circulating free (cf)DNA extracted from plasma or cerebrospinal fluid (CSF), and shallow WGS on the tissue DNA extracted from the biopsy in order to evaluate the correlation between the two biomaterials. After library construction and sequencing (Hiseq3000 or Ion Proton), copy number variations were called with WisecondorX.
Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).
