Whole-Genome Sequence of Salmonella enterica Serovar Bispebjerg from Turkey Reveals Its Pathogenic Potential.

We report the genome sequence of a Salmonella enterica subsp. enterica serovar Bispebjerg strain that was isolated from a turkey flock in 2011. The genome analysis of the strain, a rare and multihost serovar, revealed its pathogenic potential due to antimicrobial resistance and a plethora of Salmonella pathogenicity islands and virulence factors.

Phylodynamic analysis and evaluation of the balance between anthropic and environmental factors affecting IBV spreading among Italian poultry farms.

Infectious bronchitis virus (IBV) control is mainly based on wide vaccine administration. Although effective, its efficacy is not absolute, the viral circulation is not prevented and some side effects cannot be denied. Despite this, the determinants of IBV epidemiology and the factors affecting its circulation are still largely unknown and poorly investigated. In the present study, 361 IBV QX (the most relevant field genotype in Italy) sequences were obtained between 2012 and 2016 from the two main Italian integrated poultry companies. Several biostatistical and bioinformatics approaches were used to reconstruct the history of the QX genotype in Italy and to assess the effect of different environmental, climatic and social factors on its spreading patterns. Moreover, two structured coalescent models were considered in order to investigate if an actual compartmentalization occurs between the two integrated poultry companies and the role of a third "ghost" deme, representative of minor industrial poultry companies and the rural sector. The obtained results suggest that the integration of the poultry companies is an effective barrier against IBV spreading, since the strains sampled from the two companies formed two essentially-independent clades. Remarkably, the only exceptions were represented by farms located in the high densely populated poultry area of Northern Italy. The inclusion of a third deme in the model revealed the likely role of other poultry companies and rural farms (particularly concentrated in Northern Italy) as sources of strain introduction into one of the major poultry companies, whose farms are mainly located in the high densely populated poultry area of Northern Italy. Accordingly, when the effect of different environmental and urban parameters on IBV geographic spreading was investigated, no factor seems to contribute to IBV dispersal velocity, being poultry population density the only exception. Finally, the different viral population pattern observed in the two companies over the same time period supports the pivotal role of management and control strategies on IBV epidemiology. Overall, the present study results stress the crucial relevance of human action rather than environmental factors, highlighting the direct benefits that could derive from improved management and organization of the poultry sector on a larger scale.

Astroviruses as causative agents of poultry enteritis: genetic characterization and longitudinal studies on field conditions.

Astroviruses (AstVs) are nonenveloped RNA small round viruses (SRVs) with a genome of 6.8-7.9 kb. Known avian AstVs are spread worldwide; they have been associated with poult enteritis and mortality syndrome in the United States and reported in Italy in intensive turkey and guinea fowl flocks. Nevertheless, their real prevalence and their pathogenic role in avian enteritis affecting Italian flocks is far from clear. Negative staining electron microscopy (nsEM) is used for the routine diagnosis of avian enteric SRVs, although it cannot distinguish morphologically similar particles. Enzyme-linked immunosorbent assay (ELISA), reverse-transcription PCR (RT-PCR), and genomic sequencing are now used for this specific purpose. We analyzed 329 samples of chicken, turkey, and guinea fowl intestinal contents from Italian poultry flocks. Most samples were from enteritis outbreaks, but we also included samples from three longitudinal studies (one on 11 broiler flocks and the other two on a guinea fowl flock). We first examined the samples with nsEM. SRVs, including AstVs, are often associated with rotaviruses and were the most commonly detected morphotypes in avian enteric diseases. We then analyzed 124 of the samples with an RT-PCR targeting the open reading frame (ORF)-1b of AstV. This gene codes for an RNA-dependent polymerase. We then sequenced and genetically analyzed the RT-PCR positive samples. Phylogenetic analysis distinguished three defined clusters: the first included guinea fowl AstVs and turkey AstVs-2; the second, chicken AstVs; and the third was formed by avian nephritis viruses (ANVs). No strains clustered with turkey AstVs-1. The results indicate that ORF-1b presents certain genetic variability, even among AstVs from the same species. In longitudinal studies, samples retrieved from the same shed were homogeneous, with some exceptions suggesting possible coexistence of different genetic types in the same unit. The finding of ANV-like viruses in commercial guinea fowls underlines the genetic variability of AstVs and strengthens the hypothesis of a varied intraherd situation.

Genetic and antigenic characterization of infectious bursal disease viruses isolated in Italy during the period 2002-2005.

During the period 2002-2005, 109 infectious bursal disease virus (IBDV) field strains were isolated from bird flocks located in various parts of Italy. Out of these strains, 91 were isolated from broilers, 12 from pullets, and six from backyard flocks. Forty-two IBDV strains were further investigated and characterized on the basis of the geographical origin, source, and clinical signs. Antigenic and genetic characterizations were carried out using a monoclonal antibody (MAb)-based antigen-capture (AC) enzyme-linked immunosorbent assay (ELISA) or a virus neutralization assay and a reverse transcription, amplification, and direct sequencing of a genome fragment encoding the VP2 variable domain. The viruses were compared with reference IBDV strains, F52/70 (classical, 1970), 89163 (typical very virulent [vv]IBDV, 1989), 91168 (antigenically modified vvIBDV, 1991) and 94432 (antigenically modified vvIBDV, 1994) among others. All 42 strains were genetically characterized, and the comparison of their nucleotide sequences revealed the presence of six clusters having 100% identity, named group 1, 2, 3, 4, 5, and 6. Twelve strains, representative of each molecular group and/or with interesting amino acid sequence, were also antigenically characterized. The antigenic characterization showed six strains--151573, 157185 (group 1), 192294 (group 2), 77882 (group 3), 217 (group 4), and 192304--with the profile typical of vvIBDV (lack of binding of MAbs 3 and 4). Two strains, 77165 and 204875 (group 6), were also related to vvIBDV but did not react with MAb 5. Three isolates exhibited a profile of cell culture-adapted viruses and classical strains but with some differences: strain 157776 reacted with all MAbs; strain 168026 with all MAbs except MAb 4, which weakly neutralized it; and strain 72293 with all MAbs except MAb 9, which is rather unusual. The last strain, 213622, showed a very uncommon antigenic profile with missing or reduced binding of MAbs 3, 4, 5, 6, 8, and 9. Genetic characterization revealed 37 strains identified as vvIBDV viruses divided in 26 isolates (including groups 1, 2, 3, and 4) with the four amino acids residues typical of vvIBDV (222A, 256I, 294I, 299S) and 11 isolates (including groups 5, 6, and 213622) with some other amino acid exchanges. Four isolates (72293, 168026, 196783, and 222220) presented an amino acid sequence closely related to attenuated classical viruses whereas the last isolate (157776) exhibited a rather different sequence with some mutations typical of vvIBDV and others for cell culture-adapted viruses. Results of the antigenic and genetic characterization revealed that the majority of viruses (n = 37) were related to vvIBDV strains but, among these, 11 strains presented antigenically and genetically modified characteristics and originated, in major part, from the area where viruses have been circulating for a long time. The remaining viruses (n = 5) were related but not identical to attenuated classical viruses and came from areas where vaccination with intermediate strains is applied.