Edible lamellibranch molluscs can be involved in foodborne disease and infections of varying severity. They are filter feeding animals able to retain and concentrate in their organism bacteria, parasites, viruses and biotoxins marine algae present in their external environment. Major shellfish harvesting and relaying areas from different areas in Sardinia region were defined and studied by analysing different physicochemical parameters in the water and the levels of Escherichia coli (E. coli), Norovirus (NoVs) genogroup I (NoVGI), NoVs genogroup II (NoVGII) and hepatitis A virus (HAV) in the shellfish harvested and farmed from 2009 to 2011. During that period the identification of the viral agents was carried out by one step real-time reverse transcriptase-polymerase chain reaction and Escherichia coli according to ISO TS 16649-3:2005 standard method. A total of 1266 shellfish samples were tested for NoVGI, NoVGII, HAV and faecal indicators. Norovirus contamination was found in 337 samples (26.6%); only one sample of mussels was positive for HAV (0.08%); while E. coli prevalence was 3.8% in shellfish. The probability of observing shellfish samples positive for NoVs, HAV and E. coli presence was associated with harvesting, growing and relaying areas, period of sampling, environmental parameters, animal species (P<0.05). Although the higher prevalence rate of human enteropathogenic viruses was found in the winter period, we did not observe a significant relationship between the effect of seawater temperature (seasonality) and NoVs presence all over the study period; in fact, according to statistical analysis, the presence of human enteric viruses does not appear to be related to water temperature.

Background Streptococcus uberis is one of the main causative agents of ovine mastitis, however little is known about this global, environmental pathogen and its genomic mechanisms of disease. In this study, we performed genomic analysis on 46 S. uberis isolates collected from mastitis-infected sheep in Sardinia (Italy). Results Genomes were assigned into lineage clusters using PopPUNK, which found 27 distinct isolate clusters, indicating considerable genetic variability consistent with environmental isolates. Geographic trends were identified including regional linkage of several isolate clusters. Multi-locus Sequence Typing (MLST) performed poorly and provided no new insights. Genomes were then screened for antimicrobial resistance genes, which were compared to phenotypic resistance profiles. Isolates showed consistent phenotypic resistance to aminoglycosides with variable resistance to novobiocin and tetracycline. In general, identification of antimicrobial resistance genes did not correlate with phenotypic resistance profiles, indicating unknown genetic determinants. A multi-antimicrobial resistance cassette (aminoglycoside, lincosamide and streptogramin) was identified in the chromosome of three genomes, flanked by vestigial phage recombinases. This locus appears to have spread horizontally within discrete S. uberis populations within a 40 km radius (Sassari region). Genomes were screened for putative virulence factors, which identified 16 genes conserved between sheep and cow isolates, with no host-specific genes shared uniformly across all host-specific isolates. Pangenomic analysis was then performed to identify core genes which were putatively surface-exposed, for identification of potential vaccine targets. As all genomes encoded sortase, core genes were screened for the sortase cleavage motif. Of the 1445 core S. uberis genes, 64 were putative sortase substrates and were predominantly adhesins, permeases and peptidases, consistent with compounds found within ruminant milk such as xanthine, fibronectin and lactoferrin. Conclusions This study demonstrated the importance of whole genome sequencing for surveillance of S. uberis and tracking horizontal acquisition of antimicrobial resistance genes, as well as providing insight into genetic determinants of disease, which cannot be inferred from the MLST schemes. Future mastitis surveillance should be informed by genomic analysis.

The authors report results of analysis carried out during 2009-2010 for detection of P.S.P. toxins in mussels bred in Sardinia areas and management non-compliance

Noroviruses (NoVs), known as Norwalk-Like Viruses (NLV) or Small-Round-Structured-Viruses (SRVS), are among the most frequent causes of acute viral gastroenteritis in human beings, often associated with food poisoning, if raw or poorly cooked bivalve molluscs (mussels, clams and oysters) are ingested. In compliance with EU regulations, the safety of these products is evaluated according to bacteriological paramenters (Salmonella and E.coli) as provided for by Regulation (EC) No. 2073/2005, biotoxicological parameters, as provided for by Regulation (EC) No. 853/2004, and chemical parameters, as provided for by Regulation (EC) No. 1881/06. This essay focuses on the evaluation of NoV concentration levels in Mytilus galloprovincialis populations, farmed in 2009 in two different Mussels Depuration Centers (CDMs) in Sardinia (Italy). During the assessment procedures, Noroviruses were detected for the first time on the regional territory with one-step TaqMan real-time RT-PCR

Background: Streptococcus uberis is one of the main causative agents of ovine mastitis, however little is known about this global, environmental pathogen and its genomic mechanisms of disease. In this study, we performed genomic analysis on 46 S. uberis isolates collected from mastitis-infected sheep in Sardinia (Italy). Results: Genomes were assigned into lineage clusters using PopPUNK, which found 27 distinct isolate clusters, indicating considerable genetic variability consistent with environmental isolates. Geographic trends were identified including regional linkage of several isolate clusters. Multi-locus Sequence Typing (MLST) performed poorly and provided no new insights.Genomes were then screened for antimicrobial resistance genes, which were compared to phenotypic resistance profiles. Isolates showed consistent phenotypic resistance to aminoglycosides with variable resistance to novobiocin and tetracycline. In general, identification of antimicrobial resistance genes did not correlate with phenotypic resistance profiles, indicating unknown genetic determinants. A multi-antimicrobial resistance cassette (aminoglycoside, lincosamide and streptogramin) was identified in the chromosome of three genomes, flanked by vestigial phage recombinases. This locus appears to have spread horizontally within discrete S. uberis populations within a 40 km radius (Sassari region).Genomes were screened for putative virulence factors, which identified 16 genes conserved between sheep and cow isolates, with no host-specific genes shared uniformly across all host-specific isolates.Pangenomic analysis was then performed to identify core genes which were putatively surface-exposed, for identification of potential vaccine targets. As all genomes encoded sortase, core genes were screened for the sortase cleavage motif. Of the 1445 core S. uberis genes, 64 were putative sortase substrates and were predominantly adhesins, permeases and peptidases, consistent with compounds found within ruminant milk such as xanthine, fibronectin and lactoferrin. Conclusions: This study demonstrated the importance of whole genome sequencing for surveillance of S. uberis and tracking horizontal acquisition of antimicrobial resistance genes, as well as providing insight into genetic determinants of disease, which cannot be inferred from the MLST schemes. Future mastitis surveillance should be informed by genomic analysis.